diff --git a/releases/EDAM.owl b/releases/EDAM.owl index d517bfc..4e58f23 100644 --- a/releases/EDAM.owl +++ b/releases/EDAM.owl @@ -32,22 +32,21 @@ 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. Hervé Ménager topics "EDAM topics" - 17:11:2014 23:35 EDAM_format http://edamontology.org/format_ "EDAM data formats" Jon Ison, Matus Kalas, Herve Menager Matúš Kalaš - 1.5 + 1.7 Jon Ison + 3489 concept_properties "EDAM concept properties" EDAM_data http://edamontology.org/data_ "EDAM types of data" - 3442 application/rdf+xml + 08:12:2014 13:30 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" - bioinformatics "Bioinformatics" data "EDAM types of data" identifiers "EDAM types of identifiers" EDAM @@ -169,14 +168,6 @@ - - - - - - - - @@ -333,22 +324,15 @@ edam false false + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality" relations - bioinformatics 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" - - - - 'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject. - - - - @@ -358,38 +342,31 @@ 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 - bioinformatics OBO_REL:is_a false + http://wsio.org/has_function - - - - 'OBI:has_function' only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes, with objects that are a 'function' (snap:Function). It does not define explicitly that the object is a function of the subject. + 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 - - + - true In very unusual cases. + true - - 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 - - - @@ -403,7 +380,6 @@ 'A has_identifier B' defines for the subject A, that it has the object B as its identifier. edam OBO_REL:is_a - bioinformatics relations false false @@ -419,37 +395,30 @@ has input edam true - bioinformatics 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 - - - In very unusual cases. - true - - - - - OBO_REL:has_participant 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. + OBO_REL:has_participant - 'OBI:has_specified_input' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant). + In very unusual cases. + true - - + @@ -466,29 +435,22 @@ OBO_REL:has_participant relations OBO_REL:is_a - bioinformatics + "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 - - - OBO_REL:has_participant 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it. + OBO_REL:has_participant - 'OBI:has_specified_output' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant). - - - - - - true In very unusual cases. + true @@ -499,21 +461,20 @@ has topic + "http://purl.obolibrary.org/obo/OBI_0000298" false - bioinformatics + "http://purl.obolibrary.org/obo/IAO_0000136" false + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality" 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. + http://annotation-ontology.googlecode.com/svn/trunk/annotation-core.owl#hasTopic" true relations - - - - @@ -524,24 +485,6 @@ - 'is about' is narrower in the sense that it only relates subjects that are information artifacts and the relation is not necessarily the one of having a topic. It is broader in the sense that it relates with any object. - - - - - - 'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject. - - - - - - 'ao:hasTopic' is narrower in the sense that it only relates subjects that are an annotation, and it is broader in the sense that it relates with any resource. - - - - - In very unusual cases. true @@ -560,15 +503,14 @@ edam 'A is_format_of B' defines for the subject A, that it is a data format of the object B. false + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in" false false OBO_REL:is_a - bioinformatics false - OBO_REL:quality_of @@ -583,10 +525,11 @@ is function of - bioinformatics + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in" false false 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. @@ -597,8 +540,6 @@ 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. - - In very unusual cases. @@ -626,12 +567,11 @@ is identifier of false - 'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B. 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 - bioinformatics edam false false @@ -650,32 +590,25 @@ 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 - bioinformatics relations + http://wsio.org/is_input_of false - - - In very unusual cases. true + In very unusual cases. - 'OBI:is_specified_input_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011). - - - - - 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 inputs or input arguments. @@ -688,38 +621,31 @@ 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 - bioinformatics false OBO_REL:is_a - - - In very unusual cases. true + In very unusual cases. - 'OBI:is_specified_output_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011). - - - - - - '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 + '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. @@ -737,13 +663,12 @@ false true false - bioinformatics 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). + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in" - @@ -760,8 +685,8 @@ - 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 @@ -779,6 +704,25 @@ + + + + Correlation + + + + + + + + 1.7 + Identify a correlation, i.e. a statistical relationship between two random variables or two sets of data. + + + + + + @@ -788,7 +732,6 @@ A type of computational resource used in bioinformatics. beta12orEarlier beta12orEarlier - @@ -803,67 +746,36 @@ Datum + http://semanticscience.org/resource/SIO_000069" + http://www.ifomis.org/bfo/1.1/snap#Continuant" + http://www.onto-med.de/ontologies/gfo.owl#Perpetuant" + http://purl.org/biotop/biotop.owl#DigitalEntity" + http://wsio.org/data_002 beta12orEarlier - Data record Data set + Data record + "http://purl.obolibrary.org/obo/IAO_0000027" + "http://purl.obolibrary.org/obo/IAO_0000030" + http://semanticscience.org/resource/SIO_000088" 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. - - - - - - - - - - Data does theoretically not need to have a purpose, but in all regular cases it does. Remark: EDAM Data sub-ontology focuses on scientific data (SIO_000472), in particular the bioinformatics (SIO_010065) and biological (SIO_010019). - - - - - - GFO 'Perpetuant' is in general broader than data, but it may be seen narrower in the sense of being a concrete individual. - - - - - Data set EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - IAO 'data item' is a closely related ontological category (concept) broader in the sense of being any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant), standing in relation of aboutness to some entity (http://purl.obolibrary.org/obo/IAO_0000030), and to data that is intended to be a truthful statement about something. - - - - - - 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). - IAO 'information content entity' is a closely related ontological category (concept) broader in the sense of covering any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant) and standing in relation of aboutness to some entity. - - - - - - Data does however not necessarily contain statements and not necessarily about an entity. - - - - - - EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). Datum + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). @@ -911,7 +823,6 @@ An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc. beta12orEarlier - @@ -992,15 +903,15 @@ 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 - - Almost exact but limited to identifying resources. @@ -1033,7 +944,6 @@ beta12orEarlier Mass of a molecule. - @@ -1048,7 +958,6 @@ PDBML:pdbx_formal_charge beta12orEarlier Net charge of a molecule. - @@ -1063,7 +972,6 @@ beta12orEarlier A specification of a chemical structure. Chemical structure specification - @@ -1078,7 +986,6 @@ 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. - @@ -1093,7 +1000,6 @@ 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 - @@ -1107,7 +1013,6 @@ A molecular sequence and associated metadata. beta12orEarlier - @@ -1123,7 +1028,6 @@ 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. - @@ -1142,6 +1046,8 @@ + + @@ -1169,7 +1075,6 @@ Strand beta12orEarlier DNA strand specification - @@ -1215,7 +1120,6 @@ 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). - @@ -1232,7 +1136,6 @@ Sequence search hits Sequence database hits beta12orEarlier - @@ -1249,7 +1152,6 @@ Secondary database hits Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). In this way the query is classified as a member of a known protein family or group. See concepts under 'Protein features'. Secondary database search hits - @@ -1310,7 +1212,6 @@ beta12orEarlier A dotplot of sequence similarities identified from word-matching or character comparison. - @@ -1325,17 +1226,16 @@ - + Alignment of multiple molecular sequences. + http://purl.bioontology.org/ontology/MSH/D016415" beta12orEarlier - - - + http://semanticscience.org/resource/SIO_010066 + http://en.wikipedia.org/wiki/Sequence_alignment - @@ -1362,7 +1262,6 @@ beta12orEarlier A value representing molecular sequence similarity. - @@ -1392,7 +1291,6 @@ 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. - @@ -1406,7 +1304,6 @@ A profile-profile alignment (each profile typically representing a sequence alignment). beta12orEarlier - @@ -1421,7 +1318,6 @@ 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 - @@ -1438,7 +1334,6 @@ A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation. Moby:phylogenetic_distance_matrix beta12orEarlier - @@ -1450,13 +1345,12 @@ Phylogenetic character data + http://www.evolutionaryontology.org/cdao.owl#Character" beta12orEarlier 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. - - @@ -1472,18 +1366,17 @@ + http://www.evolutionaryontology.org/cdao.owl#Tree" 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. + http://purl.bioontology.org/ontology/MSH/D010802" Moby:phylogenetic_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'. Moby:Tree Phylogeny - - - @@ -1497,7 +1390,6 @@ 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 - @@ -1536,7 +1428,6 @@ beta12orEarlier Secondary structure assignment (predicted or real) of a protein. Secondary structure (protein) - @@ -1552,7 +1443,6 @@ beta12orEarlier Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. A report of predicted or actual super-secondary structure of protein sequence(s). - @@ -1567,7 +1457,6 @@ beta12orEarlier Alignment of the (1D representations of) secondary structure of two or more proteins. - @@ -1605,7 +1494,6 @@ 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. - @@ -1620,7 +1508,6 @@ beta12orEarlier Alignment of the (1D representations of) secondary structure of two or more RNA molecules. Moby:RNAStructAlignmentML - @@ -1654,12 +1541,11 @@ 3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure. - Structure data The coordinate data may be predicted or real. - beta12orEarlier + Structure data Coordinate model - - + beta12orEarlier + http://purl.bioontology.org/ontology/MSH/D015394" @@ -1691,7 +1577,6 @@ Structure search hits beta12orEarlier Results (hits) from searching a database of tertiary structure. - @@ -1706,13 +1591,12 @@ - + 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. - @@ -1727,7 +1611,6 @@ 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 - @@ -1741,7 +1624,6 @@ A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison. beta12orEarlier - @@ -1763,7 +1645,6 @@ Some type of structural (3D) profile or template (representing a structure or structure alignment). 3D profile beta12orEarlier - @@ -1778,7 +1659,6 @@ A 3D profile-3D profile alignment (each profile representing structures or a structure alignment). Structural profile alignment beta12orEarlier - @@ -1808,7 +1688,6 @@ Matrix of values used for scoring sequence-structure compatibility. beta12orEarlier - @@ -1822,7 +1701,6 @@ An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)). beta12orEarlier - @@ -1867,7 +1745,6 @@ An informative 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 - @@ -1884,7 +1761,6 @@ beta12orEarlier A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model. Protein physicochemical property - @@ -1906,7 +1782,6 @@ This might include conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, role and functions etc. beta12orEarlier Protein structure report (3D motif) - @@ -1944,7 +1819,6 @@ beta12orEarlier Protein domain assignment Summary of structural domains or 3D folds in a protein or polypeptide chain. - @@ -1978,7 +1852,6 @@ 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. Protein report (folding) beta12orEarlier - @@ -2012,7 +1885,6 @@ 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. - @@ -2033,7 +1905,6 @@ 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 report (interaction) beta12orEarlier - @@ -2055,7 +1926,6 @@ Protein family annotation An informative report on a specific protein family or other classification or group of protein sequences or structures. beta12orEarlier - @@ -2069,7 +1939,6 @@ The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large. beta12orEarlier - @@ -2083,7 +1952,6 @@ beta12orEarlier Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction. - @@ -2115,7 +1983,6 @@ 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. - @@ -2136,7 +2003,6 @@ 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 - @@ -2160,7 +2026,6 @@ 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) - @@ -2200,7 +2065,6 @@ Sequence variation annotation SO:0001059 Sequence variation report - @@ -2221,7 +2085,6 @@ This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. An informative report on a specific chromosome. beta12orEarlier - @@ -2236,7 +2099,6 @@ 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. - @@ -2258,7 +2120,6 @@ beta12orEarlier Nucleic acid features (primers) Report on matches to PCR primers and hybridization oligos in a nucleic acid sequence. - @@ -2280,7 +2141,6 @@ beta12orEarlier Experiment annotation (PCR) Information about a PCR experiment, e.g. quantitative real-time PCR. - @@ -2296,7 +2156,6 @@ 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. - @@ -2311,10 +2170,9 @@ 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 - - @@ -2335,7 +2193,6 @@ Radiation hybrid scores (RH) scores for one or more markers. Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. beta12orEarlier - @@ -2350,7 +2207,6 @@ An informative report on the linkage of alleles. Gene annotation (linkage) beta12orEarlier - @@ -2361,11 +2217,10 @@ Gene expression profile - + Gene expression pattern beta12orEarlier Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments. - @@ -2386,10 +2241,9 @@ beta12orEarlier 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. Microarray experiment metadata + Experimental design annotation Experiment metadata (microarray) Information on a microarray experiment such as conditions, protocol, sample:data relationships etc. - Experimental design annotation - @@ -2466,7 +2320,6 @@ 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 - @@ -2480,7 +2333,6 @@ beta12orEarlier X-ray crystallography data. - @@ -2494,7 +2346,6 @@ beta12orEarlier Protein nuclear magnetic resonance (NMR) raw data. - @@ -2508,7 +2359,6 @@ Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data. beta12orEarlier - @@ -2529,7 +2379,6 @@ EM volume map Volume map data from electron microscopy. beta12orEarlier - @@ -2550,7 +2399,6 @@ 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 - @@ -2568,10 +2416,8 @@ - Two-dimensional gel electrophoresis image. + Two-dimensional gel electrophoresis image beta12orEarlier - Two-dimensional gel electrophoresis image - @@ -2591,7 +2437,6 @@ Spectra from mass spectrometry. beta12orEarlier - @@ -2614,7 +2459,6 @@ A set of peptide masses (peptide mass fingerprint) from mass spectrometry. Protein fingerprint Peak list - @@ -2634,7 +2478,6 @@ beta12orEarlier Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database. - @@ -2693,7 +2536,6 @@ beta12orEarlier Basic information, annotation or documentation concerning a workflow (but not the workflow itself). - @@ -2714,7 +2556,6 @@ A biological model represented in mathematical terms. beta12orEarlier Biological model - @@ -2728,7 +2569,6 @@ A value representing estimated statistical significance of some observed data; typically sequence database hits. beta12orEarlier - @@ -2755,24 +2595,18 @@ Version information + http://www.ebi.ac.uk/swo/maturity/SWO_9000061" + http://usefulinc.com/ns/doap#Version true Information on a version of software or data, for example name, version number and release date. beta12orEarlier + http://semanticscience.org/resource/SIO_000653" 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" - - - - - - Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. - - - - @@ -2784,7 +2618,6 @@ 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 - @@ -2804,7 +2637,6 @@ beta12orEarlier An index of data of biological relevance. - @@ -2825,7 +2657,6 @@ beta12orEarlier Database index annotation A report of an analysis of an index of biological data. - @@ -2839,7 +2670,6 @@ beta12orEarlier Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc. - @@ -2853,7 +2683,6 @@ Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation. beta12orEarlier - @@ -2883,7 +2712,6 @@ Textual metadata on a software author or end-user, for example a person or other software. beta12orEarlier - @@ -2906,7 +2734,6 @@ An informative report on a specific chemical compound. Small molecule report Small molecule annotation - @@ -2922,7 +2749,6 @@ 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 - @@ -2952,7 +2778,6 @@ A term (name) from an ontology. beta12orEarlier Ontology class name - @@ -2968,7 +2793,6 @@ Ontology term metadata Ontology class metadata beta12orEarlier - @@ -2980,14 +2804,13 @@ Keyword - Moby:Global_Keyword + Moby:QueryString Moby:Wildcard_Query + Moby:Global_Keyword + Keyword(s) or phrase(s) used (typically) for text-searching purposes. + Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. 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. - @@ -3003,10 +2826,9 @@ 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. - Moby:GCP_SimpleCitation - @@ -3026,7 +2848,6 @@ beta12orEarlier A document of scientific text, typically a full text article from a scientific journal. - @@ -3042,7 +2863,6 @@ Text mining output beta12orEarlier An abstract of the results of text mining. - @@ -3087,7 +2907,6 @@ 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 - @@ -3102,7 +2921,6 @@ beta12orEarlier An identifier of a bioinformatics tool, e.g. an application or web service. - @@ -3177,7 +2995,6 @@ beta12orEarlier Name or other identifier of a molecule. - @@ -3193,7 +3010,6 @@ beta12orEarlier Identifier (e.g. character symbol) of a specific atom. Atom identifier - @@ -3209,7 +3025,6 @@ beta12orEarlier Name of a specific molecule. - @@ -3263,7 +3078,6 @@ Name of a chromosome. beta12orEarlier - @@ -3278,7 +3092,6 @@ beta12orEarlier Identifier of a peptide chain. - @@ -3299,7 +3112,6 @@ Identifier of a protein. beta12orEarlier - @@ -3316,7 +3128,6 @@ beta12orEarlier Unique name of a chemical compound. Chemical name - @@ -3331,7 +3142,6 @@ Unique registry number of a chemical compound. beta12orEarlier - @@ -3367,7 +3177,6 @@ Identifier of a drug. beta12orEarlier - @@ -3389,7 +3198,6 @@ Residue identifier beta12orEarlier Identifier of an amino acid. - @@ -3404,7 +3212,6 @@ Name or other identifier of a nucleotide. beta12orEarlier - @@ -3419,7 +3226,6 @@ Identifier of a monosaccharide. beta12orEarlier - @@ -3436,7 +3242,6 @@ beta12orEarlier Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound. ChEBI chemical name - @@ -3452,7 +3257,6 @@ beta12orEarlier IUPAC chemical name IUPAC recommended name of a chemical compound. - @@ -3468,7 +3272,6 @@ International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO). beta12orEarlier INN chemical name - @@ -3484,7 +3287,6 @@ beta12orEarlier Brand chemical name Brand name of a chemical compound. - @@ -3500,7 +3302,6 @@ Synonymous name of a chemical compound. Synonymous chemical name beta12orEarlier - @@ -3516,7 +3317,6 @@ beta12orEarlier CAS registry number of a chemical compound. CAS chemical registry number - @@ -3532,7 +3332,6 @@ Beilstein registry number of a chemical compound. beta12orEarlier Beilstein chemical registry number - @@ -3548,7 +3347,6 @@ Gmelin registry number of a chemical compound. beta12orEarlier Gmelin chemical registry number - @@ -3565,7 +3363,6 @@ Component identifier code Short ligand name 3-letter code word for a ligand (HET group) from a PDB file, for example ATP. - @@ -3580,7 +3377,6 @@ beta12orEarlier String of one or more ASCII characters representing an amino acid. - @@ -3596,7 +3392,6 @@ String of one or more ASCII characters representing a nucleotide. beta12orEarlier - @@ -3625,7 +3420,6 @@ Chain identifier WHATIF: chain beta12orEarlier - @@ -3641,7 +3435,6 @@ beta12orEarlier Name of a protein. - @@ -3656,7 +3449,6 @@ Name or other identifier of an enzyme or record from a database of enzymes. beta12orEarlier - @@ -3677,7 +3469,6 @@ 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]+ - @@ -3693,7 +3484,6 @@ beta12orEarlier Name of an enzyme. - @@ -3708,7 +3498,6 @@ beta12orEarlier Name of a restriction enzyme. - @@ -3739,7 +3528,6 @@ 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. - @@ -3758,7 +3546,6 @@ beta12orEarlier WHATIF: PDBx_atom_site WHATIF: number - @@ -3772,7 +3559,6 @@ Specification of range(s) of sequence positions. beta12orEarlier - @@ -3819,7 +3605,6 @@ 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 - @@ -3834,7 +3619,6 @@ 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 - @@ -3850,7 +3634,6 @@ 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 - @@ -3866,7 +3649,6 @@ The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications. UFO beta12orEarlier - @@ -3902,7 +3684,6 @@ beta12orEarlier An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database. Moby:GeneAccessionList - @@ -3919,7 +3700,6 @@ Moby_namespace:Global_GeneCommonName beta12orEarlier Moby_namespace:Global_GeneSymbol - @@ -3942,7 +3722,6 @@ http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene Gene identifier (NCBI) NCBI geneid - @@ -4004,7 +3783,6 @@ beta12orEarlier Identifier of a gene or feature from the CGD database. CGD ID - @@ -4019,7 +3797,6 @@ Identifier of a gene from DictyBase. beta12orEarlier - @@ -4036,7 +3813,6 @@ Unique identifier for a gene (or other feature) from the Ensembl database. Gene ID (Ensembl) beta12orEarlier - @@ -4054,7 +3830,6 @@ SGD identifier S[0-9]+ Identifier of an entry from the SGD database. - @@ -4072,7 +3847,6 @@ beta12orEarlier GeneDB identifier Moby_namespace:GeneDB - @@ -4088,7 +3862,6 @@ Identifier of an entry from the TIGR database. beta12orEarlier - @@ -4105,7 +3878,6 @@ Identifier of an gene from the TAIR database. beta12orEarlier Gene:[0-9]{7} - @@ -4128,7 +3900,6 @@ This is typically a character or string concatenated with a PDB identifier and a chain identifier. Identifier of a protein structural domain. beta12orEarlier - @@ -4143,7 +3914,6 @@ beta12orEarlier Identifier of a protein domain (or other node) from the SCOP database. - @@ -4160,7 +3930,6 @@ CATH domain identifier beta12orEarlier 1nr3A00 - @@ -4176,7 +3945,6 @@ 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. - @@ -4190,12 +3958,11 @@ SCOP sunid 33229 - 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. SCOP unique identifier sunid - Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229. + 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. @@ -4213,7 +3980,6 @@ A code number identifying a node from the CATH database. CATH code 3.30.1190.10.1.1.1.1.1 - @@ -4228,7 +3994,6 @@ beta12orEarlier The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes). - @@ -4244,7 +4009,6 @@ beta12orEarlier Organism species The name of a species (typically a taxonomic group) of organism. - @@ -4260,7 +4024,6 @@ The name of a strain of an organism variant, typically a plant, virus or bacterium. beta12orEarlier - @@ -4275,7 +4038,6 @@ beta12orEarlier A string of characters that name or otherwise identify a resource on the Internet. - @@ -4296,7 +4058,6 @@ beta12orEarlier Database identifier An identifier of a biological or bioinformatics database. - @@ -4311,7 +4072,6 @@ The name of a directory. beta12orEarlier - @@ -4326,7 +4086,6 @@ beta12orEarlier The name (or part of a name) of a file (of any type). - @@ -4348,7 +4107,6 @@ Name of an ontology of biological or bioinformatics concepts and relations. beta12orEarlier - @@ -4365,7 +4123,6 @@ Moby:Link Moby:URL A Uniform Resource Locator (URL). - @@ -4379,7 +4136,6 @@ A Uniform Resource Name (URN). beta12orEarlier - @@ -4395,7 +4151,6 @@ 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 - @@ -4410,7 +4165,6 @@ beta12orEarlier The name of a biological or bioinformatics database. - @@ -4428,7 +4182,6 @@ true The name of a molecular sequence database. - @@ -4441,7 +4194,6 @@ The name of a file (of any type) with restricted possible values. beta12orEarlier - @@ -4457,7 +4209,6 @@ beta12orEarlier A file extension is the characters appearing after the final '.' in the file name. The extension of a file name. - @@ -4473,7 +4224,6 @@ A file base name is the file name stripped of its directory specification and extension. The base name of a file. beta12orEarlier - @@ -4495,7 +4245,6 @@ Name of a QSAR descriptor. beta12orEarlier - @@ -4532,7 +4281,6 @@ beta12orEarlier An identifier of molecular sequence(s) or entries from a molecular sequence database. - @@ -4554,7 +4302,6 @@ beta12orEarlier An identifier of a set of molecular sequence(s). - @@ -4592,7 +4339,6 @@ beta12orEarlier Identifier of a molecular sequence alignment, for example a record from an alignment database. - @@ -4629,7 +4375,6 @@ Identifier of a phylogenetic tree for example from a phylogenetic tree database. beta12orEarlier - @@ -4651,7 +4396,6 @@ beta12orEarlier Substitution matrix identifier An identifier of a comparison matrix. - @@ -4667,7 +4411,6 @@ A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database. beta12orEarlier - @@ -4690,7 +4433,6 @@ beta12orEarlier Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment). Structural profile identifier - @@ -4712,7 +4454,6 @@ Identifier of an entry from a database of tertiary structure alignments. beta12orEarlier - @@ -4734,7 +4475,6 @@ beta12orEarlier Identifier of an index of amino acid physicochemical and biochemical property data. - @@ -4746,10 +4486,17 @@ Protein interaction ID - + + + + + + + + Identifier of a report of protein interactions from a protein interaction database (typically). + Molecular interaction ID beta12orEarlier - @@ -4771,7 +4518,6 @@ beta12orEarlier Identifier of a protein family. Protein secondary database record identifier - @@ -4788,18 +4534,17 @@ - + - + beta12orEarlier Unique name of a codon usage table. - @@ -4821,7 +4566,6 @@ beta12orEarlier Identifier of a transcription factor (or a TF binding site). - @@ -4842,7 +4586,6 @@ Identifier of an entry from a database of microarray data. beta12orEarlier - @@ -4864,7 +4607,6 @@ beta12orEarlier Identifier of an entry from a database of electron microscopy data. - @@ -4887,7 +4629,6 @@ Gene expression profile identifier beta12orEarlier Accession of a report of gene expression (e.g. a gene expression profile) from a database. - @@ -4909,7 +4650,6 @@ beta12orEarlier Identifier of an entry from a database of genotypes and phenotypes. - @@ -4930,7 +4670,6 @@ beta12orEarlier Identifier of an entry from a database of biological pathways or networks. - @@ -4946,7 +4685,6 @@ Identifier of a biological or biomedical workflow, typically from a database of workflows. beta12orEarlier - @@ -4962,7 +4700,6 @@ Data resource definition identifier Identifier of a data type definition from some provider. beta12orEarlier - @@ -4984,7 +4721,6 @@ Identifier of a mathematical model, typically an entry from a database. beta12orEarlier Biological model identifier - @@ -5007,7 +4743,6 @@ Identifier of an entry from a database of chemicals. Chemical compound identifier beta12orEarlier - @@ -5024,7 +4759,6 @@ Ontology concept ID beta12orEarlier A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations. - @@ -5047,7 +4781,6 @@ Article identifier Unique identifier of a scientific article. beta12orEarlier - @@ -5064,7 +4797,6 @@ beta12orEarlier FB[a-zA-Z_0-9]{2}[0-9]{7} Identifier of an object from the FlyBase database. - @@ -5080,7 +4812,6 @@ beta12orEarlier Name of an object from the WormBase database, usually a human-readable name. - @@ -5096,7 +4827,6 @@ A WormBase class describes the type of object such as 'sequence' or 'protein'. Class of an object from the WormBase database. beta12orEarlier - @@ -5113,7 +4843,6 @@ Sequence accession number A persistent, unique identifier of a molecular sequence database entry. beta12orEarlier - @@ -5146,7 +4875,6 @@ The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications. beta12orEarlier EMBOSS USA - @@ -5168,7 +4896,6 @@ beta12orEarlier Protein sequence accession number Accession number of a protein sequence database entry. - @@ -5190,7 +4917,6 @@ Nucleotide sequence accession number beta12orEarlier Accession number of a nucleotide sequence database entry. - @@ -5207,7 +4933,6 @@ RefSeq ID beta12orEarlier Accession number of a RefSeq database entry. - @@ -5247,7 +4972,6 @@ PIR ID beta12orEarlier An identifier of PIR sequence database entry. - @@ -5278,7 +5002,6 @@ Primary identifier of a Gramene database entry. Gramene primary ID beta12orEarlier - @@ -5293,7 +5016,6 @@ beta12orEarlier Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases. - @@ -5307,12 +5029,11 @@ Sequence cluster ID (UniGene) A unique identifier of an entry (gene cluster) from the NCBI UniGene database. - UniGene cluster ID - UniGene identifier beta12orEarlier + UniGene cluster ID UniGene ID UniGene cluster id - + UniGene identifier @@ -5329,7 +5050,6 @@ beta12orEarlier Identifier of a dbEST database entry. dbEST ID - @@ -5345,7 +5065,6 @@ Identifier of a dbSNP database entry. dbSNP identifier beta12orEarlier - @@ -5397,7 +5116,6 @@ beta12orEarlier An identifier of a cluster of molecular sequence(s). - @@ -5413,7 +5131,6 @@ Unique identifier of an entry from the COG database. beta12orEarlier COG ID - @@ -5434,7 +5151,6 @@ beta12orEarlier Identifier of a sequence motif, for example an entry from a motif database. - @@ -5457,7 +5173,6 @@ A sequence profile typically represents a sequence alignment. beta12orEarlier Identifier of a sequence profile. - @@ -5472,7 +5187,6 @@ beta12orEarlier Identifier of an entry from the ELMdb database of protein functional sites. - @@ -5489,7 +5203,6 @@ PS[0-9]{5} Accession number of an entry from the Prosite database. beta12orEarlier - @@ -5510,7 +5223,6 @@ beta12orEarlier Unique identifier or name of a HMMER hidden Markov model. - @@ -5525,7 +5237,6 @@ Unique identifier or name of a profile from the JASPAR database. beta12orEarlier - @@ -5588,7 +5299,6 @@ beta12orEarlier Accession number of an entry from the TreeBASE database. - @@ -5603,7 +5313,6 @@ Accession number of an entry from the TreeFam database. beta12orEarlier - @@ -5642,10 +5351,9 @@ Unique name or identifier of a comparison matrix. - Substitution matrix name See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix. + Substitution matrix name beta12orEarlier - @@ -5663,7 +5371,6 @@ PDBID [a-zA-Z_0-9]{4} An identifier of an entry from the PDB database. - @@ -5678,7 +5385,6 @@ Identifier of an entry from the AAindex database. beta12orEarlier - @@ -5693,7 +5399,6 @@ beta12orEarlier Accession number of an entry from the BIND database. - @@ -5709,7 +5414,6 @@ Accession number of an entry from the IntAct database. beta12orEarlier EBI\-[0-9]+ - @@ -5725,7 +5429,6 @@ Name of a protein family. beta12orEarlier - @@ -5746,7 +5449,6 @@ Name of an InterPro entry, usually indicating the type of protein matches for that entry. beta12orEarlier - @@ -5772,7 +5474,6 @@ 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. - @@ -5794,7 +5495,6 @@ InterPro secondary accession number beta12orEarlier Secondary accession number of an InterPro entry. - @@ -5809,7 +5509,6 @@ Unique identifier of an entry from the Gene3D database. beta12orEarlier - @@ -5825,7 +5524,6 @@ Unique identifier of an entry from the PIRSF database. beta12orEarlier PIRSF[0-9]{6} - @@ -5841,7 +5539,6 @@ The unique identifier of an entry in the PRINTS database. PR[0-9]{5} beta12orEarlier - @@ -5857,7 +5554,6 @@ beta12orEarlier Accession number of a Pfam entry. PF[0-9]{5} - @@ -5873,7 +5569,6 @@ SM[0-9]{5} beta12orEarlier Accession number of an entry from the SMART database. - @@ -5888,7 +5583,6 @@ beta12orEarlier Unique identifier (number) of a hidden Markov model from the Superfamily database. - @@ -5904,7 +5598,6 @@ beta12orEarlier Accession number of an entry (family) from the TIGRFam database. TIGRFam accession number - @@ -5921,7 +5614,6 @@ beta12orEarlier PD[0-9]+ A ProDom domain family accession number. - @@ -5936,7 +5628,6 @@ Identifier of an entry from the TRANSFAC database. beta12orEarlier - @@ -5953,7 +5644,6 @@ [AEP]-[a-zA-Z_0-9]{4}-[0-9]+ beta12orEarlier Accession number of an entry from the ArrayExpress database. - @@ -5969,7 +5659,6 @@ PRIDE experiment accession number. beta12orEarlier [0-9]+ - @@ -5984,7 +5673,6 @@ Identifier of an entry from the EMDB electron microscopy database. beta12orEarlier - @@ -6000,7 +5688,6 @@ beta12orEarlier o^GDS[0-9]+ Accession number of an entry from the GEO database. - @@ -6015,7 +5702,6 @@ Identifier of an entry from the GermOnline database. beta12orEarlier - @@ -6030,7 +5716,6 @@ beta12orEarlier Identifier of an entry from the EMAGE database. - @@ -6052,7 +5737,6 @@ beta12orEarlier Identifier of an entry from a database of disease. - @@ -6067,7 +5751,6 @@ beta12orEarlier Identifier of an entry from the HGVbase database. - @@ -6098,7 +5781,6 @@ Identifier of an entry from the OMIM database. [*#+%^]?