diff --git a/releases/EDAM.owl b/releases/EDAM.owl index 4e58f23..f6ea6ce 100644 --- a/releases/EDAM.owl +++ b/releases/EDAM.owl @@ -30,18 +30,18 @@ EDAM: An ontology of bioinformatics operations, types of data and identifiers, data formats, and topics EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries. + 1.8 + 16:12:2014 11:00 Hervé Ménager topics "EDAM topics" + 3546 EDAM_format http://edamontology.org/format_ "EDAM data formats" Jon Ison, Matus Kalas, Herve Menager Matúš Kalaš - 1.7 Jon Ison - 3489 concept_properties "EDAM concept properties" EDAM_data http://edamontology.org/data_ "EDAM types of data" 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. @@ -286,6 +286,12 @@ + + + + + + @@ -356,16 +362,16 @@ - 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. - + - In very unusual cases. - true + OBO_REL:bearer_of + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. - + @@ -443,16 +449,16 @@ - '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 + true + In very unusual cases. - + - In very unusual cases. - true + '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 - + @@ -462,16 +468,16 @@ has topic "http://purl.obolibrary.org/obo/OBI_0000298" + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality false "http://purl.obolibrary.org/obo/IAO_0000136" false - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality" + http://annotation-ontology.googlecode.com/svn/trunk/annotation-core.owl#hasTopic OBO_REL:is_a edam 'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B). false Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined. - http://annotation-ontology.googlecode.com/svn/trunk/annotation-core.owl#hasTopic" true relations @@ -497,13 +503,13 @@ is format of + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in OBO_REL:quality_of Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined. relations edam 'A is_format_of B' defines for the subject A, that it is a data format of the object B. false - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in" false false OBO_REL:is_a @@ -525,9 +531,9 @@ is function of - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in" false false + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in relations http://wsio.org/is_function_of edam @@ -548,17 +554,17 @@ - OBO_REL:inheres_in - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. - - - - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. OBO_REL:function_of + + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. + OBO_REL:inheres_in + + + @@ -603,8 +609,8 @@ - true In very unusual cases. + true @@ -638,16 +644,16 @@ - true - In very unusual cases. + '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 - '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. + true + In very unusual cases. - + @@ -659,6 +665,7 @@ edam OBO_REL:is_a false + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'. false true @@ -666,7 +673,6 @@ 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" @@ -679,14 +685,14 @@ - true In very unusual cases. + true - 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 + 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. @@ -746,36 +752,36 @@ 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://www.ifomis.org/bfo/1.1/snap#Continuant + http://purl.org/biotop/biotop.owl#DigitalEntity http://wsio.org/data_002 beta12orEarlier - Data set Data record + Data set "http://purl.obolibrary.org/obo/IAO_0000027" "http://purl.obolibrary.org/obo/IAO_0000030" - http://semanticscience.org/resource/SIO_000088" + http://semanticscience.org/resource/SIO_000069 + http://semanticscience.org/resource/SIO_000088 + http://www.onto-med.de/ontologies/gfo.owl#Perpetuant Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output. - Data set - EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + 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 - + - Data record - EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). + Data set + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - + - Datum EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + Datum @@ -822,6 +828,7 @@ An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc. + Ontologies beta12orEarlier @@ -1011,8 +1018,10 @@ Sequence record + SO:2000061 A molecular sequence and associated metadata. beta12orEarlier + http://purl.bioontology.org/ontology/MSH/D058977 @@ -1129,12 +1138,15 @@ - Database hits (sequence) + Sequence search results + Sequence database search results + A report of sequence hits and associated data from searching a database of sequences (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits. The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc. - A report of sequence hits and associated data from searching a sequence database (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits. Sequence search hits Sequence database hits + + Database hits (sequence) beta12orEarlier @@ -1145,13 +1157,15 @@ - Database hits (secondary) - - A report of hits from a search of a protein secondary or domain database. + Sequence signature matches + + Search results (protein secondary database) + This ncluding reports of hits from a search of a protein secondary or domain database. + Sequence profile matches + Report on the location of matches in one or more sequences to profiles, motifs (conserved or functional patterns) or other signatures. beta12orEarlier - 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 + Protein secondary database search results + Sequence motif matches @@ -1176,15 +1190,19 @@ - Sequence signature - - A classifier of sequences such as a sequence motif, profile or other diagnostic element. - beta12orEarlier + Sequence signature data + + + + + + + + Data concering concerning specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element. + This can include metadata about a motif or sequence profile such as its name, length, technical details about the profile construction, and so on. beta12orEarlier - true - - - + + @@ -1230,9 +1248,9 @@ Alignment of multiple molecular sequences. - http://purl.bioontology.org/ontology/MSH/D016415" beta12orEarlier http://semanticscience.org/resource/SIO_010066 + http://purl.bioontology.org/ontology/MSH/D016415 http://en.wikipedia.org/wiki/Sequence_alignment @@ -1287,7 +1305,7 @@ Sequence alignment report - + beta12orEarlier An informative report of molecular sequence alignment-derived data or metadata. Use this for any computer-generated reports on sequence alignments, and for general information (metadata) on a sequence alignment, such as a description, sequence identifiers and alignment score. @@ -1345,8 +1363,8 @@ Phylogenetic character data - http://www.evolutionaryontology.org/cdao.owl#Character" beta12orEarlier + http://www.evolutionaryontology.org/cdao.owl#Character As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments Basic character data from which a phylogenetic tree may be generated. @@ -1366,13 +1384,13 @@ - 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 + http://purl.bioontology.org/ontology/MSH/D010802 A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'. + http://www.evolutionaryontology.org/cdao.owl#Tree Moby:Tree Phylogeny @@ -1415,21 +1433,14 @@ - Protein features (secondary structure) - - - - - - - - The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks). - Protein secondary structure + Protein features report (secondary structure) + + Topic concerning secondary structure (predicted or real) of a protein. + true + 1.8 beta12orEarlier - Secondary structure assignment (predicted or real) of a protein. - Secondary structure (protein) - - + + @@ -1437,14 +1448,15 @@ - Protein features (super-secondary) - - Protein structure report (super-secondary) + Protein features report (super-secondary) + + Topic concerning super-secondary structure of protein sequence(s). beta12orEarlier + true Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. - A report of predicted or actual super-secondary structure of protein sequence(s). - - + 1.8 + + @@ -1541,11 +1553,11 @@ 3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure. + http://purl.bioontology.org/ontology/MSH/D015394 The coordinate data may be predicted or real. Structure data Coordinate model beta12orEarlier - http://purl.bioontology.org/ontology/MSH/D015394" @@ -1570,15 +1582,14 @@ - Database hits (structure) - - This includes alignment and score data. - Structure database hits - Structure search hits + Structure database search results + + true beta12orEarlier Results (hits) from searching a database of tertiary structure. - - + 1.8 + + @@ -1607,7 +1618,7 @@ Structure alignment report - + An informative report of molecular tertiary structure alignment-derived data. This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier @@ -1741,8 +1752,8 @@ Protein report - - An informative report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data. + + An informative human-readable report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data. beta12orEarlier Gene product annotation @@ -1755,9 +1766,10 @@ Protein property - The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. + Protein properties + Protein sequence statistics beta12orEarlier A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model. Protein physicochemical property @@ -1770,20 +1782,14 @@ - Protein features (3D motif) - - - - - - - - An informative report on the 3D structural motifs in a protein. - This might include conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, role and functions etc. + Protein structural motifs and surfaces + + Protein 3D motifs beta12orEarlier - Protein structure report (3D motif) - - + 1.8 + true + Topic concerning 3D structural motifs in a protein. + @@ -1806,21 +1812,14 @@ - Protein features (domains) - - - - - - - - Protein structural domains - The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc. + Protein features report (domains) + beta12orEarlier - Protein domain assignment - Summary of structural domains or 3D folds in a protein or polypeptide chain. - - + Topic concerning structural domains or 3D folds in a protein or polypeptide chain. + 1.8 + true + + @@ -1846,14 +1845,13 @@ Protein folding report - - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - Protein property (folding) + + 1.8 + true A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc. - Protein report (folding) beta12orEarlier - - + + @@ -1903,6 +1901,7 @@ An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with some other molecule(s), which might be another protein, nucleic acid or some other ligand. + Protein interaction record Protein report (interaction) beta12orEarlier @@ -1977,7 +1976,6 @@ Nucleic acid property - beta12orEarlier Nucleic acid physicochemical property @@ -2050,23 +2048,14 @@ - DNA variation (report) - - - - - - - + DNA variation + beta12orEarlier - DNA variation report - Nucleic acid features (variation) - A report on stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. - Sequence variation annotation - SO:0001059 - Sequence variation report - - + 1.8 + true + Topic concerning stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. + + @@ -2074,8 +2063,8 @@ - Chromosome (report) - + Chromosome report + @@ -2095,7 +2084,7 @@ Genotype/phenotype report - + beta12orEarlier Genotype/phenotype annotation An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes. @@ -2108,20 +2097,14 @@ - Primer binding sites (report) - - - - - - - - Primers (report) + Nucleic acid features report (primers) + + Topic concerning PCR primers and hybridization oligos in a nucleic acid sequence. beta12orEarlier - Nucleic acid features (primers) - Report on matches to PCR primers and hybridization oligos in a nucleic acid sequence. - - + 1.8 + true + + @@ -2129,20 +2112,14 @@ - PCR experiment annotation - - - - - - - - PCR assay data + PCR experiment report + + Topic concerning PCR experiments, e.g. quantitative real-time PCR. + 1.8 beta12orEarlier - Experiment annotation (PCR) - Information about a PCR experiment, e.g. quantitative real-time PCR. - - + true + + @@ -2202,9 +2179,11 @@ - Genetic linkage (report) - + Genetic linkage report + + This includes linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). An informative report on the linkage of alleles. + Linkage disequilibrium (report) Gene annotation (linkage) beta12orEarlier @@ -2231,21 +2210,13 @@ Microarray experiment report - - - - - - - + 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. - - + 1.8 + true + Topic concerning microarray experiments including conditions, protocol, sample:data relationships etc. + + @@ -2595,12 +2566,12 @@ Version information - http://www.ebi.ac.uk/swo/maturity/SWO_9000061" http://usefulinc.com/ns/doap#Version true + http://semanticscience.org/resource/SIO_000653 Information on a version of software or data, for example name, version number and release date. beta12orEarlier - http://semanticscience.org/resource/SIO_000653" + http://www.ebi.ac.uk/swo/maturity/SWO_9000061 Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. 1.5 "http://purl.obolibrary.org/obo/IAO_0000129" @@ -2647,7 +2618,7 @@ Data index report - + @@ -2732,6 +2703,7 @@ Chemical compound annotation beta12orEarlier An informative report on a specific chemical compound. + Chemical structure report Small molecule report Small molecule annotation @@ -2775,6 +2747,7 @@ Ontology term + Ontology terms A term (name) from an ontology. beta12orEarlier Ontology class name @@ -2804,13 +2777,16 @@ Keyword - Moby:QueryString - Moby:Wildcard_Query + Text + Terms 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:Wildcard_Query Moby:BooleanQueryString beta12orEarlier + Moby:QueryString + Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. + Keyword(s) or phrase(s) used (typically) for text-searching purposes. + Phrases @@ -4037,6 +4013,7 @@ URI beta12orEarlier + URIs A string of characters that name or otherwise identify a resource on the Internet. @@ -4558,12 +4535,6 @@ Transcription factor identifier - - - - - - beta12orEarlier Identifier of a transcription factor (or a TF binding site). @@ -4581,7 +4552,7 @@ - + Identifier of an entry from a database of microarray data. @@ -6101,6 +6072,7 @@ beta12orEarlier CHEBI:[0-9]+ ChEBI identifier + ChEBI IDs Identifier of an entry from the ChEBI database. @@ -6528,13 +6500,13 @@ - + - + beta12orEarlier @@ -6815,8 +6787,8 @@ 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 + http://purl.bioontology.org/ontology/MSH/D058977 beta12orEarlier Sequence features report @@ -6874,7 +6846,7 @@ - Sequence complexity (report) + Sequence complexity report Sequence property (complexity) beta12orEarlier @@ -6888,7 +6860,7 @@ - Sequence ambiguity (report) + Sequence ambiguity report beta12orEarlier Sequence property (ambiguity) @@ -6902,7 +6874,7 @@ - Sequence composition (report) + Sequence composition report Sequence property (composition) A report (typically a table) on character or word composition / frequency of a molecular sequence(s). @@ -6930,7 +6902,7 @@ Base position variability plot - + A plot of third base position variability in a nucleotide sequence. beta12orEarlier @@ -6958,8 +6930,8 @@ Base frequencies table + - A table of base frequencies of a nucleotide sequence. beta12orEarlier @@ -6972,8 +6944,8 @@ Base word frequencies table + - beta12orEarlier A table of word composition of a nucleotide sequence. @@ -6986,8 +6958,8 @@ Amino acid frequencies table + - beta12orEarlier A table of amino acid frequencies of a protein sequence. Sequence composition (amino acid frequencies) @@ -7001,8 +6973,8 @@ Amino acid word frequencies table + - beta12orEarlier Sequence composition (amino acid words) A table of amino acid word composition of a protein sequence. @@ -7067,10 +7039,12 @@ Nucleic acid features - This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. Feature table (nucleic acid) - beta12orEarlier Nucleic acid feature table + Genomic features + This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. + Genome features + beta12orEarlier An informative report on intrinsic positional features of a nucleotide sequence. @@ -7228,7 +7202,6 @@ Restriction map - beta12orEarlier Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence. @@ -7320,11 +7293,13 @@ Sequence motif matches - + + true + 1.8 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences. beta12orEarlier - - + + @@ -7365,15 +7340,14 @@ - Mobile genetic elements (report) - - Nucleic acid features (mobile genetic elements) + Mobile genetic elements + + Topic concerning regions of a nucleic acid sequence containing mobile genetic elements. + 1.8 beta12orEarlier - 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. - - + true + + @@ -7381,16 +7355,14 @@ - PolyA signal or sites (report) - + Nucleic acid features report (PolyA signal or site) + beta12orEarlier - Nucleic acid features (PolyA signal or site) - A region or site in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. - 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 - - + 1.8 + true + Topic concerning regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. + + @@ -7413,13 +7385,14 @@ - CpG island and isochore (report) - - A report or plot of CpG rich regions (isochores) in a nucleotide sequence. + Nucleic acid features report (CpG island and isochore) + + true + Topic concerning CpG rich regions (isochores) in a nucleotide sequence. beta12orEarlier - Nucleic acid features (CpG island and isochore) - - + 1.8 + + @@ -7427,14 +7400,14 @@ - Restriction sites (report) - - Nucleic acid features (restriction sites) - Report on restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. - Nucleic acid restriction sites (report) + Nucleic acid features report (restriction sites) + + Topic concerning restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. + 1.8 + true beta12orEarlier - - + + @@ -7442,13 +7415,14 @@ - Nucleosome exclusion sequences (report) - - A report on nucleosome formation potential or exclusion sequence(s). + Nucleosome exclusion sequences + + 1.8 + Report on nucleosome formation potential or exclusion sequence(s). + true beta12orEarlier - Nucleic acid features (nucleosome exclusion sequences) - - + + @@ -7456,15 +7430,14 @@ - Splice sites (report) - - Nucleic acid report (RNA splicing) - Nucleic acid features (splice sites) - Nucleic acid report (RNA splice model) - A report on splice sites in a nucleotide sequence or alternative RNA splicing events. + Nucleic acid features report (splice sites) + + 1.8 + true + Topic concerning splice sites in a nucleotide sequence or alternative RNA splicing events. beta12orEarlier - - + + @@ -7472,13 +7445,14 @@ - Matrix/scaffold attachment sites (report) - - Nucleic acid features (matrix/scaffold attachment sites) + Nucleic acid features report (matrix/scaffold attachment sites) + + Topic concerning matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. beta12orEarlier - A report on matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. - - + true + 1.8 + + @@ -7516,15 +7490,14 @@ - Operon (report) - + Gene features report (operon) + beta12orEarlier - A report on operons (operators, promoters and genes) from a bacterial genome. - 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) - - + Topic concerning operons (operators, promoters and genes) from a bacterial genome. + 1.8 + true + + @@ -7532,13 +7505,14 @@ - Promoters (report) - + Nucleic acid features report (promoters) + 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) - - + true + Topic concerning whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. + 1.8 + + @@ -7546,16 +7520,14 @@ - Coding region (report) - - Gene features (coding sequence) - Nucleic acid features (coding sequence) - Gene annotation (translation) + Coding region + + true + 1.8 + Topic concerning protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. beta12orEarlier - Gene features (coding region) - A report on protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. - - + + @@ -7578,21 +7550,14 @@ - Transcription factor binding sites (report) - - - - - - - - - A report on the transcription factor binding sites (TFBS) in a DNA sequence. - TFBS (report) + Transcription factor binding sites + + 1.8 + true + Topic concerning transcription factor binding sites (TFBS) in a DNA sequence. beta12orEarlier - Nucleic acid features (TFBS) - - + + @@ -7616,12 +7581,14 @@ - Protein features (signal peptides) - + Protein features report (signal peptides) + beta12orEarlier - A report on the location of signal peptides or signal peptide cleavage sites in protein sequences. - - + 1.8 + true + Topic concerning signal peptides or signal peptide cleavage sites in protein sequences. + + @@ -7629,18 +7596,14 @@ - Protein features (cleavage sites) - - - - - - - + Protein features report (cleavage sites) + beta12orEarlier - A report on cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. - - + 1.8 + Topic concerning cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. + true + + @@ -7649,13 +7612,13 @@ Protein features (post-translation modifications) - - Post-translation modification + + 1.8 + Topic concerning post-translation modifications in a protein sequence, typically describing the specific sites involved. beta12orEarlier - A report on post-translation modifications in a protein sequence, typically describing the specific sites involved. - Protein features (post-translation modification sites) - - + true + + @@ -7663,13 +7626,14 @@ - Protein features (active sites) - + Protein features report (active sites) + beta12orEarlier - Enzyme active site - A report on catalytic residues (active site) of an enzyme. - - + true + 1.8 + Topic concerning catalytic residues (active site) of an enzyme. + + @@ -7677,12 +7641,14 @@ - Protein features (binding sites) - - A report on ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. + Protein features report (binding sites) + + 1.8 + true beta12orEarlier - - + Topic concerning ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. + + @@ -7706,12 +7672,14 @@ - Protein features (nucleic acid binding sites) - + Protein features report (nucleic acid binding sites) + + 1.8 + Topic concerning RNA and DNA-binding proteins and binding sites in protein sequences. beta12orEarlier - A report on RNA and DNA-binding proteins and binding sites in protein sequences. - - + true + + @@ -7885,13 +7853,11 @@ Regular expression - + beta12orEarlier - true - 1.5 Regular expression pattern. - - + + @@ -7900,7 +7866,7 @@ Sequence motif - + @@ -7919,7 +7885,7 @@ Sequence profile - + @@ -7939,15 +7905,15 @@ Protein signature - + Protein domain signature - InterPro entry Protein family signature beta12orEarlier Protein site signature Protein region signature - An entry (sequence classifier and associated data) from the InterPro database. Protein repeat signature + InterPro entry + An informative report about a specific or conserved protein sequence pattern. @@ -8235,7 +8201,7 @@ Alignment of exactly two molecular sequences. beta12orEarlier - http://semanticscience.org/resource/SIO_010068" + http://semanticscience.org/resource/SIO_010068 @@ -8375,7 +8341,7 @@ Alignment score or penalty - + A simple floating point number defining the penalty for opening or extending a gap in an alignment. beta12orEarlier @@ -9044,16 +9010,14 @@ - Protein features (membrane regions) - - Transmembrane region report - Protein report (membrane protein) - An informative report on trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. - This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. + Protein features report (membrane regions) + + Topic concerning trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. + 1.8 beta12orEarlier - Intramembrane region report - - + true + + @@ -9088,14 +9052,9 @@ - - - - - - beta12orEarlier 3D coordinate and associated data for a protein tertiary (3D) structure. + Protein structures @@ -9256,15 +9215,14 @@ - Protein structure (C-alpha atoms) - - 1.5 + C-alpha trace + beta12orEarlier - true + Protein structure (C-alpha atoms) C-beta atoms from amino acid side-chains may be included. 3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only). - - + + @@ -9892,6 +9850,7 @@ Protein titration curve + beta12orEarlier The titration curve of a protein. @@ -10036,7 +9995,6 @@ Protein structural quality report - beta12orEarlier Protein report (structural quality) @@ -10055,7 +10013,7 @@ Protein residue interactions - + @@ -10373,19 +10331,13 @@ Protein-protein interaction report - - - - - - - - For example, an informative report about a specific protein complex (of multiple polypeptide chains). - Protein structure report (protein complex) + + 1.8 + Topic concerning protein-protein interaction(s), including interactions between protein domains. + true beta12orEarlier - An informative report on protein-protein interaction(s). - - + + @@ -10406,12 +10358,14 @@ - Protein-nucleic acid interaction report - + Protein-nucleic acid interactions report + + 1.8 beta12orEarlier - An informative report on protein-DNA/RNA interaction(s). - - + Topic concerning protein-DNA/RNA interaction(s). + true + + @@ -10590,6 +10544,7 @@ Base pairing probability matrix dotplot + Dotplot of RNA base pairing probability matrix. Such as generated by the Vienna package. beta12orEarlier @@ -10603,7 +10558,7 @@ 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. @@ -10748,13 +10703,13 @@ Linkage disequilibrium (report) - - Genetic linkage disequilibrium (report) + beta12orEarlier - Gene annotation (linkage disequilibrium) + 1.8 A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). - - + true + + @@ -10823,13 +10778,14 @@ Metabolic pathway report - + + true + 1.8 A report typically including a map (diagram) of a metabolic pathway. beta12orEarlier This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. - Pathway or network (metabolic) - - + + @@ -10837,13 +10793,14 @@ - Genetic information processing pathway - - Pathway or network (genetic information processing) - A report typically including a map (diagram) of a genetic information processing pathway. + Genetic information processing pathway report + + true + 1.8 + Topic concerning genetic information processing pathways. beta12orEarlier - - + + @@ -10851,13 +10808,14 @@ - Environmental information processing pathway - + Environmental information processing pathway report + + 1.8 beta12orEarlier - A report typically including a map (diagram) of an environmental information processing pathway. - Pathway or network (environmental information processing) - - + true + Topic concerning environmental information processing pathways. + + @@ -10866,12 +10824,13 @@ Signal transduction pathway report - + beta12orEarlier + true + 1.8 A report typically including a map (diagram) of a signal transduction pathway. - Pathway or network (signal transduction) - - + + @@ -10879,13 +10838,14 @@ - Pathway or network (cellular process) - Cellular process pathway - + Cellular process pathways report + beta12orEarlier - A report typically including a map (diagram) of a cellular process pathway. - - + true + Topic concernning cellular process pathways. + 1.8 + + @@ -10893,13 +10853,14 @@ - Disease pathway report - - A report typically including a map (diagram) of a disease pathway, typically a diagram for a human disease. + Disease pathway or network report + + Topic concerning disease pathways, typically of human disease. + 1.8 beta12orEarlier - Pathway or network (disease) - - + true + + @@ -10920,14 +10881,14 @@ - Protein interaction network - - + Protein interaction networks + beta12orEarlier - Pathway or network (protein-protein interaction) - A report typically including a map (diagram) of a network of protein interactions. - - + true + 1.8 + Topic concerning networks of protein interactions. + + @@ -11522,7 +11483,7 @@ - BioPax + BioPax term true beta12orEarlier @@ -13602,11 +13563,13 @@ Sequence record lite - + + 1.8 + true A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment. beta12orEarlier - - + + @@ -13622,11 +13585,12 @@ - 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" + http://purl.org/biotop/biotop.owl#BioMolecularSequenceInformation + Sequences + http://purl.bioontology.org/ontology/MSH/D008969 @@ -13637,14 +13601,13 @@ Nucleic acid sequence record (lite) - - - Sequence record lite (nucleic acid) + A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment. - Nucleotide sequence record (lite) + true + 1.8 beta12orEarlier - - + + @@ -13653,13 +13616,14 @@ Protein sequence record (lite) - - + + true A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment. beta12orEarlier Sequence record lite (protein) - - + 1.8 + + @@ -13672,9 +13636,8 @@ beta12orEarlier A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself. Document + http://semanticscience.org/resource/SIO_000148 You can use this term by default for any textual report, in case you can't find another, more specific term. Reports may be generated automatically or collated by hand and can include metadata on the origin, source, history, ownership or location of some thing. - Text - http://semanticscience.org/resource/SIO_000148" @@ -13760,8 +13723,10 @@ - Database hits - + Database search results + + Database hits + Search results A report of hits from searching a database of some type. beta12orEarlier @@ -13804,13 +13769,15 @@ Alignment data - + Alignment report This is a broad data type and is used a placeholder for other, more specific types. Data concerning, extracted from, or derived from the analysis of molecular alignment of some type. + true + 1.8 beta12orEarlier - - + + @@ -13819,9 +13786,9 @@ Nucleic acid report - + beta12orEarlier - An informative report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data. + An informative human-readable report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data. @@ -13832,7 +13799,7 @@ Structure report - + Structure-derived report beta12orEarlier An informative report on general information, properties or features of one or more molecular tertiary (3D) structures. @@ -13906,9 +13873,9 @@ Accession - http://semanticscience.org/resource/SIO_000675" - http://semanticscience.org/resource/SIO_000731" + http://semanticscience.org/resource/SIO_000675 A persistent (stable) and unique identifier, typically identifying an object (entry) from a database. + http://semanticscience.org/resource/SIO_000731 beta12orEarlier @@ -13920,15 +13887,14 @@ - SNP (report) - - An SNP is an individual point mutation or substitution of a single nucleotide. - SNP annotation - Single nucleotide polymorphism - Annotation on a single nucleotide polymorphism (SNP) in a DNA sequence. + SNP + + 1.8 beta12orEarlier - - + Topic concerning single nucleotide polymorphism (SNP) in a DNA sequence. + true + + @@ -13969,8 +13935,8 @@ 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://www.w3.org/2000/01/rdf-schema#label http://usefulinc.com/ns/doap#name http://semanticscience.org/resource/SIO_000116 @@ -14183,13 +14149,13 @@ - + - + beta12orEarlier @@ -14726,7 +14692,7 @@ Fickett testcode plot - + beta12orEarlier A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences. @@ -14740,6 +14706,7 @@ Sequence similarity plot + A plot of sequence similarities identified from word-matching or