diff --git a/releases/EDAM.owl b/releases/EDAM.owl index f6ea6ce..324fe04 100644 --- a/releases/EDAM.owl +++ b/releases/EDAM.owl @@ -28,31 +28,31 @@ xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:edam="&oboOther;edam#"> - EDAM: An ontology of bioinformatics operations, types of data and identifiers, data formats, and topics - EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries. - 1.8 - 16:12:2014 11:00 - Hervé Ménager - topics "EDAM topics" - 3546 - EDAM_format http://edamontology.org/format_ "EDAM data formats" - Jon Ison, Matus Kalas, Herve Menager - Matúš Kalaš - Jon Ison - concept_properties "EDAM concept properties" - EDAM_data http://edamontology.org/data_ "EDAM types of data" - application/rdf+xml - EDAM http://edamontology.org/ "EDAM relations and concept properties" - operations "EDAM operations" - EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence. - edam "EDAM" - relations "EDAM relations" - data "EDAM types of data" - identifiers "EDAM types of identifiers" - EDAM - formats "EDAM data formats" - EDAM_operation http://edamontology.org/operation_ "EDAM operations" EDAM_topic http://edamontology.org/topic_ "EDAM topics" + EDAM_operation http://edamontology.org/operation_ "EDAM operations" + formats "EDAM data formats" + EDAM + identifiers "EDAM types of identifiers" + data "EDAM types of data" + relations "EDAM relations" + edam "EDAM" + EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence. + operations "EDAM operations" + EDAM http://edamontology.org/ "EDAM relations and concept properties" + application/rdf+xml + EDAM_data http://edamontology.org/data_ "EDAM types of data" + concept_properties "EDAM concept properties" + Jon Ison + Matúš Kalaš + Jon Ison, Matus Kalas, Herve Menager + 1.9 + EDAM_format http://edamontology.org/format_ "EDAM data formats" + 3567 + topics "EDAM topics" + Hervé Ménager + 02:02:2015 + EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries. + EDAM: An ontology of bioinformatics operations, types of data and identifiers, data formats, and topics @@ -74,9 +74,9 @@ Created in - concept_properties - true Version in which a concept was created. + true + concept_properties @@ -85,10 +85,10 @@ Documentation - concept_properties - true - 'Documentation' trailing modifier (qualifier, 'documentation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page with explanation, description, documentation, or specification of the given data format. Specification + 'Documentation' trailing modifier (qualifier, 'documentation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page with explanation, description, documentation, or specification of the given data format. + true + concept_properties @@ -97,9 +97,9 @@ Example - concept_properties - true 'Example' concept property ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. + true + concept_properties @@ -114,9 +114,9 @@ Obsolete since - Version in which a concept was made obsolete. - concept_properties true + concept_properties + Version in which a concept was made obsolete. @@ -125,9 +125,9 @@ Regular expression - true - concept_properties 'Regular expression' concept property ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too. + concept_properties + true @@ -325,17 +325,17 @@ has format - false - 'A has_format B' defines for the subject A, that it has the object B as its data format. - edam - false - false - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality" - relations - OBO_REL:is_a - false - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'. "http://purl.obolibrary.org/obo/OBI_0000298" + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'. + false + OBO_REL:is_a + relations + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality" + false + false + edam + 'A has_format B' defines for the subject A, that it has the object B as its data format. + false @@ -346,32 +346,32 @@ has function - false - relations - "http://purl.obolibrary.org/obo/OBI_0000306" - 'A has_function B' defines for the subject A, that it has the object B as its function. - true - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality" - false - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts. - edam - OBO_REL:bearer_of - OBO_REL:is_a - false http://wsio.org/has_function + false + OBO_REL:is_a + OBO_REL:bearer_of + edam + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts. + false + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality" + true + 'A has_function B' defines for the subject A, that it has the object B as its function. + "http://purl.obolibrary.org/obo/OBI_0000306" + relations + false - true - In very unusual cases. + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. + OBO_REL:bearer_of - + - OBO_REL:bearer_of - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. + true + In very unusual cases. - + @@ -380,15 +380,15 @@ has identifier - false - false - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'. - 'A has_identifier B' defines for the subject A, that it has the object B as its identifier. - edam - OBO_REL:is_a - relations - false false + false + relations + OBO_REL:is_a + edam + 'A has_identifier B' defines for the subject A, that it has the object B as its identifier. + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'. + false + false @@ -399,18 +399,18 @@ has input - edam - true - false - 'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument. - false - OBO_REL:is_a - relations - Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined. - http://wsio.org/has_input - false - "http://purl.obolibrary.org/obo/OBI_0000293" OBO_REL:has_participant + "http://purl.obolibrary.org/obo/OBI_0000293" + false + http://wsio.org/has_input + Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined. + relations + OBO_REL:is_a + false + 'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument. + false + true + edam @@ -433,24 +433,24 @@ has output - false - false - false - 'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument. - true - OBO_REL:has_participant - relations - OBO_REL:is_a - "http://purl.obolibrary.org/obo/OBI_0000299" - edam - Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined. http://wsio.org/has_output + Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined. + edam + "http://purl.obolibrary.org/obo/OBI_0000299" + OBO_REL:is_a + relations + OBO_REL:has_participant + true + 'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument. + false + false + false - true In very unusual cases. + true @@ -467,19 +467,19 @@ has topic - "http://purl.obolibrary.org/obo/OBI_0000298" - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality - false - "http://purl.obolibrary.org/obo/IAO_0000136" - false - http://annotation-ontology.googlecode.com/svn/trunk/annotation-core.owl#hasTopic - OBO_REL:is_a - edam - 'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B). - false - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined. - true relations + true + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined. + false + 'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B). + edam + OBO_REL:is_a + http://annotation-ontology.googlecode.com/svn/trunk/annotation-core.owl#hasTopic + false + "http://purl.obolibrary.org/obo/IAO_0000136" + false + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality + "http://purl.obolibrary.org/obo/OBI_0000298" @@ -503,24 +503,24 @@ is format of - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in - OBO_REL:quality_of - Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined. - relations - edam - 'A is_format_of B' defines for the subject A, that it is a data format of the object B. - false - false - false - OBO_REL:is_a false + OBO_REL:is_a + false + false + false + 'A is_format_of B' defines for the subject A, that it is a data format of the object B. + edam + relations + Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined. + OBO_REL:quality_of + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in - OBO_REL:quality_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. + OBO_REL:quality_of @@ -531,33 +531,33 @@ is function of - false - false - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in - relations - http://wsio.org/is_function_of - edam - OBO_REL:function_of - 'A is_function_of B' defines for the subject A, that it is a function of the object B. - false - OBO_REL:is_a - true - OBO_REL:inheres_in Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used. + OBO_REL:inheres_in + true + OBO_REL:is_a + false + 'A is_function_of B' defines for the subject A, that it is a function of the object B. + OBO_REL:function_of + edam + http://wsio.org/is_function_of + relations + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in + false + false - In very unusual cases. - true + OBO_REL:function_of + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. - + - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. - OBO_REL:function_of + In very unusual cases. + true - + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. @@ -572,15 +572,15 @@ is identifier of - false - OBO_REL:is_a - 'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B. - Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined. - relations - false - edam - false false + false + edam + false + relations + Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined. + 'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B. + OBO_REL:is_a + false @@ -592,18 +592,18 @@ is input of - 'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B. - false - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'. - edam - "http://purl.obolibrary.org/obo/OBI_0000295" - OBO_REL:is_a - OBO_REL:participates_in - false - true - relations - http://wsio.org/is_input_of false + http://wsio.org/is_input_of + relations + true + false + OBO_REL:participates_in + OBO_REL:is_a + "http://purl.obolibrary.org/obo/OBI_0000295" + edam + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'. + false + 'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B. @@ -627,34 +627,34 @@ is output of - "http://purl.obolibrary.org/obo/OBI_0000312" - relations - true - http://wsio.org/is_output_of - OBO_REL:participates_in - 'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B. - false - edam - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'. - false - false OBO_REL:is_a + false + false + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'. + edam + false + 'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B. + OBO_REL:participates_in + http://wsio.org/is_output_of + true + relations + "http://purl.obolibrary.org/obo/OBI_0000312" - 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. - OBO_REL:participates_in - - - - true In very unusual cases. + + OBO_REL:participates_in + 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. + + + @@ -662,17 +662,17 @@ is topic of - edam - OBO_REL:is_a - false - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in - Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'. - false - true - false - OBO_REL:quality_of - relations 'A is_topic_of B' defines for the subject A, that it is a topic of the object B (a topic A is the scope of B). + relations + OBO_REL:quality_of + false + true + false + Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'. + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in + false + OBO_REL:is_a + edam @@ -685,17 +685,17 @@ - In very unusual cases. - true - - - - OBO_REL:quality_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. + + true + In very unusual cases. + + + @@ -721,8 +721,8 @@ - 1.7 Identify a correlation, i.e. a statistical relationship between two random variables or two sets of data. + 1.7 @@ -734,10 +734,10 @@ Resource type - true - A type of computational resource used in bioinformatics. - beta12orEarlier beta12orEarlier + beta12orEarlier + A type of computational resource used in bioinformatics. + true @@ -751,37 +751,37 @@ - Datum - http://www.ifomis.org/bfo/1.1/snap#Continuant - http://purl.org/biotop/biotop.owl#DigitalEntity - http://wsio.org/data_002 - beta12orEarlier - Data record - Data set - "http://purl.obolibrary.org/obo/IAO_0000027" - "http://purl.obolibrary.org/obo/IAO_0000030" - http://semanticscience.org/resource/SIO_000069 - http://semanticscience.org/resource/SIO_000088 - http://www.onto-med.de/ontologies/gfo.owl#Perpetuant Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output. + http://www.onto-med.de/ontologies/gfo.owl#Perpetuant + http://semanticscience.org/resource/SIO_000088 + http://semanticscience.org/resource/SIO_000069 + "http://purl.obolibrary.org/obo/IAO_0000030" + "http://purl.obolibrary.org/obo/IAO_0000027" + Data set + Data record + beta12orEarlier + http://wsio.org/data_002 + http://purl.org/biotop/biotop.owl#DigitalEntity + http://www.ifomis.org/bfo/1.1/snap#Continuant + Datum - EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). Data record + EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). - Data set EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + Datum + Data set EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - Datum @@ -793,10 +793,10 @@ Tool - true - beta12orEarlier - A bioinformatics package or tool, e.g. a standalone application or web service. beta12orEarlier + A bioinformatics package or tool, e.g. a standalone application or web service. + beta12orEarlier + true @@ -807,10 +807,10 @@ Database - beta12orEarlier - true - beta12orEarlier A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model. + beta12orEarlier + true + beta12orEarlier @@ -827,9 +827,9 @@ - An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc. - Ontologies beta12orEarlier + Ontologies + An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc. @@ -841,10 +841,10 @@ Directory metadata - true - beta12orEarlier - A directory on disk from which files are read. 1.5 + A directory on disk from which files are read. + beta12orEarlier + true @@ -856,10 +856,10 @@ MeSH vocabulary - beta12orEarlier - Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases. - true beta12orEarlier + true + Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases. + beta12orEarlier @@ -871,10 +871,10 @@ HGNC vocabulary - true - Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee. - beta12orEarlier beta12orEarlier + beta12orEarlier + Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee. + true @@ -886,10 +886,10 @@ UMLS vocabulary - true - beta12orEarlier - beta12orEarlier Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System). + beta12orEarlier + beta12orEarlier + true @@ -909,12 +909,12 @@ - A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things). - http://wsio.org/data_005 - "http://purl.org/dc/elements/1.1/identifier" - ID - beta12orEarlier http://semanticscience.org/resource/SIO_000115 + beta12orEarlier + ID + "http://purl.org/dc/elements/1.1/identifier" + http://wsio.org/data_005 + A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things). @@ -934,10 +934,10 @@ Database entry - true - An entry (retrievable via URL) from a biological database. - beta12orEarlier beta12orEarlier + beta12orEarlier + An entry (retrievable via URL) from a biological database. + true @@ -949,8 +949,8 @@ Molecular mass - beta12orEarlier Mass of a molecule. + beta12orEarlier @@ -962,9 +962,9 @@ Molecular charge - PDBML:pdbx_formal_charge - beta12orEarlier Net charge of a molecule. + beta12orEarlier + PDBML:pdbx_formal_charge @@ -976,9 +976,9 @@ Chemical formula - beta12orEarlier - A specification of a chemical structure. Chemical structure specification + A specification of a chemical structure. + beta12orEarlier @@ -990,9 +990,9 @@ QSAR descriptor - beta12orEarlier - QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties. A QSAR quantitative descriptor (name-value pair) of chemical structure. + QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties. + beta12orEarlier @@ -1004,9 +1004,9 @@ Raw sequence - Non-sequence characters may be used for example for gaps and translation stop. - A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters. beta12orEarlier + A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters. + Non-sequence characters may be used for example for gaps and translation stop. @@ -1018,10 +1018,10 @@ Sequence record - SO:2000061 - A molecular sequence and associated metadata. - beta12orEarlier http://purl.bioontology.org/ontology/MSH/D058977 + beta12orEarlier + A molecular sequence and associated metadata. + SO:2000061 @@ -1033,10 +1033,10 @@ Sequence set - SO:0001260 - beta12orEarlier - This concept may be used for arbitrary sequence sets and associated data arising from processing. A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method. + This concept may be used for arbitrary sequence sets and associated data arising from processing. + beta12orEarlier + SO:0001260 @@ -1048,10 +1048,10 @@ Sequence mask character - A character used to replace (mask) other characters in a molecular sequence. - 1.5 - beta12orEarlier true + beta12orEarlier + 1.5 + A character used to replace (mask) other characters in a molecular sequence. @@ -1063,11 +1063,11 @@ Sequence mask type - true - 1.5 - beta12orEarlier - Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits. A label (text token) describing the type of sequence masking to perform. + Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits. + beta12orEarlier + 1.5 + true @@ -1079,11 +1079,11 @@ DNA sense specification - The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used. - The strand of a DNA sequence (forward or reverse). - Strand - beta12orEarlier DNA strand specification + beta12orEarlier + Strand + The strand of a DNA sequence (forward or reverse). + The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used. @@ -1095,10 +1095,10 @@ Sequence length specification - 1.5 - beta12orEarlier - A specification of sequence length(s). true + A specification of sequence length(s). + beta12orEarlier + 1.5 @@ -1110,11 +1110,11 @@ Sequence metadata - true - 1.5 - This is used for such things as a report including the sequence identifier, type and length. - Basic or general information concerning molecular sequences. beta12orEarlier + Basic or general information concerning molecular sequences. + This is used for such things as a report including the sequence identifier, type and length. + 1.5 + true @@ -1126,9 +1126,9 @@ Sequence feature source - beta12orEarlier - How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived. This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human). + How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived. + beta12orEarlier @@ -1140,14 +1140,14 @@ Sequence search results - Sequence database search results - A report of sequence hits and associated data from searching a database of sequences (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits. - The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc. - Sequence search hits - Sequence database hits - - Database hits (sequence) beta12orEarlier + Database hits (sequence) + + Sequence database hits + Sequence search hits + The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc. + A report of sequence hits and associated data from searching a database of sequences (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits. + Sequence database search results @@ -1159,13 +1159,13 @@ Sequence signature matches - Search results (protein secondary database) - This ncluding reports of hits from a search of a protein secondary or domain database. - Sequence profile matches - Report on the location of matches in one or more sequences to profiles, motifs (conserved or functional patterns) or other signatures. - beta12orEarlier - Protein secondary database search results Sequence motif matches + Protein secondary database search results + beta12orEarlier + Report on the location of matches in one or more sequences to profiles, motifs (conserved or functional patterns) or other signatures. + Sequence profile matches + This ncluding reports of hits from a search of a protein secondary or domain database. + Search results (protein secondary database) @@ -1177,10 +1177,10 @@ Sequence signature model - true - beta12orEarlier - beta12orEarlier Data files used by motif or profile methods. + beta12orEarlier + beta12orEarlier + true @@ -1198,9 +1198,9 @@ - Data concering concerning specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element. - This can include metadata about a motif or sequence profile such as its name, length, technical details about the profile construction, and so on. beta12orEarlier + This can include metadata about a motif or sequence profile such as its name, length, technical details about the profile construction, and so on. + Data concering concerning specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element. @@ -1212,11 +1212,11 @@ Sequence alignment (words) - Alignment of exact matches between subsequences (words) within two or more molecular sequences. - Sequence word alignment - true - beta12orEarlier 1.5 + beta12orEarlier + true + Sequence word alignment + Alignment of exact matches between subsequences (words) within two or more molecular sequences. @@ -1228,8 +1228,8 @@ Dotplot - beta12orEarlier A dotplot of sequence similarities identified from word-matching or character comparison. + beta12orEarlier @@ -1247,11 +1247,11 @@ - Alignment of multiple molecular sequences. - beta12orEarlier - http://semanticscience.org/resource/SIO_010066 - http://purl.bioontology.org/ontology/MSH/D016415 http://en.wikipedia.org/wiki/Sequence_alignment + http://purl.bioontology.org/ontology/MSH/D016415 + http://semanticscience.org/resource/SIO_010066 + beta12orEarlier + Alignment of multiple molecular sequences. @@ -1263,10 +1263,10 @@ Sequence alignment parameter - beta12orEarlier - 1.5 - true Some simple value controlling a sequence alignment (or similar 'match') operation. + true + 1.5 + beta12orEarlier @@ -1278,8 +1278,8 @@ Sequence similarity score - beta12orEarlier A value representing molecular sequence similarity. + beta12orEarlier @@ -1291,10 +1291,10 @@ Sequence alignment metadata - 1.5 - true - beta12orEarlier Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score. + beta12orEarlier + true + 1.5 @@ -1306,9 +1306,9 @@ Sequence alignment report - beta12orEarlier - An informative report of molecular sequence alignment-derived data or metadata. Use this for any computer-generated reports on sequence alignments, and for general information (metadata) on a sequence alignment, such as a description, sequence identifiers and alignment score. + An informative report of molecular sequence alignment-derived data or metadata. + beta12orEarlier @@ -1320,8 +1320,8 @@ Sequence profile alignment - A profile-profile alignment (each profile typically representing a sequence alignment). beta12orEarlier + A profile-profile alignment (each profile typically representing a sequence alignment). @@ -1333,9 +1333,9 @@ Sequence-profile alignment - Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores. - Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment). beta12orEarlier + Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment). + Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores. @@ -1347,11 +1347,11 @@ Sequence distance matrix - Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix. - Phylogenetic distance matrix - A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation. - Moby:phylogenetic_distance_matrix beta12orEarlier + Moby:phylogenetic_distance_matrix + A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation. + Phylogenetic distance matrix + Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix. @@ -1363,10 +1363,10 @@ Phylogenetic character data - beta12orEarlier - http://www.evolutionaryontology.org/cdao.owl#Character - As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments Basic character data from which a phylogenetic tree may be generated. + As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments + http://www.evolutionaryontology.org/cdao.owl#Character + beta12orEarlier @@ -1384,15 +1384,15 @@ - Moby:myTree - beta12orEarlier - The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length. - Moby:phylogenetic_tree - http://purl.bioontology.org/ontology/MSH/D010802 - A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'. - http://www.evolutionaryontology.org/cdao.owl#Tree - Moby:Tree Phylogeny + Moby:Tree + http://www.evolutionaryontology.org/cdao.owl#Tree + A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'. + http://purl.bioontology.org/ontology/MSH/D010802 + Moby:phylogenetic_tree + The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length. + beta12orEarlier + Moby:myTree @@ -1404,10 +1404,10 @@ Comparison matrix - Substitution matrix - Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison. - The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats). beta12orEarlier + The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats). + Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison. + Substitution matrix @@ -1419,11 +1419,11 @@ Protein topology - The location and size of the secondary structure elements and intervening loop regions is usually indicated. - true - Predicted or actual protein topology represented as a string of protein secondary structure elements. - beta12orEarlier beta12orEarlier + beta12orEarlier + Predicted or actual protein topology represented as a string of protein secondary structure elements. + true + The location and size of the secondary structure elements and intervening loop regions is usually indicated. @@ -1435,10 +1435,10 @@ Protein features report (secondary structure) - Topic concerning secondary structure (predicted or real) of a protein. - true - 1.8 beta12orEarlier + 1.8 + true + Topic concerning secondary structure (predicted or real) of a protein. @@ -1450,11 +1450,11 @@ Protein features report (super-secondary) - Topic concerning super-secondary structure of protein sequence(s). - beta12orEarlier - true - Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. 1.8 + Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. + true + beta12orEarlier + Topic concerning super-secondary structure of protein sequence(s). @@ -1467,8 +1467,8 @@ Secondary structure alignment (protein) - beta12orEarlier Alignment of the (1D representations of) secondary structure of two or more proteins. + beta12orEarlier @@ -1480,10 +1480,10 @@ Secondary structure alignment metadata (protein) - true - beta12orEarlier - beta12orEarlier An informative report on protein secondary structure alignment-derived data or metadata. + beta12orEarlier + beta12orEarlier + true @@ -1501,11 +1501,11 @@ - beta12orEarlier - Secondary structure (RNA) - Moby:RNAStructML - This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc. An informative report of secondary structure (predicted or real) of an RNA molecule. + This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc. + Moby:RNAStructML + Secondary structure (RNA) + beta12orEarlier @@ -1517,9 +1517,9 @@ Secondary structure alignment (RNA) - beta12orEarlier - Alignment of the (1D representations of) secondary structure of two or more RNA molecules. Moby:RNAStructAlignmentML + Alignment of the (1D representations of) secondary structure of two or more RNA molecules. + beta12orEarlier @@ -1531,10 +1531,10 @@ Secondary structure alignment metadata (RNA) - beta12orEarlier - An informative report of RNA secondary structure alignment-derived data or metadata. - beta12orEarlier true + beta12orEarlier + An informative report of RNA secondary structure alignment-derived data or metadata. + beta12orEarlier @@ -1552,12 +1552,12 @@ - 3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure. - http://purl.bioontology.org/ontology/MSH/D015394 - The coordinate data may be predicted or real. - Structure data - Coordinate model beta12orEarlier + Coordinate model + Structure data + The coordinate data may be predicted or real. + http://purl.bioontology.org/ontology/MSH/D015394 + 3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure. @@ -1569,10 +1569,10 @@ Tertiary structure record - An entry from a molecular tertiary (3D) structure database. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + An entry from a molecular tertiary (3D) structure database. @@ -1584,10 +1584,10 @@ Structure database search results - true - beta12orEarlier - Results (hits) from searching a database of tertiary structure. 1.8 + Results (hits) from searching a database of tertiary structure. + beta12orEarlier + true @@ -1605,9 +1605,9 @@ - beta12orEarlier - A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition. Alignment (superimposition) of molecular tertiary (3D) structures. + A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition. + beta12orEarlier @@ -1619,9 +1619,9 @@ Structure alignment report - An informative report of molecular tertiary structure alignment-derived data. - This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier + This is a broad data type and is used a placeholder for other, more specific types. + An informative report of molecular tertiary structure alignment-derived data. @@ -1633,8 +1633,8 @@ Structure similarity score - A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison. beta12orEarlier + A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison. @@ -1652,10 +1652,10 @@ - Structural (3D) profile - Some type of structural (3D) profile or template (representing a structure or structure alignment). - 3D profile beta12orEarlier + 3D profile + Some type of structural (3D) profile or template (representing a structure or structure alignment). + Structural (3D) profile @@ -1667,9 +1667,9 @@ Structural (3D) profile alignment - A 3D profile-3D profile alignment (each profile representing structures or a structure alignment). - Structural profile alignment beta12orEarlier + Structural profile alignment + A 3D profile-3D profile alignment (each profile representing structures or a structure alignment). @@ -1681,11 +1681,11 @@ Sequence-3D profile alignment - true - beta12orEarlier - An alignment of a sequence to a 3D profile (representing structures or a structure alignment). - 1.5 Sequence-structural profile alignment + 1.5 + An alignment of a sequence to a 3D profile (representing structures or a structure alignment). + beta12orEarlier + true @@ -1697,8 +1697,8 @@ Protein sequence-structure scoring matrix - Matrix of values used for scoring sequence-structure compatibility. beta12orEarlier + Matrix of values used for scoring sequence-structure compatibility. @@ -1710,8 +1710,8 @@ Sequence-structure alignment - An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)). beta12orEarlier + An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)). @@ -1723,10 +1723,10 @@ Amino acid annotation - beta12orEarlier - true - 1.4 An informative report about a specific amino acid. + 1.4 + true + beta12orEarlier @@ -1738,10 +1738,10 @@ Peptide annotation - beta12orEarlier - An informative report about a specific peptide. - true 1.4 + true + An informative report about a specific peptide. + beta12orEarlier @@ -1753,9 +1753,9 @@ Protein report - An informative human-readable report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data. - beta12orEarlier Gene product annotation + beta12orEarlier + An informative human-readable report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data. @@ -1767,12 +1767,12 @@ Protein property - The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. - Protein properties - Protein sequence statistics - beta12orEarlier - A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model. Protein physicochemical property + A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model. + beta12orEarlier + Protein sequence statistics + Protein properties + The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. @@ -1784,11 +1784,11 @@ Protein structural motifs and surfaces - Protein 3D motifs - beta12orEarlier - 1.8 - true Topic concerning 3D structural motifs in a protein. + true + 1.8 + beta12orEarlier + Protein 3D motifs @@ -1799,10 +1799,10 @@ Protein domain classification - beta12orEarlier - 1.5 - Data concerning the classification of the sequences and/or structures of protein structural domain(s). true + Data concerning the classification of the sequences and/or structures of protein structural domain(s). + 1.5 + beta12orEarlier @@ -1814,10 +1814,10 @@ Protein features report (domains) - beta12orEarlier - Topic concerning structural domains or 3D folds in a protein or polypeptide chain. - 1.8 true + 1.8 + Topic concerning structural domains or 3D folds in a protein or polypeptide chain. + beta12orEarlier @@ -1829,12 +1829,12 @@ Protein architecture report - true - beta12orEarlier - Protein structure report (architecture) - Protein property (architecture) - An informative report on architecture (spatial arrangement of secondary structure) of a protein structure. 1.4 + An informative report on architecture (spatial arrangement of secondary structure) of a protein structure. + Protein property (architecture) + Protein structure report (architecture) + beta12orEarlier + true @@ -1846,10 +1846,10 @@ Protein folding report - 1.8 - true - A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc. beta12orEarlier + A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc. + true + 1.8 @@ -1861,14 +1861,14 @@ Protein features (mutation) - Protein report (mutation) - beta13 - Protein structure report (mutation) - Protein property (mutation) - beta12orEarlier - true - Data on the effect of (typically point) mutation on protein folding, stability, structure and function. This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Data on the effect of (typically point) mutation on protein folding, stability, structure and function. + true + beta12orEarlier + Protein property (mutation) + Protein structure report (mutation) + beta13 + Protein report (mutation) @@ -1880,9 +1880,9 @@ Protein interaction raw data - beta12orEarlier - Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. + beta12orEarlier @@ -1900,10 +1900,10 @@ - An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with some other molecule(s), which might be another protein, nucleic acid or some other ligand. - Protein interaction record - Protein report (interaction) beta12orEarlier + Protein report (interaction) + Protein interaction record + An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with some other molecule(s), which might be another protein, nucleic acid or some other ligand. @@ -1921,10 +1921,10 @@ - Protein classification data - Protein family annotation - An informative report on a specific protein family or other classification or group of protein sequences or structures. beta12orEarlier + An informative report on a specific protein family or other classification or group of protein sequences or structures. + Protein family annotation + Protein classification data @@ -1936,8 +1936,8 @@ Vmax - The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large. beta12orEarlier + The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large. @@ -1949,8 +1949,8 @@ Km - beta12orEarlier Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction. + beta12orEarlier @@ -1962,10 +1962,10 @@ Nucleotide base annotation - 1.4 - An informative report about a specific nucleotide base. - true beta12orEarlier + true + An informative report about a specific nucleotide base. + 1.4 @@ -1977,10 +1977,10 @@ Nucleic acid property - beta12orEarlier - Nucleic acid physicochemical property - The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule. + The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. + Nucleic acid physicochemical property + beta12orEarlier @@ -1998,9 +1998,9 @@ - This is a broad data type and is used a placeholder for other, more specific types. - Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences. beta12orEarlier + Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences. + This is a broad data type and is used a placeholder for other, more specific types. @@ -2012,18 +2012,18 @@ Gene report - Moby:GeneInfo - Gene function (report) - Moby_namespace:Human_Readable_Description - beta12orEarlier - Gene annotation - This includes any report on a particular locus or gene. This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s). - Moby:gene - Nucleic acid features (gene and transcript structure) - Gene features report - Gene and transcript structure (report) - A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. Gene structure (repot) + A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. + Gene and transcript structure (report) + Gene features report + Nucleic acid features (gene and transcript structure) + Moby:gene + This includes any report on a particular locus or gene. This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s). + Gene annotation + beta12orEarlier + Moby_namespace:Human_Readable_Description + Gene function (report) + Moby:GeneInfo @@ -2035,10 +2035,10 @@ Gene classification - beta12orEarlier - A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products. - true beta12orEarlier + true + A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products. + beta12orEarlier @@ -2050,10 +2050,10 @@ DNA variation - beta12orEarlier - 1.8 - true Topic concerning stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. + true + 1.8 + beta12orEarlier @@ -2071,9 +2071,9 @@ - This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. - An informative report on a specific chromosome. beta12orEarlier + An informative report on a specific chromosome. + This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. @@ -2085,9 +2085,9 @@ Genotype/phenotype report - beta12orEarlier - Genotype/phenotype annotation An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes. + Genotype/phenotype annotation + beta12orEarlier @@ -2099,10 +2099,10 @@ Nucleic acid features report (primers) - Topic concerning PCR primers and hybridization oligos in a nucleic acid sequence. - beta12orEarlier - 1.8 true + 1.8 + beta12orEarlier + Topic concerning PCR primers and hybridization oligos in a nucleic acid sequence. @@ -2114,10 +2114,10 @@ PCR experiment report - Topic concerning PCR experiments, e.g. quantitative real-time PCR. - 1.8 - beta12orEarlier true + beta12orEarlier + 1.8 + Topic concerning PCR experiments, e.g. quantitative real-time PCR. @@ -2130,9 +2130,9 @@ Sequence trace - beta12orEarlier - This is the raw data produced by a DNA sequencing machine. Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores. + This is the raw data produced by a DNA sequencing machine. + beta12orEarlier @@ -2144,12 +2144,12 @@ Sequence assembly - SO:0000353 - Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included. - SO:0001248 - http://en.wikipedia.org/wiki/Sequence_assembly - An assembly of fragments of a (typically genomic) DNA sequence. beta12orEarlier + An assembly of fragments of a (typically genomic) DNA sequence. + http://en.wikipedia.org/wiki/Sequence_assembly + SO:0001248 + Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included. + SO:0000353 @@ -2167,9 +2167,9 @@ Radiation Hybrid (RH) scores - Radiation hybrid scores (RH) scores for one or more markers. - Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. beta12orEarlier + Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. + Radiation hybrid scores (RH) scores for one or more markers. @@ -2181,11 +2181,11 @@ Genetic linkage report - This includes linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). - An informative report on the linkage of alleles. - Linkage disequilibrium (report) - Gene annotation (linkage) beta12orEarlier + Gene annotation (linkage) + Linkage disequilibrium (report) + An informative report on the linkage of alleles. + This includes linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). @@ -2197,9 +2197,9 @@ Gene expression profile - Gene expression pattern - beta12orEarlier Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments. + beta12orEarlier + Gene expression pattern @@ -2211,10 +2211,10 @@ Microarray experiment report - beta12orEarlier - 1.8 - true Topic concerning microarray experiments including conditions, protocol, sample:data relationships etc. + true + 1.8 + beta12orEarlier @@ -2226,10 +2226,10 @@ Oligonucleotide probe data - Data on oligonucleotide probes (typically for use with DNA microarrays). - true - beta13 beta12orEarlier + beta13 + true + Data on oligonucleotide probes (typically for use with DNA microarrays). @@ -2241,11 +2241,11 @@ SAGE experimental data - beta12orEarlier - Serial analysis of gene expression (SAGE) experimental data - Output from a serial analysis of gene expression (SAGE) experiment. - true beta12orEarlier + true + Output from a serial analysis of gene expression (SAGE) experiment. + Serial analysis of gene expression (SAGE) experimental data + beta12orEarlier @@ -2257,11 +2257,11 @@ MPSS experimental data - true - Massively parallel signature sequencing (MPSS) experimental data - beta12orEarlier - Massively parallel signature sequencing (MPSS) data. beta12orEarlier + Massively parallel signature sequencing (MPSS) data. + beta12orEarlier + Massively parallel signature sequencing (MPSS) experimental data + true @@ -2273,11 +2273,11 @@ SBS experimental data - Sequencing by synthesis (SBS) data. - Sequencing by synthesis (SBS) experimental data - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Sequencing by synthesis (SBS) experimental data + Sequencing by synthesis (SBS) data. @@ -2289,8 +2289,8 @@ Sequence tag profile (with gene assignment) - Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers. beta12orEarlier + Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers. @@ -2302,8 +2302,8 @@ Protein X-ray crystallographic data - beta12orEarlier X-ray crystallography data. + beta12orEarlier @@ -2315,8 +2315,8 @@ Protein NMR data - beta12orEarlier Protein nuclear magnetic resonance (NMR) raw data. + beta12orEarlier @@ -2328,8 +2328,8 @@ Protein circular dichroism (CD) spectroscopic data - Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data. beta12orEarlier + Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data. @@ -2347,9 +2347,9 @@ - EM volume map - Volume map data from electron microscopy. beta12orEarlier + Volume map data from electron microscopy. + EM volume map @@ -2367,9 +2367,9 @@ - This might include the location in the model of the known features of a particular macromolecule. - Annotation on a structural 3D model (volume map) from electron microscopy. beta12orEarlier + Annotation on a structural 3D model (volume map) from electron microscopy. + This might include the location in the model of the known features of a particular macromolecule. @@ -2387,8 +2387,8 @@ - Two-dimensional gel electrophoresis image beta12orEarlier + Two-dimensional gel electrophoresis image @@ -2406,8 +2406,8 @@ - Spectra from mass spectrometry. beta12orEarlier + Spectra from mass spectrometry. @@ -2426,10 +2426,10 @@ - beta12orEarlier - A set of peptide masses (peptide mass fingerprint) from mass spectrometry. - Protein fingerprint Peak list + Protein fingerprint + A set of peptide masses (peptide mass fingerprint) from mass spectrometry. + beta12orEarlier @@ -2447,8 +2447,8 @@ - beta12orEarlier Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database. + beta12orEarlier @@ -2460,10 +2460,10 @@ Pathway or network annotation - beta12orEarlier - An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway. - true beta12orEarlier + true + An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway. + beta12orEarlier @@ -2475,10 +2475,10 @@ Biological pathway map - beta12orEarlier - A map (typically a diagram) of a biological pathway. - true beta12orEarlier + true + A map (typically a diagram) of a biological pathway. + beta12orEarlier @@ -2490,10 +2490,10 @@ Data resource definition - A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper. - 1.5 - true beta12orEarlier + true + 1.5 + A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper. @@ -2505,8 +2505,8 @@ Workflow metadata - beta12orEarlier Basic information, annotation or documentation concerning a workflow (but not the workflow itself). + beta12orEarlier @@ -2524,9 +2524,9 @@ - A biological model represented in mathematical terms. - beta12orEarlier Biological model + beta12orEarlier + A biological model represented in mathematical terms. @@ -2538,8 +2538,8 @@ Statistical estimate score - A value representing estimated statistical significance of some observed data; typically sequence database hits. beta12orEarlier + A value representing estimated statistical significance of some observed data; typically sequence database hits. @@ -2551,10 +2551,10 @@ EMBOSS database resource definition - 1.5 - true - Resource definition for an EMBOSS database. beta12orEarlier + Resource definition for an EMBOSS database. + true + 1.5 @@ -2566,15 +2566,15 @@ Version information - http://usefulinc.com/ns/doap#Version - true - http://semanticscience.org/resource/SIO_000653 - Information on a version of software or data, for example name, version number and release date. - beta12orEarlier - http://www.ebi.ac.uk/swo/maturity/SWO_9000061 - Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. - 1.5 "http://purl.obolibrary.org/obo/IAO_0000129" + 1.5 + Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. + http://www.ebi.ac.uk/swo/maturity/SWO_9000061 + beta12orEarlier + Information on a version of software or data, for example name, version number and release date. + http://semanticscience.org/resource/SIO_000653 + true + http://usefulinc.com/ns/doap#Version @@ -2586,9 +2586,9 @@ Database cross-mapping - The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc. - A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases. beta12orEarlier + A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases. + The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc. @@ -2606,8 +2606,8 @@ - beta12orEarlier An index of data of biological relevance. + beta12orEarlier @@ -2625,9 +2625,9 @@ - beta12orEarlier - Database index annotation A report of an analysis of an index of biological data. + Database index annotation + beta12orEarlier @@ -2639,8 +2639,8 @@ Database metadata - beta12orEarlier Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc. + beta12orEarlier @@ -2652,8 +2652,8 @@ Tool metadata - Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation. beta12orEarlier + Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation. @@ -2665,11 +2665,11 @@ Job metadata - Textual metadata on a submitted or completed job. - Moby:PDGJOB - 1.5 - true beta12orEarlier + true + 1.5 + Moby:PDGJOB + Textual metadata on a submitted or completed job. @@ -2681,8 +2681,8 @@ User metadata - Textual metadata on a software author or end-user, for example a person or other software. beta12orEarlier + Textual metadata on a software author or end-user, for example a person or other software. @@ -2700,12 +2700,12 @@ - Chemical compound annotation - beta12orEarlier - An informative report on a specific chemical compound. - Chemical structure report - Small molecule report Small molecule annotation + Small molecule report + Chemical structure report + An informative report on a specific chemical compound. + beta12orEarlier + Chemical compound annotation @@ -2717,10 +2717,10 @@ Cell line report - beta12orEarlier - Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on. - Cell line annotation Organism strain data + Cell line annotation + Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on. + beta12orEarlier @@ -2732,10 +2732,10 @@ Scent annotation - true - 1.4 - An informative report about a specific scent. beta12orEarlier + An informative report about a specific scent. + 1.4 + true @@ -2747,10 +2747,10 @@ Ontology term - Ontology terms - A term (name) from an ontology. - beta12orEarlier Ontology class name + beta12orEarlier + A term (name) from an ontology. + Ontology terms @@ -2762,10 +2762,10 @@ Ontology concept data - Data concerning or derived from a concept from a biological ontology. - Ontology term metadata - Ontology class metadata beta12orEarlier + Ontology class metadata + Ontology term metadata + Data concerning or derived from a concept from a biological ontology. @@ -2777,16 +2777,16 @@ Keyword - Text - Terms - Moby:Global_Keyword - Moby:Wildcard_Query - Moby:BooleanQueryString - beta12orEarlier - Moby:QueryString - Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. - Keyword(s) or phrase(s) used (typically) for text-searching purposes. Phrases + Keyword(s) or phrase(s) used (typically) for text-searching purposes. + Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. + Moby:QueryString + beta12orEarlier + Moby:BooleanQueryString + Moby:Wildcard_Query + Moby:Global_Keyword + Terms + Text @@ -2798,13 +2798,13 @@ Citation - beta12orEarlier - Moby:Publication - Bibliographic reference - Reference - Moby:GCP_SimpleCitation - A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available. Bibliographic data that uniquely identifies a scientific article, book or other published material. + A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available. + Moby:GCP_SimpleCitation + Reference + Bibliographic reference + Moby:Publication + beta12orEarlier @@ -2822,8 +2822,8 @@ - beta12orEarlier A document of scientific text, typically a full text article from a scientific journal. + beta12orEarlier @@ -2834,11 +2834,11 @@ Text mining report - - A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles. - Text mining output - beta12orEarlier + An abstract of the results of text mining. + beta12orEarlier + Text mining output + A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles. @@ -2850,10 +2850,10 @@ Entity identifier - An identifier of a biological entity or phenomenon. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + An identifier of a biological entity or phenomenon. @@ -2865,10 +2865,10 @@ Data resource identifier - beta12orEarlier - beta12orEarlier - An identifier of a data resource. true + An identifier of a data resource. + beta12orEarlier + beta12orEarlier @@ -2880,9 +2880,9 @@ Identifier (typed) - An identifier that identifies a particular type of data. - This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. beta12orEarlier + This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. + An identifier that identifies a particular type of data. @@ -2895,8 +2895,8 @@ Tool identifier - beta12orEarlier An identifier of a bioinformatics tool, e.g. an application or web service. + beta12orEarlier @@ -2909,10 +2909,10 @@ Discrete entity identifier - Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence). - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence). @@ -2924,10 +2924,10 @@ Entity feature identifier - beta12orEarlier - Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing). - beta12orEarlier true + beta12orEarlier + Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing). + beta12orEarlier @@ -2939,10 +2939,10 @@ Entity collection identifier - Name or other identifier of a collection of discrete biological entities. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Name or other identifier of a collection of discrete biological entities. @@ -2954,10 +2954,10 @@ Phenomenon identifier - Name or other identifier of a physical, observable biological occurrence or event. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Name or other identifier of a physical, observable biological occurrence or event. @@ -2969,8 +2969,8 @@ Molecule identifier - beta12orEarlier Name or other identifier of a molecule. + beta12orEarlier @@ -2983,9 +2983,9 @@ Atom ID - beta12orEarlier - Identifier (e.g. character symbol) of a specific atom. Atom identifier + Identifier (e.g. character symbol) of a specific atom. + beta12orEarlier @@ -2999,8 +2999,8 @@ Molecule name - beta12orEarlier Name of a specific molecule. + beta12orEarlier @@ -3013,12 +3013,12 @@ Molecule type - Protein|DNA|RNA - A label (text token) describing the type a molecule. - beta12orEarlier - 1.5 - true For example, 'Protein', 'DNA', 'RNA' etc. + true + 1.5 + beta12orEarlier + A label (text token) describing the type a molecule. + Protein|DNA|RNA @@ -3030,10 +3030,10 @@ Chemical identifier - Unique identifier of a chemical compound. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + Unique identifier of a chemical compound. @@ -3052,8 +3052,8 @@ - Name of a chromosome. beta12orEarlier + Name of a chromosome. @@ -3066,8 +3066,8 @@ Peptide identifier - beta12orEarlier Identifier of a peptide chain. + beta12orEarlier @@ -3086,8 +3086,8 @@ - Identifier of a protein. beta12orEarlier + Identifier of a protein. @@ -3101,9 +3101,9 @@ Compound name - beta12orEarlier - Unique name of a chemical compound. Chemical name + Unique name of a chemical compound. + beta12orEarlier @@ -3116,8 +3116,8 @@ Chemical registry number - Unique registry number of a chemical compound. beta12orEarlier + Unique registry number of a chemical compound. @@ -3130,10 +3130,10 @@ Ligand identifier - beta12orEarlier - Code word for a ligand, for example from a PDB file. - beta12orEarlier true + beta12orEarlier + Code word for a ligand, for example from a PDB file. + beta12orEarlier @@ -3151,8 +3151,8 @@ - Identifier of a drug. beta12orEarlier + Identifier of a drug. @@ -3171,9 +3171,9 @@ - Residue identifier - beta12orEarlier Identifier of an amino acid. + beta12orEarlier + Residue identifier @@ -3186,8 +3186,8 @@ Nucleotide identifier - Name or other identifier of a nucleotide. beta12orEarlier + Name or other identifier of a nucleotide. @@ -3200,8 +3200,8 @@ Monosaccharide identifier - Identifier of a monosaccharide. beta12orEarlier + Identifier of a monosaccharide. @@ -3214,10 +3214,10 @@ Chemical name (ChEBI) - This is the recommended chemical name for use for example in database annotation. - beta12orEarlier - Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound. ChEBI chemical name + Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound. + beta12orEarlier + This is the recommended chemical name for use for example in database annotation. @@ -3230,9 +3230,9 @@ Chemical name (IUPAC) - beta12orEarlier - IUPAC chemical name IUPAC recommended name of a chemical compound. + IUPAC chemical name + beta12orEarlier @@ -3245,9 +3245,9 @@ Chemical name (INN) - International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO). - beta12orEarlier INN chemical name + beta12orEarlier + International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO). @@ -3260,9 +3260,9 @@ Chemical name (brand) - beta12orEarlier - Brand chemical name Brand name of a chemical compound. + Brand chemical name + beta12orEarlier @@ -3275,9 +3275,9 @@ Chemical name (synonymous) - Synonymous name of a chemical compound. - Synonymous chemical name beta12orEarlier + Synonymous chemical name + Synonymous name of a chemical compound. @@ -3290,9 +3290,9 @@ Chemical registry number (CAS) - beta12orEarlier - CAS registry number of a chemical compound. CAS chemical registry number + CAS registry number of a chemical compound. + beta12orEarlier @@ -3305,9 +3305,9 @@ Chemical registry number (Beilstein) - Beilstein registry number of a chemical compound. - beta12orEarlier Beilstein chemical registry number + beta12orEarlier + Beilstein registry number of a chemical compound. @@ -3320,9 +3320,9 @@ Chemical registry number (Gmelin) - Gmelin registry number of a chemical compound. - beta12orEarlier Gmelin chemical registry number + beta12orEarlier + Gmelin registry number of a chemical compound. @@ -3335,10 +3335,10 @@ HET group name - beta12orEarlier - Component identifier code - Short ligand name 3-letter code word for a ligand (HET group) from a PDB file, for example ATP. + Short ligand name + Component identifier code + beta12orEarlier @@ -3351,8 +3351,8 @@ Amino acid name - beta12orEarlier String of one or more ASCII characters representing an amino acid. + beta12orEarlier @@ -3366,8 +3366,8 @@ Nucleotide code - String of one or more ASCII characters representing a nucleotide. beta12orEarlier + String of one or more ASCII characters representing a nucleotide. @@ -3386,16 +3386,16 @@ - Polypeptide chain identifier - This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA - PDB chain identifier - PDB strand id - Protein chain identifier - PDBML:pdbx_PDB_strand_id - Identifier of a polypeptide chain from a protein. - Chain identifier - WHATIF: chain beta12orEarlier + WHATIF: chain + Chain identifier + Identifier of a polypeptide chain from a protein. + PDBML:pdbx_PDB_strand_id + Protein chain identifier + PDB strand id + PDB chain identifier + This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA + Polypeptide chain identifier @@ -3409,8 +3409,8 @@ Protein name - beta12orEarlier Name of a protein. + beta12orEarlier @@ -3423,8 +3423,8 @@ Enzyme identifier - Name or other identifier of an enzyme or record from a database of enzymes. beta12orEarlier + Name or other identifier of an enzyme or record from a database of enzymes. @@ -3437,14 +3437,14 @@ EC number - Enzyme Commission number - beta12orEarlier - Moby:Annotated_EC_Number - EC - An Enzyme Commission (EC) number of an enzyme. - Moby:EC_Number - EC code [0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+ + EC code + Moby:EC_Number + An Enzyme Commission (EC) number of an enzyme. + EC + Moby:Annotated_EC_Number + beta12orEarlier + Enzyme Commission number @@ -3458,8 +3458,8 @@ Enzyme name - beta12orEarlier Name of an enzyme. + beta12orEarlier @@ -3472,8 +3472,8 @@ Restriction enzyme name - beta12orEarlier Name of a restriction enzyme. + beta12orEarlier @@ -3486,10 +3486,10 @@ Sequence position specification - true - beta12orEarlier - A specification (partial or complete) of one or more positions or regions of a molecular sequence or map. 1.5 + A specification (partial or complete) of one or more positions or regions of a molecular sequence or map. + beta12orEarlier + true @@ -3502,8 +3502,8 @@ Sequence feature ID - beta12orEarlier A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file. + beta12orEarlier @@ -3516,12 +3516,12 @@ Sequence position - A position of one or more points (base or residue) in a sequence, or part of such a specification. - SO:0000735 - PDBML:_atom_site.id - beta12orEarlier - WHATIF: PDBx_atom_site WHATIF: number + WHATIF: PDBx_atom_site + beta12orEarlier + PDBML:_atom_site.id + SO:0000735 + A position of one or more points (base or residue) in a sequence, or part of such a specification. @@ -3533,8 +3533,8 @@ Sequence range - Specification of range(s) of sequence positions. beta12orEarlier + Specification of range(s) of sequence positions. @@ -3546,10 +3546,10 @@ Nucleic acid feature identifier - true - Name or other identifier of an nucleic acid feature. - beta12orEarlier beta12orEarlier + beta12orEarlier + Name or other identifier of an nucleic acid feature. + true @@ -3561,10 +3561,10 @@ Protein feature identifier - beta12orEarlier - beta12orEarlier - true Name or other identifier of a protein feature. + true + beta12orEarlier + beta12orEarlier @@ -3576,11 +3576,11 @@ Sequence feature key - A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence. - beta12orEarlier - Sequence feature type - The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key. Sequence feature method + The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key. + Sequence feature type + beta12orEarlier + A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence. @@ -3592,9 +3592,9 @@ Sequence feature qualifier - Feature qualifiers hold information about a feature beyond that provided by the feature key and location. - Typically one of the EMBL or Swiss-Prot feature qualifiers. beta12orEarlier + Typically one of the EMBL or Swiss-Prot feature qualifiers. + Feature qualifiers hold information about a feature beyond that provided by the feature key and location. @@ -3606,10 +3606,10 @@ Sequence feature label - beta12orEarlier - A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature. - Typically an EMBL or Swiss-Prot feature label. Sequence feature name + Typically an EMBL or Swiss-Prot feature label. + A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature. + beta12orEarlier @@ -3622,9 +3622,9 @@ EMBOSS Uniform Feature Object - The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications. - UFO beta12orEarlier + UFO + The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications. @@ -3636,10 +3636,10 @@ Codon name - true - String of one or more ASCII characters representing a codon. - beta12orEarlier beta12orEarlier + beta12orEarlier + String of one or more ASCII characters representing a codon. + true @@ -3657,9 +3657,9 @@ - beta12orEarlier - An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database. Moby:GeneAccessionList + An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database. + beta12orEarlier @@ -3672,10 +3672,10 @@ Gene symbol - The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name. - Moby_namespace:Global_GeneCommonName - beta12orEarlier Moby_namespace:Global_GeneSymbol + beta12orEarlier + Moby_namespace:Global_GeneCommonName + The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name. @@ -3689,15 +3689,15 @@ Gene ID (NCBI) - beta12orEarlier - NCBI gene ID - An NCBI unique identifier of a gene. - http://www.geneontology.org/doc/GO.xrf_abbs:LocusID - Gene identifier (Entrez) - Entrez gene ID - http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene - Gene identifier (NCBI) NCBI geneid + Gene identifier (NCBI) + http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene + Entrez gene ID + Gene identifier (Entrez) + http://www.geneontology.org/doc/GO.xrf_abbs:LocusID + An NCBI unique identifier of a gene. + NCBI gene ID + beta12orEarlier @@ -3710,10 +3710,10 @@ Gene identifier (NCBI RefSeq) - An NCBI RefSeq unique identifier of a gene. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + An NCBI RefSeq unique identifier of a gene. @@ -3725,10 +3725,10 @@ Gene identifier (NCBI UniGene) - true - beta12orEarlier - An NCBI UniGene unique identifier of a gene. beta12orEarlier + An NCBI UniGene unique identifier of a gene. + beta12orEarlier + true @@ -3740,11 +3740,11 @@ Gene identifier (Entrez) - beta12orEarlier - [0-9]+ - true - beta12orEarlier An Entrez unique identifier of a gene. + beta12orEarlier + true + [0-9]+ + beta12orEarlier @@ -3756,9 +3756,9 @@ Gene ID (CGD) - beta12orEarlier - Identifier of a gene or feature from the CGD database. CGD ID + Identifier of a gene or feature from the CGD database. + beta12orEarlier @@ -3771,8 +3771,8 @@ Gene ID (DictyBase) - Identifier of a gene from DictyBase. beta12orEarlier + Identifier of a gene from DictyBase. @@ -3786,9 +3786,9 @@ Ensembl gene ID - Unique identifier for a gene (or other feature) from the Ensembl database. - Gene ID (Ensembl) beta12orEarlier + Gene ID (Ensembl) + Unique identifier for a gene (or other feature) from the Ensembl database. @@ -3802,10 +3802,10 @@ Gene ID (SGD) - beta12orEarlier - SGD identifier - S[0-9]+ Identifier of an entry from the SGD database. + S[0-9]+ + SGD identifier + beta12orEarlier @@ -3818,11 +3818,11 @@ Gene ID (GeneDB) - Identifier of a gene from the GeneDB database. - [a-zA-Z_0-9\.-]* - beta12orEarlier - GeneDB identifier Moby_namespace:GeneDB + GeneDB identifier + beta12orEarlier + [a-zA-Z_0-9\.-]* + Identifier of a gene from the GeneDB database. @@ -3836,8 +3836,8 @@ TIGR identifier - Identifier of an entry from the TIGR database. beta12orEarlier + Identifier of an entry from the TIGR database. @@ -3851,9 +3851,9 @@ TAIR accession (gene) - Identifier of an gene from the TAIR database. - beta12orEarlier Gene:[0-9]{7} + beta12orEarlier + Identifier of an gene from the TAIR database. @@ -3873,9 +3873,9 @@ - This is typically a character or string concatenated with a PDB identifier and a chain identifier. - Identifier of a protein structural domain. beta12orEarlier + Identifier of a protein structural domain. + This is typically a character or string concatenated with a PDB identifier and a chain identifier. @@ -3888,8 +3888,8 @@ SCOP domain identifier - beta12orEarlier Identifier of a protein domain (or other node) from the SCOP database. + beta12orEarlier @@ -3902,10 +3902,10 @@ CATH domain ID - Identifier of a protein domain from CATH. - CATH domain identifier - beta12orEarlier 1nr3A00 + beta12orEarlier + CATH domain identifier + Identifier of a protein domain from CATH. @@ -3918,9 +3918,9 @@ SCOP concise classification string (sccs) - An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs. - beta12orEarlier A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification. + beta12orEarlier + An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs. @@ -3933,12 +3933,12 @@ SCOP sunid - 33229 - SCOP unique identifier - sunid - A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level. - beta12orEarlier Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229. + beta12orEarlier + A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level. + sunid + SCOP unique identifier + 33229 @@ -3951,11 +3951,11 @@ CATH node ID - beta12orEarlier - CATH node identifier - A code number identifying a node from the CATH database. - CATH code 3.30.1190.10.1.1.1.1.1 + CATH code + A code number identifying a node from the CATH database. + CATH node identifier + beta12orEarlier @@ -3968,8 +3968,8 @@ Kingdom name - beta12orEarlier The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes). + beta12orEarlier @@ -3982,9 +3982,9 @@ Species name - beta12orEarlier - Organism species The name of a species (typically a taxonomic group) of organism. + Organism species + beta12orEarlier @@ -3998,8 +3998,8 @@ Strain name - The name of a strain of an organism variant, typically a plant, virus or bacterium. beta12orEarlier + The name of a strain of an organism variant, typically a plant, virus or bacterium. @@ -4012,9 +4012,9 @@ URI - beta12orEarlier - URIs A string of characters that name or otherwise identify a resource on the Internet. + URIs + beta12orEarlier @@ -4032,9 +4032,9 @@ - beta12orEarlier - Database identifier An identifier of a biological or bioinformatics database. + Database identifier + beta12orEarlier @@ -4047,8 +4047,8 @@ Directory name - The name of a directory. beta12orEarlier + The name of a directory. @@ -4061,8 +4061,8 @@ File name - beta12orEarlier The name (or part of a name) of a file (of any type). + beta12orEarlier @@ -4082,8 +4082,8 @@ - Name of an ontology of biological or bioinformatics concepts and relations. beta12orEarlier + Name of an ontology of biological or bioinformatics concepts and relations. @@ -4096,10 +4096,10 @@ URL - beta12orEarlier - Moby:Link - Moby:URL A Uniform Resource Locator (URL). + Moby:URL + Moby:Link + beta12orEarlier @@ -4111,8 +4111,8 @@ URN - A Uniform Resource Name (URN). beta12orEarlier + A Uniform Resource Name (URN). @@ -4124,10 +4124,10 @@ LSID - A Life Science Identifier (LSID) - a unique identifier of some data. - Life Science Identifier - LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:<Authority>:<Namespace>:<ObjectID>[:<Version>] beta12orEarlier + LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:<Authority>:<Namespace>:<ObjectID>[:<Version>] + Life Science Identifier + A Life Science Identifier (LSID) - a unique identifier of some data. @@ -4140,8 +4140,8 @@ Database name - beta12orEarlier The name of a biological or bioinformatics database. + beta12orEarlier @@ -4154,10 +4154,10 @@ Sequence database name - beta12orEarlier - beta13 - true The name of a molecular sequence database. + true + beta13 + beta12orEarlier @@ -4169,8 +4169,8 @@ Enumerated file name - The name of a file (of any type) with restricted possible values. beta12orEarlier + The name of a file (of any type) with restricted possible values. @@ -4183,9 +4183,9 @@ File name extension - beta12orEarlier - A file extension is the characters appearing after the final '.' in the file name. The extension of a file name. + A file extension is the characters appearing after the final '.' in the file name. + beta12orEarlier @@ -4198,9 +4198,9 @@ File base name - A file base name is the file name stripped of its directory specification and extension. - The base name of a file. beta12orEarlier + The base name of a file. + A file base name is the file name stripped of its directory specification and extension. @@ -4220,8 +4220,8 @@ - Name of a QSAR descriptor. beta12orEarlier + Name of a QSAR descriptor. @@ -4234,11 +4234,11 @@ Database entry identifier - beta12orEarlier - An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type. - beta12orEarlier - This concept is required for completeness. It should never have child concepts. true + This concept is required for completeness. It should never have child concepts. + beta12orEarlier + An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type. + beta12orEarlier @@ -4256,8 +4256,8 @@ - beta12orEarlier An identifier of molecular sequence(s) or entries from a molecular sequence database. + beta12orEarlier @@ -4277,8 +4277,8 @@ - beta12orEarlier An identifier of a set of molecular sequence(s). + beta12orEarlier @@ -4291,10 +4291,10 @@ Sequence signature identifier - Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns. @@ -4314,8 +4314,8 @@ - beta12orEarlier Identifier of a molecular sequence alignment, for example a record from an alignment database. + beta12orEarlier @@ -4328,10 +4328,10 @@ Phylogenetic distance matrix identifier - beta12orEarlier - true - Identifier of a phylogenetic distance matrix. beta12orEarlier + Identifier of a phylogenetic distance matrix. + true + beta12orEarlier @@ -4350,8 +4350,8 @@ - Identifier of a phylogenetic tree for example from a phylogenetic tree database. beta12orEarlier + Identifier of a phylogenetic tree for example from a phylogenetic tree database. @@ -4370,9 +4370,9 @@ - beta12orEarlier - Substitution matrix identifier An identifier of a comparison matrix. + Substitution matrix identifier + beta12orEarlier @@ -4386,8 +4386,8 @@ Structure ID - A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database. beta12orEarlier + A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database. @@ -4407,9 +4407,9 @@ - beta12orEarlier - Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment). Structural profile identifier + Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment). + beta12orEarlier @@ -4429,8 +4429,8 @@ - Identifier of an entry from a database of tertiary structure alignments. beta12orEarlier + Identifier of an entry from a database of tertiary structure alignments. @@ -4450,8 +4450,8 @@ - beta12orEarlier Identifier of an index of amino acid physicochemical and biochemical property data. + beta12orEarlier @@ -4471,9 +4471,9 @@ - Identifier of a report of protein interactions from a protein interaction database (typically). - Molecular interaction ID beta12orEarlier + Molecular interaction ID + Identifier of a report of protein interactions from a protein interaction database (typically). @@ -4492,9 +4492,9 @@ - beta12orEarlier - Identifier of a protein family. Protein secondary database record identifier + Identifier of a protein family. + beta12orEarlier @@ -4511,17 +4511,17 @@ - + - + - beta12orEarlier Unique name of a codon usage table. + beta12orEarlier @@ -4535,8 +4535,8 @@ Transcription factor identifier - beta12orEarlier Identifier of a transcription factor (or a TF binding site). + beta12orEarlier @@ -4555,8 +4555,8 @@ - Identifier of an entry from a database of microarray data. beta12orEarlier + Identifier of an entry from a database of microarray data. @@ -4576,8 +4576,8 @@ - beta12orEarlier Identifier of an entry from a database of electron microscopy data. + beta12orEarlier @@ -4597,9 +4597,9 @@ - Gene expression profile identifier - beta12orEarlier Accession of a report of gene expression (e.g. a gene expression profile) from a database. + beta12orEarlier + Gene expression profile identifier @@ -4619,8 +4619,8 @@ - beta12orEarlier Identifier of an entry from a database of genotypes and phenotypes. + beta12orEarlier @@ -4639,8 +4639,8 @@ - beta12orEarlier Identifier of an entry from a database of biological pathways or networks. + beta12orEarlier @@ -4654,8 +4654,8 @@ Workflow ID - Identifier of a biological or biomedical workflow, typically from a database of workflows. beta12orEarlier + Identifier of a biological or biomedical workflow, typically from a database of workflows. @@ -4668,9 +4668,9 @@ Data resource definition ID - Data resource definition identifier - Identifier of a data type definition from some provider. beta12orEarlier + Identifier of a data type definition from some provider. + Data resource definition identifier @@ -4689,9 +4689,9 @@ - Identifier of a mathematical model, typically an entry from a database. - beta12orEarlier Biological model identifier + beta12orEarlier + Identifier of a mathematical model, typically an entry from a database. @@ -4710,10 +4710,10 @@ - Small molecule identifier - Identifier of an entry from a database of chemicals. - Chemical compound identifier beta12orEarlier + Chemical compound identifier + Identifier of an entry from a database of chemicals. + Small molecule identifier @@ -4727,9 +4727,9 @@ Ontology concept ID - Ontology concept ID - beta12orEarlier A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations. + beta12orEarlier + Ontology concept ID @@ -4749,9 +4749,9 @@ - Article identifier - Unique identifier of a scientific article. beta12orEarlier + Unique identifier of a scientific article. + Article identifier @@ -4765,9 +4765,9 @@ FlyBase ID - beta12orEarlier - FB[a-zA-Z_0-9]{2}[0-9]{7} Identifier of an object from the FlyBase database. + FB[a-zA-Z_0-9]{2}[0-9]{7} + beta12orEarlier @@ -4781,8 +4781,8 @@ WormBase name - beta12orEarlier Name of an object from the WormBase database, usually a human-readable name. + beta12orEarlier @@ -4795,9 +4795,9 @@ WormBase class - A WormBase class describes the type of object such as 'sequence' or 'protein'. - Class of an object from the WormBase database. beta12orEarlier + Class of an object from the WormBase database. + A WormBase class describes the type of object such as 'sequence' or 'protein'. @@ -4811,9 +4811,9 @@ Sequence accession - Sequence accession number - A persistent, unique identifier of a molecular sequence database entry. beta12orEarlier + A persistent, unique identifier of a molecular sequence database entry. + Sequence accession number @@ -4826,11 +4826,11 @@ Sequence type - beta12orEarlier - true - A label (text token) describing a type of molecular sequence. - Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc). 1.5 + Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc). + A label (text token) describing a type of molecular sequence. + true + beta12orEarlier @@ -4843,9 +4843,9 @@ EMBOSS Uniform Sequence Address - The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications. - beta12orEarlier EMBOSS USA + beta12orEarlier + The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications. @@ -4864,9 +4864,9 @@ - beta12orEarlier - Protein sequence accession number Accession number of a protein sequence database entry. + Protein sequence accession number + beta12orEarlier @@ -4885,9 +4885,9 @@ - Nucleotide sequence accession number - beta12orEarlier Accession number of a nucleotide sequence database entry. + beta12orEarlier + Nucleotide sequence accession number @@ -4900,10 +4900,10 @@ RefSeq accession - (NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+ - RefSeq ID - beta12orEarlier Accession number of a RefSeq database entry. + beta12orEarlier + RefSeq ID + (NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+ @@ -4916,12 +4916,12 @@ UniProt accession (extended) - 1.0 - Q7M1G0|P43353-2|P01012.107 - beta12orEarlier - [A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+ - Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number. true + Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number. + [A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+ + beta12orEarlier + Q7M1G0|P43353-2|P01012.107 + 1.0 @@ -4939,10 +4939,10 @@ - PIR accession number - PIR ID - beta12orEarlier An identifier of PIR sequence database entry. + beta12orEarlier + PIR ID + PIR accession number @@ -4955,10 +4955,10 @@ TREMBL accession - 1.2 - true - Identifier of a TREMBL sequence database entry. beta12orEarlier + Identifier of a TREMBL sequence database entry. + true + 1.2 @@ -4970,9 +4970,9 @@ Gramene primary identifier - Primary identifier of a Gramene database entry. - Gramene primary ID beta12orEarlier + Gramene primary ID + Primary identifier of a Gramene database entry. @@ -4985,8 +4985,8 @@ EMBL/GenBank/DDBJ ID - beta12orEarlier Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases. + beta12orEarlier @@ -4999,12 +4999,12 @@ Sequence cluster ID (UniGene) - A unique identifier of an entry (gene cluster) from the NCBI UniGene database. - beta12orEarlier - UniGene cluster ID - UniGene ID - UniGene cluster id UniGene identifier + UniGene cluster id + UniGene ID + UniGene cluster ID + beta12orEarlier + A unique identifier of an entry (gene cluster) from the NCBI UniGene database. @@ -5018,9 +5018,9 @@ dbEST accession - beta12orEarlier - Identifier of a dbEST database entry. dbEST ID + Identifier of a dbEST database entry. + beta12orEarlier @@ -5033,9 +5033,9 @@ dbSNP ID - Identifier of a dbSNP database entry. - dbSNP identifier beta12orEarlier + dbSNP identifier + Identifier of a dbSNP database entry. @@ -5048,11 +5048,11 @@ EMBOSS sequence type - The EMBOSS type of a molecular sequence. - beta12orEarlier - See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. - true beta12orEarlier + true + See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. + beta12orEarlier + The EMBOSS type of a molecular sequence. @@ -5064,10 +5064,10 @@ EMBOSS listfile - beta12orEarlier - true - List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile). 1.5 + List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile). + true + beta12orEarlier @@ -5085,8 +5085,8 @@ - beta12orEarlier An identifier of a cluster of molecular sequence(s). + beta12orEarlier @@ -5099,9 +5099,9 @@ Sequence cluster ID (COG) - Unique identifier of an entry from the COG database. - beta12orEarlier COG ID + beta12orEarlier + Unique identifier of an entry from the COG database. @@ -5120,8 +5120,8 @@ - beta12orEarlier Identifier of a sequence motif, for example an entry from a motif database. + beta12orEarlier @@ -5141,9 +5141,9 @@ - A sequence profile typically represents a sequence alignment. - beta12orEarlier Identifier of a sequence profile. + beta12orEarlier + A sequence profile typically represents a sequence alignment. @@ -5156,8 +5156,8 @@ ELM ID - beta12orEarlier Identifier of an entry from the ELMdb database of protein functional sites. + beta12orEarlier @@ -5170,10 +5170,10 @@ Prosite accession number - Prosite ID - PS[0-9]{5} - Accession number of an entry from the Prosite database. beta12orEarlier + Accession number of an entry from the Prosite database. + PS[0-9]{5} + Prosite ID @@ -5192,8 +5192,8 @@ - beta12orEarlier Unique identifier or name of a HMMER hidden Markov model. + beta12orEarlier @@ -5206,8 +5206,8 @@ JASPAR profile ID - Unique identifier or name of a profile from the JASPAR database. beta12orEarlier + Unique identifier or name of a profile from the JASPAR database. @@ -5220,11 +5220,11 @@ Sequence alignment type - A label (text token) describing the type of a sequence alignment. - Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on. - true - 1.5 beta12orEarlier + 1.5 + true + Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on. + A label (text token) describing the type of a sequence alignment. @@ -5236,10 +5236,10 @@ BLAST sequence alignment type - The type of a BLAST sequence alignment. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + The type of a BLAST sequence alignment. @@ -5251,12 +5251,12 @@ Phylogenetic tree type - nj|upgmp - 1.5 - A label (text token) describing the type of a phylogenetic tree. - true - beta12orEarlier For example 'nj', 'upgmp' etc. + beta12orEarlier + true + A label (text token) describing the type of a phylogenetic tree. + 1.5 + nj|upgmp @@ -5268,8 +5268,8 @@ TreeBASE study accession number - beta12orEarlier Accession number of an entry from the TreeBASE database. + beta12orEarlier @@ -5282,8 +5282,8 @@ TreeFam accession number - Accession number of an entry from the TreeFam database. beta12orEarlier + Accession number of an entry from the TreeFam database. @@ -5296,13 +5296,13 @@ Comparison matrix type - For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used. - Substitution matrix type - A label (text token) describing the type of a comparison matrix. - blosum|pam|gonnet|id - beta12orEarlier - true 1.5 + true + beta12orEarlier + blosum|pam|gonnet|id + A label (text token) describing the type of a comparison matrix. + Substitution matrix type + For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used. @@ -5321,10 +5321,10 @@ - Unique name or identifier of a comparison matrix. - See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix. - Substitution matrix name beta12orEarlier + Substitution matrix name + See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix. + Unique name or identifier of a comparison matrix. @@ -5337,11 +5337,11 @@ PDB ID - beta12orEarlier - PDB identifier - PDBID - [a-zA-Z_0-9]{4} An identifier of an entry from the PDB database. + [a-zA-Z_0-9]{4} + PDBID + PDB identifier + beta12orEarlier @@ -5354,8 +5354,8 @@ AAindex ID - Identifier of an entry from the AAindex database. beta12orEarlier + Identifier of an entry from the AAindex database. @@ -5368,8 +5368,8 @@ BIND accession number - beta12orEarlier Accession number of an entry from the BIND database. + beta12orEarlier @@ -5382,9 +5382,9 @@ IntAct accession number - Accession number of an entry from the IntAct database. - beta12orEarlier EBI\-[0-9]+ + beta12orEarlier + Accession number of an entry from the IntAct database. @@ -5398,8 +5398,8 @@ Protein family name - Name of a protein family. beta12orEarlier + Name of a protein family. @@ -5418,8 +5418,8 @@ - Name of an InterPro entry, usually indicating the type of protein matches for that entry. beta12orEarlier + Name of an InterPro entry, usually indicating the type of protein matches for that entry. @@ -5438,13 +5438,13 @@ - IPR[0-9]{6} - IPR015590 - InterPro primary accession number - beta12orEarlier - Every InterPro entry has a unique accession number to provide a persistent citation of database records. - InterPro primary accession Primary accession number of an InterPro entry. + InterPro primary accession + Every InterPro entry has a unique accession number to provide a persistent citation of database records. + beta12orEarlier + InterPro primary accession number + IPR015590 + IPR[0-9]{6} @@ -5463,9 +5463,9 @@ - InterPro secondary accession number - beta12orEarlier Secondary accession number of an InterPro entry. + beta12orEarlier + InterPro secondary accession number @@ -5478,8 +5478,8 @@ Gene3D ID - Unique identifier of an entry from the Gene3D database. beta12orEarlier + Unique identifier of an entry from the Gene3D database. @@ -5492,9 +5492,9 @@ PIRSF ID - Unique identifier of an entry from the PIRSF database. - beta12orEarlier PIRSF[0-9]{6} + beta12orEarlier + Unique identifier of an entry from the PIRSF database. @@ -5507,9 +5507,9 @@ PRINTS code - The unique identifier of an entry in the PRINTS database. - PR[0-9]{5} beta12orEarlier + PR[0-9]{5} + The unique identifier of an entry in the PRINTS database. @@ -5522,9 +5522,9 @@ Pfam accession number - beta12orEarlier - Accession number of a Pfam entry. PF[0-9]{5} + Accession number of a Pfam entry. + beta12orEarlier @@ -5537,9 +5537,9 @@ SMART accession number - SM[0-9]{5} - beta12orEarlier Accession number of an entry from the SMART database. + beta12orEarlier + SM[0-9]{5} @@ -5552,8 +5552,8 @@ Superfamily hidden Markov model number - beta12orEarlier Unique identifier (number) of a hidden Markov model from the Superfamily database. + beta12orEarlier @@ -5566,9 +5566,9 @@ TIGRFam ID - beta12orEarlier - Accession number of an entry (family) from the TIGRFam database. TIGRFam accession number + Accession number of an entry (family) from the TIGRFam database. + beta12orEarlier @@ -5581,10 +5581,10 @@ ProDom accession number - ProDom is a protein domain family database. - beta12orEarlier - PD[0-9]+ A ProDom domain family accession number. + PD[0-9]+ + beta12orEarlier + ProDom is a protein domain family database. @@ -5597,8 +5597,8 @@ TRANSFAC accession number - Identifier of an entry from the TRANSFAC database. beta12orEarlier + Identifier of an entry from the TRANSFAC database. @@ -5611,10 +5611,10 @@ ArrayExpress accession number - ArrayExpress experiment ID - [AEP]-[a-zA-Z_0-9]{4}-[0-9]+ - beta12orEarlier Accession number of an entry from the ArrayExpress database. + beta12orEarlier + [AEP]-[a-zA-Z_0-9]{4}-[0-9]+ + ArrayExpress experiment ID @@ -5627,9 +5627,9 @@ PRIDE experiment accession number - PRIDE experiment accession number. - beta12orEarlier [0-9]+ + beta12orEarlier + PRIDE experiment accession number. @@ -5642,8 +5642,8 @@ EMDB ID - Identifier of an entry from the EMDB electron microscopy database. beta12orEarlier + Identifier of an entry from the EMDB electron microscopy database. @@ -5656,9 +5656,9 @@ GEO accession number - beta12orEarlier - o^GDS[0-9]+ Accession number of an entry from the GEO database. + o^GDS[0-9]+ + beta12orEarlier @@ -5671,8 +5671,8 @@ GermOnline ID - Identifier of an entry from the GermOnline database. beta12orEarlier + Identifier of an entry from the GermOnline database. @@ -5685,8 +5685,8 @@ EMAGE ID - beta12orEarlier Identifier of an entry from the EMAGE database. + beta12orEarlier @@ -5706,8 +5706,8 @@ - beta12orEarlier Identifier of an entry from a database of disease. + beta12orEarlier @@ -5720,8 +5720,8 @@ HGVbase ID - beta12orEarlier Identifier of an entry from the HGVbase database. + beta12orEarlier @@ -5734,10 +5734,10 @@ HIVDB identifier - beta12orEarlier - Identifier of an entry from the HIVDB database. - beta12orEarlier true + beta12orEarlier + Identifier of an entry from the HIVDB database. + beta12orEarlier @@ -5749,9 +5749,9 @@ OMIM ID - Identifier of an entry from the OMIM database. - [*#+%^]?[0-9]{6} beta12orEarlier + [*#+%^]?[0-9]{6} + Identifier of an entry from the OMIM database. @@ -5765,8 +5765,8 @@ KEGG object identifier - Unique identifier of an object from one of the KEGG databases (excluding the GENES division). beta12orEarlier + Unique identifier of an object from one of the KEGG databases (excluding the GENES division). @@ -5779,10 +5779,10 @@ Pathway ID (reactome) - REACT_[0-9]+(\.[0-9]+)? - beta12orEarlier - Reactome ID Identifier of an entry from the Reactome database. + Reactome ID + beta12orEarlier + REACT_[0-9]+(\.[0-9]+)? @@ -5795,11 +5795,11 @@ Pathway ID (aMAZE) - Identifier of an entry from the aMAZE database. - beta12orEarlier - true - aMAZE ID beta12orEarlier + aMAZE ID + true + beta12orEarlier + Identifier of an entry from the aMAZE database. @@ -5812,9 +5812,9 @@ Pathway ID (BioCyc) - Identifier of an pathway from the BioCyc biological pathways database. - beta12orEarlier BioCyc pathway ID + beta12orEarlier + Identifier of an pathway from the BioCyc biological pathways database. @@ -5827,9 +5827,9 @@ Pathway ID (INOH) - Identifier of an entry from the INOH database. - INOH identifier beta12orEarlier + INOH identifier + Identifier of an entry from the INOH database. @@ -5842,9 +5842,9 @@ Pathway ID (PATIKA) - beta12orEarlier - PATIKA ID Identifier of an entry from the PATIKA database. + PATIKA ID + beta12orEarlier @@ -5857,10 +5857,10 @@ Pathway ID (CPDB) - beta12orEarlier - Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB. - CPDB ID This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined. + CPDB ID + Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB. + beta12orEarlier @@ -5873,10 +5873,10 @@ Pathway ID (Panther) - Panther Pathways ID - PTHR[0-9]{5} - beta12orEarlier Identifier of a biological pathway from the Panther Pathways database. + beta12orEarlier + PTHR[0-9]{5} + Panther Pathways ID @@ -5895,11 +5895,11 @@ - This is the identifier used internally by MIRIAM for a data type. - beta12orEarlier - MIR:[0-9]{8} - MIR:00100005 Unique identifier of a MIRIAM data resource. + MIR:00100005 + MIR:[0-9]{8} + beta12orEarlier + This is the identifier used internally by MIRIAM for a data type. @@ -5918,8 +5918,8 @@ - The name of a data type from the MIRIAM database. beta12orEarlier + The name of a data type from the MIRIAM database. @@ -5939,11 +5939,11 @@ - A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term. - urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202 - identifiers.org synonym - The URI (URL or URN) of a data entity from the MIRIAM database. beta12orEarlier + The URI (URL or URN) of a data entity from the MIRIAM database. + identifiers.org synonym + urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202 + A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term. @@ -5956,17 +5956,17 @@ MIRIAM data type primary name - The primary name of a data type from the MIRIAM database. - UniProt|Enzyme Nomenclature - The primary name of a MIRIAM data type is taken from a controlled vocabulary. beta12orEarlier + The primary name of a MIRIAM data type is taken from a controlled vocabulary. + UniProt|Enzyme Nomenclature + The primary name of a data type from the MIRIAM database. - UniProt|Enzyme Nomenclature A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. + UniProt|Enzyme Nomenclature @@ -5978,9 +5978,9 @@ MIRIAM data type synonymous name - beta12orEarlier - A synonymous name for a MIRIAM data type taken from a controlled vocabulary. A synonymous name of a data type from the MIRIAM database. + A synonymous name for a MIRIAM data type taken from a controlled vocabulary. + beta12orEarlier @@ -5993,8 +5993,8 @@ Taverna workflow ID - Unique identifier of a Taverna workflow. beta12orEarlier + Unique identifier of a Taverna workflow. @@ -6008,8 +6008,8 @@ Biological model name - Name of a biological (mathematical) model. beta12orEarlier + Name of a biological (mathematical) model. @@ -6022,9 +6022,9 @@ BioModel ID - (BIOMD|MODEL)[0-9]{10} - beta12orEarlier Unique identifier of an entry from the BioModel database. + beta12orEarlier + (BIOMD|MODEL)[0-9]{10} @@ -6038,10 +6038,10 @@ PubChem CID - beta12orEarlier - Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure. - PubChem compound accession identifier [0-9]+ + PubChem compound accession identifier + Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure. + beta12orEarlier @@ -6054,9 +6054,9 @@ ChemSpider ID - [0-9]+ - beta12orEarlier Identifier of an entry from the ChemSpider database. + beta12orEarlier + [0-9]+ @@ -6069,11 +6069,11 @@ ChEBI ID - beta12orEarlier - CHEBI:[0-9]+ - ChEBI identifier - ChEBI IDs Identifier of an entry from the ChEBI database. + ChEBI IDs + ChEBI identifier + CHEBI:[0-9]+ + beta12orEarlier @@ -6086,8 +6086,8 @@ BioPax concept ID - An identifier of a concept from the BioPax ontology. beta12orEarlier + An identifier of a concept from the BioPax ontology. @@ -6100,10 +6100,10 @@ GO concept ID - An identifier of a concept from The Gene Ontology. - beta12orEarlier - [0-9]{7}|GO:[0-9]{7} GO concept identifier + [0-9]{7}|GO:[0-9]{7} + beta12orEarlier + An identifier of a concept from The Gene Ontology. @@ -6116,8 +6116,8 @@ MeSH concept ID - An identifier of a concept from the MeSH vocabulary. beta12orEarlier + An identifier of a concept from the MeSH vocabulary. @@ -6130,8 +6130,8 @@ HGNC concept ID - An identifier of a concept from the HGNC controlled vocabulary. beta12orEarlier + An identifier of a concept from the HGNC controlled vocabulary. @@ -6145,12 +6145,12 @@ NCBI taxonomy ID - beta12orEarlier - 9662|3483|182682 - A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database. - NCBI tax ID - [1-9][0-9]{0,8} NCBI taxonomy identifier + [1-9][0-9]{0,8} + NCBI tax ID + A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database. + 9662|3483|182682 + beta12orEarlier @@ -6163,8 +6163,8 @@ Plant Ontology concept ID - beta12orEarlier An identifier of a concept from the Plant Ontology (PO). + beta12orEarlier @@ -6177,8 +6177,8 @@ UMLS concept ID - beta12orEarlier An identifier of a concept from the UMLS vocabulary. + beta12orEarlier @@ -6191,10 +6191,10 @@ FMA concept ID - beta12orEarlier - Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. - FMA:[0-9]+ An identifier of a concept from Foundational Model of Anatomy. + FMA:[0-9]+ + Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. + beta12orEarlier @@ -6207,8 +6207,8 @@ EMAP concept ID - An identifier of a concept from the EMAP mouse ontology. beta12orEarlier + An identifier of a concept from the EMAP mouse ontology. @@ -6221,8 +6221,8 @@ ChEBI concept ID - An identifier of a concept from the ChEBI ontology. beta12orEarlier + An identifier of a concept from the ChEBI ontology. @@ -6235,8 +6235,8 @@ MGED concept ID - An identifier of a concept from the MGED ontology. beta12orEarlier + An identifier of a concept from the MGED ontology. @@ -6249,9 +6249,9 @@ myGrid concept ID - An identifier of a concept from the myGrid ontology. - The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. beta12orEarlier + The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. + An identifier of a concept from the myGrid ontology. @@ -6264,11 +6264,11 @@ PubMed ID - 4963447 - beta12orEarlier - PubMed unique identifier of an article. - [1-9][0-9]{0,8} PMID + [1-9][0-9]{0,8} + PubMed unique identifier of an article. + beta12orEarlier + 4963447 @@ -6281,10 +6281,10 @@ DOI - Digital Object Identifier (DOI) of a published article. - Digital Object Identifier - (doi\:)?[0-9]{2}\.[0-9]{4}/.* beta12orEarlier + (doi\:)?[0-9]{2}\.[0-9]{4}/.* + Digital Object Identifier + Digital Object Identifier (DOI) of a published article. @@ -6297,10 +6297,10 @@ Medline UI - Medline unique identifier - The use of Medline UI has been replaced by the PubMed unique identifier. - Medline UI (unique identifier) of an article. beta12orEarlier + Medline UI (unique identifier) of an article. + The use of Medline UI has been replaced by the PubMed unique identifier. + Medline unique identifier @@ -6313,8 +6313,8 @@ Tool name - beta12orEarlier The name of a computer package, application, method or function. + beta12orEarlier @@ -6327,9 +6327,9 @@ Tool name (signature) - Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP. - The unique name of a signature (sequence classifier) method. beta12orEarlier + The unique name of a signature (sequence classifier) method. + Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP. @@ -6342,10 +6342,10 @@ Tool name (BLAST) - BLAST name - beta12orEarlier - The name of a BLAST tool. This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. + The name of a BLAST tool. + beta12orEarlier + BLAST name @@ -6358,9 +6358,9 @@ Tool name (FASTA) - This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. - The name of a FASTA tool. beta12orEarlier + The name of a FASTA tool. + This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. @@ -6373,8 +6373,8 @@ Tool name (EMBOSS) - beta12orEarlier The name of an EMBOSS application. + beta12orEarlier @@ -6387,8 +6387,8 @@ Tool name (EMBASSY package) - beta12orEarlier The name of an EMBASSY package. + beta12orEarlier @@ -6401,9 +6401,9 @@ QSAR descriptor (constitutional) - QSAR constitutional descriptor - beta12orEarlier A QSAR constitutional descriptor. + beta12orEarlier + QSAR constitutional descriptor @@ -6415,9 +6415,9 @@ QSAR descriptor (electronic) - QSAR electronic descriptor - A QSAR electronic descriptor. beta12orEarlier + A QSAR electronic descriptor. + QSAR electronic descriptor @@ -6429,9 +6429,9 @@ QSAR descriptor (geometrical) - beta12orEarlier - A QSAR geometrical descriptor. QSAR geometrical descriptor + A QSAR geometrical descriptor. + beta12orEarlier @@ -6443,9 +6443,9 @@ QSAR descriptor (topological) - A QSAR topological descriptor. - QSAR topological descriptor beta12orEarlier + QSAR topological descriptor + A QSAR topological descriptor. @@ -6457,9 +6457,9 @@ QSAR descriptor (molecular) - beta12orEarlier - QSAR molecular descriptor A QSAR molecular descriptor. + QSAR molecular descriptor + beta12orEarlier @@ -6471,8 +6471,8 @@ Sequence set (protein) - beta12orEarlier Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. + beta12orEarlier @@ -6484,8 +6484,8 @@ Sequence set (nucleic acid) - Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. beta12orEarlier + Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. @@ -6509,9 +6509,9 @@ - beta12orEarlier - The cluster might include sequences identifiers, short descriptions, alignment and summary information. A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information. + The cluster might include sequences identifiers, short descriptions, alignment and summary information. + beta12orEarlier @@ -6523,11 +6523,11 @@ Psiblast checkpoint file - A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration. - true - beta12orEarlier - A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. beta12orEarlier + A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. + beta12orEarlier + true + A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration. @@ -6539,10 +6539,10 @@ HMMER synthetic sequences set - true - beta12orEarlier - beta12orEarlier Sequences generated by HMMER package in FASTA-style format. + beta12orEarlier + beta12orEarlier + true @@ -6560,8 +6560,8 @@ - A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses. beta12orEarlier + A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses. @@ -6573,9 +6573,9 @@ Restriction digest - beta12orEarlier - SO:0000412 Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease. + SO:0000412 + beta12orEarlier @@ -6587,8 +6587,8 @@ PCR primers - Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set. beta12orEarlier + Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set. @@ -6600,10 +6600,10 @@ vectorstrip cloning vector definition file - beta12orEarlier - File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format. - true beta12orEarlier + true + File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format. + beta12orEarlier @@ -6615,10 +6615,10 @@ Primer3 internal oligo mishybridizing library - beta12orEarlier - A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format. - beta12orEarlier true + beta12orEarlier + A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format. + beta12orEarlier @@ -6630,10 +6630,10 @@ Primer3 mispriming library file - beta12orEarlier - beta12orEarlier - A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format. true + A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format. + beta12orEarlier + beta12orEarlier @@ -6645,10 +6645,10 @@ primersearch primer pairs sequence record - File of one or more pairs of primer sequences, as used by EMBOSS primersearch application. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + File of one or more pairs of primer sequences, as used by EMBOSS primersearch application. @@ -6661,10 +6661,10 @@ Sequence cluster (protein) - A cluster of protein sequences. - beta12orEarlier - The sequences are typically related, for example a family of sequences. Protein sequence cluster + The sequences are typically related, for example a family of sequences. + beta12orEarlier + A cluster of protein sequences. @@ -6677,10 +6677,10 @@ Sequence cluster (nucleic acid) - The sequences are typically related, for example a family of sequences. - beta12orEarlier - Nucleotide sequence cluster A cluster of nucleotide sequences. + Nucleotide sequence cluster + beta12orEarlier + The sequences are typically related, for example a family of sequences. @@ -6692,8 +6692,8 @@ Sequence length - The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths. beta12orEarlier + The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths. @@ -6705,12 +6705,12 @@ Word size - beta12orEarlier - true - Size of a sequence word. - 1.5 - Word length Word size is used for example in word-based sequence database search methods. + Word length + 1.5 + Size of a sequence word. + true + beta12orEarlier @@ -6722,11 +6722,11 @@ Window size - Size of a sequence window. - beta12orEarlier - A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring. - true 1.5 + true + A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring. + beta12orEarlier + Size of a sequence window. @@ -6738,10 +6738,10 @@ Sequence length range - 1.5 - beta12orEarlier - Specification of range(s) of length of sequences. true + Specification of range(s) of length of sequences. + beta12orEarlier + 1.5 @@ -6753,10 +6753,10 @@ Sequence information report - true - beta12orEarlier - beta12orEarlier Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc. + beta12orEarlier + beta12orEarlier + true @@ -6768,9 +6768,9 @@ Sequence property - Sequence properties report - An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis. beta12orEarlier + An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis. + Sequence properties report @@ -6782,15 +6782,15 @@ Sequence features - Feature record - Features - Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence. - General sequence features - This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. - SO:0000110 - http://purl.bioontology.org/ontology/MSH/D058977 - beta12orEarlier Sequence features report + beta12orEarlier + http://purl.bioontology.org/ontology/MSH/D058977 + SO:0000110 + This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. + General sequence features + Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence. + Features + Feature record @@ -6802,11 +6802,11 @@ Sequence features (comparative) - beta12orEarlier - true - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - beta13 Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc. + beta13 + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + true + beta12orEarlier @@ -6818,10 +6818,10 @@ Sequence property (protein) - beta12orEarlier - beta12orEarlier - A report of general sequence properties derived from protein sequence data. true + A report of general sequence properties derived from protein sequence data. + beta12orEarlier + beta12orEarlier @@ -6833,10 +6833,10 @@ Sequence property (nucleic acid) - beta12orEarlier - true - beta12orEarlier A report of general sequence properties derived from nucleotide sequence data. + beta12orEarlier + true + beta12orEarlier @@ -6848,9 +6848,9 @@ Sequence complexity report - Sequence property (complexity) - beta12orEarlier A report on sequence complexity, for example low-complexity or repeat regions in sequences. + beta12orEarlier + Sequence property (complexity) @@ -6862,9 +6862,9 @@ Sequence ambiguity report - beta12orEarlier - Sequence property (ambiguity) A report on ambiguity in molecular sequence(s). + Sequence property (ambiguity) + beta12orEarlier @@ -6876,9 +6876,9 @@ Sequence composition report - Sequence property (composition) - A report (typically a table) on character or word composition / frequency of a molecular sequence(s). beta12orEarlier + A report (typically a table) on character or word composition / frequency of a molecular sequence(s). + Sequence property (composition) @@ -6890,8 +6890,8 @@ Peptide molecular weight hits - beta12orEarlier A report on peptide fragments of certain molecular weight(s) in one or more protein sequences. + beta12orEarlier @@ -6903,8 +6903,8 @@ Base position variability plot - A plot of third base position variability in a nucleotide sequence. beta12orEarlier + A plot of third base position variability in a nucleotide sequence. @@ -6916,10 +6916,10 @@ Sequence composition table - beta12orEarlier - true - beta12orEarlier A table of character or word composition / frequency of a molecular sequence. + beta12orEarlier + true + beta12orEarlier @@ -6932,8 +6932,8 @@ Base frequencies table - A table of base frequencies of a nucleotide sequence. beta12orEarlier + A table of base frequencies of a nucleotide sequence. @@ -6946,8 +6946,8 @@ Base word frequencies table - beta12orEarlier A table of word composition of a nucleotide sequence. + beta12orEarlier @@ -6960,9 +6960,9 @@ Amino acid frequencies table - beta12orEarlier - A table of amino acid frequencies of a protein sequence. Sequence composition (amino acid frequencies) + A table of amino acid frequencies of a protein sequence. + beta12orEarlier @@ -6975,9 +6975,9 @@ Amino acid word frequencies table - beta12orEarlier - Sequence composition (amino acid words) A table of amino acid word composition of a protein sequence. + Sequence composition (amino acid words) + beta12orEarlier @@ -6989,10 +6989,10 @@ DAS sequence feature annotation - true - beta12orEarlier - Annotation of a molecular sequence in DAS format. beta12orEarlier + Annotation of a molecular sequence in DAS format. + beta12orEarlier + true @@ -7004,9 +7004,9 @@ Feature table - Annotation of positional sequence features, organized into a standard feature table. - beta12orEarlier Sequence feature table + beta12orEarlier + Annotation of positional sequence features, organized into a standard feature table. @@ -7024,9 +7024,9 @@ - A map of (typically one) DNA sequence annotated with positional or non-positional features. - beta12orEarlier DNA map + beta12orEarlier + A map of (typically one) DNA sequence annotated with positional or non-positional features. @@ -7039,13 +7039,13 @@ Nucleic acid features - Feature table (nucleic acid) - Nucleic acid feature table - Genomic features - This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. - Genome features - beta12orEarlier An informative report on intrinsic positional features of a nucleotide sequence. + beta12orEarlier + Genome features + This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. + Genomic features + Nucleic acid feature table + Feature table (nucleic acid) @@ -7058,11 +7058,11 @@ Protein features - Protein feature table - Feature table (protein) - This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. - beta12orEarlier An informative report on intrinsic positional features of a protein sequence. + beta12orEarlier + This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. + Feature table (protein) + Protein feature table @@ -7074,11 +7074,11 @@ Genetic map - Moby:GeneticMap - Linkage map - A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms. - beta12orEarlier A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies. + beta12orEarlier + A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms. + Linkage map + Moby:GeneticMap @@ -7090,9 +7090,9 @@ Sequence map - A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs. - beta12orEarlier A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment. + beta12orEarlier + A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs. @@ -7104,9 +7104,9 @@ Physical map - beta12orEarlier - Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing. A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them. + Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing. + beta12orEarlier @@ -7118,10 +7118,10 @@ Sequence signature map - beta12orEarlier - beta12orEarlier - Image of a sequence with matches to signatures, motifs or profiles. true + Image of a sequence with matches to signatures, motifs or profiles. + beta12orEarlier + beta12orEarlier @@ -7133,12 +7133,12 @@ Cytogenetic map - This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances. Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms. - Cytogenic map - Chromosome map - Cytologic map - A map showing banding patterns derived from direct observation of a stained chromosome. beta12orEarlier + A map showing banding patterns derived from direct observation of a stained chromosome. + Cytologic map + Chromosome map + Cytogenic map + This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances. Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms. @@ -7150,8 +7150,8 @@ DNA transduction map - A gene map showing distances between loci based on relative cotransduction frequencies. beta12orEarlier + A gene map showing distances between loci based on relative cotransduction frequencies. @@ -7163,8 +7163,8 @@ Gene map - beta12orEarlier Sequence map of a single gene annotated with genetic features such as introns, exons, untranslated regions, polyA signals, promoters, enhancers and (possibly) mutations defining alleles of a gene. + beta12orEarlier @@ -7176,8 +7176,8 @@ Plasmid map - beta12orEarlier Sequence map of a plasmid (circular DNA). + beta12orEarlier @@ -7189,8 +7189,8 @@ Genome map - Sequence map of a whole genome. beta12orEarlier + Sequence map of a whole genome. @@ -7203,8 +7203,8 @@ Restriction map - beta12orEarlier Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence. + beta12orEarlier @@ -7216,11 +7216,11 @@ InterPro compact match image - true - beta12orEarlier - The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches. - Image showing matches between protein sequence(s) and InterPro Entries. beta12orEarlier + Image showing matches between protein sequence(s) and InterPro Entries. + The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches. + beta12orEarlier + true @@ -7232,11 +7232,11 @@ InterPro detailed match image - true - The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. - Image showing detailed information on matches between protein sequence(s) and InterPro Entries. - beta12orEarlier beta12orEarlier + beta12orEarlier + Image showing detailed information on matches between protein sequence(s) and InterPro Entries. + The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. + true @@ -7248,11 +7248,11 @@ InterPro architecture image - Image showing the architecture of InterPro domains in a protein sequence. - The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein. + Image showing the architecture of InterPro domains in a protein sequence. @@ -7264,10 +7264,10 @@ SMART protein schematic - SMART protein schematic in PNG format. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + SMART protein schematic in PNG format. @@ -7279,10 +7279,10 @@ GlobPlot domain image - Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences. @@ -7294,10 +7294,10 @@ Sequence motif matches - true - 1.8 - Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences. beta12orEarlier + Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences. + 1.8 + true @@ -7309,12 +7309,12 @@ Sequence features (repeats) - Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. - The report might include derived data map such as classification, annotation, organization, periodicity etc. - Repeat sequence map - 1.5 - true beta12orEarlier + true + 1.5 + Repeat sequence map + The report might include derived data map such as classification, annotation, organization, periodicity etc. + Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. @@ -7327,10 +7327,10 @@ Gene and transcript structure (report) - true - A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. - beta12orEarlier 1.5 + beta12orEarlier + A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. + true @@ -7342,10 +7342,10 @@ Mobile genetic elements - Topic concerning regions of a nucleic acid sequence containing mobile genetic elements. - 1.8 - beta12orEarlier true + beta12orEarlier + 1.8 + Topic concerning regions of a nucleic acid sequence containing mobile genetic elements. @@ -7357,10 +7357,10 @@ Nucleic acid features report (PolyA signal or site) - beta12orEarlier - 1.8 - true Topic concerning regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. + true + 1.8 + beta12orEarlier @@ -7372,10 +7372,10 @@ Nucleic acid features (quadruplexes) - beta12orEarlier - A report on quadruplex-forming motifs in a nucleotide sequence. - 1.5 true + 1.5 + A report on quadruplex-forming motifs in a nucleotide sequence. + beta12orEarlier @@ -7387,10 +7387,10 @@ Nucleic acid features report (CpG island and isochore) - true - Topic concerning CpG rich regions (isochores) in a nucleotide sequence. - beta12orEarlier 1.8 + beta12orEarlier + Topic concerning CpG rich regions (isochores) in a nucleotide sequence. + true @@ -7402,10 +7402,10 @@ Nucleic acid features report (restriction sites) - Topic concerning restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. - 1.8 - true beta12orEarlier + true + 1.8 + Topic concerning restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. @@ -7417,10 +7417,10 @@ Nucleosome exclusion sequences - 1.8 - Report on nucleosome formation potential or exclusion sequence(s). - true beta12orEarlier + true + Report on nucleosome formation potential or exclusion sequence(s). + 1.8 @@ -7432,10 +7432,10 @@ Nucleic acid features report (splice sites) - 1.8 - true - Topic concerning splice sites in a nucleotide sequence or alternative RNA splicing events. beta12orEarlier + Topic concerning splice sites in a nucleotide sequence or alternative RNA splicing events. + true + 1.8 @@ -7447,10 +7447,10 @@ Nucleic acid features report (matrix/scaffold attachment sites) - Topic concerning matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. - beta12orEarlier - true 1.8 + true + beta12orEarlier + Topic concerning matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. @@ -7462,10 +7462,10 @@ Gene features (exonic splicing enhancer) - A report on exonic splicing enhancers (ESE) in an exon. - true - beta13 beta12orEarlier + beta13 + true + A report on exonic splicing enhancers (ESE) in an exon. @@ -7477,10 +7477,10 @@ Nucleic acid features (microRNA) - 1.5 - A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc. - beta12orEarlier true + beta12orEarlier + A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc. + 1.5 @@ -7492,10 +7492,10 @@ Gene features report (operon) - beta12orEarlier - Topic concerning operons (operators, promoters and genes) from a bacterial genome. - 1.8 true + 1.8 + Topic concerning operons (operators, promoters and genes) from a bacterial genome. + beta12orEarlier @@ -7507,10 +7507,10 @@ Nucleic acid features report (promoters) - beta12orEarlier - true - Topic concerning whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. 1.8 + Topic concerning whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. + true + beta12orEarlier @@ -7522,10 +7522,10 @@ Coding region - true - 1.8 - Topic concerning protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. beta12orEarlier + Topic concerning protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. + 1.8 + true @@ -7537,10 +7537,10 @@ Gene features (SECIS element) - true - A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence. - beta13 beta12orEarlier + beta13 + A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence. + true @@ -7552,10 +7552,10 @@ Transcription factor binding sites - 1.8 - true - Topic concerning transcription factor binding sites (TFBS) in a DNA sequence. beta12orEarlier + Topic concerning transcription factor binding sites (TFBS) in a DNA sequence. + true + 1.8 @@ -7567,11 +7567,11 @@ Protein features (sites) - A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites. - beta12orEarlier - Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. - beta12orEarlier true + beta12orEarlier + Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. + beta12orEarlier + A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites. @@ -7583,10 +7583,10 @@ Protein features report (signal peptides) - beta12orEarlier - 1.8 - true Topic concerning signal peptides or signal peptide cleavage sites in protein sequences. + true + 1.8 + beta12orEarlier @@ -7598,10 +7598,10 @@ Protein features report (cleavage sites) - beta12orEarlier - 1.8 - Topic concerning cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. true + Topic concerning cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. + 1.8 + beta12orEarlier @@ -7613,10 +7613,10 @@ Protein features (post-translation modifications) - 1.8 - Topic concerning post-translation modifications in a protein sequence, typically describing the specific sites involved. - beta12orEarlier true + beta12orEarlier + Topic concerning post-translation modifications in a protein sequence, typically describing the specific sites involved. + 1.8 @@ -7628,10 +7628,10 @@ Protein features report (active sites) - beta12orEarlier - true - 1.8 Topic concerning catalytic residues (active site) of an enzyme. + 1.8 + true + beta12orEarlier @@ -7643,10 +7643,10 @@ Protein features report (binding sites) - 1.8 - true - beta12orEarlier Topic concerning ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. + beta12orEarlier + true + 1.8 @@ -7658,11 +7658,11 @@ Protein features (epitopes) - true - Epitope mapping is commonly done during vaccine design. - beta12orEarlier - beta13 A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data. + beta13 + beta12orEarlier + Epitope mapping is commonly done during vaccine design. + true @@ -7674,10 +7674,10 @@ Protein features report (nucleic acid binding sites) - 1.8 - Topic concerning RNA and DNA-binding proteins and binding sites in protein sequences. - beta12orEarlier true + beta12orEarlier + Topic concerning RNA and DNA-binding proteins and binding sites in protein sequences. + 1.8 @@ -7689,10 +7689,10 @@ MHC Class I epitopes report - A report on epitopes that bind to MHC class I molecules. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + A report on epitopes that bind to MHC class I molecules. @@ -7703,11 +7703,11 @@ MHC Class II epitopes report - - A report on predicted epitopes that bind to MHC class II molecules. - true - beta12orEarlier + beta12orEarlier + beta12orEarlier + true + A report on predicted epitopes that bind to MHC class II molecules. @@ -7719,11 +7719,11 @@ Protein features (PEST sites) - 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. - beta13 - true - A report or plot of PEST sites in a protein sequence. beta12orEarlier + A report or plot of PEST sites in a protein sequence. + true + beta13 + 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. @@ -7735,10 +7735,10 @@ Sequence database hits scores list - beta12orEarlier - true - beta12orEarlier Scores from a sequence database search (for example a BLAST search). + beta12orEarlier + true + beta12orEarlier @@ -7750,10 +7750,10 @@ Sequence database hits alignments list - true - beta12orEarlier - Alignments from a sequence database search (for example a BLAST search). beta12orEarlier + Alignments from a sequence database search (for example a BLAST search). + beta12orEarlier + true @@ -7765,10 +7765,10 @@ Sequence database hits evaluation data - true - beta12orEarlier - A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search). beta12orEarlier + A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search). + beta12orEarlier + true @@ -7780,10 +7780,10 @@ MEME motif alphabet - true - beta12orEarlier - beta12orEarlier Alphabet for the motifs (patterns) that MEME will search for. + beta12orEarlier + beta12orEarlier + true @@ -7795,10 +7795,10 @@ MEME background frequencies file - beta12orEarlier - beta12orEarlier - true MEME background frequencies file. + true + beta12orEarlier + beta12orEarlier @@ -7810,10 +7810,10 @@ MEME motifs directive file - beta12orEarlier - File of directives for ordering and spacing of MEME motifs. - true beta12orEarlier + true + File of directives for ordering and spacing of MEME motifs. + beta12orEarlier @@ -7825,8 +7825,8 @@ Dirichlet distribution - beta12orEarlier Dirichlet distribution used by hidden Markov model analysis programs. + beta12orEarlier @@ -7838,10 +7838,10 @@ HMM emission and transition counts - beta12orEarlier - 1.4 - true Emission and transition counts of a hidden Markov model, generated once HMM has been determined, for example after residues/gaps have been assigned to match, delete and insert states. + true + 1.4 + beta12orEarlier @@ -7854,8 +7854,8 @@ Regular expression - beta12orEarlier Regular expression pattern. + beta12orEarlier @@ -7873,8 +7873,8 @@ - Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence. beta12orEarlier + Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence. @@ -7892,9 +7892,9 @@ - beta12orEarlier - http://semanticscience.org/resource/SIO_010531 Some type of statistical model representing a (typically multiple) sequence alignment. + http://semanticscience.org/resource/SIO_010531 + beta12orEarlier @@ -7906,14 +7906,14 @@ Protein signature - Protein domain signature - Protein family signature - beta12orEarlier - Protein site signature - Protein region signature - Protein repeat signature - InterPro entry An informative report about a specific or conserved protein sequence pattern. + InterPro entry + Protein repeat signature + Protein region signature + Protein site signature + beta12orEarlier + Protein family signature + Protein domain signature @@ -7925,10 +7925,10 @@ Prosite nucleotide pattern - beta12orEarlier - true - beta12orEarlier A nucleotide regular expression pattern from the Prosite database. + beta12orEarlier + true + beta12orEarlier @@ -7940,10 +7940,10 @@ Prosite protein pattern - true - beta12orEarlier - beta12orEarlier A protein regular expression pattern from the Prosite database. + beta12orEarlier + beta12orEarlier + true @@ -7955,9 +7955,9 @@ Position frequency matrix - A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position. - PFM beta12orEarlier + PFM + A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position. @@ -7969,10 +7969,10 @@ Position weight matrix - Contributions of individual sequences to the matrix might be uneven (weighted). - A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position. - beta12orEarlier PWM + beta12orEarlier + A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position. + Contributions of individual sequences to the matrix might be uneven (weighted). @@ -7984,9 +7984,9 @@ Information content matrix - A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position. - ICM beta12orEarlier + ICM + A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position. @@ -7998,9 +7998,9 @@ Hidden Markov model - A hidden Markov model representation of a set or alignment of sequences. - beta12orEarlier HMM + beta12orEarlier + A hidden Markov model representation of a set or alignment of sequences. @@ -8012,8 +8012,8 @@ Fingerprint - One or more fingerprints (sequence classifiers) as used in the PRINTS database. beta12orEarlier + One or more fingerprints (sequence classifiers) as used in the PRINTS database. @@ -8025,10 +8025,10 @@ Domainatrix signature - beta12orEarlier - beta12orEarlier - true A protein signature of the type used in the EMBASSY Signature package. + true + beta12orEarlier + beta12orEarlier @@ -8040,10 +8040,10 @@ HMMER NULL hidden Markov model - NULL hidden Markov model representation used by the HMMER package. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + NULL hidden Markov model representation used by the HMMER package. @@ -8055,11 +8055,11 @@ Protein family signature - A protein family signature (sequence classifier) from the InterPro database. - 1.5 - true - beta12orEarlier Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures. + beta12orEarlier + true + 1.5 + A protein family signature (sequence classifier) from the InterPro database. @@ -8071,11 +8071,11 @@ Protein domain signature - Protein domain signatures identify structural or functional domains or other units with defined boundaries. - A protein domain signature (sequence classifier) from the InterPro database. - true - 1.5 beta12orEarlier + 1.5 + true + A protein domain signature (sequence classifier) from the InterPro database. + Protein domain signatures identify structural or functional domains or other units with defined boundaries. @@ -8087,11 +8087,11 @@ Protein region signature - A protein region signature defines a region which cannot be described as a protein family or domain signature. - 1.5 - beta12orEarlier - true A protein region signature (sequence classifier) from the InterPro database. + true + beta12orEarlier + 1.5 + A protein region signature defines a region which cannot be described as a protein family or domain signature. @@ -8103,11 +8103,11 @@ Protein repeat signature - A protein repeat signature (sequence classifier) from the InterPro database. - beta12orEarlier - A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain. - 1.5 true + 1.5 + A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain. + beta12orEarlier + A protein repeat signature (sequence classifier) from the InterPro database. @@ -8119,11 +8119,11 @@ Protein site signature - 1.5 - true - A protein site signature (sequence classifier) from the InterPro database. - beta12orEarlier A protein site signature is a classifier for a specific site in a protein. + beta12orEarlier + A protein site signature (sequence classifier) from the InterPro database. + true + 1.5 @@ -8135,11 +8135,11 @@ Protein conserved site signature - beta12orEarlier - A protein conserved site signature (sequence classifier) from the InterPro database. - A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification. - true 1.4 + true + A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification. + A protein conserved site signature (sequence classifier) from the InterPro database. + beta12orEarlier @@ -8151,11 +8151,11 @@ Protein active site signature - beta12orEarlier - 1.4 - true - A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available. A protein active site signature (sequence classifier) from the InterPro database. + A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available. + true + 1.4 + beta12orEarlier @@ -8167,11 +8167,11 @@ Protein binding site signature - beta12orEarlier - A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification. - true - A protein binding site signature (sequence classifier) from the InterPro database. 1.4 + A protein binding site signature (sequence classifier) from the InterPro database. + true + A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification. + beta12orEarlier @@ -8183,11 +8183,11 @@ Protein post-translational modification signature - true - beta12orEarlier - 1.4 - A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible. A protein post-translational modification signature (sequence classifier) from the InterPro database. + A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible. + 1.4 + beta12orEarlier + true @@ -8199,9 +8199,9 @@ Sequence alignment (pair) - Alignment of exactly two molecular sequences. - beta12orEarlier http://semanticscience.org/resource/SIO_010068 + beta12orEarlier + Alignment of exactly two molecular sequences. @@ -8213,10 +8213,10 @@ Sequence alignment (multiple) - true - Alignment of more than two molecular sequences. - beta12orEarlier beta12orEarlier + beta12orEarlier + Alignment of more than two molecular sequences. + true @@ -8228,8 +8228,8 @@ Sequence alignment (nucleic acid) - Alignment of multiple nucleotide sequences. beta12orEarlier + Alignment of multiple nucleotide sequences. @@ -8242,8 +8242,8 @@ Sequence alignment (protein) - beta12orEarlier Alignment of multiple protein sequences. + beta12orEarlier @@ -8255,9 +8255,9 @@ Sequence alignment (hybrid) - beta12orEarlier - Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA. Alignment of multiple molecular sequences of different types. + Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA. + beta12orEarlier @@ -8270,8 +8270,8 @@ Sequence alignment (nucleic acid pair) - Alignment of exactly two nucleotide sequences. beta12orEarlier + Alignment of exactly two nucleotide sequences. @@ -8284,8 +8284,8 @@ Sequence alignment (protein pair) - beta12orEarlier Alignment of exactly two protein sequences. + beta12orEarlier @@ -8297,10 +8297,10 @@ Hybrid sequence alignment (pair) - Alignment of exactly two molecular sequences of different types. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + Alignment of exactly two molecular sequences of different types. @@ -8312,10 +8312,10 @@ Multiple nucleotide sequence alignment - beta12orEarlier - true - Alignment of more than two nucleotide sequences. beta12orEarlier + Alignment of more than two nucleotide sequences. + true + beta12orEarlier @@ -8327,10 +8327,10 @@ Multiple protein sequence alignment - Alignment of more than two protein sequences. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + Alignment of more than two protein sequences. @@ -8342,8 +8342,8 @@ Alignment score or penalty - A simple floating point number defining the penalty for opening or extending a gap in an alignment. beta12orEarlier + A simple floating point number defining the penalty for opening or extending a gap in an alignment. @@ -8355,10 +8355,10 @@ Score end gaps control - true - Whether end gaps are scored or not. - beta12orEarlier beta12orEarlier + beta12orEarlier + Whether end gaps are scored or not. + true @@ -8370,10 +8370,10 @@ Aligned sequence order - Controls the order of sequences in an output sequence alignment. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Controls the order of sequences in an output sequence alignment. @@ -8385,8 +8385,8 @@ Gap opening penalty - beta12orEarlier A penalty for opening a gap in an alignment. + beta12orEarlier @@ -8398,8 +8398,8 @@ Gap extension penalty - beta12orEarlier A penalty for extending a gap in an alignment. + beta12orEarlier @@ -8411,8 +8411,8 @@ Gap separation penalty - A penalty for gaps that are close together in an alignment. beta12orEarlier + A penalty for gaps that are close together in an alignment. @@ -8424,10 +8424,10 @@ Terminal gap penalty - beta12orEarlier - true - A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. beta12orEarlier + A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. + true + beta12orEarlier @@ -8440,8 +8440,8 @@ Match reward score - The score for a 'match' used in various sequence database search applications with simple scoring schemes. beta12orEarlier + The score for a 'match' used in various sequence database search applications with simple scoring schemes. @@ -8453,8 +8453,8 @@ Mismatch penalty score - The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes. beta12orEarlier + The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes. @@ -8466,8 +8466,8 @@ Drop off score - beta12orEarlier This is the threshold drop in score at which extension of word alignment is halted. + beta12orEarlier @@ -8479,10 +8479,10 @@ Gap opening penalty (integer) - beta12orEarlier - A simple floating point number defining the penalty for opening a gap in an alignment. - true beta12orEarlier + true + A simple floating point number defining the penalty for opening a gap in an alignment. + beta12orEarlier @@ -8494,10 +8494,10 @@ Gap opening penalty (float) - true - A simple floating point number defining the penalty for opening a gap in an alignment. - beta12orEarlier beta12orEarlier + beta12orEarlier + A simple floating point number defining the penalty for opening a gap in an alignment. + true @@ -8509,10 +8509,10 @@ Gap extension penalty (integer) - beta12orEarlier - beta12orEarlier - A simple floating point number defining the penalty for extending a gap in an alignment. true + A simple floating point number defining the penalty for extending a gap in an alignment. + beta12orEarlier + beta12orEarlier @@ -8524,10 +8524,10 @@ Gap extension penalty (float) - beta12orEarlier - A simple floating point number defining the penalty for extending a gap in an alignment. - true beta12orEarlier + true + A simple floating point number defining the penalty for extending a gap in an alignment. + beta12orEarlier @@ -8539,10 +8539,10 @@ Gap separation penalty (integer) - beta12orEarlier - true - beta12orEarlier A simple floating point number defining the penalty for gaps that are close together in an alignment. + beta12orEarlier + true + beta12orEarlier @@ -8554,10 +8554,10 @@ Gap separation penalty (float) - A simple floating point number defining the penalty for gaps that are close together in an alignment. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + A simple floating point number defining the penalty for gaps that are close together in an alignment. @@ -8569,8 +8569,8 @@ Terminal gap opening penalty - A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. beta12orEarlier + A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. @@ -8582,8 +8582,8 @@ Terminal gap extension penalty - beta12orEarlier A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. + beta12orEarlier @@ -8595,8 +8595,8 @@ Sequence identity - beta12orEarlier Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences. + beta12orEarlier @@ -8608,9 +8608,9 @@ Sequence similarity - Data Type is float probably. - Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension. beta12orEarlier + Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension. + Data Type is float probably. @@ -8622,10 +8622,10 @@ Sequence alignment metadata (quality report) - Data on molecular sequence alignment quality (estimated accuracy). - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Data on molecular sequence alignment quality (estimated accuracy). @@ -8637,11 +8637,11 @@ Sequence alignment report (site conservation) - true - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. - 1.4 - Data on character conservation in a molecular sequence alignment. beta12orEarlier + Data on character conservation in a molecular sequence alignment. + 1.4 + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. + true @@ -8653,10 +8653,10 @@ Sequence alignment report (site correlation) - true - Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures. - beta12orEarlier 1.4 + beta12orEarlier + Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures. + true @@ -8668,10 +8668,10 @@ Sequence-profile alignment (Domainatrix signature) - true - beta12orEarlier - Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment). beta12orEarlier + Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment). + beta12orEarlier + true @@ -8683,10 +8683,10 @@ Sequence-profile alignment (HMM) - Alignment of molecular sequence(s) to a hidden Markov model(s). - true - 1.5 beta12orEarlier + 1.5 + true + Alignment of molecular sequence(s) to a hidden Markov model(s). @@ -8698,10 +8698,10 @@ Sequence-profile alignment (fingerprint) - true - beta12orEarlier - 1.5 Alignment of molecular sequences to a protein fingerprint from the PRINTS database. + 1.5 + beta12orEarlier + true @@ -8713,10 +8713,10 @@ Phylogenetic continuous quantitative data - Continuous quantitative data that may be read during phylogenetic tree calculation. - Quantitative traits - Phylogenetic continuous quantitative characters beta12orEarlier + Phylogenetic continuous quantitative characters + Quantitative traits + Continuous quantitative data that may be read during phylogenetic tree calculation. @@ -8728,11 +8728,11 @@ Phylogenetic discrete data - Discretely coded characters - beta12orEarlier - Phylogenetic discrete states - Character data with discrete states that may be read during phylogenetic tree calculation. Discrete characters + Character data with discrete states that may be read during phylogenetic tree calculation. + Phylogenetic discrete states + beta12orEarlier + Discretely coded characters @@ -8744,9 +8744,9 @@ Phylogenetic character cliques - beta12orEarlier - Phylogenetic report (cliques) One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny. + Phylogenetic report (cliques) + beta12orEarlier @@ -8764,9 +8764,9 @@ - Phylogenetic report (invariants) - beta12orEarlier Phylogenetic invariants data for testing alternative tree topologies. + beta12orEarlier + Phylogenetic report (invariants) @@ -8778,14 +8778,14 @@ Phylogenetic report - true - This is a broad data type and is used for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis. - Phylogenetic tree-derived report - Phylogenetic report - 1.5 - Phylogenetic tree report - A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. beta12orEarlier + A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. + Phylogenetic tree report + 1.5 + Phylogenetic report + Phylogenetic tree-derived report + This is a broad data type and is used for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis. + true @@ -8797,11 +8797,11 @@ DNA substitution model - A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis. - beta12orEarlier - Sequence alignment report (DNA substitution model) - Phylogenetic tree report (DNA substitution model) Substitution model + Phylogenetic tree report (DNA substitution model) + Sequence alignment report (DNA substitution model) + beta12orEarlier + A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis. @@ -8813,10 +8813,10 @@ Phylogenetic tree report (tree shape) - Data about the shape of a phylogenetic tree. - 1.4 - true beta12orEarlier + true + 1.4 + Data about the shape of a phylogenetic tree. @@ -8828,10 +8828,10 @@ Phylogenetic tree report (tree evaluation) - Data on the confidence of a phylogenetic tree. - 1.4 - true beta12orEarlier + true + 1.4 + Data on the confidence of a phylogenetic tree. @@ -8843,9 +8843,9 @@ Phylogenetic tree distances - Distances, such as Branch Score distance, between two or more phylogenetic trees. - Phylogenetic tree report (tree distances) beta12orEarlier + Phylogenetic tree report (tree distances) + Distances, such as Branch Score distance, between two or more phylogenetic trees. @@ -8857,10 +8857,10 @@ Phylogenetic tree report (tree stratigraphic) - Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis. - true - 1.4 beta12orEarlier + 1.4 + true + Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis. @@ -8872,9 +8872,9 @@ Phylogenetic character contrasts - beta12orEarlier - Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts. Phylogenetic report (character contrasts) + Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts. + beta12orEarlier @@ -8886,11 +8886,11 @@ Comparison matrix (integers) - true - Matrix of integer numbers for sequence comparison. - beta12orEarlier - Substitution matrix (integers) beta12orEarlier + Substitution matrix (integers) + beta12orEarlier + Matrix of integer numbers for sequence comparison. + true @@ -8902,11 +8902,11 @@ Comparison matrix (floats) - Substitution matrix (floats) - Matrix of floating point numbers for sequence comparison. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Matrix of floating point numbers for sequence comparison. + Substitution matrix (floats) @@ -8918,9 +8918,9 @@ Comparison matrix (nucleotide) - Nucleotide substitution matrix - beta12orEarlier Matrix of integer or floating point numbers for nucleotide comparison. + beta12orEarlier + Nucleotide substitution matrix @@ -8933,10 +8933,10 @@ Comparison matrix (amino acid) - Amino acid substitution matrix - Matrix of integer or floating point numbers for amino acid comparison. - beta12orEarlier Amino acid comparison matrix + beta12orEarlier + Matrix of integer or floating point numbers for amino acid comparison. + Amino acid substitution matrix @@ -8948,11 +8948,11 @@ Nucleotide comparison matrix (integers) - beta12orEarlier - true - Matrix of integer numbers for nucleotide comparison. - beta12orEarlier Nucleotide substitution matrix (integers) + beta12orEarlier + Matrix of integer numbers for nucleotide comparison. + true + beta12orEarlier @@ -8964,11 +8964,11 @@ Nucleotide comparison matrix (floats) - Nucleotide substitution matrix (floats) - beta12orEarlier - Matrix of floating point numbers for nucleotide comparison. - true beta12orEarlier + true + Matrix of floating point numbers for nucleotide comparison. + beta12orEarlier + Nucleotide substitution matrix (floats) @@ -8980,11 +8980,11 @@ Amino acid comparison matrix (integers) - beta12orEarlier - true - Amino acid substitution matrix (integers) - Matrix of integer numbers for amino acid comparison. beta12orEarlier + Matrix of integer numbers for amino acid comparison. + Amino acid substitution matrix (integers) + true + beta12orEarlier @@ -8996,11 +8996,11 @@ Amino acid comparison matrix (floats) - Matrix of floating point numbers for amino acid comparison. - true - beta12orEarlier - Amino acid substitution matrix (floats) beta12orEarlier + Amino acid substitution matrix (floats) + beta12orEarlier + true + Matrix of floating point numbers for amino acid comparison. @@ -9012,10 +9012,10 @@ Protein features report (membrane regions) - Topic concerning trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. - 1.8 - beta12orEarlier true + beta12orEarlier + 1.8 + Topic concerning trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. @@ -9033,8 +9033,8 @@ - beta12orEarlier 3D coordinate and associated data for a nucleic acid tertiary (3D) structure. + beta12orEarlier @@ -9052,9 +9052,9 @@ - beta12orEarlier - 3D coordinate and associated data for a protein tertiary (3D) structure. Protein structures + 3D coordinate and associated data for a protein tertiary (3D) structure. + beta12orEarlier @@ -9066,9 +9066,9 @@ Protein-ligand complex - This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead. - beta12orEarlier The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule. + beta12orEarlier + This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead. @@ -9083,17 +9083,17 @@ - + - + - 3D coordinate and associated data for a carbohydrate (3D) structure. beta12orEarlier + 3D coordinate and associated data for a carbohydrate (3D) structure. @@ -9111,9 +9111,9 @@ - beta12orEarlier - CHEBI:23367 3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound. + CHEBI:23367 + beta12orEarlier @@ -9125,8 +9125,8 @@ DNA structure - 3D coordinate and associated data for a DNA tertiary (3D) structure. beta12orEarlier + 3D coordinate and associated data for a DNA tertiary (3D) structure. @@ -9144,8 +9144,8 @@ - 3D coordinate and associated data for an RNA tertiary (3D) structure. beta12orEarlier + 3D coordinate and associated data for an RNA tertiary (3D) structure. @@ -9157,8 +9157,8 @@ tRNA structure - beta12orEarlier 3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc. + beta12orEarlier @@ -9170,8 +9170,8 @@ Protein chain - 3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain. beta12orEarlier + 3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain. @@ -9189,8 +9189,8 @@ - beta12orEarlier 3D coordinate and associated data for the tertiary (3D) structure of a protein domain. + beta12orEarlier @@ -9202,10 +9202,10 @@ Protein structure (all atoms) - 3D coordinate and associated data for a protein tertiary (3D) structure (all atoms). - true - 1.5 beta12orEarlier + 1.5 + true + 3D coordinate and associated data for a protein tertiary (3D) structure (all atoms). @@ -9217,10 +9217,10 @@ C-alpha trace - beta12orEarlier - Protein structure (C-alpha atoms) - C-beta atoms from amino acid side-chains may be included. 3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only). + C-beta atoms from amino acid side-chains may be included. + Protein structure (C-alpha atoms) + beta12orEarlier @@ -9232,10 +9232,10 @@ Protein chain (all atoms) - true - beta12orEarlier - beta12orEarlier 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms). + beta12orEarlier + beta12orEarlier + true @@ -9247,11 +9247,11 @@ Protein chain (C-alpha atoms) - C-beta atoms from amino acid side-chains may be included. - beta12orEarlier - beta12orEarlier - 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only). true + 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only). + beta12orEarlier + beta12orEarlier + C-beta atoms from amino acid side-chains may be included. @@ -9263,10 +9263,10 @@ Protein domain (all atoms) - beta12orEarlier - true - beta12orEarlier 3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms). + beta12orEarlier + true + beta12orEarlier @@ -9278,11 +9278,11 @@ Protein domain (C-alpha atoms) - beta12orEarlier - beta12orEarlier - 3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only). - true C-beta atoms from amino acid side-chains may be included. + true + 3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only). + beta12orEarlier + beta12orEarlier @@ -9294,9 +9294,9 @@ Structure alignment (pair) - Pair structure alignment - beta12orEarlier Alignment (superimposition) of exactly two molecular tertiary (3D) structures. + beta12orEarlier + Pair structure alignment @@ -9308,10 +9308,10 @@ Structure alignment (multiple) - Alignment (superimposition) of more than two molecular tertiary (3D) structures. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Alignment (superimposition) of more than two molecular tertiary (3D) structures. @@ -9324,9 +9324,9 @@ Structure alignment (protein) - Alignment (superimposition) of protein tertiary (3D) structures. - beta12orEarlier Protein structure alignment + beta12orEarlier + Alignment (superimposition) of protein tertiary (3D) structures. @@ -9338,9 +9338,9 @@ Structure alignment (nucleic acid) - Nucleic acid structure alignment - Alignment (superimposition) of nucleic acid tertiary (3D) structures. beta12orEarlier + Alignment (superimposition) of nucleic acid tertiary (3D) structures. + Nucleic acid structure alignment @@ -9353,9 +9353,9 @@ Structure alignment (protein pair) - Alignment (superimposition) of exactly two protein tertiary (3D) structures. - beta12orEarlier Protein pair structural alignment + beta12orEarlier + Alignment (superimposition) of exactly two protein tertiary (3D) structures. @@ -9367,10 +9367,10 @@ Multiple protein tertiary structure alignment - beta12orEarlier - true - beta12orEarlier Alignment (superimposition) of more than two protein tertiary (3D) structures. + beta12orEarlier + true + beta12orEarlier @@ -9382,10 +9382,10 @@ Structure alignment (protein all atoms) - true - beta12orEarlier - Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered). 1.5 + Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered). + beta12orEarlier + true @@ -9397,12 +9397,12 @@ Structure alignment (protein C-alpha atoms) - beta12orEarlier - true - C-alpha trace - 1.5 - C-beta atoms from amino acid side-chains may be considered. Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered). + C-beta atoms from amino acid side-chains may be considered. + 1.5 + C-alpha trace + true + beta12orEarlier @@ -9414,10 +9414,10 @@ Pairwise protein tertiary structure alignment (all atoms) - beta12orEarlier - beta12orEarlier - true Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). + true + beta12orEarlier + beta12orEarlier @@ -9429,11 +9429,11 @@ Pairwise protein tertiary structure alignment (C-alpha atoms) - beta12orEarlier - Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). - beta12orEarlier - true C-beta atoms from amino acid side-chains may be included. + true + beta12orEarlier + Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). + beta12orEarlier @@ -9445,10 +9445,10 @@ Multiple protein tertiary structure alignment (all atoms) - beta12orEarlier - Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). - true beta12orEarlier + true + Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). + beta12orEarlier @@ -9460,11 +9460,11 @@ Multiple protein tertiary structure alignment (C-alpha atoms) - C-beta atoms from amino acid side-chains may be included. - beta12orEarlier - true - Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). beta12orEarlier + Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). + true + beta12orEarlier + C-beta atoms from amino acid side-chains may be included. @@ -9477,9 +9477,9 @@ Structure alignment (nucleic acid pair) - Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures. - Nucleic acid pair structure alignment beta12orEarlier + Nucleic acid pair structure alignment + Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures. @@ -9491,10 +9491,10 @@ Multiple nucleic acid tertiary structure alignment - beta12orEarlier - true - Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures. beta12orEarlier + Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures. + true + beta12orEarlier @@ -9506,9 +9506,9 @@ Structure alignment (RNA) - beta12orEarlier - Alignment (superimposition) of RNA tertiary (3D) structures. RNA structure alignment + Alignment (superimposition) of RNA tertiary (3D) structures. + beta12orEarlier @@ -9520,8 +9520,8 @@ Structural transformation matrix - beta12orEarlier Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures. + beta12orEarlier @@ -9533,11 +9533,11 @@ DaliLite hit table - beta12orEarlier - true - beta12orEarlier - The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given. DaliLite hit table of protein chain tertiary structure alignment data. + The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given. + beta12orEarlier + true + beta12orEarlier @@ -9549,10 +9549,10 @@ Molecular similarity score - beta12orEarlier - true - A score reflecting structural similarities of two molecules. beta12orEarlier + A score reflecting structural similarities of two molecules. + true + beta12orEarlier @@ -9564,9 +9564,9 @@ Root-mean-square deviation - Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates. - beta12orEarlier RMSD + beta12orEarlier + Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates. @@ -9578,9 +9578,9 @@ Tanimoto similarity score - A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types. - A measure of the similarity between two ligand fingerprints. beta12orEarlier + A measure of the similarity between two ligand fingerprints. + A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types. @@ -9592,8 +9592,8 @@ 3D-1D scoring matrix - beta12orEarlier A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments. + beta12orEarlier @@ -9606,8 +9606,8 @@ Amino acid index - A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids. beta12orEarlier + A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids. @@ -9619,9 +9619,9 @@ Amino acid index (chemical classes) - beta12orEarlier - Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids. Chemical classes (amino acids) + Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids. + beta12orEarlier @@ -9633,9 +9633,9 @@ Amino acid pair-wise contact potentials - beta12orEarlier - Statistical protein contact potentials. Contact potentials (amino acid pair-wise) + Statistical protein contact potentials. + beta12orEarlier @@ -9647,9 +9647,9 @@ Amino acid index (molecular weight) - beta12orEarlier - Molecular weight (amino acids) Molecular weights of amino acids. + Molecular weight (amino acids) + beta12orEarlier @@ -9661,9 +9661,9 @@ Amino acid index (hydropathy) - Hydropathy (amino acids) - beta12orEarlier Hydrophobic, hydrophilic or charge properties of amino acids. + beta12orEarlier + Hydropathy (amino acids) @@ -9675,9 +9675,9 @@ Amino acid index (White-Wimley data) - Experimental free energy values for the water-interface and water-octanol transitions for the amino acids. - White-Wimley data (amino acids) beta12orEarlier + White-Wimley data (amino acids) + Experimental free energy values for the water-interface and water-octanol transitions for the amino acids. @@ -9689,9 +9689,9 @@ Amino acid index (van der Waals radii) - beta12orEarlier - Van der Waals radii of atoms for different amino acid residues. van der Waals radii (amino acids) + Van der Waals radii of atoms for different amino acid residues. + beta12orEarlier @@ -9703,12 +9703,12 @@ Enzyme report - An informative report on a specific enzyme. - Enzyme report - beta12orEarlier - Protein report (enzyme) - 1.5 true + 1.5 + Protein report (enzyme) + beta12orEarlier + Enzyme report + An informative report on a specific enzyme. @@ -9720,14 +9720,14 @@ Restriction enzyme report - true - Restriction enzyme report - Protein report (restriction enzyme) - This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc. - 1.5 - beta12orEarlier - Restriction enzyme pattern data An informative report on a specific restriction enzyme such as enzyme reference data. + Restriction enzyme pattern data + beta12orEarlier + 1.5 + This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc. + Protein report (restriction enzyme) + Restriction enzyme report + true @@ -9739,9 +9739,9 @@ Peptide molecular weights - The report might include associated data such as frequency of peptide fragment molecular weights. - List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents. beta12orEarlier + List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents. + The report might include associated data such as frequency of peptide fragment molecular weights. @@ -9753,9 +9753,9 @@ Peptide hydrophobic moment - Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. - Report on the hydrophobic moment of a polypeptide sequence. beta12orEarlier + Report on the hydrophobic moment of a polypeptide sequence. + Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. @@ -9767,9 +9767,9 @@ Protein aliphatic index - The aliphatic index is the relative protein volume occupied by aliphatic side chains. - beta12orEarlier The aliphatic index of a protein. + beta12orEarlier + The aliphatic index is the relative protein volume occupied by aliphatic side chains. @@ -9781,9 +9781,9 @@ Protein sequence hydropathy plot - beta12orEarlier - A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc. Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. + A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc. + beta12orEarlier @@ -9795,8 +9795,8 @@ Protein charge plot - A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence. beta12orEarlier + A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence. @@ -9808,9 +9808,9 @@ Protein solubility - Protein solubility data - The solubility or atomic solvation energy of a protein sequence or structure. beta12orEarlier + The solubility or atomic solvation energy of a protein sequence or structure. + Protein solubility data @@ -9822,9 +9822,9 @@ Protein crystallizability - Data on the crystallizability of a protein sequence. - Protein crystallizability data beta12orEarlier + Protein crystallizability data + Data on the crystallizability of a protein sequence. @@ -9836,9 +9836,9 @@ Protein globularity - Data on the stability, intrinsic disorder or globularity of a protein sequence. - beta12orEarlier Protein globularity data + beta12orEarlier + Data on the stability, intrinsic disorder or globularity of a protein sequence. @@ -9851,8 +9851,8 @@ Protein titration curve - beta12orEarlier The titration curve of a protein. + beta12orEarlier @@ -9864,8 +9864,8 @@ Protein isoelectric point - The isoelectric point of one proteins. beta12orEarlier + The isoelectric point of one proteins. @@ -9877,8 +9877,8 @@ Protein pKa value - beta12orEarlier The pKa value of a protein. + beta12orEarlier @@ -9890,8 +9890,8 @@ Protein hydrogen exchange rate - The hydrogen exchange rate of a protein. beta12orEarlier + The hydrogen exchange rate of a protein. @@ -9903,8 +9903,8 @@ Protein extinction coefficient - beta12orEarlier The extinction coefficient of a protein. + beta12orEarlier @@ -9916,8 +9916,8 @@ Protein optical density - beta12orEarlier The optical density of a protein. + beta12orEarlier @@ -9929,11 +9929,11 @@ Protein subcellular localization - beta13 - true - beta12orEarlier - An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins). Protein report (subcellular localization) + An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins). + beta12orEarlier + true + beta13 @@ -9945,11 +9945,11 @@ Peptide immunogenicity data - This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. - Peptide immunogenicity - beta12orEarlier - Peptide immunogenicity report An report on allergenicity / immunogenicity of peptides and proteins. + Peptide immunogenicity report + beta12orEarlier + Peptide immunogenicity + This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. @@ -9961,10 +9961,10 @@ MHC peptide immunogenicity report - beta12orEarlier - true - beta13 A report on the immunogenicity of MHC class I or class II binding peptides. + beta13 + true + beta12orEarlier @@ -9977,14 +9977,14 @@ Protein structure report - Protein structure report (domain) - Protein report (structure) - beta12orEarlier - Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains. - Protein property (structural) - This includes for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure). - Protein structure-derived report Protein structural property + Protein structure-derived report + This includes for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure). + Protein property (structural) + Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains. + beta12orEarlier + Protein report (structure) + Protein structure report (domain) @@ -9996,13 +9996,13 @@ Protein structural quality report - beta12orEarlier - Protein report (structural quality) - Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc. - Protein property (structural quality) - Protein structure validation report - Protein structure report (quality evaluation) Report on the quality of a protein three-dimensional model. + Protein structure report (quality evaluation) + Protein structure validation report + Protein property (structural quality) + Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc. + Protein report (structural quality) + beta12orEarlier @@ -10020,10 +10020,10 @@ - Atom interaction data - beta12orEarlier - Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups. Residue interaction data + Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups. + beta12orEarlier + Atom interaction data @@ -10035,14 +10035,14 @@ Protein flexibility or motion report - Protein structure report (flexibility or motion) - 1.4 - true - beta12orEarlier - Protein flexibility or motion - Informative report on flexibility or motion of a protein structure. - Protein property (flexibility or motion) This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Protein property (flexibility or motion) + Informative report on flexibility or motion of a protein structure. + Protein flexibility or motion + beta12orEarlier + true + 1.4 + Protein structure report (flexibility or motion) @@ -10054,9 +10054,9 @@ Protein solvent accessibility - Data on the solvent accessible or buried surface area of a protein structure. - beta12orEarlier This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc. + beta12orEarlier + Data on the solvent accessible or buried surface area of a protein structure. @@ -10068,12 +10068,12 @@ Protein surface report - true - beta12orEarlier - Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure. - 1.4 - Protein structure report (surface) This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Protein structure report (surface) + 1.4 + Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure. + beta12orEarlier + true @@ -10085,8 +10085,8 @@ Ramachandran plot - Phi/psi angle data or a Ramachandran plot of a protein structure. beta12orEarlier + Phi/psi angle data or a Ramachandran plot of a protein structure. @@ -10098,8 +10098,8 @@ Protein dipole moment - beta12orEarlier Data on the net charge distribution (dipole moment) of a protein structure. + beta12orEarlier @@ -10111,8 +10111,8 @@ Protein distance matrix - A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure. beta12orEarlier + A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure. @@ -10124,8 +10124,8 @@ Protein contact map - beta12orEarlier An amino acid residue contact map for a protein structure. + beta12orEarlier @@ -10137,8 +10137,8 @@ Protein residue 3D cluster - Report on clusters of contacting residues in protein structures such as a key structural residue network. beta12orEarlier + Report on clusters of contacting residues in protein structures such as a key structural residue network. @@ -10150,8 +10150,8 @@ Protein hydrogen bonds - beta12orEarlier Patterns of hydrogen bonding in protein structures. + beta12orEarlier @@ -10163,11 +10163,11 @@ Protein non-canonical interactions - beta12orEarlier - 1.4 - Non-canonical atomic interactions in protein structures. - true Protein non-canonical interactions report + true + Non-canonical atomic interactions in protein structures. + 1.4 + beta12orEarlier @@ -10179,12 +10179,12 @@ CATH node - CATH classification node report - true - beta12orEarlier - 1.5 - The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links. Information on a node from the CATH database. + The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links. + 1.5 + beta12orEarlier + true + CATH classification node report @@ -10196,11 +10196,11 @@ SCOP node - beta12orEarlier - 1.5 - Information on a node from the SCOP database. - SCOP classification node true + SCOP classification node + Information on a node from the SCOP database. + 1.5 + beta12orEarlier @@ -10212,10 +10212,10 @@ EMBASSY domain classification - An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format. @@ -10226,10 +10226,10 @@ CATH class - true - Information on a protein 'class' node from the CATH database. - 1.5 beta12orEarlier + 1.5 + Information on a protein 'class' node from the CATH database. + true @@ -10241,10 +10241,10 @@ CATH architecture - true - Information on a protein 'architecture' node from the CATH database. - 1.5 beta12orEarlier + 1.5 + Information on a protein 'architecture' node from the CATH database. + true @@ -10256,10 +10256,10 @@ CATH topology - beta12orEarlier - Information on a protein 'topology' node from the CATH database. - 1.5 true + 1.5 + Information on a protein 'topology' node from the CATH database. + beta12orEarlier @@ -10271,10 +10271,10 @@ CATH homologous superfamily - Information on a protein 'homologous superfamily' node from the CATH database. - beta12orEarlier - true 1.5 + true + beta12orEarlier + Information on a protein 'homologous superfamily' node from the CATH database. @@ -10286,10 +10286,10 @@ CATH structurally similar group - Information on a protein 'structurally similar group' node from the CATH database. - beta12orEarlier - true 1.5 + true + beta12orEarlier + Information on a protein 'structurally similar group' node from the CATH database. @@ -10301,10 +10301,10 @@ CATH functional category - beta12orEarlier - 1.5 - true Information on a protein 'functional category' node from the CATH database. + true + 1.5 + beta12orEarlier @@ -10316,11 +10316,11 @@ Protein fold recognition report - beta12orEarlier - true - A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s). - beta12orEarlier Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. + beta12orEarlier + A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s). + true + beta12orEarlier @@ -10332,10 +10332,10 @@ Protein-protein interaction report - 1.8 - Topic concerning protein-protein interaction(s), including interactions between protein domains. - true beta12orEarlier + true + Topic concerning protein-protein interaction(s), including interactions between protein domains. + 1.8 @@ -10347,8 +10347,8 @@ Protein-ligand interaction report - An informative report on protein-ligand (small molecule) interaction(s). beta12orEarlier + An informative report on protein-ligand (small molecule) interaction(s). @@ -10360,10 +10360,10 @@ Protein-nucleic acid interactions report - 1.8 - beta12orEarlier - Topic concerning protein-DNA/RNA interaction(s). true + Topic concerning protein-DNA/RNA interaction(s). + beta12orEarlier + 1.8 @@ -10375,10 +10375,10 @@ Nucleic acid melting profile - beta12orEarlier - Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating. - A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence. Nucleic acid stability profile + A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence. + Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating. + beta12orEarlier @@ -10390,8 +10390,8 @@ Nucleic acid enthalpy - Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). beta12orEarlier + Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). @@ -10403,8 +10403,8 @@ Nucleic acid entropy - beta12orEarlier Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). + beta12orEarlier @@ -10416,10 +10416,10 @@ Nucleic acid melting temperature - true - beta12orEarlier - beta12orEarlier Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA). + beta12orEarlier + beta12orEarlier + true @@ -10431,9 +10431,9 @@ Nucleic acid stitch profile - A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature. - Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA). beta12orEarlier + Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA). + A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature. @@ -10445,8 +10445,8 @@ DNA base pair stacking energies data - beta12orEarlier DNA base pair stacking energies data. + beta12orEarlier @@ -10458,8 +10458,8 @@ DNA base pair twist angle data - DNA base pair twist angle data. beta12orEarlier + DNA base pair twist angle data. @@ -10471,8 +10471,8 @@ DNA base trimer roll angles data - DNA base trimer roll angles data. beta12orEarlier + DNA base trimer roll angles data. @@ -10484,10 +10484,10 @@ Vienna RNA parameters - beta12orEarlier - beta12orEarlier - true RNA parameters used by the Vienna package. + true + beta12orEarlier + beta12orEarlier @@ -10499,10 +10499,10 @@ Vienna RNA structure constraints - beta12orEarlier - beta12orEarlier - Structure constraints used by the Vienna package. true + Structure constraints used by the Vienna package. + beta12orEarlier + beta12orEarlier @@ -10514,10 +10514,10 @@ Vienna RNA concentration data - beta12orEarlier - true - beta12orEarlier RNA concentration data used by the Vienna package. + beta12orEarlier + true + beta12orEarlier @@ -10529,10 +10529,10 @@ Vienna RNA calculated energy - RNA calculated energy data generated by the Vienna package. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + RNA calculated energy data generated by the Vienna package. @@ -10545,9 +10545,9 @@ Base pairing probability matrix dotplot - Dotplot of RNA base pairing probability matrix. - Such as generated by the Vienna package. beta12orEarlier + Such as generated by the Vienna package. + Dotplot of RNA base pairing probability matrix. @@ -10559,13 +10559,13 @@ Nucleic acid folding report - RNA secondary structure folding classification - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc. - RNA secondary structure folding probablities - Nucleic acid report (folding model) - beta12orEarlier Nucleic acid report (folding) + beta12orEarlier + Nucleic acid report (folding model) + RNA secondary structure folding probablities + A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc. + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + RNA secondary structure folding classification @@ -10583,9 +10583,9 @@ - beta12orEarlier - A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table. Table of codon usage data calculated from one or more nucleic acid sequences. + A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table. + beta12orEarlier @@ -10597,9 +10597,9 @@ Genetic code - A genetic code need not include detailed codon usage information. - A genetic code for an organism. beta12orEarlier + A genetic code for an organism. + A genetic code need not include detailed codon usage information. @@ -10611,11 +10611,11 @@ Codon adaptation index - beta12orEarlier - beta12orEarlier - CAI - A simple measure of synonymous codon usage bias often used to predict gene expression levels. true + A simple measure of synonymous codon usage bias often used to predict gene expression levels. + CAI + beta12orEarlier + beta12orEarlier @@ -10627,9 +10627,9 @@ Codon usage bias plot - A plot of the synonymous codon usage calculated for windows over a nucleotide sequence. - beta12orEarlier Synonymous codon usage statistic plot + beta12orEarlier + A plot of the synonymous codon usage calculated for windows over a nucleotide sequence. @@ -10641,10 +10641,10 @@ Nc statistic - beta12orEarlier - The effective number of codons used in a gene sequence. This reflects how far codon usage of a gene departs from equal usage of synonymous codons. - beta12orEarlier true + beta12orEarlier + The effective number of codons used in a gene sequence. This reflects how far codon usage of a gene departs from equal usage of synonymous codons. + beta12orEarlier @@ -10656,8 +10656,8 @@ Codon usage fraction difference - beta12orEarlier The differences in codon usage fractions between two codon usage tables. + beta12orEarlier @@ -10669,9 +10669,9 @@ Pharmacogenomic test report - Data on the influence of genotype on drug response. - The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. beta12orEarlier + The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. + Data on the influence of genotype on drug response. @@ -10689,10 +10689,10 @@ - Disease report - beta12orEarlier - For example, an informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on. An informative report on a specific disease. + For example, an informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on. + beta12orEarlier + Disease report @@ -10704,10 +10704,10 @@ Linkage disequilibrium (report) - beta12orEarlier - 1.8 - A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). true + A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). + 1.8 + beta12orEarlier @@ -10720,9 +10720,9 @@ Heat map - A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context. - beta12orEarlier A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment. + beta12orEarlier + A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context. @@ -10734,11 +10734,11 @@ Affymetrix probe sets library file - beta12orEarlier - beta12orEarlier - CDF file - Affymetrix library file of information about which probes belong to which probe set. true + Affymetrix library file of information about which probes belong to which probe set. + CDF file + beta12orEarlier + beta12orEarlier @@ -10750,11 +10750,11 @@ Affymetrix probe sets information library file - beta12orEarlier - beta12orEarlier - GIN file - Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated. true + Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated. + GIN file + beta12orEarlier + beta12orEarlier @@ -10766,8 +10766,8 @@ Molecular weights standard fingerprint - Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS. beta12orEarlier + Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS. @@ -10779,11 +10779,11 @@ Metabolic pathway report - true - 1.8 - A report typically including a map (diagram) of a metabolic pathway. - beta12orEarlier This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. + beta12orEarlier + A report typically including a map (diagram) of a metabolic pathway. + 1.8 + true @@ -10795,10 +10795,10 @@ Genetic information processing pathway report - true - 1.8 - Topic concerning genetic information processing pathways. beta12orEarlier + Topic concerning genetic information processing pathways. + 1.8 + true @@ -10810,10 +10810,10 @@ Environmental information processing pathway report - 1.8 - beta12orEarlier - true Topic concerning environmental information processing pathways. + true + beta12orEarlier + 1.8 @@ -10825,10 +10825,10 @@ Signal transduction pathway report - beta12orEarlier - true - 1.8 A report typically including a map (diagram) of a signal transduction pathway. + 1.8 + true + beta12orEarlier @@ -10840,10 +10840,10 @@ Cellular process pathways report - beta12orEarlier - true - Topic concernning cellular process pathways. 1.8 + Topic concernning cellular process pathways. + true + beta12orEarlier @@ -10855,10 +10855,10 @@ Disease pathway or network report - Topic concerning disease pathways, typically of human disease. - 1.8 - beta12orEarlier true + beta12orEarlier + 1.8 + Topic concerning disease pathways, typically of human disease. @@ -10870,8 +10870,8 @@ Drug structure relationship map - beta12orEarlier A report typically including a map (diagram) of drug structure relationships. + beta12orEarlier @@ -10883,10 +10883,10 @@ Protein interaction networks - beta12orEarlier - true - 1.8 Topic concerning networks of protein interactions. + 1.8 + true + beta12orEarlier @@ -10898,11 +10898,11 @@ MIRIAM datatype - 1.5 - true - beta12orEarlier - An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources. A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types. + An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources. + beta12orEarlier + true + 1.5 @@ -10914,10 +10914,10 @@ E-value - Expectation value - A simple floating point number defining the lower or upper limit of an expectation value (E-value). - beta12orEarlier An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score. + beta12orEarlier + A simple floating point number defining the lower or upper limit of an expectation value (E-value). + Expectation value @@ -10929,9 +10929,9 @@ Z-value - A z-value might be specified as a threshold for reporting hits from database searches. - The z-value is the number of standard deviations a data value is above or below a mean value. beta12orEarlier + The z-value is the number of standard deviations a data value is above or below a mean value. + A z-value might be specified as a threshold for reporting hits from database searches. @@ -10943,9 +10943,9 @@ P-value - The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true. - A z-value might be specified as a threshold for reporting hits from database searches. beta12orEarlier + A z-value might be specified as a threshold for reporting hits from database searches. + The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true. @@ -10957,11 +10957,11 @@ Database version information - beta12orEarlier - Information on a database (or ontology) version, for example name, version number and release date. - 1.5 - Ontology version information true + Ontology version information + 1.5 + Information on a database (or ontology) version, for example name, version number and release date. + beta12orEarlier @@ -10973,10 +10973,10 @@ Tool version information - 1.5 - true - Information on an application version, for example name, version number and release date. beta12orEarlier + Information on an application version, for example name, version number and release date. + true + 1.5 @@ -10988,10 +10988,10 @@ CATH version information - Information on a version of the CATH database. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Information on a version of the CATH database. @@ -11003,10 +11003,10 @@ Swiss-Prot to PDB mapping - beta12orEarlier - true - beta12orEarlier Cross-mapping of Swiss-Prot codes to PDB identifiers. + beta12orEarlier + true + beta12orEarlier @@ -11018,10 +11018,10 @@ Sequence database cross-references - beta12orEarlier - true - beta12orEarlier Cross-references from a sequence record to other databases. + beta12orEarlier + true + beta12orEarlier @@ -11033,11 +11033,11 @@ Job status - Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed). - true - 1.5 - beta12orEarlier Metadata on the status of a submitted job. + beta12orEarlier + 1.5 + true + Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed). @@ -11049,10 +11049,10 @@ Job ID - true - beta12orEarlier - The (typically numeric) unique identifier of a submitted job. 1.0 + The (typically numeric) unique identifier of a submitted job. + beta12orEarlier + true @@ -11063,10 +11063,10 @@ Job type - A label (text token) describing the type of job, for example interactive or non-interactive. - beta12orEarlier - true 1.5 + true + beta12orEarlier + A label (text token) describing the type of job, for example interactive or non-interactive. @@ -11078,10 +11078,10 @@ Tool log - beta12orEarlier - true - A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages. 1.5 + A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages. + true + beta12orEarlier @@ -11093,10 +11093,10 @@ DaliLite log file - beta12orEarlier - DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures. - beta12orEarlier true + beta12orEarlier + DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures. + beta12orEarlier @@ -11108,10 +11108,10 @@ STRIDE log file - beta12orEarlier - beta12orEarlier - true STRIDE log file. + true + beta12orEarlier + beta12orEarlier @@ -11124,10 +11124,10 @@ NACCESS log file - NACCESS log file. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + NACCESS log file. @@ -11140,10 +11140,10 @@ EMBOSS wordfinder log file - true - beta12orEarlier - beta12orEarlier EMBOSS wordfinder log file. + beta12orEarlier + beta12orEarlier + true @@ -11155,10 +11155,10 @@ EMBOSS domainatrix log file - true - beta12orEarlier - EMBOSS (EMBASSY) domainatrix application log file. beta12orEarlier + EMBOSS (EMBASSY) domainatrix application log file. + beta12orEarlier + true @@ -11170,10 +11170,10 @@ EMBOSS sites log file - EMBOSS (EMBASSY) sites application log file. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + EMBOSS (EMBASSY) sites application log file. @@ -11185,10 +11185,10 @@ EMBOSS supermatcher error file - true - beta12orEarlier - beta12orEarlier EMBOSS (EMBASSY) supermatcher error file. + beta12orEarlier + beta12orEarlier + true @@ -11200,10 +11200,10 @@ EMBOSS megamerger log file - true - EMBOSS megamerger log file. - beta12orEarlier beta12orEarlier + beta12orEarlier + EMBOSS megamerger log file. + true @@ -11215,10 +11215,10 @@ EMBOSS whichdb log file - beta12orEarlier - EMBOSS megamerger log file. - true beta12orEarlier + true + EMBOSS megamerger log file. + beta12orEarlier @@ -11230,10 +11230,10 @@ EMBOSS vectorstrip log file - EMBOSS vectorstrip log file. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + EMBOSS vectorstrip log file. @@ -11245,8 +11245,8 @@ Username - beta12orEarlier A username on a computer system. + beta12orEarlier @@ -11259,8 +11259,8 @@ Password - A password on a computer system. beta12orEarlier + A password on a computer system. @@ -11273,10 +11273,10 @@ Email address - Moby:EmailAddress - A valid email address of an end-user. - Moby:Email beta12orEarlier + Moby:Email + A valid email address of an end-user. + Moby:EmailAddress @@ -11289,8 +11289,8 @@ Person name - The name of a person. beta12orEarlier + The name of a person. @@ -11303,10 +11303,10 @@ Number of iterations - beta12orEarlier - true - Number of iterations of an algorithm. 1.5 + Number of iterations of an algorithm. + true + beta12orEarlier @@ -11318,10 +11318,10 @@ Number of output entities - true - beta12orEarlier - 1.5 Number of entities (for example database hits, sequences, alignments etc) to write to an output file. + 1.5 + beta12orEarlier + true @@ -11333,10 +11333,10 @@ Hit sort order - true - beta12orEarlier - beta12orEarlier Controls the order of hits (reported matches) in an output file from a database search. + beta12orEarlier + beta12orEarlier + true @@ -11355,9 +11355,9 @@ - Drug annotation - beta12orEarlier An informative report on a specific drug. + beta12orEarlier + Drug annotation @@ -11370,9 +11370,9 @@ Phylogenetic tree image - See also 'Phylogenetic tree' - An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information. beta12orEarlier + An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information. + See also 'Phylogenetic tree' @@ -11384,8 +11384,8 @@ RNA secondary structure image - Image of RNA secondary structure, knots, pseudoknots etc. beta12orEarlier + Image of RNA secondary structure, knots, pseudoknots etc. @@ -11397,8 +11397,8 @@ Protein secondary structure image - beta12orEarlier Image of protein secondary structure. + beta12orEarlier @@ -11410,8 +11410,8 @@ Structure image - Image of one or more molecular tertiary (3D) structures. beta12orEarlier + Image of one or more molecular tertiary (3D) structures. @@ -11423,8 +11423,8 @@ Sequence alignment image - Image of two or more aligned molecular sequences possibly annotated with alignment features. beta12orEarlier + Image of two or more aligned molecular sequences possibly annotated with alignment features. @@ -11436,10 +11436,10 @@ Chemical structure image - beta12orEarlier - Small molecule structure image - The molecular identifier and formula are typically included. An image of the structure of a small chemical compound. + The molecular identifier and formula are typically included. + Small molecule structure image + beta12orEarlier @@ -11458,8 +11458,8 @@ - A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development. beta12orEarlier + A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development. @@ -11472,8 +11472,8 @@ Microarray spots image - An image of spots from a microarray experiment. beta12orEarlier + An image of spots from a microarray experiment. @@ -11485,10 +11485,10 @@ BioPax term - true - beta12orEarlier - A term from the BioPax ontology. beta12orEarlier + A term from the BioPax ontology. + beta12orEarlier + true @@ -11500,15 +11500,15 @@ GO - Moby:GOTerm - Moby:GO_Term - beta12orEarlier - A term definition from The Gene Ontology (GO). - true - Moby:Annotated_GO_Term_With_Probability - Moby:Annotated_GO_Term - Gene Ontology term beta12orEarlier + Gene Ontology term + Moby:Annotated_GO_Term + Moby:Annotated_GO_Term_With_Probability + true + A term definition from The Gene Ontology (GO). + beta12orEarlier + Moby:GO_Term + Moby:GOTerm @@ -11520,10 +11520,10 @@ MeSH - beta12orEarlier - beta12orEarlier - A term from the MeSH vocabulary. true + A term from the MeSH vocabulary. + beta12orEarlier + beta12orEarlier @@ -11535,10 +11535,10 @@ HGNC - beta12orEarlier - A term from the HGNC controlled vocabulary. - true beta12orEarlier + true + A term from the HGNC controlled vocabulary. + beta12orEarlier @@ -11550,10 +11550,10 @@ NCBI taxonomy vocabulary - A term from the NCBI taxonomy vocabulary. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + A term from the NCBI taxonomy vocabulary. @@ -11565,10 +11565,10 @@ Plant ontology term - A term from the Plant Ontology (PO). - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + A term from the Plant Ontology (PO). @@ -11580,10 +11580,10 @@ UMLS - true - A term from the UMLS vocabulary. - beta12orEarlier beta12orEarlier + beta12orEarlier + A term from the UMLS vocabulary. + true @@ -11595,11 +11595,11 @@ FMA - true - A term from Foundational Model of Anatomy. - beta12orEarlier - Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. beta12orEarlier + Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. + beta12orEarlier + A term from Foundational Model of Anatomy. + true @@ -11611,10 +11611,10 @@ EMAP - beta12orEarlier - beta12orEarlier - true A term from the EMAP mouse ontology. + true + beta12orEarlier + beta12orEarlier @@ -11626,10 +11626,10 @@ ChEBI - beta12orEarlier - true - A term from the ChEBI ontology. beta12orEarlier + A term from the ChEBI ontology. + true + beta12orEarlier @@ -11641,10 +11641,10 @@ MGED - beta12orEarlier - A term from the MGED ontology. - true beta12orEarlier + true + A term from the MGED ontology. + beta12orEarlier @@ -11656,11 +11656,11 @@ myGrid - beta12orEarlier - A term from the myGrid ontology. - true - beta12orEarlier The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. + beta12orEarlier + true + A term from the myGrid ontology. + beta12orEarlier @@ -11672,11 +11672,11 @@ GO (biological process) - A term definition for a biological process from the Gene Ontology (GO). - Data Type is an enumerated string. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Data Type is an enumerated string. + A term definition for a biological process from the Gene Ontology (GO). @@ -11688,11 +11688,11 @@ GO (molecular function) - beta12orEarlier - true - Data Type is an enumerated string. - beta12orEarlier A term definition for a molecular function from the Gene Ontology (GO). + beta12orEarlier + Data Type is an enumerated string. + true + beta12orEarlier @@ -11704,11 +11704,11 @@ GO (cellular component) - Data Type is an enumerated string. - beta12orEarlier - A term definition for a cellular component from the Gene Ontology (GO). - true beta12orEarlier + true + A term definition for a cellular component from the Gene Ontology (GO). + beta12orEarlier + Data Type is an enumerated string. @@ -11720,10 +11720,10 @@ Ontology relation type - A relation type defined in an ontology. - true - beta12orEarlier 1.5 + beta12orEarlier + true + A relation type defined in an ontology. @@ -11735,9 +11735,9 @@ Ontology concept definition - The definition of a concept from an ontology. - Ontology class definition beta12orEarlier + Ontology class definition + The definition of a concept from an ontology. @@ -11749,10 +11749,10 @@ Ontology concept comment - A comment on a concept from an ontology. - true - 1.4 beta12orEarlier + 1.4 + true + A comment on a concept from an ontology. @@ -11764,10 +11764,10 @@ Ontology concept reference - beta12orEarlier - Reference for a concept from an ontology. - true beta12orEarlier + true + Reference for a concept from an ontology. + beta12orEarlier @@ -11779,11 +11779,11 @@ doc2loc document information - Information on a published article provided by the doc2loc program. - beta12orEarlier - The doc2loc output includes the url, format, type and availability code of a document for every service provider. - true beta12orEarlier + true + The doc2loc output includes the url, format, type and availability code of a document for every service provider. + beta12orEarlier + Information on a published article provided by the doc2loc program. @@ -11795,10 +11795,10 @@ PDB residue number - A residue identifier (a string) from a PDB file. - beta12orEarlier - PDBML:PDB_residue_no WHATIF: pdb_number + PDBML:PDB_residue_no + beta12orEarlier + A residue identifier (a string) from a PDB file. @@ -11810,9 +11810,9 @@ Atomic coordinate - Cartesian coordinate - beta12orEarlier Cartesian coordinate of an atom (in a molecular structure). + beta12orEarlier + Cartesian coordinate @@ -11824,11 +11824,11 @@ Atomic x coordinate - Cartesian x coordinate of an atom (in a molecular structure). - PDBML:_atom_site.Cartn_x in PDBML - beta12orEarlier - Cartesian x coordinate WHATIF: PDBx_Cartn_x + Cartesian x coordinate + beta12orEarlier + PDBML:_atom_site.Cartn_x in PDBML + Cartesian x coordinate of an atom (in a molecular structure). @@ -11840,11 +11840,11 @@ Atomic y coordinate - Cartesian y coordinate of an atom (in a molecular structure). - PDBML:_atom_site.Cartn_y in PDBML - beta12orEarlier - Cartesian y coordinate WHATIF: PDBx_Cartn_y + Cartesian y coordinate + beta12orEarlier + PDBML:_atom_site.Cartn_y in PDBML + Cartesian y coordinate of an atom (in a molecular structure). @@ -11856,11 +11856,11 @@ Atomic z coordinate - Cartesian z coordinate - beta12orEarlier - Cartesian z coordinate of an atom (in a molecular structure). - WHATIF: PDBx_Cartn_z PDBML:_atom_site.Cartn_z + WHATIF: PDBx_Cartn_z + Cartesian z coordinate of an atom (in a molecular structure). + beta12orEarlier + Cartesian z coordinate @@ -11872,13 +11872,13 @@ PDB atom name - Identifier (a string) of a specific atom from a PDB file for a molecular structure. - WHATIF: atom_type - PDBML:pdbx_PDB_atom_name - WHATIF: alternate_atom - WHATIF: PDBx_auth_atom_id - beta12orEarlier WHATIF: PDBx_type_symbol + beta12orEarlier + WHATIF: PDBx_auth_atom_id + WHATIF: alternate_atom + PDBML:pdbx_PDB_atom_name + WHATIF: atom_type + Identifier (a string) of a specific atom from a PDB file for a molecular structure. @@ -11891,11 +11891,11 @@ Protein atom - beta12orEarlier - Data on a single atom from a protein structure. - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - CHEBI:33250 Atom data + CHEBI:33250 + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Data on a single atom from a protein structure. + beta12orEarlier @@ -11907,10 +11907,10 @@ Protein residue - Residue - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - Data on a single amino acid residue position in a protein structure. beta12orEarlier + Data on a single amino acid residue position in a protein structure. + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Residue @@ -11923,8 +11923,8 @@ Atom name - beta12orEarlier Name of an atom. + beta12orEarlier @@ -11937,9 +11937,9 @@ PDB residue name - beta12orEarlier - WHATIF: type Three-letter amino acid residue names as used in PDB files. + WHATIF: type + beta12orEarlier @@ -11952,11 +11952,11 @@ PDB model number - WHATIF: model_number - Model number - PDBML:pdbx_PDB_model_num - beta12orEarlier Identifier of a model structure from a PDB file. + beta12orEarlier + PDBML:pdbx_PDB_model_num + Model number + WHATIF: model_number @@ -11969,11 +11969,11 @@ CATH domain report - Summary of domain classification information for a CATH domain. - The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. - beta13 - true beta12orEarlier + true + beta13 + The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. + Summary of domain classification information for a CATH domain. @@ -11985,10 +11985,10 @@ CATH representative domain sequences (ATOM) - true - FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity). - beta12orEarlier beta12orEarlier + beta12orEarlier + FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity). + true @@ -12000,10 +12000,10 @@ CATH representative domain sequences (COMBS) - beta12orEarlier - beta12orEarlier - FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity). true + FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity). + beta12orEarlier + beta12orEarlier @@ -12015,10 +12015,10 @@ CATH domain sequences (ATOM) - beta12orEarlier - beta12orEarlier - FASTA sequence database for all CATH domains (based on PDB ATOM records). true + FASTA sequence database for all CATH domains (based on PDB ATOM records). + beta12orEarlier + beta12orEarlier @@ -12030,10 +12030,10 @@ CATH domain sequences (COMBS) - beta12orEarlier - true - beta12orEarlier FASTA sequence database for all CATH domains (based on COMBS sequence data). + beta12orEarlier + true + beta12orEarlier @@ -12045,9 +12045,9 @@ Sequence version - Sequence version information - Information on an molecular sequence version. beta12orEarlier + Information on an molecular sequence version. + Sequence version information @@ -12059,8 +12059,8 @@ Score - beta12orEarlier A numerical value, that is some type of scored value arising for example from a prediction method. + beta12orEarlier @@ -12072,11 +12072,11 @@ Protein report (function) - beta12orEarlier - Report on general functional properties of specific protein(s). - beta13 - For properties that can be mapped to a sequence, use 'Sequence report' instead. true + For properties that can be mapped to a sequence, use 'Sequence report' instead. + beta13 + Report on general functional properties of specific protein(s). + beta12orEarlier @@ -12088,11 +12088,11 @@ Gene name (ASPGD) - http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS - Name of a gene from Aspergillus Genome Database. - true - beta12orEarlier 1.3 + beta12orEarlier + true + Name of a gene from Aspergillus Genome Database. + http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS @@ -12104,11 +12104,11 @@ Gene name (CGD) - 1.3 - beta12orEarlier - http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS - true Name of a gene from Candida Genome Database. + true + http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS + beta12orEarlier + 1.3 @@ -12120,11 +12120,11 @@ Gene name (dictyBase) - Name of a gene from dictyBase database. - true - 1.3 - beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase + beta12orEarlier + 1.3 + true + Name of a gene from dictyBase database. @@ -12136,12 +12136,12 @@ Gene name (EcoGene primary) - beta12orEarlier - true - 1.3 - EcoGene primary gene name - Primary name of a gene from EcoGene Database. http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G + Primary name of a gene from EcoGene Database. + EcoGene primary gene name + 1.3 + true + beta12orEarlier @@ -12153,11 +12153,11 @@ Gene name (MaizeGDB) - beta12orEarlier - true - Name of a gene from MaizeGDB (maize genes) database. - 1.3 http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus + 1.3 + Name of a gene from MaizeGDB (maize genes) database. + true + beta12orEarlier @@ -12169,11 +12169,11 @@ Gene name (SGD) - Name of a gene from Saccharomyces Genome Database. - http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS - beta12orEarlier - 1.3 true + 1.3 + beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS + Name of a gene from Saccharomyces Genome Database. @@ -12185,11 +12185,11 @@ Gene name (TGD) - http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS - true - Name of a gene from Tetrahymena Genome Database. - 1.3 beta12orEarlier + 1.3 + Name of a gene from Tetrahymena Genome Database. + true + http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS @@ -12201,11 +12201,11 @@ Gene name (CGSC) - Symbol of a gene from E.coli Genetic Stock Center. - http://www.geneontology.org/doc/GO.xrf_abbs: CGSC - true - 1.3 beta12orEarlier + 1.3 + true + http://www.geneontology.org/doc/GO.xrf_abbs: CGSC + Symbol of a gene from E.coli Genetic Stock Center. @@ -12217,20 +12217,20 @@ Gene name (HGNC) - Symbol of a gene approved by the HUGO Gene Nomenclature Committee. - HGNC gene symbol - Gene name (HUGO) - HGNC:[0-9]{1,5} - HUGO gene symbol - HGNC gene name - http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene - HUGO gene name - Official gene name - HGNC symbol - true - 1.3 - HUGO symbol beta12orEarlier + HUGO symbol + 1.3 + true + HGNC symbol + Official gene name + HUGO gene name + http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene + HGNC gene name + HUGO gene symbol + HGNC:[0-9]{1,5} + Gene name (HUGO) + HGNC gene symbol + Symbol of a gene approved by the HUGO Gene Nomenclature Committee. @@ -12242,12 +12242,12 @@ Gene name (MGD) - beta12orEarlier - true - 1.3 - http://www.geneontology.org/doc/GO.xrf_abbs: MGD - Symbol of a gene from the Mouse Genome Database. MGI:[0-9]+ + Symbol of a gene from the Mouse Genome Database. + http://www.geneontology.org/doc/GO.xrf_abbs: MGD + 1.3 + true + beta12orEarlier @@ -12259,11 +12259,11 @@ Gene name (Bacillus subtilis) - true - 1.3 - beta12orEarlier - Symbol of a gene from Bacillus subtilis Genome Sequence Project. http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG + Symbol of a gene from Bacillus subtilis Genome Sequence Project. + beta12orEarlier + 1.3 + true @@ -12275,9 +12275,9 @@ Gene ID (PlasmoDB) - http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB - beta12orEarlier Identifier of a gene from PlasmoDB Plasmodium Genome Resource. + beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB @@ -12290,10 +12290,10 @@ Gene ID (EcoGene) - beta12orEarlier - EcoGene ID - EcoGene Accession Identifier of a gene from EcoGene Database. + EcoGene Accession + EcoGene ID + beta12orEarlier @@ -12306,10 +12306,10 @@ Gene ID (FlyBase) - http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase - http://www.geneontology.org/doc/GO.xrf_abbs: FB - Gene identifier from FlyBase database. beta12orEarlier + Gene identifier from FlyBase database. + http://www.geneontology.org/doc/GO.xrf_abbs: FB + http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase @@ -12322,11 +12322,11 @@ Gene ID (GeneDB Glossina morsitans) - beta12orEarlier - Gene identifier from Glossina morsitans GeneDB database. - beta13 - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans true + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans + beta13 + Gene identifier from Glossina morsitans GeneDB database. + beta12orEarlier @@ -12338,11 +12338,11 @@ Gene ID (GeneDB Leishmania major) - beta13 - beta12orEarlier - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor - true Gene identifier from Leishmania major GeneDB database. + true + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor + beta12orEarlier + beta13 @@ -12354,11 +12354,11 @@ Gene ID (GeneDB Plasmodium falciparum) - beta12orEarlier - beta13 - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum - true Gene identifier from Plasmodium falciparum GeneDB database. + true + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum + beta13 + beta12orEarlier @@ -12370,11 +12370,11 @@ Gene ID (GeneDB Schizosaccharomyces pombe) - Gene identifier from Schizosaccharomyces pombe GeneDB database. - beta13 - true - beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe + beta12orEarlier + true + beta13 + Gene identifier from Schizosaccharomyces pombe GeneDB database. @@ -12386,11 +12386,11 @@ Gene ID (GeneDB Trypanosoma brucei) - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei - beta12orEarlier - beta13 - true Gene identifier from Trypanosoma brucei GeneDB database. + true + beta13 + beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei @@ -12402,10 +12402,10 @@ Gene ID (Gramene) - Gene identifier from Gramene database. - http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE - beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene + beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE + Gene identifier from Gramene database. @@ -12418,10 +12418,10 @@ Gene ID (Virginia microbial) - http://www.geneontology.org/doc/GO.xrf_abbs: VMD - Gene identifier from Virginia Bioinformatics Institute microbial database. - http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD + Gene identifier from Virginia Bioinformatics Institute microbial database. + http://www.geneontology.org/doc/GO.xrf_abbs: VMD @@ -12434,9 +12434,9 @@ Gene ID (SGN) - beta12orEarlier - Gene identifier from Sol Genomics Network. http://www.geneontology.org/doc/GO.xrf_abbs: SGN + Gene identifier from Sol Genomics Network. + beta12orEarlier @@ -12450,11 +12450,11 @@ Gene ID (WormBase) - beta12orEarlier - http://www.geneontology.org/doc/GO.xrf_abbs: WormBase - http://www.geneontology.org/doc/GO.xrf_abbs: WB - WBGene[0-9]{8} Gene identifier used by WormBase database. + WBGene[0-9]{8} + http://www.geneontology.org/doc/GO.xrf_abbs: WB + http://www.geneontology.org/doc/GO.xrf_abbs: WormBase + beta12orEarlier @@ -12467,11 +12467,11 @@ Gene synonym - beta12orEarlier - beta12orEarlier - Any name (other than the recommended one) for a gene. - true Gene name synonym + true + Any name (other than the recommended one) for a gene. + beta12orEarlier + beta12orEarlier @@ -12484,8 +12484,8 @@ ORF name - The name of an open reading frame attributed by a sequencing project. beta12orEarlier + The name of an open reading frame attributed by a sequencing project. @@ -12498,10 +12498,10 @@ Sequence assembly component - beta12orEarlier - beta12orEarlier - true A component of a larger sequence assembly. + true + beta12orEarlier + beta12orEarlier @@ -12513,10 +12513,10 @@ Chromosome annotation (aberration) - A report on a chromosome aberration such as abnormalities in chromosome structure. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + A report on a chromosome aberration such as abnormalities in chromosome structure. @@ -12528,8 +12528,8 @@ Clone ID - An identifier of a clone (cloned molecular sequence) from a database. beta12orEarlier + An identifier of a clone (cloned molecular sequence) from a database. @@ -12542,10 +12542,10 @@ PDB insertion code - An insertion code (part of the residue number) for an amino acid residue from a PDB file. - PDBML:pdbx_PDB_ins_code - WHATIF: insertion_code beta12orEarlier + WHATIF: insertion_code + PDBML:pdbx_PDB_ins_code + An insertion code (part of the residue number) for an amino acid residue from a PDB file. @@ -12557,10 +12557,10 @@ Atomic occupancy - The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0. - beta12orEarlier - The fraction of an atom type present at a site in a molecular structure. WHATIF: PDBx_occupancy + The fraction of an atom type present at a site in a molecular structure. + beta12orEarlier + The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0. @@ -12572,9 +12572,9 @@ Isotropic B factor - beta12orEarlier - WHATIF: PDBx_B_iso_or_equiv Isotropic B factor (atomic displacement parameter) for an atom from a PDB file. + WHATIF: PDBx_B_iso_or_equiv + beta12orEarlier @@ -12586,10 +12586,10 @@ Deletion map - Deletion-based cytogenetic map - A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type. - beta12orEarlier A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel. + beta12orEarlier + A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type. + Deletion-based cytogenetic map @@ -12601,9 +12601,9 @@ QTL map - Quantitative trait locus map - beta12orEarlier A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers. + beta12orEarlier + Quantitative trait locus map @@ -12615,9 +12615,9 @@ Haplotype map - A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation. - Moby:Haplotyping_Study_obj beta12orEarlier + Moby:Haplotyping_Study_obj + A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation. @@ -12629,10 +12629,10 @@ Map set data - Moby:GCP_CorrelatedMapSet - Moby:GCP_CorrelatedLinkageMapSet - Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped. beta12orEarlier + Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped. + Moby:GCP_CorrelatedLinkageMapSet + Moby:GCP_CorrelatedMapSet @@ -12644,12 +12644,12 @@ Map feature - Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. - beta12orEarlier - Moby:MapFeature - A feature which may mapped (positioned) on a genetic or other type of map. - true beta12orEarlier + true + A feature which may mapped (positioned) on a genetic or other type of map. + Moby:MapFeature + beta12orEarlier + Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. @@ -12663,11 +12663,11 @@ Map type - beta12orEarlier - true - 1.5 - Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. A designation of the type of map (genetic map, physical map, sequence map etc) or map set. + Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. + 1.5 + true + beta12orEarlier @@ -12679,8 +12679,8 @@ Protein fold name - beta12orEarlier The name of a protein fold. + beta12orEarlier @@ -12693,13 +12693,13 @@ Taxon - Moby:BriefTaxonConcept - The name of a group of organisms belonging to the same taxonomic rank. - For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. - Taxonomic rank - beta12orEarlier - Taxonomy rank Moby:PotentialTaxon + Taxonomy rank + beta12orEarlier + Taxonomic rank + For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. + The name of a group of organisms belonging to the same taxonomic rank. + Moby:BriefTaxonConcept @@ -12718,8 +12718,8 @@ - A unique identifier of a (group of) organisms. beta12orEarlier + A unique identifier of a (group of) organisms. @@ -12732,8 +12732,8 @@ Genus name - The name of a genus of organism. beta12orEarlier + The name of a genus of organism. @@ -12746,16 +12746,16 @@ Taxonomic classification - Moby:TaxonTCS - Moby:TaxonScientificName - Taxonomic information - Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included. - Taxonomic name - Moby:iANT_organism-xml - The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature. - beta12orEarlier - Moby:GCP_Taxon Moby:TaxonName + Moby:GCP_Taxon + beta12orEarlier + The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature. + Moby:iANT_organism-xml + Taxonomic name + Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included. + Taxonomic information + Moby:TaxonScientificName + Moby:TaxonTCS @@ -12768,9 +12768,9 @@ iHOP organism ID - A unique identifier for an organism used in the iHOP database. - Moby_namespace:iHOPorganism beta12orEarlier + Moby_namespace:iHOPorganism + A unique identifier for an organism used in the iHOP database. @@ -12783,8 +12783,8 @@ Genbank common name - beta12orEarlier Common name for an organism as used in the GenBank database. + beta12orEarlier @@ -12797,8 +12797,8 @@ NCBI taxon - beta12orEarlier The name of a taxon from the NCBI taxonomy database. + beta12orEarlier @@ -12811,11 +12811,11 @@ Synonym - An alternative for a word. - true - beta12orEarlier - Alternative name beta12orEarlier + Alternative name + beta12orEarlier + true + An alternative for a word. @@ -12827,10 +12827,10 @@ Misspelling - beta12orEarlier - true - beta12orEarlier A common misspelling of a word. + beta12orEarlier + true + beta12orEarlier @@ -12842,10 +12842,10 @@ Acronym - beta12orEarlier - beta12orEarlier - An abbreviation of a phrase or word. true + An abbreviation of a phrase or word. + beta12orEarlier + beta12orEarlier @@ -12857,10 +12857,10 @@ Misnomer - true - beta12orEarlier - beta12orEarlier A term which is likely to be misleading of its meaning. + beta12orEarlier + beta12orEarlier + true @@ -12872,9 +12872,9 @@ Author ID - beta12orEarlier - Moby:Author Information on the authors of a published work. + Moby:Author + beta12orEarlier @@ -12887,8 +12887,8 @@ DragonDB author identifier - beta12orEarlier An identifier representing an author in the DragonDB database. + beta12orEarlier @@ -12901,9 +12901,9 @@ Annotated URI - Moby:DescribedLink - A URI along with annotation describing the data found at the address. beta12orEarlier + A URI along with annotation describing the data found at the address. + Moby:DescribedLink @@ -12915,10 +12915,10 @@ UniProt keywords - A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database. @@ -12930,9 +12930,9 @@ Gene ID (GeneFarm) - beta12orEarlier - Identifier of a gene from the GeneFarm database. Moby_namespace:GENEFARM_GeneID + Identifier of a gene from the GeneFarm database. + beta12orEarlier @@ -12945,9 +12945,9 @@ Blattner number - The blattner identifier for a gene. - Moby_namespace:Blattner_number beta12orEarlier + Moby_namespace:Blattner_number + The blattner identifier for a gene. @@ -12960,12 +12960,12 @@ Gene ID (MIPS Maize) - true - beta13 - Moby_namespace:MIPS_GE_Maize - beta12orEarlier - Identifier for genetic elements in MIPS Maize database. MIPS genetic element identifier (Maize) + Identifier for genetic elements in MIPS Maize database. + beta12orEarlier + Moby_namespace:MIPS_GE_Maize + beta13 + true @@ -12977,12 +12977,12 @@ Gene ID (MIPS Medicago) - Identifier for genetic elements in MIPS Medicago database. - Moby_namespace:MIPS_GE_Medicago - true - beta13 - beta12orEarlier MIPS genetic element identifier (Medicago) + beta12orEarlier + beta13 + true + Moby_namespace:MIPS_GE_Medicago + Identifier for genetic elements in MIPS Medicago database. @@ -12994,11 +12994,11 @@ Gene name (DragonDB) - 1.3 - Moby_namespace:DragonDB_Gene - beta12orEarlier - The name of an Antirrhinum Gene from the DragonDB database. true + The name of an Antirrhinum Gene from the DragonDB database. + beta12orEarlier + Moby_namespace:DragonDB_Gene + 1.3 @@ -13010,11 +13010,11 @@ Gene name (Arabidopsis) - 1.3 - beta12orEarlier - A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name. - true Moby_namespace:ArabidopsisGeneSymbol + true + A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name. + beta12orEarlier + 1.3 @@ -13028,9 +13028,9 @@ - beta12orEarlier - Moby_namespace:iHOPsymbol A unique identifier of a protein or gene used in the iHOP database. + Moby_namespace:iHOPsymbol + beta12orEarlier @@ -13043,12 +13043,12 @@ Gene name (GeneFarm) - beta12orEarlier - GeneFarm gene ID - Moby_namespace:GENEFARM_GeneName - Name of a gene from the GeneFarm database. - true 1.3 + true + Name of a gene from the GeneFarm database. + Moby_namespace:GENEFARM_GeneName + GeneFarm gene ID + beta12orEarlier @@ -13067,10 +13067,10 @@ - Locus identifier - beta12orEarlier - Locus name A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome. + Locus name + beta12orEarlier + Locus identifier @@ -13083,14 +13083,14 @@ Locus ID (AGI) - AGI identifier - beta12orEarlier - AGI locus code - Arabidopsis gene loci number - http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode - Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases) - AGI ID AT[1-5]G[0-9]{5} + AGI ID + Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases) + http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode + Arabidopsis gene loci number + AGI locus code + beta12orEarlier + AGI identifier @@ -13103,10 +13103,10 @@ Locus ID (ASPGD) - Identifier for loci from ASPGD (Aspergillus Genome Database). - http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID - http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD + http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID + Identifier for loci from ASPGD (Aspergillus Genome Database). @@ -13119,9 +13119,9 @@ Locus ID (MGG) - beta12orEarlier - http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG Identifier for loci from Magnaporthe grisea Database at the Broad Institute. + http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG + beta12orEarlier @@ -13134,12 +13134,12 @@ Locus ID (CGD) - http://www.geneontology.org/doc/GO.xrf_abbs: CGD - CGD locus identifier - CGDID - beta12orEarlier - http://www.geneontology.org/doc/GO.xrf_abbs: CGDID Identifier for loci from CGD (Candida Genome Database). + http://www.geneontology.org/doc/GO.xrf_abbs: CGDID + beta12orEarlier + CGDID + CGD locus identifier + http://www.geneontology.org/doc/GO.xrf_abbs: CGD @@ -13152,10 +13152,10 @@ Locus ID (CMR) - beta12orEarlier - http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR - Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute. http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR + Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute. + http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR + beta12orEarlier @@ -13168,11 +13168,11 @@ NCBI locus tag - Identifier for loci from NCBI database. - http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag - Locus ID (NCBI) - Moby_namespace:LocusID beta12orEarlier + Moby_namespace:LocusID + Locus ID (NCBI) + http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag + Identifier for loci from NCBI database. @@ -13186,11 +13186,11 @@ Locus ID (SGD) - SGDID - http://www.geneontology.org/doc/GO.xrf_abbs: SGD - beta12orEarlier - http://www.geneontology.org/doc/GO.xrf_abbs: SGDID Identifier for loci from SGD (Saccharomyces Genome Database). + http://www.geneontology.org/doc/GO.xrf_abbs: SGDID + beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs: SGD + SGDID @@ -13203,9 +13203,9 @@ Locus ID (MMP) - beta12orEarlier - Moby_namespace:MMP_Locus Identifier of loci from Maize Mapping Project. + Moby_namespace:MMP_Locus + beta12orEarlier @@ -13218,9 +13218,9 @@ Locus ID (DictyBase) - beta12orEarlier - Identifier of locus from DictyBase (Dictyostelium discoideum). Moby_namespace:DDB_gene + Identifier of locus from DictyBase (Dictyostelium discoideum). + beta12orEarlier @@ -13233,10 +13233,10 @@ Locus ID (EntrezGene) - Moby_namespace:EntrezGene_EntrezGeneID - Moby_namespace:EntrezGene_ID - beta12orEarlier Identifier of a locus from EntrezGene database. + beta12orEarlier + Moby_namespace:EntrezGene_ID + Moby_namespace:EntrezGene_EntrezGeneID @@ -13249,9 +13249,9 @@ Locus ID (MaizeGDB) - beta12orEarlier - Moby_namespace:MaizeGDB_Locus Identifier of locus from MaizeGDB (Maize genome database). + Moby_namespace:MaizeGDB_Locus + beta12orEarlier @@ -13264,13 +13264,13 @@ Quantitative trait locus - Moby:SO_QTL - A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment). - beta12orEarlier - beta12orEarlier - true - A QTL sometimes but does not necessarily correspond to a gene. QTL + A QTL sometimes but does not necessarily correspond to a gene. + true + beta12orEarlier + beta12orEarlier + A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment). + Moby:SO_QTL @@ -13282,9 +13282,9 @@ Gene ID (KOME) - Moby_namespace:GeneId - beta12orEarlier Identifier of a gene from the KOME database. + beta12orEarlier + Moby_namespace:GeneId @@ -13297,9 +13297,9 @@ Locus ID (Tropgene) - beta12orEarlier - Moby:Tropgene_locus Identifier of a locus from the Tropgene database. + Moby:Tropgene_locus + beta12orEarlier @@ -13312,8 +13312,8 @@ Alignment - beta12orEarlier An alignment of molecular sequences, structures or profiles derived from them. + beta12orEarlier @@ -13325,9 +13325,9 @@ Atomic property - beta12orEarlier - Data for an atom (in a molecular structure). General atomic property + Data for an atom (in a molecular structure). + beta12orEarlier @@ -13339,10 +13339,10 @@ UniProt keyword - http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW - Moby_namespace:SP_KW - A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database. beta12orEarlier + A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database. + Moby_namespace:SP_KW + http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW @@ -13354,10 +13354,10 @@ Ordered locus name - beta12orEarlier - A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome. - true beta12orEarlier + true + A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome. + beta12orEarlier @@ -13371,21 +13371,21 @@ - PDBML:_atom_site.id - Moby:GCP_MapPoint - Moby:GCP_MapPosition - Moby:GCP_MapInterval - Moby:Locus - Moby:MapPosition - beta12orEarlier - Moby:HitPosition - This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. Data might include sequence region name, strand, coordinate system name, assembly name, start position and end position. - Moby:GenePosition - A position in a map (for example a genetic map), either a single position (point) or a region / interval. - Sequence co-ordinates - Locus - Moby:Position Map position + Moby:Position + Locus + Sequence co-ordinates + A position in a map (for example a genetic map), either a single position (point) or a region / interval. + Moby:GenePosition + This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. Data might include sequence region name, strand, coordinate system name, assembly name, start position and end position. + Moby:HitPosition + beta12orEarlier + Moby:MapPosition + Moby:Locus + Moby:GCP_MapInterval + Moby:GCP_MapPosition + Moby:GCP_MapPoint + PDBML:_atom_site.id @@ -13397,9 +13397,9 @@ Amino acid property - beta12orEarlier - Amino acid data Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids. + Amino acid data + beta12orEarlier @@ -13411,11 +13411,11 @@ Annotation - A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. - This is a broad data type and is used a placeholder for other, more specific types. - beta13 - true beta12orEarlier + true + beta13 + This is a broad data type and is used a placeholder for other, more specific types. + A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. @@ -13433,9 +13433,9 @@ - An attribute of a molecular map (genetic or physical), or data extracted from or derived from the analysis of such a map. - beta12orEarlier Map attribute + beta12orEarlier + An attribute of a molecular map (genetic or physical), or data extracted from or derived from the analysis of such a map. @@ -13447,10 +13447,10 @@ Vienna RNA structural data - beta12orEarlier - beta12orEarlier - Data used by the Vienna RNA analysis package. true + Data used by the Vienna RNA analysis package. + beta12orEarlier + beta12orEarlier @@ -13462,10 +13462,10 @@ Sequence mask parameter - Data used to replace (mask) characters in a molecular sequence. - true - 1.5 beta12orEarlier + 1.5 + true + Data used to replace (mask) characters in a molecular sequence. @@ -13478,9 +13478,9 @@ Enzyme kinetics data - This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier Data concerning chemical reaction(s) catalysed by enzyme(s). + beta12orEarlier + This is a broad data type and is used a placeholder for other, more specific types. @@ -13492,8 +13492,8 @@ Michaelis Menten plot - beta12orEarlier A plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent. + beta12orEarlier @@ -13505,8 +13505,8 @@ Hanes Woolf plot - A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v). beta12orEarlier + A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v). @@ -13518,12 +13518,12 @@ Experimental data - beta13 - Experimental measurement data - beta12orEarlier - Raw data from or annotation on laboratory experiments. - true This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + true + Raw data from or annotation on laboratory experiments. + beta12orEarlier + Experimental measurement data + beta13 @@ -13536,10 +13536,10 @@ Genome version information - 1.5 - Information on a genome version. - true beta12orEarlier + true + Information on a genome version. + 1.5 @@ -13551,8 +13551,8 @@ Evidence - beta12orEarlier Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc. + beta12orEarlier @@ -13564,10 +13564,10 @@ Sequence record lite - 1.8 - true - A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment. beta12orEarlier + A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment. + true + 1.8 @@ -13585,12 +13585,12 @@ - One or more molecular sequences, possibly with associated annotation. - beta12orEarlier - This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles. - http://purl.org/biotop/biotop.owl#BioMolecularSequenceInformation - Sequences http://purl.bioontology.org/ontology/MSH/D008969 + Sequences + http://purl.org/biotop/biotop.owl#BioMolecularSequenceInformation + This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles. + beta12orEarlier + One or more molecular sequences, possibly with associated annotation. @@ -13602,10 +13602,10 @@ Nucleic acid sequence record (lite) - A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment. - true - 1.8 beta12orEarlier + 1.8 + true + A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment. @@ -13617,11 +13617,11 @@ Protein sequence record (lite) - true - A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment. - beta12orEarlier - Sequence record lite (protein) 1.8 + Sequence record lite (protein) + beta12orEarlier + A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment. + true @@ -13633,11 +13633,11 @@ Report - beta12orEarlier - A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself. - Document - http://semanticscience.org/resource/SIO_000148 You can use this term by default for any textual report, in case you can't find another, more specific term. Reports may be generated automatically or collated by hand and can include metadata on the origin, source, history, ownership or location of some thing. + http://semanticscience.org/resource/SIO_000148 + Document + A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself. + beta12orEarlier @@ -13649,9 +13649,9 @@ Molecular property (general) - beta12orEarlier - General data for a molecule. General molecular property + General data for a molecule. + beta12orEarlier @@ -13663,11 +13663,11 @@ Structural data - beta13 - Data concerning molecular structural data. - true - beta12orEarlier This is a broad data type and is used a placeholder for other, more specific types. + beta12orEarlier + true + Data concerning molecular structural data. + beta13 @@ -13680,11 +13680,11 @@ Sequence motif (nucleic acid) - RNA sequence motif - beta12orEarlier - A nucleotide sequence motif. - DNA sequence motif Nucleic acid sequence motif + DNA sequence motif + A nucleotide sequence motif. + beta12orEarlier + RNA sequence motif @@ -13696,9 +13696,9 @@ Sequence motif (protein) - Protein sequence motif - An amino acid sequence motif. beta12orEarlier + An amino acid sequence motif. + Protein sequence motif @@ -13710,10 +13710,10 @@ Search parameter - Some simple value controlling a search operation, typically a search of a database. - true - 1.5 beta12orEarlier + 1.5 + true + Some simple value controlling a search operation, typically a search of a database. @@ -13725,10 +13725,10 @@ Database search results - Database hits - Search results - A report of hits from searching a database of some type. beta12orEarlier + A report of hits from searching a database of some type. + Search results + Database hits @@ -13740,10 +13740,10 @@ Secondary structure - The secondary structure assignment (predicted or real) of a nucleic acid or protein. - beta12orEarlier - true 1.5 + true + beta12orEarlier + The secondary structure assignment (predicted or real) of a nucleic acid or protein. @@ -13755,10 +13755,10 @@ Matrix - An array of numerical values. - This is a broad data type and is used a placeholder for other, more specific types. - Array beta12orEarlier + Array + This is a broad data type and is used a placeholder for other, more specific types. + An array of numerical values. @@ -13770,12 +13770,12 @@ Alignment data - Alignment report - This is a broad data type and is used a placeholder for other, more specific types. - Data concerning, extracted from, or derived from the analysis of molecular alignment of some type. - true - 1.8 beta12orEarlier + 1.8 + true + Data concerning, extracted from, or derived from the analysis of molecular alignment of some type. + This is a broad data type and is used a placeholder for other, more specific types. + Alignment report @@ -13787,8 +13787,8 @@ Nucleic acid report - beta12orEarlier An informative human-readable report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data. + beta12orEarlier @@ -13800,9 +13800,9 @@ Structure report - Structure-derived report - beta12orEarlier An informative report on general information, properties or features of one or more molecular tertiary (3D) structures. + beta12orEarlier + Structure-derived report @@ -13814,11 +13814,11 @@ Nucleic acid structure data - A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s). - beta12orEarlier - Nucleic acid structural property - This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties. Nucleic acid property (structural) + This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties. + Nucleic acid structural property + beta12orEarlier + A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s). @@ -13830,10 +13830,10 @@ Molecular property - Physicochemical property - A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule. - SO:0000400 beta12orEarlier + SO:0000400 + A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule. + Physicochemical property @@ -13845,8 +13845,8 @@ DNA base structural data - beta12orEarlier Structural data for DNA base pairs or runs of bases, such as energy or angle data. + beta12orEarlier @@ -13858,10 +13858,10 @@ Database entry version information - Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on. - 1.5 - beta12orEarlier true + beta12orEarlier + 1.5 + Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on. @@ -13873,10 +13873,10 @@ Accession - http://semanticscience.org/resource/SIO_000675 - A persistent (stable) and unique identifier, typically identifying an object (entry) from a database. - http://semanticscience.org/resource/SIO_000731 beta12orEarlier + http://semanticscience.org/resource/SIO_000731 + A persistent (stable) and unique identifier, typically identifying an object (entry) from a database. + http://semanticscience.org/resource/SIO_000675 @@ -13889,10 +13889,10 @@ SNP - 1.8 - beta12orEarlier - Topic concerning single nucleotide polymorphism (SNP) in a DNA sequence. true + Topic concerning single nucleotide polymorphism (SNP) in a DNA sequence. + beta12orEarlier + 1.8 @@ -13904,9 +13904,9 @@ Data reference - beta12orEarlier - Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology. A list of database accessions or identifiers are usually included. + Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology. + beta12orEarlier @@ -13918,9 +13918,9 @@ Job identifier - beta12orEarlier - An identifier of a submitted job. http://wsio.org/data_009 + An identifier of a submitted job. + beta12orEarlier @@ -13933,12 +13933,12 @@ Name - Symbolic name - A name of a thing, which need not necessarily uniquely identify it. - beta12orEarlier - "http://www.w3.org/2000/01/rdf-schema#label - http://usefulinc.com/ns/doap#name http://semanticscience.org/resource/SIO_000116 + http://usefulinc.com/ns/doap#name + "http://www.w3.org/2000/01/rdf-schema#label + beta12orEarlier + A name of a thing, which need not necessarily uniquely identify it. + Symbolic name @@ -13958,11 +13958,11 @@ Type - true - beta12orEarlier - 1.5 - http://purl.org/dc/elements/1.1/type A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values). + http://purl.org/dc/elements/1.1/type + 1.5 + beta12orEarlier + true @@ -13974,8 +13974,8 @@ User ID - beta12orEarlier An identifier of a software end-user (typically a person). + beta12orEarlier @@ -13989,8 +13989,8 @@ KEGG organism code - beta12orEarlier A three-letter code used in the KEGG databases to uniquely identify organisms. + beta12orEarlier @@ -14003,13 +14003,13 @@ Gene name (KEGG GENES) - 1.3 - true - Moby_namespace:GeneId - Name of an entry (gene) from the KEGG GENES database. - [a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]* - KEGG GENES entry name beta12orEarlier + KEGG GENES entry name + [a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]* + Name of an entry (gene) from the KEGG GENES database. + Moby_namespace:GeneId + true + 1.3 @@ -14022,8 +14022,8 @@ BioCyc ID - beta12orEarlier Identifier of an object from one of the BioCyc databases. + beta12orEarlier @@ -14037,10 +14037,10 @@ Compound ID (BioCyc) - beta12orEarlier - BioCyc compound ID - Identifier of a compound from the BioCyc chemical compounds database. BioCyc compound identifier + Identifier of a compound from the BioCyc chemical compounds database. + BioCyc compound ID + beta12orEarlier @@ -14060,8 +14060,8 @@ - Identifier of a biological reaction from the BioCyc reactions database. beta12orEarlier + Identifier of a biological reaction from the BioCyc reactions database. @@ -14075,9 +14075,9 @@ Enzyme ID (BioCyc) - Identifier of an enzyme from the BioCyc enzymes database. - beta12orEarlier BioCyc enzyme ID + beta12orEarlier + Identifier of an enzyme from the BioCyc enzymes database. @@ -14097,8 +14097,8 @@ - Identifier of a biological reaction from a database. beta12orEarlier + Identifier of a biological reaction from a database. @@ -14111,9 +14111,9 @@ Identifier (hybrid) - This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. - beta12orEarlier An identifier that is re-used for data objects of fundamentally different types (typically served from a single database). + beta12orEarlier + This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. @@ -14132,8 +14132,8 @@ - Identifier of a molecular property. beta12orEarlier + Identifier of a molecular property. @@ -14149,18 +14149,18 @@ - + - + - beta12orEarlier - Codon usage table identifier Identifier of a codon usage table, for example a genetic code. + Codon usage table identifier + beta12orEarlier @@ -14173,8 +14173,8 @@ FlyBase primary identifier - Primary identifier of an object from the FlyBase database. beta12orEarlier + Primary identifier of an object from the FlyBase database. @@ -14187,8 +14187,8 @@ WormBase identifier - Identifier of an object from the WormBase database. beta12orEarlier + Identifier of an object from the WormBase database. @@ -14202,9 +14202,9 @@ WormBase wormpep ID - beta12orEarlier - CE[0-9]{5} Protein identifier used by WormBase database. + CE[0-9]{5} + beta12orEarlier @@ -14217,10 +14217,10 @@ Nucleic acid features (codon) - beta12orEarlier - An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon. - true beta12orEarlier + true + An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon. + beta12orEarlier @@ -14238,8 +14238,8 @@ - beta12orEarlier An identifier of a map of a molecular sequence. + beta12orEarlier @@ -14252,8 +14252,8 @@ Person identifier - beta12orEarlier An identifier of a software end-user (typically a person). + beta12orEarlier @@ -14272,8 +14272,8 @@ - beta12orEarlier Name or other identifier of a nucleic acid molecule. + beta12orEarlier @@ -14286,8 +14286,8 @@ Translation frame specification - Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome). beta12orEarlier + Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome). @@ -14305,8 +14305,8 @@ - beta12orEarlier An identifier of a genetic code. + beta12orEarlier @@ -14320,8 +14320,8 @@ Genetic code name - beta12orEarlier Informal name for a genetic code, typically an organism name. + beta12orEarlier @@ -14335,8 +14335,8 @@ File format name - beta12orEarlier Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on. + beta12orEarlier @@ -14349,10 +14349,10 @@ Sequence profile type - beta12orEarlier - A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc. - 1.5 true + 1.5 + A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc. + beta12orEarlier @@ -14364,8 +14364,8 @@ Operating system name - Name of a computer operating system such as Linux, PC or Mac. beta12orEarlier + Name of a computer operating system such as Linux, PC or Mac. @@ -14378,10 +14378,10 @@ Mutation type - A type of point or block mutation, including insertion, deletion, change, duplication and moves. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + A type of point or block mutation, including insertion, deletion, change, duplication and moves. @@ -14393,8 +14393,8 @@ Logical operator - A logical operator such as OR, AND, XOR, and NOT. beta12orEarlier + A logical operator such as OR, AND, XOR, and NOT. @@ -14407,11 +14407,11 @@ Results sort order - A control of the order of data that is output, for example the order of sequences in an alignment. - 1.5 - true - beta12orEarlier Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on. + beta12orEarlier + true + 1.5 + A control of the order of data that is output, for example the order of sequences in an alignment. @@ -14423,10 +14423,10 @@ Toggle - beta12orEarlier - true - A simple parameter that is a toggle (boolean value), typically a control for a modal tool. beta12orEarlier + A simple parameter that is a toggle (boolean value), typically a control for a modal tool. + true + beta12orEarlier @@ -14438,10 +14438,10 @@ Sequence width - The width of an output sequence or alignment. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + The width of an output sequence or alignment. @@ -14453,8 +14453,8 @@ Gap penalty - A penalty for introducing or extending a gap in an alignment. beta12orEarlier + A penalty for introducing or extending a gap in an alignment. @@ -14466,9 +14466,9 @@ Nucleic acid melting temperature - Melting temperature - A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate. beta12orEarlier + A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate. + Melting temperature @@ -14480,8 +14480,8 @@ Concentration - The concentration of a chemical compound. beta12orEarlier + The concentration of a chemical compound. @@ -14493,10 +14493,10 @@ Window step size - Size of the incremental 'step' a sequence window is moved over a sequence. - true - beta12orEarlier 1.5 + beta12orEarlier + true + Size of the incremental 'step' a sequence window is moved over a sequence. @@ -14508,10 +14508,10 @@ EMBOSS graph - An image of a graph generated by the EMBOSS suite. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + An image of a graph generated by the EMBOSS suite. @@ -14523,10 +14523,10 @@ EMBOSS report - true - beta12orEarlier - beta12orEarlier An application report generated by the EMBOSS suite. + beta12orEarlier + beta12orEarlier + true @@ -14538,10 +14538,10 @@ Sequence offset - An offset for a single-point sequence position. - 1.5 - beta12orEarlier true + beta12orEarlier + 1.5 + An offset for a single-point sequence position. @@ -14553,10 +14553,10 @@ Threshold - A value that serves as a threshold for a tool (usually to control scoring or output). - true - beta12orEarlier 1.5 + beta12orEarlier + true + A value that serves as a threshold for a tool (usually to control scoring or output). @@ -14568,12 +14568,12 @@ Protein report (transcription factor) - beta12orEarlier - Transcription factor binding site data - An informative report on a transcription factor protein. - This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites. - true beta13 + true + This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites. + An informative report on a transcription factor protein. + Transcription factor binding site data + beta12orEarlier @@ -14585,10 +14585,10 @@ Database category name - beta12orEarlier - beta12orEarlier - The name of a category of biological or bioinformatics database. true + The name of a category of biological or bioinformatics database. + beta12orEarlier + beta12orEarlier @@ -14600,10 +14600,10 @@ Sequence profile name - beta12orEarlier - true - Name of a sequence profile. beta12orEarlier + Name of a sequence profile. + true + beta12orEarlier @@ -14615,10 +14615,10 @@ Color - beta12orEarlier - true - beta12orEarlier Specification of one or more colors. + beta12orEarlier + true + beta12orEarlier @@ -14630,12 +14630,12 @@ Rendering parameter - Graphical parameter - Graphics parameter - A parameter that is used to control rendering (drawing) to a device or image. - 1.5 - beta12orEarlier true + beta12orEarlier + 1.5 + A parameter that is used to control rendering (drawing) to a device or image. + Graphics parameter + Graphical parameter @@ -14648,8 +14648,8 @@ Sequence name - beta12orEarlier Any arbitrary name of a molecular sequence. + beta12orEarlier @@ -14662,10 +14662,10 @@ Date - true - beta12orEarlier - A temporal date. 1.5 + A temporal date. + beta12orEarlier + true @@ -14677,10 +14677,10 @@ Word composition - beta12orEarlier - true - Word composition data for a molecular sequence. beta12orEarlier + Word composition data for a molecular sequence. + true + beta12orEarlier @@ -14693,8 +14693,8 @@ Fickett testcode plot - beta12orEarlier A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences. + beta12orEarlier @@ -14707,11 +14707,11 @@ Sequence similarity plot - A plot of sequence similarities identified from word-matching or character comparison. - Sequence similarity plot - Sequence conservation report - beta12orEarlier Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. + beta12orEarlier + Sequence conservation report + Sequence similarity plot + A plot of sequence similarities identified from word-matching or character comparison. @@ -14723,8 +14723,8 @@ Helical wheel - An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties. beta12orEarlier + An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties. @@ -14736,9 +14736,9 @@ Helical net - An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix. - Useful for highlighting amphipathicity and other properties. beta12orEarlier + Useful for highlighting amphipathicity and other properties. + An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix. @@ -14750,10 +14750,10 @@ Protein sequence properties plot - A plot of general physicochemical properties of a protein sequence. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + A plot of general physicochemical properties of a protein sequence. @@ -14766,8 +14766,8 @@ Protein ionization curve - A plot of pK versus pH for a protein. beta12orEarlier + A plot of pK versus pH for a protein. @@ -14780,8 +14780,8 @@ Sequence composition plot - A plot of character or word composition / frequency of a molecular sequence. beta12orEarlier + A plot of character or word composition / frequency of a molecular sequence. @@ -14794,8 +14794,8 @@ Nucleic acid density plot - Density plot (of base composition) for a nucleotide sequence. beta12orEarlier + Density plot (of base composition) for a nucleotide sequence. @@ -14807,8 +14807,8 @@ Sequence trace image - beta12orEarlier Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases). + beta12orEarlier @@ -14820,10 +14820,10 @@ Nucleic acid features (siRNA) - A report on siRNA duplexes in mRNA. - beta12orEarlier - 1.5 true + 1.5 + beta12orEarlier + A report on siRNA duplexes in mRNA. @@ -14835,11 +14835,11 @@ Sequence set (stream) - beta12orEarlier - A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing. - This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time. - true beta12orEarlier + true + This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time. + A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing. + beta12orEarlier @@ -14851,9 +14851,9 @@ FlyBase secondary identifier - beta12orEarlier - Secondary identifier are used to handle entries that were merged with or split from other entries in the database. Secondary identifier of an object from the FlyBase database. + Secondary identifier are used to handle entries that were merged with or split from other entries in the database. + beta12orEarlier @@ -14866,10 +14866,10 @@ Cardinality - beta12orEarlier - true - beta12orEarlier The number of a certain thing. + beta12orEarlier + true + beta12orEarlier @@ -14881,10 +14881,10 @@ Exactly 1 - true - A single thing. - beta12orEarlier beta12orEarlier + beta12orEarlier + A single thing. + true @@ -14895,10 +14895,10 @@ 1 or more - beta12orEarlier - true - beta12orEarlier One or more things. + beta12orEarlier + true + beta12orEarlier @@ -14909,10 +14909,10 @@ Exactly 2 - beta12orEarlier - true - beta12orEarlier Exactly two things. + beta12orEarlier + true + beta12orEarlier @@ -14923,10 +14923,10 @@ 2 or more - true - beta12orEarlier - beta12orEarlier Two or more things. + beta12orEarlier + beta12orEarlier + true @@ -14937,12 +14937,12 @@ Sequence checksum - Hash value - Hash - Hash sum - Hash code - beta12orEarlier A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing. + beta12orEarlier + Hash code + Hash sum + Hash + Hash value @@ -14954,10 +14954,10 @@ Protein features report (chemical modifications) - true - Topic concerning chemical modification of a protein. - beta12orEarlier 1.8 + beta12orEarlier + Topic concerning chemical modification of a protein. + true @@ -14969,10 +14969,10 @@ Error - true - 1.5 - Data on an error generated by computer system or tool. beta12orEarlier + Data on an error generated by computer system or tool. + 1.5 + true @@ -14984,8 +14984,8 @@ Database entry metadata - Basic information on any arbitrary database entry. beta12orEarlier + Basic information on any arbitrary database entry. @@ -14997,10 +14997,10 @@ Gene cluster - A cluster of similar genes. - beta12orEarlier - true beta13 + true + beta12orEarlier + A cluster of similar genes. @@ -15012,10 +15012,10 @@ Sequence record full - 1.8 - A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. - beta12orEarlier true + beta12orEarlier + A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. + 1.8 @@ -15027,8 +15027,8 @@ Plasmid identifier - beta12orEarlier An identifier of a plasmid in a database. + beta12orEarlier @@ -15042,8 +15042,8 @@ Mutation ID - A unique identifier of a specific mutation catalogued in a database. beta12orEarlier + A unique identifier of a specific mutation catalogued in a database. @@ -15056,10 +15056,10 @@ Mutation annotation (basic) - beta12orEarlier - true - beta12orEarlier Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style. + beta12orEarlier + true + beta12orEarlier @@ -15071,10 +15071,10 @@ Mutation annotation (prevalence) - beta12orEarlier - An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).. - true beta12orEarlier + true + An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).. + beta12orEarlier @@ -15086,10 +15086,10 @@ Mutation annotation (prognostic) - true - beta12orEarlier - An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study. beta12orEarlier + An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study. + beta12orEarlier + true @@ -15101,10 +15101,10 @@ Mutation annotation (functional) - beta12orEarlier - beta12orEarlier - true An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on. + true + beta12orEarlier + beta12orEarlier @@ -15116,8 +15116,8 @@ Codon number - The number of a codon, for instance, at which a mutation is located. beta12orEarlier + The number of a codon, for instance, at which a mutation is located. @@ -15129,10 +15129,10 @@ Tumor annotation - beta12orEarlier - An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on. - 1.4 true + 1.4 + An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on. + beta12orEarlier @@ -15144,10 +15144,10 @@ Server metadata - true - 1.5 - beta12orEarlier Basic information about a server on the web, such as an SRS server. + beta12orEarlier + 1.5 + true @@ -15159,8 +15159,8 @@ Database field name - beta12orEarlier The name of a field in a database. + beta12orEarlier @@ -15173,9 +15173,9 @@ Sequence cluster ID (SYSTERS) - beta12orEarlier - Unique identifier of a sequence cluster from the SYSTERS database. SYSTERS cluster ID + Unique identifier of a sequence cluster from the SYSTERS database. + beta12orEarlier @@ -15194,8 +15194,8 @@ - Data concerning a biological ontology. beta12orEarlier + Data concerning a biological ontology. @@ -15207,11 +15207,11 @@ Raw SCOP domain classification - These are the parsable data files provided by SCOP. - beta13 - Raw SCOP domain classification data files. - beta12orEarlier true + beta12orEarlier + Raw SCOP domain classification data files. + beta13 + These are the parsable data files provided by SCOP. @@ -15223,11 +15223,11 @@ Raw CATH domain classification - beta12orEarlier - beta13 - true - These are the parsable data files provided by CATH. Raw CATH domain classification data files. + These are the parsable data files provided by CATH. + true + beta13 + beta12orEarlier @@ -15239,10 +15239,10 @@ Heterogen annotation - An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files. - beta12orEarlier - true 1.4 + true + beta12orEarlier + An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files. @@ -15254,10 +15254,10 @@ Phylogenetic property values - beta12orEarlier - true - Phylogenetic property values data. beta12orEarlier + Phylogenetic property values data. + true + beta12orEarlier @@ -15269,11 +15269,11 @@ Sequence set (bootstrapped) - A collection of sequences output from a bootstrapping (resampling) procedure. - true - Bootstrapping is often performed in phylogenetic analysis. - beta12orEarlier 1.5 + beta12orEarlier + Bootstrapping is often performed in phylogenetic analysis. + true + A collection of sequences output from a bootstrapping (resampling) procedure. @@ -15285,10 +15285,10 @@ Phylogenetic consensus tree - beta12orEarlier - beta12orEarlier - A consensus phylogenetic tree derived from comparison of multiple trees. true + A consensus phylogenetic tree derived from comparison of multiple trees. + beta12orEarlier + beta12orEarlier @@ -15300,10 +15300,10 @@ Schema - 1.5 - A data schema for organising or transforming data of some type. - true beta12orEarlier + true + A data schema for organising or transforming data of some type. + 1.5 @@ -15315,10 +15315,10 @@ DTD - 1.5 - beta12orEarlier - true A DTD (document type definition). + true + beta12orEarlier + 1.5 @@ -15330,11 +15330,11 @@ XML Schema - 1.5 - true - An XML Schema. - XSD beta12orEarlier + XSD + An XML Schema. + true + 1.5 @@ -15346,10 +15346,10 @@ Relax-NG schema - true - A relax-NG schema. - 1.5 beta12orEarlier + 1.5 + A relax-NG schema. + true @@ -15361,10 +15361,10 @@ XSLT stylesheet - true - An XSLT stylesheet. - beta12orEarlier 1.5 + beta12orEarlier + An XSLT stylesheet. + true @@ -15376,8 +15376,8 @@ Data resource definition name - The name of a data type. beta12orEarlier + The name of a data type. @@ -15390,8 +15390,8 @@ OBO file format name - beta12orEarlier Name of an OBO file format such as OBO-XML, plain and so on. + beta12orEarlier @@ -15404,9 +15404,9 @@ Gene ID (MIPS) - MIPS genetic element identifier - beta12orEarlier Identifier for genetic elements in MIPS database. + beta12orEarlier + MIPS genetic element identifier @@ -15419,10 +15419,10 @@ Sequence identifier (protein) - true - beta12orEarlier - beta12orEarlier An identifier of protein sequence(s) or protein sequence database entries. + beta12orEarlier + beta12orEarlier + true @@ -15434,10 +15434,10 @@ Sequence identifier (nucleic acid) - beta12orEarlier - true - beta12orEarlier An identifier of nucleotide sequence(s) or nucleotide sequence database entries. + beta12orEarlier + true + beta12orEarlier @@ -15449,11 +15449,11 @@ EMBL accession - An accession number of an entry from the EMBL sequence database. - EMBL identifier - EMBL accession number - beta12orEarlier EMBL ID + beta12orEarlier + EMBL accession number + EMBL identifier + An accession number of an entry from the EMBL sequence database. @@ -15472,12 +15472,12 @@ - UniProt entry name - UniProt identifier - beta12orEarlier - UniProtKB entry name - An identifier of a polypeptide in the UniProt database. UniProtKB identifier + An identifier of a polypeptide in the UniProt database. + UniProtKB entry name + beta12orEarlier + UniProt identifier + UniProt entry name @@ -15490,11 +15490,11 @@ GenBank accession - GenBank accession number - beta12orEarlier - Accession number of an entry from the GenBank sequence database. - GenBank identifier GenBank ID + GenBank identifier + Accession number of an entry from the GenBank sequence database. + beta12orEarlier + GenBank accession number @@ -15507,11 +15507,11 @@ Gramene secondary identifier - Gramene secondary ID - Secondary (internal) identifier of a Gramene database entry. - Gramene internal ID - Gramene internal identifier beta12orEarlier + Gramene internal identifier + Gramene internal ID + Secondary (internal) identifier of a Gramene database entry. + Gramene secondary ID @@ -15525,8 +15525,8 @@ Sequence variation ID - beta12orEarlier An identifier of an entry from a database of molecular sequence variation. + beta12orEarlier @@ -15540,10 +15540,10 @@ Gene ID - Gene code - A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol. - beta12orEarlier Gene accession + beta12orEarlier + A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol. + Gene code @@ -15556,11 +15556,11 @@ Gene name (AceView) - beta12orEarlier - Name of an entry (gene) from the AceView genes database. - true - 1.3 AceView gene name + 1.3 + true + Name of an entry (gene) from the AceView genes database. + beta12orEarlier @@ -15572,11 +15572,11 @@ Gene ID (ECK) - http://www.geneontology.org/doc/GO.xrf_abbs: ECK - Identifier of an E. coli K-12 gene from EcoGene Database. - E. coli K-12 gene identifier - beta12orEarlier ECK accession + beta12orEarlier + E. coli K-12 gene identifier + Identifier of an E. coli K-12 gene from EcoGene Database. + http://www.geneontology.org/doc/GO.xrf_abbs: ECK @@ -15589,9 +15589,9 @@ Gene ID (HGNC) - Identifier for a gene approved by the HUGO Gene Nomenclature Committee. - beta12orEarlier HGNC ID + beta12orEarlier + Identifier for a gene approved by the HUGO Gene Nomenclature Committee. @@ -15605,9 +15605,9 @@ Gene name - beta12orEarlier - Allele name The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol. + Allele name + beta12orEarlier @@ -15620,11 +15620,11 @@ Gene name (NCBI) - true - Name of an entry (gene) from the NCBI genes database. - NCBI gene name - 1.3 beta12orEarlier + 1.3 + NCBI gene name + Name of an entry (gene) from the NCBI genes database. + true @@ -15636,8 +15636,8 @@ SMILES string - beta12orEarlier A specification of a chemical structure in SMILES format. + beta12orEarlier @@ -15649,8 +15649,8 @@ STRING ID - beta12orEarlier Unique identifier of an entry from the STRING database of protein-protein interactions. + beta12orEarlier @@ -15663,10 +15663,10 @@ Virus annotation - beta12orEarlier - 1.4 - true An informative report on a specific virus. + true + 1.4 + beta12orEarlier @@ -15678,10 +15678,10 @@ Virus annotation (taxonomy) - 1.4 - true - beta12orEarlier An informative report on the taxonomy of a specific virus. + beta12orEarlier + true + 1.4 @@ -15693,9 +15693,9 @@ Reaction ID (SABIO-RK) - [0-9]+ - beta12orEarlier Identifier of a biological reaction from the SABIO-RK reactions database. + beta12orEarlier + [0-9]+ @@ -15708,8 +15708,8 @@ Carbohydrate report - beta12orEarlier Annotation on or information derived from one or more specific carbohydrate 3D structure(s). + beta12orEarlier @@ -15721,11 +15721,11 @@ GI number - Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. - A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record. - gi number - NCBI GI number beta12orEarlier + NCBI GI number + gi number + A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record. + Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. @@ -15738,11 +15738,11 @@ NCBI version - accession.version - An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number. - Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number. - NCBI accession.version beta12orEarlier + NCBI accession.version + Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number. + An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number. + accession.version @@ -15755,8 +15755,8 @@ Cell line name - The name of a cell line. beta12orEarlier + The name of a cell line. @@ -15769,8 +15769,8 @@ Cell line name (exact) - The name of a cell line. beta12orEarlier + The name of a cell line. @@ -15783,8 +15783,8 @@ Cell line name (truncated) - beta12orEarlier The name of a cell line. + beta12orEarlier @@ -15797,8 +15797,8 @@ Cell line name (no punctuation) - beta12orEarlier The name of a cell line. + beta12orEarlier @@ -15811,8 +15811,8 @@ Cell line name (assonant) - beta12orEarlier The name of a cell line. + beta12orEarlier @@ -15826,9 +15826,9 @@ Enzyme ID - Enzyme accession - A unique, persistent identifier of an enzyme. beta12orEarlier + A unique, persistent identifier of an enzyme. + Enzyme accession @@ -15841,8 +15841,8 @@ REBASE enzyme number - beta12orEarlier Identifier of an enzyme from the REBASE enzymes database. + beta12orEarlier @@ -15855,9 +15855,9 @@ DrugBank ID - Unique identifier of a drug from the DrugBank database. - DB[0-9]{5} beta12orEarlier + DB[0-9]{5} + Unique identifier of a drug from the DrugBank database. @@ -15870,11 +15870,11 @@ GI number (protein) - protein gi - Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. - A unique identifier assigned to NCBI protein sequence records. - protein gi number beta12orEarlier + protein gi number + A unique identifier assigned to NCBI protein sequence records. + Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. + protein gi @@ -15887,9 +15887,9 @@ Bit score - beta12orEarlier - Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches. A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system. + Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches. + beta12orEarlier @@ -15901,9 +15901,9 @@ Translation phase specification - Phase - Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence. beta12orEarlier + Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence. + Phase @@ -15915,10 +15915,10 @@ Resource metadata - beta12orEarlier - Provenance metadata - This is a broad data type and is used a placeholder for other, more specific types. Data concerning or describing some core computational resource, as distinct from primary data. This includes metadata on the origin, source, history, ownership or location of some thing. + This is a broad data type and is used a placeholder for other, more specific types. + Provenance metadata + beta12orEarlier @@ -15936,8 +15936,8 @@ - Any arbitrary identifier of an ontology. beta12orEarlier + Any arbitrary identifier of an ontology. @@ -15951,8 +15951,8 @@ Ontology concept name - beta12orEarlier The name of a concept in an ontology. + beta12orEarlier @@ -15965,8 +15965,8 @@ Genome build identifier - An identifier of a build of a particular genome. beta12orEarlier + An identifier of a build of a particular genome. @@ -15979,8 +15979,8 @@ Pathway or network name - beta12orEarlier The name of a biological pathway or network. + beta12orEarlier @@ -15994,10 +15994,10 @@ Pathway ID (KEGG) - KEGG pathway ID - [a-zA-Z_0-9]{2,3}[0-9]{5} - beta12orEarlier Identifier of a pathway from the KEGG pathway database. + beta12orEarlier + [a-zA-Z_0-9]{2,3}[0-9]{5} + KEGG pathway ID @@ -16010,9 +16010,9 @@ Pathway ID (NCI-Nature) - Identifier of a pathway from the NCI-Nature pathway database. - [a-zA-Z_0-9]+ beta12orEarlier + [a-zA-Z_0-9]+ + Identifier of a pathway from the NCI-Nature pathway database. @@ -16026,8 +16026,8 @@ Pathway ID (ConsensusPathDB) - Identifier of a pathway from the ConsensusPathDB pathway database. beta12orEarlier + Identifier of a pathway from the ConsensusPathDB pathway database. @@ -16040,10 +16040,10 @@ Sequence cluster ID (UniRef) - beta12orEarlier - UniRef entry accession - UniRef cluster id Unique identifier of an entry from the UniRef database. + UniRef cluster id + UniRef entry accession + beta12orEarlier @@ -16056,10 +16056,10 @@ Sequence cluster ID (UniRef100) - Unique identifier of an entry from the UniRef100 database. - UniRef100 entry accession - beta12orEarlier UniRef100 cluster id + beta12orEarlier + UniRef100 entry accession + Unique identifier of an entry from the UniRef100 database. @@ -16072,10 +16072,10 @@ Sequence cluster ID (UniRef90) - Unique identifier of an entry from the UniRef90 database. - UniRef90 cluster id - beta12orEarlier UniRef90 entry accession + beta12orEarlier + UniRef90 cluster id + Unique identifier of an entry from the UniRef90 database. @@ -16088,10 +16088,10 @@ Sequence cluster ID (UniRef50) - Unique identifier of an entry from the UniRef50 database. - UniRef50 entry accession - UniRef50 cluster id beta12orEarlier + UniRef50 cluster id + UniRef50 entry accession + Unique identifier of an entry from the UniRef50 database. @@ -16110,10 +16110,10 @@ - This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier - Ontological data Data concerning or derived from an ontology. + Ontological data + beta12orEarlier + This is a broad data type and is used a placeholder for other, more specific types. @@ -16125,9 +16125,9 @@ RNA family report - RNA family annotation - An informative report on a specific RNA family or other group of classified RNA sequences. beta12orEarlier + An informative report on a specific RNA family or other group of classified RNA sequences. + RNA family annotation @@ -16145,8 +16145,8 @@ - Identifier of an RNA family, typically an entry from a RNA sequence classification database. beta12orEarlier + Identifier of an RNA family, typically an entry from a RNA sequence classification database. @@ -16160,8 +16160,8 @@ RFAM accession - beta12orEarlier Stable accession number of an entry (RNA family) from the RFAM database. + beta12orEarlier @@ -16174,10 +16174,10 @@ Protein signature type - 1.5 - A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database. - true beta12orEarlier + true + A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database. + 1.5 @@ -16189,10 +16189,10 @@ Domain-nucleic acid interaction report - beta12orEarlier - An informative report on protein domain-DNA/RNA interaction(s). - true 1.5 + true + An informative report on protein domain-DNA/RNA interaction(s). + beta12orEarlier @@ -16204,10 +16204,10 @@ Domain-domain interactions - true - beta12orEarlier - An informative report on protein domain-protein domain interaction(s). 1.8 + An informative report on protein domain-protein domain interaction(s). + beta12orEarlier + true @@ -16219,10 +16219,10 @@ Domain-domain interaction (indirect) - Data on indirect protein domain-protein domain interaction(s). - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + Data on indirect protein domain-protein domain interaction(s). @@ -16240,8 +16240,8 @@ - beta12orEarlier Accession number of a nucleotide or protein sequence database entry. + beta12orEarlier @@ -16254,11 +16254,11 @@ 2D PAGE data - Data concerning two-dimensional polygel electrophoresis. - true - beta12orEarlier - beta13 This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + beta13 + beta12orEarlier + true + Data concerning two-dimensional polygel electrophoresis. @@ -16271,10 +16271,10 @@ 2D PAGE report - true - 1.8 - beta12orEarlier Topic concerning two-dimensional gel electrophoresis experiments, gels or spots in a gel. + beta12orEarlier + 1.8 + true @@ -16287,8 +16287,8 @@ Pathway or network accession - beta12orEarlier A persistent, unique identifier of a biological pathway or network (typically a database entry). + beta12orEarlier @@ -16301,8 +16301,8 @@ Secondary structure alignment - beta12orEarlier Alignment of the (1D representations of) secondary structure of two or more molecules. + beta12orEarlier @@ -16315,8 +16315,8 @@ ASTD ID - Identifier of an object from the ASTD database. beta12orEarlier + Identifier of an object from the ASTD database. @@ -16329,8 +16329,8 @@ ASTD ID (exon) - Identifier of an exon from the ASTD database. beta12orEarlier + Identifier of an exon from the ASTD database. @@ -16343,8 +16343,8 @@ ASTD ID (intron) - Identifier of an intron from the ASTD database. beta12orEarlier + Identifier of an intron from the ASTD database. @@ -16357,8 +16357,8 @@ ASTD ID (polya) - beta12orEarlier Identifier of a polyA signal from the ASTD database. + beta12orEarlier @@ -16371,8 +16371,8 @@ ASTD ID (tss) - beta12orEarlier Identifier of a transcription start site from the ASTD database. + beta12orEarlier @@ -16385,11 +16385,11 @@ 2D PAGE spot report - true - 1.8 - An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel. - beta12orEarlier 2D PAGE spot annotation + beta12orEarlier + An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel. + 1.8 + true @@ -16402,8 +16402,8 @@ Spot ID - Unique identifier of a spot from a two-dimensional (protein) gel. beta12orEarlier + Unique identifier of a spot from a two-dimensional (protein) gel. @@ -16416,8 +16416,8 @@ Spot serial number - beta12orEarlier Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database. + beta12orEarlier @@ -16430,8 +16430,8 @@ Spot ID (HSC-2DPAGE) - beta12orEarlier Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database. + beta12orEarlier @@ -16444,10 +16444,10 @@ Protein-motif interaction - beta12orEarlier - Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs. - true beta13 + true + Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs. + beta12orEarlier @@ -16459,8 +16459,8 @@ Strain identifier - beta12orEarlier Identifier of a strain of an organism variant, typically a plant, virus or bacterium. + beta12orEarlier @@ -16474,8 +16474,8 @@ CABRI accession - beta12orEarlier A unique identifier of an item from the CABRI database. + beta12orEarlier @@ -16488,10 +16488,10 @@ Experiment report (genotyping) - beta12orEarlier - 1.8 - Report of genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. true + Report of genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. + 1.8 + beta12orEarlier @@ -16510,8 +16510,8 @@ - Identifier of an entry from a database of genotype experiment metadata. beta12orEarlier + Identifier of an entry from a database of genotype experiment metadata. @@ -16524,8 +16524,8 @@ EGA accession - Identifier of an entry from the EGA database. beta12orEarlier + Identifier of an entry from the EGA database. @@ -16538,9 +16538,9 @@ IPI protein ID - beta12orEarlier - IPI[0-9]{8} Identifier of a protein entry catalogued in the International Protein Index (IPI) database. + IPI[0-9]{8} + beta12orEarlier @@ -16553,9 +16553,9 @@ RefSeq accession (protein) - beta12orEarlier - Accession number of a protein from the RefSeq database. RefSeq protein ID + Accession number of a protein from the RefSeq database. + beta12orEarlier @@ -16568,9 +16568,9 @@ EPD ID - EPD identifier - Identifier of an entry (promoter) from the EPD database. beta12orEarlier + Identifier of an entry (promoter) from the EPD database. + EPD identifier @@ -16584,8 +16584,8 @@ TAIR accession - Identifier of an entry from the TAIR database. beta12orEarlier + Identifier of an entry from the TAIR database. @@ -16598,8 +16598,8 @@ TAIR accession (At gene) - Identifier of an Arabidopsis thaliana gene from the TAIR database. beta12orEarlier + Identifier of an Arabidopsis thaliana gene from the TAIR database. @@ -16612,8 +16612,8 @@ UniSTS accession - Identifier of an entry from the UniSTS database. beta12orEarlier + Identifier of an entry from the UniSTS database. @@ -16626,8 +16626,8 @@ UNITE accession - Identifier of an entry from the UNITE database. beta12orEarlier + Identifier of an entry from the UNITE database. @@ -16640,8 +16640,8 @@ UTR accession - Identifier of an entry from the UTR database. beta12orEarlier + Identifier of an entry from the UTR database. @@ -16654,11 +16654,11 @@ UniParc accession - UPI - UniParc ID - Accession number of a UniParc (protein sequence) database entry. - UPI[A-F0-9]{10} beta12orEarlier + UPI[A-F0-9]{10} + Accession number of a UniParc (protein sequence) database entry. + UniParc ID + UPI @@ -16671,8 +16671,8 @@ mFLJ/mKIAA number - Identifier of an entry from the Rouge or HUGE databases. beta12orEarlier + Identifier of an entry from the Rouge or HUGE databases. @@ -16685,10 +16685,10 @@ Fungi annotation - An informative report on a specific fungus. - 1.4 - beta12orEarlier true + beta12orEarlier + 1.4 + An informative report on a specific fungus. @@ -16700,10 +16700,10 @@ Fungi annotation (anamorph) - true - 1.4 - An informative report on a specific fungus anamorph. beta12orEarlier + An informative report on a specific fungus anamorph. + 1.4 + true @@ -16715,10 +16715,10 @@ Gene features report (exon) - beta12orEarlier - 1.8 - Topic concerning exons in a nucleotide sequences. true + Topic concerning exons in a nucleotide sequences. + 1.8 + beta12orEarlier @@ -16731,10 +16731,10 @@ Ensembl protein ID - Unique identifier for a protein from the Ensembl database. - Protein ID (Ensembl) - beta12orEarlier Ensembl ID (protein) + beta12orEarlier + Protein ID (Ensembl) + Unique identifier for a protein from the Ensembl database. @@ -16747,10 +16747,10 @@ Gene transcriptional features report - Topic concerning transcription of DNA into RNA including the regulation of transcription. - true - beta12orEarlier 1.8 + beta12orEarlier + true + Topic concerning transcription of DNA into RNA including the regulation of transcription. @@ -16762,10 +16762,10 @@ Toxin annotation - true - 1.4 - An informative report on a specific toxin. beta12orEarlier + An informative report on a specific toxin. + 1.4 + true @@ -16777,10 +16777,10 @@ Protein report (membrane protein) - beta12orEarlier - An informative report on a membrane protein. - true beta12orEarlier + true + An informative report on a membrane protein. + beta12orEarlier @@ -16794,8 +16794,8 @@ - beta12orEarlier An informative report on tentative or known protein-drug interaction(s). + beta12orEarlier @@ -16807,11 +16807,11 @@ Map data - Data concerning a map of molecular sequence(s). - beta13 - true - This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier + This is a broad data type and is used a placeholder for other, more specific types. + true + beta13 + Data concerning a map of molecular sequence(s). @@ -16824,10 +16824,10 @@ Phylogenetic data - beta12orEarlier - This is a broad data type and is used a placeholder for other, more specific types. - Phylogenetic data Data concerning phylogeny, typically of molecular sequences, including reports of information concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. + Phylogenetic data + This is a broad data type and is used a placeholder for other, more specific types. + beta12orEarlier @@ -16839,11 +16839,11 @@ Protein data - beta12orEarlier - true - Data concerning one or more protein molecules. - beta13 This is a broad data type and is used a placeholder for other, more specific types. + beta13 + Data concerning one or more protein molecules. + true + beta12orEarlier @@ -16855,11 +16855,11 @@ Nucleic acid data - This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier - beta13 - Data concerning one or more nucleic acid molecules. true + Data concerning one or more nucleic acid molecules. + beta13 + beta12orEarlier + This is a broad data type and is used a placeholder for other, more specific types. @@ -16871,10 +16871,10 @@ Article data - Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal. - Article report - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. beta12orEarlier + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. + Article report + Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal. @@ -16887,13 +16887,13 @@ Parameter - Tool parameter - Parameters - Typically a simple numerical or string value that controls the operation of a tool. - http://www.e-lico.eu/ontologies/dmo/DMOP/DMOP.owl#Parameter - beta12orEarlier - Tool-specific parameter http://semanticscience.org/resource/SIO_000144 + Tool-specific parameter + beta12orEarlier + http://www.e-lico.eu/ontologies/dmo/DMOP/DMOP.owl#Parameter + Typically a simple numerical or string value that controls the operation of a tool. + Parameters + Tool parameter @@ -16905,12 +16905,12 @@ Molecular data - This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier - beta13 - Data concerning a specific type of molecule. - true Molecule-specific data + true + Data concerning a specific type of molecule. + beta13 + beta12orEarlier + This is a broad data type and is used a placeholder for other, more specific types. @@ -16922,11 +16922,11 @@ Molecule report - true - 1.5 - Molecular report - beta12orEarlier An informative report on a specific molecule. + beta12orEarlier + Molecular report + 1.5 + true @@ -16939,9 +16939,9 @@ Organism report - Organism annotation - beta12orEarlier An informative report on a specific organism. + beta12orEarlier + Organism annotation @@ -16953,10 +16953,10 @@ Experiment report - Annotation on a wet lab experiment, such as experimental conditions. - Experiment annotation - beta12orEarlier Experiment metadata + beta12orEarlier + Experiment annotation + Annotation on a wet lab experiment, such as experimental conditions. @@ -16968,10 +16968,10 @@ Nucleic acid features report (mutation) - beta12orEarlier - true - 1.8 Topic concerning DNA mutation. + 1.8 + true + beta12orEarlier @@ -16983,9 +16983,9 @@ Sequence attribute - beta12orEarlier - Sequence parameter An attribute of a molecular sequence, possibly in reference to some other sequence. + Sequence parameter + beta12orEarlier @@ -16997,10 +16997,10 @@ Sequence tag profile - Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In all cases this is a list of short sequence tags and the number of times it is observed. - Sequencing-based expression profile - beta12orEarlier SAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from. + beta12orEarlier + Sequencing-based expression profile + Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In all cases this is a list of short sequence tags and the number of times it is observed. @@ -17012,8 +17012,8 @@ Mass spectrometry data - Data concerning a mass spectrometry measurement. beta12orEarlier + Data concerning a mass spectrometry measurement. @@ -17025,9 +17025,9 @@ Protein structure raw data - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - Raw data from experimental methods for determining protein structure. beta12orEarlier + Raw data from experimental methods for determining protein structure. + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. @@ -17039,8 +17039,8 @@ Mutation identifier - beta12orEarlier An identifier of a mutation. + beta12orEarlier @@ -17053,11 +17053,11 @@ Alignment data - beta12orEarlier - Data concerning an alignment of two or more molecular sequences, structures or derived data. - beta13 - true This is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles. + true + beta13 + Data concerning an alignment of two or more molecular sequences, structures or derived data. + beta12orEarlier @@ -17070,12 +17070,12 @@ Data index data - This is a broad data type and is used a placeholder for other, more specific types. - Database index - beta13 - beta12orEarlier - Data concerning an index of data. true + Data concerning an index of data. + beta12orEarlier + beta13 + Database index + This is a broad data type and is used a placeholder for other, more specific types. @@ -17087,8 +17087,8 @@ Amino acid name (single letter) - Single letter amino acid identifier, e.g. G. beta12orEarlier + Single letter amino acid identifier, e.g. G. @@ -17101,8 +17101,8 @@ Amino acid name (three letter) - Three letter amino acid identifier, e.g. GLY. beta12orEarlier + Three letter amino acid identifier, e.g. GLY. @@ -17115,8 +17115,8 @@ Amino acid name (full name) - Full name of an amino acid, e.g. Glycine. beta12orEarlier + Full name of an amino acid, e.g. Glycine. @@ -17135,8 +17135,8 @@ - Identifier of a toxin. beta12orEarlier + Identifier of a toxin. @@ -17149,8 +17149,8 @@ ArachnoServer ID - beta12orEarlier Unique identifier of a toxin from the ArachnoServer database. + beta12orEarlier @@ -17163,11 +17163,11 @@ Expressed gene list - A simple summary of expressed genes. - Gene annotation (expressed gene list) - 1.5 - true beta12orEarlier + true + 1.5 + Gene annotation (expressed gene list) + A simple summary of expressed genes. @@ -17179,8 +17179,8 @@ BindingDB Monomer ID - beta12orEarlier Unique identifier of a monomer from the BindingDB database. + beta12orEarlier @@ -17193,10 +17193,10 @@ GO concept name - The name of a concept from the GO ontology. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + The name of a concept from the GO ontology. @@ -17208,9 +17208,9 @@ GO concept ID (biological process) - An identifier of a 'biological process' concept from the the Gene Ontology. - beta12orEarlier [0-9]{7}|GO:[0-9]{7} + beta12orEarlier + An identifier of a 'biological process' concept from the the Gene Ontology. @@ -17223,9 +17223,9 @@ GO concept ID (molecular function) - An identifier of a 'molecular function' concept from the the Gene Ontology. - [0-9]{7}|GO:[0-9]{7} beta12orEarlier + [0-9]{7}|GO:[0-9]{7} + An identifier of a 'molecular function' concept from the the Gene Ontology. @@ -17238,10 +17238,10 @@ GO concept name (cellular component) - beta12orEarlier - beta12orEarlier - true The name of a concept for a cellular component from the GO ontology. + true + beta12orEarlier + beta12orEarlier @@ -17253,8 +17253,8 @@ Northern blot image - An image arising from a Northern Blot experiment. beta12orEarlier + An image arising from a Northern Blot experiment. @@ -17267,8 +17267,8 @@ Blot ID - beta12orEarlier Unique identifier of a blot from a Northern Blot. + beta12orEarlier @@ -17281,8 +17281,8 @@ BlotBase blot ID - Unique identifier of a blot from a Northern Blot from the BlotBase database. beta12orEarlier + Unique identifier of a blot from a Northern Blot from the BlotBase database. @@ -17295,9 +17295,9 @@ Hierarchy - Hierarchy annotation - Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation. beta12orEarlier + Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation. + Hierarchy annotation @@ -17309,10 +17309,10 @@ Hierarchy identifier - true - beta12orEarlier - beta12orEarlier Identifier of an entry from a database of biological hierarchies. + beta12orEarlier + beta12orEarlier + true @@ -17324,8 +17324,8 @@ Brite hierarchy ID - Identifier of an entry from the Brite database of biological hierarchies. beta12orEarlier + Identifier of an entry from the Brite database of biological hierarchies. @@ -17338,10 +17338,10 @@ Cancer type - beta12orEarlier - beta12orEarlier - A type (represented as a string) of cancer. true + A type (represented as a string) of cancer. + beta12orEarlier + beta12orEarlier @@ -17353,8 +17353,8 @@ BRENDA organism ID - beta12orEarlier A unique identifier for an organism used in the BRENDA database. + beta12orEarlier @@ -17367,9 +17367,9 @@ UniGene taxon - beta12orEarlier - UniGene organism abbreviation The name of a taxon using the controlled vocabulary of the UniGene database. + UniGene organism abbreviation + beta12orEarlier @@ -17382,8 +17382,8 @@ UTRdb taxon - The name of a taxon using the controlled vocabulary of the UTRdb database. beta12orEarlier + The name of a taxon using the controlled vocabulary of the UTRdb database. @@ -17396,9 +17396,9 @@ Catalogue ID - Catalogue identifier - An identifier of a catalogue of biological resources. beta12orEarlier + An identifier of a catalogue of biological resources. + Catalogue identifier @@ -17412,8 +17412,8 @@ CABRI catalogue name - beta12orEarlier The name of a catalogue of biological resources from the CABRI database. + beta12orEarlier @@ -17426,10 +17426,10 @@ Secondary structure alignment metadata - true - beta12orEarlier - beta12orEarlier An informative report on protein secondary structure alignment-derived data or metadata. + beta12orEarlier + beta12orEarlier + true @@ -17441,10 +17441,10 @@ Molecule interaction report - Molecular interaction data - Molecular interaction report - beta12orEarlier An informative report on the physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules). + beta12orEarlier + Molecular interaction report + Molecular interaction data @@ -17461,10 +17461,10 @@ - Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network). - Pathway - beta12orEarlier Network + beta12orEarlier + Pathway + Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network). @@ -17476,11 +17476,11 @@ Small molecule data - Data concerning one or more small molecules. - beta13 - beta12orEarlier - This is a broad data type and is used a placeholder for other, more specific types. true + This is a broad data type and is used a placeholder for other, more specific types. + beta12orEarlier + beta13 + Data concerning one or more small molecules. @@ -17492,10 +17492,10 @@ Genotype and phenotype data - Data concerning a particular genotype, phenotype or a genotype / phenotype relation. - beta13 - true beta12orEarlier + true + beta13 + Data concerning a particular genotype, phenotype or a genotype / phenotype relation. @@ -17513,10 +17513,10 @@ - This is a broad data type and is used a placeholder for other, more specific types. See also http://edamontology.org/data_0931 - Microarray data - Image or hybridisation data for a microarray, typically a study of gene expression. beta12orEarlier + Image or hybridisation data for a microarray, typically a study of gene expression. + Microarray data + This is a broad data type and is used a placeholder for other, more specific types. See also http://edamontology.org/data_0931 @@ -17529,11 +17529,11 @@ Compound ID (KEGG) - KEGG compound identifier - KEGG compound ID - beta12orEarlier - Unique identifier of a chemical compound from the KEGG database. C[0-9]+ + Unique identifier of a chemical compound from the KEGG database. + beta12orEarlier + KEGG compound ID + KEGG compound identifier @@ -17547,8 +17547,8 @@ RFAM name - beta12orEarlier Name (not necessarily stable) an entry (RNA family) from the RFAM database. + beta12orEarlier @@ -17562,9 +17562,9 @@ Reaction ID (KEGG) - beta12orEarlier - R[0-9]+ Identifier of a biological reaction from the KEGG reactions database. + R[0-9]+ + beta12orEarlier @@ -17578,9 +17578,9 @@ Drug ID (KEGG) - D[0-9]+ - Unique identifier of a drug from the KEGG Drug database. beta12orEarlier + Unique identifier of a drug from the KEGG Drug database. + D[0-9]+ @@ -17594,10 +17594,10 @@ Ensembl ID - Ensembl IDs - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database. - ENS[A-Z]*[FPTG][0-9]{11} beta12orEarlier + ENS[A-Z]*[FPTG][0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database. + Ensembl IDs @@ -17616,9 +17616,9 @@ - [A-Z][0-9]+(\.[-[0-9]+])? - beta12orEarlier An identifier of a disease from the International Classification of Diseases (ICD) database. + beta12orEarlier + [A-Z][0-9]+(\.[-[0-9]+])? @@ -17631,11 +17631,11 @@ Sequence cluster ID (CluSTr) - CluSTr cluster ID - beta12orEarlier - CluSTr ID - [0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])? Unique identifier of a sequence cluster from the CluSTr database. + [0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])? + CluSTr ID + beta12orEarlier + CluSTr cluster ID @@ -17649,9 +17649,9 @@ KEGG Glycan ID - beta12orEarlier - Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND). G[0-9]+ + Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND). + beta12orEarlier @@ -17664,11 +17664,11 @@ TCDB ID - A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins. - [0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+ - TC number - OBO file for regular expression. beta12orEarlier + OBO file for regular expression. + TC number + [0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+ + A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins. @@ -17681,9 +17681,9 @@ MINT ID - beta12orEarlier - Unique identifier of an entry from the MINT database of protein-protein interactions. MINT\-[0-9]{1,5} + Unique identifier of an entry from the MINT database of protein-protein interactions. + beta12orEarlier @@ -17696,9 +17696,9 @@ DIP ID - DIP[\:\-][0-9]{3}[EN] - beta12orEarlier Unique identifier of an entry from the DIP database of protein-protein interactions. + beta12orEarlier + DIP[\:\-][0-9]{3}[EN] @@ -17711,9 +17711,9 @@ Signaling Gateway protein ID - A[0-9]{6} - Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database. beta12orEarlier + Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database. + A[0-9]{6} @@ -17727,8 +17727,8 @@ Protein modification ID - Identifier of a protein modification catalogued in a database. beta12orEarlier + Identifier of a protein modification catalogued in a database. @@ -17741,9 +17741,9 @@ RESID ID - beta12orEarlier - AA[0-9]{4} Identifier of a protein modification catalogued in the RESID database. + AA[0-9]{4} + beta12orEarlier @@ -17757,9 +17757,9 @@ RGD ID - Identifier of an entry from the RGD database. - beta12orEarlier [0-9]{4,7} + beta12orEarlier + Identifier of an entry from the RGD database. @@ -17779,9 +17779,9 @@ - beta12orEarlier - Identifier of a protein sequence from the TAIR database. AASequence:[0-9]{10} + Identifier of a protein sequence from the TAIR database. + beta12orEarlier @@ -17794,10 +17794,10 @@ Compound ID (HMDB) - Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB). - HMDB ID - beta12orEarlier HMDB[0-9]{5} + beta12orEarlier + HMDB ID + Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB). @@ -17810,10 +17810,10 @@ LIPID MAPS ID - LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})? - Identifier of an entry from the LIPID MAPS database. - LM ID beta12orEarlier + LM ID + Identifier of an entry from the LIPID MAPS database. + LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})? @@ -17826,10 +17826,10 @@ PeptideAtlas ID - PAp[0-9]{8} - beta12orEarlier - PDBML:pdbx_PDB_strand_id Identifier of a peptide from the PeptideAtlas peptide databases. + PDBML:pdbx_PDB_strand_id + beta12orEarlier + PAp[0-9]{8} @@ -17842,10 +17842,10 @@ Molecular interaction ID - 1.7 - beta12orEarlier - true Identifier of a report of molecular interactions from a database (typically). + true + beta12orEarlier + 1.7 @@ -17857,9 +17857,9 @@ BioGRID interaction ID - A unique identifier of an interaction from the BioGRID database. - beta12orEarlier [0-9]+ + beta12orEarlier + A unique identifier of an interaction from the BioGRID database. @@ -17872,10 +17872,10 @@ Enzyme ID (MEROPS) - S[0-9]{2}\.[0-9]{3} - beta12orEarlier - Unique identifier of a peptidase enzyme from the MEROPS database. MEROPS ID + Unique identifier of a peptidase enzyme from the MEROPS database. + beta12orEarlier + S[0-9]{2}\.[0-9]{3} @@ -17889,8 +17889,8 @@ Mobile genetic element ID - beta12orEarlier An identifier of a mobile genetic element. + beta12orEarlier @@ -17903,9 +17903,9 @@ ACLAME ID - An identifier of a mobile genetic element from the Aclame database. - mge:[0-9]+ beta12orEarlier + mge:[0-9]+ + An identifier of a mobile genetic element from the Aclame database. @@ -17919,9 +17919,9 @@ SGD ID - Identifier of an entry from the Saccharomyces genome database (SGD). - beta12orEarlier PWY[a-zA-Z_0-9]{2}\-[0-9]{3} + beta12orEarlier + Identifier of an entry from the Saccharomyces genome database (SGD). @@ -17935,8 +17935,8 @@ Book ID - Unique identifier of a book. beta12orEarlier + Unique identifier of a book. @@ -17949,9 +17949,9 @@ ISBN - The International Standard Book Number (ISBN) is for identifying printed books. - (ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X) beta12orEarlier + (ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X) + The International Standard Book Number (ISBN) is for identifying printed books. @@ -17964,10 +17964,10 @@ Compound ID (3DMET) - Identifier of a metabolite from the 3DMET database. - beta12orEarlier - 3DMET ID B[0-9]{5} + 3DMET ID + beta12orEarlier + Identifier of a metabolite from the 3DMET database. @@ -17980,9 +17980,9 @@ MatrixDB interaction ID - beta12orEarlier - A unique identifier of an interaction from the MatrixDB database. ([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])_.*|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*) + A unique identifier of an interaction from the MatrixDB database. + beta12orEarlier @@ -17996,10 +17996,10 @@ cPath ID - A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database. - beta12orEarlier - These identifiers are unique within the cPath database, however, they are not stable between releases. [0-9]+ + These identifiers are unique within the cPath database, however, they are not stable between releases. + beta12orEarlier + A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database. @@ -18013,9 +18013,9 @@ PubChem bioassay ID - beta12orEarlier - [0-9]+ Identifier of an assay from the PubChem database. + [0-9]+ + beta12orEarlier @@ -18029,9 +18029,9 @@ PubChem ID - Identifier of an entry from the PubChem database. - beta12orEarlier PubChem identifier + beta12orEarlier + Identifier of an entry from the PubChem database. @@ -18044,10 +18044,10 @@ Reaction ID (MACie) - Identifier of an enzyme reaction mechanism from the MACie database. - MACie entry number - M[0-9]{4} beta12orEarlier + M[0-9]{4} + MACie entry number + Identifier of an enzyme reaction mechanism from the MACie database. @@ -18060,12 +18060,12 @@ Gene ID (miRBase) - miRNA identifier - MI[0-9]{7} - Identifier for a gene from the miRBase database. - miRNA ID - miRNA name beta12orEarlier + miRNA name + miRNA ID + Identifier for a gene from the miRBase database. + MI[0-9]{7} + miRNA identifier @@ -18078,9 +18078,9 @@ Gene ID (ZFIN) - ZDB\-GENE\-[0-9]+\-[0-9]+ - beta12orEarlier Identifier for a gene from the Zebrafish information network genome (ZFIN) database. + beta12orEarlier + ZDB\-GENE\-[0-9]+\-[0-9]+ @@ -18093,9 +18093,9 @@ Reaction ID (Rhea) - beta12orEarlier - Identifier of an enzyme-catalysed reaction from the Rhea database. [0-9]{5} + Identifier of an enzyme-catalysed reaction from the Rhea database. + beta12orEarlier @@ -18108,10 +18108,10 @@ Pathway ID (Unipathway) - Identifier of a biological pathway from the Unipathway database. - beta12orEarlier - upaid UPA[0-9]{5} + upaid + beta12orEarlier + Identifier of a biological pathway from the Unipathway database. @@ -18124,10 +18124,10 @@ Compound ID (ChEMBL) - [0-9]+ - beta12orEarlier - ChEMBL ID Identifier of a small molecular from the ChEMBL database. + ChEMBL ID + beta12orEarlier + [0-9]+ @@ -18140,9 +18140,9 @@ LGICdb identifier - [a-zA-Z_0-9]+ - beta12orEarlier Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database. + beta12orEarlier + [a-zA-Z_0-9]+ @@ -18155,9 +18155,9 @@ Reaction kinetics ID (SABIO-RK) - beta12orEarlier - [0-9]+ Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database. + [0-9]+ + beta12orEarlier @@ -18171,9 +18171,9 @@ PharmGKB ID - PA[0-9]+ - Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). beta12orEarlier + Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). + PA[0-9]+ @@ -18187,9 +18187,9 @@ Pathway ID (PharmGKB) - beta12orEarlier - Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). PA[0-9]+ + Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). + beta12orEarlier @@ -18203,9 +18203,9 @@ Disease ID (PharmGKB) - PA[0-9]+ - beta12orEarlier Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). + beta12orEarlier + PA[0-9]+ @@ -18219,9 +18219,9 @@ Drug ID (PharmGKB) - PA[0-9]+ - Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). beta12orEarlier + Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). + PA[0-9]+ @@ -18234,9 +18234,9 @@ Drug ID (TTD) - beta12orEarlier - Identifier of a drug from the Therapeutic Target Database (TTD). DAP[0-9]+ + Identifier of a drug from the Therapeutic Target Database (TTD). + beta12orEarlier @@ -18249,9 +18249,9 @@ Target ID (TTD) - beta12orEarlier - Identifier of a target protein from the Therapeutic Target Database (TTD). TTDS[0-9]+ + Identifier of a target protein from the Therapeutic Target Database (TTD). + beta12orEarlier @@ -18264,9 +18264,9 @@ Cell type identifier - A unique identifier of a type or group of cells. - Cell type ID beta12orEarlier + Cell type ID + A unique identifier of a type or group of cells. @@ -18279,9 +18279,9 @@ NeuronDB ID - A unique identifier of a neuron from the NeuronDB database. - beta12orEarlier [0-9]+ + beta12orEarlier + A unique identifier of a neuron from the NeuronDB database. @@ -18294,9 +18294,9 @@ NeuroMorpho ID - [a-zA-Z_0-9]+ - A unique identifier of a neuron from the NeuroMorpho database. beta12orEarlier + A unique identifier of a neuron from the NeuroMorpho database. + [a-zA-Z_0-9]+ @@ -18309,10 +18309,10 @@ Compound ID (ChemIDplus) - beta12orEarlier - [0-9]+ - ChemIDplus ID Identifier of a chemical from the ChemIDplus database. + ChemIDplus ID + [0-9]+ + beta12orEarlier @@ -18325,9 +18325,9 @@ Pathway ID (SMPDB) - SMP[0-9]{5} - Identifier of a pathway from the Small Molecule Pathway Database (SMPDB). beta12orEarlier + Identifier of a pathway from the Small Molecule Pathway Database (SMPDB). + SMP[0-9]{5} @@ -18340,9 +18340,9 @@ BioNumbers ID - beta12orEarlier - [0-9]+ Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology. + [0-9]+ + beta12orEarlier @@ -18355,9 +18355,9 @@ T3DB ID - Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database. - T3D[0-9]+ beta12orEarlier + T3D[0-9]+ + Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database. @@ -18373,17 +18373,17 @@ - + - + - Identifier of a carbohydrate. beta12orEarlier + Identifier of a carbohydrate. @@ -18396,9 +18396,9 @@ GlycomeDB ID - [0-9]+ - beta12orEarlier Identifier of an entry from the GlycomeDB database. + beta12orEarlier + [0-9]+ @@ -18411,9 +18411,9 @@ LipidBank ID - Identifier of an entry from the LipidBank database. - [a-zA-Z_0-9]+[0-9]+ beta12orEarlier + [a-zA-Z_0-9]+[0-9]+ + Identifier of an entry from the LipidBank database. @@ -18426,9 +18426,9 @@ CDD ID - Identifier of a conserved domain from the Conserved Domain Database. - cd[0-9]{5} beta12orEarlier + cd[0-9]{5} + Identifier of a conserved domain from the Conserved Domain Database. @@ -18441,10 +18441,10 @@ MMDB ID - MMDB accession - An identifier of an entry from the MMDB database. - beta12orEarlier [0-9]{1,5} + beta12orEarlier + An identifier of an entry from the MMDB database. + MMDB accession @@ -18457,9 +18457,9 @@ iRefIndex ID - [0-9]+ - beta12orEarlier Unique identifier of an entry from the iRefIndex database of protein-protein interactions. + beta12orEarlier + [0-9]+ @@ -18472,9 +18472,9 @@ ModelDB ID - beta12orEarlier - [0-9]+ Unique identifier of an entry from the ModelDB database. + [0-9]+ + beta12orEarlier @@ -18487,9 +18487,9 @@ Pathway ID (DQCS) - beta12orEarlier - Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS). [0-9]+ + Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS). + beta12orEarlier @@ -18502,11 +18502,11 @@ Ensembl ID (Homo sapiens) - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division). - ENS([EGTP])[0-9]{11} - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + ENS([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division). @@ -18518,11 +18518,11 @@ Ensembl ID ('Bos taurus') - ENSBTA([EGTP])[0-9]{11} - beta12orEarlier - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division). beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division). + true + beta12orEarlier + ENSBTA([EGTP])[0-9]{11} @@ -18534,11 +18534,11 @@ Ensembl ID ('Canis familiaris') - beta12orEarlier - ENSCAF([EGTP])[0-9]{11} - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division). beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division). + true + ENSCAF([EGTP])[0-9]{11} + beta12orEarlier @@ -18550,11 +18550,11 @@ Ensembl ID ('Cavia porcellus') - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division). - beta12orEarlier - true ENSCPO([EGTP])[0-9]{11} + true + beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division). + beta12orEarlier @@ -18566,11 +18566,11 @@ Ensembl ID ('Ciona intestinalis') - ENSCIN([EGTP])[0-9]{11} - beta12orEarlier - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division). true + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division). + beta12orEarlier + beta12orEarlier + ENSCIN([EGTP])[0-9]{11} @@ -18582,11 +18582,11 @@ Ensembl ID ('Ciona savignyi') - true - beta12orEarlier - beta12orEarlier - ENSCSAV([EGTP])[0-9]{11} Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division). + ENSCSAV([EGTP])[0-9]{11} + beta12orEarlier + beta12orEarlier + true @@ -18598,11 +18598,11 @@ Ensembl ID ('Danio rerio') - ENSDAR([EGTP])[0-9]{11} - beta12orEarlier - beta12orEarlier - true Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division). + true + beta12orEarlier + beta12orEarlier + ENSDAR([EGTP])[0-9]{11} @@ -18614,11 +18614,11 @@ Ensembl ID ('Dasypus novemcinctus') - true - ENSDNO([EGTP])[0-9]{11} - beta12orEarlier - beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division). + beta12orEarlier + beta12orEarlier + ENSDNO([EGTP])[0-9]{11} + true @@ -18630,11 +18630,11 @@ Ensembl ID ('Echinops telfairi') - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division). - beta12orEarlier - beta12orEarlier - true ENSETE([EGTP])[0-9]{11} + true + beta12orEarlier + beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division). @@ -18646,11 +18646,11 @@ Ensembl ID ('Erinaceus europaeus') - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division). - beta12orEarlier - ENSEEU([EGTP])[0-9]{11} true + ENSEEU([EGTP])[0-9]{11} + beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division). + beta12orEarlier @@ -18662,11 +18662,11 @@ Ensembl ID ('Felis catus') - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division). - ENSFCA([EGTP])[0-9]{11} - true beta12orEarlier + true + ENSFCA([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division). + beta12orEarlier @@ -18678,11 +18678,11 @@ Ensembl ID ('Gallus gallus') - beta12orEarlier - true - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division). ENSGAL([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division). + beta12orEarlier + true + beta12orEarlier @@ -18694,11 +18694,11 @@ Ensembl ID ('Gasterosteus aculeatus') - beta12orEarlier - ENSGAC([EGTP])[0-9]{11} - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division). beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division). + true + ENSGAC([EGTP])[0-9]{11} + beta12orEarlier @@ -18710,11 +18710,11 @@ Ensembl ID ('Homo sapiens') - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division). - beta12orEarlier - beta12orEarlier ENSHUM([EGTP])[0-9]{11} + beta12orEarlier + beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division). + true @@ -18726,11 +18726,11 @@ Ensembl ID ('Loxodonta africana') - beta12orEarlier - ENSLAF([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division). - true beta12orEarlier + true + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division). + ENSLAF([EGTP])[0-9]{11} + beta12orEarlier @@ -18742,11 +18742,11 @@ Ensembl ID ('Macaca mulatta') - beta12orEarlier - true - ENSMMU([EGTP])[0-9]{11} - beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division). + beta12orEarlier + ENSMMU([EGTP])[0-9]{11} + true + beta12orEarlier @@ -18758,11 +18758,11 @@ Ensembl ID ('Monodelphis domestica') - beta12orEarlier - ENSMOD([EGTP])[0-9]{11} - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division). beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division). + true + ENSMOD([EGTP])[0-9]{11} + beta12orEarlier @@ -18774,11 +18774,11 @@ Ensembl ID ('Mus musculus') - beta12orEarlier - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division). - true ENSMUS([EGTP])[0-9]{11} + true + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division). + beta12orEarlier + beta12orEarlier @@ -18790,11 +18790,11 @@ Ensembl ID ('Myotis lucifugus') - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division). - beta12orEarlier - true - ENSMLU([EGTP])[0-9]{11} beta12orEarlier + ENSMLU([EGTP])[0-9]{11} + true + beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division). @@ -18806,11 +18806,11 @@ Ensembl ID ("Ornithorhynchus anatinus") - beta12orEarlier - ENSOAN([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division). - true beta12orEarlier + true + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division). + ENSOAN([EGTP])[0-9]{11} + beta12orEarlier @@ -18822,11 +18822,11 @@ Ensembl ID ('Oryctolagus cuniculus') - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division). - true - ENSOCU([EGTP])[0-9]{11} beta12orEarlier + ENSOCU([EGTP])[0-9]{11} + true + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division). + beta12orEarlier @@ -18838,11 +18838,11 @@ Ensembl ID ('Oryzias latipes') - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division). - beta12orEarlier - true ENSORL([EGTP])[0-9]{11} + true + beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division). + beta12orEarlier @@ -18854,11 +18854,11 @@ Ensembl ID ('Otolemur garnettii') - ENSSAR([EGTP])[0-9]{11} - beta12orEarlier - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division). beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division). + true + beta12orEarlier + ENSSAR([EGTP])[0-9]{11} @@ -18870,11 +18870,11 @@ Ensembl ID ('Pan troglodytes') - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division). - ENSPTR([EGTP])[0-9]{11} - beta12orEarlier beta12orEarlier + beta12orEarlier + ENSPTR([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division). + true @@ -18886,11 +18886,11 @@ Ensembl ID ('Rattus norvegicus') - beta12orEarlier - ENSRNO([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division). - true beta12orEarlier + true + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division). + ENSRNO([EGTP])[0-9]{11} + beta12orEarlier @@ -18902,11 +18902,11 @@ Ensembl ID ('Spermophilus tridecemlineatus') - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division). - ENSSTO([EGTP])[0-9]{11} - beta12orEarlier true + beta12orEarlier + ENSSTO([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division). + beta12orEarlier @@ -18918,11 +18918,11 @@ Ensembl ID ('Takifugu rubripes') - true - ENSFRU([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division). - beta12orEarlier beta12orEarlier + beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division). + ENSFRU([EGTP])[0-9]{11} + true @@ -18934,11 +18934,11 @@ Ensembl ID ('Tupaia belangeri') - ENSTBE([EGTP])[0-9]{11} - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division). - beta12orEarlier beta12orEarlier + beta12orEarlier + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division). + true + ENSTBE([EGTP])[0-9]{11} @@ -18950,11 +18950,11 @@ Ensembl ID ('Xenopus tropicalis') - ENSXET([EGTP])[0-9]{11} - true - beta12orEarlier - beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division). + beta12orEarlier + beta12orEarlier + true + ENSXET([EGTP])[0-9]{11} @@ -18966,8 +18966,8 @@ CATH identifier - Identifier of a protein domain (or other node) from the CATH database. beta12orEarlier + Identifier of a protein domain (or other node) from the CATH database. @@ -18980,9 +18980,9 @@ CATH node ID (family) - 2.10.10.10 - A code number identifying a family from the CATH database. beta12orEarlier + A code number identifying a family from the CATH database. + 2.10.10.10 @@ -18995,9 +18995,9 @@ Enzyme ID (CAZy) - CAZy ID - beta12orEarlier Identifier of an enzyme from the CAZy enzymes database. + beta12orEarlier + CAZy ID @@ -19010,10 +19010,10 @@ Clone ID (IMAGE) - beta12orEarlier - A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence). - IMAGE cloneID I.M.A.G.E. cloneID + IMAGE cloneID + A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence). + beta12orEarlier @@ -19026,10 +19026,10 @@ GO concept ID (cellular compartment) - GO concept identifier (cellular compartment) - beta12orEarlier - [0-9]{7}|GO:[0-9]{7} An identifier of a 'cellular compartment' concept from the Gene Ontology. + [0-9]{7}|GO:[0-9]{7} + beta12orEarlier + GO concept identifier (cellular compartment) @@ -19042,8 +19042,8 @@ Chromosome name (BioCyc) - beta12orEarlier Name of a chromosome as used in the BioCyc database. + beta12orEarlier @@ -19056,8 +19056,8 @@ CleanEx entry name - An identifier of a gene expression profile from the CleanEx database. beta12orEarlier + An identifier of a gene expression profile from the CleanEx database. @@ -19070,8 +19070,8 @@ CleanEx dataset code - An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database. beta12orEarlier + An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database. @@ -19084,8 +19084,8 @@ Genome report - beta12orEarlier An informative report of general information concerning a genome as a whole. + beta12orEarlier @@ -19097,9 +19097,9 @@ Protein ID (CORUM) - Unique identifier for a protein complex from the CORUM database. - CORUM complex ID beta12orEarlier + CORUM complex ID + Unique identifier for a protein complex from the CORUM database. @@ -19112,8 +19112,8 @@ CDD PSSM-ID - Unique identifier of a position-specific scoring matrix from the CDD database. beta12orEarlier + Unique identifier of a position-specific scoring matrix from the CDD database. @@ -19126,9 +19126,9 @@ Protein ID (CuticleDB) - Unique identifier for a protein from the CuticleDB database. - beta12orEarlier CuticleDB ID + beta12orEarlier + Unique identifier for a protein from the CuticleDB database. @@ -19141,8 +19141,8 @@ DBD ID - beta12orEarlier Identifier of a predicted transcription factor from the DBD database. + beta12orEarlier @@ -19161,8 +19161,8 @@ - General annotation on an oligonucleotide probe. beta12orEarlier + General annotation on an oligonucleotide probe. @@ -19175,8 +19175,8 @@ Oligonucleotide ID - beta12orEarlier Identifier of an oligonucleotide from a database. + beta12orEarlier @@ -19189,8 +19189,8 @@ dbProbe ID - beta12orEarlier Identifier of an oligonucleotide probe from the dbProbe database. + beta12orEarlier @@ -19203,8 +19203,8 @@ Dinucleotide property - Physicochemical property data for one or more dinucleotides. beta12orEarlier + Physicochemical property data for one or more dinucleotides. @@ -19216,8 +19216,8 @@ DiProDB ID - Identifier of an dinucleotide property from the DiProDB database. beta12orEarlier + Identifier of an dinucleotide property from the DiProDB database. @@ -19230,10 +19230,10 @@ Protein features report (disordered structure) - Topic concerning disordered structure in a protein. - beta12orEarlier - true 1.8 + true + beta12orEarlier + Topic concerning disordered structure in a protein. @@ -19245,9 +19245,9 @@ Protein ID (DisProt) - Unique identifier for a protein from the DisProt database. - beta12orEarlier DisProt ID + beta12orEarlier + Unique identifier for a protein from the DisProt database. @@ -19260,11 +19260,11 @@ Embryo report - 1.5 - beta12orEarlier - Embryo annotation - true Annotation on an embryo or concerning embryological development. + true + Embryo annotation + beta12orEarlier + 1.5 @@ -19277,9 +19277,9 @@ Ensembl transcript ID - Unique identifier for a gene transcript from the Ensembl database. - Transcript ID (Ensembl) beta12orEarlier + Transcript ID (Ensembl) + Unique identifier for a gene transcript from the Ensembl database. @@ -19292,10 +19292,10 @@ Inhibitor annotation - true - An informative report on one or more small molecules that are enzyme inhibitors. - beta12orEarlier 1.4 + beta12orEarlier + An informative report on one or more small molecules that are enzyme inhibitors. + true @@ -19308,9 +19308,9 @@ Promoter ID - Moby:GeneAccessionList - An identifier of a promoter of a gene that is catalogued in a database. beta12orEarlier + An identifier of a promoter of a gene that is catalogued in a database. + Moby:GeneAccessionList @@ -19323,8 +19323,8 @@ EST accession - beta12orEarlier Identifier of an EST sequence. + beta12orEarlier @@ -19337,8 +19337,8 @@ COGEME EST ID - Identifier of an EST sequence from the COGEME database. beta12orEarlier + Identifier of an EST sequence from the COGEME database. @@ -19351,9 +19351,9 @@ COGEME unisequence ID - beta12orEarlier - A unisequence is a single sequence assembled from ESTs. Identifier of a unisequence from the COGEME database. + A unisequence is a single sequence assembled from ESTs. + beta12orEarlier @@ -19366,9 +19366,9 @@ Protein family ID (GeneFarm) - Accession number of an entry (family) from the TIGRFam database. - beta12orEarlier GeneFarm family ID + beta12orEarlier + Accession number of an entry (family) from the TIGRFam database. @@ -19381,8 +19381,8 @@ Family name - The name of a family of organism. beta12orEarlier + The name of a family of organism. @@ -19395,10 +19395,10 @@ Genus name (virus) - beta12orEarlier - beta13 - The name of a genus of viruses. true + The name of a genus of viruses. + beta13 + beta12orEarlier @@ -19410,10 +19410,10 @@ Family name (virus) - beta12orEarlier - true - The name of a family of viruses. beta13 + The name of a family of viruses. + true + beta12orEarlier @@ -19425,10 +19425,10 @@ Database name (SwissRegulon) - beta12orEarlier - The name of a SwissRegulon database. - beta13 true + beta13 + The name of a SwissRegulon database. + beta12orEarlier @@ -19440,9 +19440,9 @@ Sequence feature ID (SwissRegulon) - This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end". - A feature identifier as used in the SwissRegulon database. beta12orEarlier + A feature identifier as used in the SwissRegulon database. + This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end". @@ -19455,9 +19455,9 @@ FIG ID - beta12orEarlier - A unique identifier of gene in the NMPDR database. A FIG ID consists of four parts: a prefix, genome id, locus type and id number. + A unique identifier of gene in the NMPDR database. + beta12orEarlier @@ -19470,8 +19470,8 @@ Gene ID (Xenbase) - beta12orEarlier A unique identifier of gene in the Xenbase database. + beta12orEarlier @@ -19484,8 +19484,8 @@ Gene ID (Genolist) - A unique identifier of gene in the Genolist database. beta12orEarlier + A unique identifier of gene in the Genolist database. @@ -19498,11 +19498,11 @@ Gene name (Genolist) - Name of an entry (gene) from the Genolist genes database. - 1.3 - Genolist gene name - true beta12orEarlier + true + Genolist gene name + 1.3 + Name of an entry (gene) from the Genolist genes database. @@ -19514,9 +19514,9 @@ ABS ID - Identifier of an entry (promoter) from the ABS database. - beta12orEarlier ABS identifier + beta12orEarlier + Identifier of an entry (promoter) from the ABS database. @@ -19529,8 +19529,8 @@ AraC-XylS ID - beta12orEarlier Identifier of a transcription factor from the AraC-XylS database. + beta12orEarlier @@ -19543,10 +19543,10 @@ Gene name (HUGO) - Name of an entry (gene) from the HUGO database. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Name of an entry (gene) from the HUGO database. @@ -19558,8 +19558,8 @@ Locus ID (PseudoCAP) - Identifier of a locus from the PseudoCAP database. beta12orEarlier + Identifier of a locus from the PseudoCAP database. @@ -19572,8 +19572,8 @@ Locus ID (UTR) - Identifier of a locus from the UTR database. beta12orEarlier + Identifier of a locus from the UTR database. @@ -19586,8 +19586,8 @@ MonosaccharideDB ID - beta12orEarlier Unique identifier of a monosaccharide from the MonosaccharideDB database. + beta12orEarlier @@ -19600,10 +19600,10 @@ Database name (CMD) - beta13 - The name of a subdivision of the Collagen Mutation Database (CMD) database. - true beta12orEarlier + true + The name of a subdivision of the Collagen Mutation Database (CMD) database. + beta13 @@ -19614,11 +19614,11 @@ Database name (Osteogenesis) - - The name of a subdivision of the Osteogenesis database. - beta13 - true + beta12orEarlier + true + beta13 + The name of a subdivision of the Osteogenesis database. @@ -19630,8 +19630,8 @@ Genome identifier - beta12orEarlier An identifier of a particular genome. + beta12orEarlier @@ -19644,8 +19644,8 @@ GenomeReviews ID - An identifier of a particular genome. beta12orEarlier + An identifier of a particular genome. @@ -19658,9 +19658,9 @@ GlycoMap ID - Identifier of an entry from the GlycosciencesDB database. - beta12orEarlier [0-9]+ + beta12orEarlier + Identifier of an entry from the GlycosciencesDB database. @@ -19673,8 +19673,8 @@ Carbohydrate conformational map - A conformational energy map of the glycosidic linkages in a carbohydrate molecule. beta12orEarlier + A conformational energy map of the glycosidic linkages in a carbohydrate molecule. @@ -19686,10 +19686,10 @@ Gene features report (intron) - 1.8 - beta12orEarlier - true Topic concerning introns in a nucleotide sequences. + true + beta12orEarlier + 1.8 @@ -19702,8 +19702,8 @@ Transcription factor name - beta12orEarlier The name of a transcription factor. + beta12orEarlier @@ -19716,8 +19716,8 @@ TCID - beta12orEarlier Identifier of a membrane transport proteins from the transport classification database (TCDB). + beta12orEarlier @@ -19730,9 +19730,9 @@ Pfam domain name - PF[0-9]{5} - Name of a domain from the Pfam database. beta12orEarlier + Name of a domain from the Pfam database. + PF[0-9]{5} @@ -19745,9 +19745,9 @@ Pfam clan ID - Accession number of a Pfam clan. - CL[0-9]{4} beta12orEarlier + CL[0-9]{4} + Accession number of a Pfam clan. @@ -19760,9 +19760,9 @@ Gene ID (VectorBase) - Identifier for a gene from the VectorBase database. - beta12orEarlier VectorBase ID + beta12orEarlier + Identifier for a gene from the VectorBase database. @@ -19775,8 +19775,8 @@ UTRSite ID - beta12orEarlier Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs. + beta12orEarlier @@ -19795,10 +19795,10 @@ - beta12orEarlier - An informative report about a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc. - Sequence profile report Sequence motif report + Sequence profile report + An informative report about a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc. + beta12orEarlier @@ -19810,11 +19810,11 @@ Locus annotation - beta12orEarlier - An informative report on a particular locus. - beta12orEarlier - true Locus report + true + beta12orEarlier + An informative report on a particular locus. + beta12orEarlier @@ -19826,8 +19826,8 @@ Protein name (UniProt) - beta12orEarlier Official name of a protein as used in the UniProt database. + beta12orEarlier @@ -19840,11 +19840,11 @@ Term ID list - 1.5 - The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included. - true - beta12orEarlier One or more terms from one or more controlled vocabularies which are annotations on an entity. + beta12orEarlier + true + The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included. + 1.5 @@ -19856,8 +19856,8 @@ HAMAP ID - beta12orEarlier Name of a protein family from the HAMAP database. + beta12orEarlier @@ -19870,8 +19870,8 @@ Identifier with metadata - beta12orEarlier Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance. + beta12orEarlier @@ -19883,10 +19883,10 @@ Gene symbol annotation - beta12orEarlier - Annotation about a gene symbol. - beta12orEarlier true + beta12orEarlier + Annotation about a gene symbol. + beta12orEarlier @@ -19905,8 +19905,8 @@ - beta12orEarlier Identifier of a RNA transcript. + beta12orEarlier @@ -19919,8 +19919,8 @@ HIT ID - beta12orEarlier Identifier of an RNA transcript from the H-InvDB database. + beta12orEarlier @@ -19933,8 +19933,8 @@ HIX ID - beta12orEarlier A unique identifier of gene cluster in the H-InvDB database. + beta12orEarlier @@ -19947,8 +19947,8 @@ HPA antibody id - Identifier of a antibody from the HPA database. beta12orEarlier + Identifier of a antibody from the HPA database. @@ -19961,8 +19961,8 @@ IMGT/HLA ID - beta12orEarlier Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database. + beta12orEarlier @@ -19975,8 +19975,8 @@ Gene ID (JCVI) - beta12orEarlier A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI). + beta12orEarlier @@ -19989,8 +19989,8 @@ Kinase name - The name of a kinase protein. beta12orEarlier + The name of a kinase protein. @@ -20004,8 +20004,8 @@ ConsensusPathDB entity ID - beta12orEarlier Identifier of a physical entity from the ConsensusPathDB database. + beta12orEarlier @@ -20019,8 +20019,8 @@ ConsensusPathDB entity name - Name of a physical entity from the ConsensusPathDB database. beta12orEarlier + Name of a physical entity from the ConsensusPathDB database. @@ -20033,8 +20033,8 @@ CCAP strain number - beta12orEarlier The number of a strain of algae and protozoa from the CCAP database. + beta12orEarlier @@ -20048,8 +20048,8 @@ Stock number - An identifier of stock from a catalogue of biological resources. beta12orEarlier + An identifier of stock from a catalogue of biological resources. @@ -20062,8 +20062,8 @@ Stock number (TAIR) - A stock number from The Arabidopsis information resource (TAIR). beta12orEarlier + A stock number from The Arabidopsis information resource (TAIR). @@ -20076,8 +20076,8 @@ REDIdb ID - Identifier of an entry from the RNA editing database (REDIdb). beta12orEarlier + Identifier of an entry from the RNA editing database (REDIdb). @@ -20090,8 +20090,8 @@ SMART domain name - beta12orEarlier Name of a domain from the SMART database. + beta12orEarlier @@ -20104,9 +20104,9 @@ Protein family ID (PANTHER) - Accession number of an entry (family) from the PANTHER database. - Panther family ID beta12orEarlier + Panther family ID + Accession number of an entry (family) from the PANTHER database. @@ -20119,9 +20119,9 @@ RNAVirusDB ID - A unique identifier for a virus from the RNAVirusDB database. - Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. beta12orEarlier + Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. + A unique identifier for a virus from the RNAVirusDB database. @@ -20135,8 +20135,8 @@ Virus ID - An accession of annotation on a (group of) viruses (catalogued in a database). beta12orEarlier + An accession of annotation on a (group of) viruses (catalogued in a database). @@ -20149,8 +20149,8 @@ NCBI Genome Project ID - beta12orEarlier An identifier of a genome project assigned by NCBI. + beta12orEarlier @@ -20163,8 +20163,8 @@ NCBI genome accession - beta12orEarlier A unique identifier of a whole genome assigned by the NCBI. + beta12orEarlier @@ -20177,10 +20177,10 @@ Sequence profile data - beta12orEarlier - true - Data concerning, extracted from, or derived from the analysis of a sequence profile, such as its name, length, technical details about the profile or it's construction, the biological role or annotation, and so on. 1.8 + Data concerning, extracted from, or derived from the analysis of a sequence profile, such as its name, length, technical details about the profile or it's construction, the biological role or annotation, and so on. + true + beta12orEarlier @@ -20192,9 +20192,9 @@ Protein ID (TopDB) - Unique identifier for a membrane protein from the TopDB database. - TopDB ID beta12orEarlier + TopDB ID + Unique identifier for a membrane protein from the TopDB database. @@ -20207,9 +20207,9 @@ Gel ID - beta12orEarlier - Identifier of a two-dimensional (protein) gel. Gel identifier + Identifier of a two-dimensional (protein) gel. + beta12orEarlier @@ -20223,8 +20223,8 @@ Reference map name (SWISS-2DPAGE) - Name of a reference map gel from the SWISS-2DPAGE database. beta12orEarlier + Name of a reference map gel from the SWISS-2DPAGE database. @@ -20237,9 +20237,9 @@ Protein ID (PeroxiBase) - Unique identifier for a peroxidase protein from the PeroxiBase database. - beta12orEarlier PeroxiBase ID + beta12orEarlier + Unique identifier for a peroxidase protein from the PeroxiBase database. @@ -20252,8 +20252,8 @@ SISYPHUS ID - Identifier of an entry from the SISYPHUS database of tertiary structure alignments. beta12orEarlier + Identifier of an entry from the SISYPHUS database of tertiary structure alignments. @@ -20267,8 +20267,8 @@ ORF ID - Accession of an open reading frame (catalogued in a database). beta12orEarlier + Accession of an open reading frame (catalogued in a database). @@ -20281,8 +20281,8 @@ ORF identifier - beta12orEarlier An identifier of an open reading frame. + beta12orEarlier @@ -20295,8 +20295,8 @@ Linucs ID - beta12orEarlier Identifier of an entry from the GlycosciencesDB database. + beta12orEarlier @@ -20309,9 +20309,9 @@ Protein ID (LGICdb) - Unique identifier for a ligand-gated ion channel protein from the LGICdb database. - LGICdb ID beta12orEarlier + LGICdb ID + Unique identifier for a ligand-gated ion channel protein from the LGICdb database. @@ -20324,8 +20324,8 @@ MaizeDB ID - Identifier of an EST sequence from the MaizeDB database. beta12orEarlier + Identifier of an EST sequence from the MaizeDB database. @@ -20338,8 +20338,8 @@ Gene ID (MfunGD) - A unique identifier of gene in the MfunGD database. beta12orEarlier + A unique identifier of gene in the MfunGD database. @@ -20358,8 +20358,8 @@ - An identifier of a disease from the Orpha database. beta12orEarlier + An identifier of a disease from the Orpha database. @@ -20372,8 +20372,8 @@ Protein ID (EcID) - Unique identifier for a protein from the EcID database. beta12orEarlier + Unique identifier for a protein from the EcID database. @@ -20387,8 +20387,8 @@ Clone ID (RefSeq) - beta12orEarlier A unique identifier of a cDNA molecule catalogued in the RefSeq database. + beta12orEarlier @@ -20401,8 +20401,8 @@ Protein ID (ConoServer) - Unique identifier for a cone snail toxin protein from the ConoServer database. beta12orEarlier + Unique identifier for a cone snail toxin protein from the ConoServer database. @@ -20415,8 +20415,8 @@ GeneSNP ID - beta12orEarlier Identifier of a GeneSNP database entry. + beta12orEarlier @@ -20432,17 +20432,17 @@ - + - + - beta12orEarlier Identifier of a lipid. + beta12orEarlier @@ -20455,10 +20455,10 @@ Databank - beta12orEarlier - A flat-file (textual) data archive. - beta12orEarlier true + beta12orEarlier + A flat-file (textual) data archive. + beta12orEarlier @@ -20469,10 +20469,10 @@ Web portal - beta12orEarlier - true - beta12orEarlier A web site providing data (web pages) on a common theme to a HTTP client. + beta12orEarlier + true + beta12orEarlier @@ -20483,9 +20483,9 @@ Gene ID (VBASE2) - VBASE2 ID - beta12orEarlier Identifier for a gene from the VBASE2 database. + beta12orEarlier + VBASE2 ID @@ -20498,9 +20498,9 @@ DPVweb ID - A unique identifier for a virus from the DPVweb database. - beta12orEarlier DPVweb virus ID + beta12orEarlier + A unique identifier for a virus from the DPVweb database. @@ -20513,9 +20513,9 @@ Pathway ID (BioSystems) - [0-9]+ - Identifier of a pathway from the BioSystems pathway database. beta12orEarlier + Identifier of a pathway from the BioSystems pathway database. + [0-9]+ @@ -20528,10 +20528,10 @@ Experimental data (proteomics) - beta12orEarlier - beta12orEarlier - Data concerning a proteomics experiment. true + Data concerning a proteomics experiment. + beta12orEarlier + beta12orEarlier @@ -20543,8 +20543,8 @@ Abstract - An abstract of a scientific article. beta12orEarlier + An abstract of a scientific article. @@ -20556,8 +20556,8 @@ Lipid structure - 3D coordinate and associated data for a lipid structure. beta12orEarlier + 3D coordinate and associated data for a lipid structure. @@ -20569,8 +20569,8 @@ Drug structure - 3D coordinate and associated data for the (3D) structure of a drug. beta12orEarlier + 3D coordinate and associated data for the (3D) structure of a drug. @@ -20582,8 +20582,8 @@ Toxin structure - beta12orEarlier 3D coordinate and associated data for the (3D) structure of a toxin. + beta12orEarlier @@ -20596,9 +20596,9 @@ Position-specific scoring matrix - A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment. - PSSM beta12orEarlier + PSSM + A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment. @@ -20610,8 +20610,8 @@ Distance matrix - beta12orEarlier A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity. + beta12orEarlier @@ -20623,8 +20623,8 @@ Structural distance matrix - beta12orEarlier Distances (values representing similarity) between a group of molecular structures. + beta12orEarlier @@ -20636,10 +20636,10 @@ Article metadata - 1.5 - Bibliographic data concerning scientific article(s). - beta12orEarlier true + beta12orEarlier + Bibliographic data concerning scientific article(s). + 1.5 @@ -20651,9 +20651,9 @@ Ontology concept - A concept from a biological ontology. - This includes any fields from the concept definition such as concept name, definition, comments and so on. beta12orEarlier + This includes any fields from the concept definition such as concept name, definition, comments and so on. + A concept from a biological ontology. @@ -20665,8 +20665,8 @@ Codon usage bias - beta12orEarlier A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences. + beta12orEarlier @@ -20678,10 +20678,10 @@ Northern blot report - 1.8 - beta12orEarlier - true Topic concerning Northern Blot experiments. + true + beta12orEarlier + 1.8 @@ -20693,10 +20693,10 @@ Nucleic acid features report (VNTR) - Topic concerning variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. - true - beta12orEarlier 1.8 + beta12orEarlier + true + Topic concerning variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. @@ -20708,10 +20708,10 @@ Nucleic acid features report (microsatellite) - beta12orEarlier - 1.8 - Topic concerning microsatellite polymorphism in a DNA sequence. true + Topic concerning microsatellite polymorphism in a DNA sequence. + 1.8 + beta12orEarlier @@ -20724,10 +20724,10 @@ Nucleic acid features report (RFLP) - Topic concerning restriction fragment length polymorphisms (RFLP) in a DNA sequence. - 1.8 - true beta12orEarlier + true + 1.8 + Topic concerning restriction fragment length polymorphisms (RFLP) in a DNA sequence. @@ -20739,10 +20739,10 @@ Radiation hybrid map - RH map - beta12orEarlier - A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome. The radiation method can break very closely linked markers providing a more detailed map. Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map. + A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome. + beta12orEarlier + RH map @@ -20754,8 +20754,8 @@ ID list - beta12orEarlier A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data. + beta12orEarlier @@ -20767,8 +20767,8 @@ Phylogenetic gene frequencies data - Gene frequencies data that may be read during phylogenetic tree calculation. beta12orEarlier + Gene frequencies data that may be read during phylogenetic tree calculation. @@ -20780,10 +20780,10 @@ Sequence set (polymorphic) - A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata. - true - beta12orEarlier beta13 + beta12orEarlier + true + A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata. @@ -20795,10 +20795,10 @@ DRCAT resource - true - beta12orEarlier - An entry (resource) from the DRCAT bioinformatics resource catalogue. 1.5 + An entry (resource) from the DRCAT bioinformatics resource catalogue. + beta12orEarlier + true @@ -20810,8 +20810,8 @@ Protein complex - 3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another. beta12orEarlier + 3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another. @@ -20823,8 +20823,8 @@ Protein structural motif - 3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role. beta12orEarlier + 3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role. @@ -20836,8 +20836,8 @@ Lipid report - Annotation on or information derived from one or more specific lipid 3D structure(s). beta12orEarlier + Annotation on or information derived from one or more specific lipid 3D structure(s). @@ -20849,10 +20849,10 @@ Secondary structure image - true - Image of one or more molecular secondary structures. - beta12orEarlier 1.4 + beta12orEarlier + Image of one or more molecular secondary structures. + true @@ -20864,11 +20864,11 @@ Secondary structure report - 1.5 - An informative report on general information, properties or features of one or more molecular secondary structures. - true - beta12orEarlier Secondary structure-derived report + beta12orEarlier + true + An informative report on general information, properties or features of one or more molecular secondary structures. + 1.5 @@ -20880,10 +20880,10 @@ DNA features - beta12orEarlier - true - DNA sequence-specific feature annotation (not in a feature table). beta12orEarlier + DNA sequence-specific feature annotation (not in a feature table). + true + beta12orEarlier @@ -20895,12 +20895,12 @@ RNA features report - Nucleic acid features (RNA features) - RNA features - Features concerning RNA or regions of DNA that encode an RNA molecule. - 1.5 - beta12orEarlier true + beta12orEarlier + 1.5 + Features concerning RNA or regions of DNA that encode an RNA molecule. + RNA features + Nucleic acid features (RNA features) @@ -20912,10 +20912,10 @@ Plot - Biological data that has been plotted as a graph of some type. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Biological data that has been plotted as a graph of some type. @@ -20927,9 +20927,9 @@ Nucleic acid features report (polymorphism) - beta12orEarlier - Topic concerning DNA polymorphism. true + Topic concerning DNA polymorphism. + beta12orEarlier @@ -20942,10 +20942,10 @@ Protein sequence record - Sequence record (protein) - Protein sequence record - beta12orEarlier A protein sequence and associated metadata. + beta12orEarlier + Protein sequence record + Sequence record (protein) @@ -20958,12 +20958,12 @@ Nucleic acid sequence record - Sequence record (nucleic acid) - DNA sequence record - beta12orEarlier - A nucleic acid sequence and associated metadata. - Nucleotide sequence record RNA sequence record + Nucleotide sequence record + A nucleic acid sequence and associated metadata. + beta12orEarlier + DNA sequence record + Sequence record (nucleic acid) @@ -20975,10 +20975,10 @@ Protein sequence record (full) - true - beta12orEarlier - 1.8 A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. + 1.8 + beta12orEarlier + true @@ -20990,10 +20990,10 @@ Nucleic acid sequence record (full) - 1.8 - beta12orEarlier - A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. true + A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. + beta12orEarlier + 1.8 @@ -21006,8 +21006,8 @@ Biological model accession - Accession of a mathematical model, typically an entry from a database. beta12orEarlier + Accession of a mathematical model, typically an entry from a database. @@ -21021,8 +21021,8 @@ Cell type name - beta12orEarlier The name of a type or group of cells. + beta12orEarlier @@ -21036,8 +21036,8 @@ Cell type accession - Accession of a type or group of cells (catalogued in a database). beta12orEarlier + Accession of a type or group of cells (catalogued in a database). @@ -21051,10 +21051,10 @@ Compound accession - Chemical compound accession - beta12orEarlier - Accession of an entry from a database of chemicals. Small molecule accession + Accession of an entry from a database of chemicals. + beta12orEarlier + Chemical compound accession @@ -21068,8 +21068,8 @@ Drug accession - beta12orEarlier Accession of a drug. + beta12orEarlier @@ -21083,8 +21083,8 @@ Toxin name - beta12orEarlier Name of a toxin. + beta12orEarlier @@ -21098,8 +21098,8 @@ Toxin accession - Accession of a toxin (catalogued in a database). beta12orEarlier + Accession of a toxin (catalogued in a database). @@ -21113,8 +21113,8 @@ Monosaccharide accession - beta12orEarlier Accession of a monosaccharide (catalogued in a database). + beta12orEarlier @@ -21128,8 +21128,8 @@ Drug name - Common name of a drug. beta12orEarlier + Common name of a drug. @@ -21143,8 +21143,8 @@ Carbohydrate accession - beta12orEarlier Accession of an entry from a database of carbohydrates. + beta12orEarlier @@ -21158,8 +21158,8 @@ Molecule accession - beta12orEarlier Accession of a specific molecule (catalogued in a database). + beta12orEarlier @@ -21173,8 +21173,8 @@ Data resource definition accession - Accession of a data definition (catalogued in a database). beta12orEarlier + Accession of a data definition (catalogued in a database). @@ -21188,8 +21188,8 @@ Genome accession - beta12orEarlier An accession of a particular genome (in a database). + beta12orEarlier @@ -21203,8 +21203,8 @@ Map accession - beta12orEarlier An accession of a map of a molecular sequence (deposited in a database). + beta12orEarlier @@ -21218,8 +21218,8 @@ Lipid accession - Accession of an entry from a database of lipids. beta12orEarlier + Accession of an entry from a database of lipids. @@ -21233,8 +21233,8 @@ Peptide ID - Accession of a peptide deposited in a database. beta12orEarlier + Accession of a peptide deposited in a database. @@ -21248,9 +21248,9 @@ Protein accession - Accession of a protein deposited in a database. - beta12orEarlier Protein accessions + beta12orEarlier + Accession of a protein deposited in a database. @@ -21264,8 +21264,8 @@ Organism accession - beta12orEarlier An accession of annotation on a (group of) organisms (catalogued in a database). + beta12orEarlier @@ -21279,15 +21279,15 @@ Organism name - The name of an organism (or group of organisms). - Moby:OrganismsLongName - beta12orEarlier - Moby:InfraspecificEpithet - Moby:FirstEpithet - Moby:BriefOccurrenceRecord - Moby:OccurrenceRecord - Moby:OrganismsShortName Moby:Organism_Name + Moby:OrganismsShortName + Moby:OccurrenceRecord + Moby:BriefOccurrenceRecord + Moby:FirstEpithet + Moby:InfraspecificEpithet + beta12orEarlier + Moby:OrganismsLongName + The name of an organism (or group of organisms). @@ -21301,8 +21301,8 @@ Protein family accession - Accession of a protein family (that is deposited in a database). beta12orEarlier + Accession of a protein family (that is deposited in a database). @@ -21317,8 +21317,8 @@ - Accession of an entry from a database of transcription factors or binding sites. beta12orEarlier + Accession of an entry from a database of transcription factors or binding sites. @@ -21338,8 +21338,8 @@ - Identifier of a strain of an organism variant, typically a plant, virus or bacterium. beta12orEarlier + Identifier of a strain of an organism variant, typically a plant, virus or bacterium. @@ -21352,8 +21352,8 @@ Virus identifier - beta12orEarlier An accession of annotation on a (group of) viruses (catalogued in a database). + beta12orEarlier @@ -21366,8 +21366,8 @@ Sequence features metadata - Metadata on sequence features. beta12orEarlier + Metadata on sequence features. @@ -21379,8 +21379,8 @@ Gramene identifier - Identifier of a Gramene database entry. beta12orEarlier + Identifier of a Gramene database entry. @@ -21393,11 +21393,11 @@ DDBJ accession - An identifier of an entry from the DDBJ sequence database. - DDBJ ID - DDBJ identifier - DDBJ accession number beta12orEarlier + DDBJ accession number + DDBJ identifier + DDBJ ID + An identifier of an entry from the DDBJ sequence database. @@ -21410,8 +21410,8 @@ ConsensusPathDB identifier - An identifier of an entity from the ConsensusPathDB database. beta12orEarlier + An identifier of an entity from the ConsensusPathDB database. @@ -21424,11 +21424,11 @@ Sequence data - Data concerning, extracted from, or derived from the analysis of molecular sequence(s). - true - beta12orEarlier - 1.8 This is a broad data type and is used a placeholder for other, more specific types. + 1.8 + beta12orEarlier + true + Data concerning, extracted from, or derived from the analysis of molecular sequence(s). @@ -21440,11 +21440,11 @@ Codon usage - This is a broad data type and is used a placeholder for other, more specific types. - Data concerning codon usage. - beta13 - true beta12orEarlier + true + beta13 + Data concerning codon usage. + This is a broad data type and is used a placeholder for other, more specific types. @@ -21456,10 +21456,10 @@ Article report - true - Data derived from the analysis of a scientific text such as a full text article from a scientific journal. - 1.5 beta12orEarlier + 1.5 + Data derived from the analysis of a scientific text such as a full text article from a scientific journal. + true @@ -21471,9 +21471,9 @@ Sequence report - Sequence-derived report - beta12orEarlier An informative report of information about molecular sequence(s), including basic information (metadata), and reports generated from molecular sequence analysis, including positional features and non-positional properties. + beta12orEarlier + Sequence-derived report @@ -21485,8 +21485,8 @@ Protein secondary structure report - beta12orEarlier An informative report about the properties or features of one or more protein secondary structures. + beta12orEarlier @@ -21499,8 +21499,8 @@ Hopp and Woods plot - beta12orEarlier A Hopp and Woods plot of predicted antigenicity of a peptide or protein. + beta12orEarlier @@ -21513,9 +21513,9 @@ Nucleic acid melting curve - beta12orEarlier - A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA). Shows the proportion of nucleic acid which are double-stranded versus temperature. + A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA). + beta12orEarlier @@ -21527,9 +21527,9 @@ Nucleic acid probability profile - Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature - beta12orEarlier A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). + beta12orEarlier + Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature @@ -21541,10 +21541,10 @@ Nucleic acid temperature profile - Melting map - beta12orEarlier - Plots melting temperature versus base position. A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). + Plots melting temperature versus base position. + beta12orEarlier + Melting map @@ -21556,10 +21556,10 @@ Gene regulatory network report - beta12orEarlier - true - A report typically including a map (diagram) of a gene regulatory network. 1.8 + A report typically including a map (diagram) of a gene regulatory network. + true + beta12orEarlier @@ -21571,13 +21571,13 @@ 2D PAGE gel report - 2D PAGE image annotation - beta12orEarlier - 2D PAGE gel annotation - true - 1.8 - 2D PAGE image report An informative report on a two-dimensional (2D PAGE) gel. + 2D PAGE image report + 1.8 + true + 2D PAGE gel annotation + beta12orEarlier + 2D PAGE image annotation @@ -21589,8 +21589,8 @@ Oligonucleotide probe sets annotation - General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set. beta12orEarlier + General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set. @@ -21602,11 +21602,11 @@ Microarray image - true - An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data. - Gene expression image - beta12orEarlier 1.5 + beta12orEarlier + Gene expression image + An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data. + true @@ -21618,11 +21618,11 @@ Image - Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type. - beta12orEarlier - Image data - http://semanticscience.org/resource/SIO_000079 http://semanticscience.org/resource/SIO_000081 + Biological or biomedical data has been rendered into an image, typically for display on screen. + http://semanticscience.org/resource/SIO_000079 + Image data + beta12orEarlier @@ -21635,8 +21635,8 @@ Sequence image - beta12orEarlier Image of a molecular sequence, possibly with sequence features or properties shown. + beta12orEarlier @@ -21648,9 +21648,9 @@ Protein hydropathy data - beta12orEarlier - A report on protein properties concerning hydropathy. Protein hydropathy report + A report on protein properties concerning hydropathy. + beta12orEarlier @@ -21661,11 +21661,11 @@ Workflow data - - true - Data concerning a computational workflow. - beta13 + beta12orEarlier + beta13 + Data concerning a computational workflow. + true @@ -21677,10 +21677,10 @@ Workflow - A computational workflow. - 1.5 - beta12orEarlier true + beta12orEarlier + 1.5 + A computational workflow. @@ -21692,10 +21692,10 @@ Secondary structure data - Data concerning molecular secondary structure data. - beta12orEarlier - true beta13 + true + beta12orEarlier + Data concerning molecular secondary structure data. @@ -21708,10 +21708,10 @@ Protein sequence (raw) - A raw protein sequence (string of characters). - Raw sequence (protein) - beta12orEarlier Raw protein sequence + beta12orEarlier + Raw sequence (protein) + A raw protein sequence (string of characters). @@ -21724,11 +21724,11 @@ Nucleic acid sequence (raw) - A raw nucleic acid sequence. - Raw sequence (nucleic acid) - Nucleotide sequence (raw) - beta12orEarlier Nucleic acid raw sequence + beta12orEarlier + Nucleotide sequence (raw) + Raw sequence (nucleic acid) + A raw nucleic acid sequence. @@ -21740,10 +21740,10 @@ Protein sequence - http://purl.org/biotop/biotop.owl#AminoAcidSequenceInformation - beta12orEarlier - Protein sequences One or more protein sequences, possibly with associated annotation. + Protein sequences + beta12orEarlier + http://purl.org/biotop/biotop.owl#AminoAcidSequenceInformation @@ -21755,13 +21755,13 @@ Nucleic acid sequence - http://purl.org/biotop/biotop.owl#NucleotideSequenceInformation - Nucleic acid sequences - Nucleotide sequences - Nucleotide sequence - DNA sequence - beta12orEarlier One or more nucleic acid sequences, possibly with associated annotation. + beta12orEarlier + DNA sequence + Nucleotide sequence + Nucleotide sequences + Nucleic acid sequences + http://purl.org/biotop/biotop.owl#NucleotideSequenceInformation @@ -21773,11 +21773,11 @@ Reaction data - Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction. - Reaction annotation - beta12orEarlier - This is a broad data type and is used a placeholder for other, more specific types. Enzyme kinetics annotation + This is a broad data type and is used a placeholder for other, more specific types. + beta12orEarlier + Reaction annotation + Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction. @@ -21789,9 +21789,9 @@ Peptide property - Data concerning small peptides. - Peptide data beta12orEarlier + Peptide data + Data concerning small peptides. @@ -21803,10 +21803,10 @@ Protein classification - beta12orEarlier - An informative report concerning the classification of protein sequences or structures. - Protein classification data This is a broad data type and is used a placeholder for other, more specific types. + Protein classification data + An informative report concerning the classification of protein sequences or structures. + beta12orEarlier @@ -21817,11 +21817,11 @@ Sequence motif data - This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier - Data concerning specific or conserved pattern in molecular sequences. - 1.8 true + 1.8 + Data concerning specific or conserved pattern in molecular sequences. + beta12orEarlier + This is a broad data type and is used a placeholder for other, more specific types. @@ -21833,11 +21833,11 @@ Sequence profile data - Data concerning models representing a (typically multiple) sequence alignment. - beta13 - This is a broad data type and is used a placeholder for other, more specific types. - true beta12orEarlier + true + This is a broad data type and is used a placeholder for other, more specific types. + beta13 + Data concerning models representing a (typically multiple) sequence alignment. @@ -21849,10 +21849,10 @@ Pathway or network data - beta12orEarlier - true - beta13 Data concerning a specific biological pathway or network. + beta13 + true + beta12orEarlier @@ -21871,8 +21871,8 @@ - An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation. beta12orEarlier + An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation. @@ -21884,10 +21884,10 @@ Nucleic acid thermodynamic data - beta12orEarlier - Nucleic acid thermodynamic property - A thermodynamic or kinetic property of a nucleic acid molecule. Nucleic acid property (thermodynamic or kinetic) + A thermodynamic or kinetic property of a nucleic acid molecule. + Nucleic acid thermodynamic property + beta12orEarlier @@ -21899,10 +21899,10 @@ Nucleic acid classification - Nucleic acid classification data - Data concerning the classification of nucleic acid sequences or structures. - beta12orEarlier This is a broad data type and is used a placeholder for other, more specific types. + beta12orEarlier + Data concerning the classification of nucleic acid sequences or structures. + Nucleic acid classification data @@ -21913,12 +21913,12 @@ Classification report - 1.5 - A report on a classification of molecular sequences, structures or other entities. - Classification data - true - beta12orEarlier This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. + beta12orEarlier + true + Classification data + A report on a classification of molecular sequences, structures or other entities. + 1.5 @@ -21930,10 +21930,10 @@ Protein features report (key folding sites) - true - 1.8 - beta12orEarlier Topic concerning key residues involved in protein folding. + beta12orEarlier + 1.8 + true @@ -21945,9 +21945,9 @@ Protein torsion angle data - beta12orEarlier - Torsion angle data for a protein structure. Torsion angle data + Torsion angle data for a protein structure. + beta12orEarlier @@ -21960,9 +21960,9 @@ Protein structure image - Structure image (protein) - beta12orEarlier An image of protein structure. + beta12orEarlier + Structure image (protein) @@ -21974,8 +21974,8 @@ Phylogenetic character weights - beta12orEarlier Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted. + beta12orEarlier @@ -21987,13 +21987,13 @@ Annotation track - Sequence annotation track - Genome track - Genome-browser track - Genome annotation track - Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser. - Genomic track beta12orEarlier + Genomic track + Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser. + Genome annotation track + Genome-browser track + Genome track + Sequence annotation track @@ -22011,16 +22011,16 @@ - UniProt accession number - UniProtKB accession - Accession number of a UniProt (protein sequence) database entry. - TrEMBL entry accession - Swiss-Prot entry accession - [OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2} - UniProt entry accession - P43353|Q7M1G0|Q9C199|A5A6J6 - beta12orEarlier UniProtKB accession number + beta12orEarlier + P43353|Q7M1G0|Q9C199|A5A6J6 + UniProt entry accession + [OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2} + Swiss-Prot entry accession + TrEMBL entry accession + Accession number of a UniProt (protein sequence) database entry. + UniProtKB accession + UniProt accession number @@ -22034,10 +22034,10 @@ NCBI genetic code ID - beta12orEarlier - 16 - [1-9][0-9]? Identifier of a genetic code in the NCBI list of genetic codes. + [1-9][0-9]? + 16 + beta12orEarlier @@ -22056,8 +22056,8 @@ - beta12orEarlier Identifier of a concept in an ontology of biological or bioinformatics concepts and relations. + beta12orEarlier @@ -22070,10 +22070,10 @@ GO concept name (biological process) - beta12orEarlier - beta12orEarlier - The name of a concept for a biological process from the GO ontology. true + The name of a concept for a biological process from the GO ontology. + beta12orEarlier + beta12orEarlier @@ -22085,10 +22085,10 @@ GO concept name (molecular function) - beta12orEarlier - The name of a concept for a molecular function from the GO ontology. - beta12orEarlier true + beta12orEarlier + The name of a concept for a molecular function from the GO ontology. + beta12orEarlier @@ -22106,10 +22106,10 @@ - Taxonomic data - Data concerning the classification, identification and naming of organisms. - beta12orEarlier This is a broad data type and is used a placeholder for other, more specific types. + beta12orEarlier + Data concerning the classification, identification and naming of organisms. + Taxonomic data @@ -22121,9 +22121,9 @@ Protein ID (EMBL/GenBank/DDBJ) - This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein. - EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators. beta13 + EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators. + This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein. @@ -22136,11 +22136,11 @@ Core data - beta13 - true - 1.5 - A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation. Core data entities typically have a format and may be identified by an accession number. + A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation. + 1.5 + true + beta13 @@ -22158,8 +22158,8 @@ - Name or other identifier of molecular sequence feature(s). beta13 + Name or other identifier of molecular sequence feature(s). @@ -22178,8 +22178,8 @@ - An identifier of a molecular tertiary structure, typically an entry from a structure database. beta13 + An identifier of a molecular tertiary structure, typically an entry from a structure database. @@ -22198,8 +22198,8 @@ - beta13 An identifier of an array of numerical values, such as a comparison matrix. + beta13 @@ -22212,10 +22212,10 @@ Protein sequence composition - A report (typically a table) on character or word composition / frequency of protein sequence(s). - true - 1.8 beta13 + 1.8 + true + A report (typically a table) on character or word composition / frequency of protein sequence(s). @@ -22227,10 +22227,10 @@ Nucleic acid sequence composition (report) - beta13 - true - A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s). 1.8 + A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s). + true + beta13 @@ -22242,10 +22242,10 @@ Protein domain classification node - 1.5 - true - A node from a classification of protein structural domain(s). beta13 + A node from a classification of protein structural domain(s). + true + 1.5 @@ -22257,9 +22257,9 @@ CAS number - Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service. - CAS registry number beta13 + CAS registry number + Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service. @@ -22272,8 +22272,8 @@ ATC code - beta13 Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC). + beta13 @@ -22286,9 +22286,9 @@ UNII - Unique Ingredient Identifier - A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA). beta13 + A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA). + Unique Ingredient Identifier @@ -22301,10 +22301,10 @@ Geotemporal metadata - Basic information concerning geographical location or time. - true - beta13 1.5 + beta13 + true + Basic information concerning geographical location or time. @@ -22316,8 +22316,8 @@ System metadata - beta13 Metadata concerning the software, hardware or other aspects of a computer system. + beta13 @@ -22330,8 +22330,8 @@ Sequence feature name - beta13 A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. + beta13 @@ -22344,16 +22344,16 @@ Experimental measurement - Raw experimental data - Measurement data - Measurement metadata - Experimentally measured data - Measured data - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - Measurement - Experimental measurement data - Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware. beta13 + Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware. + Experimental measurement data + Measurement + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Measured data + Experimentally measured data + Measurement metadata + Measurement data + Raw experimental data @@ -22366,9 +22366,9 @@ Raw microarray data - Such data as found in Affymetrix CEL or GPR files. - Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment. beta13 + Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment. + Such data as found in Affymetrix CEL or GPR files. @@ -22386,12 +22386,12 @@ - Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip. - Gene expression report - beta13 - Microarray probe set data - Gene annotation (expression) Data generated from processing and analysis of probe set data from a microarray experiment. + Gene annotation (expression) + Microarray probe set data + beta13 + Gene expression report + Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip. @@ -22404,11 +22404,11 @@ Gene expression matrix - Gene expression data matrix - The final processed (normalised) data for a set of hybridisations in a microarray experiment. - Normalised microarray data - beta13 This combines data from all hybridisations. + beta13 + Normalised microarray data + The final processed (normalised) data for a set of hybridisations in a microarray experiment. + Gene expression data matrix @@ -22420,9 +22420,9 @@ Sample annotation - beta13 - This might include compound and dose in a dose response experiment. Annotation on a biological sample, for example experimental factors and their values. + This might include compound and dose in a dose response experiment. + beta13 @@ -22434,9 +22434,9 @@ Microarray metadata - beta13 - Annotation on the array itself used in a microarray experiment. This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc. + Annotation on the array itself used in a microarray experiment. + beta13 @@ -22448,11 +22448,11 @@ Microarray protocol annotation - Annotation on laboratory and/or data processing protocols used in an microarray experiment. - 1.8 - beta13 - This might describe e.g. the normalisation methods used to process the raw data. true + This might describe e.g. the normalisation methods used to process the raw data. + beta13 + 1.8 + Annotation on laboratory and/or data processing protocols used in an microarray experiment. @@ -22464,8 +22464,8 @@ Microarray hybridisation data - beta13 Data concerning the hybridisations measured during a microarray experiment. + beta13 @@ -22477,10 +22477,10 @@ Protein features report (topological domains) - true - Topic concerning topological domains such as cytoplasmic regions in a protein. - beta13 1.8 + beta13 + Topic concerning topological domains such as cytoplasmic regions in a protein. + true @@ -22492,10 +22492,10 @@ Sequence features (compositionally-biased regions) - A report of regions in a molecular sequence that are biased to certain characters. - true - beta13 1.5 + beta13 + true + A report of regions in a molecular sequence that are biased to certain characters. @@ -22507,10 +22507,10 @@ Nucleic acid features (difference and change) - true - 1.5 - A report on features in a nucleic acid sequence that indicate changes to or differences between sequences. beta13 + A report on features in a nucleic acid sequence that indicate changes to or differences between sequences. + 1.5 + true @@ -22522,10 +22522,10 @@ Nucleic acid features report (expression signal) - 1.8 - Topic concerning regions within a nucleic acid sequence containing a signal that alters a biological function. - beta13 true + beta13 + Topic concerning regions within a nucleic acid sequence containing a signal that alters a biological function. + 1.8 @@ -22537,11 +22537,11 @@ Nucleic acid features report (binding) - This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). - beta13 - true - Topic concerning nucleic acids binding to some other molecule. 1.8 + Topic concerning nucleic acids binding to some other molecule. + true + beta13 + This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). @@ -22553,10 +22553,10 @@ Nucleic acid repeats (report) - Topic concerning repetitive elements within a nucleic acid sequence. - beta13 - 1.8 true + 1.8 + beta13 + Topic concerning repetitive elements within a nucleic acid sequence. @@ -22568,10 +22568,10 @@ Nucleic acid features report (replication and recombination) - 1.8 - true - Topic concerning DNA replication or recombination. beta13 + Topic concerning DNA replication or recombination. + true + 1.8 @@ -22584,12 +22584,12 @@ Nucleic acid structure report - beta13 - Quadruplexes (report) - Nucleic acid features (structure) - d-loop (report) - Stem loop (report) A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures. + Stem loop (report) + d-loop (report) + Nucleic acid features (structure) + Quadruplexes (report) + beta13 @@ -22601,10 +22601,10 @@ Protein features report (repeats) - true - Topic concerning short repetitive subsequences (repeat sequences) in a protein sequence. - beta13 1.8 + beta13 + Topic concerning short repetitive subsequences (repeat sequences) in a protein sequence. + true @@ -22616,10 +22616,10 @@ Sequence motif matches (protein) - true - beta13 - 1.8 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences. + 1.8 + beta13 + true @@ -22631,10 +22631,10 @@ Sequence motif matches (nucleic acid) - 1.8 - true - beta13 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences. + beta13 + true + 1.8 @@ -22646,11 +22646,11 @@ Nucleic acid features (d-loop) - A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. - A report on displacement loops in a mitochondrial DNA sequence. - 1.5 - true beta13 + true + 1.5 + A report on displacement loops in a mitochondrial DNA sequence. + A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. @@ -22662,11 +22662,11 @@ Nucleic acid features (stem loop) - A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs. - 1.5 - A report on stem loops in a DNA sequence. - true beta13 + true + A report on stem loops in a DNA sequence. + 1.5 + A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs. @@ -22678,16 +22678,16 @@ Gene transcript report + This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). + Nucleic acid features (mRNA features) + beta13 + Transcript (report) + mRNA features + Gene transcript annotation + Clone or EST (report) + mRNA (report) An informative report on features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. This includes reports on a specific gene transcript, clone or EST. - mRNA (report) - Clone or EST (report) - Gene transcript annotation - mRNA features - Transcript (report) - beta13 - Nucleic acid features (mRNA features) - This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). @@ -22699,10 +22699,10 @@ Nucleic acid features report (signal or transit peptide) - beta13 - Topic concerning coding sequences for a signal or transit peptide. - 1.8 true + 1.8 + Topic concerning coding sequences for a signal or transit peptide. + beta13 @@ -22714,10 +22714,10 @@ Non-coding RNA - 1.8 - true - beta13 Topic concerning features of non-coding or functional RNA molecules, including tRNA and rRNA. + beta13 + true + 1.8 @@ -22729,11 +22729,11 @@ Transcriptional features (report) - beta13 - Features concerning transcription of DNA into RNA including the regulation of transcription. - This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. - true 1.5 + true + This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. + Features concerning transcription of DNA into RNA including the regulation of transcription. + beta13 @@ -22745,10 +22745,10 @@ Nucleic acid features report (STS) - beta13 - true - 1.8 Topic concerning sequence tagged sites (STS) in nucleic acid sequences. + 1.8 + true + beta13 @@ -22760,10 +22760,10 @@ Nucleic acid features (immunoglobulin gene structure) - A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments. - 1.5 - beta13 true + beta13 + 1.5 + A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments. @@ -22775,10 +22775,10 @@ SCOP class - Information on a 'class' node from the SCOP database. - true - beta13 1.5 + beta13 + true + Information on a 'class' node from the SCOP database. @@ -22790,10 +22790,10 @@ SCOP fold - true - 1.5 - Information on a 'fold' node from the SCOP database. beta13 + Information on a 'fold' node from the SCOP database. + 1.5 + true @@ -22805,10 +22805,10 @@ SCOP superfamily - true - 1.5 - Information on a 'superfamily' node from the SCOP database. beta13 + Information on a 'superfamily' node from the SCOP database. + 1.5 + true @@ -22820,10 +22820,10 @@ SCOP family - beta13 - Information on a 'family' node from the SCOP database. - true 1.5 + true + Information on a 'family' node from the SCOP database. + beta13 @@ -22835,10 +22835,10 @@ SCOP protein - 1.5 - beta13 - true Information on a 'protein' node from the SCOP database. + true + beta13 + 1.5 @@ -22850,10 +22850,10 @@ SCOP species - Information on a 'species' node from the SCOP database. - beta13 - true 1.5 + true + beta13 + Information on a 'species' node from the SCOP database. @@ -22865,10 +22865,10 @@ Mass spectrometry experiment - beta13 - true - Topic concerning mass spectrometry experiments. 1.8 + Topic concerning mass spectrometry experiments. + true + beta13 @@ -22880,15 +22880,15 @@ Gene family report - Gene homology (report) - Gene family annotation - Nucleic acid classification - Gene annotation (homology) - Homology information - Gene annotation (homology information) - beta13 - This includes reports on on gene homologues between species. An informative report on a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene, or any other classification of nucleic acid sequences or structures that reflects gene structure. + This includes reports on on gene homologues between species. + beta13 + Gene annotation (homology information) + Homology information + Gene annotation (homology) + Nucleic acid classification + Gene family annotation + Gene homology (report) @@ -22900,8 +22900,8 @@ Protein image - An image of a protein. beta13 + An image of a protein. @@ -22913,8 +22913,8 @@ Protein alignment - beta13 An alignment of protein sequences and/or structures. + beta13 @@ -22926,10 +22926,10 @@ NGS experiment - true - Topic concerning sequencing experiment, including samples, sampling, preparation, sequencing, and analysis. - 1.0 1.8 + 1.0 + Topic concerning sequencing experiment, including samples, sampling, preparation, sequencing, and analysis. + true @@ -22941,10 +22941,10 @@ Sequence assembly report - Assembly report - This might include an overall quality assement of the assembly and summary statistics including counts, average length and number of bases for reads, matches and non-matches, contigs, reads in pairs etc. - 1.1 An informative report about a DNA sequence assembly. + 1.1 + This might include an overall quality assement of the assembly and summary statistics including counts, average length and number of bases for reads, matches and non-matches, contigs, reads in pairs etc. + Assembly report @@ -22956,9 +22956,9 @@ Genome index - An index of a genome sequence. - Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. 1.1 + Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. + An index of a genome sequence. @@ -22970,11 +22970,11 @@ GWAS report - Genome-wide association study - true - Report concerning genome-wide association study experiments. - 1.1 1.8 + 1.1 + Report concerning genome-wide association study experiments. + true + Genome-wide association study @@ -22986,9 +22986,9 @@ Cytoband position - Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on. - The position of a cytogenetic band in a genome. 1.2 + The position of a cytogenetic band in a genome. + Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on. @@ -23001,11 +23001,11 @@ Cell type ontology ID - beta12orEarlier - 1.2 - CL_[0-9]{7} - Cell type ontology concept ID. CL ID + Cell type ontology concept ID. + CL_[0-9]{7} + 1.2 + beta12orEarlier @@ -23018,8 +23018,8 @@ Kinetic model - Mathematical model of a network, that contains biochemical kinetics. 1.2 + Mathematical model of a network, that contains biochemical kinetics. @@ -23031,12 +23031,12 @@ COSMIC ID - 1.3 - cosmic id - cosmic identifier - Identifier of a COSMIC database entry. - cosmic ID COSMIC identifier + cosmic ID + Identifier of a COSMIC database entry. + cosmic identifier + cosmic id + 1.3 @@ -23049,12 +23049,12 @@ HGMD ID - HGMD identifier - hgmd id - beta12orEarlier - hgmd identifier - hgmd ID Identifier of a HGMD database entry. + hgmd ID + hgmd identifier + beta12orEarlier + hgmd id + HGMD identifier @@ -23067,9 +23067,9 @@ Sequence assembly ID - 1.3 - Unique identifier of sequence assembly. Sequence assembly version + Unique identifier of sequence assembly. + 1.3 @@ -23082,10 +23082,10 @@ Sequence feature type - 1.5 - 1.3 - A label (text token) describing a type of sequence feature such as gene, transcript, cds, exon, repeat, simple, misc, variation, somatic variation, structural variation, somatic structural variation, constrained or regulatory. true + A label (text token) describing a type of sequence feature such as gene, transcript, cds, exon, repeat, simple, misc, variation, somatic variation, structural variation, somatic structural variation, constrained or regulatory. + 1.3 + 1.5 @@ -23097,10 +23097,10 @@ Gene homology (report) - 1.5 - An informative report on gene homologues between species. - true beta12orEarlier + true + An informative report on gene homologues between species. + 1.5 @@ -23113,10 +23113,10 @@ Ensembl gene tree ID - 1.3 - Unique identifier for a gene tree from the Ensembl database. - Ensembl ID (gene tree) ENSGT00390000003602 + Ensembl ID (gene tree) + Unique identifier for a gene tree from the Ensembl database. + 1.3 @@ -23129,8 +23129,8 @@ Gene tree - A phylogenetic tree that is an estimate of the character's phylogeny. 1.3 + A phylogenetic tree that is an estimate of the character's phylogeny. @@ -23142,8 +23142,8 @@ Species tree - 1.3 A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled. + 1.3 @@ -23162,9 +23162,9 @@ - Name or other identifier of an entry from a biosample database. - Sample accession 1.3 + Sample accession + Name or other identifier of an entry from a biosample database. @@ -23178,8 +23178,8 @@ MGI accession - 1.3 Identifier of an object from the MGI database. + 1.3 @@ -23193,10 +23193,10 @@ Phenotype name - Phenotype - Phenotypes - Name of a phenotype. 1.3 + Name of a phenotype. + Phenotypes + Phenotype @@ -23209,10 +23209,10 @@ Transition matrix - 1.4 - HMM transition matrix - Consider for example an HMM with two states (AT-rich and GC-rich). The transition matrix will hold the probabilities of switching from the AT-rich to the GC-rich state, and vica versa. A HMM transition matrix contains the probabilities of switching from one HMM state to another. + Consider for example an HMM with two states (AT-rich and GC-rich). The transition matrix will hold the probabilities of switching from the AT-rich to the GC-rich state, and vica versa. + HMM transition matrix + 1.4 @@ -23223,10 +23223,10 @@ Emission matrix - HMM emission matrix - Consider for example an HMM with two states (AT-rich and GC-rich). The emission matrix holds the probabilities of choosing each of the four nucleotides (A, C, G and T) in the AT-rich state and in the GC-rich state. - 1.4 A HMM emission matrix holds the probabilities of choosing the four nucleotides (A, C, G and T) in each of the states of a HMM. + 1.4 + Consider for example an HMM with two states (AT-rich and GC-rich). The emission matrix holds the probabilities of choosing each of the four nucleotides (A, C, G and T) in the AT-rich state and in the GC-rich state. + HMM emission matrix @@ -23237,8 +23237,8 @@ Hidden Markov model - 1.4 A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. + 1.4 @@ -23249,8 +23249,8 @@ Format identifier - 1.4 An identifier of a data format. + 1.4 @@ -23261,12 +23261,12 @@ Raw image - Raw biological or biomedical image generated by some experimental technique. - Image data - beta12orEarlier - http://semanticscience.org/resource/SIO_000081 - Amino acid data 1.5 + Amino acid data + http://semanticscience.org/resource/SIO_000081 + beta12orEarlier + Image data + Raw biological or biomedical image generated by some experimental technique. @@ -23278,9 +23278,9 @@ Carbohydrate property - 1.5 - Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all carbohydrates. Carbohydrate data + Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all carbohydrates. + 1.5 @@ -23292,10 +23292,10 @@ Proteomics experiment report - 1.5 - Report concerning proteomics experiments. - 1.8 true + 1.8 + Report concerning proteomics experiments. + 1.5 @@ -23307,10 +23307,10 @@ RNAi report - 1.8 - true - 1.5 Topic concerning RNAi experiments. + 1.5 + true + 1.8 @@ -23322,10 +23322,10 @@ Simulation experiment report - Topic concerning biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. - 1.8 - true 1.5 + true + 1.8 + Topic concerning biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. @@ -23343,15 +23343,15 @@ - An imaging technique that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body. - NMRI image - Magnetic resonance imaging image - + MRT image + 1.7 + Magnetic resonance tomography image Nuclear magnetic resonance imaging image - Magnetic resonance tomography image - 1.7 - MRT image + Magnetic resonance imaging image + + NMRI image + An imaging technique that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body. @@ -23369,8 +23369,8 @@ - An image from a cell migration track assay. 1.7 + An image from a cell migration track assay. @@ -23382,9 +23382,9 @@ Rate of association - Rate of association of a protein with another protein or some other molecule. - 1.7 kon + 1.7 + Rate of association of a protein with another protein or some other molecule. @@ -23396,9 +23396,9 @@ Gene order - 1.7 - Multiple gene identifiers in a specific order. Such data are often used for genome rearrangement tools and phylogenetic tree labeling. + Multiple gene identifiers in a specific order. + 1.7 @@ -23410,9 +23410,9 @@ Spectrum - Spectra - The spectrum of frequencies of electromagnetic radiation emitted from a molecule as a result of some spectroscopy experiment. 1.7 + The spectrum of frequencies of electromagnetic radiation emitted from a molecule as a result of some spectroscopy experiment. + Spectra @@ -23430,9 +23430,9 @@ - NMR spectra - 1.7 Spectral information for a molecule from a nuclear magnetic resonance experiment. + 1.7 + NMR spectra @@ -23444,10 +23444,10 @@ Chemical structure sketch - A sketch of a small molecule made with some specialised drawing package. - Small molecule sketch - 1.8 Chemical structure sketches are used for presentational purposes but also as inputs to various analysis software. + 1.8 + Small molecule sketch + A sketch of a small molecule made with some specialised drawing package. @@ -23459,8 +23459,8 @@ Nucleic acid signature - An informative report about a specific or conserved nucleic acid sequence pattern. 1.8 + An informative report about a specific or conserved nucleic acid sequence pattern. @@ -23472,9 +23472,9 @@ DNA sequence - A DNA sequence. - 1.8 DNA sequences + 1.8 + A DNA sequence. @@ -23486,10 +23486,10 @@ RNA sequence - 1.8 - RNA sequences - DNA sequences A DNA sequence. + DNA sequences + RNA sequences + 1.8 @@ -23502,10 +23502,10 @@ RNA sequence (raw) - RNA raw sequence - A raw RNA sequence. - 1.8 Raw sequence (RNA) + 1.8 + A raw RNA sequence. + RNA raw sequence @@ -23518,10 +23518,10 @@ DNA sequence (raw) - DNA raw sequence - 1.8 - A raw DNA sequence. Raw sequence (DNA) + A raw DNA sequence. + 1.8 + DNA raw sequence @@ -23539,10 +23539,10 @@ - Variations are stored along with a reference genome. - Gene sequence variations - Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects. 1.8 + Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects. + Gene sequence variations + Variations are stored along with a reference genome. @@ -23554,8 +23554,8 @@ Bibliography - A list of publications such as scientic papers or books. 1.8 + A list of publications such as scientic papers or books. @@ -23567,8 +23567,39 @@ Ontology mapping - beta12orEarlier A mapping of supplied textual terms or phrases to ontology concepts (URIs). + beta12orEarlier + + + + + + + + + + Image metadata + + Image-associated data + This can include basic provenance and technical information about the image, scientific annotation and so on. + Any data concerning a specific biological or biomedical image. + 1.9 + Image data + Image-related data + + + + + + + + + + Clinical trial report + + Clinical trial information + A report concerning a clinical trial. + 1.9 @@ -23581,14 +23612,14 @@ SMILES - beta12orEarlier Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation. - + beta12orEarlier + - + @@ -23599,8 +23630,8 @@ InChI - beta12orEarlier Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation. + beta12orEarlier @@ -23613,9 +23644,9 @@ mf - The general MF query format consists of a series of valid atomic symbols, with an optional number or range. - beta12orEarlier Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound. + beta12orEarlier + The general MF query format consists of a series of valid atomic symbols, with an optional number or range. @@ -23628,9 +23659,9 @@ inchikey - An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification. - beta12orEarlier The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound. + beta12orEarlier + An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification. @@ -23642,8 +23673,8 @@ smarts - beta12orEarlier SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation. + beta12orEarlier @@ -23656,8 +23687,8 @@ unambiguous pure - Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters. beta12orEarlier + Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters. @@ -23670,10 +23701,10 @@ nucleotide - Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters. - beta12orEarlier - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Nucleotide_sequence Non-sequence characters may be used for example for gaps. + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Nucleotide_sequence + beta12orEarlier + Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters. @@ -23686,10 +23717,10 @@ protein - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Amino_acid_sequence - Non-sequence characters may be used for gaps and translation stop. - beta12orEarlier Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters. + beta12orEarlier + Non-sequence characters may be used for gaps and translation stop. + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Amino_acid_sequence @@ -23702,8 +23733,8 @@ consensus - Alphabet for the consensus of two or more molecular sequences. beta12orEarlier + Alphabet for the consensus of two or more molecular sequences. @@ -23716,8 +23747,8 @@ pure nucleotide - Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters. beta12orEarlier + Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters. @@ -23730,8 +23761,8 @@ unambiguous pure nucleotide - Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters . beta12orEarlier + Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters . @@ -23743,9 +23774,9 @@ dna - Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters. - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#DNA_sequence beta12orEarlier + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#DNA_sequence + Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters. @@ -23757,9 +23788,9 @@ rna - beta12orEarlier - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#RNA_sequence Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters. + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#RNA_sequence + beta12orEarlier @@ -23772,8 +23803,8 @@ unambiguous pure dna - beta12orEarlier Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters. + beta12orEarlier @@ -23786,8 +23817,8 @@ pure dna - beta12orEarlier Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters. + beta12orEarlier @@ -23800,8 +23831,8 @@ unambiguous pure rna sequence - beta12orEarlier Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters. + beta12orEarlier @@ -23814,8 +23845,8 @@ pure rna - beta12orEarlier Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters. + beta12orEarlier @@ -23828,8 +23859,8 @@ unambiguous pure protein - Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters. beta12orEarlier + Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters. @@ -23842,8 +23873,8 @@ pure protein - Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters. beta12orEarlier + Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters. @@ -23855,11 +23886,11 @@ UniGene entry format - true - beta12orEarlier - A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. - Format of an entry from UniGene. beta12orEarlier + Format of an entry from UniGene. + A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. + beta12orEarlier + true @@ -23871,10 +23902,10 @@ COG sequence cluster format - Format of an entry from the COG database of clusters of (related) protein sequences. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Format of an entry from the COG database of clusters of (related) protein sequences. @@ -23887,9 +23918,9 @@ EMBL feature location - Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database. - Feature location beta12orEarlier + Feature location + Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database. @@ -23902,8 +23933,8 @@ quicktandem - beta12orEarlier Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program). + beta12orEarlier @@ -23916,8 +23947,8 @@ Sanger inverted repeats - Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program). beta12orEarlier + Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program). @@ -23930,8 +23961,8 @@ EMBOSS repeat - beta12orEarlier Report format for tandem repeats in a sequence (an EMBOSS report format). + beta12orEarlier @@ -23944,8 +23975,8 @@ est2genome format - Format of a report on exon-intron structure generated by EMBOSS est2genome. beta12orEarlier + Format of a report on exon-intron structure generated by EMBOSS est2genome. @@ -23958,8 +23989,8 @@ restrict format - beta12orEarlier Report format for restriction enzyme recognition sites used by EMBOSS restrict program. + beta12orEarlier @@ -23972,8 +24003,8 @@ restover format - Report format for restriction enzyme recognition sites used by EMBOSS restover program. beta12orEarlier + Report format for restriction enzyme recognition sites used by EMBOSS restover program. @@ -23986,8 +24017,8 @@ REBASE restriction sites - Report format for restriction enzyme recognition sites used by REBASE database. beta12orEarlier + Report format for restriction enzyme recognition sites used by REBASE database. @@ -24000,9 +24031,9 @@ FASTA search results format - This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.) - beta12orEarlier Format of results of a sequence database search using FASTA. + beta12orEarlier + This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.) @@ -24015,9 +24046,9 @@ BLAST results - This includes score data, alignment data and summary table. - beta12orEarlier Format of results of a sequence database search using some variant of BLAST. + beta12orEarlier + This includes score data, alignment data and summary table. @@ -24030,8 +24061,8 @@ mspcrunch - Format of results of a sequence database search using some variant of MSPCrunch. beta12orEarlier + Format of results of a sequence database search using some variant of MSPCrunch. @@ -24044,8 +24075,8 @@ Smith-Waterman format - Format of results of a sequence database search using some variant of Smith Waterman. beta12orEarlier + Format of results of a sequence database search using some variant of Smith Waterman. @@ -24058,9 +24089,9 @@ dhf - Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information. - beta12orEarlier The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. + beta12orEarlier + Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information. @@ -24073,9 +24104,9 @@ lhf - The hits are putative ligand-binding sequences and are found from a search of a sequence database. - Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information. beta12orEarlier + Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information. + The hits are putative ligand-binding sequences and are found from a search of a sequence database. @@ -24088,8 +24119,8 @@ InterPro hits format - beta12orEarlier Results format for searches of the InterPro database. + beta12orEarlier @@ -24101,9 +24132,9 @@ InterPro protein view report format - beta12orEarlier - The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group. Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries. + The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group. + beta12orEarlier @@ -24115,9 +24146,9 @@ InterPro match table format - The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated. - beta12orEarlier Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry. + beta12orEarlier + The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated. @@ -24130,8 +24161,8 @@ HMMER Dirichlet prior - Dirichlet distribution HMMER format. beta12orEarlier + Dirichlet distribution HMMER format. @@ -24144,8 +24175,8 @@ MEME Dirichlet prior - Dirichlet distribution MEME format. beta12orEarlier + Dirichlet distribution MEME format. @@ -24158,8 +24189,8 @@ HMMER emission and transition - beta12orEarlier Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model. + beta12orEarlier @@ -24172,8 +24203,8 @@ prosite-pattern - beta12orEarlier Format of a regular expression pattern from the Prosite database. + beta12orEarlier @@ -24186,8 +24217,8 @@ EMBOSS sequence pattern - beta12orEarlier Format of an EMBOSS sequence pattern. + beta12orEarlier @@ -24200,8 +24231,8 @@ meme-motif - beta12orEarlier A motif in the format generated by the MEME program. + beta12orEarlier @@ -24214,8 +24245,8 @@ prosite-profile - beta12orEarlier Sequence profile (sequence classifier) format used in the PROSITE database. + beta12orEarlier @@ -24228,8 +24259,8 @@ JASPAR format - A profile (sequence classifier) in the format used in the JASPAR database. beta12orEarlier + A profile (sequence classifier) in the format used in the JASPAR database. @@ -24242,8 +24273,8 @@ MEME background Markov model - beta12orEarlier Format of the model of random sequences used by MEME. + beta12orEarlier @@ -24256,8 +24287,8 @@ HMMER format - beta12orEarlier Format of a hidden Markov model representation used by the HMMER package. + beta12orEarlier @@ -24271,8 +24302,8 @@ - FASTA-style format for multiple sequences aligned by HMMER package to an HMM. beta12orEarlier + FASTA-style format for multiple sequences aligned by HMMER package to an HMM. @@ -24285,8 +24316,8 @@ DIALIGN format - beta12orEarlier Format of multiple sequences aligned by DIALIGN package. + beta12orEarlier @@ -24299,9 +24330,9 @@ daf - beta12orEarlier - EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family. The format is clustal-like and includes annotation of domain family classification information. + EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family. + beta12orEarlier @@ -24314,8 +24345,8 @@ Sequence-MEME profile alignment - Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package. beta12orEarlier + Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package. @@ -24328,8 +24359,8 @@ HMMER profile alignment (sequences versus HMMs) - beta12orEarlier Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database. + beta12orEarlier @@ -24342,8 +24373,8 @@ HMMER profile alignment (HMM versus sequences) - beta12orEarlier Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database. + beta12orEarlier @@ -24356,9 +24387,9 @@ Phylip distance matrix - Format of PHYLIP phylogenetic distance matrix data. - beta12orEarlier Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float). + beta12orEarlier + Format of PHYLIP phylogenetic distance matrix data. @@ -24371,8 +24402,8 @@ ClustalW dendrogram - Dendrogram (tree file) format generated by ClustalW. beta12orEarlier + Dendrogram (tree file) format generated by ClustalW. @@ -24385,8 +24416,8 @@ Phylip tree raw - beta12orEarlier Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted. + beta12orEarlier @@ -24399,8 +24430,8 @@ Phylip continuous quantitative characters - PHYLIP file format for continuous quantitative character data. beta12orEarlier + PHYLIP file format for continuous quantitative character data. @@ -24412,10 +24443,10 @@ Phylogenetic property values format - true - beta12orEarlier - beta12orEarlier Format of phylogenetic property data. + beta12orEarlier + beta12orEarlier + true @@ -24428,8 +24459,8 @@ Phylip character frequencies format - PHYLIP file format for phylogenetics character frequency data. beta12orEarlier + PHYLIP file format for phylogenetics character frequency data. @@ -24442,8 +24473,8 @@ Phylip discrete states format - beta12orEarlier Format of PHYLIP discrete states data. + beta12orEarlier @@ -24456,8 +24487,8 @@ Phylip cliques format - Format of PHYLIP cliques data. beta12orEarlier + Format of PHYLIP cliques data. @@ -24470,8 +24501,8 @@ Phylip tree format - beta12orEarlier Phylogenetic tree data format used by the PHYLIP program. + beta12orEarlier @@ -24484,8 +24515,8 @@ TreeBASE format - The format of an entry from the TreeBASE database of phylogenetic data. beta12orEarlier + The format of an entry from the TreeBASE database of phylogenetic data. @@ -24498,8 +24529,8 @@ TreeFam format - The format of an entry from the TreeFam database of phylogenetic data. beta12orEarlier + The format of an entry from the TreeFam database of phylogenetic data. @@ -24512,8 +24543,8 @@ Phylip tree distance format - beta12orEarlier Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package. + beta12orEarlier @@ -24526,9 +24557,9 @@ dssp - Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins). - The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format. beta12orEarlier + The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format. + Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins). @@ -24541,8 +24572,8 @@ hssp - beta12orEarlier Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins). + beta12orEarlier @@ -24555,10 +24586,10 @@ Dot-bracket format - Vienna RNA format - Vienna RNA secondary structure format - Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server. beta12orEarlier + Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server. + Vienna RNA secondary structure format + Vienna RNA format @@ -24571,8 +24602,8 @@ Vienna local RNA secondary structure format - beta12orEarlier Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server. + beta12orEarlier @@ -24590,9 +24621,9 @@ - Format of an entry (or part of an entry) from the PDB database. - PDB entry format beta12orEarlier + PDB entry format + Format of an entry (or part of an entry) from the PDB database. @@ -24605,9 +24636,9 @@ PDB - Entry format of PDB database in PDB format. - beta12orEarlier PDB format + beta12orEarlier + Entry format of PDB database in PDB format. @@ -24620,10 +24651,10 @@ mmCIF - mmcif - beta12orEarlier - Entry format of PDB database in mmCIF format. Chemical MIME (http://www.ch.ic.ac.uk/chemime): chemical/x-mmcif + Entry format of PDB database in mmCIF format. + beta12orEarlier + mmcif @@ -24636,8 +24667,8 @@ PDBML - beta12orEarlier Entry format of PDB database in PDBML (XML) format. + beta12orEarlier @@ -24649,10 +24680,10 @@ Domainatrix 3D-1D scoring matrix format - Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications. @@ -24664,8 +24695,8 @@ aaindex - beta12orEarlier Amino acid index format used by the AAindex database. + beta12orEarlier @@ -24677,11 +24708,11 @@ IntEnz enzyme report format - true - IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions. - Format of an entry from IntEnz (The Integrated Relational Enzyme Database). - beta12orEarlier beta12orEarlier + beta12orEarlier + Format of an entry from IntEnz (The Integrated Relational Enzyme Database). + IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions. + true @@ -24693,10 +24724,10 @@ BRENDA enzyme report format - beta12orEarlier - beta12orEarlier - Format of an entry from the BRENDA enzyme database. true + Format of an entry from the BRENDA enzyme database. + beta12orEarlier + beta12orEarlier @@ -24708,10 +24739,10 @@ KEGG REACTION enzyme report format - beta12orEarlier - Format of an entry from the KEGG REACTION database of biochemical reactions. - beta12orEarlier true + beta12orEarlier + Format of an entry from the KEGG REACTION database of biochemical reactions. + beta12orEarlier @@ -24723,10 +24754,10 @@ KEGG ENZYME enzyme report format - beta12orEarlier - Format of an entry from the KEGG ENZYME database. - true beta12orEarlier + true + Format of an entry from the KEGG ENZYME database. + beta12orEarlier @@ -24738,10 +24769,10 @@ REBASE proto enzyme report format - beta12orEarlier - beta12orEarlier - true Format of an entry from the proto section of the REBASE enzyme database. + true + beta12orEarlier + beta12orEarlier @@ -24753,10 +24784,10 @@ REBASE withrefm enzyme report format - Format of an entry from the withrefm section of the REBASE enzyme database. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Format of an entry from the withrefm section of the REBASE enzyme database. @@ -24769,9 +24800,9 @@ Pcons report format - Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality. - beta12orEarlier Format of output of the Pcons Model Quality Assessment Program (MQAP). + beta12orEarlier + Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality. @@ -24784,9 +24815,9 @@ ProQ report format - Format of output of the ProQ protein model quality predictor. - ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features. beta12orEarlier + ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features. + Format of output of the ProQ protein model quality predictor. @@ -24798,11 +24829,11 @@ SMART domain assignment report format - beta12orEarlier - The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues. - Format of SMART domain assignment data. - true beta12orEarlier + true + Format of SMART domain assignment data. + The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues. + beta12orEarlier @@ -24814,10 +24845,10 @@ BIND entry format - beta12orEarlier - true - beta12orEarlier Entry format for the BIND database of protein interaction. + beta12orEarlier + true + beta12orEarlier @@ -24829,10 +24860,10 @@ IntAct entry format - true - Entry format for the IntAct database of protein interaction. - beta12orEarlier beta12orEarlier + beta12orEarlier + Entry format for the IntAct database of protein interaction. + true @@ -24841,14 +24872,14 @@ - - InterPro entry format - - beta12orEarlier - This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry. - beta12orEarlier - true + + InterPro entry format + Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences. + true + beta12orEarlier + This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry. + beta12orEarlier @@ -24860,11 +24891,11 @@ InterPro entry abstract format - Entry format for the textual abstract of signatures in an InterPro entry and its protein matches. - beta12orEarlier - References are included and a functional inference is made where possible. - beta12orEarlier true + beta12orEarlier + References are included and a functional inference is made where possible. + beta12orEarlier + Entry format for the textual abstract of signatures in an InterPro entry and its protein matches. @@ -24876,10 +24907,10 @@ Gene3D entry format - beta12orEarlier - beta12orEarlier - true Entry format for the Gene3D protein secondary database. + true + beta12orEarlier + beta12orEarlier @@ -24891,10 +24922,10 @@ PIRSF entry format - beta12orEarlier - true - Entry format for the PIRSF protein secondary database. beta12orEarlier + Entry format for the PIRSF protein secondary database. + true + beta12orEarlier @@ -24906,10 +24937,10 @@ PRINTS entry format - Entry format for the PRINTS protein secondary database. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Entry format for the PRINTS protein secondary database. @@ -24921,10 +24952,10 @@ Panther Families and HMMs entry format - true - Entry format for the Panther library of protein families and subfamilies. - beta12orEarlier beta12orEarlier + beta12orEarlier + Entry format for the Panther library of protein families and subfamilies. + true @@ -24936,10 +24967,10 @@ Pfam entry format - beta12orEarlier - beta12orEarlier - true Entry format for the Pfam protein secondary database. + true + beta12orEarlier + beta12orEarlier @@ -24951,10 +24982,10 @@ SMART entry format - beta12orEarlier - Entry format for the SMART protein secondary database. - beta12orEarlier true + beta12orEarlier + Entry format for the SMART protein secondary database. + beta12orEarlier @@ -24966,10 +24997,10 @@ Superfamily entry format - true - beta12orEarlier - beta12orEarlier Entry format for the Superfamily protein secondary database. + beta12orEarlier + beta12orEarlier + true @@ -24981,10 +25012,10 @@ TIGRFam entry format - beta12orEarlier - Entry format for the TIGRFam protein secondary database. - true beta12orEarlier + true + Entry format for the TIGRFam protein secondary database. + beta12orEarlier @@ -24996,10 +25027,10 @@ ProDom entry format - true - beta12orEarlier - beta12orEarlier Entry format for the ProDom protein domain classification database. + beta12orEarlier + beta12orEarlier + true @@ -25011,10 +25042,10 @@ FSSP entry format - beta12orEarlier - true - beta12orEarlier Entry format for the FSSP database. + beta12orEarlier + true + beta12orEarlier @@ -25027,8 +25058,8 @@ findkm - A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax). beta12orEarlier + A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax). @@ -25040,10 +25071,10 @@ Ensembl gene report format - true - beta12orEarlier - Entry format of Ensembl genome database. beta12orEarlier + Entry format of Ensembl genome database. + beta12orEarlier + true @@ -25055,10 +25086,10 @@ DictyBase gene report format - beta12orEarlier - Entry format of DictyBase genome database. - beta12orEarlier true + beta12orEarlier + Entry format of DictyBase genome database. + beta12orEarlier @@ -25070,10 +25101,10 @@ CGD gene report format - Entry format of Candida Genome database. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Entry format of Candida Genome database. @@ -25085,10 +25116,10 @@ DragonDB gene report format - true - beta12orEarlier - Entry format of DragonDB genome database. beta12orEarlier + Entry format of DragonDB genome database. + beta12orEarlier + true @@ -25100,10 +25131,10 @@ EcoCyc gene report format - true - beta12orEarlier - beta12orEarlier Entry format of EcoCyc genome database. + beta12orEarlier + beta12orEarlier + true @@ -25115,10 +25146,10 @@ FlyBase gene report format - Entry format of FlyBase genome database. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + Entry format of FlyBase genome database. @@ -25130,10 +25161,10 @@ Gramene gene report format - true - Entry format of Gramene genome database. - beta12orEarlier beta12orEarlier + beta12orEarlier + Entry format of Gramene genome database. + true @@ -25145,10 +25176,10 @@ KEGG GENES gene report format - beta12orEarlier - Entry format of KEGG GENES genome database. - beta12orEarlier true + beta12orEarlier + Entry format of KEGG GENES genome database. + beta12orEarlier @@ -25160,10 +25191,10 @@ MaizeGDB gene report format - Entry format of the Maize genetics and genomics database (MaizeGDB). - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Entry format of the Maize genetics and genomics database (MaizeGDB). @@ -25175,10 +25206,10 @@ MGD gene report format - true - beta12orEarlier - beta12orEarlier Entry format of the Mouse Genome Database (MGD). + beta12orEarlier + beta12orEarlier + true @@ -25190,10 +25221,10 @@ RGD gene report format - beta12orEarlier - Entry format of the Rat Genome Database (RGD). - beta12orEarlier true + beta12orEarlier + Entry format of the Rat Genome Database (RGD). + beta12orEarlier @@ -25205,10 +25236,10 @@ SGD gene report format - Entry format of the Saccharomyces Genome Database (SGD). - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + Entry format of the Saccharomyces Genome Database (SGD). @@ -25220,10 +25251,10 @@ GeneDB gene report format - beta12orEarlier - beta12orEarlier - true Entry format of the Sanger GeneDB genome database. + true + beta12orEarlier + beta12orEarlier @@ -25235,10 +25266,10 @@ TAIR gene report format - true - Entry format of The Arabidopsis Information Resource (TAIR) genome database. - beta12orEarlier beta12orEarlier + beta12orEarlier + Entry format of The Arabidopsis Information Resource (TAIR) genome database. + true @@ -25250,10 +25281,10 @@ WormBase gene report format - true - beta12orEarlier - beta12orEarlier Entry format of the WormBase genomes database. + beta12orEarlier + beta12orEarlier + true @@ -25265,10 +25296,10 @@ ZFIN gene report format - Entry format of the Zebrafish Information Network (ZFIN) genome database. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Entry format of the Zebrafish Information Network (ZFIN) genome database. @@ -25280,10 +25311,10 @@ TIGR gene report format - beta12orEarlier - beta12orEarlier - Entry format of the TIGR genome database. true + Entry format of the TIGR genome database. + beta12orEarlier + beta12orEarlier @@ -25295,10 +25326,10 @@ dbSNP polymorphism report format - beta12orEarlier - true - Entry format for the dbSNP database. beta12orEarlier + Entry format for the dbSNP database. + true + beta12orEarlier @@ -25310,10 +25341,10 @@ OMIM entry format - Format of an entry from the OMIM database of genotypes and phenotypes. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Format of an entry from the OMIM database of genotypes and phenotypes. @@ -25325,10 +25356,10 @@ HGVbase entry format - beta12orEarlier - beta12orEarlier - Format of a record from the HGVbase database of genotypes and phenotypes. true + Format of a record from the HGVbase database of genotypes and phenotypes. + beta12orEarlier + beta12orEarlier @@ -25340,10 +25371,10 @@ HIVDB entry format - Format of a record from the HIVDB database of genotypes and phenotypes. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Format of a record from the HIVDB database of genotypes and phenotypes. @@ -25355,10 +25386,10 @@ KEGG DISEASE entry format - beta12orEarlier - true - Format of an entry from the KEGG DISEASE database. beta12orEarlier + Format of an entry from the KEGG DISEASE database. + true + beta12orEarlier @@ -25371,8 +25402,8 @@ Primer3 primer - beta12orEarlier Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program. + beta12orEarlier @@ -25385,8 +25416,8 @@ ABI - beta12orEarlier A format of raw sequence read data from an Applied Biosystems sequencing machine. + beta12orEarlier @@ -25399,8 +25430,8 @@ mira - beta12orEarlier Format of MIRA sequence trace information file. + beta12orEarlier @@ -25413,12 +25444,12 @@ CAF - beta12orEarlier Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata. + beta12orEarlier - + @@ -25429,8 +25460,8 @@ exp - beta12orEarlier Sequence assembly project file EXP format. + beta12orEarlier @@ -25443,12 +25474,12 @@ SCF - beta12orEarlier Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata. + beta12orEarlier - + @@ -25459,12 +25490,12 @@ PHD - PHD sequence trace format to store serialised chromatogram data (reads). beta12orEarlier + PHD sequence trace format to store serialised chromatogram data (reads). - + @@ -25481,9 +25512,9 @@ - Affymetrix image data file format - Format of Affymetrix data file of raw image data. beta12orEarlier + Format of Affymetrix data file of raw image data. + Affymetrix image data file format @@ -25502,9 +25533,9 @@ - Format of Affymetrix data file of information about (raw) expression levels of the individual probes. - Affymetrix probe raw data format beta12orEarlier + Affymetrix probe raw data format + Format of Affymetrix data file of information about (raw) expression levels of the individual probes. @@ -25517,8 +25548,8 @@ affymetrix - beta12orEarlier Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering. + beta12orEarlier @@ -25530,10 +25561,10 @@ ArrayExpress entry format - beta12orEarlier - Entry format for the ArrayExpress microarrays database. - true beta12orEarlier + true + Entry format for the ArrayExpress microarrays database. + beta12orEarlier @@ -25546,9 +25577,9 @@ affymetrix-exp - beta12orEarlier - Affymetrix experimental conditions data file format Affymetrix data file format for information about experimental conditions and protocols. + Affymetrix experimental conditions data file format + beta12orEarlier @@ -25567,9 +25598,9 @@ - Format of Affymetrix data file of information about (normalised) expression levels of the individual probes. - beta12orEarlier Affymetrix probe normalised data format + beta12orEarlier + Format of Affymetrix data file of information about (normalised) expression levels of the individual probes. @@ -25581,10 +25612,10 @@ EMDB entry format - beta12orEarlier - true - Format of an entry from the Electron Microscopy DataBase (EMDB). beta12orEarlier + Format of an entry from the Electron Microscopy DataBase (EMDB). + true + beta12orEarlier @@ -25596,10 +25627,10 @@ KEGG PATHWAY entry format - true - The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks. - beta12orEarlier beta12orEarlier + beta12orEarlier + The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks. + true @@ -25611,10 +25642,10 @@ MetaCyc entry format - beta12orEarlier - The format of an entry from the MetaCyc metabolic pathways database. - beta12orEarlier true + beta12orEarlier + The format of an entry from the MetaCyc metabolic pathways database. + beta12orEarlier @@ -25626,10 +25657,10 @@ HumanCyc entry format - beta12orEarlier - beta12orEarlier - true The format of a report from the HumanCyc metabolic pathways database. + true + beta12orEarlier + beta12orEarlier @@ -25641,10 +25672,10 @@ INOH entry format - beta12orEarlier - The format of an entry from the INOH signal transduction pathways database. - true beta12orEarlier + true + The format of an entry from the INOH signal transduction pathways database. + beta12orEarlier @@ -25656,10 +25687,10 @@ PATIKA entry format - true - beta12orEarlier - The format of an entry from the PATIKA biological pathways database. beta12orEarlier + The format of an entry from the PATIKA biological pathways database. + beta12orEarlier + true @@ -25671,10 +25702,10 @@ Reactome entry format - beta12orEarlier - true - The format of an entry from the reactome biological pathways database. beta12orEarlier + The format of an entry from the reactome biological pathways database. + true + beta12orEarlier @@ -25686,10 +25717,10 @@ aMAZE entry format - beta12orEarlier - The format of an entry from the aMAZE biological pathways and molecular interactions database. - true beta12orEarlier + true + The format of an entry from the aMAZE biological pathways and molecular interactions database. + beta12orEarlier @@ -25701,10 +25732,10 @@ CPDB entry format - beta12orEarlier - true - beta12orEarlier The format of an entry from the CPDB database. + beta12orEarlier + true + beta12orEarlier @@ -25716,10 +25747,10 @@ Panther Pathways entry format - The format of an entry from the Panther Pathways database. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + The format of an entry from the Panther Pathways database. @@ -25732,8 +25763,8 @@ Taverna workflow format - beta12orEarlier Format of Taverna workflows. + beta12orEarlier @@ -25745,11 +25776,11 @@ BioModel mathematical model format - Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. - true - Format of mathematical models from the BioModel database. - beta12orEarlier beta12orEarlier + beta12orEarlier + Format of mathematical models from the BioModel database. + true + Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. @@ -25761,10 +25792,10 @@ KEGG LIGAND entry format - true - beta12orEarlier - beta12orEarlier The format of an entry from the KEGG LIGAND chemical database. + beta12orEarlier + beta12orEarlier + true @@ -25776,10 +25807,10 @@ KEGG COMPOUND entry format - beta12orEarlier - true - The format of an entry from the KEGG COMPOUND database. beta12orEarlier + The format of an entry from the KEGG COMPOUND database. + true + beta12orEarlier @@ -25791,10 +25822,10 @@ KEGG PLANT entry format - true - The format of an entry from the KEGG PLANT database. - beta12orEarlier beta12orEarlier + beta12orEarlier + The format of an entry from the KEGG PLANT database. + true @@ -25806,10 +25837,10 @@ KEGG GLYCAN entry format - beta12orEarlier - The format of an entry from the KEGG GLYCAN database. - beta12orEarlier true + beta12orEarlier + The format of an entry from the KEGG GLYCAN database. + beta12orEarlier @@ -25821,10 +25852,10 @@ PubChem entry format - beta12orEarlier - true - The format of an entry from PubChem. beta12orEarlier + The format of an entry from PubChem. + true + beta12orEarlier @@ -25836,10 +25867,10 @@ ChemSpider entry format - true - beta12orEarlier - The format of an entry from a database of chemical structures and property predictions. beta12orEarlier + The format of an entry from a database of chemical structures and property predictions. + beta12orEarlier + true @@ -25851,11 +25882,11 @@ ChEBI entry format - ChEBI includes an ontological classification defining relations between entities or classes of entities. - true - The format of an entry from Chemical Entities of Biological Interest (ChEBI). - beta12orEarlier beta12orEarlier + beta12orEarlier + The format of an entry from Chemical Entities of Biological Interest (ChEBI). + true + ChEBI includes an ontological classification defining relations between entities or classes of entities. @@ -25867,10 +25898,10 @@ MSDchem ligand dictionary entry format - beta12orEarlier - true - beta12orEarlier The format of an entry from the MSDchem ligand dictionary. + beta12orEarlier + true + beta12orEarlier @@ -25883,8 +25914,8 @@ HET group dictionary entry format - beta12orEarlier The format of an entry from the HET group dictionary (HET groups from PDB files). + beta12orEarlier @@ -25896,10 +25927,10 @@ KEGG DRUG entry format - beta12orEarlier - beta12orEarlier - true The format of an entry from the KEGG DRUG database. + true + beta12orEarlier + beta12orEarlier @@ -25912,8 +25943,8 @@ PubMed citation - Format of bibliographic reference as used by the PubMed database. beta12orEarlier + Format of bibliographic reference as used by the PubMed database. @@ -25926,9 +25957,9 @@ Medline Display Format - Bibliographic reference information including citation information is included - Format for abstracts of scientific articles from the Medline database. beta12orEarlier + Format for abstracts of scientific articles from the Medline database. + Bibliographic reference information including citation information is included @@ -25941,8 +25972,8 @@ CiteXplore-core - CiteXplore 'core' citation format including title, journal, authors and abstract. beta12orEarlier + CiteXplore 'core' citation format including title, journal, authors and abstract. @@ -25955,8 +25986,8 @@ CiteXplore-all - beta12orEarlier CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references. + beta12orEarlier @@ -25969,8 +26000,8 @@ pmc - Article format of the PubMed Central database. beta12orEarlier + Article format of the PubMed Central database. @@ -25983,8 +26014,8 @@ iHOP text mining abstract format - iHOP abstract format. beta12orEarlier + iHOP abstract format. @@ -25997,9 +26028,9 @@ Oscar3 - beta12orEarlier - Text mining abstract format from the Oscar 3 application. Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document. + Text mining abstract format from the Oscar 3 application. + beta12orEarlier @@ -26011,10 +26042,10 @@ PDB atom record format - Format of an ATOM record (describing data for an individual atom) from a PDB file. - beta12orEarlier - beta13 true + beta13 + beta12orEarlier + Format of an ATOM record (describing data for an individual atom) from a PDB file. @@ -26026,11 +26057,11 @@ CATH chain report format - true - beta12orEarlier - Format of CATH domain classification information for a polypeptide chain. - beta12orEarlier The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain. + beta12orEarlier + Format of CATH domain classification information for a polypeptide chain. + beta12orEarlier + true @@ -26042,11 +26073,11 @@ CATH PDB report format - The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file. - Format of CATH domain classification information for a protein PDB file. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Format of CATH domain classification information for a protein PDB file. + The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file. @@ -26058,10 +26089,10 @@ NCBI gene report format - beta12orEarlier - beta12orEarlier - Entry (gene) format of the NCBI database. true + Entry (gene) format of the NCBI database. + beta12orEarlier + beta12orEarlier @@ -26073,12 +26104,12 @@ GeneIlluminator gene report format - true - Moby:GI_Gene - beta12orEarlier - beta12orEarlier - This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation. Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service. + This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation. + beta12orEarlier + beta12orEarlier + Moby:GI_Gene + true @@ -26090,11 +26121,11 @@ BacMap gene card format - Moby:BacMapGeneCard - beta12orEarlier - beta12orEarlier - true Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database. + true + beta12orEarlier + beta12orEarlier + Moby:BacMapGeneCard @@ -26106,11 +26137,11 @@ ColiCard report format - beta12orEarlier - Moby:ColiCard - beta12orEarlier - true Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB). + true + beta12orEarlier + Moby:ColiCard + beta12orEarlier @@ -26123,8 +26154,8 @@ PlasMapper TextMap - Map of a plasmid (circular DNA) in PlasMapper TextMap format. beta12orEarlier + Map of a plasmid (circular DNA) in PlasMapper TextMap format. @@ -26137,9 +26168,9 @@ newick - Phylogenetic tree Newick (text) format. - beta12orEarlier nh + beta12orEarlier + Phylogenetic tree Newick (text) format. @@ -26152,8 +26183,8 @@ TreeCon format - Phylogenetic tree TreeCon (text) format. beta12orEarlier + Phylogenetic tree TreeCon (text) format. @@ -26166,8 +26197,8 @@ Nexus format - beta12orEarlier Phylogenetic tree Nexus (text) format. + beta12orEarlier @@ -26181,41 +26212,41 @@ - http://www.onto-med.de/ontologies/gfo.owl#Perpetuant - The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data. - http://purl.org/biotop/biotop.owl#Quality - Data format - http://www.ifomis.org/bfo/1.1/snap#Quality - http://en.wikipedia.org/wiki/List_of_file_formats - A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. - http://wsio.org/compression_004 - "http://purl.org/dc/elements/1.1/format" - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality - http://www.ifomis.org/bfo/1.1/snap#Continuant - beta12orEarlier - http://semanticscience.org/resource/SIO_000618 - http://semanticscience.org/resource/SIO_000612 - "http://purl.obolibrary.org/obo/IAO_0000098" - Exchange format - http://www.onto-med.de/ontologies/gfo.owl#Symbol_structure - Data model - File format - http://purl.org/biotop/biotop.owl#MachineLanguage http://en.wikipedia.org/wiki/File_format + http://purl.org/biotop/biotop.owl#MachineLanguage + File format + Data model + http://www.onto-med.de/ontologies/gfo.owl#Symbol_structure + Exchange format + "http://purl.obolibrary.org/obo/IAO_0000098" + http://semanticscience.org/resource/SIO_000612 + http://semanticscience.org/resource/SIO_000618 + beta12orEarlier + http://www.ifomis.org/bfo/1.1/snap#Continuant + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality + "http://purl.org/dc/elements/1.1/format" + http://wsio.org/compression_004 + A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. + http://en.wikipedia.org/wiki/List_of_file_formats + http://www.ifomis.org/bfo/1.1/snap#Quality + Data format + http://purl.org/biotop/biotop.owl#Quality + The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data. + http://www.onto-med.de/ontologies/gfo.owl#Perpetuant - A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) - Data model + File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. + File format - + - File format - File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. + Data model + A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) - + @@ -26225,10 +26256,10 @@ Atomic data format - true - Data format for an individual atom. - beta13 beta12orEarlier + beta13 + Data format for an individual atom. + true @@ -26246,8 +26277,8 @@ - beta12orEarlier Data format for a molecular sequence record. + beta12orEarlier @@ -26265,8 +26296,8 @@ - Data format for molecular sequence feature information. beta12orEarlier + Data format for molecular sequence feature information. @@ -26284,8 +26315,8 @@ - beta12orEarlier Data format for molecular sequence alignment information. + beta12orEarlier @@ -26297,8 +26328,8 @@ acedb - ACEDB sequence format. beta12orEarlier + ACEDB sequence format. @@ -26310,10 +26341,10 @@ clustal sequence format - beta12orEarlier - Clustalw output format. - beta12orEarlier true + beta12orEarlier + Clustalw output format. + beta12orEarlier @@ -26326,8 +26357,8 @@ codata - beta12orEarlier Codata entry format. + beta12orEarlier @@ -26339,8 +26370,8 @@ dbid - Fasta format variant with database name before ID. beta12orEarlier + Fasta format variant with database name before ID. @@ -26353,10 +26384,10 @@ EMBL format - beta12orEarlier - EMBL - EMBL sequence format EMBL entry format. + EMBL sequence format + EMBL + beta12orEarlier @@ -26369,8 +26400,8 @@ Staden experiment format - beta12orEarlier Staden experiment file format. + beta12orEarlier @@ -26383,10 +26414,10 @@ FASTA - FASTA format including NCBI-style IDs. - FASTA sequence format - FASTA format beta12orEarlier + FASTA format + FASTA sequence format + FASTA format including NCBI-style IDs. @@ -26398,9 +26429,10 @@ FASTQ - FASTAQ - beta12orEarlier FASTQ short read format ignoring quality scores. + beta12orEarlier + FASTAQ + fq @@ -26412,8 +26444,8 @@ FASTQ-illumina - beta12orEarlier FASTQ Illumina 1.3 short read format. + beta12orEarlier @@ -26425,8 +26457,8 @@ FASTQ-sanger - beta12orEarlier FASTQ short read format with phred quality. + beta12orEarlier @@ -26438,8 +26470,8 @@ FASTQ-solexa - beta12orEarlier FASTQ Solexa/Illumina 1.0 short read format. + beta12orEarlier @@ -26452,8 +26484,8 @@ fitch program - beta12orEarlier Fitch program format. + beta12orEarlier @@ -26466,10 +26498,10 @@ GCG - GCG sequence file format. - GCG SSF (single sequence file) file format. - beta12orEarlier GCG SSF + beta12orEarlier + GCG SSF (single sequence file) file format. + GCG sequence file format. @@ -26482,8 +26514,8 @@ GenBank format - Genbank entry format. beta12orEarlier + Genbank entry format. @@ -26495,9 +26527,9 @@ genpept - Currently identical to refseqp format - Genpept protein entry format. beta12orEarlier + Genpept protein entry format. + Currently identical to refseqp format @@ -26510,8 +26542,8 @@ GFF2-seq - beta12orEarlier GFF feature file format with sequence in the header. + beta12orEarlier @@ -26524,8 +26556,8 @@ GFF3-seq - beta12orEarlier GFF3 feature file format with sequence. + beta12orEarlier @@ -26537,8 +26569,8 @@ giFASTA format - beta12orEarlier FASTA sequence format including NCBI-style GIs. + beta12orEarlier @@ -26551,8 +26583,8 @@ hennig86 - Hennig86 output sequence format. beta12orEarlier + Hennig86 output sequence format. @@ -26565,8 +26597,8 @@ ig - beta12orEarlier Intelligenetics sequence format. + beta12orEarlier @@ -26579,8 +26611,8 @@ igstrict - Intelligenetics sequence format (strict version). beta12orEarlier + Intelligenetics sequence format (strict version). @@ -26593,8 +26625,8 @@ jackknifer - beta12orEarlier Jackknifer interleaved and non-interleaved sequence format. + beta12orEarlier @@ -26607,8 +26639,8 @@ mase format - Mase program sequence format. beta12orEarlier + Mase program sequence format. @@ -26621,8 +26653,8 @@ mega-seq - Mega interleaved and non-interleaved sequence format. beta12orEarlier + Mega interleaved and non-interleaved sequence format. @@ -26634,9 +26666,9 @@ MSF - GCG MSF (multiple sequence file) file format. - beta12orEarlier GCG MSF + beta12orEarlier + GCG MSF (multiple sequence file) file format. @@ -26648,10 +26680,10 @@ nbrf/pir - pir - beta12orEarlier - nbrf NBRF/PIR entry sequence format. + nbrf + beta12orEarlier + pir @@ -26665,8 +26697,8 @@ - Nexus/paup interleaved sequence format. beta12orEarlier + Nexus/paup interleaved sequence format. @@ -26680,9 +26712,9 @@ - PDB sequence format (ATOM lines). - beta12orEarlier pdb format in EMBOSS. + beta12orEarlier + PDB sequence format (ATOM lines). @@ -26696,9 +26728,9 @@ - PDB nucleotide sequence format (ATOM lines). - pdbnuc format in EMBOSS. beta12orEarlier + pdbnuc format in EMBOSS. + PDB nucleotide sequence format (ATOM lines). @@ -26712,9 +26744,9 @@ - beta12orEarlier - PDB nucleotide sequence format (SEQRES lines). pdbnucseq format in EMBOSS. + PDB nucleotide sequence format (SEQRES lines). + beta12orEarlier @@ -26728,9 +26760,9 @@ - pdbseq format in EMBOSS. - beta12orEarlier PDB sequence format (SEQRES lines). + beta12orEarlier + pdbseq format in EMBOSS. @@ -26742,8 +26774,8 @@ Pearson format - Plain old FASTA sequence format (unspecified format for IDs). beta12orEarlier + Plain old FASTA sequence format (unspecified format for IDs). @@ -26755,10 +26787,10 @@ phylip sequence format - beta12orEarlier - true - Phylip interleaved sequence format. beta12orEarlier + Phylip interleaved sequence format. + true + beta12orEarlier @@ -26770,10 +26802,10 @@ phylipnon sequence format - beta12orEarlier - beta12orEarlier - Phylip non-interleaved sequence format. true + Phylip non-interleaved sequence format. + beta12orEarlier + beta12orEarlier @@ -26786,8 +26818,8 @@ raw - Raw sequence format with no non-sequence characters. beta12orEarlier + Raw sequence format with no non-sequence characters. @@ -26800,9 +26832,9 @@ refseqp - Currently identical to genpept format - Refseq protein entry sequence format. beta12orEarlier + Refseq protein entry sequence format. + Currently identical to genpept format @@ -26814,10 +26846,10 @@ selex sequence format - Selex sequence format. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Selex sequence format. @@ -26830,14 +26862,14 @@ Staden format - Staden suite sequence format. beta12orEarlier + Staden suite sequence format. - - + + @@ -26848,10 +26880,10 @@ Stockholm format - beta12orEarlier Stockholm multiple sequence alignment format (used by Pfam and Rfam). - + beta12orEarlier + @@ -26864,8 +26896,8 @@ strider format - beta12orEarlier DNA strider output sequence format. + beta12orEarlier @@ -26877,10 +26909,10 @@ UniProtKB format - UniProtKB entry sequence format. - beta12orEarlier - SwissProt format UniProt format + SwissProt format + beta12orEarlier + UniProtKB entry sequence format. @@ -26893,8 +26925,8 @@ plain text format (unformatted) - Plain text sequence format (essentially unformatted). beta12orEarlier + Plain text sequence format (essentially unformatted). @@ -26906,10 +26938,10 @@ treecon sequence format - Treecon output sequence format. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + Treecon output sequence format. @@ -26922,8 +26954,8 @@ ASN.1 sequence format - beta12orEarlier NCBI ASN.1-based sequence format. + beta12orEarlier @@ -26936,9 +26968,9 @@ DAS format - beta12orEarlier - DAS sequence (XML) format (any type). das sequence format + DAS sequence (XML) format (any type). + beta12orEarlier @@ -26951,9 +26983,9 @@ dasdna - The use of this format is deprecated. - DAS sequence (XML) format (nucleotide-only). beta12orEarlier + DAS sequence (XML) format (nucleotide-only). + The use of this format is deprecated. @@ -26966,8 +26998,8 @@ debug-seq - beta12orEarlier EMBOSS debugging trace sequence format of full internal data content. + beta12orEarlier @@ -26980,8 +27012,8 @@ jackknifernon - Jackknifer output sequence non-interleaved format. beta12orEarlier + Jackknifer output sequence non-interleaved format. @@ -26993,10 +27025,10 @@ meganon sequence format - true - Mega non-interleaved output sequence format. - beta12orEarlier beta12orEarlier + beta12orEarlier + Mega non-interleaved output sequence format. + true @@ -27008,9 +27040,9 @@ NCBI format - There are several variants of this. - beta12orEarlier NCBI FASTA sequence format with NCBI-style IDs. + beta12orEarlier + There are several variants of this. @@ -27024,8 +27056,8 @@ - beta12orEarlier Nexus/paup non-interleaved sequence format. + beta12orEarlier @@ -27037,12 +27069,12 @@ GFF2 - General Feature Format (GFF) of sequence features. beta12orEarlier + General Feature Format (GFF) of sequence features. - + @@ -27052,12 +27084,12 @@ GFF3 - Generic Feature Format version 3 (GFF3) of sequence features. beta12orEarlier + Generic Feature Format version 3 (GFF3) of sequence features. - + @@ -27067,10 +27099,10 @@ pir - beta12orEarlier - PIR feature format. - 1.7 true + 1.7 + PIR feature format. + beta12orEarlier @@ -27082,10 +27114,10 @@ swiss feature - beta12orEarlier - beta12orEarlier - Swiss-Prot feature format. true + Swiss-Prot feature format. + beta12orEarlier + beta12orEarlier @@ -27098,10 +27130,10 @@ DASGFF - beta12orEarlier - DASGFF feature - das feature DAS GFF (XML) feature format. + das feature + DASGFF feature + beta12orEarlier @@ -27114,8 +27146,8 @@ debug-feat - beta12orEarlier EMBOSS debugging trace feature format of full internal data content. + beta12orEarlier @@ -27127,10 +27159,10 @@ EMBL feature - beta12orEarlier - true - EMBL feature format. beta12orEarlier + EMBL feature format. + true + beta12orEarlier @@ -27142,10 +27174,10 @@ GenBank feature - true - beta12orEarlier - Genbank feature format. beta12orEarlier + Genbank feature format. + beta12orEarlier + true @@ -27158,9 +27190,9 @@ ClustalW format - ClustalW format for (aligned) sequences. - beta12orEarlier clustal + beta12orEarlier + ClustalW format for (aligned) sequences. @@ -27173,8 +27205,8 @@ debug - beta12orEarlier EMBOSS alignment format for debugging trace of full internal data content. + beta12orEarlier @@ -27187,8 +27219,8 @@ FASTA-aln - Fasta format for (aligned) sequences. beta12orEarlier + Fasta format for (aligned) sequences. @@ -27200,8 +27232,8 @@ markx0 - Pearson MARKX0 alignment format. beta12orEarlier + Pearson MARKX0 alignment format. @@ -27213,8 +27245,8 @@ markx1 - beta12orEarlier Pearson MARKX1 alignment format. + beta12orEarlier @@ -27226,8 +27258,8 @@ markx10 - Pearson MARKX10 alignment format. beta12orEarlier + Pearson MARKX10 alignment format. @@ -27239,8 +27271,8 @@ markx2 - Pearson MARKX2 alignment format. beta12orEarlier + Pearson MARKX2 alignment format. @@ -27252,8 +27284,8 @@ markx3 - Pearson MARKX3 alignment format. beta12orEarlier + Pearson MARKX3 alignment format. @@ -27266,8 +27298,8 @@ match - beta12orEarlier Alignment format for start and end of matches between sequence pairs. + beta12orEarlier @@ -27279,8 +27311,8 @@ mega - beta12orEarlier Mega format for (typically aligned) sequences. + beta12orEarlier @@ -27292,8 +27324,8 @@ meganon - beta12orEarlier Mega non-interleaved format for (typically aligned) sequences. + beta12orEarlier @@ -27305,10 +27337,10 @@ msf alignment format - MSF format for (aligned) sequences. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + MSF format for (aligned) sequences. @@ -27320,10 +27352,10 @@ nexus alignment format - true - beta12orEarlier - beta12orEarlier Nexus/paup format for (aligned) sequences. + beta12orEarlier + beta12orEarlier + true @@ -27335,10 +27367,10 @@ nexusnon alignment format - beta12orEarlier - Nexus/paup non-interleaved format for (aligned) sequences. - true beta12orEarlier + true + Nexus/paup non-interleaved format for (aligned) sequences. + beta12orEarlier @@ -27350,8 +27382,8 @@ pair - beta12orEarlier EMBOSS simple sequence pair alignment format. + beta12orEarlier @@ -27363,12 +27395,12 @@ PHYLIP format - Phylip format for (aligned) sequences. - PHYLIP interleaved format - http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format - ph - beta12orEarlier phy + beta12orEarlier + ph + http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format + PHYLIP interleaved format + Phylip format for (aligned) sequences. @@ -27380,10 +27412,10 @@ phylipnon - Phylip non-interleaved format for (aligned) sequences. - PHYLIP sequential format - beta12orEarlier http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format + beta12orEarlier + PHYLIP sequential format + Phylip non-interleaved format for (aligned) sequences. @@ -27396,8 +27428,8 @@ scores format - beta12orEarlier Alignment format for score values for pairs of sequences. + beta12orEarlier @@ -27411,8 +27443,8 @@ - SELEX format for (aligned) sequences. beta12orEarlier + SELEX format for (aligned) sequences. @@ -27425,8 +27457,8 @@ EMBOSS simple format - beta12orEarlier EMBOSS simple multiple alignment format. + beta12orEarlier @@ -27439,8 +27471,8 @@ srs format - Simple multiple sequence (alignment) format for SRS. beta12orEarlier + Simple multiple sequence (alignment) format for SRS. @@ -27453,8 +27485,8 @@ srspair - Simple sequence pair (alignment) format for SRS. beta12orEarlier + Simple sequence pair (alignment) format for SRS. @@ -27467,8 +27499,8 @@ T-Coffee format - beta12orEarlier T-Coffee program alignment format. + beta12orEarlier @@ -27482,8 +27514,8 @@ - beta12orEarlier Treecon format for (aligned) sequences. + beta12orEarlier @@ -27501,8 +27533,8 @@ - beta12orEarlier Data format for a phylogenetic tree. + beta12orEarlier @@ -27520,8 +27552,8 @@ - Data format for a biological pathway or network. beta12orEarlier + Data format for a biological pathway or network. @@ -27539,8 +27571,8 @@ - Data format for a sequence-profile alignment. beta12orEarlier + Data format for a sequence-profile alignment. @@ -27552,10 +27584,10 @@ Sequence-profile alignment (HMM) format - Data format for a sequence-HMM profile alignment. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Data format for a sequence-HMM profile alignment. @@ -27573,8 +27605,8 @@ - beta12orEarlier Data format for an amino acid index. + beta12orEarlier @@ -27592,9 +27624,9 @@ - Data format for a full-text scientific article. - Literature format beta12orEarlier + Literature format + Data format for a full-text scientific article. @@ -27612,8 +27644,8 @@ - Data format for an abstract (report) from text mining. beta12orEarlier + Data format for an abstract (report) from text mining. @@ -27631,8 +27663,8 @@ - beta12orEarlier Data format for reports on enzyme kinetics. + beta12orEarlier @@ -27650,9 +27682,9 @@ - Format of a report on a chemical compound. - Chemical compound annotation format beta12orEarlier + Chemical compound annotation format + Format of a report on a chemical compound. @@ -27670,8 +27702,8 @@ - beta12orEarlier Format of a report on a particular locus, gene, gene system or groups of genes. + beta12orEarlier @@ -27683,8 +27715,8 @@ Workflow format - Format of a workflow. beta12orEarlier + Format of a workflow. @@ -27696,8 +27728,8 @@ Tertiary structure format - Data format for a molecular tertiary structure. beta12orEarlier + Data format for a molecular tertiary structure. @@ -27709,10 +27741,10 @@ Biological model format - true - 1.2 - beta12orEarlier Data format for a biological model. + beta12orEarlier + 1.2 + true @@ -27730,8 +27762,8 @@ - Text format of a chemical formula. beta12orEarlier + Text format of a chemical formula. @@ -27749,8 +27781,8 @@ - Format of raw (unplotted) phylogenetic data. beta12orEarlier + Format of raw (unplotted) phylogenetic data. @@ -27768,8 +27800,8 @@ - beta12orEarlier Format of phylogenetic continuous quantitative character data. + beta12orEarlier @@ -27787,8 +27819,8 @@ - beta12orEarlier Format of phylogenetic discrete states data. + beta12orEarlier @@ -27806,8 +27838,8 @@ - beta12orEarlier Format of phylogenetic cliques data. + beta12orEarlier @@ -27825,8 +27857,8 @@ - Format of phylogenetic invariants data. beta12orEarlier + Format of phylogenetic invariants data. @@ -27838,10 +27870,10 @@ Electron microscopy model format - Annotation format for electron microscopy models. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Annotation format for electron microscopy models. @@ -27859,8 +27891,8 @@ - beta12orEarlier Format for phylogenetic tree distance data. + beta12orEarlier @@ -27872,10 +27904,10 @@ Polymorphism report format - Format for sequence polymorphism data. - 1.0 - true beta12orEarlier + true + 1.0 + Format for sequence polymorphism data. @@ -27892,8 +27924,8 @@ - Format for reports on a protein family. beta12orEarlier + Format for reports on a protein family. @@ -27911,9 +27943,9 @@ - Molecular interaction format - Format for molecular interaction data. beta12orEarlier + Format for molecular interaction data. + Molecular interaction format @@ -27931,8 +27963,8 @@ - Format for sequence assembly data. beta12orEarlier + Format for sequence assembly data. @@ -27944,8 +27976,8 @@ Microarray experiment data format - Format for microarray experimental data. beta12orEarlier + Format for microarray experimental data. @@ -27963,8 +27995,8 @@ - beta12orEarlier Format for sequence trace data (i.e. including base call information). + beta12orEarlier @@ -27982,8 +28014,8 @@ - beta12orEarlier Format for a report on gene expression. + beta12orEarlier @@ -27995,10 +28027,10 @@ Genotype and phenotype annotation format - beta12orEarlier - Format of a report on genotype / phenotype information. - true beta12orEarlier + true + Format of a report on genotype / phenotype information. + beta12orEarlier @@ -28016,8 +28048,8 @@ - beta12orEarlier Format of a map of (typically one) molecular sequence annotated with features. + beta12orEarlier @@ -28029,8 +28061,8 @@ Nucleic acid features (primers) format - Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence. beta12orEarlier + Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence. @@ -28048,8 +28080,8 @@ - beta12orEarlier Format of a report of general information about a specific protein. + beta12orEarlier @@ -28061,10 +28093,10 @@ Protein report (enzyme) format - beta12orEarlier - true - beta12orEarlier Format of a report of general information about a specific enzyme. + beta12orEarlier + true + beta12orEarlier @@ -28082,8 +28114,8 @@ - Format of a matrix of 3D-1D scores (amino acid environment probabilities). beta12orEarlier + Format of a matrix of 3D-1D scores (amino acid environment probabilities). @@ -28101,8 +28133,8 @@ - beta12orEarlier Format of a report on the quality of a protein three-dimensional model. + beta12orEarlier @@ -28120,8 +28152,8 @@ - beta12orEarlier Format of a report on sequence hits and associated data from searching a sequence database. + beta12orEarlier @@ -28139,8 +28171,8 @@ - Format of a matrix of genetic distances between molecular sequences. beta12orEarlier + Format of a matrix of genetic distances between molecular sequences. @@ -28158,8 +28190,8 @@ - beta12orEarlier Format of a sequence motif. + beta12orEarlier @@ -28177,8 +28209,8 @@ - beta12orEarlier Format of a sequence profile. + beta12orEarlier @@ -28196,8 +28228,8 @@ - Format of a hidden Markov model. beta12orEarlier + Format of a hidden Markov model. @@ -28215,8 +28247,8 @@ - beta12orEarlier Data format of a dirichlet distribution. + beta12orEarlier @@ -28231,17 +28263,17 @@ - + - + - beta12orEarlier Data format for the emission and transition counts of a hidden Markov model. + beta12orEarlier @@ -28259,8 +28291,8 @@ - Format for secondary structure (predicted or real) of an RNA molecule. beta12orEarlier + Format for secondary structure (predicted or real) of an RNA molecule. @@ -28272,8 +28304,8 @@ Protein secondary structure format - beta12orEarlier Format for secondary structure (predicted or real) of a protein molecule. + beta12orEarlier @@ -28291,8 +28323,8 @@ - Format used to specify range(s) of sequence positions. beta12orEarlier + Format used to specify range(s) of sequence positions. @@ -28305,8 +28337,8 @@ pure - beta12orEarlier Alphabet for molecular sequence with possible unknown positions but without non-sequence characters. + beta12orEarlier @@ -28319,8 +28351,8 @@ unpure - beta12orEarlier Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters. + beta12orEarlier @@ -28333,8 +28365,8 @@ unambiguous sequence - beta12orEarlier Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters. + beta12orEarlier @@ -28347,8 +28379,8 @@ ambiguous - Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters. beta12orEarlier + Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters. @@ -28360,8 +28392,8 @@ Sequence features (repeats) format - Format used for map of repeats in molecular (typically nucleotide) sequences. beta12orEarlier + Format used for map of repeats in molecular (typically nucleotide) sequences. @@ -28373,8 +28405,8 @@ Nucleic acid features (restriction sites) format - Format used for report on restriction enzyme recognition sites in nucleotide sequences. beta12orEarlier + Format used for report on restriction enzyme recognition sites in nucleotide sequences. @@ -28386,8 +28418,8 @@ Gene features (coding region) format - Format used for report on coding regions in nucleotide sequences. beta12orEarlier + Format used for report on coding regions in nucleotide sequences. @@ -28405,8 +28437,8 @@ - Format used for clusters of molecular sequences. beta12orEarlier + Format used for clusters of molecular sequences. @@ -28418,8 +28450,8 @@ Sequence cluster format (protein) - beta12orEarlier Format used for clusters of protein sequences. + beta12orEarlier @@ -28431,8 +28463,8 @@ Sequence cluster format (nucleic acid) - beta12orEarlier Format used for clusters of nucleotide sequences. + beta12orEarlier @@ -28444,10 +28476,10 @@ Gene cluster format - Format used for clusters of genes. - beta12orEarlier - beta13 true + beta13 + beta12orEarlier + Format used for clusters of genes. @@ -28460,9 +28492,9 @@ EMBL-like (text) - A text format resembling EMBL entry format. - beta12orEarlier This concept may be used for the many non-standard EMBL-like text formats. + beta12orEarlier + A text format resembling EMBL entry format. @@ -28475,9 +28507,9 @@ FASTQ-like format (text) - beta12orEarlier - This concept may be used for non-standard FASTQ short read-like formats. A text format resembling FASTQ short read format. + This concept may be used for non-standard FASTQ short read-like formats. + beta12orEarlier @@ -28489,8 +28521,8 @@ EMBLXML - beta12orEarlier XML format for EMBL entries. + beta12orEarlier @@ -28502,8 +28534,8 @@ cdsxml - beta12orEarlier XML format for EMBL entries. + beta12orEarlier @@ -28515,8 +28547,8 @@ insdxml - XML format for EMBL entries. beta12orEarlier + XML format for EMBL entries. @@ -28528,8 +28560,8 @@ geneseq - beta12orEarlier Geneseq sequence format. + beta12orEarlier @@ -28542,8 +28574,8 @@ UniProt-like (text) - beta12orEarlier A text sequence format resembling uniprotkb entry format. + beta12orEarlier @@ -28555,10 +28587,10 @@ UniProt format - 1.8 - UniProt entry sequence format. - true beta12orEarlier + true + UniProt entry sequence format. + 1.8 @@ -28570,10 +28602,10 @@ ipi - true - ipi sequence format. - beta12orEarlier 1.8 + beta12orEarlier + ipi sequence format. + true @@ -28586,8 +28618,8 @@ medline - beta12orEarlier Abstract format used by MedLine database. + beta12orEarlier @@ -28605,8 +28637,8 @@ - beta12orEarlier Format used for ontologies. + beta12orEarlier @@ -28618,8 +28650,8 @@ OBO format - A serialisation format conforming to the Open Biomedical Ontologies (OBO) model. beta12orEarlier + A serialisation format conforming to the Open Biomedical Ontologies (OBO) model. @@ -28632,8 +28664,8 @@ OWL format - beta12orEarlier A serialisation format conforming to the Web Ontology Language (OWL) model. + beta12orEarlier @@ -28646,10 +28678,10 @@ FASTA-like (text) - A text format resembling FASTA format. - beta12orEarlier - http://filext.com/file-extension/FASTA This concept may also be used for the many non-standard FASTA-like formats. + http://filext.com/file-extension/FASTA + beta12orEarlier + A text format resembling FASTA format. @@ -28661,10 +28693,10 @@ Sequence record full format - true - Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database. - beta12orEarlier 1.8 + beta12orEarlier + Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database. + true @@ -28676,10 +28708,10 @@ Sequence record lite format - Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment. - beta12orEarlier - 1.8 true + 1.8 + beta12orEarlier + Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment. @@ -28690,10 +28722,10 @@ EMBL format (XML) - - This is a placeholder for other more specific concepts. It should not normally be used for annotation. - An XML format for EMBL entries. + beta12orEarlier + An XML format for EMBL entries. + This is a placeholder for other more specific concepts. It should not normally be used for annotation. @@ -28706,9 +28738,9 @@ GenBank-like format (text) - beta12orEarlier - This concept may be used for the non-standard GenBank-like text formats. A text format resembling GenBank entry (plain text) format. + This concept may be used for the non-standard GenBank-like text formats. + beta12orEarlier @@ -28720,8 +28752,8 @@ Sequence feature table format (text) - beta12orEarlier Text format for a sequence feature table. + beta12orEarlier @@ -28733,10 +28765,10 @@ Strain data format - 1.0 - true - beta12orEarlier Format of a report on organism strain data / cell line. + beta12orEarlier + true + 1.0 @@ -28747,10 +28779,10 @@ CIP strain data format - beta12orEarlier - beta12orEarlier - true Format for a report of strain data as used for CIP database entries. + true + beta12orEarlier + beta12orEarlier @@ -28762,10 +28794,10 @@ phylip property values - beta12orEarlier - beta12orEarlier - PHYLIP file format for phylogenetic property data. true + PHYLIP file format for phylogenetic property data. + beta12orEarlier + beta12orEarlier @@ -28777,10 +28809,10 @@ STRING entry format (HTML) - Entry format (HTML) for the STRING database of protein interaction. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Entry format (HTML) for the STRING database of protein interaction. @@ -28793,8 +28825,8 @@ STRING entry format (XML) - beta12orEarlier Entry format (XML) for the STRING database of protein interaction. + beta12orEarlier @@ -28807,8 +28839,8 @@ GFF - beta12orEarlier GFF feature format (of indeterminate version). + beta12orEarlier @@ -28820,11 +28852,11 @@ GTF - beta12orEarlier Gene Transfer Format (GTF), a restricted version of GFF. + beta12orEarlier - + @@ -28837,8 +28869,8 @@ FASTA-HTML - beta12orEarlier FASTA format wrapped in HTML elements. + beta12orEarlier @@ -28851,8 +28883,8 @@ EMBL-HTML - beta12orEarlier EMBL entry format wrapped in HTML elements. + beta12orEarlier @@ -28864,10 +28896,10 @@ BioCyc enzyme report format - Format of an entry from the BioCyc enzyme database. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + Format of an entry from the BioCyc enzyme database. @@ -28879,10 +28911,10 @@ ENZYME enzyme report format - true - beta12orEarlier - beta12orEarlier Format of an entry from the Enzyme nomenclature database (ENZYME). + beta12orEarlier + beta12orEarlier + true @@ -28894,10 +28926,10 @@ PseudoCAP gene report format - Format of a report on a gene from the PseudoCAP database. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + Format of a report on a gene from the PseudoCAP database. @@ -28909,10 +28941,10 @@ GeneCards gene report format - true - beta12orEarlier - beta12orEarlier Format of a report on a gene from the GeneCards database. + beta12orEarlier + beta12orEarlier + true @@ -28924,24 +28956,18 @@ Textual format - beta12orEarlier - http://www.iana.org/assignments/media-types/media-types.xhtml#text - Plain text - http://filext.com/file-extension/TXT - Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual). - Textual format. - http://www.iana.org/assignments/media-types/text/plain http://filext.com/file-extension/TSV - Tabular format + http://www.iana.org/assignments/media-types/text/plain + Textual format. + Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual). + txt + http://filext.com/file-extension/TXT + Plain text + http://www.iana.org/assignments/media-types/media-types.xhtml#text + beta12orEarlier - - Many textual formats used in bioinformatics are tabular (tab-separated values, TSV). Typically with an additional header in their own format. - Tabular format - - - @@ -28956,10 +28982,10 @@ - Hypertext Markup Language - http://filext.com/file-extension/HTML - beta12orEarlier HTML format. + beta12orEarlier + http://filext.com/file-extension/HTML + Hypertext Markup Language @@ -28971,11 +28997,11 @@ XML - Extensible Markup Language - http://filext.com/file-extension/XML - beta12orEarlier - eXtensible Markup Language (XML) format. Data in XML format can be serialised into text, or binary format. + eXtensible Markup Language (XML) format. + beta12orEarlier + http://filext.com/file-extension/XML + Extensible Markup Language @@ -28987,9 +29013,9 @@ Binary format - Binary format. - beta12orEarlier Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004. + beta12orEarlier + Binary format. @@ -29001,10 +29027,10 @@ URI format - beta12orEarlier - Typical textual representation of a URI. - true beta13 + true + Typical textual representation of a URI. + beta12orEarlier @@ -29016,10 +29042,10 @@ NCI-Nature pathway entry format - beta12orEarlier - The format of an entry from the NCI-Nature pathways database. - true beta12orEarlier + true + The format of an entry from the NCI-Nature pathways database. + beta12orEarlier @@ -29031,9 +29057,9 @@ Format (typed) - A broad class of format distinguished by the scientific nature of the data that is identified. - beta12orEarlier This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches. + beta12orEarlier + A broad class of format distinguished by the scientific nature of the data that is identified. @@ -29052,7 +29078,7 @@ - + @@ -29064,14 +29090,14 @@ - + - BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more). - beta12orEarlier BioXSD XML format - + beta12orEarlier + BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more). + @@ -29084,8 +29110,8 @@ RDF format - A serialisation format conforming to the Resource Description Framework (RDF) model. beta12orEarlier + A serialisation format conforming to the Resource Description Framework (RDF) model. @@ -29098,8 +29124,8 @@ GenBank-HTML - Genbank entry format wrapped in HTML elements. beta12orEarlier + Genbank entry format wrapped in HTML elements. @@ -29111,10 +29137,10 @@ Protein features (domains) format - Format of a report on protein features (domain composition). - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Format of a report on protein features (domain composition). @@ -29126,9 +29152,9 @@ EMBL-like format - This concept may be used for the many non-standard EMBL-like formats. - A format resembling EMBL entry (plain text) format. beta12orEarlier + A format resembling EMBL entry (plain text) format. + This concept may be used for the many non-standard EMBL-like formats. @@ -29140,9 +29166,9 @@ FASTQ-like format - beta12orEarlier - This concept may be used for non-standard FASTQ short read-like formats. A format resembling FASTQ short read format. + This concept may be used for non-standard FASTQ short read-like formats. + beta12orEarlier @@ -29154,9 +29180,9 @@ FASTA-like - A format resembling FASTA format. - beta12orEarlier This concept may be used for the many non-standard FASTA-like formats. + beta12orEarlier + A format resembling FASTA format. @@ -29169,8 +29195,8 @@ uniprotkb-like format - A sequence format resembling uniprotkb entry format. beta12orEarlier + A sequence format resembling uniprotkb entry format. @@ -29188,8 +29214,8 @@ - beta12orEarlier Format for a sequence feature table. + beta12orEarlier @@ -29202,8 +29228,8 @@ OBO - OBO ontology text format. beta12orEarlier + OBO ontology text format. @@ -29216,8 +29242,8 @@ OBO-XML - OBO ontology XML format. beta12orEarlier + OBO ontology XML format. @@ -29229,8 +29255,8 @@ Sequence record format (text) - beta12orEarlier Data format for a molecular sequence record. + beta12orEarlier @@ -29242,8 +29268,8 @@ Sequence record format (XML) - Data format for a molecular sequence record. beta12orEarlier + Data format for a molecular sequence record. @@ -29255,8 +29281,8 @@ Sequence feature table format (XML) - beta12orEarlier XML format for a sequence feature table. + beta12orEarlier @@ -29268,8 +29294,8 @@ Alignment format (text) - beta12orEarlier Text format for molecular sequence alignment information. + beta12orEarlier @@ -29281,8 +29307,8 @@ Alignment format (XML) - beta12orEarlier XML format for molecular sequence alignment information. + beta12orEarlier @@ -29294,8 +29320,8 @@ Phylogenetic tree format (text) - Text format for a phylogenetic tree. beta12orEarlier + Text format for a phylogenetic tree. @@ -29307,8 +29333,8 @@ Phylogenetic tree format (XML) - XML format for a phylogenetic tree. beta12orEarlier + XML format for a phylogenetic tree. @@ -29321,9 +29347,9 @@ EMBL-like (XML) - beta12orEarlier - This concept may be used for the any non-standard EMBL-like XML formats. An XML format resembling EMBL entry format. + This concept may be used for the any non-standard EMBL-like XML formats. + beta12orEarlier @@ -29335,9 +29361,9 @@ GenBank-like format - This concept may be used for the non-standard GenBank-like formats. - beta12orEarlier A format resembling GenBank entry (plain text) format. + beta12orEarlier + This concept may be used for the non-standard GenBank-like formats. @@ -29349,10 +29375,10 @@ STRING entry format - true - beta12orEarlier - Entry format for the STRING database of protein interaction. beta12orEarlier + Entry format for the STRING database of protein interaction. + beta12orEarlier + true @@ -29364,8 +29390,8 @@ Sequence assembly format (text) - Text format for sequence assembly data. beta12orEarlier + Text format for sequence assembly data. @@ -29377,10 +29403,10 @@ Amino acid identifier format - beta12orEarlier - true - Text format (representation) of amino acid residues. beta13 + Text format (representation) of amino acid residues. + true + beta12orEarlier @@ -29393,8 +29419,8 @@ completely unambiguous - Alphabet for a molecular sequence without any unknown positions or ambiguity characters. beta12orEarlier + Alphabet for a molecular sequence without any unknown positions or ambiguity characters. @@ -29407,8 +29433,8 @@ completely unambiguous pure - Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters. beta12orEarlier + Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters. @@ -29421,8 +29447,8 @@ completely unambiguous pure nucleotide - beta12orEarlier Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters . + beta12orEarlier @@ -29435,8 +29461,8 @@ completely unambiguous pure dna - Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters. beta12orEarlier + Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters. @@ -29449,8 +29475,8 @@ completely unambiguous pure rna sequence - beta12orEarlier Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters. + beta12orEarlier @@ -29468,9 +29494,9 @@ - Format of a raw molecular sequence (i.e. the alphabet used). - beta12orEarlier http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence + beta12orEarlier + Format of a raw molecular sequence (i.e. the alphabet used). @@ -29484,12 +29510,12 @@ - BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. beta12orEarlier + BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. - + @@ -29501,13 +29527,13 @@ - Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. - beta12orEarlier The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project. + beta12orEarlier + Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. - + @@ -29518,10 +29544,10 @@ SBML - beta12orEarlier Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation. - + beta12orEarlier + @@ -29534,8 +29560,8 @@ completely unambiguous pure protein - Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters. beta12orEarlier + Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters. @@ -29550,17 +29576,17 @@ - + - + - beta12orEarlier Format of a bibliographic reference. + beta12orEarlier @@ -29578,8 +29604,8 @@ - beta12orEarlier Format of a sequence annotation track. + beta12orEarlier @@ -29597,8 +29623,8 @@ - Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences. beta12orEarlier + Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences. @@ -29616,8 +29642,8 @@ - beta12orEarlier Format of sequence variation annotation. + beta12orEarlier @@ -29630,8 +29656,8 @@ markx0 variant - beta12orEarlier Some variant of Pearson MARKX alignment format. + beta12orEarlier @@ -29645,8 +29671,8 @@ - beta12orEarlier Some variant of Mega format for (typically aligned) sequences. + beta12orEarlier @@ -29660,8 +29686,8 @@ - Some variant of Phylip format for (aligned) sequences. beta12orEarlier + Some variant of Phylip format for (aligned) sequences. @@ -29674,9 +29700,9 @@ AB1 - AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF). - AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence. beta12orEarlier + AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence. + AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF). @@ -29689,10 +29715,10 @@ ACE - beta12orEarlier ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards). - + beta12orEarlier + @@ -29705,11 +29731,11 @@ BED - Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser. - BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track). beta12orEarlier - + BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track). + Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser. + @@ -29722,10 +29748,10 @@ bigBed - bigBed format for large sequence annotation tracks, similar to textual BED format. beta12orEarlier - + bigBed format for large sequence annotation tracks, similar to textual BED format. + @@ -29738,10 +29764,10 @@ WIG - beta12orEarlier Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser. - + beta12orEarlier + @@ -29754,10 +29780,10 @@ bigWig - bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format. beta12orEarlier - + bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format. + @@ -29771,10 +29797,10 @@ - beta12orEarlier PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track. - + beta12orEarlier + @@ -29788,11 +29814,11 @@ - beta12orEarlier - Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format. Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth. - + Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format. + beta12orEarlier + @@ -29805,11 +29831,11 @@ 2bit - 2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'. beta12orEarlier + 2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'. - + @@ -29822,10 +29848,10 @@ .nib - .nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'. beta12orEarlier - + .nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'. + @@ -29838,11 +29864,11 @@ genePred - beta12orEarlier - genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables. genePred table format for gene prediction tracks. - + genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables. + beta12orEarlier + @@ -29855,10 +29881,10 @@ pgSnp - beta12orEarlier Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser. - + beta12orEarlier + @@ -29871,10 +29897,10 @@ axt - axt format of alignments, typically produced from BLASTZ. beta12orEarlier - + axt format of alignments, typically produced from BLASTZ. + @@ -29887,12 +29913,12 @@ LAV - LAV format of alignments generated by BLASTZ and LASTZ. beta12orEarlier + LAV format of alignments generated by BLASTZ and LASTZ. - + @@ -29903,12 +29929,12 @@ Pileup - Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s). beta12orEarlier + Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s). - + @@ -29919,12 +29945,12 @@ VCF - Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). beta12orEarlier + Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). - + @@ -29935,12 +29961,12 @@ SRF - beta12orEarlier Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive. + beta12orEarlier - + @@ -29951,12 +29977,12 @@ ZTR - beta12orEarlier ZTR format for storing chromatogram data from DNA sequencing instruments. + beta12orEarlier - + @@ -29967,12 +29993,12 @@ GVF - beta12orEarlier Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation. + beta12orEarlier - + @@ -29983,8 +30009,8 @@ BCF - BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). beta12orEarlier + BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). @@ -30003,8 +30029,8 @@ - beta13 Format of a matrix (array) of numerical values. + beta13 @@ -30022,8 +30048,8 @@ - beta13 Format of data concerning the classification of the sequences and/or structures of protein structural domain(s). + beta13 @@ -30035,9 +30061,9 @@ Raw SCOP domain classification format - beta13 - These are the parsable data files provided by SCOP. Format of raw SCOP domain classification data files. + These are the parsable data files provided by SCOP. + beta13 @@ -30049,9 +30075,9 @@ Raw CATH domain classification format - Format of raw CATH domain classification data files. - beta13 These are the parsable data files provided by CATH. + beta13 + Format of raw CATH domain classification data files. @@ -30063,9 +30089,9 @@ CATH domain report format - The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. - beta13 Format of summary of domain classification information for a CATH domain. + beta13 + The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. @@ -30078,12 +30104,12 @@ SBRML - Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models. 1.0 + Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models. - + @@ -30093,10 +30119,10 @@ BioPAX - 1.0 BioPAX is an exchange format for pathway data, with its data model defined in OWL. - + 1.0 + @@ -30110,12 +30136,12 @@ - 1.0 EBI Application Result XML is a format returned by sequence similarity search Web services at EBI. + 1.0 - + @@ -30126,13 +30152,13 @@ PSI MI XML (MIF) - MIF - XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI. 1.0 + XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI. + MIF - + @@ -30143,10 +30169,10 @@ phyloXML - 1.0 phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data. - + 1.0 + @@ -30159,10 +30185,10 @@ NeXML - NeXML is a standardised XML format for rich phyloinformatic data. 1.0 - + NeXML is a standardised XML format for rich phyloinformatic data. + @@ -30176,12 +30202,12 @@ - MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED). 1.0 + MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED). - + @@ -30193,12 +30219,12 @@ - 1.0 MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED). + 1.0 - + @@ -30209,10 +30235,10 @@ GCDML - 1.0 GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC). - + 1.0 + @@ -30225,10 +30251,10 @@ GTrack - GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG). 1.0 - + GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG). + @@ -30246,8 +30272,8 @@ - beta12orEarlier Data format for a report of information derived from a biological pathway or network. + beta12orEarlier @@ -30265,8 +30291,8 @@ - Data format for annotation on a laboratory experiment. beta12orEarlier + Data format for annotation on a laboratory experiment. @@ -30285,13 +30311,13 @@ - Reflects a UCSC Browser DB table. - Cytoband format for chromosome cytobands. 1.2 + Cytoband format for chromosome cytobands. + Reflects a UCSC Browser DB table. - + @@ -30303,12 +30329,12 @@ - CopasiML, the native format of COPASI. 1.2 + CopasiML, the native format of COPASI. - + @@ -30319,10 +30345,10 @@ CellML - 1.2 CellML, the format for mathematical models of biological and other networks. - + 1.2 + @@ -30335,10 +30361,10 @@ PSI MI TAB (MITAB) - Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI. 1.2 - + Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI. + @@ -30350,12 +30376,12 @@ PSI-PAR - 1.2 Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema. + 1.2 - + @@ -30366,11 +30392,11 @@ mzML - mzML format for raw spectrometer output data, standardised by HUPO PSI MSS. - 1.2 mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center. - + 1.2 + mzML format for raw spectrometer output data, standardised by HUPO PSI MSS. + @@ -30388,8 +30414,8 @@ - Format for mass spectrometry data. 1.2 + Format for mass spectrometry data. @@ -30402,10 +30428,10 @@ TraML - 1.2 TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS. - + 1.2 + @@ -30418,10 +30444,10 @@ mzIdentML - 1.2 mzIdentML is the exchange format for peptides and proteins identified from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of proteomics search engines. - + 1.2 + @@ -30434,10 +30460,10 @@ mzQuantML - 1.2 mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics. - + 1.2 + @@ -30450,10 +30476,10 @@ GelML - GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS. 1.2 - + GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS. + @@ -30466,10 +30492,10 @@ spML - spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics. 1.2 - + spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics. + @@ -30482,8 +30508,8 @@ OWL Functional Syntax - 1.2 A human-readable encoding for the Web Ontology Language (OWL). + 1.2 @@ -30496,9 +30522,9 @@ Manchester OWL Syntax - This format was influenced by the OWL Abstract Syntax and the DL style syntax. - 1.2 A syntax for writing OWL class expressions. + 1.2 + This format was influenced by the OWL Abstract Syntax and the DL style syntax. @@ -30511,9 +30537,9 @@ KRSS2 Syntax - 1.2 - A superset of the "Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort". This format is used in Protege 4. + A superset of the "Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort". + 1.2 @@ -30526,9 +30552,9 @@ Turtle - The Terse RDF Triple Language (Turtle) is a human-friendly serialization format for RDF (Resource Description Framework) graphs. - 1.2 The SPARQL Query Language incorporates a very similar syntax. + 1.2 + The Terse RDF Triple Language (Turtle) is a human-friendly serialization format for RDF (Resource Description Framework) graphs. @@ -30541,9 +30567,9 @@ N-Triples - A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format. - 1.2 N-Triples should not be confused with Notation 3 which is a superset of Turtle. + 1.2 + A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format. @@ -30556,8 +30582,8 @@ Notation3 - A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind. N3 + A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind. @@ -30571,11 +30597,11 @@ - RDF/XML is a serialization syntax for OWL DL, but not for OWL Full. - http://www.ebi.ac.uk/SWO/data/SWO_3000006 - 1.2 - Resource Description Framework (RDF) XML format. RDF + Resource Description Framework (RDF) XML format. + 1.2 + http://www.ebi.ac.uk/SWO/data/SWO_3000006 + RDF/XML is a serialization syntax for OWL DL, but not for OWL Full. @@ -30588,9 +30614,9 @@ OWL/XML - OWL - 1.2 OWL ontology XML serialisation format. + 1.2 + OWL @@ -30603,10 +30629,10 @@ A2M - 1.3 The A2M format is used as the primary format for multiple alignments of protein or nucleic-acid sequences in the SAM suite of tools. It is a small modification of FASTA format for sequences and is compatible with most tools that read FASTA. - + 1.3 + @@ -30619,13 +30645,13 @@ SFF - 1.3 - Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing. Standard flowgram format + Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing. + 1.3 - + @@ -30635,9 +30661,9 @@ MAP - Plink MAP - 1.3 The MAP file describes SNPs and is used by the Plink package. + 1.3 + Plink MAP @@ -30650,9 +30676,9 @@ PED - The PED file describes individuals and genetic data and is used by the Plink package. - 1.3 Plink PED + 1.3 + The PED file describes individuals and genetic data and is used by the Plink package. @@ -30665,8 +30691,8 @@ Individual genetic data format - 1.3 Data format for a metadata on an individual and their genetic data. + 1.3 @@ -30679,9 +30705,9 @@ PED/MAP - 1.3 - Plink PED/MAP The PED/MAP file describes data used by the Plink package. + Plink PED/MAP + 1.3 @@ -30695,10 +30721,10 @@ CT - Connectivity Table file format - Connect format - beta12orEarlier File format of a CT (Connectivity Table) file from the RNAstructure package. + beta12orEarlier + Connect format + Connectivity Table file format @@ -30713,8 +30739,8 @@ SS - XRNA old input style format. beta12orEarlier + XRNA old input style format. @@ -30729,8 +30755,8 @@ - beta12orEarlier RNA Markup Language. + beta12orEarlier @@ -30744,8 +30770,8 @@ GDE - beta12orEarlier Format for the Genetic Data Environment (GDE). + beta12orEarlier @@ -30758,9 +30784,9 @@ BLC - A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) pacakge. - Block file format 1.3 + Block file format + A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) pacakge. @@ -30798,8 +30824,8 @@ - BAM indexing format 1.3 + BAM indexing format @@ -30812,8 +30838,8 @@ HMMER2 - 1.3 HMMER profile HMM file for HMMER versions 2.x + 1.3 @@ -30826,8 +30852,8 @@ HMMER3 - HMMER profile HMM file for HMMER versions 3.x 1.3 + HMMER profile HMM file for HMMER versions 3.x @@ -30840,8 +30866,8 @@ PO - 1.3 EMBOSS simple sequence pair alignment format. + 1.3 @@ -30855,8 +30881,8 @@ BLAST XML results format - 1.3 XML format as produced by the NCBI Blast package + 1.3 @@ -30869,10 +30895,10 @@ CRAM - 1.7 - http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf - http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf Reference-based compression of alignment format + http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf + http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf + 1.7 @@ -30884,8 +30910,8 @@ JSON - Javascript Object Notation format; a lightweight, text-based format to represent structured data using key-value pairs. 1.7 + Javascript Object Notation format; a lightweight, text-based format to represent structured data using key-value pairs. @@ -30897,8 +30923,8 @@ EPS - 1.7 Encapsulated PostScript format + 1.7 @@ -30910,8 +30936,8 @@ GIF - Graphics Interchange Format. 1.7 + Graphics Interchange Format. @@ -30924,9 +30950,9 @@ xls - 1.7 - Microsoft Excel format Microsoft Excel spreadsheet format. + Microsoft Excel format + 1.7 @@ -30938,12 +30964,13 @@ TSV - CSV - http://filext.com/file-extension/TSV - 1.7 - Tabular data represented as tab-separated values in a text file. - http://www.iana.org/assignments/media-types/text/csv + Tabular format http://filext.com/file-extension/CSV + http://www.iana.org/assignments/media-types/text/csv + Tabular data represented as tab-separated values in a text file. + 1.7 + http://filext.com/file-extension/TSV + CSV @@ -30961,8 +30988,8 @@ - Format of a file of gene expression data, e.g. a gene expression matrix or profile. 1.7 + Format of a file of gene expression data, e.g. a gene expression matrix or profile. @@ -30975,8 +31002,8 @@ Cytoscape input file format - 1.7 Format of the cytoscape input file of gene expression ratios or values are specified over one or more experiments. + 1.7 @@ -30994,10 +31021,10 @@ - Bowtie format for indexed reference genome for "small" genomes. - 1.7 - Bowtie index format https://github.com/BenLangmead/bowtie/blob/master/MANUAL + Bowtie index format + 1.7 + Bowtie format for indexed reference genome for "small" genomes. @@ -31009,11 +31036,11 @@ RSF - GCG RSF - 1.7 - Rich sequence format. - RSF-format files contain one or more sequences that may or may not be related. In addition to the sequence data, each sequence can be annotated with descriptive sequence information (from the GCG manual). http://www.molbiol.ox.ac.uk/tutorials/Seqlab_GCG.pdf + RSF-format files contain one or more sequences that may or may not be related. In addition to the sequence data, each sequence can be annotated with descriptive sequence information (from the GCG manual). + Rich sequence format. + 1.7 + GCG RSF @@ -31027,8 +31054,8 @@ - Some format based on the GCG format. 1.7 + Some format based on the GCG format. @@ -31041,9 +31068,9 @@ BSML - 1.7 - Bioinformatics Sequence Markup Language format. http://rothlab.ucdavis.edu/genhelp/chapter_2_using_sequences.html#_Creating_and_Editing_Single_Sequenc + Bioinformatics Sequence Markup Language format. + 1.7 @@ -31061,10 +31088,10 @@ - Bowtie format for indexed reference genome for "large" genomes. - Bowtie long index format - https://github.com/BenLangmead/bowtie/blob/master/MANUAL 1.7 + https://github.com/BenLangmead/bowtie/blob/master/MANUAL + Bowtie long index format + Bowtie format for indexed reference genome for "large" genomes. @@ -31077,8 +31104,8 @@ Ensembl variation file format - 1.8 Ensembl standard format for variation data. + 1.8 @@ -31092,10 +31119,10 @@ docx - Microsoft Word format. - doc - Microsoft Word format 1.8 + Microsoft Word format + doc + Microsoft Word format. @@ -31107,11 +31134,11 @@ Document format - doc - 1.8 - Format of documents including word processor, spreadsheet and presentation. - Microsoft Word format Portable Document Format + Microsoft Word format + Format of documents including word processor, spreadsheet and presentation. + 1.8 + doc @@ -31124,8 +31151,136 @@ PDF - Portable Document Format 1.8 + Portable Document Format + + + + + + + + + + Image format + + + + + + + + Format used for images and image metadata. + 1.9 + + + + + + + + + + DICOM format + + + 1.9 + Medical image format corresponding to the Digital Imaging and Communications in Medicine (DICOM) standard. + + + + + + + + + + + + + nii + + + Medical image and metadata format of the Neuroimaging Informatics Technology Initiative. + + + NIfTI-1 format + 1.9 + + + + + + + + + + + mhd + + + Metalmage format + 1.9 + Text-based tagged file format for medical images generated using the MetaImage software package. + + + + + + + + + + + nrrd + + + 1.9 + Nearly Raw Rasta Data format designed to support scientific visualization and image processing involving N-dimensional raster data. + + + + + + + + + + + R file format + + File format used for scripts written in the R programming language for execution within the R software environment, typically for statistical computation and graphics. + + 1.9 + + + + + + + + + + SPSS + + 1.9 + File format used for scripts for the Statistical Package for the Social Sciences. + + + + + + + + + + + MHT + MIME HTML format for Web pages, which can include external resources, including images, Flash animations and so on. + + EMBL entry format wrapped in HTML elements. + 1.9 + MHTML @@ -31138,38 +31293,38 @@ Operation - http://en.wikipedia.org/wiki/Subroutine - http://en.wikipedia.org/wiki/Function_(computer_science) - http://www.onto-med.de/ontologies/gfo.owl#Function - http://www.ifomis.org/bfo/1.1/snap#Quality - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#process - http://wsio.org/operation_001 - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality - http://www.onto-med.de/ontologies/gfo.owl#Process - Function (programming) - Lambda abstraction - Mathematical function - Computational procedure - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method - http://www.ifomis.org/bfo/1.1/snap#Continuant - http://www.ifomis.org/bfo/1.1/span#Process - http://semanticscience.org/resource/SIO_000649 - Computational subroutine - Computational operation - Process - beta12orEarlier - sumo:Function - Mathematical operation - http://www.ebi.ac.uk/swo/SWO_0000003 - http://semanticscience.org/resource/SIO_000017 - Computational method - http://en.wikipedia.org/wiki/Function_(mathematics) - http://www.ifomis.org/bfo/1.1/snap#Function - http://purl.org/biotop/biotop.owl#Function - Function - A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state. - Computational tool http://www.onto-med.de/ontologies/gfo.owl#Perpetuant + Computational tool + A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state. + Function + http://purl.org/biotop/biotop.owl#Function + http://www.ifomis.org/bfo/1.1/snap#Function + http://en.wikipedia.org/wiki/Function_(mathematics) + Computational method + http://semanticscience.org/resource/SIO_000017 + http://www.ebi.ac.uk/swo/SWO_0000003 + Mathematical operation + sumo:Function + beta12orEarlier + Process + Computational operation + Computational subroutine + http://semanticscience.org/resource/SIO_000649 + http://www.ifomis.org/bfo/1.1/span#Process + http://www.ifomis.org/bfo/1.1/snap#Continuant + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method + Computational procedure + Mathematical function + Lambda abstraction + Function (programming) + http://www.onto-med.de/ontologies/gfo.owl#Process + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality + http://wsio.org/operation_001 + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#process + http://www.ifomis.org/bfo/1.1/snap#Quality + http://www.onto-med.de/ontologies/gfo.owl#Function + http://en.wikipedia.org/wiki/Function_(computer_science) + http://en.wikipedia.org/wiki/Subroutine @@ -31186,8 +31341,8 @@ - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. Function + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. @@ -31201,22 +31356,22 @@ - - + + - - + + - Search - Database retrieval - Search or query a data resource and retrieve entries and / or annotation. - Retrieval - Query beta12orEarlier + Query + Retrieval + Search or query a data resource and retrieve entries and / or annotation. + Database retrieval + Search @@ -31228,10 +31383,10 @@ Data retrieval (database cross-reference) - beta13 - true - Search database to retrieve all relevant references to a particular entity or entry. beta12orEarlier + Search database to retrieve all relevant references to a particular entity or entry. + true + beta13 @@ -31245,19 +31400,19 @@ - - + + - - + + - This is a broad concept and is used a placeholder for other, more specific concepts. - beta12orEarlier Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. + beta12orEarlier + This is a broad concept and is used a placeholder for other, more specific concepts. @@ -31275,10 +31430,10 @@ - Database indexing - Generate an index of (typically a file of) biological data. - beta12orEarlier Data indexing + beta12orEarlier + Generate an index of (typically a file of) biological data. + Database indexing @@ -31290,11 +31445,11 @@ Data index analysis - 1.6 - true - beta12orEarlier - Analyse an index of biological data. Database index analysis + Analyse an index of biological data. + beta12orEarlier + true + 1.6 @@ -31306,10 +31461,10 @@ Annotation retrieval (sequence) - beta12orEarlier - Retrieve basic information about a molecular sequence. - beta12orEarlier true + beta12orEarlier + Retrieve basic information about a molecular sequence. + beta12orEarlier @@ -31322,8 +31477,8 @@ Sequence generation - Generate a molecular sequence by some means. beta12orEarlier + Generate a molecular sequence by some means. @@ -31336,8 +31491,8 @@ Sequence editing - beta12orEarlier Edit or change a molecular sequence, either randomly or specifically. + beta12orEarlier @@ -31349,9 +31504,9 @@ Sequence merging - Sequence splicing - Merge two or more (typically overlapping) molecular sequences. beta12orEarlier + Merge two or more (typically overlapping) molecular sequences. + Sequence splicing @@ -31364,8 +31519,8 @@ Sequence conversion - beta12orEarlier Convert a molecular sequence from one type to another. + beta12orEarlier @@ -31389,8 +31544,8 @@ - Calculate sequence complexity, for example to find low-complexity regions in sequences. beta12orEarlier + Calculate sequence complexity, for example to find low-complexity regions in sequences. @@ -31404,18 +31559,18 @@ - - + + - - + + - beta12orEarlier Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes. + beta12orEarlier @@ -31440,8 +31595,8 @@ - Calculate character or word composition or frequency of a molecular sequence. beta12orEarlier + Calculate character or word composition or frequency of a molecular sequence. @@ -31459,9 +31614,9 @@ - Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length. - beta12orEarlier Find and/or analyse repeat sequences in (typically nucleotide) sequences. + beta12orEarlier + Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length. @@ -31475,20 +31630,20 @@ - - + + - - + + - Motif discovery - Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery). - beta12orEarlier Motifs and patterns might be conserved or over-represented (occur with improbable frequency). + beta12orEarlier + Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery). + Motif discovery @@ -31512,17 +31667,17 @@ - Motif recognition - Sequence motif detection - Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s). - Sequence profile search - Sequence signature detection - Sequence motif recognition - Motif detection - Protein secondary database search - Sequence motif search - Motif search beta12orEarlier + Motif search + Sequence motif search + Protein secondary database search + Motif detection + Sequence motif recognition + Sequence signature detection + Sequence profile search + Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s). + Sequence motif detection + Motif recognition @@ -31546,8 +31701,8 @@ - Find motifs shared by molecular sequences. beta12orEarlier + Find motifs shared by molecular sequences. @@ -31559,11 +31714,11 @@ Transcription regulatory sequence analysis - true - For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. - Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences. - beta13 beta12orEarlier + beta13 + Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences. + For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. + true @@ -31576,9 +31731,9 @@ Conserved transcription regulatory sequence identification - Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites). - beta12orEarlier For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes. + beta12orEarlier + Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites). @@ -31603,10 +31758,10 @@ - Protein structural property calculation - beta12orEarlier - Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure. This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. + Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure. + beta12orEarlier + Protein structural property calculation @@ -31619,9 +31774,9 @@ Protein flexibility and motion analysis - Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure. - Analyse flexibility and motion in protein structure. beta12orEarlier + Analyse flexibility and motion in protein structure. + Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure. @@ -31640,10 +31795,10 @@ - Protein structural feature identification - beta12orEarlier - This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc. Identify or screen for 3D structural motifs in protein structure(s). + This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc. + beta12orEarlier + Protein structural feature identification @@ -31662,8 +31817,8 @@ - Identify structural domains in a protein structure from first principles (for example calculations on structural compactness). beta12orEarlier + Identify structural domains in a protein structure from first principles (for example calculations on structural compactness). @@ -31675,8 +31830,8 @@ Protein architecture analysis - Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s). beta12orEarlier + Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s). @@ -31700,16 +31855,16 @@ - WHATIF: SymShellOneXML - WHATIF: SymShellFiveXML - Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s). - WHATIF:ListContactsNormal - WHATIF:ListSideChainContactsNormal - beta12orEarlier - WHATIF:ListSideChainContactsRelaxed - WHATIF: SymShellTwoXML - WHATIF:ListContactsRelaxed WHATIF: SymShellTenXML + WHATIF:ListContactsRelaxed + WHATIF: SymShellTwoXML + WHATIF:ListSideChainContactsRelaxed + beta12orEarlier + WHATIF:ListSideChainContactsNormal + WHATIF:ListContactsNormal + Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s). + WHATIF: SymShellFiveXML + WHATIF: SymShellOneXML @@ -31727,8 +31882,8 @@ - Calculate, visualise or analyse phi/psi angles of a protein structure. beta12orEarlier + Calculate, visualise or analyse phi/psi angles of a protein structure. @@ -31754,10 +31909,10 @@ - Protein property rendering - beta12orEarlier - This includes methods to render and visualise the properties of a protein sequence. Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. + This includes methods to render and visualise the properties of a protein sequence. + beta12orEarlier + Protein property rendering @@ -31772,19 +31927,19 @@ - - + + - - + + - Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins. - This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. beta12orEarlier + This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. + Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins. @@ -31809,12 +31964,12 @@ - SO:0000110 - Motif database search - beta12orEarlier - Sequence feature recognition - Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions. Sequence feature prediction + Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions. + Sequence feature recognition + beta12orEarlier + Motif database search + SO:0000110 @@ -31826,10 +31981,10 @@ Data retrieval (feature table) - beta12orEarlier - true - Extract a sequence feature table from a sequence database entry. beta13 + Extract a sequence feature table from a sequence database entry. + true + beta12orEarlier @@ -31841,10 +31996,10 @@ Feature table query - Query the features (in a feature table) of molecular sequence(s). - true - beta12orEarlier 1.6 + beta12orEarlier + true + Query the features (in a feature table) of molecular sequence(s). @@ -31865,20 +32020,20 @@ - - + + - - + + - Feature table comparison - Feature comparison - Compare the feature tables of two or more molecular sequences. beta12orEarlier + Compare the feature tables of two or more molecular sequences. + Feature comparison + Feature table comparison @@ -31890,10 +32045,10 @@ Data retrieval (sequence alignment) - Display basic information about a sequence alignment. - beta13 - true beta12orEarlier + true + beta13 + Display basic information about a sequence alignment. @@ -31911,8 +32066,8 @@ - beta12orEarlier Analyse a molecular sequence alignment. + beta12orEarlier @@ -31925,9 +32080,9 @@ Sequence alignment comparison - See also 'Sequence profile alignment'. - beta12orEarlier Compare (typically by aligning) two molecular sequence alignments. + beta12orEarlier + See also 'Sequence profile alignment'. @@ -31940,8 +32095,8 @@ Sequence alignment conversion - Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence). beta12orEarlier + Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence). @@ -31953,10 +32108,10 @@ Nucleic acid property processing - beta13 - Process (read and / or write) physicochemical property data of nucleic acids. - true beta12orEarlier + true + Process (read and / or write) physicochemical property data of nucleic acids. + beta13 @@ -31975,8 +32130,8 @@ - Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence. beta12orEarlier + Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence. @@ -31994,8 +32149,8 @@ - Predict splicing alternatives or transcript isoforms from analysis of sequence data. beta12orEarlier + Predict splicing alternatives or transcript isoforms from analysis of sequence data. @@ -32014,10 +32169,10 @@ - Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. - beta12orEarlier - Frameshift error detection Detect frameshifts in DNA sequences, including frameshift sites and signals, and frameshift errors from sequencing projects. + Frameshift error detection + beta12orEarlier + Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. @@ -32030,8 +32185,8 @@ Vector sequence detection - Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences. beta12orEarlier + Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences. @@ -32051,10 +32206,10 @@ - beta12orEarlier - Secondary structure prediction (protein) - Predict secondary structure of protein sequences. Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc. + Predict secondary structure of protein sequences. + Secondary structure prediction (protein) + beta12orEarlier @@ -32072,9 +32227,9 @@ - Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. - Predict super-secondary structure of protein sequence(s). beta12orEarlier + Predict super-secondary structure of protein sequence(s). + Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. @@ -32087,8 +32242,8 @@ Transmembrane protein prediction - beta12orEarlier Predict and/or classify transmembrane proteins or transmembrane (helical) domains or regions in protein sequences. + beta12orEarlier @@ -32106,9 +32261,9 @@ - Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods). - Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions. beta12orEarlier + Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions. + Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods). @@ -32123,18 +32278,18 @@ - - + + - - + + - beta12orEarlier Predict tertiary structure of a molecular (biopolymer) sequence. + beta12orEarlier @@ -32153,9 +32308,9 @@ - beta12orEarlier - Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences. Methods usually involve multiple sequence alignment analysis. + Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences. + beta12orEarlier @@ -32179,8 +32334,8 @@ - beta12orEarlier Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. + beta12orEarlier @@ -32193,8 +32348,8 @@ Protein-protein interaction prediction (from protein sequence) - Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences. beta12orEarlier + Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences. @@ -32208,8 +32363,8 @@ - Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures. beta12orEarlier + Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures. @@ -32224,18 +32379,18 @@ - - + + - - + + - Analyse a network of protein interactions. beta12orEarlier + Analyse a network of protein interactions. @@ -32248,8 +32403,8 @@ Protein interaction network comparison - Compare two or more networks of protein interactions. beta12orEarlier + Compare two or more networks of protein interactions. @@ -32275,9 +32430,9 @@ - Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). - beta12orEarlier Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc). + beta12orEarlier + Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). @@ -32303,10 +32458,10 @@ - Nucleic acid folding - Nucleic acid folding modelling - Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data. beta12orEarlier + Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data. + Nucleic acid folding modelling + Nucleic acid folding @@ -32318,11 +32473,11 @@ Data retrieval (restriction enzyme annotation) - beta12orEarlier - Retrieve information on restriction enzymes or restriction enzyme sites. - true - Restriction enzyme information retrieval beta13 + Restriction enzyme information retrieval + true + Retrieve information on restriction enzymes or restriction enzyme sites. + beta12orEarlier @@ -32334,11 +32489,11 @@ Genetic marker identification - A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc. - Identify genetic markers in DNA sequences. - beta13 - beta12orEarlier true + beta12orEarlier + beta13 + Identify genetic markers in DNA sequences. + A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc. @@ -32357,14 +32512,15 @@ - Functional mapping - Genetic map construction - Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances. - Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers. - Genetic map generation - Linkage mapping - This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). beta12orEarlier + QTL mapping + This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). + Linkage mapping + Genetic map generation + Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers. + Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances. + Genetic map construction + Functional mapping @@ -32388,9 +32544,9 @@ - Analyse genetic linkage. - For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc. beta12orEarlier + For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc. + Analyse genetic linkage. @@ -32409,9 +32565,9 @@ - Codon usage table construction - beta12orEarlier Calculate codon usage statistics and create a codon usage table. + beta12orEarlier + Codon usage table construction @@ -32424,8 +32580,8 @@ Codon usage table comparison - Compare two or more codon usage tables. beta12orEarlier + Compare two or more codon usage tables. @@ -32440,7 +32596,7 @@ - + @@ -32451,26 +32607,26 @@ - - + + - - + + - - + + - synon: Codon usage table analysis - Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences. - synon: Codon usage data analysis beta12orEarlier + synon: Codon usage data analysis + Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences. + synon: Codon usage table analysis @@ -32485,18 +32641,18 @@ - - + + - - + + - beta12orEarlier Identify and plot third base position variability in a nucleotide sequence. + beta12orEarlier @@ -32508,8 +32664,8 @@ Sequence word comparison - beta12orEarlier Find exact character or word matches between molecular sequences without full sequence alignment. + beta12orEarlier @@ -32534,10 +32690,10 @@ - Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences. - beta12orEarlier - Phylogenetic distance matrix generation Sequence distance matrix construction + Phylogenetic distance matrix generation + beta12orEarlier + Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences. @@ -32555,8 +32711,8 @@ - Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria. beta12orEarlier + Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria. @@ -32572,21 +32728,21 @@ - - + + - - + + - Sequence cluster generation - Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences. - beta12orEarlier - Sequence cluster construction The clusters may be output or used internally for some other purpose. + Sequence cluster construction + beta12orEarlier + Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences. + Sequence cluster generation @@ -32596,7 +32752,7 @@ - Sequence alignment generation + Sequence alignment @@ -32606,11 +32762,11 @@ - Sequence alignment computation - Sequence alignment - Align (identify equivalent sites within) molecular sequences. - beta12orEarlier Sequence alignment construction + beta12orEarlier + Align (identify equivalent sites within) molecular sequences. + Sequence alignment generation + Sequence alignment computation @@ -32622,12 +32778,12 @@ Hybrid sequence alignment construction - Hybrid sequence alignment generation - Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA). - beta12orEarlier - beta13 - true Hybrid sequence alignment + true + beta13 + beta12orEarlier + Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA). + Hybrid sequence alignment generation @@ -32639,13 +32795,13 @@ Structure-based sequence alignment - Align molecular sequences using sequence and structural information. - Structure-based sequence alignment generation - Sequence alignment (structure-based) - beta12orEarlier - Structure-based sequence alignment construction - Sequence alignment generation (structure-based) Structure-based sequence alignment + Sequence alignment generation (structure-based) + Structure-based sequence alignment construction + beta12orEarlier + Sequence alignment (structure-based) + Structure-based sequence alignment generation + Align molecular sequences using sequence and structural information. @@ -32665,12 +32821,12 @@ - Multiple structure alignment generation - Multiple structure alignment construction - beta12orEarlier - Structure alignment construction - Structure alignment generation Align (superimpose) molecular tertiary structures. + Structure alignment generation + Structure alignment construction + beta12orEarlier + Multiple structure alignment construction + Multiple structure alignment generation @@ -32685,8 +32841,8 @@ - - + + @@ -32697,13 +32853,13 @@ - - + + - Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment. - beta12orEarlier Sequence profile construction + beta12orEarlier + Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment. @@ -32734,10 +32890,10 @@ - beta12orEarlier - Structural profile construction - Generate some type of structural (3D) profile or template from a structure or structure alignment. Structural profile generation + Generate some type of structural (3D) profile or template from a structure or structure alignment. + Structural profile construction + beta12orEarlier @@ -32751,28 +32907,28 @@ - - + + - - + + - - + + - Sequence profile alignment generation - Align sequence profiles (representing sequence alignments). - Sequence profile alignment construction - See also 'Sequence alignment comparison'. - beta12orEarlier Sequence profile alignment + beta12orEarlier + See also 'Sequence alignment comparison'. + Sequence profile alignment construction + Align sequence profiles (representing sequence alignments). + Sequence profile alignment generation @@ -32797,15 +32953,15 @@ - Align structural (3D) profiles or templates (representing structures or structure alignments). - Structural profile alignment construction - Structural profile alignment generation - Structural profile alignment - Structural profile alignment construction (multiple) - Multiple 3D profile alignment construction - 3D profile alignment - 3D profile alignment (multiple) beta12orEarlier + 3D profile alignment (multiple) + 3D profile alignment + Multiple 3D profile alignment construction + Structural profile alignment construction (multiple) + Structural profile alignment + Structural profile alignment generation + Structural profile alignment construction + Align structural (3D) profiles or templates (representing structures or structure alignments). @@ -32835,12 +32991,12 @@ - A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Sequence-profile alignment - Align molecular sequence(s) to sequence profile(s). - beta12orEarlier - Sequence-profile alignment generation Sequence-profile alignment construction + Sequence-profile alignment generation + beta12orEarlier + Align molecular sequence(s) to sequence profile(s). + Sequence-profile alignment + A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. @@ -32855,22 +33011,22 @@ - - + + - - + + - Sequence-3D profile alignment - Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Sequence-3D profile alignment generation - Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment). - Sequence-3D profile alignment construction beta12orEarlier + Sequence-3D profile alignment construction + Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment). + Sequence-3D profile alignment generation + Methods might perform one-to-one, one-to-many or many-to-many comparisons. + Sequence-3D profile alignment @@ -32895,10 +33051,10 @@ - Sequence-structure alignment - Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Align molecular sequence to structure in 3D space (threading). beta12orEarlier + Align molecular sequence to structure in 3D space (threading). + Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons. + Sequence-structure alignment @@ -32919,11 +33075,11 @@ - Protein fold prediction - Recognize (predict and identify) known protein structural domains or folds in protein sequence(s). - Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. - Protein domain prediction beta12orEarlier + Protein domain prediction + Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. + Recognize (predict and identify) known protein structural domains or folds in protein sequence(s). + Protein fold prediction @@ -32941,11 +33097,11 @@ - This includes documentation, general information and other metadata on entities such as databases, database entries and tools. - beta12orEarlier - Data retrieval (metadata) - Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described. Data retrieval (documentation) + Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described. + Data retrieval (metadata) + beta12orEarlier + This includes documentation, general information and other metadata on entities such as databases, database entries and tools. @@ -32959,18 +33115,18 @@ - - + + - - + + - Query the biomedical and informatics literature. beta12orEarlier + Query the biomedical and informatics literature. @@ -32990,19 +33146,19 @@ - - + + - - + + - Process and analyse text (typically the biomedical and informatics literature) to extract information from it. - beta12orEarlier Text data mining + beta12orEarlier + Process and analyse text (typically the biomedical and informatics literature) to extract information from it. @@ -33020,8 +33176,8 @@ - Perform in-silico (virtual) PCR. beta12orEarlier + Perform in-silico (virtual) PCR. @@ -33035,8 +33191,8 @@ - - + + @@ -33047,14 +33203,14 @@ - - + + - beta12orEarlier - Design or predict oligonucleotide primers for PCR and DNA amplification etc. - Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set. PCR primer prediction + Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set. + Design or predict oligonucleotide primers for PCR and DNA amplification etc. + beta12orEarlier @@ -33069,20 +33225,20 @@ - - + + - - + + - + @@ -33091,9 +33247,9 @@ - Microarray probe prediction - beta12orEarlier Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families. + beta12orEarlier + Microarray probe prediction @@ -33118,9 +33274,9 @@ - Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence. - For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps. beta12orEarlier + For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps. + Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence. @@ -33145,9 +33301,9 @@ - This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. - Standardize or normalize microarray data. beta12orEarlier + Standardize or normalize microarray data. + This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. @@ -33159,10 +33315,10 @@ Sequencing-based expression profile data processing - beta12orEarlier - beta12orEarlier - true Process (read and / or write) SAGE, MPSS or SBS experimental data. + true + beta12orEarlier + beta12orEarlier @@ -33181,8 +33337,8 @@ - Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles. beta12orEarlier + Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles. @@ -33201,12 +33357,12 @@ - Gene expression profile generation - beta12orEarlier - Generate a gene expression profile or pattern, for example from microarray data. - Functional profiling - Gene expression profile construction Expression profiling + Gene expression profile construction + Functional profiling + Generate a gene expression profile or pattern, for example from microarray data. + beta12orEarlier + Gene expression profile generation @@ -33225,8 +33381,8 @@ - Compare gene expression profiles or patterns. beta12orEarlier + Compare gene expression profiles or patterns. @@ -33238,10 +33394,10 @@ Functional profiling - beta12orEarlier - Interpret (in functional terms) and annotate gene expression data. - beta12orEarlier true + beta12orEarlier + Interpret (in functional terms) and annotate gene expression data. + beta12orEarlier @@ -33253,11 +33409,11 @@ EST and cDNA sequence analysis - true - beta12orEarlier - beta12orEarlier - For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. Analyse EST or cDNA sequences. + For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. + beta12orEarlier + beta12orEarlier + true @@ -33269,11 +33425,11 @@ Structural genomics target selection - true - Methods will typically navigate a graph of protein families of known structure. - beta12orEarlier - Identify and select targets for protein structural determination. beta12orEarlier + Identify and select targets for protein structural determination. + beta12orEarlier + Methods will typically navigate a graph of protein families of known structure. + true @@ -33288,17 +33444,17 @@ - + - + - Assign secondary structure from protein coordinate or experimental data. beta12orEarlier + Assign secondary structure from protein coordinate or experimental data. @@ -33313,18 +33469,18 @@ - - + + - - + + - Assign a protein tertiary structure (3D coordinates) from raw experimental data. beta12orEarlier + Assign a protein tertiary structure (3D coordinates) from raw experimental data. @@ -33346,22 +33502,22 @@ - + - + - beta12orEarlier - The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc. - WHATIF: UseFileDB - Protein structure validation - WHATIF: CorrectedPDBasXML - Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc. Evaluate the quality or correctness a protein three-dimensional model. + Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc. + WHATIF: CorrectedPDBasXML + Protein structure validation + WHATIF: UseFileDB + The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc. + beta12orEarlier @@ -33374,10 +33530,10 @@ Molecular model refinement - Refine (after evaluation) a model of a molecular structure (typically a protein structure) to reduce steric clashes, volume irregularities etc. - beta12orEarlier - WHATIF: CorrectedPDBasXML Protein model refinement + WHATIF: CorrectedPDBasXML + beta12orEarlier + Refine (after evaluation) a model of a molecular structure (typically a protein structure) to reduce steric clashes, volume irregularities etc. @@ -33402,10 +33558,10 @@ - beta12orEarlier - Construct a phylogenetic tree. - Phylogenetic tree construction Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. + Phylogenetic tree construction + Construct a phylogenetic tree. + beta12orEarlier @@ -33429,8 +33585,8 @@ - Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions. beta12orEarlier + Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions. @@ -33443,9 +33599,9 @@ Phylogenetic tree comparison - For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc. - Compare two or more phylogenetic trees. beta12orEarlier + Compare two or more phylogenetic trees. + For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc. @@ -33470,8 +33626,8 @@ - beta12orEarlier Edit a phylogenetic tree. + beta12orEarlier @@ -33489,9 +33645,9 @@ - Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing). - beta12orEarlier A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation. + beta12orEarlier + Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing). @@ -33503,8 +33659,8 @@ Protein folding simulation - Simulate the folding of a protein. beta12orEarlier + Simulate the folding of a protein. @@ -33517,8 +33673,8 @@ Protein folding pathway prediction - beta12orEarlier Predict the folding pathway(s) or non-native structural intermediates of a protein. + beta12orEarlier @@ -33537,8 +33693,8 @@ - Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). beta12orEarlier + Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). @@ -33554,19 +33710,19 @@ - + - + - beta12orEarlier - Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function. - Protein mutation modelling Methods might predict silent or pathological mutations. + Protein mutation modelling + Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function. + beta12orEarlier @@ -33578,10 +33734,10 @@ Immunogen design - beta12orEarlier - beta12orEarlier - Design molecules that elicit an immune response (immunogens). true + Design molecules that elicit an immune response (immunogens). + beta12orEarlier + beta12orEarlier @@ -33595,18 +33751,18 @@ - - + + - - + + - beta12orEarlier Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). + beta12orEarlier @@ -33620,18 +33776,18 @@ - - + + - - + + - Calculate Km, Vmax and derived data for an enzyme reaction. beta12orEarlier + Calculate Km, Vmax and derived data for an enzyme reaction. @@ -33643,13 +33799,13 @@ Formatting - File format conversion - File reformatting - Reformatting - File formatting - Format conversion - Reformat a file of data (or equivalent entity in memory). beta12orEarlier + Reformat a file of data (or equivalent entity in memory). + Format conversion + File formatting + Reformatting + File reformatting + File format conversion @@ -33662,9 +33818,9 @@ Format validation - beta12orEarlier - File format validation Test and validate the format and content of a data file. + File format validation + beta12orEarlier @@ -33691,12 +33847,12 @@ - + - Rendering - Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures. beta12orEarlier + Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures. + Rendering @@ -33711,21 +33867,21 @@ - - + + - - + + - This excludes direct retrieval methods (e.g. the dbfetch program). - beta12orEarlier Search a sequence database by sequence comparison and retrieve similar sequences. sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. + beta12orEarlier + This excludes direct retrieval methods (e.g. the dbfetch program). @@ -33743,8 +33899,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Search a tertiary structure database, typically by sequence and/or structure comparison, or some other means, and retrieve structures and associated data. beta12orEarlier + Search a tertiary structure database, typically by sequence and/or structure comparison, or some other means, and retrieve structures and associated data. @@ -33756,10 +33912,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein secondary database search - Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group. - true - beta12orEarlier 1.8 + beta12orEarlier + true + Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group. @@ -33771,10 +33927,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Motif database search - 1.8 - true - Screen a sequence against a motif or pattern database. beta12orEarlier + Screen a sequence against a motif or pattern database. + true + 1.8 @@ -33786,10 +33942,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence profile database search - 1.4 - Search a database of sequence profiles with a query sequence. - beta12orEarlier true + beta12orEarlier + Search a database of sequence profiles with a query sequence. + 1.4 @@ -33801,10 +33957,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Transmembrane protein database search - beta12orEarlier - Search a database of transmembrane proteins, for example for sequence or structural similarities. - beta12orEarlier true + beta12orEarlier + Search a database of transmembrane proteins, for example for sequence or structural similarities. + beta12orEarlier @@ -33816,10 +33972,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence retrieval (by code) - beta12orEarlier - 1.6 - true Query a database and retrieve sequences with a given entry code or accession number. + true + 1.6 + beta12orEarlier @@ -33831,10 +33987,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence retrieval (by keyword) - 1.6 - beta12orEarlier - Query a database and retrieve sequences containing a given keyword. true + Query a database and retrieve sequences containing a given keyword. + beta12orEarlier + 1.6 @@ -33847,10 +34003,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence similarity search - Search a sequence database and retrieve sequences that are similar to a query sequence. - beta12orEarlier - Sequence database search (by sequence) Structure database search (by sequence) + Sequence database search (by sequence) + beta12orEarlier + Search a sequence database and retrieve sequences that are similar to a query sequence. @@ -33862,10 +34018,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by motif or pattern) - true - beta12orEarlier - Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. 1.8 + Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. + beta12orEarlier + true @@ -33877,10 +34033,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by amino acid composition) - beta12orEarlier - 1.6 - Search a sequence database and retrieve sequences of a given amino acid composition. true + Search a sequence database and retrieve sequences of a given amino acid composition. + 1.6 + beta12orEarlier @@ -33892,8 +34048,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by property) - beta12orEarlier Search a sequence database and retrieve sequences with a specified property, typically a physicochemical or compositional property. + beta12orEarlier @@ -33905,12 +34061,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by sequence using word-based methods) - Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method. - Sequence similarity search (word-based methods) - true - 1.6 - Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps. beta12orEarlier + Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps. + 1.6 + true + Sequence similarity search (word-based methods) + Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method. @@ -33922,12 +34078,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by sequence using profile-based methods) - 1.6 - This includes tools based on PSI-BLAST. - beta12orEarlier - Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query. - Sequence similarity search (profile-based methods) true + Sequence similarity search (profile-based methods) + Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query. + beta12orEarlier + This includes tools based on PSI-BLAST. + 1.6 @@ -33939,12 +34095,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by sequence using local alignment-based methods) - This includes tools based on the Smith-Waterman algorithm or FASTA. - Sequence similarity search (local alignment-based methods) - true - beta12orEarlier - 1.6 Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method. + 1.6 + beta12orEarlier + true + Sequence similarity search (local alignment-based methods) + This includes tools based on the Smith-Waterman algorithm or FASTA. @@ -33956,12 +34112,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by sequence using global alignment-based methods) - true - beta12orEarlier - Sequence similarity search (global alignment-based methods) - 1.6 - Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method. This includes tools based on the Needleman and Wunsch algorithm. + Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method. + 1.6 + Sequence similarity search (global alignment-based methods) + beta12orEarlier + true @@ -33973,12 +34129,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by sequence for primer sequences) - Sequence similarity search (primer sequences) - STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. - 1.6 - Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences. - beta12orEarlier true + beta12orEarlier + Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences. + 1.6 + STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. + Sequence similarity search (primer sequences) @@ -33990,12 +34146,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by molecular weight) - Peptide mass fingerprinting - beta12orEarlier - true - Protein fingerprinting - 1.6 Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry. + 1.6 + Protein fingerprinting + true + beta12orEarlier + Peptide mass fingerprinting @@ -34007,10 +34163,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by isoelectric point) - true - Search sequence(s) or a sequence database for sequences of a given isoelectric point. - beta12orEarlier 1.6 + beta12orEarlier + Search sequence(s) or a sequence database for sequences of a given isoelectric point. + true @@ -34022,10 +34178,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure retrieval (by code) - true - beta12orEarlier - 1.6 Query a tertiary structure database and retrieve entries with a given entry code or accession number. + 1.6 + beta12orEarlier + true @@ -34037,10 +34193,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure retrieval (by keyword) - beta12orEarlier - Query a tertiary structure database and retrieve entries containing a given keyword. - 1.6 true + 1.6 + Query a tertiary structure database and retrieve entries containing a given keyword. + beta12orEarlier @@ -34052,10 +34208,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure database search (by sequence) - 1.8 - Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence. - true beta12orEarlier + true + Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence. + 1.8 @@ -34074,10 +34230,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Structure retrieval by structure - Structure database search (by structure) - Search a database of molecular structure and retrieve structures that are similar to a query structure. beta12orEarlier + Search a database of molecular structure and retrieve structures that are similar to a query structure. + Structure database search (by structure) + Structure retrieval by structure @@ -34101,8 +34257,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Annotate a molecular sequence record with terms from a controlled vocabulary. beta12orEarlier + Annotate a molecular sequence record with terms from a controlled vocabulary. @@ -34114,8 +34270,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Genome annotation - Annotate a genome sequence with terms from a controlled vocabulary. beta12orEarlier + Annotate a genome sequence with terms from a controlled vocabulary. @@ -34127,8 +34283,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid sequence reverse and complement - Generate the reverse and / or complement of a nucleotide sequence. beta12orEarlier + Generate the reverse and / or complement of a nucleotide sequence. @@ -34140,8 +34296,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Random sequence generation - beta12orEarlier Generate a random sequence, for example, with a specific character composition. + beta12orEarlier @@ -34160,8 +34316,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Generate digest fragments for a nucleotide sequence containing restriction sites. beta12orEarlier + Generate digest fragments for a nucleotide sequence containing restriction sites. @@ -34186,8 +34342,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses. beta12orEarlier + Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses. @@ -34199,8 +34355,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence mutation and randomization - Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition. beta12orEarlier + Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition. @@ -34212,9 +34368,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence masking - beta12orEarlier - For example, SNPs or repeats in a DNA sequence might be masked. Mask characters in a molecular sequence (replacing those characters with a mask character). + For example, SNPs or repeats in a DNA sequence might be masked. + beta12orEarlier @@ -34226,8 +34382,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence cutting - beta12orEarlier Cut (remove) characters or a region from a molecular sequence. + beta12orEarlier @@ -34239,8 +34395,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Restriction site creation - beta12orEarlier Create (or remove) restriction sites in sequences, for example using silent mutations. + beta12orEarlier @@ -34258,8 +34414,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Translate a DNA sequence into protein. beta12orEarlier + Translate a DNA sequence into protein. @@ -34277,8 +34433,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Transcribe a nucleotide sequence into mRNA sequence(s). beta12orEarlier + Transcribe a nucleotide sequence into mRNA sequence(s). @@ -34290,10 +34446,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence composition calculation (nucleic acid) - beta12orEarlier - 1.8 - Calculate base frequency or word composition of a nucleotide sequence. true + Calculate base frequency or word composition of a nucleotide sequence. + 1.8 + beta12orEarlier @@ -34305,10 +34461,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence composition calculation (protein) - true - beta12orEarlier - Calculate amino acid frequency or word composition of a protein sequence. 1.8 + Calculate amino acid frequency or word composition of a protein sequence. + beta12orEarlier + true @@ -34321,8 +34477,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Repeat sequence detection - Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. beta12orEarlier + Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. @@ -34335,8 +34491,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Repeat sequence organisation analysis - Analyse repeat sequence organization such as periodicity. beta12orEarlier + Analyse repeat sequence organization such as periodicity. @@ -34350,8 +34506,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Analyse the hydrophobic, hydrophilic or charge properties of a protein structure. + beta12orEarlier @@ -34375,8 +34531,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Calculate solvent accessible or buried surface areas in protein structures. beta12orEarlier + Calculate solvent accessible or buried surface areas in protein structures. @@ -34389,8 +34545,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein hydropathy cluster calculation - Identify clusters of hydrophobic or charged residues in a protein structure. beta12orEarlier + Identify clusters of hydrophobic or charged residues in a protein structure. @@ -34408,8 +34564,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Calculate whether a protein structure has an unusually large net charge (dipole moment). beta12orEarlier + Calculate whether a protein structure has an unusually large net charge (dipole moment). @@ -34427,8 +34583,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc. beta12orEarlier + Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc. @@ -34441,10 +34597,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein binding site prediction (from structure) - Binding site prediction (from structure) - Ligand-binding and active site prediction (from structure) - beta12orEarlier Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures. + beta12orEarlier + Ligand-binding and active site prediction (from structure) + Binding site prediction (from structure) @@ -34462,8 +34618,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Analyse RNA or DNA-binding sites in protein structure. + beta12orEarlier @@ -34475,8 +34631,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein peeling - Decompose a structure into compact or globular fragments (protein peeling). beta12orEarlier + Decompose a structure into compact or globular fragments (protein peeling). @@ -34494,8 +34650,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure. beta12orEarlier + Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure. @@ -34513,8 +34669,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure. beta12orEarlier + Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure. @@ -34532,9 +34688,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Calculate clusters of contacting residues in protein structures. Cluster of contacting residues might be key structural residues. + Calculate clusters of contacting residues in protein structures. + beta12orEarlier @@ -34552,12 +34708,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Identify potential hydrogen bonds between amino acids and other groups. - WHATIF:ShowHydrogenBondsM - beta12orEarlier - The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy. - WHATIF:HasHydrogenBonds WHATIF:ShowHydrogenBonds + WHATIF:HasHydrogenBonds + The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy. + beta12orEarlier + WHATIF:ShowHydrogenBondsM + Identify potential hydrogen bonds between amino acids and other groups. @@ -34570,8 +34726,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue non-canonical interaction detection - Calculate non-canonical atomic interactions in protein structures. beta12orEarlier + Calculate non-canonical atomic interactions in protein structures. @@ -34589,8 +34745,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Calculate a Ramachandran plot of a protein structure. + beta12orEarlier @@ -34604,18 +34760,18 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - Validate a Ramachandran plot of a protein structure. beta12orEarlier + Validate a Ramachandran plot of a protein structure. @@ -34639,8 +34795,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Calculate the molecular weight of a protein sequence or fragments. + beta12orEarlier @@ -34658,8 +34814,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Predict extinction coefficients or optical density of a protein sequence. beta12orEarlier + Predict extinction coefficients or optical density of a protein sequence. @@ -34683,8 +34839,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Calculate pH-dependent properties from pKa calculations of a protein sequence. + beta12orEarlier @@ -34697,8 +34853,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein hydropathy calculation (from sequence) - beta12orEarlier Hydropathy calculation on a protein sequence. + beta12orEarlier @@ -34717,8 +34873,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Plot a protein titration curve. beta12orEarlier + Plot a protein titration curve. @@ -34736,8 +34892,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Calculate isoelectric point of a protein sequence. beta12orEarlier + Calculate isoelectric point of a protein sequence. @@ -34755,8 +34911,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Estimate hydrogen exchange rate of a protein sequence. + beta12orEarlier @@ -34768,8 +34924,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein hydrophobic region calculation - beta12orEarlier Calculate hydrophobic or hydrophilic / charged regions of a protein sequence. + beta12orEarlier @@ -34787,8 +34943,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein. beta12orEarlier + Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein. @@ -34807,9 +34963,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity. - Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. beta12orEarlier + Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. + Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity. @@ -34827,8 +34983,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc. + beta12orEarlier @@ -34846,8 +35002,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Predict the solubility or atomic solvation energy of a protein sequence. + beta12orEarlier @@ -34865,8 +35021,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Predict crystallizability of a protein sequence. beta12orEarlier + Predict crystallizability of a protein sequence. @@ -34878,8 +35034,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein signal peptide detection (eukaryotes) - Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins. beta12orEarlier + Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins. @@ -34891,8 +35047,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein signal peptide detection (bacteria) - beta12orEarlier Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins. + beta12orEarlier @@ -34904,8 +35060,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern MHC peptide immunogenicity prediction - beta12orEarlier Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc. + beta12orEarlier @@ -34917,12 +35073,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein feature prediction (from sequence) - Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure. - 1.6 - Sequence feature detection (protein) - true - beta12orEarlier Methods typically involve scanning for known motifs, patterns and regular expressions. + beta12orEarlier + true + Sequence feature detection (protein) + 1.6 + Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure. @@ -34937,22 +35093,22 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - Nucleic acid feature prediction - Nucleic acid feature recognition - beta12orEarlier - Methods typically involve scanning for known motifs, patterns and regular expressions. - Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions. Sequence feature detection (nucleic acid) + Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions. + Methods typically involve scanning for known motifs, patterns and regular expressions. + beta12orEarlier + Nucleic acid feature recognition + Nucleic acid feature prediction @@ -34971,9 +35127,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Epitope mapping is commonly done during vaccine design. - Predict antigenic determinant sites (epitopes) in protein sequences. beta12orEarlier + Predict antigenic determinant sites (epitopes) in protein sequences. + Epitope mapping is commonly done during vaccine design. @@ -34991,9 +35147,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc. - beta12orEarlier Predict post-translation modification sites in protein sequences. + beta12orEarlier + Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc. @@ -35012,9 +35168,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Detect or predict signal peptides and signal peptide cleavage sites in protein sequences. - Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc. beta12orEarlier + Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc. + Detect or predict signal peptides and signal peptide cleavage sites in protein sequences. @@ -35027,11 +35183,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein binding site prediction (from sequence) - beta12orEarlier - Protein binding site detection - Ligand-binding and active site prediction (from sequence) - Predict catalytic residues, active sites or other ligand-binding sites in protein sequences. Binding site prediction (from sequence) + Predict catalytic residues, active sites or other ligand-binding sites in protein sequences. + Ligand-binding and active site prediction (from sequence) + Protein binding site detection + beta12orEarlier @@ -35043,8 +35199,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein-nucleic acid binding prediction - Predict RNA and DNA-binding binding sites in protein sequences. beta12orEarlier + Predict RNA and DNA-binding binding sites in protein sequences. @@ -35057,8 +35213,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein folding site prediction - beta12orEarlier Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization. + beta12orEarlier @@ -35076,8 +35232,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Detect or predict cleavage sites (enzymatic or chemical) in protein sequences. beta12orEarlier + Detect or predict cleavage sites (enzymatic or chemical) in protein sequences. @@ -35089,10 +35245,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Epitope mapping (MHC Class I) - Predict epitopes that bind to MHC class I molecules. - beta12orEarlier - true 1.8 + true + beta12orEarlier + Predict epitopes that bind to MHC class I molecules. @@ -35104,10 +35260,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Epitope mapping (MHC Class II) - beta12orEarlier - true - 1.8 Predict epitopes that bind to MHC class II molecules. + 1.8 + true + beta12orEarlier @@ -35120,8 +35276,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Whole gene prediction - Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc. beta12orEarlier + Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc. @@ -35133,9 +35289,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene component prediction - Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences. - beta12orEarlier Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. + beta12orEarlier + Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences. @@ -35147,8 +35303,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Transposon prediction - Detect or predict transposons, retrotransposons / retrotransposition signatures etc. beta12orEarlier + Detect or predict transposons, retrotransposons / retrotransposition signatures etc. @@ -35160,8 +35316,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern PolyA signal detection - beta12orEarlier Detect polyA signals in nucleotide sequences. + beta12orEarlier @@ -35175,20 +35331,20 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. - Detect quadruplex-forming motifs in nucleotide sequences. - Quadruplex structure prediction beta12orEarlier + Quadruplex structure prediction + Detect quadruplex-forming motifs in nucleotide sequences. + Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. @@ -35206,11 +35362,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - CpG island and isochores detection - CpG island and isochores rendering - Find CpG rich regions in a nucleotide sequence or isochores in genome sequences. - beta12orEarlier An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence. + beta12orEarlier + Find CpG rich regions in a nucleotide sequence or isochores in genome sequences. + CpG island and isochores rendering + CpG island and isochores detection @@ -35228,8 +35384,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map. beta12orEarlier + Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map. @@ -35241,8 +35397,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleosome formation or exclusion sequence prediction - Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA. beta12orEarlier + Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA. @@ -35260,9 +35416,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Methods might require a pre-mRNA or genomic DNA sequence. - Identify, predict or analyse splice sites in nucleotide sequences. beta12orEarlier + Identify, predict or analyse splice sites in nucleotide sequences. + Methods might require a pre-mRNA or genomic DNA sequence. @@ -35274,8 +35430,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Integrated gene prediction - beta12orEarlier Predict whole gene structure using a combination of multiple methods to achieve better predictions. + beta12orEarlier @@ -35287,8 +35443,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Operon prediction - beta12orEarlier Find operons (operators, promoters and genes) in bacteria genes. + beta12orEarlier @@ -35300,10 +35456,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Coding region prediction - beta12orEarlier - ORF finding - ORF prediction Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences. + ORF prediction + ORF finding + beta12orEarlier @@ -35321,9 +35477,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. Predict selenocysteine insertion sequence (SECIS) in a DNA sequence. + SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. + beta12orEarlier @@ -35341,11 +35497,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc. - Transcription regulatory element prediction - Translational regulatory element prediction Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences. + Translational regulatory element prediction + Transcription regulatory element prediction + This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc. + beta12orEarlier @@ -35363,8 +35519,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Predict translation initiation sites, possibly by searching a database of sites. + beta12orEarlier @@ -35376,9 +35532,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Promoter prediction - beta12orEarlier - Methods might recognize CG content, CpG islands, splice sites, polyA signals etc. Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences. + Methods might recognize CG content, CpG islands, splice sites, polyA signals etc. + beta12orEarlier @@ -35390,9 +35546,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Transcription regulatory element prediction (DNA-cis) - Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences. - Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. beta12orEarlier + Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. + Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences. @@ -35404,9 +35560,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Transcription regulatory element prediction (RNA-cis) - beta12orEarlier - Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences. Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity. + Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences. + beta12orEarlier @@ -35424,10 +35580,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Functional RNA identification - Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets. - Trans-regulatory elements regulate genes distant from the gene from which they were transcribed. beta12orEarlier + Trans-regulatory elements regulate genes distant from the gene from which they were transcribed. + Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets. + Functional RNA identification @@ -35439,9 +35595,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Matrix/scaffold attachment site prediction - beta12orEarlier - Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences. MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation. + Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences. + beta12orEarlier @@ -35453,8 +35609,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Transcription factor binding site prediction - Identify or predict transcription factor binding sites in DNA sequences. beta12orEarlier + Identify or predict transcription factor binding sites in DNA sequences. @@ -35472,9 +35628,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Identify or predict exonic splicing enhancers (ESE) in exons. An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA. + Identify or predict exonic splicing enhancers (ESE) in exons. + beta12orEarlier @@ -35487,10 +35643,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence alignment validation - beta12orEarlier - Evaluate molecular sequence alignment accuracy. - Sequence alignment quality evaluation Evaluation might be purely sequence-based or use structural information. + Sequence alignment quality evaluation + Evaluate molecular sequence alignment accuracy. + beta12orEarlier @@ -35502,10 +35658,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence alignment analysis (conservation) - Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc. - Residue conservation analysis - Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence. beta12orEarlier + Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence. + Residue conservation analysis + Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc. @@ -35518,9 +35674,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence alignment analysis (site correlation) - beta12orEarlier - This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. Analyse correlations between sites in a molecular sequence alignment. + This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. + beta12orEarlier @@ -35532,10 +35688,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Chimeric sequence detection - Sequence alignment analysis (chimeric sequence detection) - Detects chimeric sequences (chimeras) from a sequence alignment. - A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles. beta12orEarlier + A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles. + Detects chimeric sequences (chimeras) from a sequence alignment. + Sequence alignment analysis (chimeric sequence detection) @@ -35547,10 +35703,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Recombination detection - Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. - Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment. - beta12orEarlier Sequence alignment analysis (recombination detection) + beta12orEarlier + Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment. + Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. @@ -35562,10 +35718,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Indel detection - Identify insertion, deletion and duplication events from a sequence alignment. - Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. - Sequence alignment analysis (indel detection) beta12orEarlier + Sequence alignment analysis (indel detection) + Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. + Identify insertion, deletion and duplication events from a sequence alignment. @@ -35577,10 +35733,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleosome formation potential prediction - beta12orEarlier - Predict nucleosome formation potential of DNA sequences. - beta12orEarlier true + beta12orEarlier + Predict nucleosome formation potential of DNA sequences. + beta12orEarlier @@ -35598,8 +35754,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy. + beta12orEarlier @@ -35618,9 +35774,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - A melting profile is used to visualise and analyse partly melted DNA conformations. Calculate and plot a DNA or DNA/RNA melting profile. + A melting profile is used to visualise and analyse partly melted DNA conformations. + beta12orEarlier @@ -35638,9 +35794,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Calculate and plot a DNA or DNA/RNA stitch profile. - beta12orEarlier A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range. + beta12orEarlier + Calculate and plot a DNA or DNA/RNA stitch profile. @@ -35658,8 +35814,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Calculate and plot a DNA or DNA/RNA melting curve. + beta12orEarlier @@ -35677,8 +35833,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Calculate and plot a DNA or DNA/RNA probability profile. beta12orEarlier + Calculate and plot a DNA or DNA/RNA probability profile. @@ -35696,8 +35852,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Calculate and plot a DNA or DNA/RNA temperature profile. + beta12orEarlier @@ -35715,9 +35871,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - This includes properties such as. - beta12orEarlier Calculate curvature and flexibility / stiffness of a nucleotide sequence. + beta12orEarlier + This includes properties such as. @@ -35729,8 +35885,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern microRNA detection - beta12orEarlier Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in a DNA sequence. + beta12orEarlier @@ -35748,8 +35904,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Identify or predict tRNA genes in genomic sequences (tRNA). + beta12orEarlier @@ -35767,8 +35923,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences. beta12orEarlier + Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences. @@ -35780,8 +35936,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein secondary structure prediction (integrated) - beta12orEarlier Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions. + beta12orEarlier @@ -35793,8 +35949,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein secondary structure prediction (helices) - Predict helical secondary structure of protein sequences. beta12orEarlier + Predict helical secondary structure of protein sequences. @@ -35806,8 +35962,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein secondary structure prediction (turns) - beta12orEarlier Predict turn structure (for example beta hairpin turns) of protein sequences. + beta12orEarlier @@ -35819,8 +35975,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein secondary structure prediction (coils) - Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences. beta12orEarlier + Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences. @@ -35832,8 +35988,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein secondary structure prediction (disulfide bonds) - Predict cysteine bonding state and disulfide bond partners in protein sequences. beta12orEarlier + Predict cysteine bonding state and disulfide bond partners in protein sequences. @@ -35846,9 +36002,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern GPCR prediction - Predict G protein-coupled receptors (GPCR). - G protein-coupled receptor (GPCR) prediction beta12orEarlier + G protein-coupled receptor (GPCR) prediction + Predict G protein-coupled receptors (GPCR). @@ -35866,9 +36022,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - G protein-coupled receptor (GPCR) analysis - beta12orEarlier Analyse G-protein coupled receptor proteins (GPCRs). + beta12orEarlier + G protein-coupled receptor (GPCR) analysis @@ -35885,18 +36041,18 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - Predict tertiary structure (backbone and side-chain conformation) of protein sequences. beta12orEarlier + Predict tertiary structure (backbone and side-chain conformation) of protein sequences. @@ -35922,9 +36078,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Predict tertiary structure of DNA or RNA. - Methods might identify thermodynamically stable or evolutionarily conserved structures. beta12orEarlier + Methods might identify thermodynamically stable or evolutionarily conserved structures. + Predict tertiary structure of DNA or RNA. @@ -35936,9 +36092,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Ab initio structure prediction - beta12orEarlier - de novo structure prediction Predict tertiary structure of protein sequence(s) without homologs of known structure. + de novo structure prediction + beta12orEarlier @@ -35958,13 +36114,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Protein structure comparative modelling - Homology structure modelling - Homology modelling - The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc. - Build a three-dimensional protein model based on known (for example homologs) structures. - beta12orEarlier Comparative modelling + beta12orEarlier + Build a three-dimensional protein model based on known (for example homologs) structures. + The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc. + Homology modelling + Homology structure modelling + Protein structure comparative modelling @@ -35979,8 +36135,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + @@ -35991,15 +36147,15 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - Protein docking - Docking simulation - This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on. - beta12orEarlier Model the structure of a protein in complex with a small molecule or another macromolecule. + beta12orEarlier + This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on. + Docking simulation + Protein docking @@ -36011,9 +36167,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein modelling (backbone) - beta12orEarlier - Methods might require a preliminary C(alpha) trace. Model protein backbone conformation. + Methods might require a preliminary C(alpha) trace. + beta12orEarlier @@ -36025,9 +36181,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein modelling (side chains) - Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc. - Methods might use a residue rotamer library. beta12orEarlier + Methods might use a residue rotamer library. + Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc. @@ -36039,8 +36195,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein modelling (loops) - Model loop conformation in protein structures. beta12orEarlier + Model loop conformation in protein structures. @@ -36064,11 +36220,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Virtual ligand screening - Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques. - Ligand-binding simulation - Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. beta12orEarlier + Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. + Ligand-binding simulation + Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques. + Virtual ligand screening @@ -36082,20 +36238,20 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection. - beta12orEarlier - RNA inverse folding Nucleic acid folding family identification + RNA inverse folding + beta12orEarlier + Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection. @@ -36109,10 +36265,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. - beta12orEarlier - Single nucleotide polymorphism detection Find single nucleotide polymorphisms (SNPs) between sequences. + Single nucleotide polymorphism detection + beta12orEarlier + This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. @@ -36130,8 +36286,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers. + beta12orEarlier @@ -36143,11 +36299,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Functional mapping - beta12orEarlier - Map the genetic architecture of dynamic complex traits. - This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). - true beta12orEarlier + true + This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). + Map the genetic architecture of dynamic complex traits. + beta12orEarlier @@ -36166,12 +36322,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Haplotype reconstruction - Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). - beta12orEarlier - Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. - Haplotype inference Haplotype map generation + Haplotype inference + Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. + beta12orEarlier + Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). + Haplotype reconstruction @@ -36189,9 +36345,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). - Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes. beta12orEarlier + Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes. + Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). @@ -36210,8 +36366,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Predict genetic code from analysis of codon usage data. beta12orEarlier + Predict genetic code from analysis of codon usage data. @@ -36231,8 +36387,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Draw a dotplot of sequence similarities identified from word-matching or character comparison. beta12orEarlier + Draw a dotplot of sequence similarities identified from word-matching or character comparison. @@ -36250,12 +36406,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Pairwise sequence alignment construction - Align exactly two molecular sequences. - Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Pairwise sequence alignment Pairwise sequence alignment generation + Pairwise sequence alignment + Methods might perform one-to-one, one-to-many or many-to-many comparisons. + Align exactly two molecular sequences. + Pairwise sequence alignment construction + beta12orEarlier @@ -36267,12 +36423,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Multiple sequence alignment - Multiple sequence alignment generation - beta12orEarlier - Multiple sequence alignment - This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment. - Align two or more molecular sequences. Multiple sequence alignment construction + Align two or more molecular sequences. + This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment. + Multiple sequence alignment + beta12orEarlier + Multiple sequence alignment generation @@ -36284,14 +36440,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pairwise sequence alignment generation (local) - Pairwise sequence alignment construction (local) - 1.6 - Local alignment methods identify regions of local similarity. - true - Pairwise sequence alignment (local) - Locally align exactly two molecular sequences. - Local pairwise sequence alignment construction beta12orEarlier + Local pairwise sequence alignment construction + Locally align exactly two molecular sequences. + Pairwise sequence alignment (local) + true + Local alignment methods identify regions of local similarity. + 1.6 + Pairwise sequence alignment construction (local) @@ -36304,14 +36460,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pairwise sequence alignment generation (global) - Pairwise sequence alignment (global) - Global alignment methods identify similarity across the entire length of the sequences. - beta12orEarlier - Globally align exactly two molecular sequences. - true - 1.6 - Global pairwise sequence alignment construction Pairwise sequence alignment construction (global) + Global pairwise sequence alignment construction + 1.6 + true + Globally align exactly two molecular sequences. + beta12orEarlier + Global alignment methods identify similarity across the entire length of the sequences. + Pairwise sequence alignment (global) @@ -36324,14 +36480,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Local sequence alignment - Locally align two or more molecular sequences. - Sequence alignment (local) - Sequence alignment generation (local) - Multiple sequence alignment construction (local) - Local alignment methods identify regions of local similarity. - beta12orEarlier - Local multiple sequence alignment construction Multiple sequence alignment (local) + Local multiple sequence alignment construction + beta12orEarlier + Local alignment methods identify regions of local similarity. + Multiple sequence alignment construction (local) + Sequence alignment generation (local) + Sequence alignment (local) + Locally align two or more molecular sequences. @@ -36343,14 +36499,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Global sequence alignment - Global alignment methods identify similarity across the entire length of the sequences. - Sequence alignment generation (global) - Globally align two or more molecular sequences. - Multiple sequence alignment construction (global) - Sequence alignment (global) - beta12orEarlier - Multiple sequence alignment (global) Global multiple sequence alignment construction + Multiple sequence alignment (global) + beta12orEarlier + Sequence alignment (global) + Multiple sequence alignment construction (global) + Globally align two or more molecular sequences. + Sequence alignment generation (global) + Global alignment methods identify similarity across the entire length of the sequences. @@ -36362,13 +36518,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Constrained sequence alignment - Constrained multiple sequence alignment construction - Sequence alignment (constrained) - Multiple sequence alignment (constrained) - Sequence alignment generation (constrained) - Multiple sequence alignment construction (constrained) - Align two or more molecular sequences with user-defined constraints. beta12orEarlier + Align two or more molecular sequences with user-defined constraints. + Multiple sequence alignment construction (constrained) + Sequence alignment generation (constrained) + Multiple sequence alignment (constrained) + Sequence alignment (constrained) + Constrained multiple sequence alignment construction @@ -36380,13 +36536,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Consensus-based sequence alignment - Multiple sequence alignment (consensus) - Multiple sequence alignment construction (consensus) - Sequence alignment generation (consensus) - Align two or more molecular sequences using multiple methods to achieve higher quality. - beta12orEarlier - Sequence alignment (consensus) Consensus multiple sequence alignment construction + Sequence alignment (consensus) + beta12orEarlier + Align two or more molecular sequences using multiple methods to achieve higher quality. + Sequence alignment generation (consensus) + Multiple sequence alignment construction (consensus) + Multiple sequence alignment (consensus) @@ -36404,14 +36560,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Multiple sequence alignment (phylogenetic tree-based) - Multiple sequence alignment construction (phylogenetic tree-based) - Sequence alignment (phylogenetic tree-based) - Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree. - Phylogenetic tree-based multiple sequence alignment construction - beta12orEarlier - This is supposed to give a more biologically meaningful alignment than standard alignments. Sequence alignment generation (phylogenetic tree-based) + This is supposed to give a more biologically meaningful alignment than standard alignments. + beta12orEarlier + Phylogenetic tree-based multiple sequence alignment construction + Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree. + Sequence alignment (phylogenetic tree-based) + Multiple sequence alignment construction (phylogenetic tree-based) + Multiple sequence alignment (phylogenetic tree-based) @@ -36423,12 +36579,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Secondary structure alignment generation - Align molecular secondary structure (represented as a 1D string). - true - Secondary structure alignment - Secondary structure alignment construction - 1.6 beta12orEarlier + 1.6 + Secondary structure alignment construction + Secondary structure alignment + true + Align molecular secondary structure (represented as a 1D string). @@ -36447,11 +36603,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Protein secondary structure alignment - Secondary structure alignment (protein) - beta12orEarlier - Align protein secondary structures. Protein secondary structure alignment construction + Align protein secondary structures. + beta12orEarlier + Secondary structure alignment (protein) + Protein secondary structure alignment @@ -36476,12 +36632,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Secondary structure alignment (RNA) - RNA secondary structure alignment construction - Align RNA secondary structures. - RNA secondary structure alignment RNA secondary structure alignment generation + RNA secondary structure alignment + Align RNA secondary structures. + RNA secondary structure alignment construction + Secondary structure alignment (RNA) + beta12orEarlier @@ -36493,10 +36649,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pairwise structure alignment - Align (superimpose) exactly two molecular tertiary structures. - Pairwise structure alignment construction - Pairwise structure alignment generation beta12orEarlier + Pairwise structure alignment generation + Pairwise structure alignment construction + Align (superimpose) exactly two molecular tertiary structures. @@ -36508,12 +36664,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Multiple structure alignment construction - beta12orEarlier - Multiple structure alignment - true - 1.6 - This includes methods that use an existing alignment. Align (superimpose) two or more molecular tertiary structures. + This includes methods that use an existing alignment. + 1.6 + true + Multiple structure alignment + beta12orEarlier @@ -36525,10 +36681,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure alignment (protein) - Align protein tertiary structures. - beta12orEarlier - true beta13 + true + beta12orEarlier + Align protein tertiary structures. @@ -36540,10 +36696,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure alignment (RNA) - beta12orEarlier - Align RNA tertiary structures. - true beta13 + true + Align RNA tertiary structures. + beta12orEarlier @@ -36555,14 +36711,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pairwise structure alignment generation (local) - beta12orEarlier - Local pairwise structure alignment construction - true - 1.6 - Pairwise structure alignment construction (local) - Local alignment methods identify regions of local similarity, common substructures etc. - Pairwise structure alignment (local) Locally align (superimpose) exactly two molecular tertiary structures. + Pairwise structure alignment (local) + Local alignment methods identify regions of local similarity, common substructures etc. + Pairwise structure alignment construction (local) + 1.6 + true + Local pairwise structure alignment construction + beta12orEarlier @@ -36575,14 +36731,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pairwise structure alignment generation (global) - Pairwise structure alignment (global) - Globally align (superimpose) exactly two molecular tertiary structures. - Pairwise structure alignment construction (global) - 1.6 - beta12orEarlier - true - Global alignment methods identify similarity across the entire structures. Global pairwise structure alignment construction + Global alignment methods identify similarity across the entire structures. + true + beta12orEarlier + 1.6 + Pairwise structure alignment construction (global) + Globally align (superimpose) exactly two molecular tertiary structures. + Pairwise structure alignment (global) @@ -36595,14 +36751,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Local structure alignment - Structure alignment generation (local) - Multiple structure alignment (local) - Multiple structure alignment construction (local) - Locally align (superimpose) two or more molecular tertiary structures. - beta12orEarlier - Structure alignment construction (local) - Local alignment methods identify regions of local similarity, common substructures etc. Local multiple structure alignment construction + Local alignment methods identify regions of local similarity, common substructures etc. + Structure alignment construction (local) + beta12orEarlier + Locally align (superimpose) two or more molecular tertiary structures. + Multiple structure alignment construction (local) + Multiple structure alignment (local) + Structure alignment generation (local) @@ -36614,14 +36770,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Global structure alignment - Globally align (superimpose) two or more molecular tertiary structures. - Global multiple structure alignment construction - Global alignment methods identify similarity across the entire structures. - beta12orEarlier - Multiple structure alignment construction (global) - Structure alignment generation (global) - Multiple structure alignment (global) Structure alignment construction (global) + Multiple structure alignment (global) + Structure alignment generation (global) + Multiple structure alignment construction (global) + beta12orEarlier + Global alignment methods identify similarity across the entire structures. + Global multiple structure alignment construction + Globally align (superimpose) two or more molecular tertiary structures. @@ -36633,14 +36789,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Profile-to-profile alignment (pairwise) - Sequence profile alignment generation (pairwise) - Align exactly two molecular profiles. - beta12orEarlier - Sequence profile alignment (pairwise) - Sequence profile alignment construction (pairwise) - Pairwise sequence profile alignment construction - Methods might perform one-to-one, one-to-many or many-to-many comparisons. Sequence alignment generation (pairwise profile) + Methods might perform one-to-one, one-to-many or many-to-many comparisons. + Pairwise sequence profile alignment construction + Sequence profile alignment construction (pairwise) + Sequence profile alignment (pairwise) + beta12orEarlier + Align exactly two molecular profiles. + Sequence profile alignment generation (pairwise) @@ -36652,14 +36808,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence alignment generation (multiple profile) - Multiple sequence profile alignment construction - Sequence profile alignment construction (multiple) - Sequence profile alignment (multiple) - beta12orEarlier - Sequence profile alignment generation (multiple) - true - 1.6 Align two or more molecular profiles. + 1.6 + true + Sequence profile alignment generation (multiple) + beta12orEarlier + Sequence profile alignment (multiple) + Sequence profile alignment construction (multiple) + Multiple sequence profile alignment construction @@ -36671,13 +36827,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 3D profile-to-3D profile alignment (pairwise) - Structural profile alignment generation (pairwise) - beta12orEarlier - Align exactly two molecular Structural (3D) profiles. - Structural profile alignment construction (pairwise) - Structural (3D) profile alignment (pairwise) - Pairwise structural (3D) profile alignment construction Methods might perform one-to-one, one-to-many or many-to-many comparisons. + Pairwise structural (3D) profile alignment construction + Structural (3D) profile alignment (pairwise) + Structural profile alignment construction (pairwise) + Align exactly two molecular Structural (3D) profiles. + beta12orEarlier + Structural profile alignment generation (pairwise) @@ -36689,13 +36845,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structural profile alignment generation (multiple) - 1.6 - Structural (3D) profile alignment (multiple) - beta12orEarlier - Multiple structural (3D) profile alignment construction - Align two or more molecular 3D profiles. - Structural profile alignment construction (multiple) true + Structural profile alignment construction (multiple) + Align two or more molecular 3D profiles. + Multiple structural (3D) profile alignment construction + beta12orEarlier + Structural (3D) profile alignment (multiple) + 1.6 @@ -36707,12 +36863,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (tool metadata) - Tool information retrieval - true - beta12orEarlier - Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function. - 1.6 Data retrieval (tool annotation) + 1.6 + Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function. + beta12orEarlier + true + Tool information retrieval @@ -36724,12 +36880,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (database metadata) - 1.6 - Database information retrieval - Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword. - Data retrieval (database annotation) - true beta12orEarlier + true + Data retrieval (database annotation) + Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword. + Database information retrieval + 1.6 @@ -36747,8 +36903,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Predict primers for large scale sequencing. + beta12orEarlier @@ -36760,8 +36916,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern PCR primer design (for genotyping polymorphisms) - Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs). beta12orEarlier + Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs). @@ -36779,8 +36935,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Predict primers for gene transcription profiling. + beta12orEarlier @@ -36792,8 +36948,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern PCR primer design (for conserved primers) - beta12orEarlier Predict primers that are conserved across multiple genomes or species. + beta12orEarlier @@ -36811,8 +36967,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Predict primers based on gene structure, promoters, exon-exon junctions etc. + beta12orEarlier @@ -36824,8 +36980,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern PCR primer design (for methylation PCRs) - Predict primers for methylation PCRs. beta12orEarlier + Predict primers for methylation PCRs. @@ -36837,9 +36993,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence assembly (mapping assembly) - The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. - beta12orEarlier Sequence assembly by combining fragments using an existing backbone sequence, typically a reference genome. + beta12orEarlier + The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. @@ -36851,9 +37007,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence assembly (de-novo assembly) - beta12orEarlier - De-novo assemblers are much slower and more memory intensive than mapping assemblers. Sequence assembly by combining fragments without the aid of a reference sequence or genome. + De-novo assemblers are much slower and more memory intensive than mapping assemblers. + beta12orEarlier @@ -36865,8 +37021,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence assembly (genome assembly) - beta12orEarlier Sequence assembly capable on a very large scale such as assembly of whole genomes. + beta12orEarlier @@ -36878,9 +37034,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence assembly (EST assembly) - Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification. - Sequence assembly for EST sequences (transcribed mRNA). beta12orEarlier + Sequence assembly for EST sequences (transcribed mRNA). + Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification. @@ -36899,10 +37055,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts. - Tag to gene assignment Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. + Tag to gene assignment + Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts. + beta12orEarlier @@ -36914,11 +37070,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern SAGE data processing - true - Process (read and / or write) serial analysis of gene expression (SAGE) data. - beta12orEarlier - Serial analysis of gene expression data processing beta12orEarlier + Serial analysis of gene expression data processing + beta12orEarlier + Process (read and / or write) serial analysis of gene expression (SAGE) data. + true @@ -36930,11 +37086,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern MPSS data processing - beta12orEarlier - Massively parallel signature sequencing data processing - true - Process (read and / or write) massively parallel signature sequencing (MPSS) data. beta12orEarlier + Process (read and / or write) massively parallel signature sequencing (MPSS) data. + true + Massively parallel signature sequencing data processing + beta12orEarlier @@ -36946,11 +37102,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern SBS data processing - true - Process (read and / or write) sequencing by synthesis (SBS) data. - beta12orEarlier - Sequencing by synthesis data processing beta12orEarlier + Sequencing by synthesis data processing + beta12orEarlier + Process (read and / or write) sequencing by synthesis (SBS) data. + true @@ -36969,10 +37125,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Generate a heat map of gene expression from microarray data. - Heat map construction - The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions. beta12orEarlier + The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions. + Heat map construction + Generate a heat map of gene expression from microarray data. @@ -36984,11 +37140,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene expression profile analysis - 1.6 - Analyse one or more gene expression profiles, typically to interpret them in functional terms. - beta12orEarlier - Functional profiling true + Functional profiling + beta12orEarlier + Analyse one or more gene expression profiles, typically to interpret them in functional terms. + 1.6 @@ -37008,8 +37164,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway. beta12orEarlier + Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway. @@ -37022,8 +37178,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein secondary structure assignment (from coordinate data) - Assign secondary structure from protein coordinate data. beta12orEarlier + Assign secondary structure from protein coordinate data. @@ -37041,8 +37197,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Assign secondary structure from circular dichroism (CD) spectroscopic data. + beta12orEarlier @@ -37054,10 +37210,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein structure assignment (from X-ray crystallographic data) - beta12orEarlier - Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data. - 1.7 true + 1.7 + Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data. + beta12orEarlier @@ -37069,10 +37225,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein structure assignment (from NMR data) - 1.7 - true - Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data. beta12orEarlier + Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data. + true + 1.7 @@ -37084,9 +37240,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic tree generation (data centric) - Construct a phylogenetic tree from a specific type of data. - beta12orEarlier Phylogenetic tree construction (data centric) + beta12orEarlier + Construct a phylogenetic tree from a specific type of data. @@ -37098,9 +37254,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic tree generation (method centric) - beta12orEarlier - Construct a phylogenetic tree using a specific method. Phylogenetic tree construction (method centric) + Construct a phylogenetic tree using a specific method. + beta12orEarlier @@ -37113,10 +37269,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic tree generation (from molecular sequences) - Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. - Phylogenetic tree construction (from molecular sequences) - beta12orEarlier Phylogenetic tree construction from molecular sequences. + beta12orEarlier + Phylogenetic tree construction (from molecular sequences) + Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. @@ -37134,9 +37290,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Phylogenetic tree construction from continuous quantitative character data. - beta12orEarlier Phylogenetic tree construction (from continuous quantitative characters) + beta12orEarlier + Phylogenetic tree construction from continuous quantitative character data. @@ -37160,9 +37316,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Phylogenetic tree construction from gene frequency data. Phylogenetic tree construction (from gene frequencies) + Phylogenetic tree construction from gene frequency data. + beta12orEarlier @@ -37180,9 +37336,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Phylogenetic tree generation (from polymorphism data) Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data. + Phylogenetic tree generation (from polymorphism data) + beta12orEarlier @@ -37194,9 +37350,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic species tree construction - beta12orEarlier - Phylogenetic species tree generation Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison. + Phylogenetic species tree generation + beta12orEarlier @@ -37208,10 +37364,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic tree generation (parsimony methods) - beta12orEarlier - This includes evolutionary parsimony (invariants) methods. - Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment. Phylogenetic tree construction (parsimony methods) + Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment. + This includes evolutionary parsimony (invariants) methods. + beta12orEarlier @@ -37223,10 +37379,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic tree generation (minimum distance methods) - Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances. - Phylogenetic tree construction (minimum distance methods) - beta12orEarlier This includes neighbor joining (NJ) clustering method. + beta12orEarlier + Phylogenetic tree construction (minimum distance methods) + Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances. @@ -37238,10 +37394,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic tree generation (maximum likelihood and Bayesian methods) - beta12orEarlier - Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm. - Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution. Phylogenetic tree construction (maximum likelihood and Bayesian methods) + Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution. + Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm. + beta12orEarlier @@ -37253,9 +37409,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic tree generation (quartet methods) - Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely. - Phylogenetic tree construction (quartet methods) beta12orEarlier + Phylogenetic tree construction (quartet methods) + Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely. @@ -37267,9 +37423,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic tree generation (AI methods) - beta12orEarlier - Phylogenetic tree construction (AI methods) Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms. + Phylogenetic tree construction (AI methods) + beta12orEarlier @@ -37294,9 +37450,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Identify a plausible model of DNA substitution that explains a DNA sequence alignment. - beta12orEarlier Sequence alignment analysis (phylogenetic modelling) + beta12orEarlier + Identify a plausible model of DNA substitution that explains a DNA sequence alignment. @@ -37308,9 +37464,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic tree analysis (shape) - beta12orEarlier - Analyse the shape (topology) of a phylogenetic tree. Phylogenetic tree topology analysis + Analyse the shape (topology) of a phylogenetic tree. + beta12orEarlier @@ -37323,8 +37479,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic tree bootstrapping - beta12orEarlier Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree. + beta12orEarlier @@ -37348,8 +37504,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Predict families of genes and gene function based on their position in a phylogenetic tree. + beta12orEarlier @@ -37361,9 +37517,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic tree analysis (natural selection) - Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive). - Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait. beta12orEarlier + Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait. + Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive). @@ -37376,10 +37532,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic tree generation (consensus) - Phylogenetic tree construction (consensus) - beta12orEarlier - Methods typically test for topological similarity between trees using for example a congruence index. Compare two or more phylogenetic trees to produce a consensus tree. + Methods typically test for topological similarity between trees using for example a congruence index. + beta12orEarlier + Phylogenetic tree construction (consensus) @@ -37391,8 +37547,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic sub/super tree detection - Compare two or more phylogenetic trees to detect subtrees or supertrees. beta12orEarlier + Compare two or more phylogenetic trees to detect subtrees or supertrees. @@ -37410,8 +37566,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Compare two or more phylogenetic trees to calculate distances between trees. beta12orEarlier + Compare two or more phylogenetic trees to calculate distances between trees. @@ -37423,9 +37579,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic tree annotation - Annotate a phylogenetic tree with terms from a controlled vocabulary. - http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation beta12orEarlier + http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation + Annotate a phylogenetic tree with terms from a controlled vocabulary. @@ -37445,19 +37601,19 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - Predict and optimise peptide ligands that elicit an immunological response. - Peptide immunogen prediction beta12orEarlier + Peptide immunogen prediction + Predict and optimise peptide ligands that elicit an immunological response. @@ -37473,17 +37629,17 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + - + - Predict or optimise DNA to elicit (via DNA vaccination) an immunological response. beta12orEarlier + Predict or optimise DNA to elicit (via DNA vaccination) an immunological response. @@ -37507,9 +37663,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Sequence file format conversion - Reformat (a file or other report of) molecular sequence(s). beta12orEarlier + Reformat (a file or other report of) molecular sequence(s). + Sequence file format conversion @@ -37523,18 +37679,18 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + - + - beta12orEarlier Reformat (a file or other report of) molecular sequence alignment(s). + beta12orEarlier @@ -37559,8 +37715,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Reformat a codon usage table. + beta12orEarlier @@ -37585,9 +37741,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Sequence rendering - Visualise, format or render a molecular sequence, possibly with sequence features or properties shown. beta12orEarlier + Visualise, format or render a molecular sequence, possibly with sequence features or properties shown. + Sequence rendering @@ -37602,19 +37758,19 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - beta12orEarlier - Visualise, format or print a molecular sequence alignment. Sequence alignment rendering + Visualise, format or print a molecular sequence alignment. + beta12orEarlier @@ -37628,19 +37784,19 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - Visualise, format or render sequence clusters. - beta12orEarlier Sequence cluster rendering + beta12orEarlier + Visualise, format or render sequence clusters. @@ -37659,9 +37815,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Phylogenetic tree rendering Render or visualise a phylogenetic tree. + Phylogenetic tree rendering + beta12orEarlier @@ -37680,9 +37836,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Visualise RNA secondary structure, knots, pseudoknots etc. RNA secondary structure rendering + Visualise RNA secondary structure, knots, pseudoknots etc. + beta12orEarlier @@ -37692,8 +37848,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Protein secondary structure visualisation Protein secondary structure rendering + Protein secondary structure visualisation @@ -37701,8 +37857,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Render and visualise protein secondary structure. + beta12orEarlier @@ -37727,9 +37883,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation. Structure rendering + Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation. + beta12orEarlier @@ -37749,8 +37905,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Visualise microarray data. + beta12orEarlier @@ -37760,8 +37916,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Protein interaction network visualisation Protein interaction network rendering + Protein interaction network visualisation @@ -37769,9 +37925,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Identify and analyse networks of protein interactions. - beta12orEarlier + beta12orEarlier + Identify and analyse networks of protein interactions. @@ -37789,10 +37945,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Draw or visualise a DNA map. - Map rendering - DNA map drawing beta12orEarlier + DNA map drawing + Map rendering + Draw or visualise a DNA map. @@ -37804,10 +37960,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence motif rendering - beta12orEarlier - beta12orEarlier - true Render a sequence with motifs. + true + beta12orEarlier + beta12orEarlier @@ -37826,8 +37982,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Draw or visualise restriction maps in DNA sequences. + beta12orEarlier @@ -37839,10 +37995,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern DNA linear map rendering - Draw a linear maps of DNA. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Draw a linear maps of DNA. @@ -37854,9 +38010,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Plasmid map drawing - Draw a circular maps of DNA, for example a plasmid map. - DNA circular map rendering beta12orEarlier + DNA circular map rendering + Draw a circular maps of DNA, for example a plasmid map. @@ -37874,9 +38030,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Operon rendering - beta12orEarlier Visualise operon structure etc. + beta12orEarlier + Operon rendering @@ -37888,10 +38044,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid folding family identification - beta12orEarlier - Identify folding families of related RNAs. - beta12orEarlier true + beta12orEarlier + Identify folding families of related RNAs. + beta12orEarlier @@ -37903,8 +38059,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid folding energy calculation - Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants. beta12orEarlier + Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants. @@ -37916,11 +38072,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Annotation retrieval - true - beta12orEarlier - Retrieve existing annotation (or documentation), typically annotation on a database entity. - Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations. beta12orEarlier + Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations. + Retrieve existing annotation (or documentation), typically annotation on a database entity. + beta12orEarlier + true @@ -37939,9 +38095,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. - Predict general functional properties of a protein. beta12orEarlier + Predict general functional properties of a protein. + For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. @@ -37960,8 +38116,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Compare the functional properties of two or more proteins. + beta12orEarlier @@ -37973,10 +38129,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence submission - true - 1.6 - beta12orEarlier Submit a molecular sequence to a database. + beta12orEarlier + 1.6 + true @@ -37994,8 +38150,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Analyse a known network of gene regulation. beta12orEarlier + Analyse a known network of gene regulation. @@ -38014,10 +38170,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Prepare or load a user-specified data file so that it is available for use. - WHATIF:UploadPDB Data loading + WHATIF:UploadPDB + Prepare or load a user-specified data file so that it is available for use. + beta12orEarlier @@ -38029,12 +38185,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence retrieval - true - beta12orEarlier - Query a sequence data resource (typically a database) and retrieve sequences and / or annotation. - 1.6 - Data retrieval (sequences) This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. + Data retrieval (sequences) + 1.6 + Query a sequence data resource (typically a database) and retrieve sequences and / or annotation. + beta12orEarlier + true @@ -38046,13 +38202,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure retrieval - 1.6 - Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation. - This includes direct retrieval methods but not those that perform calculations on the sequence or structure. - WHATIF:DownloadPDB - beta12orEarlier - WHATIF:EchoPDB true + WHATIF:EchoPDB + beta12orEarlier + WHATIF:DownloadPDB + This includes direct retrieval methods but not those that perform calculations on the sequence or structure. + Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation. + 1.6 @@ -38065,10 +38221,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Surface rendering - A dot has three coordinates (x,y,z) and (typically) a color. - Calculate the positions of dots that are homogeneously distributed over the surface of a molecule. - WHATIF:GetSurfaceDots beta12orEarlier + WHATIF:GetSurfaceDots + Calculate the positions of dots that are homogeneously distributed over the surface of a molecule. + A dot has three coordinates (x,y,z) and (typically) a color. @@ -38080,11 +38236,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein atom surface calculation (accessible) - Waters are not considered. - Calculate the solvent accessibility ('accessible surface') for each atom in a structure. - WHATIF:AtomAccessibilitySolvent - WHATIF:AtomAccessibilitySolventPlus beta12orEarlier + WHATIF:AtomAccessibilitySolventPlus + WHATIF:AtomAccessibilitySolvent + Calculate the solvent accessibility ('accessible surface') for each atom in a structure. + Waters are not considered. @@ -38096,11 +38252,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein atom surface calculation (accessible molecular) - WHATIF:AtomAccessibilityMolecularPlus - WHATIF:AtomAccessibilityMolecular - Waters are not considered. - Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure. beta12orEarlier + Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure. + Waters are not considered. + WHATIF:AtomAccessibilityMolecular + WHATIF:AtomAccessibilityMolecularPlus @@ -38112,10 +38268,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue surface calculation (accessible) - Calculate the solvent accessibility ('accessible surface') for each residue in a structure. - Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). - beta12orEarlier WHATIF:ResidueAccessibilitySolvent + beta12orEarlier + Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + Calculate the solvent accessibility ('accessible surface') for each residue in a structure. @@ -38127,10 +38283,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue surface calculation (vacuum accessible) - beta12orEarlier - WHATIF:ResidueAccessibilityVacuum - Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. + WHATIF:ResidueAccessibilityVacuum + beta12orEarlier @@ -38142,10 +38298,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue surface calculation (accessible molecular) - beta12orEarlier - Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). - WHATIF:ResidueAccessibilityMolecular Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure. + WHATIF:ResidueAccessibilityMolecular + Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + beta12orEarlier @@ -38157,10 +38313,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue surface calculation (vacuum molecular) - WHATIF:ResidueAccessibilityVacuumMolecular - Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. - beta12orEarlier Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + beta12orEarlier + Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. + WHATIF:ResidueAccessibilityVacuumMolecular @@ -38172,9 +38328,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein surface calculation (accessible molecular) - Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole. - beta12orEarlier WHATIF:TotAccessibilityMolecular + beta12orEarlier + Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole. @@ -38186,9 +38342,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein surface calculation (accessible) - beta12orEarlier - Calculate the solvent accessibility ('accessible surface') for a structure as a whole. WHATIF:TotAccessibilitySolvent + Calculate the solvent accessibility ('accessible surface') for a structure as a whole. + beta12orEarlier @@ -38200,9 +38356,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Backbone torsion angle calculation - Calculate for each residue in a protein structure all its backbone torsion angles. - WHATIF:ResidueTorsionsBB beta12orEarlier + WHATIF:ResidueTorsionsBB + Calculate for each residue in a protein structure all its backbone torsion angles. @@ -38214,9 +38370,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Full torsion angle calculation - WHATIF:ResidueTorsions - Calculate for each residue in a protein structure all its torsion angles. beta12orEarlier + Calculate for each residue in a protein structure all its torsion angles. + WHATIF:ResidueTorsions @@ -38228,9 +38384,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Cysteine torsion angle calculation - WHATIF:CysteineTorsions - Calculate for each cysteine (bridge) all its torsion angles. beta12orEarlier + Calculate for each cysteine (bridge) all its torsion angles. + WHATIF:CysteineTorsions @@ -38242,10 +38398,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Tau angle calculation - For each amino acid in a protein structure calculate the backbone angle tau. - Tau is the backbone angle N-Calpha-C (angle over the C-alpha). - beta12orEarlier WHATIF:ShowTauAngle + beta12orEarlier + Tau is the backbone angle N-Calpha-C (angle over the C-alpha). + For each amino acid in a protein structure calculate the backbone angle tau. @@ -38257,9 +38413,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Cysteine bridge detection - beta12orEarlier - Detect cysteine bridges (from coordinate data) in a protein structure. WHATIF:ShowCysteineBridge + Detect cysteine bridges (from coordinate data) in a protein structure. + beta12orEarlier @@ -38271,10 +38427,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Free cysteine detection - WHATIF:ShowCysteineFree - Detect free cysteines in a protein structure. - A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal. beta12orEarlier + A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal. + Detect free cysteines in a protein structure. + WHATIF:ShowCysteineFree @@ -38286,9 +38442,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Metal-bound cysteine detection - Detect cysteines that are bound to metal in a protein structure. - WHATIF:ShowCysteineMetal beta12orEarlier + WHATIF:ShowCysteineMetal + Detect cysteines that are bound to metal in a protein structure. @@ -38302,10 +38458,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - WHATIF:HasNucleicContacts - Calculate protein residue contacts with nucleic acids in a structure. - WHATIF:ShowProteiNucleicContacts beta12orEarlier + WHATIF:ShowProteiNucleicContacts + Calculate protein residue contacts with nucleic acids in a structure. + WHATIF:HasNucleicContacts @@ -38318,10 +38474,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue contact calculation (residue-metal) - WHATIF:HasMetalContactsPlus - Calculate protein residue contacts with metal in a structure. - beta12orEarlier WHATIF:HasMetalContacts + beta12orEarlier + Calculate protein residue contacts with metal in a structure. + WHATIF:HasMetalContactsPlus @@ -38333,10 +38489,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue contact calculation (residue-negative ion) - WHATIF:HasNegativeIonContacts - beta12orEarlier - WHATIF:HasNegativeIonContactsPlus Calculate ion contacts in a structure (all ions for all side chain atoms). + WHATIF:HasNegativeIonContactsPlus + beta12orEarlier + WHATIF:HasNegativeIonContacts @@ -38348,9 +38504,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue bump detection - Detect 'bumps' between residues in a structure, i.e. those with pairs of atoms whose Van der Waals' radii interpenetrate more than a defined distance. - beta12orEarlier WHATIF:ShowBumps + beta12orEarlier + Detect 'bumps' between residues in a structure, i.e. those with pairs of atoms whose Van der Waals' radii interpenetrate more than a defined distance. @@ -38362,10 +38518,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue symmetry contact calculation - beta12orEarlier - A symmetry contact is a contact between two atoms in different asymmetric unit. - WHATIF:SymmetryContact Calculate the number of symmetry contacts made by residues in a protein structure. + WHATIF:SymmetryContact + A symmetry contact is a contact between two atoms in different asymmetric unit. + beta12orEarlier @@ -38378,11 +38534,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue contact calculation (residue-ligand) - WHATIF:ShowDrugContacts - WHATIF:ShowLigandContacts - WHATIF:ShowDrugContactsShort - Calculate contacts between residues and ligands in a protein structure. beta12orEarlier + Calculate contacts between residues and ligands in a protein structure. + WHATIF:ShowDrugContactsShort + WHATIF:ShowLigandContacts + WHATIF:ShowDrugContacts @@ -38394,13 +38550,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Salt bridge calculation - Calculate (and possibly score) salt bridges in a protein structure. - WHATIF:ShowSaltBridgesH - WHATIF:HasSaltBridge - beta12orEarlier - WHATIF:ShowSaltBridges - WHATIF:HasSaltBridgePlus Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance. + WHATIF:HasSaltBridgePlus + WHATIF:ShowSaltBridges + beta12orEarlier + WHATIF:HasSaltBridge + WHATIF:ShowSaltBridgesH + Calculate (and possibly score) salt bridges in a protein structure. @@ -38412,19 +38568,19 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Rotamer likelihood prediction - beta12orEarlier - WHATIF:ShowLikelyRotamers100 - WHATIF:ShowLikelyRotamers200 - WHATIF:ShowLikelyRotamers300 - WHATIF:ShowLikelyRotamers400 - WHATIF:ShowLikelyRotamers700 - Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. - WHATIF:ShowLikelyRotamers900 - WHATIF:ShowLikelyRotamers600 - WHATIF:ShowLikelyRotamers800 - Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure. - WHATIF:ShowLikelyRotamers500 WHATIF:ShowLikelyRotamers + WHATIF:ShowLikelyRotamers500 + Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure. + WHATIF:ShowLikelyRotamers800 + WHATIF:ShowLikelyRotamers600 + WHATIF:ShowLikelyRotamers900 + Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. + WHATIF:ShowLikelyRotamers700 + WHATIF:ShowLikelyRotamers400 + WHATIF:ShowLikelyRotamers300 + WHATIF:ShowLikelyRotamers200 + WHATIF:ShowLikelyRotamers100 + beta12orEarlier @@ -38436,9 +38592,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Proline mutation value calculation - beta12orEarlier - WHATIF:ProlineMutationValue Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein. + WHATIF:ProlineMutationValue + beta12orEarlier @@ -38450,9 +38606,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue packing validation - WHATIF: PackingQuality - Identify poorly packed residues in protein structures. beta12orEarlier + Identify poorly packed residues in protein structures. + WHATIF: PackingQuality @@ -38464,10 +38620,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Dihedral angle validation - WHATIF: ImproperQualityMax - beta12orEarlier - Identify for each residue in a protein structure any improper dihedral (phi/psi) angles. WHATIF: ImproperQualitySum + Identify for each residue in a protein structure any improper dihedral (phi/psi) angles. + beta12orEarlier + WHATIF: ImproperQualityMax @@ -38479,11 +38635,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern PDB file sequence retrieval - beta12orEarlier - true - WHATIF: PDB_sequence - beta12orEarlier Extract a molecular sequence from a PDB file. + beta12orEarlier + WHATIF: PDB_sequence + true + beta12orEarlier @@ -38495,10 +38651,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern HET group detection - A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. - beta12orEarlier - WHATIF: HETGroupNames Identify HET groups in PDB files. + WHATIF: HETGroupNames + beta12orEarlier + A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. @@ -38510,11 +38666,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern DSSP secondary structure assignment - true - beta12orEarlier - WHATIF: ResidueDSSP - beta12orEarlier Determine for residue the DSSP determined secondary structure in three-state (HSC). + beta12orEarlier + WHATIF: ResidueDSSP + beta12orEarlier + true @@ -38526,9 +38682,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure formatting - WHATIF: PDBasXML - beta12orEarlier Reformat (a file or other report of) tertiary structure data. + beta12orEarlier + WHATIF: PDBasXML @@ -38546,8 +38702,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Assign cysteine bonding state and disulfide bond partners in protein structures. + beta12orEarlier @@ -38559,10 +38715,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue validation - The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues). - WHATIF: UseResidueDB - beta12orEarlier Identify poor quality amino acid positions in protein structures. + beta12orEarlier + WHATIF: UseResidueDB + The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues). @@ -38574,11 +38730,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure retrieval (water) - Query a tertiary structure database and retrieve water molecules. - true - WHATIF:MovedWaterPDB - 1.6 beta12orEarlier + 1.6 + WHATIF:MovedWaterPDB + true + Query a tertiary structure database and retrieve water molecules. @@ -38596,8 +38752,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Identify or predict siRNA duplexes in RNA. beta12orEarlier + Identify or predict siRNA duplexes in RNA. @@ -38610,8 +38766,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence alignment refinement - beta12orEarlier Refine an existing sequence alignment. + beta12orEarlier @@ -38623,10 +38779,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Listfile processing - beta12orEarlier - true - Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses). 1.6 + Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses). + true + beta12orEarlier @@ -38639,8 +38795,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence file editing - Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, creation of subset or a new file of sequences. beta12orEarlier + Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, creation of subset or a new file of sequences. @@ -38652,10 +38808,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence alignment file processing - true - 1.6 - Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences. beta12orEarlier + Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences. + 1.6 + true @@ -38667,10 +38823,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Small molecule data processing - Process (read and / or write) physicochemical property data for small molecules. - beta12orEarlier - true beta13 + true + beta12orEarlier + Process (read and / or write) physicochemical property data for small molecules. @@ -38682,11 +38838,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (ontology annotation) - beta12orEarlier - Search and retrieve documentation on a bioinformatics ontology. - true - Ontology information retrieval beta13 + Ontology information retrieval + true + Search and retrieve documentation on a bioinformatics ontology. + beta12orEarlier @@ -38698,11 +38854,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (ontology concept) - Ontology retrieval - beta12orEarlier - beta13 - true Query an ontology and retrieve concepts or relations. + true + beta13 + beta12orEarlier + Ontology retrieval @@ -38720,8 +38876,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences. + beta12orEarlier @@ -38733,10 +38889,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure file processing - true - beta12orEarlier - 1.6 Perform basic (non-analytical) operations on a file of molecular tertiary structural data. + 1.6 + beta12orEarlier + true @@ -38748,11 +38904,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (sequence profile) - beta12orEarlier - beta13 - This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. - true Query a profile data resource and retrieve one or more profile(s) and / or associated annotation. + true + This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. + beta13 + beta12orEarlier @@ -38764,10 +38920,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Statistical calculation - true - beta12orEarlier - Perform a statistical data operation of some type, e.g. calibration or validation. Statistical analysis + Perform a statistical data operation of some type, e.g. calibration or validation. + beta12orEarlier + true @@ -38793,10 +38949,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data. - A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. - 3D-1D scoring matrix construction beta12orEarlier + 3D-1D scoring matrix construction + A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. + Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data. @@ -38815,9 +38971,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Transmembrane protein rendering - beta12orEarlier Visualise transmembrane proteins, typically the transmembrane regions within a sequence. + beta12orEarlier + Transmembrane protein rendering @@ -38829,10 +38985,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Demonstration - beta13 - An operation performing purely illustrative (pedagogical) purposes. - true beta12orEarlier + true + An operation performing purely illustrative (pedagogical) purposes. + beta13 @@ -38843,10 +38999,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (pathway or network) - beta13 - Query a biological pathways database and retrieve annotation on one or more pathways. - true beta12orEarlier + true + Query a biological pathways database and retrieve annotation on one or more pathways. + beta13 @@ -38858,10 +39014,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (identifier) - true - beta13 - Query a database and retrieve one or more data identifiers. beta12orEarlier + Query a database and retrieve one or more data identifiers. + beta13 + true @@ -38874,8 +39030,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid density plotting - Calculate a density plot (of base composition) for a nucleotide sequence. beta12orEarlier + Calculate a density plot (of base composition) for a nucleotide sequence. @@ -38893,9 +39049,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Sequence analysis (general) - beta12orEarlier Analyse one or more known molecular sequences. + beta12orEarlier + Sequence analysis (general) @@ -38907,10 +39063,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence motif processing - beta12orEarlier - Process (read and / or write) molecular sequence motifs. - 1.6 true + 1.6 + Process (read and / or write) molecular sequence motifs. + beta12orEarlier @@ -38922,10 +39078,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein interaction data processing - beta12orEarlier - true - Process (read and / or write) protein interaction data. 1.6 + Process (read and / or write) protein interaction data. + true + beta12orEarlier @@ -38940,19 +39096,19 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - Analyse protein tertiary structural data. - beta12orEarlier Structure analysis (protein) + beta12orEarlier + Analyse protein tertiary structural data. @@ -38964,10 +39120,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Annotation processing - Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity. - beta12orEarlier - beta12orEarlier true + beta12orEarlier + beta12orEarlier + Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity. @@ -38979,10 +39135,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence feature analysis - beta12orEarlier - Analyse features in molecular sequences. - true beta12orEarlier + true + Analyse features in molecular sequences. + beta12orEarlier @@ -39000,12 +39156,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Data file processing - File handling - Report handling - beta12orEarlier - File processing Basic (non-analytical) operations of some data, either a file or equivalent entity in memory. + File processing + beta12orEarlier + Report handling + File handling + Data file processing @@ -39017,10 +39173,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene expression analysis - beta12orEarlier - true - beta12orEarlier Analyse gene expression and regulation data. + beta12orEarlier + true + beta12orEarlier @@ -39032,11 +39188,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structural profile processing - true - 3D profile processing - Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type. - 1.6 beta12orEarlier + 1.6 + Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type. + 3D profile processing + true @@ -39048,11 +39204,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data index processing - beta12orEarlier - 1.6 - Process (read and / or write) an index of (typically a file of) biological data. - true Database index processing + true + Process (read and / or write) an index of (typically a file of) biological data. + 1.6 + beta12orEarlier @@ -39064,10 +39220,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence profile processing - 1.6 - Process (read and / or write) some type of sequence profile. - beta12orEarlier true + beta12orEarlier + Process (read and / or write) some type of sequence profile. + 1.6 @@ -39085,9 +39241,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report. - beta12orEarlier This is a broad concept and is used a placeholder for other, more specific concepts. + beta12orEarlier + Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report. @@ -39112,10 +39268,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Protein folding modelling - Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report. This is a broad concept and is used a placeholder for other, more specific concepts. + Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report. + Protein folding modelling + beta12orEarlier @@ -39129,19 +39285,19 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - Secondary structure analysis (protein) - beta12orEarlier Analyse known protein secondary structure data. + beta12orEarlier + Secondary structure analysis (protein) @@ -39153,10 +39309,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Physicochemical property data processing - beta12orEarlier - Process (read and / or write) data on the physicochemical property of a molecule. - true beta13 + true + Process (read and / or write) data on the physicochemical property of a molecule. + beta12orEarlier @@ -39175,9 +39331,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Predict oligonucleotide primers or probes. - beta12orEarlier Primer and probe prediction + beta12orEarlier + Predict oligonucleotide primers or probes. @@ -39189,11 +39345,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Operation (typed) - beta12orEarlier - Process (read and / or write) data of a specific type, for example applying analytical methods. - Processing - Calculation Computation + Calculation + Processing + Process (read and / or write) data of a specific type, for example applying analytical methods. + beta12orEarlier @@ -39211,9 +39367,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query. - Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database. beta12orEarlier + Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database. + Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query. @@ -39231,9 +39387,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords. - beta12orEarlier Information retrieval + beta12orEarlier + Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords. @@ -39245,11 +39401,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Prediction and recognition - Detection - Predict, recognise, detect or identify some properties of a biomolecule. - Prediction - Recognition beta12orEarlier + Recognition + Prediction + Predict, recognise, detect or identify some properties of a biomolecule. + Detection @@ -39261,8 +39417,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Comparison - Compare two or more things to identify similarities. beta12orEarlier + Compare two or more things to identify similarities. @@ -39274,8 +39430,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Optimisation and refinement - Refine or optimise some data model. beta12orEarlier + Refine or optimise some data model. @@ -39293,8 +39449,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Model or simulate some biological entity or system. beta12orEarlier + Model or simulate some biological entity or system. @@ -39306,10 +39462,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data handling - beta12orEarlier - Perform basic operations on some data or a database. - beta12orEarlier true + beta12orEarlier + Perform basic operations on some data or a database. + beta12orEarlier @@ -39321,9 +39477,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Validation - Validate some data. - Validation and standardisation beta12orEarlier + Validation and standardisation + Validate some data. @@ -39335,9 +39491,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Mapping - beta12orEarlier - Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts. This is a broad concept and is used a placeholder for other, more specific concepts. + Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts. + beta12orEarlier @@ -39349,9 +39505,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Design - true - Design a biological entity (typically a molecular sequence or structure) with specific properties. beta12orEarlier + Design a biological entity (typically a molecular sequence or structure) with specific properties. + true @@ -39363,10 +39519,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Microarray data processing - true - beta12orEarlier - Process (read and / or write) microarray data. beta12orEarlier + Process (read and / or write) microarray data. + beta12orEarlier + true @@ -39378,8 +39534,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Codon usage table processing - beta12orEarlier Process (read and / or write) a codon usage table. + beta12orEarlier @@ -39391,10 +39547,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (codon usage table) - beta13 - true - beta12orEarlier Retrieve a codon usage table and / or associated annotation. + beta12orEarlier + true + beta13 @@ -39406,10 +39562,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene expression profile processing - beta12orEarlier - true - Process (read and / or write) a gene expression profile. 1.6 + Process (read and / or write) a gene expression profile. + true + beta12orEarlier @@ -39428,11 +39584,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - GO term enrichment - Analyse a set of genes (genes corresponding to an expression profile, or any other set) with respect to concepts from an ontology of gene functions. - The Gene Ontology (GO) is invariably used, the input is a set of Gene IDs and the output of the analysis is typically a ranked list of GO terms, each associated with a p-value. - Gene expression profile annotation beta12orEarlier + Gene expression profile annotation + The Gene Ontology (GO) is invariably used, the input is a set of Gene IDs and the output of the analysis is typically a ranked list of GO terms, each associated with a p-value. + Analyse a set of genes (genes corresponding to an expression profile, or any other set) with respect to concepts from an ontology of gene functions. + GO term enrichment @@ -39457,8 +39613,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Predict a network of gene regulation. + beta12orEarlier @@ -39476,8 +39632,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Generate, analyse or handle a biological pathway or network. + beta12orEarlier @@ -39495,8 +39651,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Process (read and / or write) RNA secondary structure data. beta12orEarlier + Process (read and / or write) RNA secondary structure data. @@ -39508,10 +39664,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure processing (RNA) - true - beta13 - beta12orEarlier Process (read and / or write) RNA tertiary structure data. + beta12orEarlier + beta13 + true @@ -39529,8 +39685,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Predict RNA tertiary structure. beta12orEarlier + Predict RNA tertiary structure. @@ -39548,8 +39704,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Predict DNA tertiary structure. + beta12orEarlier @@ -39567,8 +39723,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Process (read and / or write) a phylogenetic tree. beta12orEarlier + Process (read and / or write) a phylogenetic tree. @@ -39580,10 +39736,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein secondary structure processing - beta12orEarlier - true - 1.6 Process (read and / or write) protein secondary structure data. + 1.6 + true + beta12orEarlier @@ -39595,10 +39751,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein interaction network processing - 1.6 - Process (read and / or write) a network of protein interactions. - beta12orEarlier true + beta12orEarlier + Process (read and / or write) a network of protein interactions. + 1.6 @@ -39610,11 +39766,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence processing - 1.6 - beta12orEarlier - true - Process (read and / or write) one or more molecular sequences and associated annotation. Sequence processing (general) + Process (read and / or write) one or more molecular sequences and associated annotation. + true + beta12orEarlier + 1.6 @@ -39626,10 +39782,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence processing (protein) - 1.6 - true - beta12orEarlier Process (read and / or write) a protein sequence and associated annotation. + beta12orEarlier + true + 1.6 @@ -39641,10 +39797,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence processing (nucleic acid) - Process (read and / or write) a nucleotide sequence and associated annotation. - beta12orEarlier - true 1.6 + true + beta12orEarlier + Process (read and / or write) a nucleotide sequence and associated annotation. @@ -39659,14 +39815,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + @@ -39675,8 +39831,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Compare two or more molecular sequences. + beta12orEarlier @@ -39688,10 +39844,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence cluster processing - 1.6 - beta12orEarlier - true Process (read and / or write) a sequence cluster. + true + beta12orEarlier + 1.6 @@ -39703,10 +39859,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Feature table processing - beta12orEarlier - true - 1.6 Process (read and / or write) a sequence feature table. + 1.6 + true + beta12orEarlier @@ -39730,10 +39886,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Gene finding - Detect, predict and identify genes or components of genes in DNA sequences. - beta12orEarlier Gene and gene component prediction + beta12orEarlier + Detect, predict and identify genes or components of genes in DNA sequences. + Gene finding @@ -39752,9 +39908,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Classify G-protein coupled receptors (GPCRs) into families and subfamilies. - G protein-coupled receptor (GPCR) classification beta12orEarlier + G protein-coupled receptor (GPCR) classification + Classify G-protein coupled receptors (GPCRs) into families and subfamilies. @@ -39774,8 +39930,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Predict G-protein coupled receptor (GPCR) coupling selectivity. + beta12orEarlier @@ -39787,10 +39943,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure processing (protein) - Process (read and / or write) a protein tertiary structure. - beta12orEarlier - 1.6 true + 1.6 + beta12orEarlier + Process (read and / or write) a protein tertiary structure. @@ -39802,9 +39958,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein atom surface calculation - beta12orEarlier - Calculate the solvent accessibility for each atom in a structure. Waters are not considered. + Calculate the solvent accessibility for each atom in a structure. + beta12orEarlier @@ -39816,8 +39972,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue surface calculation - Calculate the solvent accessibility for each residue in a structure. beta12orEarlier + Calculate the solvent accessibility for each residue in a structure. @@ -39829,8 +39985,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein surface calculation - Calculate the solvent accessibility of a structure as a whole. beta12orEarlier + Calculate the solvent accessibility of a structure as a whole. @@ -39842,10 +39998,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence alignment processing - 1.6 - Process (read and / or write) a molecular sequence alignment. - true beta12orEarlier + true + Process (read and / or write) a molecular sequence alignment. + 1.6 @@ -39869,8 +40025,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Identify or predict protein-protein interactions, interfaces, binding sites etc. + beta12orEarlier @@ -39882,10 +40038,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure processing - beta12orEarlier - Process (read and / or write) a molecular tertiary structure. - 1.6 true + 1.6 + Process (read and / or write) a molecular tertiary structure. + beta12orEarlier @@ -39897,10 +40053,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Map annotation - 1.6 - beta12orEarlier - true Annotate a DNA map of some type with terms from a controlled vocabulary. + true + beta12orEarlier + 1.6 @@ -39912,11 +40068,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (protein annotation) - beta12orEarlier - Protein information retrieval - true - beta13 Retrieve information on a protein. + beta13 + true + Protein information retrieval + beta12orEarlier @@ -39928,10 +40084,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (phylogenetic tree) - true - Retrieve a phylogenetic tree from a data resource. - beta13 beta12orEarlier + beta13 + Retrieve a phylogenetic tree from a data resource. + true @@ -39943,10 +40099,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (protein interaction annotation) - beta12orEarlier - beta13 - true Retrieve information on a protein interaction. + true + beta13 + beta12orEarlier @@ -39958,11 +40114,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (protein family annotation) - true - Retrieve information on a protein family. - beta13 - Protein family information retrieval beta12orEarlier + Protein family information retrieval + beta13 + Retrieve information on a protein family. + true @@ -39974,11 +40130,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (RNA family annotation) - beta13 - beta12orEarlier - RNA family information retrieval - Retrieve information on an RNA family. true + Retrieve information on an RNA family. + RNA family information retrieval + beta12orEarlier + beta13 @@ -39990,11 +40146,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (gene annotation) - beta13 - true - Retrieve information on a specific gene. - Gene information retrieval beta12orEarlier + Gene information retrieval + Retrieve information on a specific gene. + true + beta13 @@ -40006,11 +40162,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (genotype and phenotype annotation) - true - beta13 - beta12orEarlier - Genotype and phenotype information retrieval Retrieve information on a specific genotype or phenotype. + Genotype and phenotype information retrieval + beta12orEarlier + beta13 + true @@ -40023,8 +40179,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein architecture comparison - beta12orEarlier Compare the architecture of two or more protein structures. + beta12orEarlier @@ -40038,9 +40194,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Identify the architecture of a protein structure. - Includes methods that try to suggest the most likely biological unit for a given protein X-ray crystal structure based on crystal symmetry and scoring of putative protein-protein interfaces. beta12orEarlier + Includes methods that try to suggest the most likely biological unit for a given protein X-ray crystal structure based on crystal symmetry and scoring of putative protein-protein interfaces. + Identify the architecture of a protein structure. @@ -40057,7 +40213,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + @@ -40069,11 +40225,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + - beta12orEarlier Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation. + beta12orEarlier @@ -40098,9 +40254,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Sequence analysis (nucleic acid) - beta12orEarlier Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences). + beta12orEarlier + Sequence analysis (nucleic acid) @@ -40119,9 +40275,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Sequence analysis (protein) Analyse a protein sequence (using methods that are only applicable to protein sequences). + Sequence analysis (protein) + beta12orEarlier @@ -40139,8 +40295,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Analyse known molecular tertiary structures. beta12orEarlier + Analyse known molecular tertiary structures. @@ -40165,8 +40321,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Analyse nucleic acid tertiary structural data. + beta12orEarlier @@ -40178,10 +40334,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Secondary structure processing - beta12orEarlier - true - Process (read and / or write) a molecular secondary structure. 1.6 + Process (read and / or write) a molecular secondary structure. + true + beta12orEarlier @@ -40200,8 +40356,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Compare two or more molecular tertiary structures. beta12orEarlier + Compare two or more molecular tertiary structures. @@ -40219,9 +40375,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Render a helical wheel representation of protein secondary structure. - beta12orEarlier Helical wheel rendering + beta12orEarlier + Render a helical wheel representation of protein secondary structure. @@ -40239,9 +40395,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Render a topology diagram of protein secondary structure. - beta12orEarlier Topology diagram rendering + beta12orEarlier + Render a topology diagram of protein secondary structure. @@ -40261,10 +40417,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Compare protein tertiary structures. - Methods might identify structural neighbors, find structural similarities or define a structural core. - Structure comparison (protein) beta12orEarlier + Structure comparison (protein) + Methods might identify structural neighbors, find structural similarities or define a structural core. + Compare protein tertiary structures. @@ -40278,10 +40434,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Protein secondary structure - Secondary structure comparison (protein) - beta12orEarlier Compare protein secondary structures. + beta12orEarlier + Secondary structure comparison (protein) + Protein secondary structure @@ -40300,10 +40456,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Protein targeting prediction - Predict the subcellular localization of a protein sequence. The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. + Predict the subcellular localization of a protein sequence. + Protein targeting prediction + beta12orEarlier @@ -40315,8 +40471,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue contact calculation (residue-residue) - Calculate contacts between residues in a protein structure. beta12orEarlier + Calculate contacts between residues in a protein structure. @@ -40329,8 +40485,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Hydrogen bond calculation (inter-residue) - beta12orEarlier Identify potential hydrogen bonds between amino acid residues. + beta12orEarlier @@ -40355,8 +40511,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Predict the interactions of proteins with other molecules. + beta12orEarlier @@ -40368,10 +40524,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Codon usage data processing - true - Process (read and / or write) codon usage data. - beta13 beta12orEarlier + beta13 + Process (read and / or write) codon usage data. + true @@ -40389,12 +40545,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Process (read and / or write) gene expression (typically microarray) data, including analysis of one or more gene expression profiles, typically to interpret them in functional terms. - Gene expression data processing - Microarray data processing - Gene expression (microarray) data processing - Gene expression profile analysis beta12orEarlier + Gene expression profile analysis + Gene expression (microarray) data processing + Microarray data processing + Gene expression data processing + Process (read and / or write) gene expression (typically microarray) data, including analysis of one or more gene expression profiles, typically to interpret them in functional terms. @@ -40406,10 +40562,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene regulatory network processing - true - Process (read and / or write) a network of gene regulation. - beta12orEarlier 1.6 + beta12orEarlier + Process (read and / or write) a network of gene regulation. + true @@ -40426,10 +40582,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Network analysis - Pathway analysis Analyse a known biological pathway or network. + Pathway analysis + Network analysis + beta12orEarlier @@ -40441,10 +40597,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequencing-based expression profile data analysis - true - beta12orEarlier - beta12orEarlier Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts. + beta12orEarlier + beta12orEarlier + true @@ -40464,9 +40620,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Splicing analysis Analyse, characterize and model alternative splicing events from comparing multiple nucleic acid sequences. + Splicing analysis + beta12orEarlier @@ -40478,10 +40634,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Microarray raw data analysis - Analyse raw microarray data. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Analyse raw microarray data. @@ -40499,9 +40655,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Nucleic acid data processing Process (read and / or write) nucleic acid sequence or structural data. + Nucleic acid data processing + beta12orEarlier @@ -40519,9 +40675,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Process (read and / or write) protein sequence or structural data. - Protein data processing beta12orEarlier + Protein data processing + Process (read and / or write) protein sequence or structural data. @@ -40533,10 +40689,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence data processing - true - beta13 - Process (read and / or write) molecular sequence data. beta12orEarlier + Process (read and / or write) molecular sequence data. + beta13 + true @@ -40547,10 +40703,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structural data processing - beta12orEarlier - true - beta13 Process (read and / or write) molecular structural data. + beta13 + true + beta12orEarlier @@ -40562,10 +40718,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Text processing - 1.6 - Process (read and / or write) text. - beta12orEarlier true + beta12orEarlier + Process (read and / or write) text. + 1.6 @@ -40585,9 +40741,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Sequence alignment analysis (protein) - beta12orEarlier Analyse a protein sequence alignment, typically to detect features or make predictions. + beta12orEarlier + Sequence alignment analysis (protein) @@ -40607,9 +40763,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Analyse a protein sequence alignment, typically to detect features or make predictions. - Sequence alignment analysis (nucleic acid) beta12orEarlier + Sequence alignment analysis (nucleic acid) + Analyse a protein sequence alignment, typically to detect features or make predictions. @@ -40623,9 +40779,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier - Compare two or more nucleic acid sequences. Sequence comparison (nucleic acid) + Compare two or more nucleic acid sequences. + beta12orEarlier @@ -40639,9 +40795,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Compare two or more protein sequences. - Sequence comparison (protein) beta12orEarlier + Sequence comparison (protein) + Compare two or more protein sequences. @@ -40659,8 +40815,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Back-translate a protein sequence into DNA. beta12orEarlier + Back-translate a protein sequence into DNA. @@ -40672,10 +40828,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence editing (nucleic acid) - beta12orEarlier - Edit or change a nucleic acid sequence, either randomly or specifically. - true 1.8 + true + Edit or change a nucleic acid sequence, either randomly or specifically. + beta12orEarlier @@ -40687,10 +40843,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence editing (protein) - 1.8 - true - beta12orEarlier Edit or change a protein sequence, either randomly or specifically. + beta12orEarlier + true + 1.8 @@ -40702,8 +40858,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence generation (nucleic acid) - beta12orEarlier Generate a nucleic acid sequence by some means. + beta12orEarlier @@ -40716,8 +40872,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence generation (protein) - beta12orEarlier Generate a protein sequence by some means. + beta12orEarlier @@ -40729,11 +40885,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid sequence visualisation - beta12orEarlier - 1.8 - Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. - true Visualise, format or render a nucleic acid sequence. + true + Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. + 1.8 + beta12orEarlier @@ -40745,11 +40901,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein sequence visualisation - Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. - 1.8 - Visualise, format or render a protein sequence. - beta12orEarlier true + beta12orEarlier + Visualise, format or render a protein sequence. + 1.8 + Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. @@ -40763,9 +40919,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Structure comparison (nucleic acid) - beta12orEarlier Compare nucleic acid tertiary structures. + beta12orEarlier + Structure comparison (nucleic acid) @@ -40777,10 +40933,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure processing (nucleic acid) - Process (read and / or write) nucleic acid tertiary structure data. - true - beta12orEarlier 1.6 + beta12orEarlier + true + Process (read and / or write) nucleic acid tertiary structure data. @@ -40801,17 +40957,17 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + - + - Generate a map of a DNA sequence annotated with positional or non-positional features of some type. beta12orEarlier + Generate a map of a DNA sequence annotated with positional or non-positional features of some type. @@ -40823,11 +40979,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Map data processing - 1.6 - true - beta12orEarlier - Process (read and / or write) a DNA map of some type. DNA map data processing + Process (read and / or write) a DNA map of some type. + beta12orEarlier + true + 1.6 @@ -40841,18 +40997,18 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information). beta12orEarlier + Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information). @@ -40870,10 +41026,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures. - Binding site prediction - beta12orEarlier Ligand-binding and active site prediction + beta12orEarlier + Binding site prediction + Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures. @@ -40891,10 +41047,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS). - An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences. - Sequence mapping beta12orEarlier + Sequence mapping + An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences. + Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS). @@ -40913,11 +41069,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Alignment construction - beta12orEarlier - Alignment generation - Alignment Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits. + Alignment + Alignment generation + beta12orEarlier + Alignment construction @@ -40930,8 +41086,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein fragment weight comparison - Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data. beta12orEarlier + Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data. @@ -40949,8 +41105,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Compare the physicochemical properties of two or more proteins (or reference data). + beta12orEarlier @@ -40968,8 +41124,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Compare two or more molecular secondary structures. + beta12orEarlier @@ -40982,8 +41138,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Hopp and Woods plotting - Generate a Hopp and Woods plot of antigenicity of a protein. beta12orEarlier + Generate a Hopp and Woods plot of antigenicity of a protein. @@ -40995,8 +41151,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Microarray cluster textual view generation - Visualise gene clusters with gene names. beta12orEarlier + Visualise gene clusters with gene names. @@ -41008,11 +41164,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Microarray wave graph plotting - Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis. - This view can be rendered as a pie graph. The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades. - beta12orEarlier - Microarray cluster temporal graph rendering Microarray wave graph rendering + Microarray cluster temporal graph rendering + beta12orEarlier + This view can be rendered as a pie graph. The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades. + Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis. @@ -41024,11 +41180,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Microarray dendrograph plotting - Microarray view rendering - Microarray checks view rendering - beta12orEarlier - Generate a dendrograph of raw, preprocessed or clustered microarray data. Microarray dendrograph rendering + Generate a dendrograph of raw, preprocessed or clustered microarray data. + beta12orEarlier + Microarray checks view rendering + Microarray view rendering @@ -41040,10 +41196,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Microarray proximity map plotting - Microarray proximity map rendering - Generate a plot of distances (distance matrix) between genes. - Microarray distance map rendering beta12orEarlier + Microarray distance map rendering + Generate a plot of distances (distance matrix) between genes. + Microarray proximity map rendering @@ -41055,10 +41211,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Microarray tree or dendrogram rendering - Microarray matrix tree plot rendering - Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression. - beta12orEarlier Microarray 2-way dendrogram rendering + beta12orEarlier + Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression. + Microarray matrix tree plot rendering @@ -41070,9 +41226,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Microarray principal component plotting - Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values. - Microarray principal component rendering beta12orEarlier + Microarray principal component rendering + Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values. @@ -41084,9 +41240,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Microarray scatter plot plotting - Microarray scatter plot rendering - beta12orEarlier Generate a scatter plot of microarray data, typically after principal component analysis. + beta12orEarlier + Microarray scatter plot rendering @@ -41098,9 +41254,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Whole microarray graph plotting - Whole microarray graph rendering - beta12orEarlier Visualise gene expression data where each band (or line graph) corresponds to a sample. + beta12orEarlier + Whole microarray graph rendering @@ -41112,8 +41268,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Microarray tree-map rendering - Visualise gene expression data after hierarchical clustering for representing hierarchical relationships. beta12orEarlier + Visualise gene expression data after hierarchical clustering for representing hierarchical relationships. @@ -41125,8 +41281,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Microarray Box-Whisker plot plotting - Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles. beta12orEarlier + Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles. @@ -41140,18 +41296,18 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. beta12orEarlier + Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. @@ -41163,9 +41319,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Analysis - beta12orEarlier - For non-analytical operations, see the 'Processing' branch. Apply analytical methods to existing data of a specific type. + For non-analytical operations, see the 'Processing' branch. + beta12orEarlier @@ -41178,10 +41334,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Alignment analysis - 1.8 - beta12orEarlier - true Process or analyse an alignment of molecular sequences or structures. + true + beta12orEarlier + 1.8 @@ -41201,19 +41357,19 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - Article analysis - beta12orEarlier Analyse a body of scientific text (typically a full text article from a scientific journal.) + beta12orEarlier + Article analysis @@ -41225,10 +41381,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Molecular interaction analysis - true - beta13 - beta12orEarlier Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact. + beta12orEarlier + beta13 + true @@ -41251,8 +41407,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions. beta12orEarlier + Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions. @@ -41264,8 +41420,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue contact calculation - beta12orEarlier Calculate contacts between residues and some other group in a protein structure. + beta12orEarlier @@ -41277,10 +41433,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Alignment processing - beta12orEarlier - 1.6 - Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data. true + Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data. + 1.6 + beta12orEarlier @@ -41293,10 +41449,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure alignment processing - true - beta12orEarlier - 1.6 Process (read and / or write) a molecular tertiary (3D) structure alignment. + 1.6 + beta12orEarlier + true @@ -41314,8 +41470,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Calculate codon usage bias. + beta12orEarlier @@ -41334,8 +41490,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Generate a codon usage bias plot. beta12orEarlier + Generate a codon usage bias plot. @@ -41353,8 +41509,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta12orEarlier Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc. + beta12orEarlier @@ -41366,8 +41522,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Classification - Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category. beta12orEarlier + Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category. @@ -41379,10 +41535,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Molecular interaction data processing - Process (read and / or write) molecular interaction data. - beta12orEarlier - true beta13 + true + beta12orEarlier + Process (read and / or write) molecular interaction data. @@ -41394,8 +41550,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence classification - Assign molecular sequence(s) to a group or category. beta12orEarlier + Assign molecular sequence(s) to a group or category. @@ -41408,8 +41564,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure classification - beta12orEarlier Assign molecular structure(s) to a group or category. + beta12orEarlier @@ -41421,8 +41577,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein comparison - beta12orEarlier Compare two or more proteins (or some aspect) to identify similarities. + beta12orEarlier @@ -41434,8 +41590,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid comparison - Compare two or more nucleic acids to identify similarities. beta12orEarlier + Compare two or more nucleic acids to identify similarities. @@ -41447,8 +41603,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Prediction and recognition (protein) - Predict, recognise, detect or identify some properties of proteins. beta12orEarlier + Predict, recognise, detect or identify some properties of proteins. @@ -41460,8 +41616,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Prediction and recognition (nucleic acid) - Predict, recognise, detect or identify some properties of nucleic acids. beta12orEarlier + Predict, recognise, detect or identify some properties of nucleic acids. @@ -41479,8 +41635,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically. beta13 + Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically. @@ -41492,8 +41648,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence alignment editing - beta13 Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically. + beta13 @@ -41512,9 +41668,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta13 - Pathway or network rendering Render (visualise) a biological pathway or network. + Pathway or network rendering + beta13 @@ -41526,11 +41682,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein function prediction (from sequence) - 1.6 - For functional properties that are positional, use 'Protein site detection' instead. - Predict general (non-positional) functional properties of a protein from analysing its sequence. - true beta13 + true + Predict general (non-positional) functional properties of a protein from analysing its sequence. + For functional properties that are positional, use 'Protein site detection' instead. + 1.6 @@ -41544,14 +41700,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - beta13 - Sequence feature detection (protein) - Protein secondary database search - Protein site detection - Sequence profile database search - Protein site prediction - Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions. Protein site recognition + Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions. + Protein site prediction + Sequence profile database search + Protein site detection + Protein secondary database search + Sequence feature detection (protein) + beta13 @@ -41564,8 +41720,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein property calculation (from sequence) - Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. beta13 + Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. @@ -41577,10 +41733,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein feature prediction (from structure) - Predict, recognise and identify positional features in proteins from analysing protein structure. - true - 1.6 beta13 + 1.6 + true + Predict, recognise and identify positional features in proteins from analysing protein structure. @@ -41605,12 +41761,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Protein feature prediction - Protein feature recognition - beta13 - Predict, recognise and identify positional features in proteins from analysing protein sequences or structures. Features includes functional sites or regions, secondary structure, structural domains and so on. Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a discriminatory element. This includes methods that search a secondary protein database (Prosite, Blocks, ProDom, Prints, Pfam etc.) to assign a protein sequence(s) to a known protein family or group. + Predict, recognise and identify positional features in proteins from analysing protein sequences or structures. + beta13 + Protein feature recognition + Protein feature prediction @@ -41622,11 +41778,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Database search (by sequence) - beta13 - Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries. - 1.6 - true Sequence screening + true + 1.6 + Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries. + beta13 @@ -41650,8 +41806,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Predict a network of protein interactions. beta13 + Predict a network of protein interactions. @@ -41664,8 +41820,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid design - Design (or predict) nucleic acid sequences with specific chemical or physical properties. beta13 + Design (or predict) nucleic acid sequences with specific chemical or physical properties. @@ -41677,8 +41833,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Editing - Edit a data entity, either randomly or specifically. beta13 + Edit a data entity, either randomly or specifically. @@ -41693,8 +41849,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + @@ -41705,12 +41861,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - Evaluate a DNA sequence assembly, typically for purposes of quality control. 1.1 + Evaluate a DNA sequence assembly, typically for purposes of quality control. @@ -41722,10 +41878,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Genome alignment - Genome alignment - 1.1 - Genome alignment construction Align two or more (tpyically huge) molecular sequences that represent genomes. + Genome alignment construction + 1.1 + Genome alignment @@ -41737,8 +41893,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Localized reassembly - 1.1 Reconstruction of a sequence assembly in a localised area. + 1.1 @@ -41750,11 +41906,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence assembly visualisation - Assembly visualisation - 1.1 - Render and visualise a DNA sequence assembly. - Sequence assembly rendering Assembly rendering + Sequence assembly rendering + Render and visualise a DNA sequence assembly. + 1.1 + Assembly visualisation @@ -41772,11 +41928,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Phred base-calling - Base calling - Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer. - 1.1 Phred base calling + 1.1 + Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer. + Base calling + Phred base-calling @@ -41788,11 +41944,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Bisulfite mapping - Bisulfite sequence mapping - Bisulfite sequence alignment - The mapping of methylation sites in a DNA (genome) sequence. - Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected. 1.1 + Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected. + The mapping of methylation sites in a DNA (genome) sequence. + Bisulfite sequence alignment + Bisulfite sequence mapping @@ -41810,8 +41966,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced. beta12orEarlier + Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced. @@ -41823,9 +41979,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Trim ends - For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. - Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. 1.1 + Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. + For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. @@ -41837,8 +41993,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Trim vector - 1.1 Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences. + 1.1 @@ -41850,8 +42006,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Trim to reference - Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. 1.1 + Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. @@ -41863,8 +42019,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence trimming - Cut (remove) the end from a molecular sequence. 1.1 + Cut (remove) the end from a molecular sequence. @@ -41876,9 +42032,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Genome feature comparison - 1.1 - Compare the features of two genome sequences. Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on. + Compare the features of two genome sequences. + 1.1 @@ -41896,10 +42052,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Detect errors in DNA sequences generated from sequencing projects). - beta12orEarlier - Short-read error correction Short read error correction + Short-read error correction + beta12orEarlier + Detect errors in DNA sequences generated from sequencing projects). @@ -41911,9 +42067,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Genotyping - Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence. - Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on. 1.1 + Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on. + Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence. @@ -41926,11 +42082,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Genetic variation analysis - Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model. - Genetic variation annotation - Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript. - Sequence variation analysis 1.1 + Sequence variation analysis + Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript. + Genetic variation annotation + Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model. @@ -41943,18 +42099,18 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Read mapping - Short sequence read mapping - Align short oligonucleotide sequences (reads) to a larger (genomic) sequence. - Short read alignment - 1.1 - Read alignment - Oligonucleotide alignment - The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. - Oligonucleotide alignment construction - Short read mapping - Oligonucleotide alignment generation - Oligonucleotide mapping Short oligonucleotide alignment + Oligonucleotide mapping + Oligonucleotide alignment generation + Short read mapping + Oligonucleotide alignment construction + The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. + Oligonucleotide alignment + Read alignment + 1.1 + Short read alignment + Align short oligonucleotide sequences (reads) to a larger (genomic) sequence. + Short sequence read mapping @@ -41966,8 +42122,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Split read mapping - 1.1 A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation. + 1.1 @@ -41979,9 +42135,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern DNA barcoding - Sample barcoding - 1.1 Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms. + 1.1 + Sample barcoding @@ -41993,9 +42149,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern SNP calling - 1.1 - Operations usually score confidence in the prediction or some other statistical measure of evidence. Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism. + Operations usually score confidence in the prediction or some other statistical measure of evidence. + 1.1 @@ -42007,9 +42163,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Mutation detection - 1.1 - Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware. Polymorphism detection + Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware. + 1.1 @@ -42021,9 +42177,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Chromatogram visualisation - 1.1 - Chromatogram viewing Visualise, format or render an image of a Chromatogram. + Chromatogram viewing + 1.1 @@ -42035,8 +42191,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Methylation analysis - Determine cytosine methylation states in nucleic acid sequences. 1.1 + Determine cytosine methylation states in nucleic acid sequences. @@ -42049,8 +42205,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Methylation calling - Determine cytosine methylation status of specific positions in a nucleic acid sequences. 1.1 + Determine cytosine methylation status of specific positions in a nucleic acid sequences. @@ -42062,9 +42218,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Methylation level analysis (global) - Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay. - Global methylation analysis 1.1 + Global methylation analysis + Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay. @@ -42076,10 +42232,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Methylation level analysis (gene-specific) - 1.1 - Measure the level of methyl cytosines in specific genes. - Many different techniques are available for this. Gene-specific methylation analysis + Many different techniques are available for this. + Measure the level of methyl cytosines in specific genes. + 1.1 @@ -42091,13 +42247,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Genome visualisation - Genome browsing - Genome viewing - Genome visualisation - Genome rendering - Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence. - Genome visualization 1.1 + Genome visualization + Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence. + Genome rendering + Genome visualisation + Genome viewing + Genome browsing @@ -42109,9 +42265,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Genome comparison - Genomic region matching - 1.1 Compare the sequence or features of two or more genomes, for example, to find matching regions. + 1.1 + Genomic region matching @@ -42129,9 +42285,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - 1.1 - Generate an index of a genome sequence. Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. + Generate an index of a genome sequence. + 1.1 @@ -42143,9 +42299,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Genome indexing (Burrows-Wheeler) - 1.1 - Generate an index of a genome sequence using the Burrows-Wheeler algorithm. The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. + Generate an index of a genome sequence using the Burrows-Wheeler algorithm. + 1.1 @@ -42157,10 +42313,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Genome indexing (suffix arrays) - A suffix array consists of the lexicographically sorted list of suffixes of a genome. - suffix arrays - Generate an index of a genome sequence using a suffix arrays algorithm. 1.1 + Generate an index of a genome sequence using a suffix arrays algorithm. + suffix arrays + A suffix array consists of the lexicographically sorted list of suffixes of a genome. @@ -42172,11 +42328,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Spectral analysis - Mass spectrum analysis - Analyse a spectrum from a mass spectrometry (or other) experiment. - Spectrum analysis - 1.1 Spectral analysis + 1.1 + Spectrum analysis + Analyse a spectrum from a mass spectrometry (or other) experiment. + Mass spectrum analysis @@ -42194,10 +42350,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Identify peaks in a spectrum from a mass spectrometry, NMR, or some other spectrum-generating experiment. - Peak assignment - Peak finding 1.1 + Peak finding + Peak assignment + Identify peaks in a spectrum from a mass spectrometry, NMR, or some other spectrum-generating experiment. @@ -42216,11 +42372,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Scaffold generation - Scaffold may be positioned along a chromosome physical map to create a "golden path". - 1.1 - Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps. Scaffold construction + Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps. + 1.1 + Scaffold may be positioned along a chromosome physical map to create a "golden path". + Scaffold generation @@ -42232,9 +42388,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Scaffold gap completion - 1.1 - Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced. Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences. + Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced. + 1.1 @@ -42247,10 +42403,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequencing quality control - 1.1 - Sequencing QC - Analyse raw sequence data from a sequencing pipeline and identify problems. Raw sequence data quality control. + Analyse raw sequence data from a sequencing pipeline and identify problems. + Sequencing QC + 1.1 @@ -42263,10 +42419,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Read pre-processing - 1.1 - Pre-process sequence reads to ensure (or improve) quality and reliability. - This is a broad concept and is used a placeholder for other, more specific concepts. For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on. Sequence read pre-processing + This is a broad concept and is used a placeholder for other, more specific concepts. For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on. + Pre-process sequence reads to ensure (or improve) quality and reliability. + 1.1 @@ -42284,8 +42440,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - 1.1 Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples. + 1.1 @@ -42297,10 +42453,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Peak calling - 1.1 - Protein binding peak detection - Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data. Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). + Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data. + Protein binding peak detection + 1.1 @@ -42312,10 +42468,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Differential expression analysis - 1.1 - Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups. - Differentially expressed gene identification Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups. + Differentially expressed gene identification + Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups. + 1.1 @@ -42327,9 +42483,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene set testing - Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc. - Gene sets can be defined beforehand by biological function, chromosome locations and so on. 1.1 + Gene sets can be defined beforehand by biological function, chromosome locations and so on. + Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc. @@ -42342,9 +42498,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Variant classification - Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.) - 1.1 Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins. + 1.1 + Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.) @@ -42356,9 +42512,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Variant prioritization - 1.1 - Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes. Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. + Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes. + 1.1 @@ -42370,10 +42526,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Variant calling - Methods often utilise a database of aligned reads. - Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence. - 1.1 Variant mapping + 1.1 + Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence. + Methods often utilise a database of aligned reads. @@ -42385,9 +42541,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structural variation discovery - Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. - 1.1 Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s). + 1.1 + Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. @@ -42399,11 +42555,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Exome analysis - Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome. - Exome sequence analysis - Exome sequencing is considered a cheap alternative to whole genome sequencing. - Targeted exome capture 1.1 + Targeted exome capture + Exome sequencing is considered a cheap alternative to whole genome sequencing. + Exome sequence analysis + Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome. @@ -42415,8 +42571,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Read depth analysis - Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications. 1.1 + Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications. @@ -42434,11 +42590,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - expression QTL profiling - Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes. - eQTL profiling - 1.1 expression quantitative trait loci profiling + 1.1 + eQTL profiling + Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes. + expression QTL profiling @@ -42450,10 +42606,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Copy number estimation - Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors. - 1.1 - Transcript copy number estimation Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number). + Transcript copy number estimation + 1.1 + Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors. @@ -42465,8 +42621,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Primer removal - Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products). 1.2 + Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products). @@ -42490,8 +42646,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - 1.2 Infer a transcriptome sequence by analysis of short sequence reads. + 1.2 @@ -42503,11 +42659,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Transcriptome assembly (de novo) - Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other. - 1.2 - 1.6 - true de novo transcriptome assembly + true + 1.6 + 1.2 + Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other. @@ -42519,10 +42675,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Transcriptome assembly (mapping) - true - 1.2 - 1.6 Infer a transcriptome sequence by mapping short reads to a reference genome. + 1.6 + 1.2 + true @@ -42536,18 +42692,18 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + - + - Convert one set of sequence coordinates to another, e.g. convert coordinates of one assembly to another, cDNA to genomic, CDS to genomic, protein translation to genomic etc. 1.3 + Convert one set of sequence coordinates to another, e.g. convert coordinates of one assembly to another, cDNA to genomic, CDS to genomic, protein translation to genomic etc. @@ -42559,8 +42715,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Document similarity calculation - 1.3 Calculate similarity between 2 or more documents. + 1.3 @@ -42573,8 +42729,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Document clustering - 1.3 Cluster (group) documents on the basis of their calculated similarity. + 1.3 @@ -42587,11 +42743,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Named entity recognition - 1.3 - Recognise named entities (text tokens) within documents. - Entity extraction - Entity chunking Entity identification + Entity chunking + Entity extraction + Recognise named entities (text tokens) within documents. + 1.3 @@ -42604,11 +42760,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern ID mapping - Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration. - Accession mapping - 1.3 - The mapping can be achieved by comparing identifier values or some other means, e.g. exact matches to a provided sequence. Identifier mapping + The mapping can be achieved by comparing identifier values or some other means, e.g. exact matches to a provided sequence. + 1.3 + Accession mapping + Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration. @@ -42620,9 +42776,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Anonymisation - Data anonymisation - 1.3 Process data in such a way that makes it hard to trace to the person which the data concerns. + 1.3 + Data anonymisation @@ -42640,14 +42796,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - 1.3 - Search for and retrieve a data identifier of some kind, e.g. a database entry accession. - Accession retrieval - Data retrieval (id) - Identifier retrieval - Data retrieval (ID) - Data retrieval (accession) id retrieval + Data retrieval (accession) + Data retrieval (ID) + Identifier retrieval + Data retrieval (id) + Accession retrieval + Search for and retrieve a data identifier of some kind, e.g. a database entry accession. + 1.3 @@ -42671,8 +42827,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - 1.4 Generate a checksum of a molecular sequence. + 1.4 @@ -42690,9 +42846,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - 1.4 - Construct a bibliography from the scientific literature. Bibliography construction + Construct a bibliography from the scientific literature. + 1.4 @@ -42704,8 +42860,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein quaternary structure prediction - Predict the structure of a multi-subunit protein and particularly how the subunits fit together. 1.4 + Predict the structure of a multi-subunit protein and particularly how the subunits fit together. @@ -42717,8 +42873,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein surface analysis - Analyse the surface properties of proteins. 1.4 + Analyse the surface properties of proteins. @@ -42730,8 +42886,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Ontology comparison - Compare two or more ontologies, e.g. identify differences. 1.4 + Compare two or more ontologies, e.g. identify differences. @@ -42742,11 +42898,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Ontology comparison - - Compare two or more ontologies, e.g. identify differences. + 1.4 - - + Compare two or more ontologies, e.g. identify differences. + 1.9 + + @@ -42758,22 +42915,22 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - Format inference - 'Format recognition' is not a bioinformatics-specific operation, but of great relevance in bioinformatics. Should be removed from EDAM if/when captured satisfactorily in a suitable domain-generic ontology. - Format recognition - Format identification - 1.4 Recognition of which format the given data is in. + 1.4 + Format identification + Format recognition + 'Format recognition' is not a bioinformatics-specific operation, but of great relevance in bioinformatics. Should be removed from EDAM if/when captured satisfactorily in a suitable domain-generic ontology. + Format inference @@ -42792,9 +42949,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Splitting - 1.4 - Split a file containing multiple data items into many files, each containing one item File splitting + Split a file containing multiple data items into many files, each containing one item + 1.4 @@ -42806,10 +42963,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Generation - Construct some data entity. - For non-analytical operations, see the 'Processing' branch. - beta12orEarlier Construction + beta12orEarlier + For non-analytical operations, see the 'Processing' branch. + Construct some data entity. @@ -42822,11 +42979,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid sequence feature detection - Nucleic acid site detection - 1.6 - Nucleic acid site recognition - Predict, recognise and identify functional or other key sites within nucleic acid sequences, typically by scanning for known motifs, patterns and regular expressions. Nucleic acid site prediction + Predict, recognise and identify functional or other key sites within nucleic acid sequences, typically by scanning for known motifs, patterns and regular expressions. + Nucleic acid site recognition + 1.6 + Nucleic acid site detection @@ -42838,14 +42995,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Deposition - For non-analytical operations, see the 'Processing' branch. - Database deposition - Data deposition - Data submission - Submission - Database submission + Deposit some data in a database or some other type of repository or software system. 1.6 - Deposit some data in a database. + Database submission + Submission + Data submission + Data deposition + Database deposition + For non-analytical operations, see the 'Processing' branch. @@ -42857,8 +43014,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Clustering - Group together some data entities on the basis of similarities such that entities in the same group (cluster) are more similar to each other than to those in other groups (clusters). 1.6 + Group together some data entities on the basis of similarities such that entities in the same group (cluster) are more similar to each other than to those in other groups (clusters). @@ -42871,7 +43028,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Assembly 1.6 - XXX + Construct some entity (typically a molecule sequence) from component pieces. @@ -42883,8 +43040,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Conversion - Non-analytical data conversion. 1.6 + Non-analytical data conversion. @@ -42896,8 +43053,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Standardization and normalization - Standardize or normalize data. 1.6 + Standardize or normalize data. @@ -42909,8 +43066,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Aggregation - 1.6 Combine multiple files or data items into a single file or object. + 1.6 @@ -42922,8 +43079,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Article comparison - 1.6 Compare two or more scientific articles. + 1.6 @@ -42935,8 +43092,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Calculation - 1.6 Mathemetical determination of the value of something, typically a properly of a molecule. + 1.6 @@ -42949,8 +43106,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pathway or network prediction - Predict a molecular pathway or network. 1.6 + Predict a molecular pathway or network. @@ -42962,8 +43119,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Genome assembly - The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated. 1.6 + The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated. @@ -42975,8 +43132,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Plotting - 1.6 Generate a graph, or other visual representation, of data, showing the relationship between two or more variables. + 1.6 @@ -42994,8 +43151,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - The analysis of a image (typically a digital image) of some type in order to extract information from it. 1.7 + The analysis of a image (typically a digital image) of some type in order to extract information from it. + Image processing @@ -43008,8 +43166,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Diffraction data analysis - Analysis of data from a diffraction experiment. 1.7 + Analysis of data from a diffraction experiment. @@ -43027,8 +43185,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Analysis of cell migration images in order to study cell migration, typically in order to study the processes that play a role in the disease progression. 1.7 + Analysis of cell migration images in order to study cell migration, typically in order to study the processes that play a role in the disease progression. @@ -43040,8 +43198,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Diffraction data reduction - Processing of diffraction data into a corrected, ordered, and simplified form. 1.7 + Processing of diffraction data into a corrected, ordered, and simplified form. @@ -43059,8 +43217,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - 1.7 Measurement of neurites; projections (axons or dendrites) from the cell body of a neuron, from analysis of neuron images. + 1.7 @@ -43072,10 +43230,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Diffraction data integration - The evaluation of diffraction intensities and integration of diffraction maxima from a diffraction experiment. - Diffraction profile fitting - Diffraction summation integration 1.7 + Diffraction summation integration + Diffraction profile fitting + The evaluation of diffraction intensities and integration of diffraction maxima from a diffraction experiment. @@ -43087,8 +43245,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phasing - 1.7 Phase a macromolecular crystal structure, for example by using molecular replacement or experimental phasing methods. + 1.7 @@ -43100,9 +43258,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Molecular replacement - The technique solves the phase problem, i.e. retrieve information concern phases of the structure. - A technique used to construct an atomic model of an unknown structure from diffraction data, based upon an atomic model of a known structure, either a related protein or the same protein from a different crystal form. 1.7 + A technique used to construct an atomic model of an unknown structure from diffraction data, based upon an atomic model of a known structure, either a related protein or the same protein from a different crystal form. + The technique solves the phase problem, i.e. retrieve information concern phases of the structure. @@ -43114,9 +43272,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Rigid body refinement - A method used to refine a structure by moving the whole molecule or parts of it as a rigid unit, rather than moving individual atoms. - Rigid body refinement usually follows molecular replacement in the assignment of a structure from diffraction data. 1.7 + Rigid body refinement usually follows molecular replacement in the assignment of a structure from diffraction data. + A method used to refine a structure by moving the whole molecule or parts of it as a rigid unit, rather than moving individual atoms. @@ -43135,9 +43293,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Single particle analysis is used to improve the information that can be obtained by relatively low resolution techniques, , e.g. an image of a protein or virus from transmission electron microscopy (TEM). - 1.7 An image processing technique that combines and analyze multiple images of a particulate sample, in order to produce an image with clearer features that are more easily interpreted. + 1.7 + Single particle analysis is used to improve the information that can be obtained by relatively low resolution techniques, , e.g. an image of a protein or virus from transmission electron microscopy (TEM). @@ -43150,9 +43308,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Single particle alignment and classification - A micrograph can include particles in multiple different orientations and/or conformations. Particles are compared and organised into sets based on their similarity. Typically iterations of classification and alignment and are performed to optimise the final image; average images produced by classification are used as a reference image for subsequent alignment of the whole image set. - 1.7 Compare (align and classify) multiple particle images from a micrograph in order to produce a representative image of the particle. + 1.7 + A micrograph can include particles in multiple different orientations and/or conformations. Particles are compared and organised into sets based on their similarity. Typically iterations of classification and alignment and are performed to optimise the final image; average images produced by classification are used as a reference image for subsequent alignment of the whole image set. @@ -43170,9 +43328,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Functional sequence clustering - Clustering of molecular sequences on the basis of their function, typically using information from an ontology of gene function, or some other measure of functional phenotype. 1.7 + Clustering of molecular sequences on the basis of their function, typically using information from an ontology of gene function, or some other measure of functional phenotype. + Functional sequence clustering @@ -43184,8 +43342,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Taxonomic classification - Classifiication of molecular sequences by assignment to some taxonomic hierarchy. 1.7 + Classifiication of molecular sequences by assignment to some taxonomic hierarchy. @@ -43204,9 +43362,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - 1.7 - The prediction of the degree of pathogenicity of a microorganism from analysis of molecular sequences. Pathogenicity prediction + The prediction of the degree of pathogenicity of a microorganism from analysis of molecular sequences. + 1.7 @@ -43219,10 +43377,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene expression correlation analysis + 1.7 + Gene co-expression network analysis Analyse the correlation patterns among genes across across a variety of experiments, microarray samples etc. - Gene co-expression network analysis - 1.7 @@ -43241,8 +43399,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - 1.7 Compute the covariance model for (a family of) RNA secondary structures. + 1.7 @@ -43254,9 +43412,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern RNA secondary structure prediction (shape-based) - 1.7 - Predict RNA secondary structure by analysis, e.g. probabilistic analysis, of the shape of RNA folds. RNA shape prediction + Predict RNA secondary structure by analysis, e.g. probabilistic analysis, of the shape of RNA folds. + 1.7 @@ -43268,8 +43426,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid alignment folding prediction (alignment-based) - Prediction of nucleic-acid folding using sequence alignments as a source of data. 1.7 + Prediction of nucleic-acid folding using sequence alignments as a source of data. @@ -43281,9 +43439,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern k-mer counting - k-mer counting is used in genome and transcriptome assembly, metagenomic sequencing, and for error correction of sequence reads. - 1.7 Count k-mers (substrings of length k) in DNA sequence data. + 1.7 + k-mer counting is used in genome and transcriptome assembly, metagenomic sequencing, and for error correction of sequence reads. @@ -43301,9 +43459,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - 1.7 - Note that this is somewhat different from simply analysing an existing tree or constructing a completely new one. Reconstructing the inner node labels of a phylogenetic tree from its leafes. + Note that this is somewhat different from simply analysing an existing tree or constructing a completely new one. + 1.7 @@ -43315,8 +43473,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Probabilistic data generation - 1.7 Generate some data from a choosen probibalistic model, possibly to evaluate algorithms. + 1.7 @@ -43329,8 +43487,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Probabilistic sequence generation - Generate sequences from some probabilistic model, e.g. a model that simulates evolution. 1.7 + Generate sequences from some probabilistic model, e.g. a model that simulates evolution. @@ -43349,8 +43507,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Identify or predict causes for antibiotic resistance from molecular sequence analysis. 1.7 + Identify or predict causes for antibiotic resistance from molecular sequence analysis. @@ -43369,10 +43527,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Analyse a dataset with respect to concepts from an ontology. - 1.8 - Term enrichment A relevant ontology will be used. The input is typically a set of identifiers or other data, and the output of the analysis is typically a ranked list of ontology terms, each associated with a p-value. + Term enrichment + 1.8 + Analyse a dataset with respect to concepts from an ontology. @@ -43391,8 +43549,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Analyse a dataset with respect to concepts from an ontology of chemical structure. 1.8 + Analyse a dataset with respect to concepts from an ontology of chemical structure. @@ -43404,8 +43562,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Incident curve plotting - Plot an incident curve such as a survival curve, death curve, mortality curve. 1.8 + Plot an incident curve such as a survival curve, death curve, mortality curve. @@ -43417,9 +43575,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Variant pattern analysis - 1.8 - Identify and map patterns of genomic variations. Methods often utilise a database of aligned reads. + Identify and map patterns of genomic variations. + 1.8 @@ -43431,8 +43589,172 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Mathematical modelling - beta12orEarlier Model some biological system using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models. + beta12orEarlier + + + + + + + + + + Microscope image visualisation + + + + + + + + Visualise images resulting from various types of microscopy. + 1.9 + Microscopy image visualisation + + + + + + + + + + Image annotation + + 1.9 + Annotate an image of some sort, typically with terms from a controlled vocabulary. + + + + + + + + + + Imputation + + Data imputation + Replace missing data with substituted values, usually by using some statistical or other mathematical approach. + true + 1.9 + + + + + + + + + + Ontology visualisation + + 1.9 + Visualise, format or render data from an ontology, typically a tree of terms. + Ontology browsing + + + + + + + + + + Maximum occurence analysis + + A method for making numerical assessments about the maximum percent of time that a conformer of a flexible macromolecule can exist and still be compatible with the experimental data. + beta12orEarlier + + + + + + + + + + Database comparison + + + 1.9 + Data model comparison + Compare the models or schemas used by two or more databases, or any other general comparison of databases rather than a detailed comparison of the entries themselves. + Schema comparison + + + + + + + + + + Network simulation + + + + + + + + Simulate the bevaviour of a biological pathway or network. + Pathway simulation + Network topology simulation + 1.9 + + + + + + + + + + RNA-seq read count analysis + + Analyze read counts from RNA-seq experiments. + 1.9 + + + + + + + + + + Chemical redundancy removal + + 1.9 + Identify and remove redudancy from a set of small molecule structures. + + + + + + + + + + RNA-seq time series data analysis + + 1.9 + Analyze time series data from an RNA-seq experiment. + + + + + + + + + + Simulated gene expression data generation + + 1.9 + Simulate gene expression data, e.g. for purposes of benchmarking. @@ -43444,17 +43766,17 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Topic - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method - sumo:FieldOfStudy - http://www.ifomis.org/bfo/1.1/snap#Continuant - beta12orEarlier - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality - A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other. - http://www.onto-med.de/ontologies/gfo.owl#Perpetuant - http://www.ifomis.org/bfo/1.1/snap#Quality - http://www.onto-med.de/ontologies/gfo.owl#Category - http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research http://purl.org/biotop/biotop.owl#Quality + http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research + http://www.onto-med.de/ontologies/gfo.owl#Category + http://www.ifomis.org/bfo/1.1/snap#Quality + http://www.onto-med.de/ontologies/gfo.owl#Perpetuant + A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other. + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality + beta12orEarlier + http://www.ifomis.org/bfo/1.1/snap#Continuant + sumo:FieldOfStudy + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method @@ -43466,15 +43788,15 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acids - Topic concerning the processing and analysis of nucleic acid sequence, structural and other data. - beta12orEarlier - http://purl.bioontology.org/ontology/MSH/D017422 - Nucleic acid physicochemistry - Nucleic acid properties - http://purl.bioontology.org/ontology/MSH/D017423 - Nucleic acid informatics - Nucleic acid analysis Nucleic acid bioinformatics + Nucleic acid analysis + Nucleic acid informatics + http://purl.bioontology.org/ontology/MSH/D017423 + Nucleic acid properties + Nucleic acid physicochemistry + http://purl.bioontology.org/ontology/MSH/D017422 + beta12orEarlier + Topic concerning the processing and analysis of nucleic acid sequence, structural and other data. @@ -43486,13 +43808,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Proteins - beta12orEarlier - http://purl.bioontology.org/ontology/MSH/D020539 - Protein analysis - Protein databases - Protein informatics - Protein bioinformatics Topic concerning archival, processing and analysis of protein data, typically molecular sequence and structural data. + Protein bioinformatics + Protein informatics + Protein databases + Protein analysis + http://purl.bioontology.org/ontology/MSH/D020539 + beta12orEarlier @@ -43504,10 +43826,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Metabolites - beta12orEarlier - This concept excludes macromolecules such as proteins and nucleic acids. - Topic concerning the structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. Metabolite structures + Topic concerning the structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. + This concept excludes macromolecules such as proteins and nucleic acids. + beta12orEarlier @@ -43519,12 +43841,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence analysis - Topic concerning the archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles. - BioCatalogue:Sequence Analysis - http://purl.bioontology.org/ontology/MSH/D017421 - Sequences - Sequence databases beta12orEarlier + Sequence databases + Sequences + http://purl.bioontology.org/ontology/MSH/D017421 + BioCatalogue:Sequence Analysis + Topic concerning the archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles. @@ -43537,15 +43859,15 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure analysis - beta12orEarlier - Structure data resources - This includes related concepts such as structural properties, alignments and structural motifs. - Structure databases - Structural bioinformatics - Structure analysis - http://purl.bioontology.org/ontology/MSH/D015394 - Topic concerning the curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules. Computational structural biology + Topic concerning the curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules. + http://purl.bioontology.org/ontology/MSH/D015394 + Structure analysis + Structural bioinformatics + Structure databases + This includes related concepts such as structural properties, alignments and structural motifs. + Structure data resources + beta12orEarlier @@ -43558,8 +43880,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure prediction - beta12orEarlier Topic concerning the prediction of molecular (secondary or tertiary) structure. + beta12orEarlier @@ -43571,10 +43893,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Alignment - beta12orEarlier - Topic concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment). - true beta12orEarlier + true + Topic concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment). + beta12orEarlier @@ -43587,18 +43909,18 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogeny - BioCatalogue:Evolutionary Distance Measurements - This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc. - BioCatalogue:Phylogeny - Phylogenetic simulation - http://purl.bioontology.org/ontology/MSH/D010802 - Topic concerning the study of evolutionary relationships amongst organisms. - Phylogenetic clocks - Phylogenetic dating - BioCatalogue:Tree Inference - beta12orEarlier - Phylogenetic stratigraphy Phylogeny reconstruction + Phylogenetic stratigraphy + beta12orEarlier + BioCatalogue:Tree Inference + Phylogenetic dating + Phylogenetic clocks + Topic concerning the study of evolutionary relationships amongst organisms. + http://purl.bioontology.org/ontology/MSH/D010802 + Phylogenetic simulation + BioCatalogue:Phylogeny + This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc. + BioCatalogue:Evolutionary Distance Measurements @@ -43612,9 +43934,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Functional genomics - BioCatalogue:Functional Genomics - Topic concerning the study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc. beta12orEarlier + Topic concerning the study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc. + BioCatalogue:Functional Genomics @@ -43627,15 +43949,15 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Ontology and terminology - Ontologies - BioCatalogue:Ontology Lookup - Topic concerning the conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource. - Ontology - Applied ontology - http://purl.bioontology.org/ontology/MSH/D002965 - beta12orEarlier - Terminology BioCatalogue:Ontology + Terminology + beta12orEarlier + http://purl.bioontology.org/ontology/MSH/D002965 + Applied ontology + Ontology + Topic concerning the conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource. + BioCatalogue:Ontology Lookup + Ontologies @@ -43645,20 +43967,20 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - Data search, query and retrieval - - Data query - Topic concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information. - BioCatalogue:Structure Retrieval - BioCatalogue:Image Retrieval - BioCatalogue:Sequence Retrieval - BioCatalogue:Data Retrieval - BioCatalogue:Identifier Retrieval - Data search - This includes, for example, search, query and retrieval of molecular sequences and associated data. - Data retrieval + + Data search, query and retrieval + beta12orEarlier + Data retrieval + This includes, for example, search, query and retrieval of molecular sequences and associated data. + Data search + BioCatalogue:Identifier Retrieval + BioCatalogue:Data Retrieval + BioCatalogue:Sequence Retrieval + BioCatalogue:Image Retrieval + BioCatalogue:Structure Retrieval + Topic concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information. + Data query @@ -43671,10 +43993,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Bioinformatics - beta12orEarlier - Topic concerning the archival, curation, processing and analysis of complex biological data. - http://purl.bioontology.org/ontology/MSH/D016247 This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation. + http://purl.bioontology.org/ontology/MSH/D016247 + Topic concerning the archival, curation, processing and analysis of complex biological data. + beta12orEarlier @@ -43687,10 +44009,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data visualisation - beta12orEarlier - Data rendering and visualisation - Topic for the rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data. Data rendering + Topic for the rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data. + Data rendering and visualisation + beta12orEarlier @@ -43702,9 +44024,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid thermodynamics - 1.3 - true Topic concerning the study of the thermodynamic properties of a nucleic acid. + true + 1.3 @@ -43716,16 +44038,16 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid structure analysis - RNA structure - Nucleic acid thermodynamics - Nucleic acid structure - beta12orEarlier - RNA structure alignment - Topic concerning the archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation. - RNA alignment - Nucleic acid denaturation - DNA melting Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc. + DNA melting + Nucleic acid denaturation + RNA alignment + Topic concerning the archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation. + RNA structure alignment + beta12orEarlier + Nucleic acid structure + Nucleic acid thermodynamics + RNA structure @@ -43737,8 +44059,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern RNA - Topic concerning RNA sequences and structures. beta12orEarlier + Topic concerning RNA sequences and structures. @@ -43750,10 +44072,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid restriction - true - Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids. - beta12orEarlier 1.3 + beta12orEarlier + Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids. + true @@ -43765,14 +44087,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Mapping - This includes resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. It also includes resources for physical (sequence) maps of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. - beta12orEarlier - DNA mapping - Synteny - Linkage mapping - Linkage - Genetic linkage Topic concerning the mapping of complete (typically nucleotide) sequences. + Genetic linkage + Linkage + Linkage mapping + Synteny + DNA mapping + beta12orEarlier + This includes resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. It also includes resources for physical (sequence) maps of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. @@ -43784,11 +44106,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Genetic codes and codon usage - Codon usage analysis - 1.3 - Topic concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on. - true beta12orEarlier + true + Topic concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on. + 1.3 + Codon usage analysis @@ -43800,9 +44122,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein expression - beta12orEarlier - Topic concerning the translation of mRNA into protein and subsequent protein processing in the cell. Translation + Topic concerning the translation of mRNA into protein and subsequent protein processing in the cell. + beta12orEarlier @@ -43815,14 +44137,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene finding - BioCatalogue:Gene Prediction - Gene discovery - Topic that aims to identify, predict, model or analyse genes or gene structure in DNA sequences. - This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. - 1.3 - true - Gene prediction beta12orEarlier + Gene prediction + true + 1.3 + This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. + Topic that aims to identify, predict, model or analyse genes or gene structure in DNA sequences. + Gene discovery + BioCatalogue:Gene Prediction @@ -43834,10 +44156,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Transcription - true - beta12orEarlier - Topic concerning the transcription of DNA into mRNA. 1.3 + Topic concerning the transcription of DNA into mRNA. + beta12orEarlier + true @@ -43849,11 +44171,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Promoters - beta13 - Topic concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins). - BioCatalogue:Promoter Prediction - beta12orEarlier true + beta12orEarlier + BioCatalogue:Promoter Prediction + Topic concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins). + beta13 @@ -43865,10 +44187,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid folding - beta12orEarlier - Topic concerning the folding (in 3D space) of nucleic acid molecules. - true beta12orEarlier + true + Topic concerning the folding (in 3D space) of nucleic acid molecules. + beta12orEarlier @@ -43881,11 +44203,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene structure + This includes the study of promoters, coding regions etc. + beta12orEarlier + Gene features Topic concerning gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc. - Gene features - beta12orEarlier - This includes the study of promoters, coding regions etc. @@ -43897,14 +44219,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Proteomics - BioCatalogue:Proteomics - Protein expression - Topic concerning protein and peptide identification, especially in the study of whole proteomes of organisms. - http://purl.bioontology.org/ontology/MSH/D040901 - Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein expression data, for example in different cells or tissues. - Peptide identification - Protein and peptide identification beta12orEarlier + Protein and peptide identification + Peptide identification + Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein expression data, for example in different cells or tissues. + http://purl.bioontology.org/ontology/MSH/D040901 + Topic concerning protein and peptide identification, especially in the study of whole proteomes of organisms. + Protein expression + BioCatalogue:Proteomics @@ -43918,9 +44240,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structural genomics - Topic concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism. - beta12orEarlier BioCatalogue:Structural Genomics + beta12orEarlier + Topic concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism. @@ -43933,10 +44255,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein properties - beta12orEarlier - Protein physicochemistry - Protein hydropathy Topic concerning the study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein. + Protein hydropathy + Protein physicochemistry + beta12orEarlier @@ -43949,16 +44271,16 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein interactions - BioCatalogue:Protein Interaction - Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions. - BioCatalogue:Ligand Interaction - Protein-DNA interaction - beta12orEarlier - Protein-ligand interactions - Protein-protein interactions - This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. - Protein-RNA interaction Protein-nucleic acid interactions + Protein-RNA interaction + This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. + Protein-protein interactions + Protein-ligand interactions + beta12orEarlier + Protein-DNA interaction + BioCatalogue:Ligand Interaction + Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions. + BioCatalogue:Protein Interaction @@ -43970,13 +44292,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein folding, stability and design - Rational protein design - Protein design - Protein residue interactions - beta12orEarlier - Protein stability - Protein folding Topic concerning protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. + Protein folding + Protein stability + beta12orEarlier + Protein residue interactions + Protein design + Rational protein design @@ -43988,10 +44310,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Two-dimensional gel electrophoresis - true - beta12orEarlier - beta13 Topic concerning two-dimensional gel electrophoresis image and related data. + beta13 + beta12orEarlier + true @@ -44003,8 +44325,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Mass spectrometry - Topic concerning an analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase. beta12orEarlier + Topic concerning an analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase. @@ -44017,10 +44339,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein microarrays - beta13 - beta12orEarlier - true Topic concerning protein microarray data. + true + beta12orEarlier + beta13 @@ -44032,10 +44354,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein hydropathy - 1.3 - true - beta12orEarlier Topic for the study of the hydrophobic, hydrophilic and charge properties of a protein. + beta12orEarlier + true + 1.3 @@ -44047,11 +44369,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein targeting and localization - beta12orEarlier - Protein localization - Topic concerning the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export. - Protein sorting Protein targeting + Protein sorting + Topic concerning the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export. + Protein localization + beta12orEarlier @@ -44063,10 +44385,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein cleavage sites and proteolysis - 1.3 - beta12orEarlier - Topic concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence. true + Topic concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence. + beta12orEarlier + 1.3 @@ -44078,11 +44400,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein structure comparison - beta12orEarlier - Use this concept for methods that are exclusively for protein structure. - true - beta12orEarlier Topic concerning the comparison of two or more protein structures. + beta12orEarlier + true + Use this concept for methods that are exclusively for protein structure. + beta12orEarlier @@ -44095,11 +44417,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue interactions - beta12orEarlier - 1.3 - true - Protein residue interactions The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures. + Protein residue interactions + true + 1.3 + beta12orEarlier @@ -44111,11 +44433,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein-protein interactions - Topic concerning protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc. - 1.3 - beta12orEarlier - true Protein interaction networks + true + beta12orEarlier + 1.3 + Topic concerning protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc. @@ -44127,10 +44449,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein-ligand interactions - 1.3 - true - Topic concerning protein-ligand (small molecule) interactions. beta12orEarlier + Topic concerning protein-ligand (small molecule) interactions. + true + 1.3 @@ -44142,10 +44464,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein-nucleic acid interactions - true - 1.3 - Topic concerning protein-DNA/RNA interactions. beta12orEarlier + Topic concerning protein-DNA/RNA interactions. + 1.3 + true @@ -44157,10 +44479,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein design - true - Topic concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. - beta12orEarlier 1.3 + beta12orEarlier + Topic concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. + true @@ -44172,10 +44494,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern G protein-coupled receptors (GPCR) - beta12orEarlier - beta12orEarlier - Topic concerning G-protein coupled receptors (GPCRs). true + Topic concerning G-protein coupled receptors (GPCRs). + beta12orEarlier + beta12orEarlier @@ -44187,8 +44509,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Carbohydrates - Topic concerning carbohydrates, typically including structural information. beta12orEarlier + Topic concerning carbohydrates, typically including structural information. @@ -44200,8 +44522,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Lipids - Topic concerning lipids and their structures. beta12orEarlier + Topic concerning lipids and their structures. @@ -44213,10 +44535,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Small molecules - beta12orEarlier - CHEBI:23367 - Topic concerning small molecules of biological significance, typically archival, curation, processing and analysis of structural information. Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. + Topic concerning small molecules of biological significance, typically archival, curation, processing and analysis of structural information. + CHEBI:23367 + beta12orEarlier @@ -44228,10 +44550,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence editing - Edit, convert or otherwise change a molecular sequence, either randomly or specifically. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Edit, convert or otherwise change a molecular sequence, either randomly or specifically. @@ -44244,14 +44566,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence composition, complexity and repeats - BioCatalogue:Repeats - Sequence composition - Topic concerning the archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences. - Sequence repeats - Low complexity sequences - Sequence complexity - beta12orEarlier Repeat sequences + beta12orEarlier + Sequence complexity + Low complexity sequences + Sequence repeats + Topic concerning the archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences. + Sequence composition + BioCatalogue:Repeats @@ -44263,11 +44585,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence motifs - Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites. - 1.3 - true - Motifs beta12orEarlier + Motifs + true + 1.3 + Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites. @@ -44279,11 +44601,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence comparison - Topic concerning the comparison of two or more molecular sequences, for example sequence alignment and clustering. - BioCatalogue:Protein Sequence Similarity - beta12orEarlier - The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. BioCatalogue:Nucleotide Sequence Similarity + The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. + beta12orEarlier + BioCatalogue:Protein Sequence Similarity + Topic concerning the comparison of two or more molecular sequences, for example sequence alignment and clustering. @@ -44295,15 +44617,15 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence sites, features and motifs - beta12orEarlier - HMMs - Sequence sites - Sequence profiles + Sequence features + Functional sites + Sequence motifs Topic concerning the archival, detection, prediction and analysis of positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. - Sequence motifs - Functional sites - Sequence features + Sequence profiles + Sequence sites + HMMs + beta12orEarlier @@ -44315,11 +44637,11 @@ positional features such as functional and other key sites, in molecular sequenc Sequence database search - The query is a sequence-based entity such as another sequence, a motif or profile. - true - beta12orEarlier - Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence). beta12orEarlier + Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence). + beta12orEarlier + true + The query is a sequence-based entity such as another sequence, a motif or profile. @@ -44331,12 +44653,12 @@ positional features such as functional and other key sites, in molecular sequenc Sequence clustering - Sequence clusters - 1.7 - Topic concerning the comparison and grouping together of molecular sequences on the basis of their similarities. - true - beta12orEarlier This includes systems that generate, process and analyse sequence clusters. + beta12orEarlier + true + Topic concerning the comparison and grouping together of molecular sequences on the basis of their similarities. + 1.7 + Sequence clusters @@ -44349,14 +44671,14 @@ positional features such as functional and other key sites, in molecular sequenc Protein structural motifs and surfaces - Protein surfaces - Protein structural motifs - beta12orEarlier - Topic concerning (3D) structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules. - Protein 3D motifs - Structural motifs - Protein structural features This includes conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches, role and functions etc. + Protein structural features + Structural motifs + Protein 3D motifs + Topic concerning (3D) structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules. + beta12orEarlier + Protein structural motifs + Protein surfaces @@ -44368,11 +44690,11 @@ positional features such as functional and other key sites, in molecular sequenc Structural (3D) profiles - Structural profiles - 1.3 - beta12orEarlier - true The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment. + true + beta12orEarlier + 1.3 + Structural profiles @@ -44385,9 +44707,9 @@ positional features such as functional and other key sites, in molecular sequenc Protein structure prediction - BioCatalogue:Protein Structure Prediction - Topic concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features. beta12orEarlier + Topic concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features. + BioCatalogue:Protein Structure Prediction @@ -44400,12 +44722,12 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid structure prediction - Topic concerning the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. - Nucleic acid folding - beta12orEarlier - RNA structure prediction - Nucleic acid design DNA structure prediction + Nucleic acid design + RNA structure prediction + beta12orEarlier + Nucleic acid folding + Topic concerning the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. @@ -44417,10 +44739,10 @@ positional features such as functional and other key sites, in molecular sequenc Ab initio structure prediction - beta12orEarlier - true - Topic concerning the prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates. 1.7 + Topic concerning the prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates. + true + beta12orEarlier @@ -44432,10 +44754,10 @@ positional features such as functional and other key sites, in molecular sequenc Homology modelling - Topic concerning the modelling of the three-dimensional structure of a protein using known sequence and structural data. - beta12orEarlier - true 1.4 + true + beta12orEarlier + Topic concerning the modelling of the three-dimensional structure of a protein using known sequence and structural data. @@ -44447,11 +44769,12 @@ positional features such as functional and other key sites, in molecular sequenc Molecular dynamics - beta12orEarlier - Molecular motions - Molecular flexibility - Topic concerning the simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation. This includes resources concerning flexibility and motion in protein and other molecular structures. + Protein dynamics + Molecular flexibility + Topic concerning the study and simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation. + Molecular motions + beta12orEarlier @@ -44463,8 +44786,8 @@ positional features such as functional and other key sites, in molecular sequenc Molecular docking - Topic concerning the modelling the structure of proteins in complex with small molecules or other macromolecules. beta12orEarlier + Topic concerning the modelling the structure of proteins in complex with small molecules or other macromolecules. @@ -44476,10 +44799,10 @@ positional features such as functional and other key sites, in molecular sequenc Protein secondary structure prediction - true - 1.3 - beta12orEarlier Topic concerning the prediction of secondary or supersecondary structure of protein sequences. + beta12orEarlier + 1.3 + true @@ -44492,10 +44815,10 @@ positional features such as functional and other key sites, in molecular sequenc Protein tertiary structure prediction - Topic concerning the prediction of tertiary structure of protein sequences. - beta12orEarlier - true 1.3 + true + beta12orEarlier + Topic concerning the prediction of tertiary structure of protein sequences. @@ -44508,9 +44831,9 @@ positional features such as functional and other key sites, in molecular sequenc Protein fold recognition - beta12orEarlier - Topic concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s). For example threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). + Topic concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s). + beta12orEarlier @@ -44522,11 +44845,11 @@ positional features such as functional and other key sites, in molecular sequenc Sequence alignment - true - 1.7 - Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments). - beta12orEarlier This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on. + beta12orEarlier + Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments). + 1.7 + true @@ -44538,11 +44861,11 @@ positional features such as functional and other key sites, in molecular sequenc Structure alignment - beta12orEarlier - 1.7 - true - This includes the generation, storage, analysis, rendering etc. of structure alignments. Topic concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment). + This includes the generation, storage, analysis, rendering etc. of structure alignments. + true + 1.7 + beta12orEarlier @@ -44554,11 +44877,11 @@ positional features such as functional and other key sites, in molecular sequenc Threading - true - beta12orEarlier - Topic concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). - 1.3 Sequence-structure alignment + 1.3 + Topic concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). + beta12orEarlier + true @@ -44570,11 +44893,11 @@ positional features such as functional and other key sites, in molecular sequenc Sequence profiles and HMMs - Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. - 1.3 - beta12orEarlier - Topic concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment. true + Topic concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment. + beta12orEarlier + 1.3 + Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. @@ -44586,13 +44909,13 @@ positional features such as functional and other key sites, in molecular sequenc Phylogeny reconstruction - BioCatalogue:Tree Inference - beta12orEarlier - Currently too specific for the topic sub-ontology (but might be unobsoleted). - true - 1.3 - Topic concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree. BioCatalogue:Evolutionary Distance Measurements + Topic concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree. + 1.3 + true + Currently too specific for the topic sub-ontology (but might be unobsoleted). + beta12orEarlier + BioCatalogue:Tree Inference @@ -44605,8 +44928,8 @@ positional features such as functional and other key sites, in molecular sequenc Phylogenomics - Topic concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction. beta12orEarlier + Topic concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction. @@ -44619,12 +44942,12 @@ positional features such as functional and other key sites, in molecular sequenc Virtual PCR - Topic concerning simulated polymerase chain reaction (PCR). - true - PCR - beta12orEarlier - Polymerase chain reaction beta13 + Polymerase chain reaction + beta12orEarlier + PCR + true + Topic concerning simulated polymerase chain reaction (PCR). @@ -44636,10 +44959,10 @@ positional features such as functional and other key sites, in molecular sequenc Sequence assembly - This covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. - beta12orEarlier - Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence. Assembly + Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence. + beta12orEarlier + This covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. @@ -44652,12 +44975,12 @@ positional features such as functional and other key sites, in molecular sequenc Genetic variation - Topic concerning stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. - beta12orEarlier - Polymorphism - Mutation - DNA variation http://purl.bioontology.org/ontology/MSH/D014644 + DNA variation + Mutation + Polymorphism + beta12orEarlier + Topic concerning stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. @@ -44669,13 +44992,13 @@ positional features such as functional and other key sites, in molecular sequenc Microarrays - beta12orEarlier - DNA microarrays - Topic concerning microarrays, for example, to process microarray data or design probes and experiments. - 1.3 - http://purl.bioontology.org/ontology/MSH/D046228 - true BioCatalogue:Microarrays + true + http://purl.bioontology.org/ontology/MSH/D046228 + 1.3 + Topic concerning microarrays, for example, to process microarray data or design probes and experiments. + DNA microarrays + beta12orEarlier @@ -44687,10 +45010,10 @@ positional features such as functional and other key sites, in molecular sequenc Pharmacology - Topic concerning the study of drugs and their effects or responses in living systems. - Pharmacoinformatics - beta12orEarlier Computational pharmacology + beta12orEarlier + Pharmacoinformatics + Topic concerning the study of drugs and their effects or responses in living systems. @@ -44699,22 +45022,22 @@ positional features such as functional and other key sites, in molecular sequenc - - - Gene expression - - Codon usage - DNA microarrays - Gene expression analysis - http://purl.bioontology.org/ontology/MSH/D015870 - Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc. - http://edamontology.org/topic_0197 - Topic concerning the analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. - beta12orEarlier - Expression profiling - Gene expression profiling - BioCatalogue:Microarrays + + + Gene expression + This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on. + BioCatalogue:Microarrays + Gene expression profiling + Expression profiling + beta12orEarlier + Topic concerning the analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. + http://edamontology.org/topic_0197 + Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc. + http://purl.bioontology.org/ontology/MSH/D015870 + Gene expression analysis + DNA microarrays + Codon usage @@ -44727,8 +45050,8 @@ positional features such as functional and other key sites, in molecular sequenc Gene regulation - beta12orEarlier Topic concerning primarily the regulation of gene expression. + beta12orEarlier @@ -44741,8 +45064,8 @@ positional features such as functional and other key sites, in molecular sequenc Pharmacogenomics - Topic concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. beta12orEarlier + Topic concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. @@ -44756,10 +45079,10 @@ positional features such as functional and other key sites, in molecular sequenc Medicinal chemistry - beta12orEarlier - Drug design - Topic concerning the design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes. This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. + Topic concerning the design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes. + Drug design + beta12orEarlier @@ -44772,10 +45095,10 @@ positional features such as functional and other key sites, in molecular sequenc Fish - 1.3 - true - Topic concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation. beta12orEarlier + Topic concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation. + true + 1.3 @@ -44787,10 +45110,10 @@ positional features such as functional and other key sites, in molecular sequenc Flies - beta12orEarlier - true - 1.3 Topic concerning flies, e.g. information on a specific fly genome including molecular sequences, genes and annotation. + 1.3 + true + beta12orEarlier @@ -44801,14 +45124,12 @@ positional features such as functional and other key sites, in molecular sequenc Mice or rats - - Topic concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation. - 1.3 - beta12orEarlier - true + The resource may be specific to a group of mice / rats or all mice / rats. - - + beta12orEarlier + Topic concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation. + + @@ -44818,10 +45139,10 @@ positional features such as functional and other key sites, in molecular sequenc Worms - beta12orEarlier - 1.3 - true Topic concerning worms, e.g. information on a specific worm genome including molecular sequences, genes and annotation. + true + 1.3 + beta12orEarlier @@ -44833,10 +45154,10 @@ positional features such as functional and other key sites, in molecular sequenc Literature analysis - true - The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query. - 1.3 beta12orEarlier + 1.3 + The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query. + true @@ -44848,12 +45169,12 @@ positional features such as functional and other key sites, in molecular sequenc Data mining - Literature mining - Text mining - Literature analysis - Text data mining - beta12orEarlier Topic concerning the analysis of the biomedical and informatics literature. + beta12orEarlier + Text data mining + Literature analysis + Text mining + Literature mining @@ -44866,9 +45187,9 @@ positional features such as functional and other key sites, in molecular sequenc Data deposition, annotation and curation - beta12orEarlier - Database curation Topic concerning the organisation and maintenance of a collection of biological database entries (or other such entities) including the annotation of entries, typically with terms from a controlled vocabulary. + Database curation + beta12orEarlier @@ -44881,11 +45202,11 @@ positional features such as functional and other key sites, in molecular sequenc File management - Utility software - This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. - beta12orEarlier - Topic concerning basic manipulations of files or reports of generic biological data. Routine data management + Topic concerning basic manipulations of files or reports of generic biological data. + beta12orEarlier + This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. + Utility software @@ -44897,10 +45218,10 @@ positional features such as functional and other key sites, in molecular sequenc Sequence annotation - Annotate a molecular sequence. - true - beta12orEarlier beta12orEarlier + beta12orEarlier + true + Annotate a molecular sequence. @@ -44912,11 +45233,11 @@ positional features such as functional and other key sites, in molecular sequenc Genome annotation - BioCatalogue:Genome Annotation - Annotate a genome. - beta12orEarlier - true beta12orEarlier + true + beta12orEarlier + Annotate a genome. + BioCatalogue:Genome Annotation @@ -44930,17 +45251,17 @@ positional features such as functional and other key sites, in molecular sequenc NMR - Rotational Frame Nuclear Overhauser Effect Spectroscopy - Topic concerning an analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules. - NMR spectroscopy - Spectroscopy - Nuclear magnetic resonance spectroscopy - Heteronuclear Overhauser Effect Spectroscopy - beta12orEarlier - HOESY - Nuclear Overhauser Effect Spectroscopy - NOESY ROESY + NOESY + Nuclear Overhauser Effect Spectroscopy + HOESY + beta12orEarlier + Heteronuclear Overhauser Effect Spectroscopy + Nuclear magnetic resonance spectroscopy + Spectroscopy + NMR spectroscopy + Topic concerning an analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules. + Rotational Frame Nuclear Overhauser Effect Spectroscopy @@ -44953,9 +45274,9 @@ positional features such as functional and other key sites, in molecular sequenc Sequence classification - Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences. - Topic concerning the classification of molecular sequences based on some measure of their similarity. beta12orEarlier + Topic concerning the classification of molecular sequences based on some measure of their similarity. + Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences. @@ -44967,10 +45288,10 @@ positional features such as functional and other key sites, in molecular sequenc Protein classification - beta12orEarlier - Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc. - true 1.3 + true + Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc. + beta12orEarlier @@ -44982,11 +45303,11 @@ positional features such as functional and other key sites, in molecular sequenc Sequence motif or profile - Topic concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type. - beta12orEarlier - This includes comparison, discovery, recognition etc. of sequence motifs. - true beta12orEarlier + true + This includes comparison, discovery, recognition etc. of sequence motifs. + beta12orEarlier + Topic concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type. @@ -44999,12 +45320,12 @@ positional features such as functional and other key sites, in molecular sequenc Protein modifications - beta12orEarlier - EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000) - MOD:00000 - Protein post-translational modification - Topic concerning protein chemical modifications, e.g. post-translational modifications. GO:0006464 + Topic concerning protein chemical modifications, e.g. post-translational modifications. + Protein post-translational modification + MOD:00000 + EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000) + beta12orEarlier @@ -45016,16 +45337,16 @@ positional features such as functional and other key sites, in molecular sequenc Molecular interactions, pathways and networks - BioCatalogue:Pathways - http://edamontology.org/topic_3076 - Topic concerning molecular interactions, biological pathways, networks and other models. - Biological pathways - Biological models - Molecular interactions - beta13 - Network or pathway analysis - Biological networks BioCatalogue:Pathway Retrieval + Biological networks + Network or pathway analysis + beta13 + Molecular interactions + Biological models + Biological pathways + Topic concerning molecular interactions, biological pathways, networks and other models. + http://edamontology.org/topic_3076 + BioCatalogue:Pathways @@ -45038,10 +45359,10 @@ positional features such as functional and other key sites, in molecular sequenc Informatics - beta12orEarlier - beta12orEarlier - A database concerning biological data management and modelling, including datatypes, workflows and models. A sub-discipline of bioinformatics; the application of information technology to a specialised biological area. true + A database concerning biological data management and modelling, including datatypes, workflows and models. A sub-discipline of bioinformatics; the application of information technology to a specialised biological area. + beta12orEarlier + beta12orEarlier @@ -45053,10 +45374,10 @@ positional features such as functional and other key sites, in molecular sequenc Literature data resources - beta12orEarlier - 1.3 - true Data resources for the biological or biomedical literature, either a primary source of literature or some derivative. + true + 1.3 + beta12orEarlier @@ -45068,9 +45389,9 @@ positional features such as functional and other key sites, in molecular sequenc Laboratory information management - Laboratory resources - beta12orEarlier Topic concerning laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on. + beta12orEarlier + Laboratory resources @@ -45084,13 +45405,13 @@ positional features such as functional and other key sites, in molecular sequenc Cell and tissue culture - beta12orEarlier - Cell culture - Topic concerning general cell culture or data on a specific cell lines. - true - 1.3 Tissue culture - + 1.3 + true + Topic concerning general cell culture or data on a specific cell lines. + Cell culture + beta12orEarlier + @@ -45101,13 +45422,13 @@ positional features such as functional and other key sites, in molecular sequenc Ecology - Environmental science - Ecoinformatics - Computational ecology - beta12orEarlier - Ecological informatics - http://purl.bioontology.org/ontology/MSH/D004777 Topic concerning the ecological and environmental sciences and especially the application of information technology (ecoinformatics). + http://purl.bioontology.org/ontology/MSH/D004777 + Ecological informatics + beta12orEarlier + Computational ecology + Ecoinformatics + Environmental science @@ -45121,16 +45442,16 @@ positional features such as functional and other key sites, in molecular sequenc Electron microscopy - Single particle electron microscopy - Electron diffraction experiment - Electron crystallography - beta12orEarlier - Transmission electron microscopy + SEM + Scanning electron microscopy + TEM Topic concerning the study of matter by studying the interference pattern from firing electrons at a sample, to analyse structures at resolutions higher than can be achieved using light. - TEM - Scanning electron microscopy - SEM + Transmission electron microscopy + beta12orEarlier + Electron crystallography + Electron diffraction experiment + Single particle electron microscopy @@ -45143,10 +45464,10 @@ positional features such as functional and other key sites, in molecular sequenc Cell cycle - true - beta12orEarlier - Topic concerning the cell cycle including key genes and proteins. beta13 + Topic concerning the cell cycle including key genes and proteins. + beta12orEarlier + true @@ -45158,10 +45479,10 @@ positional features such as functional and other key sites, in molecular sequenc Peptides and amino acids - Peptides - Amino acids - Topic concerning the physicochemical, biochemical or structural properties of amino acids or peptides. beta12orEarlier + Topic concerning the physicochemical, biochemical or structural properties of amino acids or peptides. + Amino acids + Peptides @@ -45173,21 +45494,21 @@ positional features such as functional and other key sites, in molecular sequenc Organelles - 1.3 - Rough endoplasmic reticulum - Golgi apparatus - Mitochondria - true - Nucleus - Ribosome - Centriole - Lysosome - beta12orEarlier - Topic concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome). - Smooth endoplasmic reticulum - Organelle genes and proteins - Cytoplasm Cell membrane + Cytoplasm + Organelle genes and proteins + Smooth endoplasmic reticulum + Topic concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome). + beta12orEarlier + Lysosome + Centriole + Ribosome + Nucleus + true + Mitochondria + Golgi apparatus + Rough endoplasmic reticulum + 1.3 @@ -45199,11 +45520,11 @@ positional features such as functional and other key sites, in molecular sequenc Ribosomes - true - 1.3 - Topic concerning ribosomes, typically of ribosome-related genes and proteins. - Ribosome genes and proteins beta12orEarlier + Ribosome genes and proteins + Topic concerning ribosomes, typically of ribosome-related genes and proteins. + 1.3 + true @@ -45215,10 +45536,10 @@ positional features such as functional and other key sites, in molecular sequenc Scents - true - beta13 - beta12orEarlier A database about scents. + beta12orEarlier + beta13 + true @@ -45231,10 +45552,10 @@ positional features such as functional and other key sites, in molecular sequenc Drugs and target structures - Target structures - beta12orEarlier - Topic concerning the structures of drugs, drug target, their interactions and binding affinities. Drug structures + Topic concerning the structures of drugs, drug target, their interactions and binding affinities. + beta12orEarlier + Target structures @@ -45245,12 +45566,12 @@ positional features such as functional and other key sites, in molecular sequenc - Organisms + Model organisms - Model organisms - Topic concerning a specific organism, or group of organisms, used to study a particular aspect of biology. - beta12orEarlier This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism. + beta12orEarlier + Topic concerning a specific organism, or group of organisms, used to study a particular aspect of biology. + Organisms @@ -45263,10 +45584,10 @@ positional features such as functional and other key sites, in molecular sequenc Genomics - beta12orEarlier - Topic concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. - http://purl.bioontology.org/ontology/MSH/D023281 BioCatalogue:Genomics + http://purl.bioontology.org/ontology/MSH/D023281 + Topic concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. + beta12orEarlier @@ -45279,12 +45600,12 @@ positional features such as functional and other key sites, in molecular sequenc Gene families - Gene and protein families - Genes, gene family or system - Topic concerning particular gene(s), gene family or other gene group or system and their encoded proteins. - Gene system - Gene family beta12orEarlier + Gene family + Gene system + Topic concerning particular gene(s), gene family or other gene group or system and their encoded proteins. + Genes, gene family or system + Gene and protein families @@ -45297,8 +45618,8 @@ positional features such as functional and other key sites, in molecular sequenc Chromosomes - Topic concerning chromosomes. beta12orEarlier + Topic concerning chromosomes. @@ -45310,10 +45631,11 @@ positional features such as functional and other key sites, in molecular sequenc Genotype and phenotype - beta12orEarlier - Genotyping - Topic concerning the study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on. Genotype and phenotype resources + Topic concerning the study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on. + Genotyping + Phenotyping + beta12orEarlier @@ -45326,10 +45648,10 @@ positional features such as functional and other key sites, in molecular sequenc Gene expression and microarray - beta12orEarlier - beta12orEarlier - true Topic concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc. + true + beta12orEarlier + beta12orEarlier @@ -45342,16 +45664,16 @@ positional features such as functional and other key sites, in molecular sequenc Sequence design - beta12orEarlier - Primers - Primer design - in silico cloning - Topic concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR). - Probe design - Gene design - http://purl.bioontology.org/ontology/MSH/D015335 - This includes the design of primers for PCR and DNA amplification or the design of molecular probes. Probes + This includes the design of primers for PCR and DNA amplification or the design of molecular probes. + http://purl.bioontology.org/ontology/MSH/D015335 + Gene design + Probe design + Topic concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR). + in silico cloning + Primer design + Primers + beta12orEarlier @@ -45363,9 +45685,9 @@ positional features such as functional and other key sites, in molecular sequenc Pathology - Diseases - beta12orEarlier Topic concerning diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases. + beta12orEarlier + Diseases @@ -45378,11 +45700,11 @@ positional features such as functional and other key sites, in molecular sequenc Specific protein resources - beta12orEarlier - Specific protein - true - Topic concerning a particular protein, protein family or other group of proteins. 