[0-9]{6} beta12orEarlier - @@ -6114,7 +5796,6 @@ Unique identifier of an object from one of the KEGG databases (excluding the GENES division). beta12orEarlier - @@ -6131,7 +5812,6 @@ beta12orEarlier Reactome ID Identifier of an entry from the Reactome database. - @@ -6164,7 +5844,6 @@ Identifier of an pathway from the BioCyc biological pathways database. beta12orEarlier BioCyc pathway ID - @@ -6180,7 +5859,6 @@ Identifier of an entry from the INOH database. INOH identifier beta12orEarlier - @@ -6196,7 +5874,6 @@ beta12orEarlier PATIKA ID Identifier of an entry from the PATIKA database. - @@ -6213,7 +5890,6 @@ 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. - @@ -6230,7 +5906,6 @@ PTHR[0-9]{5} beta12orEarlier Identifier of a biological pathway from the Panther Pathways database. - @@ -6249,12 +5924,11 @@ + 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. - beta12orEarlier - This is the identifier used internally by MIRIAM for a data type. - @@ -6275,7 +5949,6 @@ The name of a data type from the MIRIAM database. beta12orEarlier - @@ -6295,12 +5968,11 @@ - 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. + 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 - @@ -6317,14 +5989,13 @@ UniProt|Enzyme Nomenclature The primary name of a MIRIAM data type is taken from a controlled vocabulary. beta12orEarlier - - A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. UniProt|Enzyme Nomenclature + A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. @@ -6339,7 +6010,6 @@ 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. - @@ -6354,7 +6024,6 @@ Unique identifier of a Taverna workflow. beta12orEarlier - @@ -6370,7 +6039,6 @@ Name of a biological (mathematical) model. beta12orEarlier - @@ -6386,7 +6054,6 @@ (BIOMD|MODEL)[0-9]{10} beta12orEarlier Unique identifier of an entry from the BioModel database. - @@ -6404,7 +6071,6 @@ Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure. PubChem compound accession identifier [0-9]+ - @@ -6420,7 +6086,6 @@ [0-9]+ beta12orEarlier Identifier of an entry from the ChemSpider database. - @@ -6437,7 +6102,6 @@ CHEBI:[0-9]+ ChEBI identifier Identifier of an entry from the ChEBI database. - @@ -6452,7 +6116,6 @@ An identifier of a concept from the BioPax ontology. beta12orEarlier - @@ -6469,7 +6132,6 @@ beta12orEarlier [0-9]{7}|GO:[0-9]{7} GO concept identifier - @@ -6484,7 +6146,6 @@ An identifier of a concept from the MeSH vocabulary. beta12orEarlier - @@ -6499,7 +6160,6 @@ An identifier of a concept from the HGNC controlled vocabulary. beta12orEarlier - @@ -6519,7 +6179,6 @@ NCBI tax ID [1-9][0-9]{0,8} NCBI taxonomy identifier - @@ -6534,7 +6193,6 @@ beta12orEarlier An identifier of a concept from the Plant Ontology (PO). - @@ -6549,7 +6207,6 @@ beta12orEarlier An identifier of a concept from the UMLS vocabulary. - @@ -6566,7 +6223,6 @@ 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. - @@ -6581,7 +6237,6 @@ An identifier of a concept from the EMAP mouse ontology. beta12orEarlier - @@ -6596,7 +6251,6 @@ An identifier of a concept from the ChEBI ontology. beta12orEarlier - @@ -6611,7 +6265,6 @@ An identifier of a concept from the MGED ontology. beta12orEarlier - @@ -6627,7 +6280,6 @@ 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 - @@ -6645,7 +6297,6 @@ PubMed unique identifier of an article. [1-9][0-9]{0,8} PMID - @@ -6662,7 +6313,6 @@ Digital Object Identifier (doi\:)?[0-9]{2}\.[0-9]{4}/.* beta12orEarlier - @@ -6679,7 +6329,6 @@ The use of Medline UI has been replaced by the PubMed unique identifier. Medline UI (unique identifier) of an article. beta12orEarlier - @@ -6694,7 +6343,6 @@ beta12orEarlier The name of a computer package, application, method or function. - @@ -6710,7 +6358,6 @@ 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 - @@ -6727,7 +6374,6 @@ beta12orEarlier The name of a BLAST tool. This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. - @@ -6743,7 +6389,6 @@ This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. The name of a FASTA tool. beta12orEarlier - @@ -6758,7 +6403,6 @@ beta12orEarlier The name of an EMBOSS application. - @@ -6773,7 +6417,6 @@ beta12orEarlier The name of an EMBASSY package. - @@ -6789,7 +6432,6 @@ QSAR constitutional descriptor beta12orEarlier A QSAR constitutional descriptor. - @@ -6804,7 +6446,6 @@ QSAR electronic descriptor A QSAR electronic descriptor. beta12orEarlier - @@ -6819,7 +6460,6 @@ beta12orEarlier A QSAR geometrical descriptor. QSAR geometrical descriptor - @@ -6834,7 +6474,6 @@ A QSAR topological descriptor. QSAR topological descriptor beta12orEarlier - @@ -6849,7 +6488,6 @@ beta12orEarlier QSAR molecular descriptor A QSAR molecular descriptor. - @@ -6863,7 +6501,6 @@ beta12orEarlier Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. - @@ -6877,7 +6514,6 @@ Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. beta12orEarlier - @@ -6892,7 +6528,7 @@ - + @@ -6904,7 +6540,6 @@ 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. - @@ -6955,7 +6590,6 @@ A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses. beta12orEarlier - @@ -6970,7 +6604,6 @@ beta12orEarlier SO:0000412 Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease. - @@ -6984,7 +6617,6 @@ Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set. beta12orEarlier - @@ -7061,7 +6693,6 @@ beta12orEarlier The sequences are typically related, for example a family of sequences. Protein sequence cluster - @@ -7078,7 +6709,6 @@ beta12orEarlier Nucleotide sequence cluster A cluster of nucleotide sequences. - @@ -7092,7 +6722,6 @@ The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths. beta12orEarlier - @@ -7170,7 +6799,6 @@ Sequence properties report An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis. beta12orEarlier - @@ -7187,11 +6815,10 @@ 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. + http://purl.bioontology.org/ontology/MSH/D058977" SO:0000110 beta12orEarlier Sequence features report - - @@ -7252,7 +6879,6 @@ Sequence property (complexity) beta12orEarlier A report on sequence complexity, for example low-complexity or repeat regions in sequences. - @@ -7267,7 +6893,6 @@ beta12orEarlier Sequence property (ambiguity) A report on ambiguity in molecular sequence(s). - @@ -7282,7 +6907,6 @@ Sequence property (composition) A report (typically a table) on character or word composition / frequency of a molecular sequence(s). beta12orEarlier - @@ -7296,7 +6920,6 @@ beta12orEarlier A report on peptide fragments of certain molecular weight(s) in one or more protein sequences. - @@ -7310,7 +6933,6 @@ A plot of third base position variability in a nucleotide sequence. beta12orEarlier - @@ -7340,7 +6962,6 @@ A table of base frequencies of a nucleotide sequence. beta12orEarlier - @@ -7355,7 +6976,6 @@ beta12orEarlier A table of word composition of a nucleotide sequence. - @@ -7371,7 +6991,6 @@ beta12orEarlier A table of amino acid frequencies of a protein sequence. Sequence composition (amino acid frequencies) - @@ -7387,7 +7006,6 @@ beta12orEarlier Sequence composition (amino acid words) A table of amino acid word composition of a protein sequence. - @@ -7417,7 +7035,6 @@ Annotation of positional sequence features, organized into a standard feature table. beta12orEarlier Sequence feature table - @@ -7438,7 +7055,6 @@ A map of (typically one) DNA sequence annotated with positional or non-positional features. beta12orEarlier DNA map - @@ -7456,7 +7072,6 @@ beta12orEarlier Nucleic acid feature table An informative report on intrinsic positional features of a nucleotide sequence. - @@ -7474,7 +7089,6 @@ 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. - @@ -7491,7 +7105,6 @@ 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. - @@ -7506,7 +7119,6 @@ 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. - @@ -7521,7 +7133,6 @@ 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. - @@ -7554,7 +7165,6 @@ Cytologic map A map showing banding patterns derived from direct observation of a stained chromosome. beta12orEarlier - @@ -7568,7 +7178,6 @@ A gene map showing distances between loci based on relative cotransduction frequencies. beta12orEarlier - @@ -7582,7 +7191,6 @@ 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. - @@ -7596,7 +7204,6 @@ beta12orEarlier Sequence map of a plasmid (circular DNA). - @@ -7610,7 +7217,6 @@ Sequence map of a whole genome. beta12orEarlier - @@ -7626,7 +7232,6 @@ beta12orEarlier Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence. - @@ -7718,7 +7323,6 @@ Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences. beta12orEarlier - @@ -7768,7 +7372,6 @@ A report on a region of a nucleic acid sequence containin mobile genetic elements. Nucleic acid features (transposons) This includes transposons, Plasmids, Bacteriophage elements and Group II introns. - @@ -7786,7 +7389,6 @@ 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 PolyA signal - @@ -7816,7 +7418,6 @@ A report or plot of CpG rich regions (isochores) in a nucleotide sequence. beta12orEarlier Nucleic acid features (CpG island and isochore) - @@ -7832,7 +7433,6 @@ Report on restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. Nucleic acid restriction sites (report) beta12orEarlier - @@ -7847,7 +7447,6 @@ A report on nucleosome formation potential or exclusion sequence(s). beta12orEarlier Nucleic acid features (nucleosome exclusion sequences) - @@ -7864,7 +7463,6 @@ Nucleic acid report (RNA splice model) A report on splice sites in a nucleotide sequence or alternative RNA splicing events. beta12orEarlier - @@ -7879,7 +7477,6 @@ Nucleic acid features (matrix/scaffold attachment sites) beta12orEarlier A report on matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. - @@ -7926,7 +7523,6 @@ 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. Gene features (operon) - @@ -7941,7 +7537,6 @@ beta12orEarlier A report on 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) - @@ -7959,7 +7554,6 @@ beta12orEarlier Gene features (coding region) A report on protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. - @@ -7997,7 +7591,6 @@ TFBS (report) beta12orEarlier Nucleic acid features (TFBS) - @@ -8027,7 +7620,6 @@ beta12orEarlier A report on the location of signal peptides or signal peptide cleavage sites in protein sequences. - @@ -8047,7 +7639,6 @@ beta12orEarlier A report on cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. - @@ -8063,7 +7654,6 @@ beta12orEarlier A report on post-translation modifications in a protein sequence, typically describing the specific sites involved. Protein features (post-translation modification sites) - @@ -8078,7 +7668,6 @@ beta12orEarlier Enzyme active site A report on catalytic residues (active site) of an enzyme. - @@ -8092,7 +7681,6 @@ A report on ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. beta12orEarlier - @@ -8122,7 +7710,6 @@ beta12orEarlier A report on RNA and DNA-binding proteins and binding sites in protein sequences. - @@ -8272,7 +7859,6 @@ beta12orEarlier Dirichlet distribution used by hidden Markov model analysis programs. - @@ -8323,7 +7909,6 @@ Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence. beta12orEarlier - @@ -8342,11 +7927,10 @@ beta12orEarlier + http://semanticscience.org/resource/SIO_010531 Some type of statistical model representing a (typically multiple) sequence alignment. - - @@ -8364,7 +7948,6 @@ Protein region signature An entry (sequence classifier and associated data) from the InterPro database. Protein repeat signature - @@ -8409,7 +7992,6 @@ A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position. PFM beta12orEarlier - @@ -8425,7 +8007,6 @@ A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position. beta12orEarlier PWM - @@ -8440,7 +8021,6 @@ 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 - @@ -8455,7 +8035,6 @@ A hidden Markov model representation of a set or alignment of sequences. beta12orEarlier HMM - @@ -8469,7 +8048,6 @@ One or more fingerprints (sequence classifiers) as used in the PRINTS database. beta12orEarlier - @@ -8657,10 +8235,9 @@ Alignment of exactly two molecular sequences. beta12orEarlier - + http://semanticscience.org/resource/SIO_010068" - @@ -8687,7 +8264,6 @@ Alignment of multiple nucleotide sequences. beta12orEarlier - @@ -8702,7 +8278,6 @@ beta12orEarlier Alignment of multiple protein sequences. - @@ -8717,7 +8292,6 @@ beta12orEarlier Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA. Alignment of multiple molecular sequences of different types. - @@ -8732,7 +8306,6 @@ Alignment of exactly two nucleotide sequences. beta12orEarlier - @@ -8747,7 +8320,6 @@ beta12orEarlier Alignment of exactly two protein sequences. - @@ -8806,7 +8378,6 @@ A simple floating point number defining the penalty for opening or extending a gap in an alignment. beta12orEarlier - @@ -8850,7 +8421,6 @@ beta12orEarlier A penalty for opening a gap in an alignment. - @@ -8864,7 +8434,6 @@ beta12orEarlier A penalty for extending a gap in an alignment. - @@ -8878,7 +8447,6 @@ A penalty for gaps that are close together in an alignment. beta12orEarlier - @@ -8908,7 +8476,6 @@ The score for a 'match' used in various sequence database search applications with simple scoring schemes. beta12orEarlier - @@ -8922,7 +8489,6 @@ The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes. beta12orEarlier - @@ -8936,7 +8502,6 @@ beta12orEarlier This is the threshold drop in score at which extension of word alignment is halted. - @@ -9040,7 +8605,6 @@ 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 - @@ -9054,7 +8618,6 @@ 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. - @@ -9068,7 +8631,6 @@ beta12orEarlier Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences. - @@ -9083,7 +8645,6 @@ 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 - @@ -9190,7 +8751,6 @@ Quantitative traits Phylogenetic continuous quantitative characters beta12orEarlier - @@ -9207,7 +8767,6 @@ Phylogenetic discrete states Character data with discrete states that may be read during phylogenetic tree calculation. Discrete characters - @@ -9222,7 +8781,6 @@ 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. - @@ -9243,7 +8801,6 @@ Phylogenetic report (invariants) beta12orEarlier Phylogenetic invariants data for testing alternative tree topologies. - @@ -9279,7 +8836,6 @@ Sequence alignment report (DNA substitution model) Phylogenetic tree report (DNA substitution model) Substitution model - @@ -9324,7 +8880,6 @@ Distances, such as Branch Score distance, between two or more phylogenetic trees. Phylogenetic tree report (tree distances) beta12orEarlier - @@ -9354,7 +8909,6 @@ beta12orEarlier Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts. Phylogenetic report (character contrasts) - @@ -9401,7 +8955,6 @@ Nucleotide substitution matrix beta12orEarlier Matrix of integer or floating point numbers for nucleotide comparison. - @@ -9418,7 +8971,6 @@ Matrix of integer or floating point numbers for amino acid comparison. beta12orEarlier Amino acid comparison matrix - @@ -9500,7 +9052,6 @@ 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. beta12orEarlier Intramembrane region report - @@ -9520,7 +9071,6 @@ beta12orEarlier 3D coordinate and associated data for a nucleic acid tertiary (3D) structure. - @@ -9535,18 +9085,17 @@ - + - + beta12orEarlier 3D coordinate and associated data for a protein tertiary (3D) structure. - @@ -9561,7 +9110,6 @@ 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. - @@ -9587,7 +9135,6 @@ 3D coordinate and associated data for a carbohydrate (3D) structure. beta12orEarlier - @@ -9608,7 +9155,6 @@ beta12orEarlier CHEBI:23367 3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound. - @@ -9622,7 +9168,6 @@ 3D coordinate and associated data for a DNA tertiary (3D) structure. beta12orEarlier - @@ -9642,7 +9187,6 @@ 3D coordinate and associated data for an RNA tertiary (3D) structure. beta12orEarlier - @@ -9656,7 +9200,6 @@ beta12orEarlier 3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc. - @@ -9670,7 +9213,6 @@ 3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain. beta12orEarlier - @@ -9690,7 +9232,6 @@ beta12orEarlier 3D coordinate and associated data for the tertiary (3D) structure of a protein domain. - @@ -9798,7 +9339,6 @@ Pair structure alignment beta12orEarlier Alignment (superimposition) of exactly two molecular tertiary (3D) structures. - @@ -9829,7 +9369,6 @@ Alignment (superimposition) of protein tertiary (3D) structures. beta12orEarlier Protein structure alignment - @@ -9844,7 +9383,6 @@ Nucleic acid structure alignment Alignment (superimposition) of nucleic acid tertiary (3D) structures. beta12orEarlier - @@ -9860,7 +9398,6 @@ Alignment (superimposition) of exactly two protein tertiary (3D) structures. beta12orEarlier Protein pair structural alignment - @@ -9985,7 +9522,6 @@ Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures. Nucleic acid pair structure alignment beta12orEarlier - @@ -10015,7 +9551,6 @@ beta12orEarlier Alignment (superimposition) of RNA tertiary (3D) structures. RNA structure alignment - @@ -10029,7 +9564,6 @@ beta12orEarlier Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures. - @@ -10075,7 +9609,6 @@ Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates. beta12orEarlier RMSD - @@ -10090,7 +9623,6 @@ 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 - @@ -10104,7 +9636,6 @@ beta12orEarlier A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments. - @@ -10119,7 +9650,6 @@ A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids. beta12orEarlier - @@ -10134,7 +9664,6 @@ beta12orEarlier Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids. Chemical classes (amino acids) - @@ -10149,7 +9678,6 @@ beta12orEarlier Statistical protein contact potentials. Contact potentials (amino acid pair-wise) - @@ -10164,7 +9692,6 @@ beta12orEarlier Molecular weight (amino acids) Molecular weights of amino acids. - @@ -10179,7 +9706,6 @@ Hydropathy (amino acids) beta12orEarlier Hydrophobic, hydrophilic or charge properties of amino acids. - @@ -10194,7 +9720,6 @@ Experimental free energy values for the water-interface and water-octanol transitions for the amino acids. White-Wimley data (amino acids) beta12orEarlier - @@ -10209,7 +9734,6 @@ beta12orEarlier Van der Waals radii of atoms for different amino acid residues. van der Waals radii (amino acids) - @@ -10260,7 +9784,6 @@ 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 - @@ -10275,7 +9798,6 @@ Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. Report on the hydrophobic moment of a polypeptide sequence. beta12orEarlier - @@ -10290,7 +9812,6 @@ The aliphatic index is the relative protein volume occupied by aliphatic side chains. beta12orEarlier The aliphatic index of a protein. - @@ -10305,7 +9826,6 @@ 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. - @@ -10319,7 +9839,6 @@ 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 - @@ -10334,7 +9853,6 @@ Protein solubility data The solubility or atomic solvation energy of a protein sequence or structure. beta12orEarlier - @@ -10349,7 +9867,6 @@ Data on the crystallizability of a protein sequence. Protein crystallizability data beta12orEarlier - @@ -10364,7 +9881,6 @@ Data on the stability, intrinsic disorder or globularity of a protein sequence. beta12orEarlier Protein globularity data - @@ -10378,7 +9894,6 @@ beta12orEarlier The titration curve of a protein. - @@ -10392,7 +9907,6 @@ The isoelectric point of one proteins. beta12orEarlier - @@ -10406,7 +9920,6 @@ beta12orEarlier The pKa value of a protein. - @@ -10420,7 +9933,6 @@ The hydrogen exchange rate of a protein. beta12orEarlier - @@ -10434,7 +9946,6 @@ beta12orEarlier The extinction coefficient of a protein. - @@ -10448,7 +9959,6 @@ beta12orEarlier The optical density of a protein. - @@ -10481,7 +9991,6 @@ beta12orEarlier Peptide immunogenicity report An report on allergenicity / immunogenicity of peptides and proteins. - @@ -10517,7 +10026,6 @@ 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 - @@ -10537,7 +10045,6 @@ Protein structure validation report Protein structure report (quality evaluation) Report on the quality of a protein three-dimensional model. - @@ -10559,7 +10066,6 @@ 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 - @@ -10593,7 +10099,6 @@ 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. - @@ -10624,7 +10129,6 @@ Phi/psi angle data or a Ramachandran plot of a protein structure. beta12orEarlier - @@ -10638,7 +10142,6 @@ beta12orEarlier Data on the net charge distribution (dipole moment) of a protein structure. - @@ -10652,7 +10155,6 @@ A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure. beta12orEarlier - @@ -10666,7 +10168,6 @@ beta12orEarlier An amino acid residue contact map for a protein structure. - @@ -10680,7 +10181,6 @@ Report on clusters of contacting residues in protein structures such as a key structural residue network. beta12orEarlier - @@ -10694,7 +10194,6 @@ beta12orEarlier Patterns of hydrogen bonding in protein structures. - @@ -10885,7 +10384,6 @@ Protein structure report (protein complex) beta12orEarlier An informative report on protein-protein interaction(s). - @@ -10899,7 +10397,6 @@ An informative report on protein-ligand (small molecule) interaction(s). beta12orEarlier - @@ -10913,7 +10410,6 @@ beta12orEarlier An informative report on protein-DNA/RNA interaction(s). - @@ -10929,7 +10425,6 @@ 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 - @@ -10943,7 +10438,6 @@ Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). beta12orEarlier - @@ -10957,7 +10451,6 @@ beta12orEarlier Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). - @@ -10987,7 +10480,6 @@ 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 - @@ -11001,7 +10493,6 @@ beta12orEarlier DNA base pair stacking energies data. - @@ -11015,7 +10506,6 @@ DNA base pair twist angle data. beta12orEarlier - @@ -11029,7 +10519,6 @@ DNA base trimer roll angles data. beta12orEarlier - @@ -11104,7 +10593,6 @@ Dotplot of RNA base pairing probability matrix. Such as generated by the Vienna package. beta12orEarlier - @@ -11116,12 +10604,13 @@ 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) - @@ -11142,7 +10631,6 @@ 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. - @@ -11157,7 +10645,6 @@ A genetic code need not include detailed codon usage information. A genetic code for an organism. beta12orEarlier - @@ -11188,7 +10675,6 @@ A plot of the synonymous codon usage calculated for windows over a nucleotide sequence. beta12orEarlier Synonymous codon usage statistic plot - @@ -11217,7 +10703,6 @@ beta12orEarlier The differences in codon usage fractions between two codon usage tables. - @@ -11232,7 +10717,6 @@ 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 - @@ -11254,7 +10738,6 @@ 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. - @@ -11270,7 +10753,6 @@ beta12orEarlier Gene annotation (linkage disequilibrium) A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). - @@ -11286,7 +10768,6 @@ 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. - @@ -11332,7 +10813,6 @@ Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS. beta12orEarlier - @@ -11348,7 +10828,6 @@ beta12orEarlier This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. Pathway or network (metabolic) - @@ -11363,7 +10842,6 @@ Pathway or network (genetic information processing) A report typically including a map (diagram) of a genetic information processing pathway. beta12orEarlier - @@ -11378,7 +10856,6 @@ beta12orEarlier A report typically including a map (diagram) of an environmental information processing pathway. Pathway or network (environmental information processing) - @@ -11393,7 +10870,6 @@ beta12orEarlier A report typically including a map (diagram) of a signal transduction pathway. Pathway or network (signal transduction) - @@ -11408,7 +10884,6 @@ beta12orEarlier A report typically including a map (diagram) of a cellular process pathway. - @@ -11423,7 +10898,6 @@ A report typically including a map (diagram) of a disease pathway, typically a diagram for a human disease. beta12orEarlier Pathway or network (disease) - @@ -11437,7 +10911,6 @@ beta12orEarlier A report typically including a map (diagram) of drug structure relationships. - @@ -11453,7 +10926,6 @@ beta12orEarlier Pathway or network (protein-protein interaction) A report typically including a map (diagram) of a network of protein interactions. - @@ -11485,7 +10957,6 @@ 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. - @@ -11500,7 +10971,6 @@ 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 - @@ -11515,7 +10985,6 @@ 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 - @@ -11817,7 +11286,6 @@ beta12orEarlier A username on a computer system. - @@ -11832,7 +11300,6 @@ A password on a computer system. beta12orEarlier - @@ -11849,7 +11316,6 @@ A valid email address of an end-user. Moby:Email beta12orEarlier - @@ -11864,7 +11330,6 @@ The name of a person. beta12orEarlier - @@ -11933,7 +11398,6 @@ beta12orEarlier An informative report on a specific drug. - @@ -11948,7 +11412,6 @@ 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 - @@ -11962,7 +11425,6 @@ Image of RNA secondary structure, knots, pseudoknots etc. beta12orEarlier - @@ -11976,7 +11438,6 @@ beta12orEarlier Image of protein secondary structure. - @@ -11990,7 +11451,6 @@ Image of one or more molecular tertiary (3D) structures. beta12orEarlier - @@ -12004,7 +11464,6 @@ Image of two or more aligned molecular sequences possibly annotated with alignment features. beta12orEarlier - @@ -12020,7 +11479,6 @@ Small molecule structure image The molecular identifier and formula are typically included. An image of the structure of a small chemical compound. - @@ -12041,7 +11499,6 @@ A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development. beta12orEarlier - @@ -12056,7 +11513,6 @@ An image of spots from a microarray experiment. beta12orEarlier - @@ -12321,7 +11777,6 @@ The definition of a concept from an ontology. Ontology class definition beta12orEarlier - @@ -12383,7 +11838,6 @@ beta12orEarlier PDBML:PDB_residue_no WHATIF: pdb_number - @@ -12398,7 +11852,6 @@ Cartesian coordinate beta12orEarlier Cartesian coordinate of an atom (in a molecular structure). - @@ -12415,7 +11868,6 @@ beta12orEarlier Cartesian x coordinate WHATIF: PDBx_Cartn_x - @@ -12432,7 +11884,6 @@ beta12orEarlier Cartesian y coordinate WHATIF: PDBx_Cartn_y - @@ -12449,7 +11900,6 @@ Cartesian z coordinate of an atom (in a molecular structure). WHATIF: PDBx_Cartn_z PDBML:_atom_site.Cartn_z - @@ -12468,7 +11918,6 @@ WHATIF: PDBx_auth_atom_id beta12orEarlier WHATIF: PDBx_type_symbol - @@ -12486,7 +11935,6 @@ 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 - @@ -12502,7 +11950,6 @@ 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 - @@ -12517,7 +11964,6 @@ beta12orEarlier Name of an atom. - @@ -12533,7 +11979,6 @@ beta12orEarlier WHATIF: type Three-letter amino acid residue names as used in PDB files. - @@ -12551,7 +11996,6 @@ PDBML:pdbx_PDB_model_num beta12orEarlier Identifier of a model structure from a PDB file. - @@ -12643,7 +12087,6 @@ Sequence version information Information on an molecular sequence version. beta12orEarlier - @@ -12657,7 +12100,6 @@ beta12orEarlier A numerical value, that is some type of scored value arising for example from a prediction method. - @@ -12875,7 +12317,6 @@ http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB beta12orEarlier Identifier of a gene from PlasmoDB Plasmodium Genome Resource. - @@ -12892,7 +12333,6 @@ EcoGene ID EcoGene Accession Identifier of a gene from EcoGene Database. - @@ -12909,7 +12349,6 @@ http://www.geneontology.org/doc/GO.xrf_abbs: FB Gene identifier from FlyBase database. beta12orEarlier - @@ -13006,7 +12445,6 @@ http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene - @@ -13023,7 +12461,6 @@ Gene identifier from Virginia Bioinformatics Institute microbial database. http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD beta12orEarlier - @@ -13039,7 +12476,6 @@ beta12orEarlier Gene identifier from Sol Genomics Network. http://www.geneontology.org/doc/GO.xrf_abbs: SGN - @@ -13053,12 +12489,11 @@ Gene ID (WormBase) - http://www.geneontology.org/doc/GO.xrf_abbs: WormBase - Gene identifier used by WormBase database. 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. @@ -13090,7 +12525,6 @@ The name of an open reading frame attributed by a sequencing project. beta12orEarlier - @@ -13135,7 +12569,6 @@ An identifier of a clone (cloned molecular sequence) from a database. beta12orEarlier - @@ -13152,7 +12585,6 @@ PDBML:pdbx_PDB_ins_code WHATIF: insertion_code beta12orEarlier - @@ -13168,7 +12600,6 @@ beta12orEarlier The fraction of an atom type present at a site in a molecular structure. WHATIF: PDBx_occupancy - @@ -13183,7 +12614,6 @@ beta12orEarlier WHATIF: PDBx_B_iso_or_equiv Isotropic B factor (atomic displacement parameter) for an atom from a PDB file. - @@ -13199,7 +12629,6 @@ 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. - @@ -13214,7 +12643,6 @@ Quantitative trait locus map beta12orEarlier A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers. - @@ -13229,7 +12657,6 @@ A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation. Moby:Haplotyping_Study_obj beta12orEarlier - @@ -13245,7 +12672,6 @@ Moby:GCP_CorrelatedLinkageMapSet Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped. beta12orEarlier - @@ -13294,7 +12720,6 @@ beta12orEarlier The name of a protein fold. - @@ -13314,7 +12739,6 @@ beta12orEarlier Taxonomy rank Moby:PotentialTaxon - @@ -13335,7 +12759,6 @@ A unique identifier of a (group of) organisms. beta12orEarlier - @@ -13350,7 +12773,6 @@ The name of a genus of organism. beta12orEarlier - @@ -13373,7 +12795,6 @@ beta12orEarlier Moby:GCP_Taxon Moby:TaxonName - @@ -13389,7 +12810,6 @@ A unique identifier for an organism used in the iHOP database. Moby_namespace:iHOPorganism beta12orEarlier - @@ -13404,7 +12824,6 @@ beta12orEarlier Common name for an organism as used in the GenBank database. - @@ -13419,7 +12838,6 @@ beta12orEarlier The name of a taxon from the NCBI taxonomy database. - @@ -13496,7 +12914,6 @@ beta12orEarlier Moby:Author Information on the authors of a published work. - @@ -13511,7 +12928,6 @@ beta12orEarlier An identifier representing an author in the DragonDB database. - @@ -13527,7 +12943,6 @@ Moby:DescribedLink A URI along with annotation describing the data found at the address. beta12orEarlier - @@ -13557,7 +12972,6 @@ beta12orEarlier Identifier of a gene from the GeneFarm database. Moby_namespace:GENEFARM_GeneID - @@ -13573,7 +12987,6 @@ The blattner identifier for a gene. Moby_namespace:Blattner_number beta12orEarlier - @@ -13657,7 +13070,6 @@ beta12orEarlier Moby_namespace:iHOPsymbol A unique identifier of a protein or gene used in the iHOP database. - @@ -13694,11 +13106,10 @@ - beta12orEarlier - 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 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. @@ -13719,7 +13130,6 @@ Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases) AGI ID AT[1-5]G[0-9]{5} - @@ -13736,7 +13146,6 @@ http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD beta12orEarlier - @@ -13752,7 +13161,6 @@ beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG Identifier for loci from Magnaporthe grisea Database at the Broad Institute. - @@ -13766,12 +13174,11 @@ 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 - CGD locus identifier Identifier for loci from CGD (Candida Genome Database). - @@ -13788,7 +13195,6 @@ 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 - @@ -13806,7 +13212,6 @@ Locus ID (NCBI) Moby_namespace:LocusID beta12orEarlier - @@ -13821,11 +13226,10 @@ SGDID - Identifier for loci from SGD (Saccharomyces Genome Database). 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). @@ -13841,7 +13245,6 @@ beta12orEarlier Moby_namespace:MMP_Locus Identifier of loci from Maize Mapping Project. - @@ -13857,7 +13260,6 @@ beta12orEarlier Identifier of locus from DictyBase (Dictyostelium discoideum). Moby_namespace:DDB_gene - @@ -13874,7 +13276,6 @@ Moby_namespace:EntrezGene_ID beta12orEarlier Identifier of a locus from EntrezGene database. - @@ -13890,7 +13291,6 @@ beta12orEarlier Moby_namespace:MaizeGDB_Locus Identifier of locus from MaizeGDB (Maize genome database). - @@ -13924,7 +13324,6 @@ Moby_namespace:GeneId beta12orEarlier Identifier of a gene from the KOME database. - @@ -13940,7 +13339,6 @@ beta12orEarlier Moby:Tropgene_locus Identifier of a locus from the Tropgene database. - @@ -13955,7 +13353,6 @@ beta12orEarlier An alignment of molecular sequences, structures or profiles derived from them. - @@ -13970,7 +13367,6 @@ beta12orEarlier Data for an atom (in a molecular structure). General atomic property - @@ -13986,7 +13382,6 @@ Moby_namespace:SP_KW A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database. beta12orEarlier - @@ -14030,7 +13425,6 @@ Locus Moby:Position Map position - @@ -14045,7 +13439,6 @@ beta12orEarlier Amino acid data Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids. - @@ -14082,7 +13475,6 @@ 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 - @@ -14128,7 +13520,6 @@ 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). - @@ -14142,7 +13533,6 @@ 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. - @@ -14156,7 +13546,6 @@ 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 - @@ -14203,7 +13592,6 @@ 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. - @@ -14217,7 +13605,6 @@ A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment. beta12orEarlier - @@ -14235,14 +13622,13 @@ + http://purl.org/biotop/biotop.owl#BioMolecularSequenceInformation" 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.bioontology.org/ontology/MSH/D008969" - @@ -14257,7 +13643,6 @@ A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment. Nucleotide sequence record (lite) beta12orEarlier - @@ -14273,7 +13658,6 @@ A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment. beta12orEarlier Sequence record lite (protein) - @@ -14290,10 +13674,9 @@ Document 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. Text - + http://semanticscience.org/resource/SIO_000148" - @@ -14306,7 +13689,6 @@ beta12orEarlier General data for a molecule. General molecular property - @@ -14340,7 +13722,6 @@ A nucleotide sequence motif. DNA sequence motif Nucleic acid sequence motif - @@ -14355,7 +13736,6 @@ Protein sequence motif An amino acid sequence motif. beta12orEarlier - @@ -14384,7 +13764,6 @@ A report of hits from searching a database of some type. beta12orEarlier - @@ -14411,10 +13790,10 @@ Matrix - An array of numerical values where (typically) the rows and columns correspond to molecular entities and the values are comparative data, for example, distances between molecular sequences. + An array of numerical values. This is a broad data type and is used a placeholder for other, more specific types. + Array beta12orEarlier - @@ -14430,7 +13809,6 @@ 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. beta12orEarlier - @@ -14444,7 +13822,6 @@ beta12orEarlier An informative report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data. - @@ -14459,7 +13836,6 @@ Structure-derived report beta12orEarlier An informative report on general information, properties or features of one or more molecular tertiary (3D) structures. - @@ -14476,7 +13852,6 @@ Nucleic acid structural property This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties. Nucleic acid property (structural) - @@ -14492,7 +13867,6 @@ A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule. SO:0000400 beta12orEarlier - @@ -14506,7 +13880,6 @@ beta12orEarlier Structural data for DNA base pairs or runs of bases, such as energy or angle data. - @@ -14533,14 +13906,13 @@ Accession + http://semanticscience.org/resource/SIO_000675" + http://semanticscience.org/resource/SIO_000731" A persistent (stable) and unique identifier, typically identifying an object (entry) from a database. beta12orEarlier - - - @@ -14555,7 +13927,6 @@ Single nucleotide polymorphism Annotation on a single nucleotide polymorphism (SNP) in a DNA sequence. beta12orEarlier - @@ -14570,7 +13941,6 @@ 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. - @@ -14584,11 +13954,10 @@ beta12orEarlier An identifier of a submitted job. - + http://wsio.org/data_009 - @@ -14600,13 +13969,13 @@ Symbolic name A name of a thing, which need not necessarily uniquely identify it. + "http://www.w3.org/2000/01/rdf-schema#label" beta12orEarlier - + http://usefulinc.com/ns/doap#name + http://semanticscience.org/resource/SIO_000116 - - @@ -14626,10 +13995,10 @@ 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). - @@ -14641,7 +14010,6 @@ beta12orEarlier An identifier of a software end-user (typically a person). - @@ -14657,7 +14025,6 @@ beta12orEarlier A three-letter code used in the KEGG databases to uniquely identify organisms. - @@ -14691,7 +14058,6 @@ beta12orEarlier Identifier of an object from one of the BioCyc databases. - @@ -14709,7 +14075,6 @@ BioCyc compound ID Identifier of a compound from the BioCyc chemical compounds database. BioCyc compound identifier - @@ -14731,7 +14096,6 @@ Identifier of a biological reaction from the BioCyc reactions database. beta12orEarlier - @@ -14748,7 +14112,6 @@ Identifier of an enzyme from the BioCyc enzymes database. beta12orEarlier BioCyc enzyme ID - @@ -14770,7 +14133,6 @@ Identifier of a biological reaction from a database. beta12orEarlier - @@ -14786,7 +14148,6 @@ 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). - @@ -14807,7 +14168,6 @@ Identifier of a molecular property. beta12orEarlier - @@ -14823,19 +14183,18 @@ - + - + beta12orEarlier Codon usage table identifier Identifier of a codon usage table, for example a genetic code. - @@ -14850,7 +14209,6 @@ Primary identifier of an object from the FlyBase database. beta12orEarlier - @@ -14865,7 +14223,6 @@ Identifier of an object from the WormBase database. beta12orEarlier - @@ -14882,7 +14239,6 @@ beta12orEarlier CE[0-9]{5} Protein identifier used by WormBase database. - @@ -14918,7 +14274,6 @@ beta12orEarlier An identifier of a map of a molecular sequence. - @@ -14933,7 +14288,6 @@ beta12orEarlier An identifier of a software end-user (typically a person). - @@ -14954,7 +14308,6 @@ beta12orEarlier Name or other identifier of a nucleic acid molecule. - @@ -14969,7 +14322,6 @@ Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome). beta12orEarlier - @@ -14989,7 +14341,6 @@ beta12orEarlier An identifier of a genetic code. - @@ -15005,7 +14356,6 @@ beta12orEarlier Informal name for a genetic code, typically an organism name. - @@ -15021,7 +14371,6 @@ beta12orEarlier Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on. - @@ -15051,7 +14400,6 @@ Name of a computer operating system such as Linux, PC or Mac. beta12orEarlier - @@ -15081,7 +14429,6 @@ A logical operator such as OR, AND, XOR, and NOT. beta12orEarlier - @@ -15142,7 +14489,6 @@ A penalty for introducing or extending a gap in an alignment. beta12orEarlier - @@ -15157,7 +14503,6 @@ 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 - @@ -15171,7 +14516,6 @@ The concentration of a chemical compound. beta12orEarlier - @@ -15340,7 +14684,6 @@ beta12orEarlier Any arbitrary name of a molecular sequence. - @@ -15386,7 +14729,6 @@ beta12orEarlier A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences. - @@ -15398,14 +14740,11 @@ Sequence similarity plot - A plot of sequence similarities identified from word-matching or character comparison. - Sequence conservation report - 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. 