character comparison. Sequence similarity plot Sequence conservation report @@ -14798,6 +14765,7 @@ Protein ionization curve + A plot of pK versus pH for a protein. beta12orEarlier @@ -14811,6 +14779,7 @@ Sequence composition plot + A plot of character or word composition / frequency of a molecular sequence. beta12orEarlier @@ -14823,7 +14792,8 @@ Nucleic acid density plot - + + Density plot (of base composition) for a nucleotide sequence. beta12orEarlier @@ -14982,15 +14952,14 @@ - Protein features (chemical modification) - - Protein modification annotation - GO:0006464 - MOD:00000 + Protein features report (chemical modifications) + + true + Topic concerning chemical modification of a protein. beta12orEarlier - A report on a chemical modification of a protein. - - + 1.8 + + @@ -15042,13 +15011,13 @@ Sequence record full - - SO:2000061 + + 1.8 A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. beta12orEarlier - http://purl.bioontology.org/ontology/MSH/D058977" - - + true + + @@ -16233,12 +16202,14 @@ - Domain-domain interaction report - + Domain-domain interactions + + true beta12orEarlier An informative report on protein domain-protein domain interaction(s). - - + 1.8 + + @@ -16298,19 +16269,14 @@ - 2D PAGE experiment report - - - - - - - - An informative report on a two-dimensional gel electrophoresis experiment, gel or spots in a gel. + 2D PAGE report + + true + 1.8 beta12orEarlier - Experiment annotation (2D PAGE) - - + Topic concerning two-dimensional gel electrophoresis experiments, gels or spots in a gel. + + @@ -16418,12 +16384,14 @@ 2D PAGE spot report - + + true + 1.8 An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel. beta12orEarlier 2D PAGE spot annotation - - + + @@ -16518,15 +16486,14 @@ - Genotyping experiment report - - Metadata on a genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. + Experiment report (genotyping) + beta12orEarlier - Experiment report (genotyping) - Genotyping experiment metadata - Experiment annotation (genotype) - - + 1.8 + Report of genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. + true + + @@ -16746,13 +16713,14 @@ - Exons (report) - - Gene features (exon) + Gene features report (exon) + beta12orEarlier - An informative report on an exon in a nucleotide sequences. - - + 1.8 + Topic concerning exons in a nucleotide sequences. + true + + @@ -16777,23 +16745,14 @@ - Transcriptional features (report) - - Enhancers (report) - Terminators (report) + Gene transcriptional features report + + Topic concerning transcription of DNA into RNA including the regulation of transcription. + true beta12orEarlier - Attenuators (report) - GC signals (report) - TATA signals (report) - CAAT signals (report) - -10 signals (report) - This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. - An informative report on features concerning transcription of DNA into RNA including the regulation of transcription. - Nucleic acid features (transcriptional) - -35 signals (report) - Ribosome binding sites (report) - - + 1.8 + + @@ -16832,13 +16791,13 @@ Protein-drug interaction report - + + + beta12orEarlier - 1.5 - true - An informative report on protein-drug interaction(s) including binding affinity data. - - + An informative report on tentative or known protein-drug interaction(s). + + @@ -16912,9 +16871,9 @@ Article data + Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal. Article report This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. - Data concerning, extracted from, or derived from the analysis of a scientific text such as a full text article from a scientific journal. beta12orEarlier @@ -16928,11 +16887,11 @@ Parameter - Parameter or primitive Tool parameter + Parameters Typically a simple numerical or string value that controls the operation of a tool. + http://www.e-lico.eu/ontologies/dmo/DMOP/DMOP.owl#Parameter beta12orEarlier - http://www.e-lico.eu/ontologies/dmo/DMOP/DMOP.owl#Parameter" Tool-specific parameter http://semanticscience.org/resource/SIO_000144 @@ -16979,7 +16938,7 @@ Organism report - + Organism annotation beta12orEarlier An informative report on a specific organism. @@ -16993,7 +16952,7 @@ Experiment report - + Annotation on a wet lab experiment, such as experimental conditions. Experiment annotation beta12orEarlier @@ -17007,14 +16966,14 @@ - DNA mutation report - - Annotation on a mutation. - Mutation annotation - Nucleic acid features (mutation) + Nucleic acid features report (mutation) + beta12orEarlier - - + true + 1.8 + Topic concerning DNA mutation. + + @@ -17023,7 +16982,7 @@ Sequence attribute - + beta12orEarlier Sequence parameter An attribute of a molecular sequence, possibly in reference to some other sequence. @@ -17503,6 +17462,7 @@ Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network). + Pathway beta12orEarlier Network @@ -17634,6 +17594,7 @@ Ensembl ID + Ensembl IDs Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database. ENS[A-Z]*[FPTG][0-9]{11} beta12orEarlier @@ -18412,13 +18373,13 @@ - + - + Identifier of a carbohydrate. @@ -19267,13 +19228,14 @@ - Protein features (disordered structure) - - Protein structure report (disordered structure) - An informative report about disordered structure in a protein. + Protein features report (disordered structure) + + Topic concerning disordered structure in a protein. beta12orEarlier - - + true + 1.8 + + @@ -19722,14 +19684,14 @@ - Introns (report) - - Gene features (intron) + Gene features report (intron) + + 1.8 beta12orEarlier - An informative report on an intron in a nucleotide sequences. - Nucleic acid features (intron) - - + true + Topic concerning introns in a nucleotide sequences. + + @@ -19825,8 +19787,8 @@ - Sequence motif report - + Sequence signature report + @@ -19834,8 +19796,9 @@ 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. + An informative report about a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc. + Sequence profile report + Sequence motif report @@ -19939,7 +19902,7 @@ - + beta12orEarlier @@ -20213,17 +20176,13 @@ Sequence profile data - - - - - - - + beta12orEarlier + true Data concerning, extracted from, or derived from the analysis of a sequence profile, such as its name, length, technical details about the profile or it's construction, the biological role or annotation, and so on. - - + 1.8 + + @@ -20638,6 +20597,7 @@ A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment. + PSSM beta12orEarlier @@ -20716,14 +20676,14 @@ - Northern blot experiment report - - Experiment report (Northern blot) + Northern blot report + + 1.8 beta12orEarlier - Experiment annotation (Northern blot) - General annotation on a Northern Blot experiment. - - + true + Topic concerning Northern Blot experiments. + + @@ -20731,16 +20691,14 @@ - VNTR (report) - - Nucleic acid features (VNTR) - VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. - Variable number of tandem repeat polymorphism - VNTR annotation + Nucleic acid features report (VNTR) + + Topic concerning variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. + true beta12orEarlier - Annotation on a variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. - - + 1.8 + + @@ -20748,15 +20706,15 @@ - Microsatellites (report) - + Nucleic acid features report (microsatellite) + beta12orEarlier - Nucleic acid features (microsatellite) - 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. - - + 1.8 + Topic concerning microsatellite polymorphism in a DNA sequence. + true + + + @@ -20764,15 +20722,14 @@ - RFLP (report) - - Annotation on a restriction fragment length polymorphisms (RFLP) in a DNA sequence. - An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. - Nucleic acid features (RFLP) - RFLP annotation + Nucleic acid features report (RFLP) + + Topic concerning restriction fragment length polymorphisms (RFLP) in a DNA sequence. + 1.8 + true beta12orEarlier - - + + @@ -20954,13 +20911,13 @@ Plot - + + Biological data that has been plotted as a graph of some type. beta12orEarlier true - Biological data that is plotted as a graph of some type. beta12orEarlier - - + + @@ -20968,14 +20925,13 @@ - DNA polymorphism (report) - - Annotation on a polymorphism. + Nucleic acid features report (polymorphism) + beta12orEarlier - Nucleic acid features (polymorphism) - Polymorphism annotation - - + Topic concerning DNA polymorphism. + true + + @@ -21003,9 +20959,11 @@ Sequence record (nucleic acid) + DNA sequence record beta12orEarlier A nucleic acid sequence and associated metadata. Nucleotide sequence record + RNA sequence record @@ -21016,14 +20974,13 @@ Protein sequence record (full) - - + + true beta12orEarlier + 1.8 A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. - SO:2000061 - Sequence record full (protein) - - + + @@ -21032,15 +20989,13 @@ Nucleic acid sequence record (full) - - - Nucleotide sequence record (full) - SO:2000061 + + 1.8 beta12orEarlier A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. - Sequence record full (nucleic acid) - - + true + + @@ -21295,6 +21250,7 @@ Accession of a protein deposited in a database. beta12orEarlier + Protein accessions @@ -21409,7 +21365,7 @@ Sequence features metadata - + Metadata on sequence features. beta12orEarlier @@ -21467,12 +21423,14 @@ Sequence data - + Data concerning, extracted from, or derived from the analysis of molecular sequence(s). + true beta12orEarlier + 1.8 This is a broad data type and is used a placeholder for other, more specific types. - - + + @@ -21512,7 +21470,7 @@ Sequence report - + Sequence-derived report beta12orEarlier An informative report of information about molecular sequence(s), including basic information (metadata), and reports generated from molecular sequence analysis, including positional features and non-positional properties. @@ -21526,7 +21484,7 @@ Protein secondary structure report - + beta12orEarlier An informative report about the properties or features of one or more protein secondary structures. @@ -21540,6 +21498,7 @@ Hopp and Woods plot + beta12orEarlier A Hopp and Woods plot of predicted antigenicity of a peptide or protein. @@ -21553,6 +21512,7 @@ Nucleic acid melting curve + beta12orEarlier A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA). Shows the proportion of nucleic acid which are double-stranded versus temperature. @@ -21595,19 +21555,13 @@ Gene regulatory network report - - - - - - - + beta12orEarlier + true A report typically including a map (diagram) of