1.3 + Topic concerning a particular protein, protein family or other group of proteins. + true + Specific protein + beta12orEarlier @@ -45394,8 +45716,8 @@ positional features such as functional and other key sites, in molecular sequenc Taxonomy - Topic concerning organism classification, identification and naming. beta12orEarlier + Topic concerning organism classification, identification and naming. @@ -45407,10 +45729,10 @@ positional features such as functional and other key sites, in molecular sequenc Protein sequence analysis - true - Topic concerning archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. - 1.8 beta12orEarlier + 1.8 + Topic concerning archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. + true @@ -45422,11 +45744,11 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid sequence analysis - Topic concerning the archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles. - true - 1.8 - BioCatalogue:Nucleotide Sequence Analysis beta12orEarlier + BioCatalogue:Nucleotide Sequence Analysis + 1.8 + true + Topic concerning the archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles. @@ -45439,10 +45761,10 @@ positional features such as functional and other key sites, in molecular sequenc Repeat sequences - 1.3 - Topic concerning the repetitive nature of molecular sequences. - beta12orEarlier true + beta12orEarlier + Topic concerning the repetitive nature of molecular sequences. + 1.3 @@ -45454,10 +45776,10 @@ positional features such as functional and other key sites, in molecular sequenc Low complexity sequences - beta12orEarlier - 1.3 - Topic concerning the (character) complexity of molecular sequences, particularly regions of low complexity. true + Topic concerning the (character) complexity of molecular sequences, particularly regions of low complexity. + 1.3 + beta12orEarlier @@ -45469,10 +45791,10 @@ positional features such as functional and other key sites, in molecular sequenc Proteome - true - beta13 - beta12orEarlier Topic concerning a specific proteome including protein sequences and annotation. + beta12orEarlier + beta13 + true @@ -45484,10 +45806,10 @@ positional features such as functional and other key sites, in molecular sequenc DNA - The DNA sequences might be coding or non-coding sequences. - Topic concerning DNA sequences and structure, including processes such as methylation and replication. - beta12orEarlier DNA analysis + beta12orEarlier + Topic concerning DNA sequences and structure, including processes such as methylation and replication. + The DNA sequences might be coding or non-coding sequences. @@ -45499,12 +45821,12 @@ positional features such as functional and other key sites, in molecular sequenc Coding RNA - beta12orEarlier - This includes expressed sequence tag (EST) or complementary DNA (cDNA) sequences. - Topic concerning protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames - mRNA - cDNA EST + cDNA + mRNA + Topic concerning protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames + This includes expressed sequence tag (EST) or complementary DNA (cDNA) sequences. + beta12orEarlier @@ -45517,13 +45839,13 @@ positional features such as functional and other key sites, in molecular sequenc Functional, regulatory and non-coding RNA - beta12orEarlier - Topic concerning non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA). - Non-coding RNA includes piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA). - Regulatory RNA - Functional RNA - Non-coding RNA ncRNA + Non-coding RNA + Functional RNA + Regulatory RNA + Non-coding RNA includes piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA). + Topic concerning non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA). + beta12orEarlier @@ -45535,9 +45857,9 @@ positional features such as functional and other key sites, in molecular sequenc rRNA - Topic concerning one or more ribosomal RNA (rRNA) sequences. - true 1.3 + true + Topic concerning one or more ribosomal RNA (rRNA) sequences. @@ -45549,9 +45871,9 @@ positional features such as functional and other key sites, in molecular sequenc tRNA - Topic concerning one or more transfer RNA (tRNA) sequences. - true 1.3 + true + Topic concerning one or more transfer RNA (tRNA) sequences. @@ -45563,11 +45885,11 @@ positional features such as functional and other key sites, in molecular sequenc Protein secondary structure - This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. - 1.8 - Topic concerning protein secondary structure or secondary structure alignments. - beta12orEarlier true + beta12orEarlier + Topic concerning protein secondary structure or secondary structure alignments. + 1.8 + This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. @@ -45579,10 +45901,10 @@ positional features such as functional and other key sites, in molecular sequenc RNA structure - true - beta12orEarlier - Topic concerning RNA secondary or tertiary structure and alignments. 1.3 + Topic concerning RNA secondary or tertiary structure and alignments. + beta12orEarlier + true @@ -45594,10 +45916,10 @@ positional features such as functional and other key sites, in molecular sequenc Protein tertiary structure - beta12orEarlier - true - Topic concerning protein tertiary structures. 1.8 + Topic concerning protein tertiary structures. + true + beta12orEarlier @@ -45609,10 +45931,10 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid classification - beta12orEarlier - Topic concerning classification of nucleic acid sequences and structures. - true 1.3 + true + Topic concerning classification of nucleic acid sequences and structures. + beta12orEarlier @@ -45624,11 +45946,11 @@ positional features such as functional and other key sites, in molecular sequenc Protein families - A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. - Protein secondary databases - Protein sequence classification - beta12orEarlier Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group. + beta12orEarlier + Protein sequence classification + Protein secondary databases + A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. @@ -45641,11 +45963,11 @@ positional features such as functional and other key sites, in molecular sequenc Protein domains and folds - Protein domains - BioCatalogue:Domains - Protein folds - beta12orEarlier Topic concerning protein tertiary structural domains and folds. + beta12orEarlier + Protein folds + BioCatalogue:Domains + Protein domains @@ -45657,10 +45979,10 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid sequence alignment - 1.3 - Topic concerning nucleotide sequence alignments. - true beta12orEarlier + true + Topic concerning nucleotide sequence alignments. + 1.3 @@ -45672,11 +45994,11 @@ positional features such as functional and other key sites, in molecular sequenc Protein sequence alignment - Topic concerning protein sequence alignments. - A sequence profile typically represents a sequence alignment. - true - beta12orEarlier 1.3 + beta12orEarlier + true + A sequence profile typically represents a sequence alignment. + Topic concerning protein sequence alignments. @@ -45688,11 +46010,11 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid sites and features + beta12orEarlier + 1.3 + true Topic concerning the archival, detection, prediction and analysis of positional features such as functional sites in nucleotide sequences. - true - 1.3 - beta12orEarlier @@ -45705,10 +46027,10 @@ positional features such as functional sites in nucleotide sequences. Protein sites and features - true - Topic concerning the detection, identification and analysis of positional features in proteins, such as functional sites. - 1.3 beta12orEarlier + 1.3 + Topic concerning the detection, identification and analysis of positional features in proteins, such as functional sites. + true @@ -45723,14 +46045,14 @@ positional features such as functional sites in nucleotide sequences. - Transcription factor binding sites - beta12orEarlier - Transcription factors - TFBS - Transcriptional regulatory sites - Topic concerning proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences. - BioCatalogue:Transcription Factors Transcription factor proteins either promote (as an activator) or block (as a repressor) the binding to DNA of RNA polymerase. Regulatory sites including transcription factor binding site as well as promoters, enhancers, silencers and boundary elements / insulators. + BioCatalogue:Transcription Factors + Topic concerning proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences. + Transcriptional regulatory sites + TFBS + Transcription factors + beta12orEarlier + Transcription factor binding sites @@ -45742,10 +46064,10 @@ positional features such as functional sites in nucleotide sequences. Phosphorylation sites - beta12orEarlier - Topic concerning protein phosphorylation and phosphorylation sites in protein sequences. - true 1.0 + true + Topic concerning protein phosphorylation and phosphorylation sites in protein sequences. + beta12orEarlier @@ -45758,8 +46080,8 @@ positional features such as functional sites in nucleotide sequences. Metabolic pathways - Topic concerning metabolic pathways. beta12orEarlier + Topic concerning metabolic pathways. @@ -45771,9 +46093,9 @@ positional features such as functional sites in nucleotide sequences. Signaling pathways - beta12orEarlier - Signal transduction pathways Topic concerning signaling pathways. + Signal transduction pathways + beta12orEarlier @@ -45785,9 +46107,9 @@ positional features such as functional sites in nucleotide sequences. Protein and peptide identification - true - beta12orEarlier 1.3 + beta12orEarlier + true @@ -45799,10 +46121,10 @@ positional features such as functional sites in nucleotide sequences. Workflows - 1.0 - true - beta12orEarlier Topic concerning biological or biomedical analytical workflows or pipelines. + beta12orEarlier + true + 1.0 @@ -45813,10 +46135,10 @@ positional features such as functional sites in nucleotide sequences. Data types and objects - true - 1.0 - beta12orEarlier Topic concerning structuring data into basic types and (computational) objects. + beta12orEarlier + 1.0 + true @@ -45828,8 +46150,8 @@ positional features such as functional sites in nucleotide sequences. Theoretical biology - true 1.3 + true @@ -45841,10 +46163,10 @@ positional features such as functional sites in nucleotide sequences. Mitochondria - 1.3 - Topic concerning mitochondria, typically of mitochondrial genes and proteins. - true beta12orEarlier + true + Topic concerning mitochondria, typically of mitochondrial genes and proteins. + 1.3 @@ -45856,12 +46178,12 @@ positional features such as functional sites in nucleotide sequences. Plants - beta12orEarlier - Botany - Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation. - Plant biology - The resource may be specific to a plant, a group of plants or all plants. Plant + The resource may be specific to a plant, a group of plants or all plants. + Plant biology + Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation. + Botany + beta12orEarlier @@ -45873,10 +46195,10 @@ positional features such as functional sites in nucleotide sequences. Viruses - The resource may be specific to a virus, a group of viruses or all viruses. - beta12orEarlier - Topic concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation. Virology + Topic concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation. + beta12orEarlier + The resource may be specific to a virus, a group of viruses or all viruses. @@ -45888,11 +46210,11 @@ positional features such as functional sites in nucleotide sequences. Fungi - Yeast - The resource may be specific to a fungus, a group of fungi or all fungi. - Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation. - beta12orEarlier Mycology + beta12orEarlier + Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation. + The resource may be specific to a fungus, a group of fungi or all fungi. + Yeast @@ -45904,9 +46226,9 @@ positional features such as functional sites in nucleotide sequences. Pathogens - Topic concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. - The resource may be specific to a pathogen, a group of pathogens or all pathogens. beta12orEarlier + The resource may be specific to a pathogen, a group of pathogens or all pathogens. + Topic concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. @@ -45918,10 +46240,10 @@ positional features such as functional sites in nucleotide sequences. Arabidopsis - true - 1.3 - beta12orEarlier Topic concerning Arabidopsis-specific data. + beta12orEarlier + 1.3 + true @@ -45933,10 +46255,10 @@ positional features such as functional sites in nucleotide sequences. Rice - beta12orEarlier - Topic concerning rice-specific data. - 1.3 true + 1.3 + Topic concerning rice-specific data. + beta12orEarlier @@ -45948,12 +46270,12 @@ positional features such as functional sites in nucleotide sequences. Genetic mapping and linkage - Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. - Genetic linkage - true - 1.3 - beta12orEarlier Linkage mapping + beta12orEarlier + 1.3 + true + Genetic linkage + Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. @@ -45965,9 +46287,9 @@ positional features such as functional sites in nucleotide sequences. Comparative genomics - BioCatalogue:Comparative Genomics - beta12orEarlier Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes. + beta12orEarlier + BioCatalogue:Comparative Genomics @@ -45981,9 +46303,9 @@ positional features such as functional sites in nucleotide sequences.Mobile genetic elements - Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns. - beta12orEarlier Transposons + beta12orEarlier + Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns. @@ -45995,10 +46317,10 @@ positional features such as functional sites in nucleotide sequences. Human disease - Topic concerning human diseases, typically describing the genes, mutations and proteins implicated in disease. - beta12orEarlier - true beta13 + true + beta12orEarlier + Topic concerning human diseases, typically describing the genes, mutations and proteins implicated in disease. @@ -46010,12 +46332,12 @@ positional features such as functional sites in nucleotide sequences. Immunology - beta12orEarlier - http://purl.bioontology.org/ontology/MSH/D007125 - http://purl.bioontology.org/ontology/MSH/D007120 - Computational immunology - Immunoinformatics Topic concerning the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on. + Immunoinformatics + Computational immunology + http://purl.bioontology.org/ontology/MSH/D007120 + http://purl.bioontology.org/ontology/MSH/D007125 + beta12orEarlier @@ -46028,11 +46350,11 @@ positional features such as functional sites in nucleotide sequences. Membrane and lipoproteins - Topic concerning lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane. - Transmembrane proteins - Lipoproteins - Membrane proteins beta12orEarlier + Membrane proteins + Lipoproteins + Transmembrane proteins + Topic concerning lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane. @@ -46044,9 +46366,9 @@ positional features such as functional sites in nucleotide sequences. Enzymes - Enzymology - Topic concerning proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. beta12orEarlier + Topic concerning proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. + Enzymology @@ -46058,10 +46380,10 @@ positional features such as functional sites in nucleotide sequences. Primers - Primer binding sites - beta12orEarlier - Topic concerning PCR primers and hybridization oligos in a nucleic acid sequence. Nucleic acid features (primers) + Topic concerning PCR primers and hybridization oligos in a nucleic acid sequence. + beta12orEarlier + Primer binding sites @@ -46074,12 +46396,12 @@ positional features such as functional sites in nucleotide sequences. PolyA signal or sites - Topic concerning regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. - PolyA site - A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation. - PolyA signal - Nucleic acid features (PolyA signal or site) beta12orEarlier + Nucleic acid features (PolyA signal or site) + PolyA signal + A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation. + PolyA site + Topic concerning regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. @@ -46092,9 +46414,9 @@ positional features such as functional sites in nucleotide sequences. CpG island and isochores - Topic concerning CpG rich regions (isochores) in a nucleotide sequence. - Nucleic acid features (CpG island and isochore) beta12orEarlier + Nucleic acid features (CpG island and isochore) + Topic concerning CpG rich regions (isochores) in a nucleotide sequence. @@ -46107,10 +46429,10 @@ positional features such as functional sites in nucleotide sequences. Restriction sites - Nucleic acid restriction sites (report) - beta12orEarlier - Nucleic acid features (restriction sites) Topic concerning restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. + Nucleic acid features (restriction sites) + beta12orEarlier + Nucleic acid restriction sites (report) @@ -46124,11 +46446,11 @@ positional features such as functional sites in nucleotide sequences.Splice sites - Nucleic acid report (RNA splice model) - beta12orEarlier - Nucleic acid report (RNA splicing) - Nucleic acid features (splice sites) Topic concerning splice sites in a nucleotide sequence or alternative RNA splicing events. + Nucleic acid features (splice sites) + Nucleic acid report (RNA splicing) + beta12orEarlier + Nucleic acid report (RNA splice model) @@ -46141,9 +46463,9 @@ positional features such as functional sites in nucleotide sequences. Matrix/scaffold attachment sites - Topic concerning matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. - beta12orEarlier Nucleic acid features (matrix/scaffold attachment sites) + beta12orEarlier + Topic concerning matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. @@ -46156,11 +46478,11 @@ positional features such as functional sites in nucleotide sequences. Operon - The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query. - Nucleic acid features (operon) - beta12orEarlier - Topic concerning operons (operators, promoters and genes) from a bacterial genome. Gene features (operon) + Topic concerning operons (operators, promoters and genes) from a bacterial genome. + beta12orEarlier + Nucleic acid features (operon) + The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query. @@ -46173,9 +46495,9 @@ positional features such as functional sites in nucleotide sequences. Promoters - Topic concerning whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. - Nucleic acid features (promoters) beta12orEarlier + Nucleic acid features (promoters) + Topic concerning whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. @@ -46188,13 +46510,13 @@ positional features such as functional sites in nucleotide sequences. Structural biology - Structural determination - This includes Informatics concerning data generated from the use of microscopes, including optical, electron and scanning probe microscopy. Includes methods for digitizing microscope images and viewing the produced virtual slides and associated data on a computer screen. - 1.3 - This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. - Structure determination - Structural assignment Topic concerning the molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids. + Structural assignment + Structure determination + This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. + 1.3 + This includes Informatics concerning data generated from the use of microscopes, including optical, electron and scanning probe microscopy. Includes methods for digitizing microscope images and viewing the produced virtual slides and associated data on a computer screen. + Structural determination @@ -46208,13 +46530,13 @@ positional features such as functional sites in nucleotide sequences.Protein membrane regions - Transmembrane regions - Protein transmembrane regions - Intramembrane regions - Topic concerning trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. - This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. - Protein features (membrane regions) 1.8 + Protein features (membrane regions) + This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. + Topic concerning trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. + Intramembrane regions + Protein transmembrane regions + Transmembrane regions @@ -46227,9 +46549,9 @@ positional features such as functional sites in nucleotide sequences. Structure comparison - beta12orEarlier - This might involve comparison of secondary or tertiary (3D) structural information. Topic concerning the comparison of two or more molecular structures, for example structure alignment and clustering. + This might involve comparison of secondary or tertiary (3D) structural information. + beta12orEarlier @@ -46242,11 +46564,11 @@ positional features such as functional sites in nucleotide sequences. Function analysis - beta12orEarlier - Protein function analysis - Topic concerning the study of gene and protein function including the prediction of functional properties of a protein. - BioCatalogue:Function Prediction Protein function prediction + BioCatalogue:Function Prediction + Topic concerning the study of gene and protein function including the prediction of functional properties of a protein. + Protein function analysis + beta12orEarlier @@ -46259,9 +46581,9 @@ positional features such as functional sites in nucleotide sequences. Prokaryotes and archae - Topic concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation. - beta12orEarlier The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes. + beta12orEarlier + Topic concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation. @@ -46273,11 +46595,11 @@ positional features such as functional sites in nucleotide sequences. Protein databases - Topic concerning protein data resources. - Protein data resources - beta12orEarlier - 1.3 true + 1.3 + beta12orEarlier + Protein data resources + Topic concerning protein data resources. @@ -46289,10 +46611,10 @@ positional features such as functional sites in nucleotide sequences. Structure determination - 1.3 - true - beta12orEarlier Topic concerning experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. + beta12orEarlier + true + 1.3 @@ -46304,8 +46626,8 @@ positional features such as functional sites in nucleotide sequences. Cell biology - Topic concerning cells, such as key genes and proteins involved in the cell cycle. beta12orEarlier + Topic concerning cells, such as key genes and proteins involved in the cell cycle. @@ -46317,10 +46639,10 @@ positional features such as functional sites in nucleotide sequences. Classification - true - Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships. - beta12orEarlier beta13 + beta12orEarlier + Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships. + true @@ -46332,10 +46654,10 @@ positional features such as functional sites in nucleotide sequences. Lipoproteins - beta12orEarlier - Topic concerning lipoproteins (protein-lipid assemblies). - 1.3 true + 1.3 + Topic concerning lipoproteins (protein-lipid assemblies). + beta12orEarlier @@ -46347,11 +46669,11 @@ positional features such as functional sites in nucleotide sequences. Phylogeny visualisation - beta12orEarlier - beta12orEarlier - BioCatalogue:Tree Display - Visualise a phylogeny, for example, render a phylogenetic tree. true + Visualise a phylogeny, for example, render a phylogenetic tree. + BioCatalogue:Tree Display + beta12orEarlier + beta12orEarlier @@ -46364,11 +46686,11 @@ positional features such as functional sites in nucleotide sequences.Cheminformatics - Chemoinformatics - beta12orEarlier - Topic concerning the application of information technology to chemistry in biological research environment. - BioCatalogue:Chemoinformatics Chemical informatics + BioCatalogue:Chemoinformatics + Topic concerning the application of information technology to chemistry in biological research environment. + beta12orEarlier + Chemoinformatics @@ -46381,18 +46703,18 @@ positional features such as functional sites in nucleotide sequences. Systems biology - Biological modelling - Biological system modelling - beta12orEarlier - BioCatalogue:Systems Biology - BioCatalogue:Model Analysis - http://purl.bioontology.org/ontology/MSH/D049490 - Biological models - Topic concerning the holistic modelling and analysis of complex biological systems and the interactions therein. - BioCatalogue:Model Creation - This includes databases of models and methods to construct or analyse a model. - BioCatalogue:Model Execution http://en.wikipedia.org/wiki/Systems_biology + BioCatalogue:Model Execution + This includes databases of models and methods to construct or analyse a model. + BioCatalogue:Model Creation + Topic concerning the holistic modelling and analysis of complex biological systems and the interactions therein. + Biological models + http://purl.bioontology.org/ontology/MSH/D049490 + BioCatalogue:Model Analysis + BioCatalogue:Systems Biology + beta12orEarlier + Biological system modelling + Biological modelling @@ -46405,12 +46727,12 @@ positional features such as functional sites in nucleotide sequences. Statistics - http://purl.bioontology.org/ontology/MSH/D056808 - beta12orEarlier - BioCatalogue:Biostatistics - http://en.wikipedia.org/wiki/Biostatistics - Biostatistics Topic concerning the application of statistical methods to biological problems. + Biostatistics + http://en.wikipedia.org/wiki/Biostatistics + BioCatalogue:Biostatistics + beta12orEarlier + http://purl.bioontology.org/ontology/MSH/D056808 @@ -46423,11 +46745,11 @@ positional features such as functional sites in nucleotide sequences. Structure database search - true - beta12orEarlier - Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure). - beta12orEarlier The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template. + beta12orEarlier + Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure). + beta12orEarlier + true @@ -46439,13 +46761,13 @@ positional features such as functional sites in nucleotide sequences. Molecular modelling - Molecular modeling - Homology modelling - Topic concerning the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. - beta12orEarlier - Comparative modelling - Comparative modeling Homology modeling + Comparative modeling + Comparative modelling + beta12orEarlier + Topic concerning the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. + Homology modelling + Molecular modeling @@ -46457,11 +46779,11 @@ positional features such as functional sites in nucleotide sequences. Protein function prediction - Topic concerning the prediction of functional properties of a protein. - true - BioCatalogue:Function Prediction - beta12orEarlier 1.2 + beta12orEarlier + BioCatalogue:Function Prediction + true + Topic concerning the prediction of functional properties of a protein. @@ -46473,10 +46795,10 @@ positional features such as functional sites in nucleotide sequences. SNP - Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. - A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. - Single nucleotide polymorphism beta12orEarlier + Single nucleotide polymorphism + A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. + Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. @@ -46488,10 +46810,10 @@ positional features such as functional sites in nucleotide sequences. Transmembrane protein prediction - true - beta12orEarlier - beta12orEarlier Predict transmembrane domains and topology in protein sequences. + beta12orEarlier + beta12orEarlier + true @@ -46504,11 +46826,11 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid structure comparison - Use this concept for methods that are exclusively for nucleic acid structures. - beta12orEarlier - Topic concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures. - true beta12orEarlier + true + Topic concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures. + beta12orEarlier + Use this concept for methods that are exclusively for nucleic acid structures. @@ -46521,9 +46843,9 @@ positional features such as functional sites in nucleotide sequences. Exons - beta12orEarlier - Topic concerning exons in a nucleotide sequences. Gene features (exon) + Topic concerning exons in a nucleotide sequences. + beta12orEarlier @@ -46536,19 +46858,19 @@ positional features such as functional sites in nucleotide sequences. Gene transcription features - Attenuators (report) - TATA signals (report) - beta12orEarlier - Topic concerning transcription of DNA into RNA including the regulation of transcription. - -10 signals (report) - Ribosome binding sites (report) - Terminators (report) - Enhancers (report) - This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. - Gene transcriptional features - -35 signals (report) - CAAT signals (report) GC signals (report) + CAAT signals (report) + -35 signals (report) + Gene transcriptional features + This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. + Enhancers (report) + Terminators (report) + Ribosome binding sites (report) + -10 signals (report) + Topic concerning transcription of DNA into RNA including the regulation of transcription. + beta12orEarlier + TATA signals (report) + Attenuators (report) @@ -46562,10 +46884,10 @@ positional features such as functional sites in nucleotide sequences.DNA mutation - Topic concerning DNA mutation. - Nucleic acid features (mutation) - beta12orEarlier Mutation annotation + beta12orEarlier + Nucleic acid features (mutation) + Topic concerning DNA mutation. @@ -46578,10 +46900,10 @@ positional features such as functional sites in nucleotide sequences. Oncology - Cancer biology - Cancer - beta12orEarlier Topic concerning the study of cancer, for example, genes and proteins implicated in cancer. + beta12orEarlier + Cancer + Cancer biology @@ -46595,10 +46917,10 @@ positional features such as functional sites in nucleotide sequences.Toxins and targets - beta12orEarlier - Targets - Topic concerning structural and associated data for toxic chemical substances. Toxins + Topic concerning structural and associated data for toxic chemical substances. + Targets + beta12orEarlier @@ -46611,10 +46933,10 @@ positional features such as functional sites in nucleotide sequences. Introns - beta12orEarlier - Topic concerning introns in a nucleotide sequences. - Nucleic acid features (intron) Gene features (intron) + Nucleic acid features (intron) + Topic concerning introns in a nucleotide sequences. + beta12orEarlier @@ -46627,10 +46949,10 @@ positional features such as functional sites in nucleotide sequences. Tool topic - beta12orEarlier - true - A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool. beta12orEarlier + A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool. + true + beta12orEarlier @@ -46642,10 +46964,10 @@ positional features such as functional sites in nucleotide sequences. Study topic - beta12orEarlier - true - beta12orEarlier A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding. + beta12orEarlier + true + beta12orEarlier @@ -46657,10 +46979,10 @@ positional features such as functional sites in nucleotide sequences. Nomenclature - beta12orEarlier - Topic concerning biological nomenclature (naming), symbols and terminology. - 1.3 true + 1.3 + Topic concerning biological nomenclature (naming), symbols and terminology. + beta12orEarlier @@ -46672,10 +46994,10 @@ positional features such as functional sites in nucleotide sequences. Disease genes and proteins - beta12orEarlier - Topic concerning the genes, gene variations and proteins involved in one or more specific diseases. - true 1.3 + true + Topic concerning the genes, gene variations and proteins involved in one or more specific diseases. + beta12orEarlier @@ -46687,10 +47009,10 @@ positional features such as functional sites in nucleotide sequences. Protein structure analysis - Topic concerning protein secondary or tertiary structural data and/or associated annotation. - beta12orEarlier - http://edamontology.org/topic_3040 Protein structure + http://edamontology.org/topic_3040 + beta12orEarlier + Topic concerning protein secondary or tertiary structural data and/or associated annotation. @@ -46702,13 +47024,12 @@ positional features such as functional sites in nucleotide sequences. Humans - - 1.3 - Topic concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general. - true + beta12orEarlier - - + true + Topic concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general. + + @@ -46718,12 +47039,12 @@ positional features such as functional sites in nucleotide sequences. Gene resources - true - Gene database - Informatics resource (typically a database) primarily focussed on genes. - 1.3 - beta12orEarlier Gene resource + beta12orEarlier + 1.3 + Informatics resource (typically a database) primarily focussed on genes. + Gene database + true @@ -46735,10 +47056,10 @@ positional features such as functional sites in nucleotide sequences. Yeast - 1.3 - true - beta12orEarlier Topic concerning yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation. + beta12orEarlier + true + 1.3 @@ -46750,10 +47071,10 @@ positional features such as functional sites in nucleotide sequences. Eukaryotes - beta12orEarlier - The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes. - Topic concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation. Eukaryote + Topic concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation. + The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes. + beta12orEarlier @@ -46765,9 +47086,9 @@ positional features such as functional sites in nucleotide sequences. Invertebrates - Topic concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation. - beta12orEarlier The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates. + beta12orEarlier + Topic concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation. @@ -46779,9 +47100,9 @@ positional features such as functional sites in nucleotide sequences. Vertebrates - beta12orEarlier - Topic concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates. + Topic concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. + beta12orEarlier @@ -46793,9 +47114,9 @@ positional features such as functional sites in nucleotide sequences. Unicellular eukaryotes - Topic concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation. - The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes. beta12orEarlier + The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes. + Topic concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation. @@ -46807,10 +47128,10 @@ positional features such as functional sites in nucleotide sequences. Protein structure alignment - 1.3 - true - Topic concerning protein secondary or tertiary structure alignments. beta12orEarlier + Topic concerning protein secondary or tertiary structure alignments. + true + 1.3 @@ -46823,11 +47144,11 @@ positional features such as functional sites in nucleotide sequences.X-ray diffraction - X-ray crystallography - Crystallography - Topic concerning the study of matter and their structure by means of the diffraction of X-rays, typically the diffraction pattern caused by the regularly spaced atoms of a crystalline sample. - X-ray microscopy beta12orEarlier + X-ray microscopy + Topic concerning the study of matter and their structure by means of the diffraction of X-rays, typically the diffraction pattern caused by the regularly spaced atoms of a crystalline sample. + Crystallography + X-ray crystallography @@ -46840,11 +47161,11 @@ positional features such as functional sites in nucleotide sequences. Ontologies, nomenclature and classification - Topic concerning conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics. - beta12orEarlier - http://purl.bioontology.org/ontology/MSH/D002965 - 1.3 true + 1.3 + http://purl.bioontology.org/ontology/MSH/D002965 + beta12orEarlier + Topic concerning conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics. @@ -46857,13 +47178,13 @@ positional features such as functional sites in nucleotide sequences.Immunoproteins, genes and antigens - Immunogenes - Immunoproteins - beta12orEarlier - This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc." - Antigens - Immunopeptides Topic concerning immunity-related genes, proteins and their ligands. + Immunopeptides + Antigens + This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc." + beta12orEarlier + Immunoproteins + Immunogenes @@ -46876,11 +47197,11 @@ positional features such as functional sites in nucleotide sequences. Molecules - true - beta12orEarlier - Topic concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance. - beta12orEarlier CHEBI:23367 + beta12orEarlier + Topic concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance. + beta12orEarlier + true @@ -46893,11 +47214,11 @@ positional features such as functional sites in nucleotide sequences.Toxicology - Toxicology - Computational toxicology - Toxicoinformatics - beta12orEarlier Topic concerning toxins and the adverse effects of these chemical substances on living organisms. + beta12orEarlier + Toxicoinformatics + Computational toxicology + Toxicology @@ -46910,11 +47231,11 @@ positional features such as functional sites in nucleotide sequences. High-throughput sequencing - beta12orEarlier - Topic concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously. - true - beta13 Next-generation sequencing + beta13 + true + Topic concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously. + beta12orEarlier @@ -46926,11 +47247,11 @@ positional features such as functional sites in nucleotide sequences. Structural clustering - beta12orEarlier - Topic concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters. - true - Structure classification 1.7 + Structure classification + true + Topic concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters. + beta12orEarlier @@ -46943,8 +47264,8 @@ positional features such as functional sites in nucleotide sequences.Gene regulatory networks - beta12orEarlier Topic concerning gene regulatory networks. + beta12orEarlier @@ -46956,10 +47277,10 @@ positional features such as functional sites in nucleotide sequences. Disease (specific) - beta12orEarlier - true - beta12orEarlier Informatics resources dedicated to one or more specific diseases (not diseases in general). + beta12orEarlier + true + beta12orEarlier @@ -46971,12 +47292,12 @@ positional features such as functional sites in nucleotide sequences. VNTR - Topic concerning variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. - VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. - VNTR annotation - beta12orEarlier - Variable number of tandem repeat polymorphism Nucleic acid features (VNTR) + Variable number of tandem repeat polymorphism + beta12orEarlier + VNTR annotation + VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. + Topic concerning variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. @@ -46989,11 +47310,11 @@ positional features such as functional sites in nucleotide sequences. Microsatellites - Microsatellite annotation - A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine. - Topic concerning microsatellite polymorphism in a DNA sequence. - Nucleic acid features (microsatellite) beta12orEarlier + Nucleic acid features (microsatellite) + Topic concerning microsatellite polymorphism in a DNA sequence. + A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine. + Microsatellite annotation @@ -47006,11 +47327,11 @@ positional features such as functional sites in nucleotide sequences. RFLP - Nucleic acid features (RFLP) - beta12orEarlier - RFLP annotation - An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. Topic concerning restriction fragment length polymorphisms (RFLP) in a DNA sequence. + An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. + RFLP annotation + beta12orEarlier + Nucleic acid features (RFLP) @@ -47024,10 +47345,10 @@ positional features such as functional sites in nucleotide sequences.DNA polymorphism - Topic concerning DNA polymorphism. - beta12orEarlier - Polymorphism annotation Nucleic acid features (polymorphism) + Polymorphism annotation + beta12orEarlier + Topic concerning DNA polymorphism. @@ -47040,10 +47361,10 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid design - true - beta12orEarlier - 1.3 Topic for the design of nucleic acid sequences with specific conformations. + 1.3 + beta12orEarlier + true @@ -47055,10 +47376,10 @@ positional features such as functional sites in nucleotide sequences. Primer or probe design - beta13 - true - Topic concerning the design of primers for PCR and DNA amplification or the design of molecular probes. 1.3 + Topic concerning the design of primers for PCR and DNA amplification or the design of molecular probes. + true + beta13 @@ -47070,11 +47391,11 @@ positional features such as functional sites in nucleotide sequences. Structure databases - Topic concerning molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids. - Structure data resources - 1.2 - true beta13 + true + 1.2 + Structure data resources + Topic concerning molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids. @@ -47086,10 +47407,10 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid structure - 1.2 - Topic concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation. - beta13 true + beta13 + Topic concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation. + 1.2 @@ -47101,13 +47422,13 @@ positional features such as functional sites in nucleotide sequences. Sequence databases - Topic concerning molecular sequence data resources, including sequence sites, alignments, motifs and profiles. - 1.3 - Sequence data resource - Sequence data - Sequence data resources - beta13 true + beta13 + Sequence data resources + Sequence data + Sequence data resource + 1.3 + Topic concerning molecular sequence data resources, including sequence sites, alignments, motifs and profiles. @@ -47119,11 +47440,11 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid sequences - Nucleotide sequences - true - Topic concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles. - 1.3 beta13 + 1.3 + Topic concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles. + true + Nucleotide sequences @@ -47135,10 +47456,10 @@ positional features such as functional sites in nucleotide sequences. Protein sequences - true - 1.3 - beta13 Topic concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles. + beta13 + 1.3 + true @@ -47150,8 +47471,8 @@ positional features such as functional sites in nucleotide sequences. Protein interaction networks - true 1.3 + true @@ -47163,8 +47484,8 @@ positional features such as functional sites in nucleotide sequences. Molecular biology - Topic concerning the molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life. beta13 + Topic concerning the molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life. @@ -47177,10 +47498,10 @@ positional features such as functional sites in nucleotide sequences. Mammals - 1.3 - beta13 - Topic concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation. true + Topic concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation. + beta13 + 1.3 @@ -47192,9 +47513,9 @@ positional features such as functional sites in nucleotide sequences. Biodiversity - http://purl.bioontology.org/ontology/MSH/D044822 - Topic concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet. beta13 + Topic concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet. + http://purl.bioontology.org/ontology/MSH/D044822 @@ -47207,13 +47528,13 @@ positional features such as functional sites in nucleotide sequences. Sequence clusters and classification - beta13 - Sequence clusters - true - 1.3 - Sequence families - This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. Topic concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity. + This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. + Sequence families + 1.3 + true + Sequence clusters + beta13 @@ -47225,12 +47546,12 @@ positional features such as functional sites in nucleotide sequences. Genetics - Gene resource - beta13 - Genetics data resources - http://purl.bioontology.org/ontology/MSH/D005823 - Gene database Topic concerning the study of genes, genetic variation and heredity in living organisms. + Gene database + http://purl.bioontology.org/ontology/MSH/D005823 + Genetics data resources + beta13 + Gene resource @@ -47243,8 +47564,8 @@ positional features such as functional sites in nucleotide sequences. Quantitative genetics - Topic concerning the genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight). beta13 + Topic concerning the genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight). @@ -47256,8 +47577,8 @@ positional features such as functional sites in nucleotide sequences. Population genetics - beta13 Topic concerning the distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow. + beta13 @@ -47270,10 +47591,10 @@ positional features such as functional sites in nucleotide sequences. Regulatory RNA - beta13 - true - 1.3 Topic concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA). + 1.3 + true + beta13 @@ -47285,10 +47606,10 @@ positional features such as functional sites in nucleotide sequences. Documentation and help - Documentation - beta13 - Help Topic concerning the documentation of resources such as tools, services and databases and how to get help. + Help + beta13 + Documentation @@ -47301,10 +47622,10 @@ positional features such as functional sites in nucleotide sequences. Genetic organisation - true - Topic concerning the structural and functional organisation of genes and other genetic elements. - beta13 1.3 + beta13 + Topic concerning the structural and functional organisation of genes and other genetic elements. + true @@ -47317,15 +47638,15 @@ positional features such as functional sites in nucleotide sequences.Medical informatics - Molecular medicine - Health and disease - beta13 - Healthcare informatics - Translational medicine - Biomedical informatics - Clinical informatics - Health informatics Topic concerning the application of information technology to health, disease and biomedicine. + Health informatics + Clinical informatics + Biomedical informatics + Translational medicine + Healthcare informatics + beta13 + Health and disease + Molecular medicine @@ -47338,8 +47659,8 @@ positional features such as functional sites in nucleotide sequences. Developmental biology - beta13 Topic concerning how organisms grow and develop. + beta13 @@ -47352,8 +47673,8 @@ positional features such as functional sites in nucleotide sequences. Embryology - Topic concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. beta13 + Topic concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. @@ -47366,8 +47687,8 @@ positional features such as functional sites in nucleotide sequences. Anatomy - Topic concerning the form and function of the structures of living organisms. beta13 + Topic concerning the form and function of the structures of living organisms. @@ -47380,11 +47701,11 @@ positional features such as functional sites in nucleotide sequences. Literature and reference - http://purl.bioontology.org/ontology/MSH/D011642 - Topic concerning the scientific literature, reference information and documentation. - Literature sources - beta13 Literature search + beta13 + Literature sources + Topic concerning the scientific literature, reference information and documentation. + http://purl.bioontology.org/ontology/MSH/D011642 @@ -47397,9 +47718,9 @@ positional features such as functional sites in nucleotide sequences. Biology - Topic concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on. - beta13 Biological science + beta13 + Topic concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on. @@ -47412,16 +47733,16 @@ positional features such as functional sites in nucleotide sequences. Data management - Data processing - Knowledge management - Databases - Information management - Data handling - http://purl.bioontology.org/ontology/MSH/D030541 - beta13 - Data acquisition - Databases Topic concerning the general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources. + Databases + Data acquisition + beta13 + http://purl.bioontology.org/ontology/MSH/D030541 + Data handling + Information management + Databases + Knowledge management + Data processing @@ -47434,11 +47755,11 @@ positional features such as functional sites in nucleotide sequences. Sequence feature detection - http://purl.bioontology.org/ontology/MSH/D058977 - beta13 - true - Topic concerning the detection of the positional features, such as functional and other key sites, in molecular sequences. 1.3 + Topic concerning the detection of the positional features, such as functional and other key sites, in molecular sequences. + true + beta13 + http://purl.bioontology.org/ontology/MSH/D058977 @@ -47450,10 +47771,10 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid feature detection - 1.3 - beta13 - Topic concerning the detection of positional features such as functional sites in nucleotide sequences. true + Topic concerning the detection of positional features such as functional sites in nucleotide sequences. + beta13 + 1.3 @@ -47465,10 +47786,10 @@ positional features such as functional sites in nucleotide sequences. Protein feature detection - true - 1.3 - Topic concerning the detection, identification and analysis of positional protein sequence features, such as functional sites. beta13 + Topic concerning the detection, identification and analysis of positional protein sequence features, such as functional sites. + 1.3 + true @@ -47480,13 +47801,13 @@ positional features such as functional sites in nucleotide sequences. Biological system modelling - Topic for modelling biological systems in mathematical terms. - beta13 - true - 1.2 - BioCatalogue:Model Execution BioCatalogue:Model Analysis - + BioCatalogue:Model Execution + 1.2 + true + beta13 + Topic for modelling biological systems in mathematical terms. + @@ -47497,8 +47818,8 @@ positional features such as functional sites in nucleotide sequences. Data acquisition - beta13 Topic concerning the acquisition of biological data. + beta13 @@ -47510,12 +47831,12 @@ positional features such as functional sites in nucleotide sequences. Genes and proteins resources - true - Gene and protein families - beta13 - Gene family - Topic concerning specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins. 1.3 + Topic concerning specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins. + Gene family + beta13 + Gene and protein families + true @@ -47528,9 +47849,9 @@ positional features such as functional sites in nucleotide sequences.Protein topological domains - 1.8 - Topic concerning topological domains such as cytoplasmic regions in a protein. Protein features (topological domains) + Topic concerning topological domains such as cytoplasmic regions in a protein. + 1.8 @@ -47543,8 +47864,8 @@ positional features such as functional sites in nucleotide sequences. Protein variants - Topic concerning protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. beta13 + Topic concerning protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. @@ -47558,9 +47879,9 @@ positional features such as functional sites in nucleotide sequences.Expression signals - Nucleic acid features (expression signal) - Topic concerning regions within a nucleic acid sequence containing a signal that alters a biological function. beta13 + Topic concerning regions within a nucleic acid sequence containing a signal that alters a biological function. + Nucleic acid features (expression signal) @@ -47574,10 +47895,10 @@ positional features such as functional sites in nucleotide sequences.DNA binding sites - Nucleic acid features (binding) - Topic concerning nucleic acids binding to some other molecule. - beta13 This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). + beta13 + Topic concerning nucleic acids binding to some other molecule. + Nucleic acid features (binding) @@ -47590,9 +47911,9 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid repeats - Topic concerning repetitive elements within a nucleic acid sequence. - This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. beta13 + This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. + Topic concerning repetitive elements within a nucleic acid sequence. @@ -47605,11 +47926,11 @@ positional features such as functional sites in nucleotide sequences. DNA replication and recombination - Topic concerning DNA replication or recombination. - beta13 - Nucleic acid features (replication and recombination) - Nucleosome exclusion sequences This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. + Nucleosome exclusion sequences + Nucleic acid features (replication and recombination) + beta13 + Topic concerning DNA replication or recombination. @@ -47622,10 +47943,10 @@ positional features such as functional sites in nucleotide sequences. Signal or transit peptide - A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. - Nucleic acid features (signal or transit peptide) - beta13 Topic concerning coding sequences for a signal or transit peptide. + beta13 + Nucleic acid features (signal or transit peptide) + A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. @@ -47638,10 +47959,10 @@ positional features such as functional sites in nucleotide sequences. Sequence tagged sites - Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs. - beta13 - Topic concerning sequence tagged sites (STS) in nucleic acid sequences. Nucleic acid features (STS) + Topic concerning sequence tagged sites (STS) in nucleic acid sequences. + beta13 + Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs. @@ -47654,12 +47975,12 @@ positional features such as functional sites in nucleotide sequences. Sequencing - Next gen sequencing - Next generation sequencing - NGS - 1.1 - http://purl.bioontology.org/ontology/MSH/D059014 Topic concerning the determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. + http://purl.bioontology.org/ontology/MSH/D059014 + 1.1 + NGS + Next generation sequencing + Next gen sequencing @@ -47672,13 +47993,13 @@ positional features such as functional sites in nucleotide sequences. ChIP-seq - Topic concerning the analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. - Chip-sequencing - 1.1 - Chip seq - Chip sequencing - 1.3 true + 1.3 + Chip sequencing + Chip seq + 1.1 + Chip-sequencing + Topic concerning the analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. @@ -47690,16 +48011,16 @@ positional features such as functional sites in nucleotide sequences. RNA-Seq - true - This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs. - WTSS - Small RNA-Seq - A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. - 1.3 - 1.1 - RNA-seq - Whole transcriptome shotgun sequencing Small RNA-seq + Whole transcriptome shotgun sequencing + RNA-seq + 1.1 + 1.3 + A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. + Small RNA-Seq + WTSS + This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs. + true @@ -47711,11 +48032,11 @@ positional features such as functional sites in nucleotide sequences. DNA methylation - 1.1 - http://purl.bioontology.org/ontology/MSH/D019175 - 1.3 - true Topic concerning DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc. + true + 1.3 + http://purl.bioontology.org/ontology/MSH/D019175 + 1.1 @@ -47727,9 +48048,9 @@ positional features such as functional sites in nucleotide sequences. Metabolomics - 1.1 - http://purl.bioontology.org/ontology/MSH/D055432 Topic concerning the systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism. + http://purl.bioontology.org/ontology/MSH/D055432 + 1.1 @@ -47743,10 +48064,10 @@ positional features such as functional sites in nucleotide sequences.Epigenomics - Topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc. - http://purl.bioontology.org/ontology/MSH/D057890 - 1.1 Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. + 1.1 + http://purl.bioontology.org/ontology/MSH/D057890 + Topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc. @@ -47760,12 +48081,12 @@ positional features such as functional sites in nucleotide sequences.Metagenomics - 1.1 - Topic concerning the study of genetic material recovered from environmental samples, and associated environmental data. - Environmental genomics - Community genomics - Ecogenomics http://purl.bioontology.org/ontology/MSH/D056186 + Ecogenomics + Community genomics + Environmental genomics + Topic concerning the study of genetic material recovered from environmental samples, and associated environmental data. + 1.1 @@ -47779,9 +48100,9 @@ positional features such as functional sites in nucleotide sequences.Structural variation - Genomic structural variation - Topic concerning variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations. 1.1 + Topic concerning variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations. + Genomic structural variation @@ -47793,9 +48114,9 @@ positional features such as functional sites in nucleotide sequences. DNA packaging - http://purl.bioontology.org/ontology/MSH/D042003 - Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures. beta12orEarlier + Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures. + http://purl.bioontology.org/ontology/MSH/D042003 @@ -47807,11 +48128,11 @@ positional features such as functional sites in nucleotide sequences. DNA-Seq - true - DNA-seq - 1.3 - A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements. 1.1 + A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements. + 1.3 + DNA-seq + true @@ -47823,11 +48144,11 @@ positional features such as functional sites in nucleotide sequences. RNA-Seq alignment - beta12orEarlier - RNA-seq alignment - 1.3 - Topic concerning the alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing. true + Topic concerning the alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing. + 1.3 + RNA-seq alignment + beta12orEarlier @@ -47839,11 +48160,11 @@ positional features such as functional sites in nucleotide sequences. ChIP-on-chip - ChIP-chip - 1.1 - Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. - 1.3 true + 1.3 + Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. + 1.1 + ChIP-chip @@ -47855,11 +48176,11 @@ positional features such as functional sites in nucleotide sequences. Data security - Security - Security - 1.3 - Privacy Topic concerning the protection of data, for example, patient health data. + Privacy + 1.3 + Security + Security @@ -47871,12 +48192,12 @@ positional features such as functional sites in nucleotide sequences. Sample collections - Specimen collections - biosamples - 1.3 - Topic concerning biological samples and specimens. - biobanking samples + biobanking + Topic concerning biological samples and specimens. + 1.3 + biosamples + Specimen collections @@ -47890,10 +48211,10 @@ positional features such as functional sites in nucleotide sequences.Biochemistry - Biological chemistry - Topic concerning chemical substances and physico-chemical processes and that occur within living organisms. - 1.3 Chemical biology + 1.3 + Topic concerning chemical substances and physico-chemical processes and that occur within living organisms. + Biological chemistry @@ -47907,9 +48228,9 @@ positional features such as functional sites in nucleotide sequences.Phylogenetics - http://purl.bioontology.org/ontology/MSH/D010802 - 1.3 Topic concerning the study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences). + 1.3 + http://purl.bioontology.org/ontology/MSH/D010802 @@ -47921,12 +48242,12 @@ positional features such as functional sites in nucleotide sequences. Epigenetics - 1.3 - Histone modification - http://purl.bioontology.org/ontology/MSH/D019175 - This includes sub-topics such as histone modification and DNA methylation. - DNA methylation Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence. + DNA methylation + This includes sub-topics such as histone modification and DNA methylation. + http://purl.bioontology.org/ontology/MSH/D019175 + Histone modification + 1.3 @@ -47939,8 +48260,8 @@ positional features such as functional sites in nucleotide sequences. Biotechnology - 1.3 Topic concerning the exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production. + 1.3 @@ -47954,8 +48275,8 @@ positional features such as functional sites in nucleotide sequences.Phenomics - 1.3 Topic concerning phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. + 1.3 @@ -47968,8 +48289,8 @@ positional features such as functional sites in nucleotide sequences. Evolutionary biology - 1.3 Topic concerning the evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity. + 1.3 @@ -47982,8 +48303,8 @@ positional features such as functional sites in nucleotide sequences. Physiology - Topic concerning the functions of living organisms and their constituent parts. 1.3 + Topic concerning the functions of living organisms and their constituent parts. @@ -47996,8 +48317,8 @@ positional features such as functional sites in nucleotide sequences. Microbiology - 1.3 Topic concerning the biology of microorganisms. + 1.3 @@ -48010,9 +48331,9 @@ positional features such as functional sites in nucleotide sequences. Parasitology - 1.3 - Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system. Topic concerning the biology of parasites. + Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system. + 1.3 @@ -48025,10 +48346,10 @@ positional features such as functional sites in nucleotide sequences. Medicine - Biomedical research - 1.3 - Topic concerning research in support of healing by diagnosis, treatment, and prevention of disease. Experimental medicine + Topic concerning research in support of healing by diagnosis, treatment, and prevention of disease. + 1.3 + Biomedical research @@ -48041,9 +48362,9 @@ positional features such as functional sites in nucleotide sequences. Neurobiology - Topic concerning the study of the nervous system and brain; its anatomy, physiology and function. - 1.3 Neuroscience + 1.3 + Topic concerning the study of the nervous system and brain; its anatomy, physiology and function. @@ -48056,10 +48377,10 @@ positional features such as functional sites in nucleotide sequences. Public health and epidemiology - Epidemiology - Public health - 1.3 Topic concerning the the patterns, cause, and effect of disease within populations. + 1.3 + Public health + Epidemiology @@ -48073,8 +48394,8 @@ positional features such as functional sites in nucleotide sequences.Biophysics - Topic concerning the use of physics to study biological system. 1.3 + Topic concerning the use of physics to study biological system. @@ -48088,13 +48409,13 @@ positional features such as functional sites in nucleotide sequences.Computational biology - Biomathematics - 1.3 - Theoretical biology - Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of biological systems. - Mathematical biology - This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology). BioCatalogue:Model Execution + This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology). + Mathematical biology + Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of biological systems. + Theoretical biology + 1.3 + Biomathematics @@ -48108,9 +48429,9 @@ positional features such as functional sites in nucleotide sequences.Transcriptomics - Topic concerning the analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. - 1.3 Transcriptome + 1.3 + Topic concerning the analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. @@ -48123,8 +48444,8 @@ positional features such as functional sites in nucleotide sequences. Chemistry - Topic concerning the composition and properties of matter, reactions, and the use of reactions to create new substances. 1.3 + Topic concerning the composition and properties of matter, reactions, and the use of reactions to create new substances. @@ -48137,9 +48458,9 @@ positional features such as functional sites in nucleotide sequences. Mathematics - 1.3 - Maths Topic concerning the is the study of numbers (quantity) and other topics including structure, space, and change. + Maths + 1.3 @@ -48152,8 +48473,8 @@ positional features such as functional sites in nucleotide sequences. Computer science - Topic concerning the theory and practical use of computer systems. 1.3 + Topic concerning the theory and practical use of computer systems. @@ -48166,8 +48487,8 @@ positional features such as functional sites in nucleotide sequences. Physics - 1.3 Topic concerning the study of matter, space and time, and related concepts such as energy and force. + 1.3 @@ -48181,9 +48502,9 @@ positional features such as functional sites in nucleotide sequences.RNA splicing - 1.3 - This includes the study of splice sites, splicing patterns, splice alternatives or variants, isoforms, etc. Topic concerning RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons. + This includes the study of splice sites, splicing patterns, splice alternatives or variants, isoforms, etc. + 1.3 @@ -48195,8 +48516,8 @@ positional features such as functional sites in nucleotide sequences. Molecular genetics - 1.3 Topic concerning the structure and function of genes at a molecular level. + 1.3 @@ -48209,12 +48530,12 @@ positional features such as functional sites in nucleotide sequences. Respiratory medicine - Topic concerning the study of respiratory system. - Pulmonology - Pulmonary disorders - 1.3 - Pulmonary medicine Respiratory disease + Pulmonary medicine + 1.3 + Pulmonary disorders + Pulmonology + Topic concerning the study of respiratory system. @@ -48227,10 +48548,10 @@ positional features such as functional sites in nucleotide sequences. Metabolic disease - Topic concerning the study of metabolic diseases. - true - 1.3 1.4 + 1.3 + true + Topic concerning the study of metabolic diseases. @@ -48242,10 +48563,10 @@ positional features such as functional sites in nucleotide sequences. Infectious disease - 1.3 - Topic concerning the branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions). - Communicable disease Transmissable disease + Communicable disease + Topic concerning the branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions). + 1.3 @@ -48258,8 +48579,8 @@ positional features such as functional sites in nucleotide sequences. Rare diseases - Topic concerning the study of rare diseases. 1.3 + Topic concerning the study of rare diseases. @@ -48273,8 +48594,8 @@ positional features such as functional sites in nucleotide sequences.Computational chemistry - Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems. 1.3 + Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems. @@ -48287,9 +48608,9 @@ positional features such as functional sites in nucleotide sequences. Neurology - 1.3 - Neurological disorders Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system. + Neurological disorders + 1.3 @@ -48302,11 +48623,11 @@ positional features such as functional sites in nucleotide sequences. Cardiology - Cardiovascular disease - Heart disease - Topic concerning the diseases and abnormalities of the heart and circulatory system. - 1.3 Cardiovascular medicine + 1.3 + Topic concerning the diseases and abnormalities of the heart and circulatory system. + Heart disease + Cardiovascular disease @@ -48320,9 +48641,9 @@ positional features such as functional sites in nucleotide sequences.Drug discovery - 1.3 - Topic concerning the discovery and design of drugs or potential drug compounds. This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. + Topic concerning the discovery and design of drugs or potential drug compounds. + 1.3 @@ -48335,10 +48656,10 @@ positional features such as functional sites in nucleotide sequences. Biobank - Tissue collection - Topic concerning repositories of biological samples, typically human, for basic biological and clinical research. - 1.3 biobanking + 1.3 + Topic concerning repositories of biological samples, typically human, for basic biological and clinical research. + Tissue collection @@ -48351,8 +48672,8 @@ positional features such as functional sites in nucleotide sequences. Mouse clinic - Topic concerning laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines. 1.3 + Topic concerning laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines. @@ -48365,8 +48686,8 @@ positional features such as functional sites in nucleotide sequences. Microbial collection - Topic concerning collections of microbial cells including bacteria, yeasts and moulds. 1.3 + Topic concerning collections of microbial cells including bacteria, yeasts and moulds. @@ -48379,8 +48700,8 @@ positional features such as functional sites in nucleotide sequences. Cell culture collection - 1.3 Topic concerning collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells. + 1.3 @@ -48393,8 +48714,8 @@ positional features such as functional sites in nucleotide sequences. Clone library - Topic concerning collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA. 1.3 + Topic concerning collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA. @@ -48407,8 +48728,8 @@ positional features such as functional sites in nucleotide sequences. Translational medicine - 1.3 Topic concerning 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice. + 1.3 @@ -48421,12 +48742,12 @@ positional features such as functional sites in nucleotide sequences. Compound libraries and screening - 1.3 - Chemical screening - Compound library - Topic concerning collections of chemicals, typically for use in high-throughput screening experiments. - Chemical library Translational medicine + Chemical library + Topic concerning collections of chemicals, typically for use in high-throughput screening experiments. + Compound library + Chemical screening + 1.3 @@ -48440,8 +48761,8 @@ positional features such as functional sites in nucleotide sequences.Biomedical science - 1.3 Topic concerning biological science that is (typically) performed in the context of medicine. + 1.3 @@ -48454,8 +48775,8 @@ positional features such as functional sites in nucleotide sequences. Data identity and mapping - Topic concerning the identity of biological data and the mapping of entities in different databases. 1.3 + Topic concerning the identity of biological data and the mapping of entities in different databases. @@ -48468,9 +48789,9 @@ positional features such as functional sites in nucleotide sequences. Sequence search - Topic concerning the search and retrieval from a database on the basis of molecular sequence similarity. - Sequence database search 1.3 + Sequence database search + Topic concerning the search and retrieval from a database on the basis of molecular sequence similarity. @@ -48482,9 +48803,9 @@ positional features such as functional sites in nucleotide sequences. Biomarkers - Topic concerning objective indicators of biological state often used to assess health, and determinate treatment. - 1.4 Diagnostic markers + 1.4 + Topic concerning objective indicators of biological state often used to assess health, and determinate treatment. @@ -48496,9 +48817,9 @@ positional features such as functional sites in nucleotide sequences. Laboratory techniques - 1.4 - Lab techniques Topic concerning the procedures used to conduct an experiment. + Lab techniques + 1.4 @@ -48511,8 +48832,8 @@ positional features such as functional sites in nucleotide sequences. Data analysis - 1.4 Topic concerning the process of systematically applying statistical and / or logical techniques to describe and illustrate, condense and recap, and evaluate data. + 1.4 @@ -48525,8 +48846,8 @@ positional features such as functional sites in nucleotide sequences. Data integration - 1.4 Topic concerning the combination of data from different sources to provide users with a unified view of these data. + 1.4 @@ -48539,9 +48860,9 @@ positional features such as functional sites in nucleotide sequences. Biomaterials - Topic concerning any matter, surface or construct that interacts with a biological system. - 1.4 Diagnostic markers + 1.4 + Topic concerning any matter, surface or construct that interacts with a biological system. @@ -48555,8 +48876,8 @@ positional features such as functional sites in nucleotide sequences.Chemical biology - Topic concerning the use of synthetic chemistry to study and manipulate biological systems. 1.4 + Topic concerning the use of synthetic chemistry to study and manipulate biological systems. @@ -48569,8 +48890,8 @@ positional features such as functional sites in nucleotide sequences. Analytical chemistry - Topic concerning the study of the separation, identification, and quantification of the chemical components of natural and artificial materials. 1.4 + Topic concerning the study of the separation, identification, and quantification of the chemical components of natural and artificial materials. @@ -48583,9 +48904,9 @@ positional features such as functional sites in nucleotide sequences. Synthetic chemistry - Topic concerning the use of chemistry to create new compounds. - 1.4 Synthetic organic chemistry + 1.4 + Topic concerning the use of chemistry to create new compounds. @@ -48598,9 +48919,9 @@ positional features such as functional sites in nucleotide sequences. Computer programming - Software development - 1.4 Topic concerning the process that leads from an original formulation of a computing problem to executable programs. + 1.4 + Software development @@ -48613,11 +48934,11 @@ positional features such as functional sites in nucleotide sequences. Drug development - Medicines development - Drug development science - Medicine development - Topic concerning the process of bringing a new drug to market once a lead compounds has been identified through drug discovery. 1.4 + Topic concerning the process of bringing a new drug to market once a lead compounds has been identified through drug discovery. + Medicine development + Drug development science + Medicines development @@ -48630,10 +48951,10 @@ positional features such as functional sites in nucleotide sequences. Drug formulation and delivery - 1.4 - Topic concerning the process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect. - Drug formulation Drug delivery + Drug formulation + Topic concerning the process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect. + 1.4 @@ -48646,16 +48967,16 @@ positional features such as functional sites in nucleotide sequences. Pharmacokinetics and pharmacodynamics - Drug metabolism - Drug metabolism - ADME - Drug absorption - Drug excretion - 1.4 - Drug distribution - Topic concerning the study of how a drug interacts with the body. - Pharmacokinetics Pharmacodynamics + Pharmacokinetics + Topic concerning the study of how a drug interacts with the body. + Drug distribution + 1.4 + Drug excretion + Drug absorption + ADME + Drug metabolism + Drug metabolism @@ -48666,13 +48987,13 @@ positional features such as functional sites in nucleotide sequences. - Medicine research and development Medicines research and development + Medicine research and development - Topic concerning the discovery, development and approval of medicines. - 1.4 - Drug discovery and development Health care research + Drug discovery and development + 1.4 + Topic concerning the discovery, development and approval of medicines. @@ -48685,9 +49006,9 @@ positional features such as functional sites in nucleotide sequences. Safety sciences - Topic concerning the safety (or lack) of drugs and other medical interventions. - Drug safety 1.4 + Drug safety + Topic concerning the safety (or lack) of drugs and other medical interventions. @@ -48700,9 +49021,9 @@ positional features such as functional sites in nucleotide sequences. Pharmacovigilence - Topic concerning the detection, assesment, understanding and prevention of adverse effects of medicines. - Pharmacovigilence concerns safety once a drug has gone to market. 1.4 + Pharmacovigilence concerns safety once a drug has gone to market. + Topic concerning the detection, assesment, understanding and prevention of adverse effects of medicines. @@ -48715,10 +49036,10 @@ positional features such as functional sites in nucleotide sequences. Preclinical and clinical studies - Clinical studies - 1.4 - Preclinical studies Topic concerning the testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities. + Preclinical studies + 1.4 + Clinical studies @@ -48731,11 +49052,12 @@ positional features such as functional sites in nucleotide sequences. Imaging - Topic concerning the visual representation of an object. - Diffraction experiment - Microscopy - 1.4 This includes diffraction experiments that are based upon the interference of waves, typically electromagnetic waves such as X-rays or visible light, by some object being studied, typical in order to produce an image of the object or determine its structure. + Microscopy imaging + 1.4 + Microscopy + Diffraction experiment + Topic concerning the visual representation of an object. @@ -48748,8 +49070,8 @@ positional features such as functional sites in nucleotide sequences. Biological imaging - Topic concerning the use of imaging techniques to understand biology. 1.4 + Topic concerning the use of imaging techniques to understand biology. @@ -48762,8 +49084,8 @@ positional features such as functional sites in nucleotide sequences. Medical imaging - 1.4 Topic concerning the use of imaging techniques for clinical purposes for medical research. + 1.4 @@ -48776,8 +49098,8 @@ positional features such as functional sites in nucleotide sequences. Light microscopy - 1.4 Topic concerning the use of optical instruments to magnify the image of an object. + 1.4 @@ -48790,8 +49112,8 @@ positional features such as functional sites in nucleotide sequences. Laboratory animal science - Topic concerning the use of animals and alternatives in experimental research. 1.4 + Topic concerning the use of animals and alternatives in experimental research. @@ -48804,8 +49126,8 @@ positional features such as functional sites in nucleotide sequences. Marine biology - Topic concerning the study of organisms in the ocean or brackish waters. 1.4 + Topic concerning the study of organisms in the ocean or brackish waters. @@ -48818,8 +49140,8 @@ positional features such as functional sites in nucleotide sequences. Molecular medicine - Topic concerning the identification of molecular and genetic causes of disease and the development of interventions to correct them. 1.4 + Topic concerning the identification of molecular and genetic causes of disease and the development of interventions to correct them. @@ -48832,9 +49154,9 @@ positional features such as functional sites in nucleotide sequences. Nutritional science - Nutrition science - 1.4 Topic concerning the study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals. It also includes the study of human behaviours related to food choices. + 1.4 + Nutrition science @@ -48847,8 +49169,8 @@ positional features such as functional sites in nucleotide sequences. Omics - 1.4 Topic concerning the collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms. + 1.4 @@ -48861,12 +49183,12 @@ positional features such as functional sites in nucleotide sequences. Quality affairs - 1.4 - Good laboratory practice - Quality assurance - Topic concerning the processes that need to be in place to ensure the quality of products for human or animal use. - Good manufacturing practice Good clinical practice + Good manufacturing practice + Topic concerning the processes that need to be in place to ensure the quality of products for human or animal use. + Quality assurance + Good laboratory practice + 1.4 @@ -48879,8 +49201,8 @@ positional features such as functional sites in nucleotide sequences. Regulatory affairs - 1.4 Topic concerning the protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines. + 1.4 @@ -48893,9 +49215,9 @@ positional features such as functional sites in nucleotide sequences. Regnerative medicine - Topic concerning biomedical approaches to clinical interventions that involve the use of stem cells. - 1.4 Stem cell research + 1.4 + Topic concerning biomedical approaches to clinical interventions that involve the use of stem cells. @@ -48908,8 +49230,8 @@ positional features such as functional sites in nucleotide sequences. Systems medicine - Topic concerning an interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life. 1.4 + Topic concerning an interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life. @@ -48922,8 +49244,8 @@ positional features such as functional sites in nucleotide sequences. Veterinary medicine - Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals. 1.4 + Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals. @@ -48936,9 +49258,9 @@ positional features such as functional sites in nucleotide sequences. Bioengineering - Topic concerning the application of biological concepts and methods to the analytical and synthetic methodologies of engineering. - Diagnostic markers 1.4 + Diagnostic markers + Topic concerning the application of biological concepts and methods to the analytical and synthetic methodologies of engineering. @@ -48951,11 +49273,11 @@ positional features such as functional sites in nucleotide sequences. Geriatric medicine - Geriatrics - 1.4 - Aging - Topic concerning the branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging. Ageing + Topic concerning the branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging. + Aging + 1.4 + Geriatrics @@ -48968,13 +49290,13 @@ positional features such as functional sites in nucleotide sequences. Allergy, clinical immunology and immunotherapeutics. - Immunotherapeutics - Allergy - Immunomodulators - Clinical immunology - Immune disorders - 1.4 Topic concerning health issues related to the immune system and their prevention, diagnosis and mangement. + 1.4 + Immune disorders + Clinical immunology + Immunomodulators + Allergy + Immunotherapeutics @@ -48987,10 +49309,10 @@ positional features such as functional sites in nucleotide sequences. Pain medicine - Algiatry - 1.4 - Ageing Topic concerning with the prevention of pain and the evaluation, treatment and rehabilitation of persons in pain. + Ageing + 1.4 + Algiatry @@ -49003,9 +49325,9 @@ positional features such as functional sites in nucleotide sequences. Anaesthesiology - Topic concerning anaesthesia and anaesthetics. - 1.4 Anaesthetics + 1.4 + Topic concerning anaesthesia and anaesthetics. @@ -49018,11 +49340,11 @@ positional features such as functional sites in nucleotide sequences. Critical care medicine - Topic concerning the multidisciplinary that cares for patients with acute, life-threatening illness or injury. - 1.4 - Emergency medicine - Geriatrics Acute medicine + Geriatrics + Emergency medicine + 1.4 + Topic concerning the multidisciplinary that cares for patients with acute, life-threatening illness or injury. @@ -49035,9 +49357,9 @@ positional features such as functional sites in nucleotide sequences. Dermatology - 1.4 - Topic concerning the branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails. Dermatological disorders + Topic concerning the branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails. + 1.4 @@ -49050,8 +49372,8 @@ positional features such as functional sites in nucleotide sequences. Dentistry - Topic concerning the study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures. 1.4 + Topic concerning the study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures. @@ -49064,11 +49386,11 @@ positional features such as functional sites in nucleotide sequences. Ear, nose and throat medicine - Head and neck disorders - Audiovestibular medicine - 1.4 - Otolaryngology Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat. + Otolaryngology + 1.4 + Audiovestibular medicine + Head and neck disorders @@ -49081,12 +49403,12 @@ positional features such as functional sites in nucleotide sequences. Endocrinology and metabolism - Endocrine disorders - Endocrinology - Topic concerning the branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism. - Metabolism - Metabolic disorders 1.4 + Metabolic disorders + Metabolism + Topic concerning the branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism. + Endocrinology + Endocrine disorders @@ -49099,10 +49421,10 @@ positional features such as functional sites in nucleotide sequences. Haematology - Blood disorders - 1.4 - Haematological disorders Topic concerning the branch of medicine that deals with the blood, blood-forming organs and blood diseases. + Haematological disorders + 1.4 + Blood disorders @@ -49115,9 +49437,9 @@ positional features such as functional sites in nucleotide sequences. Gastroenterology - Topic concerning the branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum. - 1.4 Gastrointestinal disorders + 1.4 + Topic concerning the branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum. @@ -49130,8 +49452,8 @@ positional features such as functional sites in nucleotide sequences. Gender medicine - 1.4 Topic concerning the study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management. + 1.4 @@ -49144,11 +49466,11 @@ positional features such as functional sites in nucleotide sequences. Gynaecology and obstetrics - Obstetrics - Gynaecological disorders - Gynaecology - Topic concerning the branch of medicine that deals with the health of the female reproductive system, pregnancy and birth. 1.4 + Topic concerning the branch of medicine that deals with the health of the female reproductive system, pregnancy and birth. + Gynaecology + Gynaecological disorders + Obstetrics @@ -49161,10 +49483,10 @@ positional features such as functional sites in nucleotide sequences. Hepatic and biliary medicine - Topic concerning the branch of medicine that deals with the liver, gallbladder, bile ducts and bile. - 1.4 - Liver disorders Hepatobiliary medicine + Liver disorders + 1.4 + Topic concerning the branch of medicine that deals with the liver, gallbladder, bile ducts and bile. @@ -49177,8 +49499,8 @@ positional features such as functional sites in nucleotide sequences. Infectious tropical disease - Topic concerning the branch of medicine that deals with the infectious diseases of the tropics. 1.4 + Topic concerning the branch of medicine that deals with the infectious diseases of the tropics. @@ -49191,8 +49513,8 @@ positional features such as functional sites in nucleotide sequences. Trauma medicine - Topic concerning the branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident. 1.4 + Topic concerning the branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident. @@ -49205,8 +49527,8 @@ positional features such as functional sites in nucleotide sequences. Medical toxicology - 1.4 Topic concerning the branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents. + 1.4 @@ -49219,9 +49541,9 @@ positional features such as functional sites in nucleotide sequences. Musculoskeletal medicine - 1.4 - Musculoskeletal disorders Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue. It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine. + Musculoskeletal disorders + 1.4 @@ -49234,10 +49556,10 @@ positional features such as functional sites in nucleotide sequences. Opthalmology - Topic concerning the branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles. - Audiovestibular medicine - Eye disoders 1.4 + Eye disoders + Audiovestibular medicine + Topic concerning the branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles. @@ -49250,9 +49572,9 @@ positional features such as functional sites in nucleotide sequences. Paediatrics - Child health - Topic concerning the branch of medicine that deals with the medical care of infants, children and adolescents. 1.4 + Topic concerning the branch of medicine that deals with the medical care of infants, children and adolescents. + Child health @@ -49265,10 +49587,10 @@ positional features such as functional sites in nucleotide sequences. Psychiatry - Mental health - Topic concerning the branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour. - Psychiatric disorders 1.4 + Psychiatric disorders + Topic concerning the branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour. + Mental health @@ -49281,12 +49603,12 @@ positional features such as functional sites in nucleotide sequences. Reproductive health - 1.4 - Fertility medicine - Audiovestibular medicine - Family planning - Reproductive disorders Topic concerning the health of the reproductive processes, functions and systems at all stages of life. + Reproductive disorders + Family planning + Audiovestibular medicine + Fertility medicine + 1.4 @@ -49299,8 +49621,8 @@ positional features such as functional sites in nucleotide sequences. Surgery - 1.4 Topic concerning the use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance. + 1.4 @@ -49313,12 +49635,12 @@ positional features such as functional sites in nucleotide sequences. Urology and nephrology - Nephrology - Urological disorders - Kidney disease - Urology - 1.4 Topic concerning the branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney. + 1.4 + Urology + Kidney disease + Urological disorders + Nephrology @@ -49331,10 +49653,10 @@ positional features such as functional sites in nucleotide sequences. Complementary medicine - Alternative medicine - 1.4 - Holistic medicine Topic concerning medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health. + Holistic medicine + 1.4 + Alternative medicine @@ -49347,14 +49669,14 @@ positional features such as functional sites in nucleotide sequences. MRI + Nuclear magnetic resonance imaging + Topic concerning techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body. + 1.7 + MRT + Magnetic resonance tomography + NMRI Magnetic resonance imaging - NMRI - Magnetic resonance tomography - MRT - 1.7 - Topic concerning techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body. - Nuclear magnetic resonance imaging @@ -49367,11 +49689,11 @@ positional features such as functional sites in nucleotide sequences.Neutron diffraction - Neutron diffraction experiment - Topic concerning the study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure. - 1.7 - Elastic neutron scattering Neutron microscopy + Elastic neutron scattering + 1.7 + Topic concerning the study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure. + Neutron diffraction experiment @@ -49383,10 +49705,10 @@ positional features such as functional sites in nucleotide sequences. Tomography - 1.7 - Topic concerning imaging in sections (sectioning), through the use of a wave-generating device (tomograph) that generates an image (a tomogram). - Electron tomography X-ray tomography + Electron tomography + Topic concerning imaging in sections (sectioning), through the use of a wave-generating device (tomograph) that generates an image (a tomogram). + 1.7 @@ -49398,10 +49720,10 @@ positional features such as functional sites in nucleotide sequences. Data mining - KDD - Knowledge Discovery in Databases - Topic concerning the discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format. 1.7 + Topic concerning the discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format. + Knowledge Discovery in Databases + KDD @@ -49413,8 +49735,8 @@ positional features such as functional sites in nucleotide sequences. Machine learning - 1.7 A topic concerning the application of artificial intelligence methods to algorithms, in order to create methods that can learn from data in order to generate an ouput, rather than relying on explicitly encoded information only. + 1.7 @@ -49426,8 +49748,8 @@ positional features such as functional sites in nucleotide sequences. Biological databases - Topic concerning databases of biological information including the results of scientific experiments, the application of high-throughput technology, computational analysis and the the scientific literature. 1.8 + Topic concerning databases of biological information including the results of scientific experiments, the application of high-throughput technology, computational analysis and the the scientific literature. @@ -49439,13 +49761,13 @@ positional features such as functional sites in nucleotide sequences. Animals - Topic concerning animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation. - Metazoa - Animal - Zoology - Animal biology - 1.8 The resource may be specific to a plant, a group of plants or all plants. + 1.8 + Animal biology + Zoology + Animal + Metazoa + Topic concerning animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation. @@ -49457,10 +49779,10 @@ positional features such as functional sites in nucleotide sequences. Protein sites, features and motifs - 1.8 - Protein functional sites - Protein sequence features Topic concerning the biologiy, archival, detection, prediction and analysis of positional features such as functional and other key sites, in protein sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. + Protein sequence features + Protein functional sites + 1.8 @@ -49472,10 +49794,10 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid sites, features and motifs - Topic concerning the biologiy, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. - Nucleic acid functional sites - 1.8 Nucleic acid sequence features + 1.8 + Nucleic acid functional sites + Topic concerning the biologiy, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. @@ -49488,11 +49810,11 @@ positional features such as functional sites in nucleotide sequences.Gene transcript features - 1.8 - This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). - mRNA features - Nucleic acid features (mRNA features) Topic concerning features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. + Nucleic acid features (mRNA features) + mRNA features + This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). + 1.8 @@ -49504,8 +49826,8 @@ positional features such as functional sites in nucleotide sequences. Protein-ligand interactions - 1.8 Topic concerning protein-ligand (small molecule) interaction(s). + 1.8 @@ -49517,8 +49839,8 @@ positional features such as functional sites in nucleotide sequences. Protein-drug interactions - 1.8 Topic concerning protein-drug interaction(s). + 1.8 @@ -49530,8 +49852,8 @@ positional features such as functional sites in nucleotide sequences. Genotyping experiment - Topic concerning genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. 1.8 + Topic concerning genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. @@ -49543,9 +49865,9 @@ positional features such as functional sites in nucleotide sequences. GWAS study - Topic concerning genome-wide association study experiments. - Genome-wide association study 1.8 + Genome-wide association study + Topic concerning genome-wide association study experiments. @@ -49557,9 +49879,9 @@ positional features such as functional sites in nucleotide sequences. Microarray experiment - This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates. - 1.8 Topic concerning microarray experiments including conditions, protocol, sample:data relationships etc. + 1.8 + This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates. @@ -49571,8 +49893,8 @@ positional features such as functional sites in nucleotide sequences. PCR experiment - Topic concerning PCR experiments, e.g. quantitative real-time PCR. 1.8 + Topic concerning PCR experiments, e.g. quantitative real-time PCR. @@ -49584,8 +49906,8 @@ positional features such as functional sites in nucleotide sequences. Proteomics experiment - Topic concerning proteomics experiments. 1.8 + Topic concerning proteomics experiments. @@ -49597,8 +49919,8 @@ positional features such as functional sites in nucleotide sequences. 2D PAGE experiment - 1.8 Topic concerning two-dimensional gel electrophoresis experiments, gels or spots in a gel. + 1.8 @@ -49610,8 +49932,8 @@ positional features such as functional sites in nucleotide sequences. Northern blot experiment - 1.8 Topic concerning Northern Blot experiments. + 1.8 @@ -49623,8 +49945,8 @@ positional features such as functional sites in nucleotide sequences. RNAi experiment - Topic concerning RNAi experiments. 1.8 + Topic concerning RNAi experiments. @@ -49636,8 +49958,8 @@ positional features such as functional sites in nucleotide sequences. Simulation experiment - Topic concerning biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. 1.8 + Topic concerning biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. @@ -49649,8 +49971,8 @@ positional features such as functional sites in nucleotide sequences. Protein-nucleic acid interactions - Topic concerning protein-DNA/RNA interaction(s). 1.8 + Topic concerning protein-DNA/RNA interaction(s). @@ -49662,10 +49984,10 @@ positional features such as functional sites in nucleotide sequences. Protein-protein interactions - Protein interaction networks - 1.8 - Domain-domain interactions Topic concerning protein-protein interaction(s), including interactions between protein domains. + Domain-domain interactions + 1.8 + Protein interaction networks @@ -49677,8 +49999,8 @@ positional features such as functional sites in nucleotide sequences. Cellular process pathways - Topic concernning cellular process pathways. 1.8 + Topic concernning cellular process pathways. @@ -49690,9 +50012,9 @@ positional features such as functional sites in nucleotide sequences. Disease pathways - 1.8 - Pathway or network (disease) Topic concerning disease pathways, typically of human disease. + Pathway or network (disease) + 1.8 @@ -49704,9 +50026,9 @@ positional features such as functional sites in nucleotide sequences. Environmental information processing pathways - Pathway or network (environmental information processing) - 1.8 Topic concerning environmental information processing pathways. + 1.8 + Pathway or network (environmental information processing) @@ -49718,9 +50040,9 @@ positional features such as functional sites in nucleotide sequences. Genetic information processing pathways - 1.8 - Pathway or network (genetic information processing) Topic concerning genetic information processing pathways. + Pathway or network (genetic information processing) + 1.8 @@ -49732,10 +50054,10 @@ positional features such as functional sites in nucleotide sequences. Protein super-secondary structure - Topic concerning super-secondary structure of protein sequence(s). - Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. - 1.8 Protein features (super-secondary) + 1.8 + Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. + Topic concerning super-secondary structure of protein sequence(s). @@ -49747,10 +50069,10 @@ positional features such as functional sites in nucleotide sequences. Protein active sites - Protein features (active sites) - Topic concerning catalytic residues (active site) of an enzyme. - 1.8 Enzyme active site + 1.8 + Topic concerning catalytic residues (active site) of an enzyme. + Protein features (active sites) @@ -49762,9 +50084,9 @@ positional features such as functional sites in nucleotide sequences. Protein binding sites - Protein features (binding sites) - Topic concerning ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. 1.8 + Topic concerning ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. + Protein features (binding sites) @@ -49776,9 +50098,9 @@ positional features such as functional sites in nucleotide sequences. Protein-nucleic acid binding sites - Protein features (nucleic acid binding sites) - 1.8 Topic concerning RNA and DNA-binding proteins and binding sites in protein sequences. + 1.8 + Protein features (nucleic acid binding sites) @@ -49790,9 +50112,9 @@ positional features such as functional sites in nucleotide sequences. Protein cleavage sites - 1.8 - Protein features (cleavage sites) Topic concerning cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. + Protein features (cleavage sites) + 1.8 @@ -49804,11 +50126,11 @@ positional features such as functional sites in nucleotide sequences. Protein chemical modifications - GO:0006464 - 1.8 - MOD:00000 - Protein features (chemical modifications) Topic concerning chemical modification of a protein. + Protein features (chemical modifications) + MOD:00000 + 1.8 + GO:0006464 @@ -49820,9 +50142,9 @@ positional features such as functional sites in nucleotide sequences. Protein disordered structure - Protein features (disordered structure) - 1.8 Topic concerning disordered structure in a protein. + 1.8 + Protein features (disordered structure) @@ -49835,11 +50157,11 @@ positional features such as functional sites in nucleotide sequences.Protein domains - Protein features (domains) - Protein structural domains - Topic concerning structural domains or 3D folds in a protein or polypeptide chain. - 1.8 The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc. + 1.8 + Topic concerning structural domains or 3D folds in a protein or polypeptide chain. + Protein structural domains + Protein features (domains) @@ -49852,9 +50174,9 @@ positional features such as functional sites in nucleotide sequences.Protein key folding sites - Topic concerning key residues involved in protein folding. - 1.8 Protein features (key folding sites) + 1.8 + Topic concerning key residues involved in protein folding. @@ -49866,10 +50188,10 @@ positional features such as functional sites in nucleotide sequences. Protein post-translational modifications - 1.8 - Topic concerning post-translation modifications in a protein sequence, typically describing the specific sites involved. - Post-translation modifications Protein features (post-translation modifications) + Post-translation modifications + Topic concerning post-translation modifications in a protein sequence, typically describing the specific sites involved. + 1.8 @@ -49882,10 +50204,10 @@ positional features such as functional sites in nucleotide sequences.Protein secondary structure - 1.8 - Topic concerning secondary structure (predicted or real) of a protein. - Protein features (secondary structure) The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks). + Protein features (secondary structure) + Topic concerning secondary structure (predicted or real) of a protein. + 1.8 @@ -49897,10 +50219,10 @@ positional features such as functional sites in nucleotide sequences. Protein sequence repeats - Protein repeats - Protein features (repeats) - Topic concerning short repetitive subsequences (repeat sequences) in a protein sequence. 1.8 + Topic concerning short repetitive subsequences (repeat sequences) in a protein sequence. + Protein features (repeats) + Protein repeats @@ -49912,9 +50234,9 @@ positional features such as functional sites in nucleotide sequences. Protein signal peptides - Topic concerning signal peptides or signal peptide cleavage sites in protein sequences. - 1.8 Protein features (signal peptides) + 1.8 + Topic concerning signal peptides or signal peptide cleavage sites in protein sequences. @@ -49927,10 +50249,10 @@ positional features such as functional sites in nucleotide sequences.Obsolete concept (EDAM) - true - An obsolete concept (redefined in EDAM). - Needed for conversion to the OBO format. 1.2 + Needed for conversion to the OBO format. + An obsolete concept (redefined in EDAM). + true