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. @@ -15419,7 +14758,6 @@ An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties. beta12orEarlier - @@ -15434,7 +14772,6 @@ 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 - @@ -15463,7 +14800,6 @@ A plot of pK versus pH for a protein. beta12orEarlier - @@ -15477,7 +14813,6 @@ A plot of character or word composition / frequency of a molecular sequence. beta12orEarlier - @@ -15491,7 +14826,6 @@ Density plot (of base composition) for a nucleotide sequence. beta12orEarlier - @@ -15505,7 +14839,6 @@ beta12orEarlier Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases). - @@ -15551,7 +14884,6 @@ 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. - @@ -15641,7 +14973,6 @@ 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. - @@ -15658,7 +14989,6 @@ MOD:00000 beta12orEarlier A report on a chemical modification of a protein. - @@ -15687,7 +15017,6 @@ Basic information on any arbitrary database entry. beta12orEarlier - @@ -15717,8 +15046,7 @@ SO:2000061 A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. beta12orEarlier - - + http://purl.bioontology.org/ontology/MSH/D058977" @@ -15732,7 +15060,6 @@ beta12orEarlier An identifier of a plasmid in a database. - @@ -15748,7 +15075,6 @@ A unique identifier of a specific mutation catalogued in a database. beta12orEarlier - @@ -15823,7 +15149,6 @@ The number of a codon, for instance, at which a mutation is located. beta12orEarlier - @@ -15867,7 +15192,6 @@ beta12orEarlier The name of a field in a database. - @@ -15883,7 +15207,6 @@ beta12orEarlier Unique identifier of a sequence cluster from the SYSTERS database. SYSTERS cluster ID - @@ -15904,7 +15227,6 @@ Data concerning a biological ontology. beta12orEarlier - @@ -16087,7 +15409,6 @@ The name of a data type. beta12orEarlier - @@ -16102,7 +15423,6 @@ beta12orEarlier Name of an OBO file format such as OBO-XML, plain and so on. - @@ -16118,7 +15438,6 @@ MIPS genetic element identifier beta12orEarlier Identifier for genetic elements in MIPS database. - @@ -16166,7 +15485,6 @@ EMBL accession number beta12orEarlier EMBL ID - @@ -16191,7 +15509,6 @@ UniProtKB entry name An identifier of a polypeptide in the UniProt database. UniProtKB identifier - @@ -16209,7 +15526,6 @@ Accession number of an entry from the GenBank sequence database. GenBank identifier GenBank ID - @@ -16227,7 +15543,6 @@ Gramene internal ID Gramene internal identifier beta12orEarlier - @@ -16243,7 +15558,6 @@ beta12orEarlier An identifier of an entry from a database of molecular sequence variation. - @@ -16261,7 +15575,6 @@ A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol. beta12orEarlier Gene accession - @@ -16295,7 +15608,6 @@ E. coli K-12 gene identifier beta12orEarlier ECK accession - @@ -16311,7 +15623,6 @@ Identifier for a gene approved by the HUGO Gene Nomenclature Committee. beta12orEarlier HGNC ID - @@ -16328,7 +15639,6 @@ 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. - @@ -16359,7 +15669,6 @@ beta12orEarlier A specification of a chemical structure in SMILES format. - @@ -16373,7 +15682,6 @@ beta12orEarlier Unique identifier of an entry from the STRING database of protein-protein interactions. - @@ -16419,7 +15727,6 @@ [0-9]+ beta12orEarlier Identifier of a biological reaction from the SABIO-RK reactions database. - @@ -16434,7 +15741,6 @@ beta12orEarlier Annotation on or information derived from one or more specific carbohydrate 3D structure(s). - @@ -16451,7 +15757,6 @@ gi number NCBI GI number beta12orEarlier - @@ -16469,7 +15774,6 @@ 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 - @@ -16484,7 +15788,6 @@ The name of a cell line. beta12orEarlier - @@ -16499,7 +15802,6 @@ The name of a cell line. beta12orEarlier - @@ -16514,7 +15816,6 @@ beta12orEarlier The name of a cell line. - @@ -16529,7 +15830,6 @@ beta12orEarlier The name of a cell line. - @@ -16544,7 +15844,6 @@ beta12orEarlier The name of a cell line. - @@ -16561,7 +15860,6 @@ Enzyme accession A unique, persistent identifier of an enzyme. beta12orEarlier - @@ -16576,7 +15874,6 @@ beta12orEarlier Identifier of an enzyme from the REBASE enzymes database. - @@ -16592,7 +15889,6 @@ Unique identifier of a drug from the DrugBank database. DB[0-9]{5} beta12orEarlier - @@ -16610,7 +15906,6 @@ A unique identifier assigned to NCBI protein sequence records. protein gi number beta12orEarlier - @@ -16626,7 +15921,6 @@ 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. - @@ -16641,7 +15935,6 @@ Phase Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence. beta12orEarlier - @@ -16657,7 +15950,6 @@ 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. - @@ -16677,7 +15969,6 @@ Any arbitrary identifier of an ontology. beta12orEarlier - @@ -16693,7 +15984,6 @@ beta12orEarlier The name of a concept in an ontology. - @@ -16708,7 +15998,6 @@ An identifier of a build of a particular genome. beta12orEarlier - @@ -16723,7 +16012,6 @@ beta12orEarlier The name of a biological pathway or network. - @@ -16741,7 +16029,6 @@ [a-zA-Z_0-9]{2,3}[0-9]{5} beta12orEarlier Identifier of a pathway from the KEGG pathway database. - @@ -16757,7 +16044,6 @@ Identifier of a pathway from the NCI-Nature pathway database. [a-zA-Z_0-9]+ beta12orEarlier - @@ -16773,7 +16059,6 @@ Identifier of a pathway from the ConsensusPathDB pathway database. beta12orEarlier - @@ -16790,7 +16075,6 @@ UniRef entry accession UniRef cluster id Unique identifier of an entry from the UniRef database. - @@ -16807,7 +16091,6 @@ UniRef100 entry accession beta12orEarlier UniRef100 cluster id - @@ -16824,7 +16107,6 @@ UniRef90 cluster id beta12orEarlier UniRef90 entry accession - @@ -16841,7 +16123,6 @@ UniRef50 entry accession UniRef50 cluster id beta12orEarlier - @@ -16864,7 +16145,6 @@ beta12orEarlier Ontological data Data concerning or derived from an ontology. - @@ -16879,7 +16159,6 @@ RNA family annotation An informative report on a specific RNA family or other group of classified RNA sequences. beta12orEarlier - @@ -16899,7 +16178,6 @@ Identifier of an RNA family, typically an entry from a RNA sequence classification database. beta12orEarlier - @@ -16915,7 +16193,6 @@ beta12orEarlier Stable accession number of an entry (RNA family) from the RFAM database. - @@ -16960,7 +16237,6 @@ beta12orEarlier An informative report on protein domain-protein domain interaction(s). - @@ -16995,7 +16271,6 @@ beta12orEarlier Accession number of a nucleotide or protein sequence database entry. - @@ -17034,7 +16309,6 @@ An informative report on a two-dimensional gel electrophoresis experiment, gel or spots in a gel. beta12orEarlier Experiment annotation (2D PAGE) - @@ -17049,7 +16323,6 @@ beta12orEarlier A persistent, unique identifier of a biological pathway or network (typically a database entry). - @@ -17064,7 +16337,6 @@ beta12orEarlier Alignment of the (1D representations of) secondary structure of two or more molecules. - @@ -17079,7 +16351,6 @@ Identifier of an object from the ASTD database. beta12orEarlier - @@ -17094,7 +16365,6 @@ Identifier of an exon from the ASTD database. beta12orEarlier - @@ -17109,7 +16379,6 @@ Identifier of an intron from the ASTD database. beta12orEarlier - @@ -17124,7 +16393,6 @@ beta12orEarlier Identifier of a polyA signal from the ASTD database. - @@ -17139,7 +16407,6 @@ beta12orEarlier Identifier of a transcription start site from the ASTD database. - @@ -17155,7 +16422,6 @@ An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel. beta12orEarlier 2D PAGE spot annotation - @@ -17170,7 +16436,6 @@ Unique identifier of a spot from a two-dimensional (protein) gel. beta12orEarlier - @@ -17185,7 +16450,6 @@ beta12orEarlier Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database. - @@ -17200,7 +16464,6 @@ beta12orEarlier Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database. - @@ -17230,7 +16493,6 @@ beta12orEarlier Identifier of a strain of an organism variant, typically a plant, virus or bacterium. - @@ -17246,7 +16508,6 @@ beta12orEarlier A unique identifier of an item from the CABRI database. - @@ -17264,7 +16525,6 @@ Experiment report (genotyping) Genotyping experiment metadata Experiment annotation (genotype) - @@ -17285,7 +16545,6 @@ Identifier of an entry from a database of genotype experiment metadata. beta12orEarlier - @@ -17300,7 +16559,6 @@ Identifier of an entry from the EGA database. beta12orEarlier - @@ -17316,7 +16574,6 @@ beta12orEarlier IPI[0-9]{8} Identifier of a protein entry catalogued in the International Protein Index (IPI) database. - @@ -17332,7 +16589,6 @@ beta12orEarlier Accession number of a protein from the RefSeq database. RefSeq protein ID - @@ -17348,7 +16604,6 @@ EPD identifier Identifier of an entry (promoter) from the EPD database. beta12orEarlier - @@ -17364,7 +16619,6 @@ Identifier of an entry from the TAIR database. beta12orEarlier - @@ -17379,7 +16633,6 @@ Identifier of an Arabidopsis thaliana gene from the TAIR database. beta12orEarlier - @@ -17394,7 +16647,6 @@ Identifier of an entry from the UniSTS database. beta12orEarlier - @@ -17409,7 +16661,6 @@ Identifier of an entry from the UNITE database. beta12orEarlier - @@ -17424,7 +16675,6 @@ Identifier of an entry from the UTR database. beta12orEarlier - @@ -17442,7 +16692,6 @@ Accession number of a UniParc (protein sequence) database entry. UPI[A-F0-9]{10} beta12orEarlier - @@ -17457,7 +16706,6 @@ Identifier of an entry from the Rouge or HUGE databases. beta12orEarlier - @@ -17503,7 +16751,6 @@ Gene features (exon) beta12orEarlier An informative report on an exon in a nucleotide sequences. - @@ -17520,7 +16767,6 @@ Protein ID (Ensembl) beta12orEarlier Ensembl ID (protein) - @@ -17546,7 +16792,6 @@ Nucleic acid features (transcriptional) -35 signals (report) Ribosome binding sites (report) - @@ -17624,7 +16869,6 @@ 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. - @@ -17673,7 +16917,6 @@ Data concerning, extracted from, or derived from the analysis of a scientific text such as a full text article from a scientific journal. beta12orEarlier - @@ -17687,21 +16930,14 @@ Parameter or primitive Tool parameter - Tool-specific parameter Typically a simple numerical or string value that controls the operation of a tool. beta12orEarlier - + http://www.e-lico.eu/ontologies/dmo/DMOP/DMOP.owl#Parameter" + Tool-specific parameter + http://semanticscience.org/resource/SIO_000144 - - - - Slightly narrower in the sense of changing the characteristics of a system/function. - - - - @@ -17747,7 +16983,6 @@ Organism annotation beta12orEarlier An informative report on a specific organism. - @@ -17763,7 +16998,6 @@ Experiment annotation beta12orEarlier Experiment metadata - @@ -17779,7 +17013,6 @@ Mutation annotation Nucleic acid features (mutation) beta12orEarlier - @@ -17794,7 +17027,6 @@ beta12orEarlier Sequence parameter An attribute of a molecular sequence, possibly in reference to some other sequence. - @@ -17810,7 +17042,6 @@ 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. - @@ -17824,7 +17055,6 @@ Data concerning a mass spectrometry measurement. beta12orEarlier - @@ -17839,7 +17069,6 @@ 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 - @@ -17853,7 +17082,6 @@ beta12orEarlier An identifier of a mutation. - @@ -17902,7 +17130,6 @@ Single letter amino acid identifier, e.g. G. beta12orEarlier - @@ -17917,7 +17144,6 @@ Three letter amino acid identifier, e.g. GLY. beta12orEarlier - @@ -17932,7 +17158,6 @@ Full name of an amino acid, e.g. Glycine. beta12orEarlier - @@ -17953,7 +17178,6 @@ Identifier of a toxin. beta12orEarlier - @@ -17968,7 +17192,6 @@ beta12orEarlier Unique identifier of a toxin from the ArachnoServer database. - @@ -17999,7 +17222,6 @@ beta12orEarlier Unique identifier of a monomer from the BindingDB database. - @@ -18030,7 +17252,6 @@ An identifier of a 'biological process' concept from the the Gene Ontology. beta12orEarlier [0-9]{7}|GO:[0-9]{7} - @@ -18046,7 +17267,6 @@ An identifier of a 'molecular function' concept from the the Gene Ontology. [0-9]{7}|GO:[0-9]{7} beta12orEarlier - @@ -18076,7 +17296,6 @@ An image arising from a Northern Blot experiment. beta12orEarlier - @@ -18091,7 +17310,6 @@ beta12orEarlier Unique identifier of a blot from a Northern Blot. - @@ -18106,7 +17324,6 @@ Unique identifier of a blot from a Northern Blot from the BlotBase database. beta12orEarlier - @@ -18122,7 +17339,6 @@ Hierarchy annotation Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation. beta12orEarlier - @@ -18151,7 +17367,6 @@ Identifier of an entry from the Brite database of biological hierarchies. beta12orEarlier - @@ -18181,7 +17396,6 @@ beta12orEarlier A unique identifier for an organism used in the BRENDA database. - @@ -18197,7 +17411,6 @@ beta12orEarlier UniGene organism abbreviation The name of a taxon using the controlled vocabulary of the UniGene database. - @@ -18212,7 +17425,6 @@ The name of a taxon using the controlled vocabulary of the UTRdb database. beta12orEarlier - @@ -18228,7 +17440,6 @@ Catalogue identifier An identifier of a catalogue of biological resources. beta12orEarlier - @@ -18244,7 +17455,6 @@ beta12orEarlier The name of a catalogue of biological resources from the CABRI database. - @@ -18295,7 +17505,6 @@ Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network). beta12orEarlier Network - @@ -18336,7 +17545,7 @@ - Microarray data + Gene expression data @@ -18345,10 +17554,9 @@ 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 - Gene expression data - @@ -18362,11 +17570,10 @@ KEGG compound identifier + KEGG compound ID beta12orEarlier Unique identifier of a chemical compound from the KEGG database. C[0-9]+ - KEGG compound ID - @@ -18382,7 +17589,6 @@ beta12orEarlier Name (not necessarily stable) an entry (RNA family) from the RFAM database. - @@ -18399,7 +17605,6 @@ beta12orEarlier R[0-9]+ Identifier of a biological reaction from the KEGG reactions database. - @@ -18416,7 +17621,6 @@ D[0-9]+ Unique identifier of a drug from the KEGG Drug database. beta12orEarlier - @@ -18433,7 +17637,6 @@ Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database. ENS[A-Z]*[FPTG][0-9]{11} beta12orEarlier - @@ -18455,7 +17658,6 @@ [A-Z][0-9]+(\.[-[0-9]+])? beta12orEarlier An identifier of a disease from the International Classification of Diseases (ICD) database. - @@ -18473,7 +17675,6 @@ CluSTr ID [0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])? Unique identifier of a sequence cluster from the CluSTr database. - @@ -18490,7 +17691,6 @@ beta12orEarlier Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND). G[0-9]+ - @@ -18508,7 +17708,6 @@ TC number OBO file for regular expression. beta12orEarlier - @@ -18524,7 +17723,6 @@ beta12orEarlier Unique identifier of an entry from the MINT database of protein-protein interactions. MINT\-[0-9]{1,5} - @@ -18540,7 +17738,6 @@ DIP[\:\-][0-9]{3}[EN] beta12orEarlier Unique identifier of an entry from the DIP database of protein-protein interactions. - @@ -18556,7 +17753,6 @@ A[0-9]{6} Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database. beta12orEarlier - @@ -18572,7 +17768,6 @@ Identifier of a protein modification catalogued in a database. beta12orEarlier - @@ -18588,7 +17783,6 @@ beta12orEarlier AA[0-9]{4} Identifier of a protein modification catalogued in the RESID database. - @@ -18605,7 +17799,6 @@ Identifier of an entry from the RGD database. beta12orEarlier [0-9]{4,7} - @@ -18628,7 +17821,6 @@ beta12orEarlier Identifier of a protein sequence from the TAIR database. AASequence:[0-9]{10} - @@ -18645,7 +17837,6 @@ HMDB ID beta12orEarlier HMDB[0-9]{5} - @@ -18662,7 +17853,6 @@ Identifier of an entry from the LIPID MAPS database. LM ID beta12orEarlier - @@ -18679,7 +17869,6 @@ beta12orEarlier PDBML:pdbx_PDB_strand_id Identifier of a peptide from the PeptideAtlas peptide databases. - @@ -18691,20 +17880,13 @@ Molecular interaction ID - - - - - - - - + + 1.7 beta12orEarlier + true Identifier of a report of molecular interactions from a database (typically). - - - - + + @@ -18713,11 +17895,10 @@ BioGRID interaction ID - + A unique identifier of an interaction from the BioGRID database. beta12orEarlier [0-9]+ - @@ -18734,7 +17915,6 @@ beta12orEarlier Unique identifier of a peptidase enzyme from the MEROPS database. MEROPS ID - @@ -18750,7 +17930,6 @@ beta12orEarlier An identifier of a mobile genetic element. - @@ -18766,7 +17945,6 @@ An identifier of a mobile genetic element from the Aclame database. mge:[0-9]+ beta12orEarlier - @@ -18783,7 +17961,6 @@ Identifier of an entry from the Saccharomyces genome database (SGD). beta12orEarlier PWY[a-zA-Z_0-9]{2}\-[0-9]{3} - @@ -18799,7 +17976,6 @@ Unique identifier of a book. beta12orEarlier - @@ -18815,7 +17991,6 @@ 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 - @@ -18832,7 +18007,6 @@ beta12orEarlier 3DMET ID B[0-9]{5} - @@ -18844,11 +18018,10 @@ 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_.*) - @@ -18866,7 +18039,6 @@ beta12orEarlier These identifiers are unique within the cPath database, however, they are not stable between releases. [0-9]+ - @@ -18883,7 +18055,6 @@ beta12orEarlier [0-9]+ Identifier of an assay from the PubChem database. - @@ -18900,7 +18071,6 @@ Identifier of an entry from the PubChem database. beta12orEarlier PubChem identifier - @@ -18917,7 +18087,6 @@ MACie entry number M[0-9]{4} beta12orEarlier - @@ -18930,13 +18099,12 @@ Gene ID (miRBase) - miRNA name - beta12orEarlier - MI[0-9]{7} miRNA identifier + MI[0-9]{7} Identifier for a gene from the miRBase database. miRNA ID - + miRNA name + beta12orEarlier @@ -18952,7 +18120,6 @@ ZDB\-GENE\-[0-9]+\-[0-9]+ beta12orEarlier Identifier for a gene from the Zebrafish information network genome (ZFIN) database. - @@ -18968,7 +18135,6 @@ beta12orEarlier Identifier of an enzyme-catalysed reaction from the Rhea database. [0-9]{5} - @@ -18985,7 +18151,6 @@ beta12orEarlier upaid UPA[0-9]{5} - @@ -19002,7 +18167,6 @@ beta12orEarlier ChEMBL ID Identifier of a small molecular from the ChEMBL database. - @@ -19018,7 +18182,6 @@ [a-zA-Z_0-9]+ beta12orEarlier Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database. - @@ -19034,7 +18197,6 @@ beta12orEarlier [0-9]+ Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database. - @@ -19051,7 +18213,6 @@ PA[0-9]+ Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). beta12orEarlier - @@ -19068,7 +18229,6 @@ beta12orEarlier Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). PA[0-9]+ - @@ -19085,7 +18245,6 @@ PA[0-9]+ beta12orEarlier Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). - @@ -19102,7 +18261,6 @@ PA[0-9]+ Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). beta12orEarlier - @@ -19118,7 +18276,6 @@ beta12orEarlier Identifier of a drug from the Therapeutic Target Database (TTD). DAP[0-9]+ - @@ -19134,7 +18291,6 @@ beta12orEarlier Identifier of a target protein from the Therapeutic Target Database (TTD). TTDS[0-9]+ - @@ -19150,7 +18306,6 @@ A unique identifier of a type or group of cells. Cell type ID beta12orEarlier - @@ -19166,7 +18321,6 @@ A unique identifier of a neuron from the NeuronDB database. beta12orEarlier [0-9]+ - @@ -19182,7 +18336,6 @@ [a-zA-Z_0-9]+ A unique identifier of a neuron from the NeuroMorpho database. beta12orEarlier - @@ -19199,7 +18352,6 @@ [0-9]+ ChemIDplus ID Identifier of a chemical from the ChemIDplus database. - @@ -19215,7 +18367,6 @@ SMP[0-9]{5} Identifier of a pathway from the Small Molecule Pathway Database (SMPDB). beta12orEarlier - @@ -19231,7 +18382,6 @@ beta12orEarlier [0-9]+ Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology. - @@ -19247,7 +18397,6 @@ Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database. T3D[0-9]+ beta12orEarlier - @@ -19263,18 +18412,17 @@ - + - + Identifier of a carbohydrate. beta12orEarlier - @@ -19290,7 +18438,6 @@ [0-9]+ beta12orEarlier Identifier of an entry from the GlycomeDB database. - @@ -19306,7 +18453,6 @@ Identifier of an entry from the LipidBank database. [a-zA-Z_0-9]+[0-9]+ beta12orEarlier - @@ -19322,7 +18468,6 @@ Identifier of a conserved domain from the Conserved Domain Database. cd[0-9]{5} beta12orEarlier - @@ -19339,7 +18484,6 @@ An identifier of an entry from the MMDB database. beta12orEarlier [0-9]{1,5} - @@ -19355,7 +18499,6 @@ [0-9]+ beta12orEarlier Unique identifier of an entry from the iRefIndex database of protein-protein interactions. - @@ -19371,7 +18514,6 @@ beta12orEarlier [0-9]+ Unique identifier of an entry from the ModelDB database. - @@ -19387,7 +18529,6 @@ beta12orEarlier Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS). [0-9]+ - @@ -19866,7 +19007,6 @@ Identifier of a protein domain (or other node) from the CATH database. beta12orEarlier - @@ -19882,7 +19022,6 @@ 2.10.10.10 A code number identifying a family from the CATH database. beta12orEarlier - @@ -19898,7 +19037,6 @@ CAZy ID beta12orEarlier Identifier of an enzyme from the CAZy enzymes database. - @@ -19915,7 +19053,6 @@ 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 - @@ -19932,7 +19069,6 @@ beta12orEarlier [0-9]{7}|GO:[0-9]{7} An identifier of a 'cellular compartment' concept from the Gene Ontology. - @@ -19947,7 +19083,6 @@ beta12orEarlier Name of a chromosome as used in the BioCyc database. - @@ -19962,7 +19097,6 @@ An identifier of a gene expression profile from the CleanEx database. beta12orEarlier - @@ -19977,7 +19111,6 @@ An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database. beta12orEarlier - @@ -19992,7 +19125,6 @@ beta12orEarlier An informative report of general information concerning a genome as a whole. - @@ -20007,7 +19139,6 @@ Unique identifier for a protein complex from the CORUM database. CORUM complex ID beta12orEarlier - @@ -20022,7 +19153,6 @@ Unique identifier of a position-specific scoring matrix from the CDD database. beta12orEarlier - @@ -20038,7 +19168,6 @@ Unique identifier for a protein from the CuticleDB database. beta12orEarlier CuticleDB ID - @@ -20053,7 +19182,6 @@ beta12orEarlier Identifier of a predicted transcription factor from the DBD database. - @@ -20074,7 +19202,6 @@ General annotation on an oligonucleotide probe. beta12orEarlier - @@ -20089,7 +19216,6 @@ beta12orEarlier Identifier of an oligonucleotide from a database. - @@ -20104,7 +19230,6 @@ beta12orEarlier Identifier of an oligonucleotide probe from the dbProbe database. - @@ -20119,7 +19244,6 @@ Physicochemical property data for one or more dinucleotides. beta12orEarlier - @@ -20133,7 +19257,6 @@ Identifier of an dinucleotide property from the DiProDB database. beta12orEarlier - @@ -20149,7 +19272,6 @@ Protein structure report (disordered structure) An informative report about disordered structure in a protein. beta12orEarlier - @@ -20164,7 +19286,6 @@ Unique identifier for a protein from the DisProt database. beta12orEarlier DisProt ID - @@ -20197,7 +19318,6 @@ Unique identifier for a gene transcript from the Ensembl database. Transcript ID (Ensembl) beta12orEarlier - @@ -20229,7 +19349,6 @@ Moby:GeneAccessionList An identifier of a promoter of a gene that is catalogued in a database. beta12orEarlier - @@ -20244,7 +19363,6 @@ beta12orEarlier Identifier of an EST sequence. - @@ -20259,7 +19377,6 @@ Identifier of an EST sequence from the COGEME database. beta12orEarlier - @@ -20275,7 +19392,6 @@ beta12orEarlier A unisequence is a single sequence assembled from ESTs. Identifier of a unisequence from the COGEME database. - @@ -20291,7 +19407,6 @@ Accession number of an entry (family) from the TIGRFam database. beta12orEarlier GeneFarm family ID - @@ -20306,7 +19421,6 @@ The name of a family of organism. beta12orEarlier - @@ -20367,7 +19481,6 @@ 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 - @@ -20383,7 +19496,6 @@ 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. - @@ -20398,7 +19510,6 @@ beta12orEarlier A unique identifier of gene in the Xenbase database. - @@ -20413,7 +19524,6 @@ A unique identifier of gene in the Genolist database. beta12orEarlier - @@ -20445,7 +19555,6 @@ Identifier of an entry (promoter) from the ABS database. beta12orEarlier ABS identifier - @@ -20460,7 +19569,6 @@ beta12orEarlier Identifier of a transcription factor from the AraC-XylS database. - @@ -20490,7 +19598,6 @@ Identifier of a locus from the PseudoCAP database. beta12orEarlier - @@ -20505,7 +19612,6 @@ Identifier of a locus from the UTR database. beta12orEarlier - @@ -20520,7 +19626,6 @@ beta12orEarlier Unique identifier of a monosaccharide from the MonosaccharideDB database. - @@ -20565,7 +19670,6 @@ beta12orEarlier An identifier of a particular genome. - @@ -20580,7 +19684,6 @@ An identifier of a particular genome. beta12orEarlier - @@ -20596,7 +19699,6 @@ Identifier of an entry from the GlycosciencesDB database. beta12orEarlier [0-9]+ - @@ -20611,7 +19713,6 @@ A conformational energy map of the glycosidic linkages in a carbohydrate molecule. beta12orEarlier - @@ -20627,7 +19728,6 @@ beta12orEarlier An informative report on an intron in a nucleotide sequences. Nucleic acid features (intron) - @@ -20642,7 +19742,6 @@ beta12orEarlier The name of a transcription factor. - @@ -20657,7 +19756,6 @@ beta12orEarlier Identifier of a membrane transport proteins from the transport classification database (TCDB). - @@ -20673,7 +19771,6 @@ PF[0-9]{5} Name of a domain from the Pfam database. beta12orEarlier - @@ -20689,7 +19786,6 @@ Accession number of a Pfam clan. CL[0-9]{4} beta12orEarlier - @@ -20705,7 +19801,6 @@ Identifier for a gene from the VectorBase database. beta12orEarlier VectorBase ID - @@ -20720,7 +19815,6 @@ beta12orEarlier Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs. - @@ -20742,7 +19836,6 @@ beta12orEarlier Sequence motif metadata Data 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. - @@ -20772,7 +19865,6 @@ beta12orEarlier Official name of a protein as used in the UniProt database. - @@ -20803,7 +19895,6 @@ beta12orEarlier Name of a protein family from the HAMAP database. - @@ -20818,7 +19909,6 @@ beta12orEarlier Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance. - @@ -20854,7 +19944,6 @@ beta12orEarlier Identifier of a RNA transcript. - @@ -20869,7 +19958,6 @@ beta12orEarlier Identifier of an RNA transcript from the H-InvDB database. - @@ -20884,7 +19972,6 @@ beta12orEarlier A unique identifier of gene cluster in the H-InvDB database. - @@ -20899,7 +19986,6 @@ Identifier of a antibody from the HPA database. beta12orEarlier - @@ -20914,7 +20000,6 @@ beta12orEarlier Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database. - @@ -20929,7 +20014,6 @@ beta12orEarlier A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI). - @@ -20944,7 +20028,6 @@ The name of a kinase protein. beta12orEarlier - @@ -20960,7 +20043,6 @@ beta12orEarlier Identifier of a physical entity from the ConsensusPathDB database. - @@ -20976,7 +20058,6 @@ Name of a physical entity from the ConsensusPathDB database. beta12orEarlier - @@ -20991,7 +20072,6 @@ beta12orEarlier The number of a strain of algae and protozoa from the CCAP database. - @@ -21007,7 +20087,6 @@ An identifier of stock from a catalogue of biological resources. beta12orEarlier - @@ -21022,7 +20101,6 @@ A stock number from The Arabidopsis information resource (TAIR). beta12orEarlier - @@ -21037,7 +20115,6 @@ Identifier of an entry from the RNA editing database (REDIdb). beta12orEarlier - @@ -21052,7 +20129,6 @@ beta12orEarlier Name of a domain from the SMART database. - @@ -21068,7 +20144,6 @@ Accession number of an entry (family) from the PANTHER database. Panther family ID beta12orEarlier - @@ -21084,7 +20159,6 @@ 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 - @@ -21100,7 +20174,6 @@ An accession of annotation on a (group of) viruses (catalogued in a database). beta12orEarlier - @@ -21115,7 +20188,6 @@ beta12orEarlier An identifier of a genome project assigned by NCBI. - @@ -21130,7 +20202,6 @@ beta12orEarlier A unique identifier of a whole genome assigned by the NCBI. - @@ -21151,7 +20222,6 @@ beta12orEarlier 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. - @@ -21166,7 +20236,6 @@ Unique identifier for a membrane protein from the TopDB database. TopDB ID beta12orEarlier - @@ -21182,7 +20251,6 @@ beta12orEarlier Identifier of a two-dimensional (protein) gel. Gel identifier - @@ -21198,7 +20266,6 @@ Name of a reference map gel from the SWISS-2DPAGE database. beta12orEarlier - @@ -21214,7 +20281,6 @@ Unique identifier for a peroxidase protein from the PeroxiBase database. beta12orEarlier PeroxiBase ID - @@ -21229,7 +20295,6 @@ Identifier of an entry from the SISYPHUS database of tertiary structure alignments. beta12orEarlier - @@ -21245,7 +20310,6 @@ Accession of an open reading frame (catalogued in a database). beta12orEarlier - @@ -21260,7 +20324,6 @@ beta12orEarlier An identifier of an open reading frame. - @@ -21275,7 +20338,6 @@ beta12orEarlier Identifier of an entry from the GlycosciencesDB database. - @@ -21291,7 +20353,6 @@ Unique identifier for a ligand-gated ion channel protein from the LGICdb database. LGICdb ID beta12orEarlier - @@ -21306,7 +20367,6 @@ Identifier of an EST sequence from the MaizeDB database. beta12orEarlier - @@ -21321,7 +20381,6 @@ A unique identifier of gene in the MfunGD database. beta12orEarlier - @@ -21342,7 +20401,6 @@ An identifier of a disease from the Orpha database. beta12orEarlier - @@ -21357,7 +20415,6 @@ Unique identifier for a protein from the EcID database. beta12orEarlier - @@ -21373,7 +20430,6 @@ beta12orEarlier A unique identifier of a cDNA molecule catalogued in the RefSeq database. - @@ -21388,7 +20444,6 @@ Unique identifier for a cone snail toxin protein from the ConoServer database. beta12orEarlier - @@ -21403,7 +20458,6 @@ beta12orEarlier Identifier of a GeneSNP database entry. - @@ -21419,18 +20473,17 @@ - + - + beta12orEarlier Identifier of a lipid. - @@ -21474,7 +20527,6 @@ VBASE2 ID beta12orEarlier Identifier for a gene from the VBASE2 database. - @@ -21490,7 +20542,6 @@ A unique identifier for a virus from the DPVweb database. beta12orEarlier DPVweb virus ID - @@ -21506,7 +20557,6 @@ [0-9]+ Identifier of a pathway from the BioSystems pathway database. beta12orEarlier - @@ -21536,7 +20586,6 @@ An abstract of a scientific article. beta12orEarlier - @@ -21550,7 +20599,6 @@ 3D coordinate and associated data for a lipid structure. beta12orEarlier - @@ -21564,7 +20612,6 @@ 3D coordinate and associated data for the (3D) structure of a drug. beta12orEarlier - @@ -21578,7 +20625,6 @@ beta12orEarlier 3D coordinate and associated data for the (3D) structure of a toxin. - @@ -21593,7 +20639,6 @@ 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. beta12orEarlier - @@ -21607,7 +20652,6 @@ beta12orEarlier A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity. - @@ -21621,7 +20665,6 @@ beta12orEarlier Distances (values representing similarity) between a group of molecular structures. - @@ -21651,7 +20694,6 @@ A concept from a biological ontology. This includes any fields from the concept definition such as concept name, definition, comments and so on. beta12orEarlier - @@ -21665,7 +20707,6 @@ beta12orEarlier A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences. - @@ -21681,7 +20722,6 @@ beta12orEarlier Experiment annotation (Northern blot) General annotation on a Northern Blot experiment. - @@ -21699,7 +20739,6 @@ VNTR annotation beta12orEarlier Annotation on a variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. - @@ -21716,7 +20755,6 @@ 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 Annotation on a microsatellite polymorphism in a DNA sequence. - @@ -21733,7 +20771,6 @@ Nucleic acid features (RFLP) RFLP annotation beta12orEarlier - @@ -21749,7 +20786,6 @@ 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. - @@ -21763,7 +20799,6 @@ beta12orEarlier A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data. - @@ -21777,7 +20812,6 @@ Gene frequencies data that may be read during phylogenetic tree calculation. beta12orEarlier - @@ -21821,7 +20855,6 @@ 3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another. beta12orEarlier - @@ -21835,7 +20868,6 @@ 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 - @@ -21849,7 +20881,6 @@ Annotation on or information derived from one or