a gene regulatory network. - Gene regulation network report - Pathway or network (gene regulation) - - + 1.8 + + @@ -21616,14 +21570,16 @@ 2D PAGE gel report - + 2D PAGE image annotation beta12orEarlier 2D PAGE gel annotation + true + 1.8 2D PAGE image report An informative report on a two-dimensional (2D PAGE) gel. - - + + @@ -21664,9 +21620,9 @@ 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" + http://semanticscience.org/resource/SIO_000079 + http://semanticscience.org/resource/SIO_000081 @@ -21784,8 +21740,9 @@ Protein sequence - http://purl.org/biotop/biotop.owl#AminoAcidSequenceInformation" + http://purl.org/biotop/biotop.owl#AminoAcidSequenceInformation beta12orEarlier + Protein sequences One or more protein sequences, possibly with associated annotation. @@ -21798,10 +21755,11 @@ Nucleic acid sequence + http://purl.org/biotop/biotop.owl#NucleotideSequenceInformation Nucleic acid sequences Nucleotide sequences Nucleotide sequence - http://purl.org/biotop/biotop.owl#NucleotideSequenceInformation" + DNA sequence beta12orEarlier One or more nucleic acid sequences, possibly with associated annotation. @@ -21858,12 +21816,14 @@ Sequence motif data - + This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier Data concerning specific or conserved pattern in molecular sequences. - - + 1.8 + true + + @@ -21904,7 +21864,7 @@ Pathway or network report - + @@ -21968,12 +21928,14 @@ - Protein features (key folding sites) - + Protein features report (key folding sites) + + true + 1.8 beta12orEarlier - A report on key residues involved in protein folding. - - + Topic concerning key residues involved in protein folding. + + @@ -22249,12 +22211,13 @@ Protein sequence composition - - Sequence property (protein composition) + A report (typically a table) on character or word composition / frequency of protein sequence(s). + true + 1.8 beta13 - - + + @@ -22263,13 +22226,13 @@ Nucleic acid sequence composition (report) - - + beta13 + true A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s). - Sequence property (nucleic acid composition) - - + 1.8 + + @@ -22456,7 +22419,7 @@ Sample annotation - + beta13 This might include compound and dose in a dose response experiment. Annotation on a biological sample, for example experimental factors and their values. @@ -22484,12 +22447,14 @@ Microarray protocol annotation - + Annotation on laboratory and/or data processing protocols used in an microarray experiment. + 1.8 beta13 This might describe e.g. the normalisation methods used to process the raw data. - - + true + + @@ -22510,19 +22475,14 @@ - Protein features (topological domains) - - - - - - - - Summary of topological domains such as cytoplasmic regions in a protein. + Protein features report (topological domains) + + true + Topic concerning topological domains such as cytoplasmic regions in a protein. beta13 - Protein topological domains - - + 1.8 + + @@ -22542,19 +22502,6 @@ - - - - Protein features (sequence variants) - - A report on the protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. - beta13 - - - - - - @@ -22573,13 +22520,14 @@ - Expression signal (report) - - Nucleic acid features (expression signal) - A report on regions within a nucleic acid sequence containing a signal that alters a biological function. + Nucleic acid features report (expression signal) + + 1.8 + Topic concerning regions within a nucleic acid sequence containing a signal that alters a biological function. beta13 - - + true + + @@ -22587,14 +22535,15 @@ - DNA binding sites (report) - - A report on regions of a nucleic acid sequence that bind some other molecule. + Nucleic acid features report (binding) + This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). beta13 - Nucleic acid features (binding) - - + true + Topic concerning nucleic acids binding to some other molecule. + 1.8 + + @@ -22602,13 +22551,14 @@ - Nucleic acid features (repeats) - + Nucleic acid repeats (report) + + Topic concerning repetitive elements within a nucleic acid sequence. 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. - - + 1.8 + true + + @@ -22616,14 +22566,14 @@ - DNA replication and recombination sites (report) - - This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. - Nucleic acid features (replication and recombination) - A report on regions within a nucleic acid sequence that are involved in DNA replcication or recombination. + Nucleic acid features report (replication and recombination) + + 1.8 + true + Topic concerning DNA replication or recombination. beta13 - - + + @@ -22649,12 +22599,14 @@ - Protein features (repeats) - + Protein features report (repeats) + + true + Topic concerning short repetitive subsequences (repeat sequences) in a protein sequence. beta13 - Location of short repetitive subsequences (repeat sequences) in a protein sequence. - - + 1.8 + + @@ -22663,11 +22615,13 @@ Sequence motif matches (protein) - + + true beta13 + 1.8 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences. - - + + @@ -22676,11 +22630,13 @@ Sequence motif matches (nucleic acid) - + + 1.8 + true beta13 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences. - - + + @@ -22741,14 +22697,14 @@ - Signal or transit peptide (report) - + Nucleic acid features report (signal or transit peptide) + beta13 - Nucleic acid features (signal or transit peptide) - A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. - A report on a coding sequence for a signal or transit peptide. - - + Topic concerning coding sequences for a signal or transit peptide. + 1.8 + true + + @@ -22756,21 +22712,14 @@ - Non-coding RNA (report) - - - - - - - - Non-coding RNA features + Non-coding RNA + + 1.8 + true beta13 - Features concerning non-coding or functional RNA molecules, including tRNA and rRNA. - ncRNA features - Nucleic acid features (non-coding RNA) - - + Topic concerning features of non-coding or functional RNA molecules, including tRNA and rRNA. + + @@ -22794,14 +22743,14 @@ - Sequence tagged sites (report) - + Nucleic acid features report (STS) + beta13 - 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) - - + true + 1.8 + Topic concerning sequence tagged sites (STS) in nucleic acid sequences. + + @@ -22914,14 +22863,14 @@ - Mass spectrometry experiment report - - General annotation on a mass spectrometry experiment. + Mass spectrometry experiment + beta13 - Experiment annotation (mass spectrometry) - Experiment report (mass spectrometry) - - + true + Topic concerning mass spectrometry experiments. + 1.8 + + @@ -22975,20 +22924,14 @@ - NGS experiment report - - - - - - - - Data on a sequencing experiment, including samples, sampling, preparation, sequencing, and analysis. - Experiment metadata (NGS) + NGS experiment + + true + Topic concerning sequencing experiment, including samples, sampling, preparation, sequencing, and analysis. 1.0 - NGS experiment metadata - - + 1.8 + + @@ -23025,14 +22968,15 @@ - GWAS study metadata - - Experiment annotation (genome-wide association study) + GWAS report + + Genome-wide association study + true + Report concerning genome-wide association study experiments. 1.1 - Genome-wide association study experiment metadata - Experiment metadata (GWAS) - - + 1.8 + + @@ -23319,8 +23263,8 @@ Raw biological or biomedical image generated by some experimental technique. Image data - http://semanticscience.org/resource/SIO_000081" beta12orEarlier + http://semanticscience.org/resource/SIO_000081 Amino acid data 1.5 @@ -23347,13 +23291,13 @@ Proteomics experiment report - - Experiment report (proteomics) - Information about a proteomics experiment. + 1.5 - Experiment annotation (proteomics experiment) - - + Report concerning proteomics experiments. + 1.8 + true + + @@ -23361,14 +23305,14 @@ - RNAi experiment report - - Experiment report (RNAi) + RNAi report + + 1.8 + true 1.5 - Experiment annotation (RNAi experiment) - Information about an RNAi experiment. - - + Topic concerning RNAi experiments. + + @@ -23377,13 +23321,13 @@ Simulation experiment report - - Experiment annotation (simulation experiment) - Experiment report (simulation) + + Topic concerning biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. + 1.8 + true 1.5 - Information about a biological computational model experiment (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. - - + + @@ -23495,6 +23439,142 @@ + + + + Chemical structure sketch + + A sketch of a small molecule made with some specialised drawing package. + Small molecule sketch + 1.8 + Chemical structure sketches are used for presentational purposes but also as inputs to various analysis software. + + + + + + + + + + Nucleic acid signature + + An informative report about a specific or conserved nucleic acid sequence pattern. + 1.8 + + + + + + + + + + DNA sequence + + A DNA sequence. + 1.8 + DNA sequences + + + + + + + + + + RNA sequence + + 1.8 + RNA sequences + DNA sequences + A DNA sequence. + + + + + + + + + + RNA sequence (raw) + + + RNA raw sequence + A raw RNA sequence. + 1.8 + Raw sequence (RNA) + + + + + + + + + + DNA sequence (raw) + + + DNA raw sequence + 1.8 + A raw DNA sequence. + Raw sequence (DNA) + + + + + + + + + + Sequence variations + + + + + + + + Variations are stored along with a reference genome. + Gene sequence variations + Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects. + 1.8 + + + + + + + + + + Bibliography + + A list of publications such as scientic papers or books. + 1.8 + + + + + + + + + + Ontology mapping + + beta12orEarlier + A mapping of supplied textual terms or phrases to ontology concepts (URIs). + + + + + + @@ -23592,7 +23672,7 @@ 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" + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Nucleotide_sequence Non-sequence characters may be used for example for gaps. @@ -23606,7 +23686,7 @@ protein - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Amino_acid_sequence" + 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. @@ -23664,7 +23744,7 @@ 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" + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#DNA_sequence beta12orEarlier @@ -23677,8 +23757,8 @@ rna - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#RNA_sequence" beta12orEarlier + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#RNA_sequence Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters. @@ -24522,12 +24602,12 @@ - PDB format + PDB Entry format of PDB