more specific lipid 3D structure(s). beta12orEarlier - @@ -21943,7 +20974,6 @@ beta12orEarlier Nucleic acid features (polymorphism) Polymorphism annotation - @@ -21960,7 +20990,6 @@ Protein sequence record beta12orEarlier A protein sequence and associated metadata. - @@ -21977,7 +21006,6 @@ beta12orEarlier A nucleic acid sequence and associated metadata. Nucleotide sequence record - @@ -21994,7 +21022,6 @@ A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. SO:2000061 Sequence record full (protein) - @@ -22012,7 +21039,6 @@ beta12orEarlier A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. Sequence record full (nucleic acid) - @@ -22027,7 +21053,6 @@ Accession of a mathematical model, typically an entry from a database. beta12orEarlier - @@ -22043,7 +21068,6 @@ beta12orEarlier The name of a type or group of cells. - @@ -22059,7 +21083,6 @@ Accession of a type or group of cells (catalogued in a database). beta12orEarlier - @@ -22077,7 +21100,6 @@ beta12orEarlier Accession of an entry from a database of chemicals. Small molecule accession - @@ -22093,7 +21115,6 @@ beta12orEarlier Accession of a drug. - @@ -22109,7 +21130,6 @@ beta12orEarlier Name of a toxin. - @@ -22125,7 +21145,6 @@ Accession of a toxin (catalogued in a database). beta12orEarlier - @@ -22141,7 +21160,6 @@ beta12orEarlier Accession of a monosaccharide (catalogued in a database). - @@ -22157,7 +21175,6 @@ Common name of a drug. beta12orEarlier - @@ -22173,7 +21190,6 @@ beta12orEarlier Accession of an entry from a database of carbohydrates. - @@ -22189,7 +21205,6 @@ beta12orEarlier Accession of a specific molecule (catalogued in a database). - @@ -22205,7 +21220,6 @@ Accession of a data definition (catalogued in a database). beta12orEarlier - @@ -22221,7 +21235,6 @@ beta12orEarlier An accession of a particular genome (in a database). - @@ -22237,7 +21250,6 @@ beta12orEarlier An accession of a map of a molecular sequence (deposited in a database). - @@ -22253,7 +21265,6 @@ Accession of an entry from a database of lipids. beta12orEarlier - @@ -22269,7 +21280,6 @@ Accession of a peptide deposited in a database. beta12orEarlier - @@ -22285,7 +21295,6 @@ Accession of a protein deposited in a database. beta12orEarlier - @@ -22301,7 +21310,6 @@ beta12orEarlier An accession of annotation on a (group of) organisms (catalogued in a database). - @@ -22324,7 +21332,6 @@ Moby:OccurrenceRecord Moby:OrganismsShortName Moby:Organism_Name - @@ -22340,7 +21347,6 @@ Accession of a protein family (that is deposited in a database). beta12orEarlier - @@ -22357,7 +21363,6 @@ Accession of an entry from a database of transcription factors or binding sites. beta12orEarlier - @@ -22379,7 +21384,6 @@ Identifier of a strain of an organism variant, typically a plant, virus or bacterium. beta12orEarlier - @@ -22394,7 +21398,6 @@ beta12orEarlier An accession of annotation on a (group of) viruses (catalogued in a database). - @@ -22409,7 +21412,6 @@ Metadata on sequence features. beta12orEarlier - @@ -22423,7 +21425,6 @@ Identifier of a Gramene database entry. beta12orEarlier - @@ -22441,7 +21442,6 @@ DDBJ identifier DDBJ accession number beta12orEarlier - @@ -22456,7 +21456,6 @@ An identifier of an entity from the ConsensusPathDB database. beta12orEarlier - @@ -22472,7 +21471,6 @@ Data concerning, extracted from, or derived from the analysis of molecular sequence(s). beta12orEarlier This is a broad data type and is used a placeholder for other, more specific types. - @@ -22518,7 +21516,6 @@ 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. - @@ -22532,7 +21529,6 @@ beta12orEarlier An informative report about the properties or features of one or more protein secondary structures. - @@ -22546,7 +21542,6 @@ beta12orEarlier A Hopp and Woods plot of predicted antigenicity of a peptide or protein. - @@ -22561,7 +21556,6 @@ 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. - @@ -22576,7 +21570,6 @@ 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). - @@ -22592,7 +21585,6 @@ beta12orEarlier Plots melting temperature versus base position. A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). - @@ -22614,7 +21606,6 @@ A report typically including a map (diagram) of a gene regulatory network. Gene regulation network report Pathway or network (gene regulation) - @@ -22631,7 +21622,6 @@ 2D PAGE gel annotation 2D PAGE image report An informative report on a two-dimensional (2D PAGE) gel. - @@ -22645,7 +21635,6 @@ 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 - @@ -22675,12 +21664,11 @@ Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type. beta12orEarlier + http://semanticscience.org/resource/SIO_000079" Image data - + http://semanticscience.org/resource/SIO_000081" - - @@ -22693,7 +21681,6 @@ beta12orEarlier Image of a molecular sequence, possibly with sequence features or properties shown. - @@ -22708,7 +21695,6 @@ beta12orEarlier A report on protein properties concerning hydropathy. Protein hydropathy report - @@ -22770,7 +21756,6 @@ Raw sequence (protein) beta12orEarlier Raw protein sequence - @@ -22788,7 +21773,6 @@ Nucleotide sequence (raw) beta12orEarlier Nucleic acid raw sequence - @@ -22800,12 +21784,11 @@ Protein sequence + http://purl.org/biotop/biotop.owl#AminoAcidSequenceInformation" beta12orEarlier One or more protein sequences, possibly with associated annotation. - - @@ -22818,12 +21801,11 @@ Nucleic acid sequences Nucleotide sequences Nucleotide sequence + http://purl.org/biotop/biotop.owl#NucleotideSequenceInformation" beta12orEarlier One or more nucleic acid sequences, possibly with associated annotation. - - @@ -22838,7 +21820,6 @@ beta12orEarlier This is a broad data type and is used a placeholder for other, more specific types. Enzyme kinetics annotation - @@ -22853,7 +21834,6 @@ Data concerning small peptides. Peptide data beta12orEarlier - @@ -22882,7 +21862,6 @@ 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. - @@ -22934,7 +21913,6 @@ An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation. beta12orEarlier - @@ -22950,7 +21928,6 @@ Nucleic acid thermodynamic property A thermodynamic or kinetic property of a nucleic acid molecule. Nucleic acid property (thermodynamic or kinetic) - @@ -22995,7 +21972,6 @@ beta12orEarlier A report on key residues involved in protein folding. - @@ -23010,7 +21986,6 @@ beta12orEarlier Torsion angle data for a protein structure. Torsion angle data - @@ -23026,7 +22001,6 @@ Structure image (protein) beta12orEarlier An image of protein structure. - @@ -23040,7 +22014,6 @@ beta12orEarlier Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted. - @@ -23055,11 +22028,10 @@ 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 - Genome annotation track beta12orEarlier - @@ -23087,7 +22059,6 @@ P43353|Q7M1G0|Q9C199|A5A6J6 beta12orEarlier UniProtKB accession number - @@ -23105,7 +22076,6 @@ 16 [1-9][0-9]? Identifier of a genetic code in the NCBI list of genetic codes. - @@ -23126,7 +22096,6 @@ beta12orEarlier Identifier of a concept in an ontology of biological or bioinformatics concepts and relations. - @@ -23179,7 +22148,6 @@ 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. - @@ -23194,7 +22162,6 @@ 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 - @@ -23231,7 +22198,6 @@ Name or other identifier of molecular sequence feature(s). beta13 - @@ -23252,7 +22218,6 @@ An identifier of a molecular tertiary structure, typically an entry from a structure database. beta13 - @@ -23273,7 +22238,6 @@ beta13 An identifier of an array of numerical values, such as a comparison matrix. - @@ -23289,7 +22253,6 @@ Sequence property (protein composition) A report (typically a table) on character or word composition / frequency of protein sequence(s). beta13 - @@ -23305,7 +22268,6 @@ beta13 A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s). Sequence property (nucleic acid composition) - @@ -23335,7 +22297,6 @@ Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service. CAS registry number beta13 - @@ -23350,7 +22311,6 @@ 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). - @@ -23366,7 +22326,6 @@ 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 - @@ -23396,7 +22355,6 @@ beta13 Metadata concerning the software, hardware or other aspects of a computer system. - @@ -23411,7 +22369,6 @@ beta13 A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. - @@ -23434,7 +22391,6 @@ Experimental measurement data Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware. beta13 - @@ -23450,7 +22406,6 @@ Such data as found in Affymetrix CEL or GPR files. Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment. beta13 - @@ -23461,7 +22416,6 @@ Processed microarray data - @@ -23475,7 +22429,6 @@ Microarray probe set data Gene annotation (expression) Data generated from processing and analysis of probe set data from a microarray experiment. - @@ -23485,14 +22438,14 @@ - Normalised microarray data - + 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. - Gene expression matrix - @@ -23507,7 +22460,6 @@ beta13 This might include compound and dose in a dose response experiment. Annotation on a biological sample, for example experimental factors and their values. - @@ -23522,7 +22474,6 @@ beta13 Annotation on the array itself used in a microarray experiment. This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc. - @@ -23537,7 +22488,6 @@ Annotation on laboratory and/or data processing protocols used in an microarray experiment. beta13 This might describe e.g. the normalisation methods used to process the raw data. - @@ -23551,7 +22501,6 @@ beta13 Data concerning the hybridisations measured during a microarray experiment. - @@ -23572,7 +22521,6 @@ Summary of topological domains such as cytoplasmic regions in a protein. beta13 Protein topological domains - @@ -23601,7 +22549,6 @@ A report on the protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. beta13 - @@ -23631,7 +22578,6 @@ Nucleic acid features (expression signal) A report on regions within a nucleic acid sequence containing a signal that alters a biological function. beta13 - @@ -23647,7 +22593,6 @@ This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). beta13 Nucleic acid features (binding) - @@ -23662,7 +22607,6 @@ beta13 A report on 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. - @@ -23678,7 +22622,6 @@ Nucleic acid features (replication and recombination) A report on regions within a nucleic acid sequence that are involved in DNA replcication or recombination. beta13 - @@ -23691,13 +22634,12 @@ Nucleic acid structure report + beta13 Quadruplexes (report) Nucleic acid features (structure) d-loop (report) - A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures. - beta13 Stem loop (report) - + A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures. @@ -23711,7 +22653,6 @@ beta13 Location of short repetitive subsequences (repeat sequences) in a protein sequence. - @@ -23725,7 +22666,6 @@ beta13 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences. - @@ -23739,7 +22679,6 @@ beta13 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences. - @@ -23793,7 +22732,6 @@ 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). - @@ -23809,7 +22747,6 @@ 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. A report on a coding sequence for a signal or transit peptide. - @@ -23832,7 +22769,6 @@ Features concerning non-coding or functional RNA molecules, including tRNA and rRNA. ncRNA features Nucleic acid features (non-coding RNA) - @@ -23864,7 +22800,6 @@ A report on sequence tagged sites (STS) in nucleic acid sequences. 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. Nucleic acid features (STS) - @@ -23985,7 +22920,6 @@ beta13 Experiment annotation (mass spectrometry) Experiment report (mass spectrometry) - @@ -24003,10 +22937,9 @@ 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. - beta13 - @@ -24020,7 +22953,6 @@ An image of a protein. beta13 - @@ -24034,7 +22966,6 @@ beta13 An alignment of protein sequences and/or structures. - @@ -24056,7 +22987,6 @@ Experiment metadata (NGS) 1.0 NGS experiment metadata - @@ -24072,7 +23002,6 @@ 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. - @@ -24087,7 +23016,6 @@ 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 - @@ -24103,7 +23031,6 @@ 1.1 Genome-wide association study experiment metadata Experiment metadata (GWAS) - @@ -24118,7 +23045,6 @@ 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 - @@ -24132,11 +23058,10 @@ beta12orEarlier - CL_[0-9]{7} 1.2 + CL_[0-9]{7} Cell type ontology concept ID. CL ID - @@ -24151,7 +23076,6 @@ Mathematical model of a network, that contains biochemical kinetics. 1.2 - @@ -24164,12 +23088,11 @@ COSMIC ID 1.3 - cosmic identifier - COSMIC identifier cosmic id + cosmic identifier Identifier of a COSMIC database entry. cosmic ID - + COSMIC identifier @@ -24182,13 +23105,12 @@ HGMD ID - hgmd identifier - Identifier of a HGMD database entry. - hgmd id HGMD identifier + hgmd id beta12orEarlier + hgmd identifier hgmd ID - + Identifier of a HGMD database entry. @@ -24204,7 +23126,6 @@ 1.3 Unique identifier of sequence assembly. Sequence assembly version - @@ -24252,7 +23173,6 @@ Unique identifier for a gene tree from the Ensembl database. Ensembl ID (gene tree) ENSGT00390000003602 - @@ -24267,7 +23187,6 @@ A phylogenetic tree that is an estimate of the character's phylogeny. 1.3 - @@ -24281,7 +23200,6 @@ 1.3 A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled. - @@ -24303,7 +23221,6 @@ Name or other identifier of an entry from a biosample database. Sample accession 1.3 - @@ -24319,7 +23236,6 @@ 1.3 Identifier of an object from the MGI database. - @@ -24337,7 +23253,6 @@ Phenotypes Name of a phenotype. 1.3 - @@ -24404,13 +23319,12 @@ Raw biological or biomedical image generated by some experimental technique. Image data + http://semanticscience.org/resource/SIO_000081" beta12orEarlier Amino acid data 1.5 - - @@ -24423,7 +23337,6 @@ 1.5 Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all carbohydrates. Carbohydrate data - @@ -24439,7 +23352,6 @@ Information about a proteomics experiment. 1.5 Experiment annotation (proteomics experiment) - @@ -24455,7 +23367,6 @@ 1.5 Experiment annotation (RNAi experiment) Information about an RNAi experiment. - @@ -24471,24 +23382,129 @@ Experiment report (simulation) 1.5 Information about a biological computational model experiment (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. - + + + + MRI image + + + + + + + + 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 + + Nuclear magnetic resonance imaging image + + Magnetic resonance tomography image + 1.7 + MRT image + + + + + + + + + + Cell migration track image + + + + + + + + An image from a cell migration track assay. + 1.7 + + + + + + + + + + Rate of association + + Rate of association of a protein with another protein or some other molecule. + 1.7 + kon + + + + + + + + + + Gene order + + 1.7 + Multiple gene identifiers in a specific order. + Such data are often used for genome rearrangement tools and phylogenetic tree labeling. + + + + + + + + + + Spectrum + + Spectra + The spectrum of frequencies of electromagnetic radiation emitted from a molecule as a result of some spectroscopy experiment. + 1.7 + + + + + + + + + + NMR spectrum + + + + + + + + NMR spectra + 1.7 + Spectral information for a molecule from a nuclear magnetic resonance experiment. + + + + + + SMILES - Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation. beta12orEarlier + Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation. - @@ -24505,7 +23521,6 @@ beta12orEarlier Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation. - @@ -24521,7 +23536,6 @@ 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. - @@ -24537,7 +23551,6 @@ 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. - @@ -24551,7 +23564,6 @@ beta12orEarlier SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation. - @@ -24566,7 +23578,6 @@ Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters. beta12orEarlier - @@ -24581,9 +23592,8 @@ 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. - - @@ -24596,11 +23606,10 @@ 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. - - @@ -24615,7 +23624,6 @@ Alphabet for the consensus of two or more molecular sequences. beta12orEarlier - @@ -24630,7 +23638,6 @@ Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters. beta12orEarlier - @@ -24645,7 +23652,6 @@ Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters . beta12orEarlier - @@ -24658,9 +23664,8 @@ 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 - - @@ -24672,10 +23677,9 @@ rna + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#RNA_sequence" beta12orEarlier Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters. - - @@ -24690,7 +23694,6 @@ beta12orEarlier Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters. - @@ -24705,7 +23708,6 @@ beta12orEarlier Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters. - @@ -24720,7 +23722,6 @@ beta12orEarlier Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters. - @@ -24735,7 +23736,6 @@ beta12orEarlier Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters. - @@ -24750,7 +23750,6 @@ Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters. beta12orEarlier - @@ -24765,7 +23764,6 @@ Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters. beta12orEarlier - @@ -24812,7 +23810,6 @@ Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database. Feature location beta12orEarlier - @@ -24827,7 +23824,6 @@ beta12orEarlier Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program). - @@ -24842,7 +23838,6 @@ Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program). beta12orEarlier - @@ -24857,7 +23852,6 @@ beta12orEarlier Report format for tandem repeats in a sequence (an EMBOSS report format). - @@ -24872,7 +23866,6 @@ Format of a report on exon-intron structure generated by EMBOSS est2genome. beta12orEarlier - @@ -24887,7 +23880,6 @@ beta12orEarlier Report format for restriction enzyme recognition sites used by EMBOSS restrict program. - @@ -24902,7 +23894,6 @@ Report format for restriction enzyme recognition sites used by EMBOSS restover program. beta12orEarlier - @@ -24917,7 +23908,6 @@ Report format for restriction enzyme recognition sites used by REBASE database. beta12orEarlier - @@ -24933,7 +23923,6 @@ 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. - @@ -24949,7 +23938,6 @@ This includes score data, alignment data and summary table. beta12orEarlier Format of results of a sequence database search using some variant of BLAST. - @@ -24964,7 +23952,6 @@ Format of results of a sequence database search using some variant of MSPCrunch. beta12orEarlier - @@ -24979,7 +23966,6 @@ Format of results of a sequence database search using some variant of Smith Waterman. beta12orEarlier - @@ -24995,7 +23981,6 @@ 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. - @@ -25011,7 +23996,6 @@ 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 - @@ -25026,7 +24010,6 @@ beta12orEarlier Results format for searches of the InterPro database. - @@ -25041,7 +24024,6 @@ 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. - @@ -25056,7 +24038,6 @@ 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. - @@ -25071,7 +24052,6 @@ Dirichlet distribution HMMER format. beta12orEarlier - @@ -25086,7 +24066,6 @@ Dirichlet distribution MEME format. beta12orEarlier - @@ -25101,7 +24080,6 @@ beta12orEarlier Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model. - @@ -25116,7 +24094,6 @@ beta12orEarlier Format of a regular expression pattern from the Prosite database. - @@ -25131,7 +24108,6 @@ beta12orEarlier Format of an EMBOSS sequence pattern. - @@ -25146,7 +24122,6 @@ beta12orEarlier A motif in the format generated by the MEME program. - @@ -25161,7 +24136,6 @@ beta12orEarlier Sequence profile (sequence classifier) format used in the PROSITE database. - @@ -25176,7 +24150,6 @@ A profile (sequence classifier) in the format used in the JASPAR database. beta12orEarlier - @@ -25191,7 +24164,6 @@ beta12orEarlier Format of the model of random sequences used by MEME. - @@ -25206,7 +24178,6 @@ beta12orEarlier Format of a hidden Markov model representation used by the HMMER package. - @@ -25222,7 +24193,6 @@ FASTA-style format for multiple sequences aligned by HMMER package to an HMM. beta12orEarlier - @@ -25237,7 +24207,6 @@ beta12orEarlier Format of multiple sequences aligned by DIALIGN package. - @@ -25253,7 +24222,6 @@ 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. - @@ -25268,7 +24236,6 @@ Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package. beta12orEarlier - @@ -25283,7 +24250,6 @@ beta12orEarlier Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database. - @@ -25298,7 +24264,6 @@ beta12orEarlier Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database. - @@ -25314,7 +24279,6 @@ 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). - @@ -25329,7 +24293,6 @@ Dendrogram (tree file) format generated by ClustalW. beta12orEarlier - @@ -25344,7 +24307,6 @@ beta12orEarlier Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted. - @@ -25359,7 +24321,6 @@ PHYLIP file format for continuous quantitative character data. beta12orEarlier - @@ -25389,7 +24350,6 @@ PHYLIP file format for phylogenetics character frequency data. beta12orEarlier - @@ -25404,7 +24364,6 @@ beta12orEarlier Format of PHYLIP discrete states data. - @@ -25419,7 +24378,6 @@ Format of PHYLIP cliques data. beta12orEarlier - @@ -25434,7 +24392,6 @@ beta12orEarlier Phylogenetic tree data format used by the PHYLIP program. - @@ -25449,7 +24406,6 @@ The format of an entry from the TreeBASE database of phylogenetic data. beta12orEarlier - @@ -25464,7 +24420,6 @@ The format of an entry from the TreeFam database of phylogenetic data. beta12orEarlier - @@ -25479,7 +24434,6 @@ beta12orEarlier Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package. - @@ -25495,7 +24449,6 @@ 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 - @@ -25510,7 +24463,6 @@ beta12orEarlier Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins). - @@ -25527,7 +24479,6 @@ Vienna RNA secondary structure format Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server. beta12orEarlier - @@ -25542,7 +24493,6 @@ beta12orEarlier Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server. - @@ -25563,7 +24513,6 @@ Format of an entry (or part of an entry) from the PDB database. PDB entry format beta12orEarlier - @@ -25579,7 +24528,6 @@ Entry format of PDB database in PDB format. beta12orEarlier PDB - @@ -25596,7 +24544,6 @@ beta12orEarlier Entry format of PDB database in mmCIF format. Chemical MIME (http://www.ch.ic.ac.uk/chemime): chemical/x-mmcif - @@ -25611,7 +24558,6 @@ beta12orEarlier Entry format of PDB database in PDBML (XML) format. - @@ -25640,7 +24586,6 @@ beta12orEarlier Amino acid index format used by the AAindex database. - @@ -25747,7 +24692,6 @@ 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). - @@ -25763,7 +24707,6 @@ 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 - @@ -26006,7 +24949,6 @@ 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 - @@ -26351,7 +25293,6 @@ beta12orEarlier Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program. - @@ -26366,7 +25307,6 @@ beta12orEarlier A format of raw sequence read data from an Applied Biosystems sequencing machine. - @@ -26381,7 +25321,6 @@ beta12orEarlier Format of MIRA sequence trace information file. - @@ -26396,7 +25335,6 @@ beta12orEarlier Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata. - @@ -26413,7 +25351,6 @@ beta12orEarlier Sequence assembly project file EXP format. - @@ -26428,7 +25365,6 @@ beta12orEarlier Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata. - @@ -26445,7 +25381,6 @@ PHD sequence trace format to store serialised chromatogram data (reads). beta12orEarlier - @@ -26469,7 +25404,6 @@ Affymetrix image data file format Format of Affymetrix data file of raw image data. beta12orEarlier - @@ -26491,7 +25425,6 @@ Format of Affymetrix data file of information about (raw) expression levels of the individual probes. Affymetrix probe raw data format beta12orEarlier - @@ -26506,7 +25439,6 @@ beta12orEarlier Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering. - @@ -26537,7 +25469,6 @@ beta12orEarlier Affymetrix experimental conditions data file format Affymetrix data file format for information about experimental conditions and protocols. - @@ -26559,7 +25490,6 @@ Format of Affymetrix data file of information about (normalised) expression levels of the individual probes. beta12orEarlier Affymetrix probe normalised data format - @@ -26724,7 +25654,6 @@ beta12orEarlier Format of Taverna workflows. - @@ -26876,7 +25805,6 @@ beta12orEarlier The format of an entry from the HET group dictionary (HET groups from PDB files). - @@ -26906,7 +25834,6 @@ Format of bibliographic reference as used by the PubMed database. beta12orEarlier - @@ -26922,7 +25849,6 @@ Bibliographic reference information including citation information is included Format for abstracts of scientific articles from the Medline database. beta12orEarlier - @@ -26937,7 +25863,6 @@ CiteXplore 'core' citation format including title, journal, authors and abstract. beta12orEarlier - @@ -26952,7 +25877,6 @@ beta12orEarlier CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references. - @@ -26967,7 +25891,6 @@ Article format of the PubMed Central database. beta12orEarlier - @@ -26982,7 +25905,6 @@ iHOP abstract format. beta12orEarlier - @@ -26998,7 +25920,6 @@ 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. - @@ -27124,7 +26045,6 @@ Map of a plasmid (circular DNA) in PlasMapper TextMap format. beta12orEarlier - @@ -27140,7 +26060,6 @@ Phylogenetic tree Newick (text) format. beta12orEarlier nh - @@ -27155,7 +26074,6 @@ Phylogenetic tree TreeCon (text) format. beta12orEarlier - @@ -27170,7 +26088,6 @@ beta12orEarlier Phylogenetic tree Nexus (text) format. - @@ -27186,46 +26103,33 @@ 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. Data format + http://en.wikipedia.org/wiki/List_of_file_formats" + http://purl.org/biotop/biotop.owl#MachineLanguage" + http://semanticscience.org/resource/SIO_000612" + http://purl.org/biotop/biotop.owl#Quality" + http://www.ifomis.org/bfo/1.1/snap#Quality" + http://en.wikipedia.org/wiki/File_format" A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. - beta12orEarlier + "http://purl.org/dc/elements/1.1/format" + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality" + http://semanticscience.org/resource/SIO_000618" + http://www.ifomis.org/bfo/1.1/snap#Continuant" + http://www.onto-med.de/ontologies/gfo.owl#Symbol_structure" + http://wsio.org/compression_004" + beta12orEarlier + "http://purl.obolibrary.org/obo/IAO_0000098" + http://www.onto-med.de/ontologies/gfo.owl#Perpetuant" Exchange format Data model File format - - - - - - - - - - - - - - - - - + + - GFO 'Perpetuant' is in general broader than format, but it may be seen narrower in the sense of being a concrete individual and in the way of exhibiting presentials. - - - - - - Compression and encoding' defines additional 'formatting' and/or encoding on top of the primary format. - - - - - - Closely related concept focusing on the specification of a data format. + 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 @@ -27233,24 +26137,6 @@ - - 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'.) - - - - - Format can be a quality of a data record. - - - - - - BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the data format. - - - - @@ -27282,7 +26168,6 @@ beta12orEarlier Data format for a molecular sequence record. - @@ -27302,7 +26187,6 @@ Data format for molecular sequence feature information. beta12orEarlier - @@ -27322,7 +26206,6 @@ beta12orEarlier Data format for molecular sequence alignment information. - @@ -27336,7 +26219,6 @@ ACEDB sequence format. beta12orEarlier - @@ -27366,7 +26248,6 @@ beta12orEarlier Codata entry format. - @@ -27380,7 +26261,6 @@ Fasta format variant with database name before ID. beta12orEarlier - @@ -27397,7 +26277,6 @@ EMBL EMBL sequence format EMBL entry format. - @@ -27412,7 +26291,6 @@ beta12orEarlier Staden experiment file format. - @@ -27429,7 +26307,6 @@ FASTA sequence format FASTA format beta12orEarlier - @@ -27441,9 +26318,9 @@ FASTQ + FASTAQ beta12orEarlier FASTQ short read format ignoring quality scores. - @@ -27457,7 +26334,6 @@ beta12orEarlier FASTQ Illumina 1.3 short read format. - @@ -27471,7 +26347,6 @@ beta12orEarlier FASTQ short read format with phred quality. - @@ -27485,7 +26360,6 @@ beta12orEarlier FASTQ Solexa/Illumina 1.0 short read format. - @@ -27500,7 +26374,6 @@ beta12orEarlier Fitch program format. - @@ -27510,12 +26383,13 @@ - gcg + GCG - + + GCG sequence file format. + GCG SSF (single sequence file) file format. beta12orEarlier - GCG sequence format. - + GCG SSF @@ -27530,7 +26404,6 @@ Genbank entry format. beta12orEarlier - @@ -27545,7 +26418,6 @@ Currently identical to refseqp format Genpept protein entry format. beta12orEarlier - @@ -27560,7 +26432,6 @@ beta12orEarlier GFF feature file format with sequence in the header. - @@ -27575,7 +26446,6 @@ beta12orEarlier GFF3 feature file format with sequence. - @@ -27589,7 +26459,6 @@ beta12orEarlier FASTA sequence format including NCBI-style GIs. - @@ -27604,7 +26473,6 @@ Hennig86 output sequence format. beta12orEarlier - @@ -27619,7 +26487,6 @@ beta12orEarlier Intelligenetics sequence format. - @@ -27634,7 +26501,6 @@ Intelligenetics sequence format (strict version). beta12orEarlier - @@ -27649,7 +26515,6 @@ beta12orEarlier Jackknifer interleaved and non-interleaved sequence format. - @@ -27664,7 +26529,6 @@ Mase program sequence format. beta12orEarlier - @@ -27679,7 +26543,6 @@ Mega interleaved and non-interleaved sequence format. beta12orEarlier - @@ -27689,13 +26552,11 @@ - msf - - - + MSF + GCG MSF (multiple sequence file) file format. beta12orEarlier - + GCG MSF @@ -27705,12 +26566,13 @@ - nbrf + nbrf/pir + pir beta12orEarlier + nbrf NBRF/PIR entry sequence format. - @@ -27726,7 +26588,6 @@ Nexus/paup interleaved sequence format. beta12orEarlier - @@ -27743,7 +26604,6 @@ PDB sequence format (ATOM lines). beta12orEarlier pdb format in EMBOSS. - @@ -27760,7 +26620,6 @@ PDB nucleotide sequence format (ATOM lines). pdbnuc format in EMBOSS. beta12orEarlier - @@ -27777,7 +26636,6 @@ beta12orEarlier PDB nucleotide sequence format (SEQRES lines). pdbnucseq format in EMBOSS. - @@ -27794,7 +26652,6 @@ pdbseq format in EMBOSS. beta12orEarlier PDB sequence format (SEQRES lines). - @@ -27808,7 +26665,6 @@ Plain old FASTA sequence format (unspecified format for IDs). beta12orEarlier - @@ -27853,7 +26709,6 @@ Raw sequence format with no non-sequence characters. beta12orEarlier - @@ -27869,7 +26724,6 @@ Currently identical to genpept format Refseq protein entry sequence format. beta12orEarlier - @@ -27899,7 +26753,6 @@ Staden suite sequence format. beta12orEarlier - @@ -27920,7 +26773,6 @@ Stockholm multiple sequence alignment format (used by Pfam and Rfam). - @@ -27935,7 +26787,6 @@ beta12orEarlier DNA strider output sequence format. - @@ -27949,7 +26800,6 @@ UniProtKB entry sequence format. beta12orEarlier - @@ -27964,7 +26814,6 @@ Plain text sequence format (essentially unformatted). beta12orEarlier - @@ -27994,7 +26843,6 @@ beta12orEarlier NCBI ASN.1-based sequence format. - @@ -28010,7 +26858,6 @@ beta12orEarlier DAS sequence (XML) format (any type). das sequence format - @@ -28026,7 +26873,6 @@ The use of this format is deprecated. DAS sequence (XML) format (nucleotide-only). beta12orEarlier - @@ -28041,7 +26887,6 @@ beta12orEarlier EMBOSS debugging trace sequence format of full internal data content. - @@ -28056,7 +26901,6 @@ Jackknifer output sequence non-interleaved format. beta12orEarlier - @@ -28086,7 +26930,6 @@ There are several variants of this. beta12orEarlier NCBI FASTA sequence format with NCBI-style IDs. - @@ -28102,7 +26945,6 @@ beta12orEarlier Nexus/paup non-interleaved sequence format. - @@ -28116,7 +26958,6 @@ General Feature Format (GFF) of sequence features. beta12orEarlier - @@ -28132,7 +26973,6 @@ Generic Feature Format version 3 (GFF3) of sequence features. beta12orEarlier - @@ -28145,13 +26985,13 @@ pir - - + beta12orEarlier PIR feature format. - - - + 1.7 + true + + @@ -28181,7 +27021,6 @@ DASGFF feature das feature DAS GFF (XML) feature format. - @@ -28196,7 +27035,6 @@ beta12orEarlier EMBOSS debugging trace feature format of full internal data content. - @@ -28241,7 +27079,6 @@ ClustalW format for (aligned) sequences. beta12orEarlier - @@ -28256,7 +27093,6 @@ beta12orEarlier EMBOSS alignment format for debugging trace of full internal data content. - @@ -28271,7 +27107,6 @@ Fasta format for (aligned) sequences. beta12orEarlier - @@ -28285,7 +27120,6 @@ Pearson MARKX0 alignment format. beta12orEarlier - @@ -28299,7 +27133,6 @@ beta12orEarlier Pearson MARKX1 alignment format. - @@ -28313,7 +27146,6 @@ Pearson MARKX10 alignment format. beta12orEarlier - @@ -28327,7 +27159,6 @@ Pearson MARKX2 alignment format. beta12orEarlier - @@ -28341,7 +27172,6 @@ Pearson MARKX3 alignment format. beta12orEarlier - @@ -28356,7 +27186,6 @@ beta12orEarlier Alignment format for start and end of matches between sequence pairs. - @@ -28370,7 +27199,6 @@ beta12orEarlier Mega format for (typically aligned) sequences. - @@ -28384,7 +27212,6 @@ beta12orEarlier Mega non-interleaved format for (typically aligned) sequences. - @@ -28443,7 +27270,6 @@ beta12orEarlier EMBOSS simple sequence pair alignment format. - @@ -28453,11 +27279,14 @@ - Phylip format + PHYLIP format Phylip format for (aligned) sequences. + PHYLIP interleaved format + http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format + ph beta12orEarlier - + phy @@ -28467,11 +27296,12 @@ - Phylipnon + phylipnon Phylip non-interleaved format for (aligned) sequences. + PHYLIP sequential format beta12orEarlier - + http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format @@ -28486,7 +27316,6 @@ beta12orEarlier Alignment format for score values for pairs of sequences. - @@ -28502,7 +27331,6 @@ SELEX format for (aligned) sequences. beta12orEarlier - @@ -28517,7 +27345,6 @@ beta12orEarlier EMBOSS simple multiple alignment format. - @@ -28532,7 +27359,6 @@ Simple multiple sequence (alignment) format for SRS. beta12orEarlier - @@ -28547,7 +27373,6 @@ Simple sequence pair (alignment) format for SRS. beta12orEarlier - @@ -28562,7 +27387,6 @@ beta12orEarlier T-Coffee program alignment format. - @@ -28578,7 +27402,6 @@ beta12orEarlier Treecon format for (aligned) sequences. - @@ -28598,7 +27421,6 @@ beta12orEarlier Data format for a phylogenetic tree. - @@ -28618,7 +27440,6 @@ Data format for a biological pathway or network. beta12orEarlier - @@ -28638,7 +27459,6 @@ Data format for a sequence-profile alignment. beta12orEarlier - @@ -28673,7 +27493,6 @@ beta12orEarlier Data format for an amino acid index. - @@ -28694,7 +27513,6 @@ Data format for a full-text scientific article. Literature format beta12orEarlier - @@ -28714,7 +27532,6 @@ Data format for an abstract (report) from text mining. beta12orEarlier - @@ -28734,7 +27551,6 @@ beta12orEarlier Data format for reports on enzyme kinetics. - @@ -28755,7 +27571,6 @@ Format of a report on a chemical compound. Chemical compound annotation format beta12orEarlier - @@ -28775,7 +27590,6 @@ beta12orEarlier Format of a report on a particular locus, gene, gene system or groups of genes. - @@ -28789,7 +27603,6 @@ Format of a workflow. beta12orEarlier - @@ -28803,7 +27616,6 @@ Data format for a molecular tertiary structure. beta12orEarlier - @@ -28838,7 +27650,6 @@ Text format of a chemical formula. beta12orEarlier - @@ -28858,7 +27669,6 @@ Format of raw (unplotted) phylogenetic data. beta12orEarlier - @@ -28878,7 +27688,6 @@ beta12orEarlier Format of phylogenetic continuous quantitative character data. - @@ -28898,7 +27707,6 @@ beta12orEarlier Format of phylogenetic discrete states data. - @@ -28918,7 +27726,6 @@ beta12orEarlier Format of phylogenetic cliques data. - @@ -28938,7 +27745,6 @@ Format of phylogenetic invariants data. beta12orEarlier - @@ -28973,7 +27779,6 @@ beta12orEarlier Format for phylogenetic tree distance data. - @@ -29007,7 +27812,6 @@ Format for reports on a protein family. beta12orEarlier - @@ -29017,17 +27821,17 @@ - Molecular interaction format + Protein interaction format - + + Molecular interaction format Format for molecular interaction data. beta12orEarlier - @@ -29047,7 +27851,6 @@ Format for sequence assembly data. beta12orEarlier - @@ -29067,7 +27870,6 @@ Format for microarray experimental data. beta12orEarlier - @@ -29087,7 +27889,6 @@ beta12orEarlier Format for sequence trace data (i.e. including base call information). - @@ -29107,7 +27908,6 @@ beta12orEarlier Format for a report on gene expression. - @@ -29142,7 +27942,6 @@ beta12orEarlier Format of a map of (typically one) molecular sequence annotated with features. - @@ -29162,7 +27961,6 @@ Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence. beta12orEarlier - @@ -29182,7 +27980,6 @@ beta12orEarlier Format of a report of general information about a specific protein. - @@ -29217,7 +28014,6 @@ Format of a matrix of 3D-1D scores (amino acid environment probabilities). beta12orEarlier - @@ -29237,7 +28033,6 @@ beta12orEarlier Format of a report on the quality of a protein three-dimensional model. - @@ -29257,7 +28052,6 @@ beta12orEarlier Format of a report on sequence hits and associated data from searching a sequence database. - @@ -29277,7 +28071,6 @@ Format of a matrix of genetic distances between molecular sequences. beta12orEarlier - @@ -29297,7 +28090,6 @@ beta12orEarlier Format of a sequence motif. - @@ -29317,7 +28109,6 @@ beta12orEarlier Format of a sequence profile. - @@ -29337,7 +28128,6 @@ Format of a hidden Markov model. beta12orEarlier - @@ -29357,7 +28147,6 @@ beta12orEarlier Data format of a dirichlet distribution. - @@ -29372,12 +28161,17 @@ - + + + + + + + beta12orEarlier Data format for the emission and transition counts of a hidden Markov model. - @@ -29397,7 +28191,6 @@ Format for secondary structure (predicted or real) of an RNA molecule. beta12orEarlier - @@ -29417,7 +28210,6 @@ beta12orEarlier Format for secondary structure (predicted or real) of a protein molecule. - @@ -29437,7 +28229,6 @@ Format used to specify range(s) of sequence positions. beta12orEarlier - @@ -29452,7 +28243,6 @@ beta12orEarlier Alphabet for molecular sequence with possible unknown positions but without non-sequence characters. - @@ -29467,7 +28257,6 @@ beta12orEarlier Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters. - @@ -29482,7 +28271,6 @@ beta12orEarlier Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters. - @@ -29497,7 +28285,6 @@ Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters. beta12orEarlier - @@ -29511,7 +28298,6 @@ Format used for map of repeats in molecular (typically nucleotide) sequences. beta12orEarlier - @@ -29531,7 +28317,6 @@ Format used for report on restriction enzyme recognition sites in nucleotide sequences. beta12orEarlier - @@ -29551,7 +28336,6 @@ Format used for report on coding regions in nucleotide sequences. beta12orEarlier - @@ -29571,7 +28355,6 @@ Format used for clusters of molecular sequences. beta12orEarlier - @@ -29585,7 +28368,6 @@ beta12orEarlier Format used for clusters of protein sequences. - @@ -29599,7 +28381,6 @@ beta12orEarlier Format used for clusters of nucleotide sequences. - @@ -29630,7 +28411,6 @@ A text format resembling EMBL entry format. beta12orEarlier This concept may be used for the many non-standard EMBL-like text formats. - @@ -29646,7 +28426,6 @@ beta12orEarlier This concept may be used for non-standard FASTQ short read-like formats. A text format resembling FASTQ short read format. - @@ -29660,7 +28439,6 @@ beta12orEarlier XML format for EMBL entries. - @@ -29674,7 +28452,6 @@ beta12orEarlier XML format for EMBL entries. - @@ -29688,7 +28465,6 @@ XML format for EMBL entries. beta12orEarlier - @@ -29702,7 +28478,6 @@ beta12orEarlier Geneseq sequence format. - @@ -29717,7 +28492,6 @@ beta12orEarlier A text sequence format resembling uniprotkb entry format. - @@ -29730,8 +28504,8 @@ UniProt format UniProt entry sequence format. + SwissProt format beta12orEarlier - @@ -29745,7 +28519,6 @@ ipi sequence format. beta12orEarlier - @@ -29760,7 +28533,6 @@ beta12orEarlier Abstract format used by MedLine database. - @@ -29780,7 +28552,6 @@ beta12orEarlier Format used for ontologies. - @@ -29794,7 +28565,6 @@ A serialisation format conforming to the Open Biomedical Ontologies (OBO) model. beta12orEarlier - @@ -29809,7 +28579,6 @@ beta12orEarlier A serialisation format conforming to the Web Ontology Language (OWL) model. - @@ -29825,8 +28594,7 @@ A text format resembling FASTA format. beta12orEarlier This concept may also be used for the many non-standard FASTA-like formats. - - + http://filext.com/file-extension/FASTA" @@ -29846,7 +28614,6 @@ Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database. beta12orEarlier - @@ -29866,7 +28633,6 @@ 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 - @@ -29881,7 +28647,6 @@ This is a placeholder for other more specific concepts. It should not normally be used for annotation. An XML format for EMBL entries. beta12orEarlier - @@ -29897,7 +28662,6 @@ beta12orEarlier This concept may be used for the non-standard GenBank-like text formats. A text format resembling GenBank entry (plain text) format. - @@ -29911,7 +28675,6 @@ beta12orEarlier Text format for a sequence feature table. - @@ -29985,7 +28748,6 @@ beta12orEarlier Entry format (XML) for the STRING database of protein interaction. - @@ -30000,7 +28762,6 @@ beta12orEarlier GFF feature format (of indeterminate version). - @@ -30017,7 +28778,6 @@ - @@ -30032,7 +28792,6 @@ beta12orEarlier FASTA format wrapped in HTML elements. - @@ -30047,7 +28806,6 @@ beta12orEarlier EMBL entry format wrapped in HTML elements. - @@ -30120,38 +28878,23 @@ Textual format beta12orEarlier + http://www.iana.org/assignments/media-types/media-types.xhtml#text Plain text 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). + http://www.iana.org/assignments/media-types/text/plain" Textual format. + http://filext.com/file-extension/TSV" + http://filext.com/file-extension/TXT" Tabular format - - - - - - - - fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. - - - - - - Tabular format Many textual formats used in bioinformatics are tabular (tab-separated values, TSV). Typically with an additional header in their own format. + Tabular format - - fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. - - - - @@ -30167,19 +28910,12 @@ Hypertext Markup Language + http://filext.com/file-extension/HTML beta12orEarlier HTML format. - - - - fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. - - - - @@ -30188,21 +28924,14 @@ XML + http://filext.com/file-extension/XML" Extensible Markup Language beta12orEarlier eXtensible Markup Language (XML) format. Data in XML format can be serialised into text, or binary format. - - - - fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. - - - - @@ -30214,7 +28943,6 @@ 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. - @@ -30259,7 +28987,6 @@ 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. - @@ -30284,13 +29011,13 @@ - + - + BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more). @@ -30298,7 +29025,6 @@ BioXSD XML format - @@ -30313,7 +29039,6 @@ A serialisation format conforming to the Resource Description Framework (RDF) model. beta12orEarlier - @@ -30328,7 +29053,6 @@ Genbank entry format wrapped in HTML elements. beta12orEarlier - @@ -30358,7 +29082,6 @@ This concept may be used for the many non-standard EMBL-like formats. A format resembling EMBL entry (plain text) format. beta12orEarlier - @@ -30373,7 +29096,6 @@ beta12orEarlier This concept may be used for non-standard FASTQ short read-like formats. A format resembling FASTQ short read format. - @@ -30388,7 +29110,6 @@ A format resembling FASTA format. beta12orEarlier This concept may be used for the many non-standard FASTA-like formats. - @@ -30403,7 +29124,6 @@ A sequence format resembling uniprotkb entry format. beta12orEarlier - @@ -30423,7 +29143,6 @@ beta12orEarlier Format for a sequence feature table. - @@ -30438,7 +29157,6 @@ OBO ontology text format. beta12orEarlier - @@ -30453,7 +29171,6 @@ OBO ontology XML format. beta12orEarlier - @@ -30467,7 +29184,6 @@ beta12orEarlier Data format for a molecular sequence record. - @@ -30481,7 +29197,6 @@ Data format for a molecular sequence record. beta12orEarlier - @@ -30495,7 +29210,6 @@ beta12orEarlier XML format for a sequence feature table. - @@ -30509,7 +29223,6 @@ beta12orEarlier Text format for molecular sequence alignment information. - @@ -30523,7 +29236,6 @@ beta12orEarlier XML format for molecular sequence alignment information. - @@ -30537,7 +29249,6 @@ Text format for a phylogenetic tree. beta12orEarlier - @@ -30551,7 +29262,6 @@ XML format for a phylogenetic tree. beta12orEarlier - @@ -30567,7 +29277,6 @@ beta12orEarlier This concept may be used for the any non-standard EMBL-like XML formats. An XML format resembling EMBL entry format. - @@ -30582,7 +29291,6 @@ This concept may be used for the non-standard GenBank-like formats. beta12orEarlier A format resembling GenBank entry (plain text) format. - @@ -30611,7 +29319,6 @@ Text format for sequence assembly data. beta12orEarlier - @@ -30641,7 +29348,6 @@ Alphabet for a molecular sequence without any unknown positions or ambiguity characters. beta12orEarlier - @@ -30656,7 +29362,6 @@ Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters. beta12orEarlier - @@ -30671,7 +29376,6 @@ beta12orEarlier Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters . - @@ -30686,7 +29390,6 @@ Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters. beta12orEarlier - @@ -30701,7 +29404,6 @@ beta12orEarlier Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters. - @@ -30721,10 +29423,9 @@ Format of a raw molecular sequence (i.e. the alphabet used). beta12orEarlier - + http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence" - @@ -30738,7 +29439,6 @@ 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 - @@ -30757,11 +29457,10 @@ 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. - - + @@ -30776,7 +29475,6 @@ Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation. - @@ -30791,7 +29489,6 @@ Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters. beta12orEarlier - @@ -30806,18 +29503,17 @@ - + - + beta12orEarlier Format of a bibliographic reference. - @@ -30837,7 +29533,6 @@ beta12orEarlier Format of a sequence annotation track. - @@ -30857,7 +29552,6 @@ Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences. beta12orEarlier - @@ -30877,7 +29571,6 @@ beta12orEarlier Format of sequence variation annotation. - @@ -30892,7 +29585,6 @@ beta12orEarlier Some variant of Pearson MARKX alignment format. - @@ -30908,7 +29600,6 @@ beta12orEarlier Some variant of Mega format for (typically aligned) sequences. - @@ -30924,7 +29615,6 @@ Some variant of Phylip format for (aligned) sequences. beta12orEarlier - @@ -30940,7 +29630,6 @@ 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 - @@ -30957,7 +29646,6 @@ ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards). - @@ -30975,7 +29663,6 @@ beta12orEarlier - @@ -30992,7 +29679,6 @@ beta12orEarlier - @@ -31009,7 +29695,6 @@ 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. - @@ -31026,7 +29711,6 @@ beta12orEarlier - @@ -31044,7 +29728,6 @@ PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track. - @@ -31063,7 +29746,6 @@ Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth. - @@ -31081,7 +29763,6 @@ - @@ -31098,7 +29779,6 @@ beta12orEarlier - @@ -31116,7 +29796,6 @@ genePred table format for gene prediction tracks. - @@ -31133,7 +29812,6 @@ Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser. - @@ -31150,7 +29828,6 @@ beta12orEarlier - @@ -31165,7 +29842,6 @@ LAV format of alignments generated by BLASTZ and LASTZ. beta12orEarlier - @@ -31182,7 +29858,6 @@ 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 - @@ -31199,7 +29874,6 @@ Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). beta12orEarlier - @@ -31216,7 +29890,6 @@ beta12orEarlier Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive. - @@ -31233,7 +29906,6 @@ beta12orEarlier ZTR format for storing chromatogram data from DNA sequencing instruments. - @@ -31250,7 +29922,6 @@ beta12orEarlier Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation. - @@ -31267,7 +29938,6 @@ BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). beta12orEarlier - @@ -31288,7 +29958,6 @@ beta13 Format of a matrix (array) of numerical values. - @@ -31308,7 +29977,6 @@ beta13 Format of data concerning the classification of the sequences and/or structures of protein structural domain(s). - @@ -31323,7 +29991,6 @@ beta13 These are the parsable data files provided by SCOP. Format of raw SCOP domain classification data files. - @@ -31338,7 +30005,6 @@ Format of raw CATH domain classification data files. beta13 These are the parsable data files provided by CATH. - @@ -31353,7 +30019,6 @@ 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. - @@ -31368,7 +30033,6 @@ Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models. 1.0 - @@ -31386,7 +30050,6 @@ BioPAX is an exchange format for pathway data, with its data model defined in OWL. - @@ -31402,7 +30065,6 @@ 1.0 EBI Application Result XML is a format returned by sequence similarity search Web services at EBI. - @@ -31420,7 +30082,6 @@ MIF XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI. 1.0 - @@ -31439,7 +30100,6 @@ phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data. - @@ -31456,7 +30116,6 @@ 1.0 - @@ -31472,7 +30131,6 @@ MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED). 1.0 - @@ -31490,7 +30148,6 @@ 1.0 MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED). - @@ -31515,7 +30172,6 @@ GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC). - @@ -31532,7 +30188,6 @@ 1.0 - @@ -31552,7 +30207,6 @@ beta12orEarlier Data format for a report of information derived from a biological pathway or network. - @@ -31566,7 +30220,6 @@ Data format for annotation on a laboratory experiment. beta12orEarlier - @@ -31585,14 +30238,13 @@ - 1.2 - Cytoband format for chromosome cytobands. Reflects a UCSC Browser DB table. - + Cytoband format for chromosome cytobands. + 1.2 - + @@ -31606,7 +30258,6 @@ CopasiML, the native format of COPASI. 1.2 - @@ -31625,7 +30276,6 @@ CellML, the format for mathematical models of biological and other networks. - @@ -31642,7 +30292,6 @@ 1.2 - @@ -31656,7 +30305,6 @@ 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. - @@ -31676,7 +30324,6 @@ mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center. - @@ -31696,7 +30343,6 @@ Format for mass spectrometry data. 1.2 - @@ -31713,7 +30359,6 @@ TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS. - @@ -31730,7 +30375,6 @@ 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. - @@ -31747,7 +30391,6 @@ 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. - @@ -31770,7 +30413,6 @@ 1.2 - @@ -31793,7 +30435,6 @@ 1.2 - @@ -31808,7 +30449,6 @@ 1.2 A human-readable encoding for the Web Ontology Language (OWL). - @@ -31824,7 +30464,6 @@ This format was influenced by the OWL Abstract Syntax and the DL style syntax. 1.2 A syntax for writing OWL class expressions. - @@ -31840,7 +30479,6 @@ 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. - @@ -31856,7 +30494,6 @@ 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. - @@ -31872,7 +30509,6 @@ 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. - @@ -31887,7 +30523,6 @@ A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind. N3 - @@ -31903,12 +30538,11 @@ RDF/XML is a serialization syntax for OWL DL, but not for OWL Full. 1.2 - RDF Resource Description Framework (RDF) XML format. - + http://www.ebi.ac.uk/SWO/data/SWO_3000006" + RDF - @@ -31922,7 +30556,6 @@ OWL 1.2 OWL ontology XML serialisation format. - @@ -31939,7 +30572,6 @@ 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. - @@ -31955,7 +30587,6 @@ 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 - @@ -31973,7 +30604,6 @@ 1.3 The MAP file describes SNPs and is used by the Plink package. - @@ -31989,7 +30619,6 @@ 1.3 Plink PED - @@ -32003,7 +30632,6 @@ 1.3 Data format for a metadata on an individual and their genetic data. - @@ -32020,7 +30648,6 @@ Plink PED/MAP The PED/MAP file describes data used by the Plink package. - @@ -32035,9 +30662,8 @@ Connectivity Table file format Connect format - File format of a CT (Connectivity Table) file from the RNAstructure package. beta12orEarlier - + File format of a CT (Connectivity Table) file from the RNAstructure package. @@ -32054,7 +30680,6 @@ XRNA old input style format. beta12orEarlier - @@ -32071,7 +30696,6 @@ beta12orEarlier RNA Markup Language. - @@ -32088,7 +30712,6 @@ beta12orEarlier Format for the Genetic Data Environment (GDE). - @@ -32103,7 +30726,6 @@ A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) pacakge. Block file format 1.3 - @@ -32115,6 +30737,7 @@ Data index format + @@ -32123,7 +30746,6 @@ 1.3 - @@ -32143,7 +30765,6 @@ BAM indexing format 1.3 - @@ -32159,7 +30780,6 @@ 1.3 HMMER profile HMM file for HMMER versions 2.x - @@ -32174,7 +30794,6 @@ HMMER profile HMM file for HMMER versions 3.x 1.3 - @@ -32188,7 +30807,6 @@ 1.3 EMBOSS simple sequence pair alignment format. - @@ -32204,7 +30822,212 @@ 1.3 XML format as produced by the NCBI Blast package - + + + + + + + + + + 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 + + + + + + + + + + JSON + + Javascript Object Notation format; a lightweight, text-based format to represent structured data using key-value pairs. + 1.7 + + + + + + + + + + EPS + + 1.7 + Encapsulated PostScript format + + + + + + + + + + GIF + + Graphics Interchange Format. + 1.7 + + + + + + + + + + xls + + 1.7 + Microsoft Excel spreadsheet format. + + + + + + + + + + TSV + + CSV + http://filext.com/file-extension/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" + + + + + + + + + + Gene expression data format + + + + + + + + Format of a file of gene expression data, e.g. a gene expression matrix or profile. + 1.7 + + + + + + + + + + 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. + + + + + + + + + + ebwt + + + + + + + + Bowtie format for indexed reference genome for "small" genomes. + 1.7 + Bowtie index format + https://github.com/BenLangmead/bowtie/blob/master/MANUAL + + + + + + + + + + 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 + + + + + + + + + + GCG format variant + + + + Some format based on the GCG format. + 1.7 + + + + + + + + + + BSML + + + 1.7 + Bioinformatics Sequence Markup Language format. + http://rothlab.ucdavis.edu/genhelp/chapter_2_using_sequences.html#_Creating_and_Editing_Single_Sequenc + + + + + + + + + + ebwtl + + + + + + + + Bowtie format for indexed reference genome for "large" genomes. + Bowtie long index format + https://github.com/BenLangmead/bowtie/blob/master/MANUAL + 1.7 @@ -32217,132 +31040,59 @@ Operation + http://purl.org/biotop/biotop.owl#Function" + http://wsio.org/operation_001" + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality" + http://www.ebi.ac.uk/swo/SWO_0000003" + http://semanticscience.org/resource/SIO_000649" Function (programming) Lambda abstraction Mathematical function + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method" + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#process" Computational procedure Computational subroutine - Process + http://www.onto-med.de/ontologies/gfo.owl#Perpetuant" + http://www.ifomis.org/bfo/1.1/span#Process" + http://en.wikipedia.org/wiki/Subroutine" Computational operation + Process beta12orEarlier sumo:Function + http://semanticscience.org/resource/SIO_000017" Mathematical operation + http://www.ifomis.org/bfo/1.1/snap#Continuant" + http://en.wikipedia.org/wiki/Function_(computer_science)" Computational method + http://www.ifomis.org/bfo/1.1/snap#Quality" + http://www.onto-med.de/ontologies/gfo.owl#Function" Function + http://en.wikipedia.org/wiki/Function_(mathematics)" + http://www.onto-med.de/ontologies/gfo.owl#Process" + http://www.ifomis.org/bfo/1.1/snap#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 - - - - - - - - - - - - - - - - - - - - - + + - However, one may think that an operation is not a process. - - - - - - However, operation is not a GFO 'Concept' present only in someone's mind. + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. + Function - - Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. Process + Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. - BFO 'function' is narrower in the sense that it is a 'realizable_entity' (snap:RealizableEntity) and a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it does not need to have input(s) and output(s). - - - - - - Function, including an operation, can have a role of a quality/property in semantic annotation of e.g. a computational tool. - - - - - - However, one may think that an operation is not a process and not a physical entity. - - - - - - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. In addition, one may think of 'biotop:Disposition' (parent of 'biotop:Function') being also a 'biotop:Quality'. - - - - - - Method may in addition focus on how to achieve the result, not just on what to achieve as with operation. - - - - - - Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. - - - - - Computational tool Computational tool provides one or more operations. - - Function - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. - - - - - Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. - - - - - - GFO 'Perpetuant' is in general broader than operation, but it may be seen narrower in the sense of being a concrete individual and exhibiting presentials. - - - - - - Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. - - - - - - Function, including an operation, can be a quality/property of e.g. a computational tool. - - - - @@ -32353,14 +31103,14 @@ - - + + - - + + Search @@ -32369,7 +31119,6 @@ Retrieval Query beta12orEarlier - @@ -32411,7 +31160,6 @@ 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. - @@ -32433,7 +31181,6 @@ Generate an index of (typically a file of) biological data. beta12orEarlier Data indexing - @@ -32445,12 +31192,12 @@ Data index analysis + 1.6 + true beta12orEarlier Analyse an index of biological data. Database index analysis - 1.6 - true @@ -32479,7 +31226,6 @@ Generate a molecular sequence by some means. beta12orEarlier - @@ -32494,7 +31240,6 @@ beta12orEarlier Edit or change a molecular sequence, either randomly or specifically. - @@ -32509,7 +31254,6 @@ Sequence splicing Merge two or more (typically overlapping) molecular sequences. beta12orEarlier - @@ -32524,7 +31268,6 @@ beta12orEarlier Convert a molecular sequence from one type to another. - @@ -32538,19 +31281,18 @@ - - + + - - + + Calculate sequence complexity, for example to find low-complexity regions in sequences. beta12orEarlier - @@ -32564,19 +31306,18 @@ - - + + - - + + beta12orEarlier Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes. - @@ -32591,19 +31332,18 @@ - - + + - - + + Calculate character or word composition or frequency of a molecular sequence. beta12orEarlier - @@ -32624,7 +31364,6 @@ 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. - @@ -32652,7 +31391,6 @@ 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). - @@ -32677,11 +31415,10 @@ Sequence motif detection - Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s). beta12orEarlier + Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s). Motif detection Motif recognition - @@ -32707,7 +31444,6 @@ Find motifs shared by molecular sequences. beta12orEarlier - @@ -32745,7 +31481,6 @@ 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. - @@ -32770,11 +31505,10 @@ - This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. 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. @@ -32790,7 +31524,6 @@ 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 - @@ -32819,7 +31552,6 @@ 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). - @@ -32834,19 +31566,18 @@ - - + + - - + + Identify structural domains in a protein structure from first principles (for example calculations on structural compactness). beta12orEarlier - @@ -32860,7 +31591,6 @@ Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s). beta12orEarlier - @@ -32874,14 +31604,14 @@ - - + + - - + + WHATIF: SymShellOneXML @@ -32894,7 +31624,6 @@ WHATIF: SymShellTwoXML WHATIF:ListContactsRelaxed WHATIF: SymShellTenXML - @@ -32914,7 +31643,6 @@ Calculate, visualise or analyse phi/psi angles of a protein structure. beta12orEarlier - @@ -32936,12 +31664,6 @@ - - - - - - @@ -32950,7 +31672,6 @@ 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. - @@ -32965,20 +31686,19 @@ - - + + - - + + 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 - @@ -32993,14 +31713,14 @@ - - + + - - + + SO:0000110 @@ -33008,7 +31728,6 @@ Sequence feature recognition Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions. Sequence feature prediction - @@ -33036,10 +31755,10 @@ Feature table query Query the features (in a feature table) of molecular sequence(s). + true beta12orEarlier + 1.6 - 1.6 - true @@ -33054,7 +31773,7 @@ - + @@ -33066,14 +31785,13 @@ - + Feature table comparison Feature comparison Compare the feature tables of two or more molecular sequences. beta12orEarlier - @@ -33102,25 +31820,12 @@ - - - - - - - - - - - - beta12orEarlier Analyse a molecular sequence alignment. - @@ -33136,7 +31841,6 @@ See also 'Sequence profile alignment'. beta12orEarlier Compare (typically by aligning) two molecular sequence alignments. - @@ -33151,7 +31855,6 @@ Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence). beta12orEarlier - @@ -33187,7 +31890,6 @@ Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence. beta12orEarlier - @@ -33207,7 +31909,6 @@ Predict splicing alternatives or transcript isoforms from analysis of sequence data. beta12orEarlier - @@ -33217,7 +31918,7 @@ - Frameshift error detection + Frameshift detection @@ -33228,8 +31929,8 @@ Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. beta12orEarlier - Detect frameshift errors in DNA sequences (from sequencing projects). - + Frameshift error detection + Detect frameshifts in DNA sequences, including frameshift sites and signals, and frameshift errors from sequencing projects. @@ -33244,7 +31945,6 @@ Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences. beta12orEarlier - @@ -33260,27 +31960,26 @@ - - + + - - + + - + beta12orEarlier Predict secondary structure of protein sequences. Secondary structure prediction (protein) 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. - @@ -33301,7 +32000,6 @@ Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. Predict super-secondary structure of protein sequence(s). beta12orEarlier - @@ -33322,7 +32020,6 @@ beta12orEarlier Predict transmembrane proteins or transmembrane (helical) domains or regions in protein sequences. - @@ -33336,20 +32033,19 @@ - - + + - - + + 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 - @@ -33364,19 +32060,18 @@ - - + + - - + + beta12orEarlier Predict tertiary structure of a molecular (biopolymer) sequence. - @@ -33398,7 +32093,6 @@ beta12orEarlier Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences. Methods usually involve multiple sequence alignment analysis. - @@ -33412,19 +32106,18 @@ - - + + - - + + 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. - @@ -33439,7 +32132,6 @@ Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences. beta12orEarlier - @@ -33455,7 +32147,6 @@ Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures. beta12orEarlier - @@ -33470,12 +32161,6 @@ - - - - - - @@ -33486,9 +32171,14 @@ + + + + + + Analyse a network of protein interactions. beta12orEarlier - @@ -33509,7 +32199,6 @@ Compare two or more networks of protein interactions. beta12orEarlier - @@ -33525,20 +32214,19 @@ - - + + - - + + + 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). - Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). - @@ -33554,21 +32242,20 @@ - - + + - - + + Nucleic acid folding Nucleic acid folding modelling Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data. beta12orEarlier - @@ -33627,7 +32314,6 @@ 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 - @@ -33641,20 +32327,19 @@ - - + + - - + + 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 - @@ -33676,7 +32361,6 @@ Codon usage table construction beta12orEarlier Calculate codon usage statistics and create a codon usage table. - @@ -33691,7 +32375,6 @@ Compare two or more codon usage tables. beta12orEarlier - @@ -33705,8 +32388,8 @@ - - + + @@ -33717,8 +32400,8 @@ - - + + @@ -33737,7 +32420,6 @@ 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 - @@ -33752,19 +32434,18 @@ - - + + - - + + beta12orEarlier Identify and plot third base position variability in a nucleotide sequence. - @@ -33778,7 +32459,6 @@ beta12orEarlier Find exact character or word matches between molecular sequences without full sequence alignment. - @@ -33804,10 +32484,9 @@ Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences. - Sequence distance matrix construction beta12orEarlier Phylogenetic distance matrix generation - + Sequence distance matrix construction @@ -33827,7 +32506,6 @@ Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria. beta12orEarlier - @@ -33844,7 +32522,7 @@ - + @@ -33858,7 +32536,6 @@ beta12orEarlier Sequence cluster construction The clusters may be output or used internally for some other purpose. - @@ -33878,24 +32555,11 @@ - - - - - - - - - - - - Sequence alignment computation Sequence alignment Align (identify equivalent sites within) molecular sequences. beta12orEarlier Sequence alignment construction - @@ -33924,20 +32588,13 @@ Structure-based sequence alignment - - - - - - Align molecular sequences using sequence and structural information. Structure-based sequence alignment generation - Structure-based sequence alignment Sequence alignment (structure-based) beta12orEarlier Structure-based sequence alignment construction Sequence alignment generation (structure-based) - + Structure-based sequence alignment @@ -33963,7 +32620,6 @@ beta12orEarlier Structure alignment construction Align (superimpose) molecular tertiary structures. - @@ -33994,10 +32650,9 @@ + Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment. beta12orEarlier Sequence profile construction - Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment. - @@ -34012,27 +32667,26 @@ - - + + - - + + - + beta12orEarlier Structural profile construction Generate some type of structural (3D) profile or template from a structure or structure alignment. Structural profile generation - @@ -34052,23 +32706,22 @@ - - + + - - + + - Align sequence profiles (representing sequence alignments). Sequence profile alignment generation + Align sequence profiles (representing sequence alignments). Sequence profile alignment construction See also 'Sequence alignment comparison'. beta12orEarlier Sequence profile alignment - @@ -34083,20 +32736,14 @@ - - - - - - - - + + - - + + Align structural (3D) profiles or templates (representing structures or structure alignments). @@ -34108,7 +32755,6 @@ 3D profile alignment 3D profile alignment (multiple) beta12orEarlier - @@ -34122,20 +32768,20 @@ - - + + - - + + - - + + A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. @@ -34144,7 +32790,6 @@ beta12orEarlier Sequence-profile alignment generation Sequence-profile alignment construction - @@ -34159,14 +32804,14 @@ - - + + - - + + Sequence-3D profile alignment @@ -34175,7 +32820,6 @@ Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment). Sequence-3D profile alignment construction beta12orEarlier - @@ -34190,12 +32834,6 @@ - - - - - - @@ -34207,10 +32845,9 @@ 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 - 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. - @@ -34227,14 +32864,14 @@ - - + + - - + + Protein fold prediction @@ -34242,7 +32879,6 @@ 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 - @@ -34265,7 +32901,6 @@ 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) - @@ -34291,7 +32926,6 @@ Query the biomedical and informatics literature. beta12orEarlier - @@ -34311,20 +32945,19 @@ - - + + - - + + Process and analyse text (typically the biomedical and informatics literature) to extract information from it. beta12orEarlier Text data mining - @@ -34344,7 +32977,6 @@ Perform in-silico (virtual) PCR. beta12orEarlier - @@ -34358,12 +32990,6 @@ - - - - - - @@ -34374,11 +33000,16 @@ + + + + + + + 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 - beta12orEarlier - @@ -34394,7 +33025,7 @@ - + @@ -34405,20 +33036,19 @@ - - + + - - + + 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. - @@ -34446,7 +33076,6 @@ 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 - @@ -34461,20 +33090,19 @@ - + - + This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. Standardize or normalize microarray data. beta12orEarlier - @@ -34510,7 +33138,6 @@ Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles. beta12orEarlier - @@ -34535,7 +33162,6 @@ Functional profiling Gene expression profile construction Expression profiling - @@ -34556,7 +33182,6 @@ Compare gene expression profiles or patterns. beta12orEarlier - @@ -34623,19 +33248,18 @@ - - + + - - + + Assign secondary structure from protein coordinate or experimental data. beta12orEarlier - @@ -34646,18 +33270,18 @@ Protein structure assignment - + - + - + @@ -34668,7 +33292,6 @@ Assign a protein tertiary structure (3D coordinates) from raw experimental data. beta12orEarlier - @@ -34679,24 +33302,24 @@ Protein model validation - + - - + + - + - + @@ -34705,17 +33328,13 @@ - - - - - - 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. - @@ -34725,13 +33344,13 @@ - Protein model refinement + Molecular model refinement - 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. - Refine (after evaluation) a model of protein structure to reduce steric clashes, volume irregularities etc. + + 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 @@ -34758,9 +33377,8 @@ beta12orEarlier Construct a phylogenetic tree. - Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. Phylogenetic tree construction - + Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. @@ -34774,19 +33392,18 @@ - - + + - - + + Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions. beta12orEarlier - @@ -34802,7 +33419,6 @@ 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 - @@ -34817,19 +33433,18 @@ - + - + beta12orEarlier Edit a phylogenetic tree. - @@ -34850,7 +33465,6 @@ 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. - @@ -34864,7 +33478,6 @@ Simulate the folding of a protein. beta12orEarlier - @@ -34879,7 +33492,6 @@ beta12orEarlier Predict the folding pathway(s) or non-native structural intermediates of a protein. - @@ -34894,19 +33506,18 @@ - - + + - - + + Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). beta12orEarlier - @@ -34932,10 +33543,9 @@ beta12orEarlier - Methods might predict silent or pathological mutations. 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. @@ -34946,7 +33556,6 @@ Immunogen design - beta12orEarlier beta12orEarlier @@ -34977,7 +33586,6 @@ beta12orEarlier Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). - @@ -34991,19 +33599,18 @@ - - + + - - + + Calculate Km, Vmax and derived data for an enzyme reaction. beta12orEarlier - @@ -35017,12 +33624,11 @@ File format conversion File reformatting + Reformatting File formatting Format conversion Reformat a file of data (or equivalent entity in memory). beta12orEarlier - Reformatting - @@ -35038,7 +33644,6 @@ beta12orEarlier File format validation Test and validate the format and content of a data file. - @@ -35071,7 +33676,6 @@ Rendering Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures. beta12orEarlier - @@ -35086,20 +33690,19 @@ - - + + - - + + This excludes direct retrieval methods (e.g. the dbfetch program). beta12orEarlier Search a sequence database by sequence comparison and retrieve similar sequences. - @@ -35113,19 +33716,18 @@ - - + + - - + + Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data. beta12orEarlier - @@ -35155,7 +33757,6 @@ beta12orEarlier Methods might use fingerprints, profiles, hidden Markov models, sequence alignment etc to provide a mapping to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). Protein sequence classification - @@ -35176,7 +33777,6 @@ Screen a sequence against a motif or pattern database. beta12orEarlier - @@ -35219,10 +33819,10 @@ Sequence retrieval (by code) beta12orEarlier + 1.6 + true Query a database and retrieve sequences with a given entry code or accession number. - 1.6 - true @@ -35233,11 +33833,11 @@ Sequence retrieval (by keyword) + 1.6 beta12orEarlier Query a database and retrieve sequences containing a given keyword. - - 1.6 true + @@ -35251,7 +33851,6 @@ Search a sequence database and retrieve sequences that are similar to a query sequence. beta12orEarlier Sequence similarity search - @@ -35272,7 +33871,6 @@ beta12orEarlier Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. - @@ -35285,10 +33883,10 @@ Sequence database search (by amino acid composition) beta12orEarlier + 1.6 Search a sequence database and retrieve sequences of a given amino acid composition. - - 1.6 true + @@ -35301,7 +33899,6 @@ beta12orEarlier Search a sequence database and retrieve sequences with a specified property, typically a physicochemical or compositional property. - @@ -35315,11 +33912,11 @@ 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 - 1.6 - true @@ -35330,13 +33927,13 @@ 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) - - 1.6 true + @@ -35349,11 +33946,11 @@ 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 - true @@ -35364,13 +33961,13 @@ 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. - 1.6 - true @@ -35383,11 +33980,11 @@ 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 - - 1.6 true + @@ -35400,11 +33997,11 @@ 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 - true @@ -35415,11 +34012,11 @@ Sequence database search (by isoelectric point) + true Search sequence(s) or a sequence database for sequences of a given isoelectric point. beta12orEarlier + 1.6 - 1.6 - true @@ -35430,11 +34027,11 @@ 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 - true @@ -35447,9 +34044,9 @@ beta12orEarlier Query a tertiary structure database and retrieve entries containing a given keyword. - - 1.6 + 1.6 true + @@ -35464,7 +34061,6 @@ Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence. Structure retrieval by sequence beta12orEarlier - @@ -35486,7 +34082,6 @@ Search a tertiary structure database and retrieve structures that are similar to a query structure. Structural similarity search beta12orEarlier - @@ -35500,19 +34095,18 @@ - + - + Annotate a molecular sequence record with terms from a controlled vocabulary. beta12orEarlier - @@ -35526,7 +34120,6 @@ Annotate a genome sequence with terms from a controlled vocabulary. beta12orEarlier - @@ -35540,7 +34133,6 @@ Generate the reverse and / or complement of a nucleotide sequence. beta12orEarlier - @@ -35554,7 +34146,6 @@ beta12orEarlier Generate a random sequence, for example, with a specific character composition. - @@ -35581,7 +34172,6 @@ Generate digest fragments for a nucleotide sequence containing restriction sites. beta12orEarlier - @@ -35596,19 +34186,18 @@ - - + + - - + + Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses. beta12orEarlier - @@ -35622,7 +34211,6 @@ Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition. beta12orEarlier - @@ -35637,7 +34225,6 @@ 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). - @@ -35651,7 +34238,6 @@ beta12orEarlier Cut (remove) characters or a region from a molecular sequence. - @@ -35671,7 +34257,6 @@ beta12orEarlier Create (or remove) restriction sites in sequences, for example using silent mutations. - @@ -35691,7 +34276,6 @@ Translate a DNA sequence into protein. beta12orEarlier - @@ -35711,7 +34295,6 @@ Transcribe a nucleotide sequence into mRNA sequence(s). beta12orEarlier - @@ -35726,7 +34309,6 @@ beta12orEarlier Calculate base frequency or word composition of a nucleotide sequence. - @@ -35741,7 +34323,6 @@ beta12orEarlier Calculate amino acid frequency or word composition of a protein sequence. - @@ -35756,7 +34337,6 @@ Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. beta12orEarlier - @@ -35771,7 +34351,6 @@ Analyse repeat sequence organization such as periodicity. beta12orEarlier - @@ -35786,7 +34365,6 @@ beta12orEarlier Analyse the hydrophobic, hydrophilic or charge properties of a protein structure. - @@ -35800,19 +34378,18 @@ - - + + - - + + Calculate solvent accessible or buried surface areas in protein structures. beta12orEarlier - @@ -35827,7 +34404,6 @@ Identify clusters of hydrophobic or charged residues in a protein structure. beta12orEarlier - @@ -35847,7 +34423,6 @@ Calculate whether a protein structure has an unusually large net charge (dipole moment). beta12orEarlier - @@ -35867,7 +34442,6 @@ Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc. beta12orEarlier - @@ -35883,7 +34457,6 @@ Ligand-binding and active site prediction (from structure) beta12orEarlier Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures. - @@ -35897,19 +34470,18 @@ - - + + - - + + beta12orEarlier Analyse RNA or DNA-binding sites in protein structure. - @@ -35929,7 +34501,6 @@ Decompose a structure into compact or globular fragments (protein peeling). beta12orEarlier - @@ -35949,7 +34520,6 @@ Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure. beta12orEarlier - @@ -35969,7 +34539,6 @@ Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure. beta12orEarlier - @@ -35990,7 +34559,6 @@ beta12orEarlier Calculate clusters of contacting residues in protein structures. Cluster of contacting residues might be key structural residues. - @@ -36009,12 +34577,11 @@ Identify potential hydrogen bonds between amino acids and other groups. - WHATIF:ShowHydrogenBonds WHATIF:ShowHydrogenBondsM beta12orEarlier The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy. WHATIF:HasHydrogenBonds - + WHATIF:ShowHydrogenBonds @@ -36029,7 +34596,6 @@ Calculate non-canonical atomic interactions in protein structures. beta12orEarlier - @@ -36049,7 +34615,6 @@ beta12orEarlier Calculate a Ramachandran plot of a protein structure. - @@ -36075,7 +34640,6 @@ Validate a Ramachandran plot of a protein structure. beta12orEarlier - @@ -36101,7 +34665,6 @@ beta12orEarlier Calculate the molecular weight of a protein sequence or fragments. - @@ -36121,7 +34684,6 @@ Predict extinction coefficients or optical density of a protein sequence. beta12orEarlier - @@ -36147,7 +34709,6 @@ beta12orEarlier Calculate pH-dependent properties from pKa calculations of a protein sequence. - @@ -36161,7 +34722,6 @@ beta12orEarlier Hydropathy calculation on a protein sequence. - @@ -36182,7 +34742,6 @@ Plot a protein titration curve. beta12orEarlier - @@ -36202,7 +34761,6 @@ Calculate isoelectric point of a protein sequence. beta12orEarlier - @@ -36222,7 +34780,6 @@ beta12orEarlier Estimate hydrogen exchange rate of a protein sequence. - @@ -36236,7 +34793,6 @@ beta12orEarlier Calculate hydrophobic or hydrophilic / charged regions of a protein sequence. - @@ -36256,7 +34812,6 @@ Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein. beta12orEarlier - @@ -36278,7 +34833,6 @@ Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity. Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. beta12orEarlier - @@ -36298,7 +34852,6 @@ beta12orEarlier Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc. - @@ -36318,7 +34871,6 @@ beta12orEarlier Predict the solubility or atomic solvation energy of a protein sequence. - @@ -36338,7 +34890,6 @@ Predict crystallizability of a protein sequence. beta12orEarlier - @@ -36352,7 +34903,6 @@ Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins. beta12orEarlier - @@ -36366,7 +34916,6 @@ beta12orEarlier Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins. - @@ -36380,7 +34929,6 @@ beta12orEarlier Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc. - @@ -36393,12 +34941,12 @@ 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. - 1.6 - true @@ -36428,7 +34976,6 @@ 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) - @@ -36443,20 +34990,19 @@ - - + + - - + + Epitope mapping is commonly done during vaccine design. Predict antigenic determinant sites (epitopes) in protein sequences. beta12orEarlier - @@ -36470,20 +35016,19 @@ - - + + - - + + 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. - @@ -36498,20 +35043,19 @@ - - + + - - + + 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 - @@ -36528,7 +35072,6 @@ 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) - @@ -36548,7 +35091,6 @@ Predict RNA and DNA-binding binding sites in protein sequences. beta12orEarlier - @@ -36569,7 +35111,6 @@ beta12orEarlier Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization. - @@ -36595,7 +35136,6 @@ Detect or predict cleavage sites (enzymatic or chemical) in protein sequences. beta12orEarlier - @@ -36609,7 +35149,6 @@ Predict epitopes that bind to MHC class I molecules. beta12orEarlier - @@ -36623,7 +35162,6 @@ beta12orEarlier Predict epitopes that bind to MHC class II molecules. - @@ -36637,7 +35175,6 @@ Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc. beta12orEarlier - @@ -36652,7 +35189,6 @@ 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. - @@ -36672,7 +35208,6 @@ Detect or predict transposons, retrotransposons / retrotransposition signatures etc. beta12orEarlier - @@ -36692,7 +35227,6 @@ beta12orEarlier Detect polyA signals in nucleotide sequences. - @@ -36706,21 +35240,20 @@ - - + + - - + + 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 - @@ -36734,22 +35267,21 @@ - - + + - - + + - CpG island and isochores rendering - beta12orEarlier 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. - @@ -36769,19 +35301,18 @@ - - + + - - + + Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map. beta12orEarlier - @@ -36801,7 +35332,6 @@ Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA. beta12orEarlier - @@ -36815,20 +35345,19 @@ - - + + - - + + Methods might require a pre-mRNA or genomic DNA sequence. Identify, predict or analyse splice sites in nucleotide sequences. beta12orEarlier - @@ -36842,7 +35371,6 @@ beta12orEarlier Predict whole gene structure using a combination of multiple methods to achieve better predictions. - @@ -36856,7 +35384,6 @@ beta12orEarlier Find operons (operators, promoters and genes) in bacteria genes. - @@ -36875,8 +35402,8 @@ beta12orEarlier + ORF prediction Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences. - @@ -36897,7 +35424,6 @@ 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. - @@ -36907,7 +35433,7 @@ - Transcription regulatory element prediction + Regulatory element prediction @@ -36917,8 +35443,9 @@ 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. - @@ -36938,7 +35465,6 @@ beta12orEarlier Predict translation initiation sites, possibly by searching a database of sites. - @@ -36959,7 +35485,6 @@ 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. - @@ -36974,7 +35499,6 @@ 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 - @@ -36989,7 +35513,6 @@ 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. - @@ -37011,7 +35534,6 @@ 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 - @@ -37032,7 +35554,6 @@ 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. - @@ -37052,7 +35573,6 @@ Identify or predict transcription factor binding sites in DNA sequences. beta12orEarlier - @@ -37066,20 +35586,19 @@ - - + + - - + + 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. - @@ -37096,7 +35615,6 @@ Evaluate molecular sequence alignment accuracy. Sequence alignment quality evaluation Evaluation might be purely sequence-based or use structural information. - @@ -37112,7 +35630,6 @@ Residue conservation analysis Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence. beta12orEarlier - @@ -37123,11 +35640,11 @@ 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. - @@ -37143,7 +35660,6 @@ 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 - @@ -37159,7 +35675,6 @@ Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment. beta12orEarlier Sequence alignment analysis (recombination detection) - @@ -37175,7 +35690,6 @@ Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. Sequence alignment analysis (indel detection) beta12orEarlier - @@ -37210,7 +35724,6 @@ beta12orEarlier Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy. - @@ -37232,7 +35745,6 @@ beta12orEarlier A melting profile is used to visualise and analyse partly melted DNA conformations. Calculate and plot a DNA or DNA/RNA melting profile. - @@ -37253,7 +35765,6 @@ 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. - @@ -37273,7 +35784,6 @@ beta12orEarlier Calculate and plot a DNA or DNA/RNA melting curve. - @@ -37293,7 +35803,6 @@ Calculate and plot a DNA or DNA/RNA probability profile. beta12orEarlier - @@ -37313,7 +35822,6 @@ beta12orEarlier Calculate and plot a DNA or DNA/RNA temperature profile. - @@ -37327,20 +35835,19 @@ - - + + - - + + This includes properties such as. beta12orEarlier Calculate curvature and flexibility / stiffness of a nucleotide sequence. - @@ -37360,7 +35867,6 @@ beta12orEarlier Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in an RNA sequence. - @@ -37380,7 +35886,6 @@ beta12orEarlier Identify or predict tRNA genes in genomic sequences (tRNA). - @@ -37400,7 +35905,6 @@ Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences. beta12orEarlier - @@ -37414,7 +35918,6 @@ beta12orEarlier Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions. - @@ -37428,7 +35931,6 @@ Predict helical secondary structure of protein sequences. beta12orEarlier - @@ -37442,7 +35944,6 @@ beta12orEarlier Predict turn structure (for example beta hairpin turns) of protein sequences. - @@ -37456,7 +35957,6 @@ Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences. beta12orEarlier - @@ -37470,7 +35970,6 @@ Predict cysteine bonding state and disulfide bond partners in protein sequences. beta12orEarlier - @@ -37486,7 +35985,6 @@ Predict G protein-coupled receptors (GPCR). G protein-coupled receptor (GPCR) prediction beta12orEarlier - @@ -37513,7 +36011,6 @@ G protein-coupled receptor (GPCR) analysis beta12orEarlier Analyse G-protein coupled receptor proteins (GPCRs). - @@ -37530,14 +36027,14 @@ - - + + - - + + @@ -37548,7 +36045,6 @@ Predict tertiary structure (backbone and side-chain conformation) of protein sequences. beta12orEarlier - @@ -37564,20 +36060,19 @@ - - + + - - + + - Methods might identify thermodynamically stable or evolutionarily conserved structures. Predict tertiary structure of DNA or RNA. + Methods might identify thermodynamically stable or evolutionarily conserved structures. beta12orEarlier - @@ -37589,15 +36084,9 @@ Ab initio structure prediction - - - - - - beta12orEarlier + de novo structure prediction Predict tertiary structure of protein sequence(s) without homologs of known structure. - @@ -37614,17 +36103,16 @@ - + 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. - beta12orEarlier Build a three-dimensional protein model based on known (for example homologs) structures. + beta12orEarlier Comparative modelling - @@ -37634,8 +36122,8 @@ - Protein docking - + Molecular docking + @@ -37655,10 +36143,11 @@ + 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. - @@ -37673,7 +36162,6 @@ beta12orEarlier Methods might require a preliminary C(alpha) trace. Model protein backbone conformation. - @@ -37688,7 +36176,6 @@ 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 - @@ -37702,7 +36189,6 @@ Model loop conformation in protein structures. beta12orEarlier - @@ -37726,11 +36212,11 @@ + Virtual ligand screening Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques. - Virtual ligand screening + Ligand-binding simulation Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. beta12orEarlier - @@ -37758,7 +36244,6 @@ beta12orEarlier RNA inverse folding Nucleic acid folding family identification - @@ -37782,7 +36267,6 @@ beta12orEarlier Single nucleotide polymorphism detection Find single nucleotide polymorphisms (SNPs) between sequences. - @@ -37802,7 +36286,6 @@ 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. - @@ -37843,7 +36326,6 @@ 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 - @@ -37864,7 +36346,6 @@ 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 - @@ -37885,7 +36366,6 @@ Predict genetic code from analysis of codon usage data. beta12orEarlier - @@ -37907,7 +36387,6 @@ Draw a dotplot of sequence similarities identified from word-matching or character comparison. beta12orEarlier - @@ -37927,11 +36406,10 @@ 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 - Align exactly two molecular sequences. Pairwise sequence alignment generation - @@ -37949,7 +36427,6 @@ 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 - @@ -37962,15 +36439,15 @@ Pairwise sequence alignment generation (local) Pairwise sequence alignment construction (local) + 1.6 Local alignment methods identify regions of local similarity. - Local pairwise sequence alignment construction - beta12orEarlier + true Pairwise sequence alignment (local) Locally align exactly two molecular sequences. + Local pairwise sequence alignment construction + beta12orEarlier - 1.6 - true @@ -37981,16 +36458,16 @@ Pairwise sequence alignment generation (global) - beta12orEarlier + Pairwise sequence alignment (global) Global alignment methods identify similarity across the entire length of the sequences. + beta12orEarlier Globally align exactly two molecular sequences. - Pairwise sequence alignment (global) - Pairwise sequence alignment construction (global) + true + 1.6 Global pairwise sequence alignment construction + Pairwise sequence alignment construction (global) - 1.6 - true @@ -38009,7 +36486,6 @@ beta12orEarlier Local multiple sequence alignment construction Multiple sequence alignment (local) - @@ -38029,7 +36505,6 @@ beta12orEarlier Multiple sequence alignment (global) Global multiple sequence alignment construction - @@ -38042,13 +36517,12 @@ Constrained sequence alignment Constrained multiple sequence alignment construction + Sequence alignment (constrained) Multiple sequence alignment (constrained) - Multiple sequence alignment construction (constrained) Sequence alignment generation (constrained) + Multiple sequence alignment construction (constrained) Align two or more molecular sequences with user-defined constraints. beta12orEarlier - Sequence alignment (constrained) - @@ -38060,14 +36534,13 @@ Consensus-based sequence alignment - Align two or more molecular sequences using multiple methods to achieve higher quality. - Sequence alignment generation (consensus) - Consensus multiple sequence alignment construction 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 @@ -38093,7 +36566,6 @@ beta12orEarlier This is supposed to give a more biologically meaningful alignment than standard alignments. Sequence alignment generation (phylogenetic tree-based) - @@ -38106,12 +36578,12 @@ 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 - true @@ -38125,22 +36597,15 @@ - - - - - - - Secondary structure alignment (protein) - Align protein secondary structures. Protein secondary structure alignment + Secondary structure alignment (protein) beta12orEarlier + Align protein secondary structures. Protein secondary structure alignment construction - @@ -38155,8 +36620,8 @@ - - + + @@ -38165,19 +36630,12 @@ - - - - - - beta12orEarlier Secondary structure alignment (RNA) RNA secondary structure alignment construction Align RNA secondary structures. RNA secondary structure alignment RNA secondary structure alignment generation - @@ -38193,7 +36651,6 @@ Pairwise structure alignment construction Pairwise structure alignment beta12orEarlier - @@ -38207,11 +36664,11 @@ beta12orEarlier Multiple structure alignment + true + 1.6 This includes methods that use an existing alignment. Align (superimpose) two or more molecular tertiary structures. - 1.6 - true @@ -38252,16 +36709,16 @@ 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) - beta12orEarlier - Local pairwise structure alignment construction Locally align (superimpose) exactly two molecular tertiary structures. - 1.6 - true @@ -38272,16 +36729,16 @@ Pairwise structure alignment generation (global) - beta12orEarlier Pairwise structure alignment (global) - Global alignment methods identify similarity across the entire structures. Globally align (superimpose) exactly two molecular tertiary structures. - Global pairwise structure alignment construction Pairwise structure alignment construction (global) + 1.6 + beta12orEarlier + true + Global alignment methods identify similarity across the entire structures. + Global pairwise structure alignment construction - 1.6 - true @@ -38293,14 +36750,13 @@ Local structure alignment Structure alignment generation (local) - Multiple structure alignment construction (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 - @@ -38320,7 +36776,6 @@ Structure alignment generation (global) Multiple structure alignment (global) Structure alignment construction (global) - @@ -38340,7 +36795,6 @@ Pairwise sequence profile alignment construction Methods might perform one-to-one, one-to-many or many-to-many comparisons. Sequence alignment generation (pairwise profile) - @@ -38352,15 +36806,15 @@ Sequence alignment generation (multiple profile) - Sequence profile alignment (multiple) - Sequence profile alignment construction (multiple) Multiple sequence profile alignment construction - Sequence profile alignment generation (multiple) + 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 @@ -38371,14 +36825,13 @@ 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) - Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Structural profile alignment generation (pairwise) - Align exactly two molecular Structural (3D) profiles. Pairwise structural (3D) profile alignment construction - + Methods might perform one-to-one, one-to-many or many-to-many comparisons. @@ -38390,14 +36843,14 @@ 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) - - 1.6 true + @@ -38409,12 +36862,12 @@ 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 - true @@ -38425,13 +36878,13 @@ 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 - 1.6 - true @@ -38450,7 +36903,6 @@ beta12orEarlier Predict primers for large scale sequencing. - @@ -38464,7 +36916,6 @@ Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs). beta12orEarlier - @@ -38484,7 +36935,6 @@ beta12orEarlier Predict primers for gene transcription profiling. - @@ -38498,7 +36948,6 @@ beta12orEarlier Predict primers that are conserved across multiple genomes or species. - @@ -38518,7 +36967,6 @@ beta12orEarlier Predict primers based on gene structure, promoters, exon-exon junctions etc. - @@ -38532,7 +36980,6 @@ Predict primers for methylation PCRs. beta12orEarlier - @@ -38547,7 +36994,6 @@ 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. - @@ -38562,7 +37008,6 @@ 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. - @@ -38576,7 +37021,6 @@ beta12orEarlier Sequence assembly capable on a very large scale such as assembly of whole genomes. - @@ -38591,7 +37035,6 @@ 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 - @@ -38614,7 +37057,6 @@ 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. - @@ -38685,7 +37127,6 @@ 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 - @@ -38697,12 +37138,12 @@ Gene expression profile analysis + 1.6 Analyse one or more gene expression profiles, typically to interpret them in functional terms. beta12orEarlier Functional profiling - - 1.6 true + @@ -38723,7 +37164,6 @@ Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway. beta12orEarlier - @@ -38738,7 +37178,6 @@ Assign secondary structure from protein coordinate data. beta12orEarlier - @@ -38758,7 +37197,6 @@ beta12orEarlier Assign secondary structure from circular dichroism (CD) spectroscopic data. - @@ -38769,18 +37207,14 @@ 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 + - + @@ -38789,18 +37223,14 @@ Protein structure assignment (from NMR data) - - - - - - - + + 1.7 + true Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data. beta12orEarlier - + - + @@ -38813,7 +37243,6 @@ Construct a phylogenetic tree from a specific type of data. beta12orEarlier Phylogenetic tree construction (data centric) - @@ -38828,7 +37257,6 @@ beta12orEarlier Construct a phylogenetic tree using a specific method. Phylogenetic tree construction (method centric) - @@ -38845,7 +37273,6 @@ Phylogenetic tree generation (from molecular sequences) beta12orEarlier Phylogenetic tree construction from molecular sequences. - @@ -38866,7 +37293,6 @@ Phylogenetic tree construction from continuous quantitative character data. beta12orEarlier Phylogenetic tree generation (from continuous quantitative characters) - @@ -38880,20 +37306,19 @@ - - + + - - + + Phylogenetic tree generation (from gene frequencies) beta12orEarlier Phylogenetic tree construction from gene frequency data. - @@ -38914,7 +37339,6 @@ 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. - @@ -38929,7 +37353,6 @@ beta12orEarlier Phylogenetic species tree generation Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison. - @@ -38945,7 +37368,6 @@ 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) - @@ -38961,7 +37383,6 @@ Phylogenetic tree construction (minimum distance methods) beta12orEarlier This includes neighbor joining (NJ) clustering method. - @@ -38977,7 +37398,6 @@ 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) - @@ -38992,7 +37412,6 @@ 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 - @@ -39007,7 +37426,6 @@ beta12orEarlier Phylogenetic tree construction (AI methods) Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms. - @@ -39035,7 +37453,6 @@ Identify a plausible model of DNA substitution that explains a DNA sequence alignment. beta12orEarlier Sequence alignment analysis (phylogenetic modelling) - @@ -39050,7 +37467,6 @@ beta12orEarlier Analyse the shape (topology) of a phylogenetic tree. Phylogenetic tree topology analysis - @@ -39065,7 +37481,6 @@ beta12orEarlier Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree. - @@ -39091,7 +37506,6 @@ beta12orEarlier Predict families of genes and gene function based on their position in a phylogenetic tree. - @@ -39106,7 +37520,6 @@ 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 - @@ -39123,7 +37536,6 @@ 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. - @@ -39137,7 +37549,6 @@ Compare two or more phylogenetic trees to detect subtrees or supertrees. beta12orEarlier - @@ -39157,7 +37568,6 @@ Compare two or more phylogenetic trees to calculate distances between trees. beta12orEarlier - @@ -39169,12 +37579,11 @@ Phylogenetic tree annotation + http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation" Annotate a phylogenetic tree with terms from a controlled vocabulary. beta12orEarlier - - @@ -39186,14 +37595,14 @@ - - + + - - + + @@ -39205,7 +37614,6 @@ Predict and optimise peptide ligands that elicit an immunological response. Peptide immunogen prediction beta12orEarlier - @@ -39221,18 +37629,17 @@ - + - + Predict or optimise DNA to elicit (via DNA vaccination) an immunological response. beta12orEarlier - @@ -39246,20 +37653,19 @@ - + - + Sequence file format conversion Reformat (a file or other report of) molecular sequence(s). beta12orEarlier - @@ -39273,19 +37679,18 @@ - + - + beta12orEarlier Reformat (a file or other report of) molecular sequence alignment(s). - @@ -39300,19 +37705,18 @@ - + - + beta12orEarlier Reformat a codon usage table. - @@ -39322,24 +37726,24 @@ - Sequence rendering + Sequence visualisation - - + + - - + + + Sequence rendering Visualise, format or render a molecular sequence, possibly with sequence features or properties shown. beta12orEarlier - @@ -39349,17 +37753,11 @@ - Sequence alignment rendering + Sequence alignment visualisation - - - - - - @@ -39372,7 +37770,7 @@ beta12orEarlier Visualise, format or print a molecular sequence alignment. - + Sequence alignment rendering @@ -39382,12 +37780,12 @@ - Sequence cluster rendering + Sequence cluster visualisation - + @@ -39398,7 +37796,7 @@ Visualise, format or render sequence clusters. beta12orEarlier - + Sequence cluster rendering @@ -39408,7 +37806,7 @@ - Phylogenetic tree rendering + Phylogenetic tree visualisation @@ -39418,8 +37816,8 @@ beta12orEarlier + Phylogenetic tree rendering Render or visualise a phylogenetic tree. - @@ -39429,7 +37827,7 @@ - RNA secondary structure rendering + RNA secondary structure visualisation @@ -39440,7 +37838,7 @@ beta12orEarlier Visualise RNA secondary structure, knots, pseudoknots etc. - + RNA secondary structure rendering @@ -39450,23 +37848,23 @@ + Protein secondary structure visualisation Protein secondary structure rendering - - + + - - + + beta12orEarlier Render and visualise protein secondary structure. - @@ -39476,7 +37874,7 @@ - Structure rendering + Structure visualisation @@ -39493,7 +37891,7 @@ beta12orEarlier Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation. - + Structure rendering @@ -39515,7 +37913,6 @@ beta12orEarlier Visualise microarray data. - @@ -39525,23 +37922,24 @@ + Protein interaction network visualisation Protein interaction network rendering - - + + - - + + Identify and analyse networks of protein interactions. beta12orEarlier - + @@ -39551,7 +37949,7 @@ - Map rendering + Map drawing @@ -39559,10 +37957,10 @@ - Render and visualise a DNA map. - DNA map rendering + Draw or visualise a DNA map. + Map rendering + DNA map drawing beta12orEarlier - @@ -39587,7 +37985,7 @@ - Restriction map rendering + Restriction map drawing @@ -39597,8 +37995,7 @@ beta12orEarlier - Visualise restriction maps in DNA sequences. - + Draw or visualise restriction maps in DNA sequences. @@ -39623,11 +38020,11 @@ - DNA circular map rendering + Plasmid map drawing Draw a circular maps of DNA, for example a plasmid map. + DNA circular map rendering beta12orEarlier - @@ -39637,7 +38034,7 @@ - Operon rendering + Operon drawing @@ -39645,9 +38042,9 @@ + Operon rendering beta12orEarlier Visualise operon structure etc. - @@ -39676,7 +38073,6 @@ Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants. beta12orEarlier - @@ -39714,7 +38110,6 @@ For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. Predict general functional properties of a protein. beta12orEarlier - @@ -39735,7 +38130,6 @@ beta12orEarlier Compare the functional properties of two or more proteins. - @@ -39747,11 +38141,11 @@ Sequence submission + true + 1.6 beta12orEarlier Submit a molecular sequence to a database. - 1.6 - true @@ -39777,7 +38171,6 @@ Analyse a known network of gene regulation. beta12orEarlier - @@ -39799,7 +38192,6 @@ Prepare or load a user-specified data file so that it is available for use. WHATIF:UploadPDB Data loading - @@ -39811,13 +38203,13 @@ 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. - 1.6 - true @@ -39828,14 +38220,14 @@ 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 - - 1.6 true + @@ -39851,7 +38243,6 @@ Calculate the positions of dots that are homogeneously distributed over the surface of a molecule. WHATIF:GetSurfaceDots beta12orEarlier - @@ -39868,7 +38259,6 @@ WHATIF:AtomAccessibilitySolvent WHATIF:AtomAccessibilitySolventPlus beta12orEarlier - @@ -39885,7 +38275,6 @@ Waters are not considered. Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure. beta12orEarlier - @@ -39901,7 +38290,6 @@ Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). beta12orEarlier WHATIF:ResidueAccessibilitySolvent - @@ -39917,7 +38305,6 @@ 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). - @@ -39933,7 +38320,6 @@ 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. - @@ -39949,7 +38335,6 @@ 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). - @@ -39964,7 +38349,6 @@ Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole. beta12orEarlier WHATIF:TotAccessibilityMolecular - @@ -39979,7 +38363,6 @@ beta12orEarlier Calculate the solvent accessibility ('accessible surface') for a structure as a whole. WHATIF:TotAccessibilitySolvent - @@ -39994,7 +38377,6 @@ Calculate for each residue in a protein structure all its backbone torsion angles. WHATIF:ResidueTorsionsBB beta12orEarlier - @@ -40009,7 +38391,6 @@ WHATIF:ResidueTorsions Calculate for each residue in a protein structure all its torsion angles. beta12orEarlier - @@ -40024,7 +38405,6 @@ WHATIF:CysteineTorsions Calculate for each cysteine (bridge) all its torsion angles. beta12orEarlier - @@ -40040,7 +38420,6 @@ Tau is the backbone angle N-Calpha-C (angle over the C-alpha). beta12orEarlier WHATIF:ShowTauAngle - @@ -40055,7 +38434,6 @@ beta12orEarlier Detect cysteine bridges (from coordinate data) in a protein structure. WHATIF:ShowCysteineBridge - @@ -40071,7 +38449,6 @@ 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 - @@ -40086,7 +38463,6 @@ Detect cysteines that are bound to metal in a protein structure. WHATIF:ShowCysteineMetal beta12orEarlier - @@ -40104,7 +38480,6 @@ Calculate protein residue contacts with nucleic acids in a structure. WHATIF:ShowProteiNucleicContacts beta12orEarlier - @@ -40121,7 +38496,6 @@ Calculate protein residue contacts with metal in a structure. beta12orEarlier WHATIF:HasMetalContacts - @@ -40137,7 +38511,6 @@ beta12orEarlier WHATIF:HasNegativeIonContactsPlus Calculate ion contacts in a structure (all ions for all side chain atoms). - @@ -40152,7 +38525,6 @@ 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 - @@ -40168,7 +38540,6 @@ 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. - @@ -40186,7 +38557,6 @@ WHATIF:ShowDrugContactsShort Calculate contacts between residues and ligands in a protein structure. beta12orEarlier - @@ -40198,14 +38568,13 @@ Salt bridge calculation - WHATIF:HasSaltBridgePlus 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. - @@ -40225,12 +38594,11 @@ 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:ShowLikelyRotamers800 WHATIF:ShowLikelyRotamers600 + WHATIF:ShowLikelyRotamers800 Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure. WHATIF:ShowLikelyRotamers500 WHATIF:ShowLikelyRotamers - @@ -40245,7 +38613,6 @@ 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. - @@ -40260,7 +38627,6 @@ WHATIF: PackingQuality Identify poorly packed residues in protein structures. beta12orEarlier - @@ -40276,7 +38642,6 @@ beta12orEarlier Identify for each residue in a protein structure any improper dihedral (phi/psi) angles. WHATIF: ImproperQualitySum - @@ -40308,7 +38673,6 @@ beta12orEarlier WHATIF: HETGroupNames Identify HET groups in PDB files. - @@ -40339,7 +38703,6 @@ WHATIF: PDBasXML beta12orEarlier Reformat (a file or other report of) tertiary structure data. - @@ -40359,7 +38722,6 @@ beta12orEarlier Assign cysteine bonding state and disulfide bond partners in protein structures. - @@ -40375,7 +38737,6 @@ WHATIF: UseResidueDB beta12orEarlier Identify poor quality amino acid positions in protein structures. - @@ -40388,11 +38749,11 @@ Structure retrieval (water) Query a tertiary structure database and retrieve water molecules. + true WHATIF:MovedWaterPDB + 1.6 beta12orEarlier - 1.6 - true @@ -40411,7 +38772,6 @@ Identify or predict siRNA duplexes in RNA. beta12orEarlier - @@ -40426,7 +38786,6 @@ beta12orEarlier Refine an existing sequence alignment. - @@ -40439,10 +38798,10 @@ Listfile processing beta12orEarlier + true Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses). + 1.6 - 1.6 - true @@ -40456,7 +38815,6 @@ 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, or create a file of sequences. - @@ -40468,11 +38826,11 @@ 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 - 1.6 - true @@ -40533,12 +38891,11 @@ - + beta12orEarlier Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences. - @@ -40550,11 +38907,11 @@ Structure file processing + true beta12orEarlier + 1.6 Perform basic (non-analytical) operations on a file of molecular tertiary structural data. - 1.6 - true @@ -40579,13 +38936,13 @@ - Statistical calculation - + Statistical analysis + + true beta12orEarlier Perform a statistical data operation of some type, e.g. calibration or validation. - 1.6 - true - + + @@ -40599,21 +38956,20 @@ - - + + - - + + 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 - @@ -40623,24 +38979,24 @@ - Transmembrane protein rendering + Transmembrane protein visualisation - - + + - - + + + Transmembrane protein rendering beta12orEarlier Visualise transmembrane proteins, typically the transmembrane regions within a sequence. - @@ -40699,7 +39055,6 @@ Calculate a density plot (of base composition) for a nucleotide sequence. beta12orEarlier - @@ -40713,26 +39068,13 @@ - - - - - - - - - - - - Sequence analysis (general) beta12orEarlier Analyse one or more known molecular sequences. - @@ -40746,9 +39088,9 @@ beta12orEarlier Process (read and / or write) molecular sequence motifs. - - 1.6 + 1.6 true + @@ -40760,10 +39102,10 @@ Protein interaction data processing beta12orEarlier + true Process (read and / or write) protein interaction data. + 1.6 - 1.6 - true @@ -40777,26 +39119,19 @@ - - - - - - - - + + - - + + + Analyse protein tertiary structural data. beta12orEarlier Structure analysis (protein) - Analyse protein tertiary structural data. - @@ -40836,7 +39171,7 @@ - Utility operaration + Utility operation @@ -40845,12 +39180,11 @@ Data file processing - Basic (non-analytical) operations of some data, either a file or equivalent entity in memory. File handling Report handling - File processing beta12orEarlier - + File processing + Basic (non-analytical) operations of some data, either a file or equivalent entity in memory. @@ -40877,12 +39211,12 @@ 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 - true @@ -40894,11 +39228,11 @@ Data index processing beta12orEarlier + 1.6 Process (read and / or write) an index of (typically a file of) biological data. + true Database index processing - 1.6 - true @@ -40909,11 +39243,11 @@ Sequence profile processing + 1.6 Process (read and / or write) some type of sequence profile. beta12orEarlier - - 1.6 true + @@ -40933,7 +39267,6 @@ 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. - @@ -40948,21 +39281,20 @@ - - + + - - + + 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. - @@ -40976,14 +39308,14 @@ - - + + - - + + @@ -40995,7 +39327,6 @@ Secondary structure analysis (protein) beta12orEarlier Analyse known protein secondary structure data. - @@ -41032,7 +39363,6 @@ Predict oligonucleotide primers or probes. beta12orEarlier Primer and probe prediction - @@ -41049,7 +39379,6 @@ Processing Calculation Computation - @@ -41070,7 +39399,6 @@ 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 - @@ -41091,7 +39419,6 @@ 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 - @@ -41108,7 +39435,6 @@ Prediction Recognition beta12orEarlier - @@ -41122,7 +39448,6 @@ Compare two or more things to identify similarities. beta12orEarlier - @@ -41136,7 +39461,6 @@ Refine or optimise some data model. beta12orEarlier - @@ -41156,7 +39480,6 @@ Model or simulate some biological entity or system. beta12orEarlier - @@ -41186,7 +39509,6 @@ Validate some data. Validation and standardisation beta12orEarlier - @@ -41213,7 +39535,6 @@ 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. - @@ -41228,7 +39549,6 @@ true Design a biological entity (typically a molecular sequence or structure) with specific properties. beta12orEarlier - @@ -41257,7 +39577,6 @@ beta12orEarlier Process (read and / or write) a codon usage table. - @@ -41285,10 +39604,10 @@ Gene expression profile processing beta12orEarlier + true Process (read and / or write) a gene expression profile. + 1.6 - 1.6 - true @@ -41302,14 +39621,15 @@ - - + + + GO term enrichment + 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 - Annotate a set of genes, e.g. an expression profile, with concepts from an ontology of gene functions. - + Annotate a set of genes (genes corresponding to an expression profile, or any other set) with concepts from an ontology of gene functions. @@ -41324,19 +39644,18 @@ - - + + - - + + beta12orEarlier Predict a network of gene regulation. - @@ -41356,7 +39675,6 @@ beta12orEarlier Generate, analyse or handle a biological pathway or network. - @@ -41376,7 +39694,6 @@ Process (read and / or write) RNA secondary structure data. beta12orEarlier - @@ -41411,7 +39728,6 @@ Predict RNA tertiary structure. beta12orEarlier - @@ -41431,7 +39747,6 @@ beta12orEarlier Predict DNA tertiary structure. - @@ -41451,7 +39766,6 @@ Process (read and / or write) a phylogenetic tree. beta12orEarlier - @@ -41464,10 +39778,10 @@ Protein secondary structure processing beta12orEarlier + true + 1.6 Process (read and / or write) protein secondary structure data. - 1.6 - true @@ -41478,11 +39792,11 @@ Protein interaction network processing + 1.6 Process (read and / or write) a network of protein interactions. beta12orEarlier - - 1.6 true + @@ -41493,12 +39807,12 @@ Sequence processing + 1.6 beta12orEarlier + true Process (read and / or write) one or more molecular sequences and associated annotation. Sequence processing (general) - 1.6 - true @@ -41509,11 +39823,11 @@ Sequence processing (protein) + 1.6 + true beta12orEarlier Process (read and / or write) a protein sequence and associated annotation. - 1.6 - true @@ -41526,9 +39840,9 @@ Process (read and / or write) a nucleotide sequence and associated annotation. beta12orEarlier - - 1.6 true + 1.6 + @@ -41542,12 +39856,6 @@ - - - - - - @@ -41558,9 +39866,14 @@ + + + + + + beta12orEarlier Compare two or more molecular sequences. - @@ -41572,11 +39885,11 @@ Sequence cluster processing + 1.6 beta12orEarlier + true Process (read and / or write) a sequence cluster. - 1.6 - true @@ -41588,10 +39901,10 @@ Feature table processing beta12orEarlier + true + 1.6 Process (read and / or write) a sequence feature table. - 1.6 - true @@ -41600,24 +39913,24 @@ - Gene and gene component prediction + Gene prediction - - + + - - + + Gene finding Detect, predict and identify genes or components of genes in DNA sequences. beta12orEarlier - + Gene and gene component prediction @@ -41639,7 +39952,6 @@ Classify G-protein coupled receptors (GPCRs) into families and subfamilies. G protein-coupled receptor (GPCR) classification beta12orEarlier - @@ -41661,7 +39973,6 @@ beta12orEarlier Predict G-protein coupled receptor (GPCR) coupling selectivity. - @@ -41675,9 +39986,9 @@ Process (read and / or write) a protein tertiary structure. beta12orEarlier - - 1.6 + 1.6 true + @@ -41691,7 +40002,6 @@ beta12orEarlier Calculate the solvent accessibility for each atom in a structure. Waters are not considered. - @@ -41705,7 +40015,6 @@ Calculate the solvent accessibility for each residue in a structure. beta12orEarlier - @@ -41719,7 +40028,6 @@ Calculate the solvent accessibility of a structure as a whole. beta12orEarlier - @@ -41731,11 +40039,11 @@ Sequence alignment processing + 1.6 Process (read and / or write) a molecular sequence alignment. + true beta12orEarlier - 1.6 - true @@ -41760,7 +40068,6 @@ beta12orEarlier Identify or predict protein-protein interactions, interfaces, binding sites etc. - @@ -41774,9 +40081,9 @@ beta12orEarlier Process (read and / or write) a molecular tertiary structure. - - 1.6 + 1.6 true + @@ -41787,11 +40094,11 @@ Map annotation + 1.6 beta12orEarlier + true Annotate a DNA map of some type with terms from a controlled vocabulary. - 1.6 - true @@ -41915,7 +40222,6 @@ beta12orEarlier Compare the architecture of two or more protein structures. - @@ -41932,7 +40238,6 @@ 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 - @@ -41948,8 +40253,8 @@ - - + + @@ -41960,13 +40265,12 @@ - - + + - Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation. beta12orEarlier - + Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation. @@ -41981,14 +40285,14 @@ - - + + - - + + @@ -42000,7 +40304,6 @@ Sequence analysis (nucleic acid) beta12orEarlier Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences). - @@ -42015,20 +40318,19 @@ - - + + - - + + beta12orEarlier Sequence analysis (protein) Analyse a protein sequence (using methods that are only applicable to protein sequences). - @@ -42042,25 +40344,12 @@ - - - - - - - - - - - - Analyse known molecular tertiary structures. beta12orEarlier - @@ -42075,25 +40364,18 @@ - - - - - - - - + + - - + + beta12orEarlier Analyse nucleic acid tertiary structural data. - @@ -42106,10 +40388,10 @@ Secondary structure processing beta12orEarlier + true Process (read and / or write) a molecular secondary structure. + 1.6 - 1.6 - true @@ -42129,7 +40411,6 @@ Compare two or more molecular tertiary structures. beta12orEarlier - @@ -42139,7 +40420,7 @@ - Helical wheel rendering + Helical wheel drawing @@ -42149,7 +40430,7 @@ Render a helical wheel representation of protein secondary structure. beta12orEarlier - + Helical wheel rendering @@ -42159,7 +40440,7 @@ - Topology diagram rendering + Topology diagram drawing @@ -42169,7 +40450,7 @@ Render a topology diagram of protein secondary structure. beta12orEarlier - + Topology diagram rendering @@ -42185,21 +40466,14 @@ - - - - - - Compare protein tertiary structures. - beta12orEarlier Methods might identify structural neighbors, find structural similarities or define a structural core. Structure comparison (protein) - + beta12orEarlier @@ -42219,11 +40493,10 @@ - beta12orEarlier - Compare protein secondary structures. Protein secondary structure Secondary structure comparison (protein) - + beta12orEarlier + Compare protein secondary structures. @@ -42246,7 +40519,6 @@ 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. - @@ -42260,7 +40532,6 @@ Calculate contacts between residues in a protein structure. beta12orEarlier - @@ -42275,7 +40546,6 @@ beta12orEarlier Identify potential hydrogen bonds between amino acid residues. - @@ -42302,7 +40572,6 @@ beta12orEarlier Predict the interactions of proteins with other molecules. - @@ -42338,10 +40607,9 @@ 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 - beta12orEarlier - Gene expression profile analysis Gene expression (microarray) data processing - + Gene expression profile analysis + beta12orEarlier @@ -42353,10 +40621,10 @@ Gene regulatory network processing + true Process (read and / or write) a network of gene regulation. beta12orEarlier - 1.6 - true + 1.6 @@ -42369,12 +40637,6 @@ - - - - - - @@ -42383,7 +40645,6 @@ Network analysis Pathway analysis Analyse a known biological pathway or network. - @@ -42414,20 +40675,19 @@ - - + + - - + + beta12orEarlier Splicing analysis Analyse, characterize and model alternative splicing events from comparing multiple nucleic acid sequences. - @@ -42463,7 +40723,6 @@ beta12orEarlier Nucleic acid data processing Process (read and / or write) nucleic acid sequence or structural data. - @@ -42484,7 +40743,6 @@ Process (read and / or write) protein sequence or structural data. Protein data processing beta12orEarlier - @@ -42525,11 +40783,11 @@ Text processing + 1.6 Process (read and / or write) text. beta12orEarlier - - 1.6 true + @@ -42548,16 +40806,9 @@ - - - - - - - beta12orEarlier Sequence alignment analysis (protein) + beta12orEarlier Analyse a protein sequence alignment, typically to detect features or make predictions. - @@ -42577,16 +40828,9 @@ - - - - - - Analyse a protein sequence alignment, typically to detect features or make predictions. Sequence alignment analysis (nucleic acid) beta12orEarlier - @@ -42603,7 +40847,6 @@ beta12orEarlier Compare two or more nucleic acid sequences. Sequence comparison (nucleic acid) - @@ -42620,7 +40863,6 @@ Compare two or more protein sequences. Sequence comparison (protein) beta12orEarlier - @@ -42640,7 +40882,6 @@ Back-translate a protein sequence into DNA. beta12orEarlier - @@ -42660,7 +40901,6 @@ beta12orEarlier Edit or change a nucleic acid sequence, either randomly or specifically. - @@ -42681,7 +40921,6 @@ beta12orEarlier Edit or change a protein sequence, either randomly or specifically. - @@ -42701,7 +40940,6 @@ beta12orEarlier Generate a nucleic acid sequence by some means. - @@ -42722,7 +40960,6 @@ beta12orEarlier Generate a protein sequence by some means. - @@ -42732,7 +40969,7 @@ - Sequence rendering (nucleic acid) + Sequence visualisation (nucleic acid) @@ -42741,9 +40978,9 @@ beta12orEarlier + Sequence rendering (nucleic acid) Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. Visualise, format or render a nucleic acid sequence. - @@ -42753,13 +40990,13 @@ - Sequence rendering (protein) + Sequence visualisation (protein) - + Protein sequence visualisation @@ -42767,7 +41004,7 @@ Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. Protein sequence rendering Visualise, format or render a protein sequence. - + Sequence rendering (protein) @@ -42784,7 +41021,6 @@ Structure comparison (nucleic acid) beta12orEarlier Compare nucleic acid tertiary structures. - @@ -42797,10 +41033,10 @@ Structure processing (nucleic acid) Process (read and / or write) nucleic acid tertiary structure data. + true beta12orEarlier + 1.6 - 1.6 - true @@ -42819,7 +41055,6 @@ Generate a map of a DNA sequence annotated with positional or non-positional features of some type. beta12orEarlier - @@ -42831,12 +41066,12 @@ Map data processing + 1.6 + true beta12orEarlier Process (read and / or write) a DNA map of some type. DNA map data processing - 1.6 - true @@ -42849,19 +41084,18 @@ - - + + - - + + Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information). beta12orEarlier - @@ -42881,20 +41115,19 @@ - - + + - - + + Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures. beta12orEarlier Ligand-binding and active site prediction - @@ -42916,7 +41149,6 @@ 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 - @@ -42938,7 +41170,6 @@ beta12orEarlier Alignment Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits. - @@ -42953,7 +41184,6 @@ Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data. beta12orEarlier - @@ -42973,7 +41203,6 @@ beta12orEarlier Compare the physicochemical properties of two or more proteins (or reference data). - @@ -42993,7 +41222,6 @@ beta12orEarlier Compare two or more molecular secondary structures. - @@ -43008,7 +41236,6 @@ Generate a Hopp and Woods plot of antigenicity of a protein. beta12orEarlier - @@ -43018,11 +41245,10 @@ - Microarray cluster textual view rendering + Microarray cluster textual view generation Visualise gene clusters with gene names. beta12orEarlier - @@ -43032,13 +41258,13 @@ - Microarray wave graph rendering + 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 @@ -43048,13 +41274,13 @@ - Microarray dendrograph rendering + Microarray dendrograph plotting Microarray view rendering Microarray checks view rendering beta12orEarlier Generate a dendrograph of raw, preprocessed or clustered microarray data. - + Microarray dendrograph rendering @@ -43064,12 +41290,12 @@ - Microarray proximity map rendering + Microarray proximity map plotting + Microarray proximity map rendering Generate a plot of distances (distance matrix) between genes. Microarray distance map rendering beta12orEarlier - @@ -43079,13 +41305,12 @@ - Microarray tree or dendrogram view rendering + Microarray tree or dendrogram rendering Microarray matrix tree plot rendering - Microarray 2-way dendrogram 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 @@ -43095,11 +41320,11 @@ - Microarray principal component rendering + 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 - @@ -43109,11 +41334,11 @@ - Microarray scatter plot rendering + Microarray scatter plot plotting + Microarray scatter plot rendering beta12orEarlier Generate a scatter plot of microarray data, typically after principal component analysis. - @@ -43123,11 +41348,11 @@ - Whole microarray graph view rendering + Whole microarray graph plotting + Whole microarray graph rendering beta12orEarlier Visualise gene expression data where each band (or line graph) corresponds to a sample. - @@ -43141,7 +41366,6 @@ Visualise gene expression data after hierarchical clustering for representing hierarchical relationships. beta12orEarlier - @@ -43151,11 +41375,10 @@ - Microarray Box-Whisker plot rendering + 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 - @@ -43169,19 +41392,18 @@ - - + + - - + + 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 - @@ -43197,7 +41419,6 @@ For non-analytical operations, see the 'Processing' branch. Apply analytical methods to existing data of a specific type. - @@ -43211,9 +41432,9 @@ Analyse an existing alignment of two or more molecular sequences, structures or derived data. beta12orEarlier - - 1.6 true + 1.6 + @@ -43245,7 +41466,6 @@ Article analysis beta12orEarlier Analyse a body of scientific text (typically a full text article from a scientific journal.) - @@ -43273,19 +41493,18 @@ - - + + - - + + Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions. beta12orEarlier - @@ -43299,7 +41518,6 @@ beta12orEarlier Calculate contacts between residues and some other group in a protein structure. - @@ -43312,11 +41530,11 @@ Alignment processing beta12orEarlier + 1.6 Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data. + true - 1.6 - true @@ -43327,11 +41545,11 @@ Structure alignment processing + true beta12orEarlier + 1.6 Process (read and / or write) a molecular tertiary (3D) structure alignment. - 1.6 - true @@ -43350,7 +41568,6 @@ beta12orEarlier Calculate codon usage bias. - @@ -43371,7 +41588,6 @@ Generate a codon usage bias plot. beta12orEarlier - @@ -43391,7 +41607,6 @@ beta12orEarlier Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc. - @@ -43405,7 +41620,6 @@ 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 - @@ -43434,7 +41648,6 @@ Assign molecular sequence(s) to a group or category. beta12orEarlier - @@ -43449,7 +41662,6 @@ beta12orEarlier Assign molecular structure(s) to a group or category. - @@ -43463,7 +41675,6 @@ beta12orEarlier Compare two or more proteins (or some aspect) to identify similarities. - @@ -43477,7 +41688,6 @@ Compare two or more nucleic acids to identify similarities. beta12orEarlier - @@ -43491,7 +41701,6 @@ Predict, recognise, detect or identify some properties of proteins. beta12orEarlier - @@ -43505,7 +41714,6 @@ Predict, recognise, detect or identify some properties of nucleic acids. beta12orEarlier - @@ -43525,7 +41733,6 @@ Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically. beta13 - @@ -43539,7 +41746,6 @@ beta13 Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically. - @@ -43549,7 +41755,7 @@ - Pathway or network rendering + Pathway or network visualisation @@ -43559,8 +41765,8 @@ beta13 + Pathway or network rendering Render (visualise) a biological pathway or network. - @@ -43572,12 +41778,12 @@ 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 - 1.6 - true @@ -43596,7 +41802,6 @@ 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 - @@ -43611,7 +41816,6 @@ 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 - @@ -43624,10 +41828,10 @@ Protein feature prediction (from structure) Predict, recognise and identify positional features in proteins from analysing protein structure. + true + 1.6 beta13 - 1.6 - true @@ -43641,20 +41845,20 @@ - - + + - - + + - + Features includes functional sites or regions and secondary structure. Sequence-based methods typically involve scanning for known motifs, patterns and regular expressions. @@ -43662,7 +41866,6 @@ Protein feature recognition beta13 Predict, recognise and identify positional features in proteins from analysing protein sequences or structures. - @@ -43676,10 +41879,10 @@ 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 - 1.6 - true @@ -43704,7 +41907,6 @@ Predict a network of protein interactions. beta13 - @@ -43719,7 +41921,6 @@ Design (or predict) nucleic acid sequences with specific chemical or physical properties. beta13 - @@ -43733,7 +41934,6 @@ Edit, convert or otherwise change a data entity, either randomly or specifically. beta13 - @@ -43766,7 +41966,6 @@ Evaluate a DNA sequence assembly, typically for purposes of quality control. 1.1 - @@ -43782,7 +41981,6 @@ 1.1 Genome alignment construction Align two or more (tpyically huge) molecular sequences that represent genomes. - @@ -43796,7 +41994,6 @@ 1.1 Reconstruction of a sequence assembly in a localised area. - @@ -43806,14 +42003,13 @@ - Sequence assembly rendering + Sequence assembly visualisation Assembly visualisation 1.1 Render and visualise a DNA sequence assembly. + Sequence assembly rendering Assembly rendering - Sequence assembly visualisation - @@ -43836,7 +42032,6 @@ Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer. 1.1 Phred base calling - @@ -43853,7 +42048,6 @@ 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 - @@ -43873,7 +42067,6 @@ Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced. beta12orEarlier - @@ -43888,7 +42081,6 @@ 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 - @@ -43902,7 +42094,6 @@ 1.1 Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences. - @@ -43916,7 +42107,6 @@ Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. 1.1 - @@ -43930,7 +42120,6 @@ Cut (remove) the end from a molecular sequence. 1.1 - @@ -43945,7 +42134,6 @@ 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. - @@ -43967,7 +42155,6 @@ beta12orEarlier Short-read error correction Short read error correction - @@ -43982,7 +42169,6 @@ 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 - @@ -44001,12 +42187,11 @@ - Genetic variation annotation - 1.1 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 @@ -44031,7 +42216,6 @@ Oligonucleotide alignment generation Oligonucleotide mapping Short oligonucleotide alignment - @@ -44045,7 +42229,6 @@ 1.1 A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation. - @@ -44060,7 +42243,6 @@ 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. - @@ -44075,7 +42257,6 @@ 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. - @@ -44090,7 +42271,6 @@ 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 - @@ -44105,7 +42285,6 @@ 1.1 Chromatogram viewing Visualise, format or render an image of a Chromatogram. - @@ -44119,7 +42298,6 @@ Determine cytosine methylation states in nucleic acid sequences. 1.1 - @@ -44134,7 +42312,6 @@ Determine cytosine methylation status of specific positions in a nucleic acid sequences. 1.1 - @@ -44149,7 +42326,6 @@ 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 - @@ -44165,7 +42341,6 @@ Measure the level of methyl cytosines in specific genes. Many different techniques are available for this. Gene-specific methylation analysis - @@ -44175,15 +42350,15 @@ - Genome rendering + 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 - @@ -44198,7 +42373,6 @@ Genomic region matching 1.1 Compare the sequence or features of two or more genomes, for example, to find matching regions. - @@ -44219,7 +42393,6 @@ 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. - @@ -44234,7 +42407,6 @@ 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. - @@ -44250,7 +42422,6 @@ suffix arrays Generate an index of a genome sequence using a suffix arrays algorithm. 1.1 - @@ -44267,7 +42438,6 @@ Spectrum analysis 1.1 Spectral analysis - @@ -44285,10 +42455,10 @@ - Identify peaks in a spectrum from a mass spectrometry experiment. + Identify peaks in a spectrum from a mass spectrometry, NMR, or some other spectrum-generating experiment. + Peak assignment Peak finding 1.1 - @@ -44307,12 +42477,11 @@ + Scaffold generation Scaffold may be positioned along a chromosome physical map to create a "golden path". 1.1 - Scaffold generation 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 - @@ -44327,7 +42496,6 @@ 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. - @@ -44344,7 +42512,6 @@ Sequencing QC Analyse raw sequence data from a sequencing pipeline and identify problems. Raw sequence data quality control. - @@ -44361,7 +42528,6 @@ 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 - @@ -44381,7 +42547,6 @@ 1.1 Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples. - @@ -44397,7 +42562,6 @@ 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'). - @@ -44413,7 +42577,6 @@ 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. - @@ -44428,7 +42591,6 @@ 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 - @@ -44444,7 +42606,6 @@ 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. - @@ -44459,7 +42620,6 @@ 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. - @@ -44475,7 +42635,6 @@ Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence. 1.1 Variant mapping - @@ -44490,7 +42649,6 @@ 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). - @@ -44507,7 +42665,6 @@ Exome sequencing is considered a cheap alternative to whole genome sequencing. Targeted exome capture 1.1 - @@ -44521,7 +42678,6 @@ Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications. 1.1 - @@ -44544,7 +42700,6 @@ eQTL profiling 1.1 expression quantitative trait loci profiling - @@ -44560,7 +42715,6 @@ 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). - @@ -44575,7 +42729,6 @@ Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products). 1.2 - @@ -44601,7 +42754,6 @@ 1.2 Infer a transcriptome sequence by analysis of short sequence reads. - @@ -44615,10 +42767,10 @@ 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 - 1.6 - true @@ -44629,11 +42781,11 @@ Transcriptome assembly (mapping) + true 1.2 + 1.6 Infer a transcriptome sequence by mapping short reads to a reference genome. - 1.6 - true @@ -44658,7 +42810,6 @@ 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 - @@ -44672,7 +42823,6 @@ 1.3 Calculate similarity between 2 or more documents. - @@ -44687,7 +42837,6 @@ 1.3 Cluster (group) documents on the basis of their calculated similarity. - @@ -44705,7 +42854,6 @@ Entity extraction Entity chunking Entity identification - @@ -44722,7 +42870,6 @@ Accession mapping 1.3 Identifier mapping - @@ -44737,7 +42884,6 @@ Data anonymisation 1.3 Process data in such a way that makes it hard to trace to the person which the data concerns. - @@ -44763,7 +42909,6 @@ Data retrieval (ID) Data retrieval (accession) id retrieval - @@ -44777,20 +42922,19 @@ - - + + - - + + Sequence checksum generation 1.4 Generate a checksum of a molecular sequence. - @@ -44805,7 +42949,6 @@ 1.4 Construct a bibliography from the scientific literature. Bibliography construction - @@ -44819,7 +42962,6 @@ Predict the structure of a multi-subunit protein and particularly how the subunits fit together. 1.4 - @@ -44833,7 +42975,6 @@ Analyse the surface properties of proteins. 1.4 - @@ -44847,7 +42988,6 @@ Compare two or more ontologies, e.g. identify differences. 1.4 - @@ -44861,7 +43001,6 @@ Compare two or more ontologies, e.g. identify differences. 1.4 - @@ -44875,14 +43014,14 @@ - - + + - - + + Format inference @@ -44892,14 +43031,13 @@ 1.4 Recognition of which format the given data is in. - The has_input "Data" (data_0006) may cause visualisation or other problems although ontologically correct. But on the other hand it may be useful to distinguish from nullary operations without inputs. - + @@ -44913,7 +43051,6 @@ 1.4 Split a file containing multiple data items into many files, each containing one item File splitting - @@ -44929,7 +43066,6 @@ For non-analytical operations, see the 'Processing' branch. beta12orEarlier Construction - @@ -44947,7 +43083,6 @@ 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 - @@ -44967,7 +43102,6 @@ Database submission 1.6 Deposit some data in a database. - @@ -44981,7 +43115,6 @@ 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). 1.6 - @@ -44997,7 +43130,6 @@ Reformatting XXX Format conversion - @@ -45011,7 +43143,6 @@ Non-analytical data conversion. 1.6 - @@ -45025,7 +43156,6 @@ Standardize or normalize data. 1.6 - @@ -45039,7 +43169,6 @@ 1.6 Combine multiple files or data items into a single file or object. - @@ -45053,7 +43182,6 @@ 1.6 Compare two or more scientific articles. - @@ -45067,7 +43195,6 @@ 1.6 Mathemetical determination of the value of something, typically a properly of a molecule. - @@ -45082,7 +43209,6 @@ Predict a molecular pathway or network. 1.6 - @@ -45096,7 +43222,6 @@ The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated. 1.6 - @@ -45110,57 +43235,405 @@ 1.6 Generate a graph, or other visual representation, of data, showing the relationship between two or more variables. - + + + + Image analysis + + + + + + + + The analysis of a image (typically a digital image) of some type in order to extract information from it. + 1.7 + + + + + + + + + + + Diffraction data analysis + + Analysis of data from a diffraction experiment. + 1.7 + + + + + + + + + + Cell migration analysis + + + + + + + + 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 + + + + + + + + + + Diffraction data reduction + + Processing of diffraction data into a corrected, ordered, and simplified form. + 1.7 + + + + + + + + + + Neurite measurement + + + + + + + + 1.7 + Measurement of neurites; projections (axons or dendrites) from the cell body of a neuron, from analysis of neuron images. + + + + + + + + + + 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 + + + + + + + + + + Phasing + + 1.7 + Phase a macromolecular crystal structure, for example by using molecular replacement or experimental phasing methods. + + + + + + + + + + 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 + + + + + + + + + + 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 + + + + + + + + + + Single particle analysis + + + + + + + + + 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. + + + + + + + + + + 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. + + + + + + + + + + Functional clustering + + + + + + + + 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 + + + + + + + + + + Taxonomic classification + + Classifiication of molecular sequences by assignment to some taxonomic hierarchy. + 1.7 + + + + + + + + + + Virulence prediction + + + + + + + + + 1.7 + The prediction of the degree of pathogenicity of a microorganism from analysis of molecular sequences. + Pathogenicity prediction + + + + + + + + + + Gene expression correlation analysis + + + Analyse the correlation patterns among genes across across a variety of experiments, microarray samples etc. + + Gene co-expression network analysis + 1.7 + + + + + + + + + + RNA structure covariance model generation + + + + + + + + + 1.7 + Compute the covariance model for (a family of) RNA secondary structures. + + + + + + + + + + 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 + + + + + + + + + + Nucleic acid alignment folding prediction (alignment-based) + + Prediction of nucleic-acid folding using sequence alignments as a source of data. + 1.7 + + + + + + + + + + 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. + + + + + + + + + + Phylogenetic tree reconstruction + + + + + + + + 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. + + + + + + + + + + Probabilistic data generation + + 1.7 + Generate some data from a choosen probibalistic model, possibly to evaluate algorithms. + + + + + + + + + + Probabilistic sequence generation + + + Generate sequences from some probabilistic model, e.g. a model that simulates evolution. + 1.7 + + + + + + + + + + Antimicrobial resistance prediction + + + + + + + + + Identify or predict causes for antibiotic resistance from molecular sequence analysis. + 1.7 + + + + + + Topic + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality" sumo:FieldOfStudy beta12orEarlier + http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research" 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.ifomis.org/bfo/1.1/snap#Continuant" + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method" + http://www.ifomis.org/bfo/1.1/snap#Quality" + http://purl.org/biotop/biotop.owl#Quality" + http://www.onto-med.de/ontologies/gfo.owl#Category" + http://www.onto-med.de/ontologies/gfo.owl#Perpetuant" - - - - - - - - Topic can be a quality of an entity. - - - - - - GFO 'Category' is in general broader than topic, but it may be seen narrower in the sense that it can be instantiated. - - - - - - GFO 'Perpetuant' is in general broader than topic, but depending on metaphysical (non-)beliefs it may be seen narrower in the sense of being a concrete individual and exhibiting presentials. - - - - - - BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the topic. - - - - @@ -45172,13 +43645,12 @@ Topic concerning the processing and analysis of nucleic acid sequence, structural and other data. beta12orEarlier Nucleic acid physicochemistry + http://purl.bioontology.org/ontology/MSH/D017422" + http://purl.bioontology.org/ontology/MSH/D017423" Nucleic acid properties - Nucleic acid informatics Nucleic acid analysis + Nucleic acid informatics Nucleic acid bioinformatics - - - @@ -45193,11 +43665,10 @@ beta12orEarlier Protein analysis Protein databases + Protein informatics Protein bioinformatics + http://purl.bioontology.org/ontology/MSH/D020539" Topic concerning archival, processing and analysis of protein data, typically molecular sequence and structural data. - Protein informatics - - @@ -45213,7 +43684,6 @@ 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 - @@ -45225,13 +43695,12 @@ Sequence analysis + http://purl.bioontology.org/ontology/MSH/D017421" + 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 Sequences Sequence databases - 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. beta12orEarlier - - @@ -45251,9 +43720,8 @@ Structural bioinformatics Structure analysis 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" Computational structural biology - - @@ -45268,7 +43736,6 @@ beta12orEarlier Topic concerning the prediction of molecular (secondary or tertiary) structure. - @@ -45284,7 +43751,6 @@ Topic concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment). true beta12orEarlier - @@ -45301,7 +43767,7 @@ 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 - BioCatalogue:Statistical Robustness + http://purl.bioontology.org/ontology/MSH/D010802" Topic concerning the study of evolutionary relationships amongst organisms. Phylogenetic clocks Phylogenetic dating @@ -45309,8 +43775,6 @@ beta12orEarlier Phylogenetic stratigraphy Phylogeny reconstruction - - @@ -45327,7 +43791,6 @@ 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 - @@ -45339,17 +43802,16 @@ 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 beta12orEarlier + http://purl.bioontology.org/ontology/MSH/D002965" Terminology BioCatalogue:Ontology - - @@ -45362,8 +43824,8 @@ Data search, query and 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 + 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 @@ -45373,7 +43835,6 @@ This includes, for example, search, query and retrieval of molecular sequences and associated data. Data retrieval beta12orEarlier - @@ -45388,9 +43849,8 @@ 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. - - @@ -45407,7 +43867,6 @@ 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 - @@ -45436,14 +43895,13 @@ RNA structure Nucleic acid thermodynamics Nucleic acid structure - RNA structure alignment 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. - @@ -45457,7 +43915,6 @@ Topic concerning RNA sequences and structures. beta12orEarlier - @@ -45484,13 +43941,13 @@ Mapping + Synteny Linkage 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. Linkage Genetic linkage beta12orEarlier Topic concerning the mapping of complete (typically nucleotide) sequences. - @@ -45521,7 +43978,6 @@ beta12orEarlier Topic concerning the translation of mRNA into protein and subsequent protein processing in the cell. Translation - @@ -45602,7 +44058,6 @@ Topic concerning resources that aim to identify, predict, model, analyse or curate gene structure in DNA sequences. This includes introns, exons, and gene fusion. beta12orEarlier This includes the study of promoters, coding regions etc. - @@ -45620,9 +44075,8 @@ 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 + http://purl.bioontology.org/ontology/MSH/D040901" beta12orEarlier - - @@ -45639,7 +44093,6 @@ Topic concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism. beta12orEarlier BioCatalogue:Structural Genomics - @@ -45656,7 +44109,6 @@ 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. - @@ -45679,7 +44131,6 @@ This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. Protein-RNA interaction Protein-nucleic acid interactions - @@ -45692,13 +44143,12 @@ Protein folding, stability and design Rational protein design - Protein stability - Protein folding 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. - @@ -45774,7 +44224,6 @@ 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 - @@ -45912,7 +44361,6 @@ Topic concerning carbohydrates, typically including structural information. beta12orEarlier - @@ -45926,7 +44374,6 @@ Topic concerning lipids and their structures. beta12orEarlier - @@ -45942,7 +44389,6 @@ 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. - @@ -45978,7 +44424,6 @@ Sequence complexity beta12orEarlier Repeat sequences - @@ -46006,12 +44451,11 @@ 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 - Topic concerning the comparison of two or more molecular sequences. - @@ -46035,7 +44479,6 @@ positional features such as functional and other key sites, in molecular sequenc Functional sites Protein functional sites Sequence features - @@ -46062,15 +44505,16 @@ 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. - + - + @@ -46082,12 +44526,11 @@ positional features such as functional and other key sites, in molecular sequenc 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. This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on. - Structural motifs Protein structural features - + 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. @@ -46119,7 +44562,6 @@ positional features such as functional and other key sites, in molecular sequenc BioCatalogue:Protein Structure Prediction Topic concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features. beta12orEarlier - @@ -46141,7 +44583,6 @@ positional features such as functional and other key sites, in molecular sequenc RNA structure prediction Nucleic acid design DNA structure prediction - @@ -46152,13 +44593,14 @@ positional features such as functional and other key sites, in molecular sequenc Ab initio structure prediction - + beta12orEarlier - de novo protein structure prediction + 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 + - + @@ -46188,7 +44630,6 @@ positional features such as functional and other key sites, in molecular sequenc 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. - @@ -46202,7 +44643,6 @@ positional features such as functional and other key sites, in molecular sequenc Topic concerning the modelling the structure of proteins in complex with small molecules or other macromolecules. beta12orEarlier - @@ -46249,7 +44689,6 @@ positional features such as functional and other key sites, in molecular sequenc 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). - @@ -46260,20 +44699,15 @@ positional features such as functional and other key sites, in molecular sequenc Sequence alignment - - BioCatalogue:Protein Multiple Alignment - BioCatalogue:Protein Pairwise 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. - BioCatalogue:Nucleotide Multiple Alignment - BioCatalogue:Protein Sequence Alignment - BioCatalogue:Nucleotide Pairwise Alignment - BioCatalogue:Nucleotide Sequence Alignment - - + - + @@ -46282,14 +44716,16 @@ 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). Structure alignment generation - + - + @@ -46352,7 +44788,6 @@ positional features such as functional and other key sites, in molecular sequenc 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 - @@ -46386,7 +44821,6 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence. Assembly - @@ -46401,10 +44835,9 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier Polymorphism Mutation + http://purl.bioontology.org/ontology/MSH/D014644" Topic concerning DNA sequence variation (mutation and polymorphism) data. DNA variation - - @@ -46420,10 +44853,10 @@ positional features such as functional and other key sites, in molecular sequenc 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 - @@ -46438,7 +44871,6 @@ positional features such as functional and other key sites, in molecular sequenc Pharmacoinformatics beta12orEarlier Computational pharmacology - @@ -46462,8 +44894,7 @@ positional features such as functional and other key sites, in molecular sequenc Gene expression profiling BioCatalogue:Microarrays This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on. - - + http://purl.bioontology.org/ontology/MSH/D015870" @@ -46478,7 +44909,6 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier Topic concerning primarily the regulation of gene expression. - @@ -46493,7 +44923,6 @@ positional features such as functional and other key sites, in molecular sequenc 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 - @@ -46511,7 +44940,6 @@ positional features such as functional and other key sites, in molecular sequenc 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. - @@ -46598,7 +45026,7 @@ positional features such as functional and other key sites, in molecular sequenc - Text mining + Data mining BioCatalogue:Document Clustering BioCatalogue:Document Similarity @@ -46607,9 +45035,9 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier Topic concerning the analysis of the biomedical and informatics literature. Literature mining + Text mining Literature analysis BioCatalogue:Named Entity Recognition - @@ -46630,7 +45058,6 @@ positional features such as functional and other key sites, in molecular sequenc Genome annotation beta12orEarlier Curation - @@ -46652,7 +45079,6 @@ positional features such as functional and other key sites, in molecular sequenc This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. Topic concerning basic manipulations of files or reports of generic biological data. File handling - @@ -46694,14 +45120,20 @@ positional features such as functional and other key sites, in molecular sequenc - NMR spectroscopy + 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 + NMR spectroscopy Spectroscopy Nuclear magnetic resonance spectroscopy + Heteronuclear Overhauser Effect Spectroscopy beta12orEarlier + HOESY + Nuclear Overhauser Effect Spectroscopy + NOESY + ROESY @@ -46717,7 +45149,6 @@ positional features such as functional and other key sites, in molecular sequenc 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 - @@ -46767,7 +45198,6 @@ positional features such as functional and other key sites, in molecular sequenc Protein post-translational modification Topic concerning protein chemical modifications, e.g. post-translational modifications. GO:0006464 - @@ -46789,7 +45219,6 @@ positional features such as functional and other key sites, in molecular sequenc Network or pathway analysis Biological networks BioCatalogue:Pathway Retrieval - @@ -46836,7 +45265,6 @@ positional features such as functional and other key sites, in molecular sequenc 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. - @@ -46868,12 +45296,11 @@ positional features such as functional and other key sites, in molecular sequenc Environmental science Ecoinformatics - beta12orEarlier Computational ecology + beta12orEarlier + http://purl.bioontology.org/ontology/MSH/D004777" Ecological informatics Topic concerning the ecological and environmental sciences and especially the application of information technology (ecoinformatics). - - @@ -46887,8 +45314,16 @@ positional features such as functional and other key sites, in molecular sequenc Electron microscopy - Topic concerning the use of electrons to analyse structures at resolutions higher than can be achieved using light. + Single particle electron microscopy + Electron diffraction experiment + Electron crystallography beta12orEarlier + Transmission electron microscopy + 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 @@ -46920,7 +45355,6 @@ positional features such as functional and other key sites, in molecular sequenc Amino acids Topic concerning the physicochemical, biochemical or structural properties of amino acids or peptides. beta12orEarlier - @@ -46994,7 +45428,6 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier Topic concerning the structures of drugs, drug target, their interactions and binding affinities. Drug structures - @@ -47011,7 +45444,6 @@ positional features such as functional and other key sites, in molecular sequenc 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. - @@ -47024,11 +45456,10 @@ positional features such as functional and other key sites, in molecular sequenc Genomics + http://purl.bioontology.org/ontology/MSH/D023281" 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. BioCatalogue:Genomics - - @@ -47048,7 +45479,6 @@ positional features such as functional and other key sites, in molecular sequenc Gene system Gene family beta12orEarlier - @@ -47063,7 +45493,6 @@ positional features such as functional and other key sites, in molecular sequenc Topic concerning chromosomes. beta12orEarlier - @@ -47079,7 +45508,6 @@ positional features such as functional and other key sites, in molecular sequenc 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 - @@ -47117,8 +45545,7 @@ positional features such as functional and other key sites, in molecular sequenc Gene design This includes the design of primers for PCR and DNA amplification or the design of molecular probes. Probes - - + http://purl.bioontology.org/ontology/MSH/D015335" @@ -47133,7 +45560,6 @@ positional features such as functional and other key sites, in molecular sequenc Diseases beta12orEarlier Topic concerning diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases. - @@ -47161,13 +45587,11 @@ positional features such as functional and other key sites, in molecular sequenc Taxonomy - - 1.3 - true + Topic concerning organism classification, identification and naming. beta12orEarlier - - + + @@ -47181,7 +45605,6 @@ positional features such as functional and other key sites, in molecular sequenc Topic concerning archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. BioCatalogue:Protein Sequence Analysis beta12orEarlier - @@ -47196,7 +45619,6 @@ positional features such as functional and other key sites, in molecular sequenc Topic concerning the archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles. BioCatalogue:Nucleotide Sequence Analysis beta12orEarlier - @@ -47257,7 +45679,6 @@ positional features such as functional and other key sites, in molecular sequenc Topic concerning DNA sequences and structure, including processes such as methylation and replication. beta12orEarlier DNA analysis - @@ -47274,7 +45695,6 @@ positional features such as functional and other key sites, in molecular sequenc cDNA Topic concerning messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences. EST - @@ -47292,7 +45712,6 @@ positional features such as functional and other key sites, in molecular sequenc 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). Functional RNA Non-coding RNA - @@ -47337,7 +45756,6 @@ positional features such as functional and other key sites, in molecular sequenc Topic concerning protein secondary structure or secondary structure alignments. beta12orEarlier Protein secondary structure analysis - @@ -47368,7 +45786,6 @@ positional features such as functional and other key sites, in molecular sequenc Protein tertiary structure analysis Topic concerning protein tertiary structures. BioCatalogue:Protein Tertiary Structure - @@ -47401,7 +45818,6 @@ positional features such as functional and other key sites, in molecular sequenc 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. - @@ -47419,7 +45835,6 @@ positional features such as functional and other key sites, in molecular sequenc Protein folds beta12orEarlier Topic concerning protein tertiary structural domains and folds. - @@ -47435,7 +45850,7 @@ positional features such as functional and other key sites, in molecular sequenc Topic concerning nucleotide sequence alignments. true beta12orEarlier - + @@ -47451,7 +45866,7 @@ positional features such as functional and other key sites, in molecular sequenc true beta12orEarlier 1.3 - + @@ -47503,7 +45918,6 @@ positional features such as functional sites in nucleotide sequences.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. - @@ -47533,7 +45947,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning metabolic pathways. beta12orEarlier - @@ -47547,7 +45960,6 @@ positional features such as functional sites in nucleotide sequences. beta12orEarlier Topic concerning signaling pathways. - @@ -47636,7 +46048,6 @@ positional features such as functional sites in nucleotide sequences.Plant biology The resource may be specific to a plant, a group of plants or all plants. Plant - @@ -47652,7 +46063,6 @@ positional features such as functional sites in nucleotide sequences.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 - @@ -47668,7 +46078,6 @@ positional features such as functional sites in nucleotide sequences.Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation. beta12orEarlier Mycology - @@ -47683,7 +46092,6 @@ positional features such as functional sites in nucleotide sequences.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 - @@ -47745,7 +46153,6 @@ positional features such as functional sites in nucleotide sequences.BioCatalogue:Comparative Genomics beta12orEarlier Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes. - @@ -47760,7 +46167,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns. beta12orEarlier - @@ -47787,13 +46193,12 @@ positional features such as functional sites in nucleotide sequences. Immunology - Computational immunology beta12orEarlier + Computational immunology Immunoinformatics + http://purl.bioontology.org/ontology/MSH/D007120" + http://purl.bioontology.org/ontology/MSH/D007125" Topic concerning the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on. - - - @@ -47811,7 +46216,6 @@ positional features such as functional sites in nucleotide sequences.Lipoproteins Membrane proteins beta12orEarlier - @@ -47826,7 +46230,6 @@ positional features such as functional sites in nucleotide sequences.Enzymology Topic concerning proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. beta12orEarlier - @@ -47845,7 +46248,6 @@ positional features such as functional sites in nucleotide sequences.Structure determination Structural assignment Topic concerning the molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids. - @@ -47858,11 +46260,9 @@ positional features such as functional sites in nucleotide sequences. Structure comparison - beta12orEarlier - Topic concerning the comparison of two or more molecular structures. 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. @@ -47880,7 +46280,6 @@ positional features such as functional sites in nucleotide sequences.Topic concerning the study of gene and protein function including the prediction of functional properties of a protein. BioCatalogue:Function Prediction Protein function prediction - @@ -47896,7 +46295,6 @@ positional features such as functional sites in nucleotide sequences.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. - @@ -47941,7 +46339,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning cells, such as key genes and proteins involved in the cell cycle. beta12orEarlier - @@ -48000,12 +46397,11 @@ positional features such as functional sites in nucleotide sequences.Cheminformatics - Chemical informatics - BioCatalogue:Chemoinformatics Chemoinformatics beta12orEarlier Topic concerning the application of information technology to chemistry in biological research environment. - + BioCatalogue:Chemoinformatics + Chemical informatics @@ -48020,7 +46416,9 @@ positional features such as functional sites in nucleotide sequences. Biological modelling Biological system modelling + http://en.wikipedia.org/wiki/Systems_biology" beta12orEarlier + http://purl.bioontology.org/ontology/MSH/D049490" BioCatalogue:Systems Biology BioCatalogue:Model Analysis Biological models @@ -48028,9 +46426,6 @@ positional features such as functional sites in nucleotide sequences.BioCatalogue:Model Creation BioCatalogue:Model Execution This includes databases of models and methods to construct or analyse a model. - - - @@ -48043,13 +46438,12 @@ positional features such as functional sites in nucleotide sequences. Statistics - Topic concerning the application of statistical methods to biological problems. beta12orEarlier BioCatalogue:Biostatistics + http://purl.bioontology.org/ontology/MSH/D056808" Biostatistics - - - + http://en.wikipedia.org/wiki/Biostatistics" + Topic concerning the application of statistical methods to biological problems. @@ -48078,14 +46472,13 @@ positional features such as functional sites in nucleotide sequences. Molecular modelling - Topic concerning the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. - Comparative modeling Molecular modeling Homology modelling - Comparative modelling + Topic concerning the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. beta12orEarlier + Comparative modelling + Comparative modeling Homology modeling - @@ -48116,7 +46509,6 @@ positional features such as functional sites in nucleotide sequences.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. beta12orEarlier - @@ -48165,7 +46557,6 @@ positional features such as functional sites in nucleotide sequences.Cancer beta12orEarlier Topic concerning the study of cancer, for example, genes and proteins implicated in cancer. - @@ -48183,7 +46574,6 @@ positional features such as functional sites in nucleotide sequences.Targets Topic concerning structural and associated data for toxic chemical substances. Toxins - @@ -48260,7 +46650,6 @@ positional features such as functional sites in nucleotide sequences.beta12orEarlier http://edamontology.org/topic_3040 Protein structure - @@ -48324,7 +46713,6 @@ positional features such as functional sites in nucleotide sequences.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 - @@ -48339,7 +46727,6 @@ positional features such as functional sites in nucleotide sequences.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. - @@ -48354,7 +46741,6 @@ positional features such as functional sites in nucleotide sequences.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. - @@ -48369,7 +46755,6 @@ positional features such as functional sites in nucleotide sequences.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 - @@ -48394,12 +46779,14 @@ positional features such as functional sites in nucleotide sequences. - X-ray crystallography + 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 - Topic concerning the study of crystals and their structure by means of the diffraction of X-rays by the regularly spaced atoms of crystalline materials. @@ -48414,10 +46801,10 @@ positional features such as functional sites in nucleotide sequences. 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 - @@ -48436,7 +46823,6 @@ positional features such as functional sites in nucleotide sequences.Antigens Immunopeptides Topic concerning immunity-related genes, proteins and their ligands. - @@ -48466,12 +46852,11 @@ positional features such as functional sites in nucleotide sequences.Toxicology - Computational toxicology - beta12orEarlier Toxicology + Computational toxicology Toxicoinformatics + beta12orEarlier Topic concerning toxins and the adverse effects of these chemical substances on living organisms. - @@ -48499,14 +46884,15 @@ 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 + - + @@ -48519,7 +46905,6 @@ positional features such as functional sites in nucleotide sequences. beta12orEarlier Topic concerning gene regulatory networks. - @@ -48671,7 +47056,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning the molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life. beta13 - @@ -48700,9 +47084,8 @@ positional features such as functional sites in nucleotide sequences.Biodiversity 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" beta13 - - @@ -48736,10 +47119,9 @@ positional features such as functional sites in nucleotide sequences.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. - - @@ -48754,7 +47136,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning the genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight). beta13 - @@ -48768,7 +47149,6 @@ positional features such as functional sites in nucleotide sequences. 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. - @@ -48800,7 +47180,6 @@ positional features such as functional sites in nucleotide sequences.beta13 Help Topic concerning the documentation of resources such as tools, services and databases and how to get help. - @@ -48838,7 +47217,6 @@ positional features such as functional sites in nucleotide sequences.Clinical informatics Health informatics Topic concerning the application of information technology to health, disease and biomedicine. - @@ -48853,7 +47231,6 @@ positional features such as functional sites in nucleotide sequences. beta13 Topic concerning how organisms grow and develop. - @@ -48868,7 +47245,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. beta13 - @@ -48883,7 +47259,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning the form and function of the structures of living organisms. beta13 - @@ -48896,12 +47271,11 @@ 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 - - @@ -48917,7 +47291,6 @@ positional features such as functional sites in nucleotide sequences.Topic concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on. beta13 Biological science - @@ -48930,14 +47303,14 @@ positional features such as functional sites in nucleotide sequences. Data management + http://purl.bioontology.org/ontology/MSH/D030541" Knowledge management Databases + Information management Data handling beta13 Databases Topic concerning the general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources. - - @@ -48953,9 +47326,9 @@ positional features such as functional sites in nucleotide sequences.beta13 true Topic concerning the detection of the positional features, such as functional and other key sites, in molecular sequences. + http://purl.bioontology.org/ontology/MSH/D058977" 1.3 - @@ -49019,7 +47392,6 @@ positional features such as functional sites in nucleotide sequences.beta13 Data deposition Deposition - @@ -49051,9 +47423,8 @@ positional features such as functional sites in nucleotide sequences.Next gen sequencing Next generation sequencing 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. - - @@ -49108,9 +47479,9 @@ positional features such as functional sites in nucleotide sequences.1.1 1.3 true + http://purl.bioontology.org/ontology/MSH/D019175" 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. - @@ -49122,9 +47493,8 @@ 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. - - @@ -49138,11 +47508,10 @@ positional features such as functional sites in nucleotide sequences.Epigenomics + http://purl.bioontology.org/ontology/MSH/D057890" Topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc. 1.1 Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. - - @@ -49156,13 +47525,12 @@ positional features such as functional sites in nucleotide sequences.Metagenomics + http://purl.bioontology.org/ontology/MSH/D056186" 1.1 Topic concerning the study of genetic material recovered from environmental samples, and associated environmental data. Environmental genomics Community genomics Ecogenomics - - @@ -49178,7 +47546,6 @@ positional features such as functional sites in nucleotide sequences.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 - @@ -49191,9 +47558,8 @@ positional features such as functional sites in nucleotide sequences.DNA packaging Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures. + http://purl.bioontology.org/ontology/MSH/D042003" beta12orEarlier - - @@ -49258,7 +47624,6 @@ positional features such as functional sites in nucleotide sequences.1.3 Privacy Topic concerning the protection of data, for example, patient health data. - @@ -49276,7 +47641,6 @@ positional features such as functional sites in nucleotide sequences.Topic concerning biological samples and specimens. biobanking samples - @@ -49294,7 +47658,6 @@ positional features such as functional sites in nucleotide sequences.Topic concerning chemical substances and physico-chemical processes and that occur within living organisms. 1.3 Chemical biology - @@ -49310,8 +47673,7 @@ positional features such as functional sites in nucleotide sequences. 1.3 Topic concerning the study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences). - - + http://purl.bioontology.org/ontology/MSH/D010802" @@ -49323,13 +47685,12 @@ positional features such as functional sites in nucleotide sequences. Epigenetics + http://purl.bioontology.org/ontology/MSH/D019175" 1.3 Histone modification - DNA methylation 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. - - @@ -49344,7 +47705,6 @@ positional features such as functional sites in nucleotide sequences. 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. - @@ -49360,7 +47720,6 @@ positional features such as functional sites in nucleotide sequences. 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. - @@ -49375,7 +47734,6 @@ positional features such as functional sites in nucleotide sequences. 1.3 Topic concerning the evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity. - @@ -49390,7 +47748,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning the functions of living organisms and their constituent parts. 1.3 - @@ -49405,7 +47762,6 @@ positional features such as functional sites in nucleotide sequences. 1.3 Topic concerning the biology of microorganisms. - @@ -49421,7 +47777,6 @@ positional features such as functional sites in nucleotide sequences.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. - @@ -49438,7 +47793,6 @@ positional features such as functional sites in nucleotide sequences.1.3 Topic concerning research in support of healing by diagnosis, treatment, and prevention of disease. Experimental medicine - @@ -49454,7 +47808,6 @@ positional features such as functional sites in nucleotide sequences.Topic concerning the study of the nervous system and brain; its anatomy, physiology and function. 1.3 Neuroscience - @@ -49471,7 +47824,6 @@ positional features such as functional sites in nucleotide sequences.Public health 1.3 Topic concerning the the patterns, cause, and effect of disease within populations. - @@ -49487,7 +47839,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning the use of physics to study biological system. 1.3 - @@ -49508,7 +47859,6 @@ positional features such as functional sites in nucleotide sequences.Mathematical biology This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology). BioCatalogue:Model Execution - @@ -49525,7 +47875,6 @@ positional features such as functional sites in nucleotide sequences.Topic concerning the analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. 1.3 Transcriptome - @@ -49540,7 +47889,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning the composition and properties of matter, reactions, and the use of reactions to create new substances. 1.3 - @@ -49555,8 +47903,7 @@ positional features such as functional sites in nucleotide sequences. 1.3 Maths - Topic concerning the composition and properties of matter, reactions, and the use of reactions to create new substances. - + Topic concerning the is the study of numbers (quantity) and other topics including structure, space, and change. @@ -49571,7 +47918,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning the theory and practical use of computer systems. 1.3 - @@ -49586,7 +47932,6 @@ positional features such as functional sites in nucleotide sequences. 1.3 Topic concerning the study of matter, space and time, and related concepts such as energy and force. - @@ -49603,7 +47948,6 @@ positional features such as functional sites in nucleotide sequences.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. - @@ -49617,7 +47961,6 @@ positional features such as functional sites in nucleotide sequences. 1.3 Topic concerning the structure and function of genes at a molecular level. - @@ -49630,13 +47973,12 @@ positional features such as functional sites in nucleotide sequences. Respiratory medicine + Topic concerning the study of respiratory system. + Pulmonology Pulmonary disorders 1.3 - Respiratory disease Pulmonary medicine - Topic concerning the study of respiratory system. - Pulmonology - + Respiratory disease @@ -49668,7 +48010,6 @@ positional features such as functional sites in nucleotide sequences.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 - @@ -49683,7 +48024,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning the study of rare diseases. 1.3 - @@ -49699,7 +48039,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems. 1.3 - @@ -49715,7 +48054,6 @@ positional features such as functional sites in nucleotide sequences.1.3 Neurological disorders Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system. - @@ -49733,7 +48071,6 @@ positional features such as functional sites in nucleotide sequences.Topic concerning the diseases and abnormalities of the heart and circulatory system. 1.3 Cardiovascular medicine - @@ -49750,7 +48087,6 @@ positional features such as functional sites in nucleotide sequences.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. - @@ -49767,7 +48103,6 @@ positional features such as functional sites in nucleotide sequences.Topic concerning repositories of biological samples, typically human, for basic biological and clinical research. 1.3 biobanking - @@ -49782,7 +48117,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines. 1.3 - @@ -49797,7 +48131,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning collections of microbial cells including bacteria, yeasts and moulds. 1.3 - @@ -49812,7 +48145,6 @@ positional features such as functional sites in nucleotide sequences. 1.3 Topic concerning collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells. - @@ -49827,7 +48159,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA. 1.3 - @@ -49842,7 +48173,6 @@ positional features such as functional sites in nucleotide sequences. 1.3 Topic concerning 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice. - @@ -49861,7 +48191,6 @@ positional features such as functional sites in nucleotide sequences.Topic concerning collections of chemicals, typically for use in high-throughput screening experiments. Chemical library Translational medicine - @@ -49877,7 +48206,6 @@ positional features such as functional sites in nucleotide sequences. 1.3 Topic concerning biological science that is (typically) performed in the context of medicine. - @@ -49892,7 +48220,6 @@ positional features such as functional sites in nucleotide sequences. Topic concerning the identity of biological data and the mapping of entities in different databases. 1.3 - @@ -49905,11 +48232,9 @@ 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 - @@ -50171,8 +48496,10 @@ 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. @@ -50454,7 +48781,7 @@ 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 @@ -50779,6 +49106,84 @@ positional features such as functional sites in nucleotide sequences. + + + MRI + + 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 + + + + + + + + + + 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 + + + + + + + + + + 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 + + + + + + + + + + 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 + + + + + + + + + + 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. + + + + + +