database in PDB format. beta12orEarlier - PDB + PDB format @@ -26101,27 +26181,27 @@ + http://www.onto-med.de/ontologies/gfo.owl#Perpetuant The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data. + http://purl.org/biotop/biotop.owl#Quality Data format - http://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" + http://www.ifomis.org/bfo/1.1/snap#Quality + http://en.wikipedia.org/wiki/List_of_file_formats A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. + http://wsio.org/compression_004 "http://purl.org/dc/elements/1.1/format" - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality" - http://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" + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality + http://www.ifomis.org/bfo/1.1/snap#Continuant beta12orEarlier + http://semanticscience.org/resource/SIO_000618 + http://semanticscience.org/resource/SIO_000612 "http://purl.obolibrary.org/obo/IAO_0000098" - http://www.onto-med.de/ontologies/gfo.owl#Perpetuant" Exchange format + http://www.onto-med.de/ontologies/gfo.owl#Symbol_structure Data model File format + http://purl.org/biotop/biotop.owl#MachineLanguage + http://en.wikipedia.org/wiki/File_format @@ -26567,7 +26647,6 @@ nbrf/pir - pir beta12orEarlier @@ -26800,6 +26879,8 @@ UniProtKB entry sequence format. beta12orEarlier + SwissProt format + UniProt format @@ -27079,6 +27160,7 @@ ClustalW format for (aligned) sequences. beta12orEarlier + clustal @@ -27862,12 +27944,6 @@ Microarray experiment data format - - - - - - Format for microarray experimental data. beta12orEarlier @@ -27953,12 +28029,6 @@ Nucleic acid features (primers) format - - - - - - Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence. beta12orEarlier @@ -28202,12 +28272,6 @@ Protein secondary structure format - - - - - - beta12orEarlier Format for secondary structure (predicted or real) of a protein molecule. @@ -28309,12 +28373,6 @@ Nucleic acid features (restriction sites) format - - - - - - Format used for report on restriction enzyme recognition sites in nucleotide sequences. beta12orEarlier @@ -28328,12 +28386,6 @@ Gene features (coding region) format - - - - - - Format used for report on coding regions in nucleotide sequences. beta12orEarlier @@ -28502,12 +28554,13 @@ UniProt format - + + 1.8 UniProt entry sequence format. - SwissProt format + true beta12orEarlier - - + + @@ -28516,11 +28569,13 @@ ipi - + + true ipi sequence format. beta12orEarlier - - + 1.8 + + @@ -28593,8 +28648,8 @@ A text format resembling FASTA format. beta12orEarlier + http://filext.com/file-extension/FASTA This concept may also be used for the many non-standard FASTA-like formats. - http://filext.com/file-extension/FASTA" @@ -28605,17 +28660,13 @@ Sequence record full format - - - - - - - + + true Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database. beta12orEarlier - - + 1.8 + + @@ -28624,17 +28675,13 @@ Sequence record lite format - - - - - - - + Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment. beta12orEarlier - - + 1.8 + true + + @@ -28880,11 +28927,11 @@ beta12orEarlier http://www.iana.org/assignments/media-types/media-types.xhtml#text Plain text + http://filext.com/file-extension/TXT Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual). - http://www.iana.org/assignments/media-types/text/plain" Textual format. - http://filext.com/file-extension/TSV" - http://filext.com/file-extension/TXT" + http://www.iana.org/assignments/media-types/text/plain + http://filext.com/file-extension/TSV Tabular format @@ -28924,8 +28971,8 @@ XML - http://filext.com/file-extension/XML" Extensible Markup Language + http://filext.com/file-extension/XML beta12orEarlier eXtensible Markup Language (XML) format. Data in XML format can be serialised into text, or binary format. @@ -29005,19 +29052,19 @@ - + - + - + BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more). @@ -29078,7 +29125,7 @@ EMBL-like format - + This concept may be used for the many non-standard EMBL-like formats. A format resembling EMBL entry (plain text) format. beta12orEarlier @@ -29106,7 +29153,7 @@ FASTA-like - + A format resembling FASTA format. beta12orEarlier This concept may be used for the many non-standard FASTA-like formats. @@ -29120,7 +29167,7 @@ uniprotkb-like format - + A sequence format resembling uniprotkb entry format. beta12orEarlier @@ -29287,7 +29334,7 @@ GenBank-like format - + This concept may be used for the non-standard GenBank-like formats. beta12orEarlier A format resembling GenBank entry (plain text) format. @@ -29423,7 +29470,7 @@ Format of a raw molecular sequence (i.e. the alphabet used). beta12orEarlier - http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence" + http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence @@ -29566,7 +29613,7 @@ - + beta12orEarlier @@ -30162,12 +30209,6 @@ GCDML - - - - - - 1.0 GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC). @@ -30218,6 +30259,12 @@ Experiment annotation format + + + + + + Data format for annotation on a laboratory experiment. beta12orEarlier @@ -30403,12 +30450,6 @@ GelML - - - - - - GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS. 1.2 @@ -30425,12 +30466,6 @@ spML - - - - - - spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics. 1.2 @@ -30537,9 +30572,9 @@ RDF/XML is a serialization syntax for OWL DL, but not for OWL Full. + http://www.ebi.ac.uk/SWO/data/SWO_3000006 1.2 Resource Description Framework (RDF) XML format. - http://www.ebi.ac.uk/SWO/data/SWO_3000006" RDF @@ -30887,8 +30922,10 @@ xls - + + 1.7 + Microsoft Excel format Microsoft Excel spreadsheet format. @@ -30902,11 +30939,11 @@ TSV CSV - http://filext.com/file-extension/CSV" - http://filext.com/file-extension/TSV" + 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" + http://www.iana.org/assignments/media-types/text/csv + http://filext.com/file-extension/CSV @@ -31034,54 +31071,109 @@ + + + + Ensembl variation file format + + + 1.8 + Ensembl standard format for variation data. + + + + + + + + + + + docx + + + Microsoft Word format. + doc + Microsoft Word format + 1.8 + + + + + + + + + + Document format + + doc + 1.8 + Format of documents including word processor, spreadsheet and presentation. + Microsoft Word format + Portable Document Format + + + + + + + + + + PDF + + + Portable Document Format + 1.8 + + + + + + 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" + http://en.wikipedia.org/wiki/Subroutine + http://en.wikipedia.org/wiki/Function_(computer_science) + http://www.onto-med.de/ontologies/gfo.owl#Function + http://www.ifomis.org/bfo/1.1/snap#Quality + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#process + http://wsio.org/operation_001 + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality + http://www.onto-med.de/ontologies/gfo.owl#Process Function (programming) Lambda abstraction Mathematical function - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method" - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#process" Computational procedure + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method + http://www.ifomis.org/bfo/1.1/snap#Continuant + http://www.ifomis.org/bfo/1.1/span#Process + http://semanticscience.org/resource/SIO_000649 Computational subroutine - 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)" + http://www.ebi.ac.uk/swo/SWO_0000003 + http://semanticscience.org/resource/SIO_000017 Computational method - http://www.ifomis.org/bfo/1.1/snap#Quality" - http://www.onto-med.de/ontologies/gfo.owl#Function" + http://en.wikipedia.org/wiki/Function_(mathematics) + http://www.ifomis.org/bfo/1.1/snap#Function + http://purl.org/biotop/biotop.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 + http://www.onto-med.de/ontologies/gfo.owl#Perpetuant - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. - Function - - - - Process Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. @@ -31093,6 +31185,12 @@ + + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. + Function + + + @@ -31103,14 +31201,14 @@ - - + + - - + + Search @@ -31147,14 +31245,14 @@ - - + + - - + + This is a broad concept and is used a placeholder for other, more specific concepts. @@ -31281,14 +31379,14 @@ - - + + - - + + Calculate sequence complexity, for example to find low-complexity regions in sequences. @@ -31377,14 +31475,14 @@ - - + + - - + + Motif discovery @@ -31400,25 +31498,31 @@ - Sequence motif recognition + Sequence signature recognition - - + + - - + + - Sequence motif detection - beta12orEarlier + Motif recognition + Sequence motif detection Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s). - Motif detection - Motif recognition + Sequence profile search + Sequence signature detection + Sequence motif recognition + Motif detection + Protein secondary database search + Sequence motif search + Motif search + beta12orEarlier @@ -31432,14 +31536,14 @@ - - + + - - + + Find motifs shared by molecular sequences. @@ -31472,12 +31576,6 @@ Conserved transcription regulatory sequence identification - - - - - - Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites). beta12orEarlier For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes. @@ -31495,14 +31593,14 @@ - - + + - - + + Protein structural property calculation @@ -31538,12 +31636,6 @@ - - - - - - @@ -31566,12 +31658,6 @@ - - - - - - @@ -31604,14 +31690,14 @@ - - + + - - + + WHATIF: SymShellOneXML @@ -31658,14 +31744,14 @@ - - + + - - + + Protein property rendering @@ -31686,14 +31772,14 @@ - - + + - - + + Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins. @@ -31713,17 +31799,18 @@ - - + + - - + + SO:0000110 + Motif database search beta12orEarlier Sequence feature recognition Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions. @@ -31773,7 +31860,7 @@ - + @@ -31785,7 +31872,7 @@ - + Feature table comparison @@ -31961,24 +32048,12 @@ - - - - - - - - - - - - beta12orEarlier - Predict secondary structure of protein sequences. Secondary structure prediction (protein) + Predict secondary structure of protein sequences. Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc. @@ -31994,7 +32069,7 @@ - + Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. @@ -32012,14 +32087,8 @@ Transmembrane protein prediction - - - - - - beta12orEarlier - Predict transmembrane proteins or transmembrane (helical) domains or regions in protein sequences. + Predict and/or classify transmembrane proteins or transmembrane (helical) domains or regions in protein sequences. @@ -32033,12 +32102,6 @@ - - - - - - @@ -32060,14 +32123,14 @@ - - + + - - + + beta12orEarlier @@ -32161,20 +32224,14 @@ - - - - - - - - + + - - + + Analyse a network of protein interactions. @@ -32191,12 +32248,6 @@ Protein interaction network comparison - - - - - - Compare two or more networks of protein interactions. beta12orEarlier @@ -32327,14 +32378,14 @@ - - + + - - + + Analyse genetic linkage. @@ -32389,19 +32440,19 @@ - + - + - - + + @@ -32412,8 +32463,8 @@ - - + + synon: Codon usage table analysis @@ -32604,7 +32655,7 @@ - Structure alignment generation + Structure alignment @@ -32614,11 +32665,11 @@ - Structure alignment Multiple structure alignment generation Multiple structure alignment construction beta12orEarlier Structure alignment construction + Structure alignment generation Align (superimpose) molecular tertiary structures. @@ -32634,8 +32685,8 @@ - - + + @@ -32646,8 +32697,8 @@ - - + + Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment. @@ -32668,7 +32719,7 @@ - + @@ -32680,7 +32731,7 @@ - + beta12orEarlier @@ -32706,14 +32757,14 @@ - - + + - - + + Sequence profile alignment generation @@ -32768,8 +32819,8 @@ - - + + @@ -32780,8 +32831,8 @@ - - + + A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. @@ -32834,14 +32885,14 @@ - - + + - - + + Sequence-structure alignment @@ -32868,12 +32919,6 @@ - - - - - - Protein fold prediction Recognize (predict and identify) known protein structural domains or folds in protein sequence(s). Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. @@ -32939,20 +32984,20 @@ - - + + - - + + - - + + Process and analyse text (typically the biomedical and informatics literature) to extract information from it. @@ -32996,14 +33041,14 @@ - - + + - - + + beta12orEarlier @@ -33090,13 +33135,13 @@ - + - + @@ -33243,19 +33288,13 @@ - - - - - - - + - + Assign secondary structure from protein coordinate or experimental data. @@ -33280,12 +33319,6 @@ - - - - - - @@ -33313,19 +33346,13 @@ - - - - - - - + beta12orEarlier @@ -33392,14 +33419,14 @@ - - + + - - + + Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions. @@ -33506,12 +33533,6 @@ - - - - - - @@ -33575,7 +33596,7 @@ - + @@ -33657,8 +33678,8 @@ - - + + @@ -33669,8 +33690,8 @@ - - + + Rendering @@ -33702,7 +33723,9 @@ This excludes direct retrieval methods (e.g. the dbfetch program). beta12orEarlier - Search a sequence database by sequence comparison and retrieve similar sequences. + Search a sequence database by sequence comparison and retrieve similar sequences. + +sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. @@ -33716,17 +33739,11 @@ - - - - - - - Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data. + Search a tertiary structure database, typically by sequence and/or structure comparison, or some other means, and retrieve structures and associated data. beta12orEarlier @@ -33738,27 +33755,13 @@ Protein secondary database search - - - - - - - - - - - - - - - Sequence profile database search + Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group. + true beta12orEarlier - 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 - - + 1.8 + + @@ -33767,18 +33770,13 @@ Motif database search - - - - - - - - + + 1.8 + true Screen a sequence against a motif or pattern database. beta12orEarlier - - + + @@ -33792,7 +33790,7 @@ Search a database of sequence profiles with a query sequence. beta12orEarlier true - + @@ -33846,11 +33844,13 @@ - Sequence database search (by sequence) - + Sequence similarity search + + Search a sequence database and retrieve sequences that are similar to a query sequence. beta12orEarlier - Sequence similarity search + Sequence database search (by sequence) + Structure database search (by sequence) @@ -33861,18 +33861,13 @@ Sequence database search (by motif or pattern) - - - - - - - - + + true beta12orEarlier Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. - - + 1.8 + + @@ -34056,13 +34051,13 @@ Structure database search (by sequence) - - + + 1.8 Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence. - Structure retrieval by sequence + true beta12orEarlier - - + + @@ -34070,8 +34065,9 @@ - Structure database search (by structure) + Structural similarity search + @@ -34079,8 +34075,8 @@ Structure retrieval by structure - Search a tertiary structure database and retrieve structures that are similar to a query structure. - Structural similarity search + Structure database search (by structure) + Search a database of molecular structure and retrieve structures that are similar to a query structure. beta12orEarlier @@ -34095,13 +34091,13 @@ - + - + @@ -34164,12 +34160,6 @@ - - - - - - Generate digest fragments for a nucleotide sequence containing restriction sites. beta12orEarlier @@ -34186,14 +34176,14 @@ - - + + - - + + Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses. @@ -34248,13 +34238,7 @@ Restriction site creation - - - - - - - + beta12orEarlier Create (or remove) restriction sites in sequences, for example using silent mutations. @@ -34305,12 +34289,13 @@ Sequence composition calculation (nucleic acid) - - + beta12orEarlier + 1.8 Calculate base frequency or word composition of a nucleotide sequence. - - + true + + @@ -34319,12 +34304,13 @@ Sequence composition calculation (protein) - - + + true beta12orEarlier Calculate amino acid frequency or word composition of a protein sequence. - - + 1.8 + + @@ -34362,6 +34348,7 @@ Protein hydropathy calculation (from structure) + beta12orEarlier Analyse the hydrophobic, hydrophilic or charge properties of a protein structure. @@ -34451,9 +34438,10 @@ - Binding site prediction (from structure) + Protein binding site prediction (from structure) + Binding site prediction (from structure) Ligand-binding and active site prediction (from structure) beta12orEarlier Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures. @@ -34470,12 +34458,6 @@ - - - - - - @@ -34493,12 +34475,6 @@ Protein peeling - - - - - - Decompose a structure into compact or globular fragments (protein peeling). beta12orEarlier @@ -34628,14 +34604,14 @@ - - + + - - + + Validate a Ramachandran plot of a protein structure. @@ -34653,14 +34629,14 @@ - - + + - - + + beta12orEarlier @@ -34697,14 +34673,14 @@ - - + + - - + + beta12orEarlier @@ -34719,6 +34695,7 @@ Protein hydropathy calculation (from sequence) + beta12orEarlier Hydropathy calculation on a protein sequence. @@ -34994,12 +34971,6 @@ - - - - - - Epitope mapping is commonly done during vaccine design. Predict antigenic determinant sites (epitopes) in protein sequences. beta12orEarlier @@ -35016,12 +34987,6 @@ - - - - - - @@ -35047,12 +35012,6 @@ - - - - - - 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 @@ -35065,10 +35024,11 @@ - Protein binding site detection + Protein binding site prediction (from sequence) beta12orEarlier + Protein binding site detection Ligand-binding and active site prediction (from sequence) Predict catalytic residues, active sites or other ligand-binding sites in protein sequences. Binding site prediction (from sequence) @@ -35083,12 +35043,6 @@ Protein-nucleic acid binding prediction - - - - - - Predict RNA and DNA-binding binding sites in protein sequences. beta12orEarlier @@ -35103,12 +35057,6 @@ Protein folding site prediction - - - - - - beta12orEarlier Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization. @@ -35128,12 +35076,6 @@ - - - - - - Detect or predict cleavage sites (enzymatic or chemical) in protein sequences. beta12orEarlier @@ -35146,11 +35088,13 @@ Epitope mapping (MHC Class I) - + Predict epitopes that bind to MHC class I molecules. beta12orEarlier - - + true + 1.8 + + @@ -35159,9 +35103,12 @@ Epitope mapping (MHC Class II) - + beta12orEarlier + true + 1.8 Predict epitopes that bind to MHC class II molecules. + @@ -35200,12 +35147,6 @@ Transposon prediction - - - - - - Detect or predict transposons, retrotransposons / retrotransposition signatures etc. beta12orEarlier @@ -35219,12 +35160,6 @@ PolyA signal detection - - - - - - beta12orEarlier Detect polyA signals in nucleotide sequences. @@ -35267,12 +35202,6 @@ - - - - - - @@ -35299,18 +35228,6 @@ - - - - - - - - - - - - Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map. beta12orEarlier @@ -35324,12 +35241,6 @@ Nucleosome formation or exclusion sequence prediction - - - - - - Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA. beta12orEarlier @@ -35349,12 +35260,6 @@ - - - - - - Methods might require a pre-mRNA or genomic DNA sequence. Identify, predict or analyse splice sites in nucleotide sequences. beta12orEarlier @@ -35395,13 +35300,8 @@ Coding region prediction - - - - - - beta12orEarlier + ORF finding ORF prediction Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences. @@ -35476,12 +35376,6 @@ Promoter prediction - - - - - - beta12orEarlier Methods might recognize CG content, CpG islands, splice sites, polyA signals etc. Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences. @@ -35545,12 +35439,6 @@ Matrix/scaffold attachment site prediction - - - - - - beta12orEarlier Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences. MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation. @@ -35565,12 +35453,6 @@ Transcription factor binding site prediction - - - - - - Identify or predict transcription factor binding sites in DNA sequences. beta12orEarlier @@ -35586,12 +35468,6 @@ - - - - - - @@ -35839,12 +35715,6 @@ - - - - - - This includes properties such as. beta12orEarlier Calculate curvature and flexibility / stiffness of a nucleotide sequence. @@ -35859,14 +35729,8 @@ microRNA detection - - - - - - beta12orEarlier - Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in an RNA sequence. + Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in a DNA sequence. @@ -35998,12 +35862,6 @@ - - - - - - @@ -36037,12 +35895,6 @@ - - - - - - Predict tertiary structure (backbone and side-chain conformation) of protein sequences. beta12orEarlier @@ -36127,20 +35979,20 @@ - - + + - + - - + + Protein docking @@ -36202,14 +36054,14 @@ - - + + - - + + Virtual ligand screening @@ -36230,14 +36082,14 @@ - - + + - - + + Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection. @@ -36257,12 +36109,6 @@ - - - - - - This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. beta12orEarlier Single nucleotide polymorphism detection @@ -36340,7 +36186,7 @@ - + Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). @@ -36620,14 +36466,14 @@ - - + + - - + + beta12orEarlier @@ -36645,11 +36491,11 @@ - Pairwise structure alignment generation + Pairwise structure alignment Align (superimpose) exactly two molecular tertiary structures. Pairwise structure alignment construction - Pairwise structure alignment + Pairwise structure alignment generation beta12orEarlier @@ -37045,7 +36891,7 @@ Tag mapping - + @@ -37213,7 +37059,6 @@ 1.7 true - @@ -37229,7 +37074,6 @@ Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data. beta12orEarlier - @@ -37266,11 +37110,11 @@ - Phylogenetic tree construction (from molecular sequences) + Phylogenetic tree generation (from molecular sequences) Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. - Phylogenetic tree generation (from molecular sequences) + Phylogenetic tree construction (from molecular sequences) beta12orEarlier Phylogenetic tree construction from molecular sequences. @@ -37282,7 +37126,7 @@ - Phylogenetic tree construction (from continuous quantitative characters) + Phylogenetic tree generation (from continuous quantitative characters) @@ -37292,7 +37136,7 @@ Phylogenetic tree construction from continuous quantitative character data. beta12orEarlier - Phylogenetic tree generation (from continuous quantitative characters) + Phylogenetic tree construction (from continuous quantitative characters) @@ -37302,7 +37146,7 @@ - Phylogenetic tree construction (from gene frequencies) + Phylogenetic tree generation (from gene frequencies) @@ -37316,9 +37160,9 @@ - Phylogenetic tree generation (from gene frequencies) beta12orEarlier Phylogenetic tree construction from gene frequency data. + Phylogenetic tree construction (from gene frequencies) @@ -37579,8 +37423,8 @@ Phylogenetic tree annotation - http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation" Annotate a phylogenetic tree with terms from a controlled vocabulary. + http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation beta12orEarlier @@ -37595,20 +37439,20 @@ - - + + - + - - + + Predict and optimise peptide ligands that elicit an immunological response. @@ -37629,13 +37473,13 @@ - + - + Predict or optimise DNA to elicit (via DNA vaccination) an immunological response. @@ -37653,13 +37497,13 @@ - + - + @@ -37679,13 +37523,13 @@ - + - + @@ -37758,14 +37602,14 @@ - - + + - - + + beta12orEarlier @@ -37784,14 +37628,14 @@ - - + + - - + + Visualise, format or render sequence clusters. @@ -37854,13 +37698,7 @@ - - - - - - - + beta12orEarlier @@ -37931,12 +37769,6 @@ - - - - - - Identify and analyse networks of protein interactions. beta12orEarlier @@ -38158,12 +37990,6 @@ - - - - - - @@ -38813,8 +38639,8 @@ Sequence file editing + Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, creation of subset or a new file of sequences. beta12orEarlier - Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, or create a file of sequences. @@ -38936,11 +38762,12 @@ - Statistical analysis - + Statistical calculation + true beta12orEarlier Perform a statistical data operation of some type, e.g. calibration or validation. + Statistical analysis @@ -38984,12 +38811,6 @@ - - - - - - @@ -39051,7 +38872,7 @@ Nucleic acid density plotting - + Calculate a density plot (of base composition) for a nucleotide sequence. beta12orEarlier @@ -39120,7 +38941,7 @@ - + @@ -39281,14 +39102,14 @@ - - + + - - + + beta12orEarlier @@ -39309,7 +39130,7 @@ - + @@ -39318,12 +39139,6 @@ - - - - - - Secondary structure analysis (protein) beta12orEarlier Analyse known protein secondary structure data. @@ -39520,18 +39335,6 @@ Mapping - - - - - - - - - - - - beta12orEarlier Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts. This is a broad concept and is used a placeholder for other, more specific concepts. @@ -39617,8 +39420,8 @@ Functional enrichment - + @@ -39626,10 +39429,10 @@ GO term enrichment + Analyse a set of genes (genes corresponding to an expression profile, or any other set) with respect to concepts from an ontology of gene functions. The Gene Ontology (GO) is invariably used, the input is a set of Gene IDs and the output of the analysis is typically a ranked list of GO terms, each associated with a p-value. Gene expression profile annotation beta12orEarlier - Annotate a set of genes (genes corresponding to an expression profile, or any other set) with concepts from an ontology of gene functions. @@ -39644,14 +39447,14 @@ - - + + - - + + beta12orEarlier @@ -39856,12 +39659,6 @@ - - - - - - @@ -39872,6 +39669,12 @@ + + + + + + beta12orEarlier Compare two or more molecular sequences. @@ -40056,14 +39859,14 @@ - - + + - - + + beta12orEarlier @@ -40254,19 +40057,19 @@ - + - - + + - - + + beta12orEarlier @@ -40295,12 +40098,6 @@ - - - - - - Sequence analysis (nucleic acid) beta12orEarlier Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences). @@ -40318,12 +40115,6 @@ - - - - - - @@ -40364,14 +40155,14 @@ - - + + - - + + beta12orEarlier @@ -40487,12 +40278,6 @@ - - - - - - Protein secondary structure Secondary structure comparison (protein) beta12orEarlier @@ -40560,14 +40345,14 @@ - - + + - - + + beta12orEarlier @@ -40675,12 +40460,6 @@ - - - - - - @@ -40892,17 +40671,13 @@ Sequence editing (nucleic acid) - - - - - - - + beta12orEarlier Edit or change a nucleic acid sequence, either randomly or specifically. - - + true + 1.8 + + @@ -40911,18 +40686,13 @@ Sequence editing (protein) - - - - - - - - + + 1.8 + true beta12orEarlier Edit or change a protein sequence, either randomly or specifically. - - + + @@ -40932,12 +40702,6 @@ Sequence generation (nucleic acid) - - - - - - beta12orEarlier Generate a nucleic acid sequence by some means. @@ -40952,12 +40716,6 @@ Sequence generation (protein) - - - - - - beta12orEarlier Generate a protein sequence by some means. @@ -40969,20 +40727,15 @@ - Sequence visualisation (nucleic acid) - - - - - - - + Nucleic acid sequence visualisation + beta12orEarlier - Sequence rendering (nucleic acid) + 1.8 Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. + true Visualise, format or render a nucleic acid sequence. - - + + @@ -40990,23 +40743,15 @@ - Sequence visualisation (protein) - - - - - - - - - Protein sequence visualisation - beta12orEarlier + Protein sequence visualisation + Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. - Protein sequence rendering + 1.8 Visualise, format or render a protein sequence. - Sequence rendering (protein) - - + beta12orEarlier + true + + @@ -41053,6 +40798,18 @@ + + + + + + + + + + + + Generate a map of a DNA sequence annotated with positional or non-positional features of some type. beta12orEarlier @@ -41105,27 +40862,16 @@ - Binding site prediction + Protein binding site prediction - - - - - - - - - - - - Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures. + Binding site prediction beta12orEarlier Ligand-binding and active site prediction @@ -41158,7 +40904,8 @@ - Alignment generation + Alignment + @@ -41168,6 +40915,7 @@ Alignment construction beta12orEarlier + Alignment generation Alignment Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits. @@ -41392,14 +41140,14 @@ - - + + - - + + 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. @@ -41430,11 +41178,11 @@ Alignment analysis - Analyse an existing alignment of two or more molecular sequences, structures or derived data. + 1.8 beta12orEarlier true - 1.6 - + Process or analyse an alignment of molecular sequences or structures. + @@ -41447,14 +41195,14 @@ - - + + - - + + @@ -41493,14 +41241,14 @@ - - + + - - + + Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions. @@ -41792,13 +41540,15 @@ - Protein site detection + Protein sequence feature detection beta13 Sequence feature detection (protein) - Protein sequence feature detection + Protein secondary database search + Protein site detection + Sequence profile database search Protein site prediction Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions. Protein site recognition @@ -41845,27 +41595,22 @@ - - - - - - - - + + - Features includes functional sites or regions and secondary structure. Sequence-based methods typically involve scanning for known motifs, patterns and regular expressions. Protein feature prediction Protein feature recognition beta13 Predict, recognise and identify positional features in proteins from analysing protein sequences or structures. + Features includes functional sites or regions, secondary structure, structural domains and so on. Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a discriminatory element. This includes methods that search a secondary protein database (Prosite, Blocks, ProDom, Prints, Pfam etc.) to assign a protein sequence(s) to a known protein family or group. + @@ -41896,7 +41641,7 @@ - + @@ -41932,7 +41677,7 @@ Editing - Edit, convert or otherwise change a data entity, either randomly or specifically. + Edit a data entity, either randomly or specifically. beta13 @@ -41954,14 +41699,14 @@ - - + + - - + + Evaluate a DNA sequence assembly, typically for purposes of quality control. @@ -42004,7 +41749,7 @@ Sequence assembly visualisation - + Assembly visualisation 1.1 Render and visualise a DNA sequence assembly. @@ -42181,12 +41926,6 @@ Genetic variation analysis - - - - - - Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model. Genetic variation annotation Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript. @@ -42351,7 +42090,7 @@ Genome visualisation - + Genome browsing Genome viewing Genome visualisation @@ -42726,7 +42465,6 @@ Primer removal - Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products). 1.2 @@ -42869,6 +42607,7 @@ Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration. Accession mapping 1.3 + The mapping can be achieved by comparing identifier values or some other means, e.g. exact matches to a provided sequence. Identifier mapping @@ -42918,21 +42657,20 @@ - Checksum generation + Sequence checksum generation - - + + - - + + - Sequence checksum generation 1.4 Generate a checksum of a molecular sequence. @@ -42946,6 +42684,12 @@ Bibliography generation + + + + + + 1.4 Construct a bibliography from the scientific literature. Bibliography construction @@ -43036,8 +42780,8 @@ 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. - + @@ -43075,10 +42819,10 @@ - Nucleic acid site detection + Nucleic acid sequence feature detection - + Nucleic acid site detection 1.6 Nucleic acid site recognition Predict, recognise and identify functional or other key sites within nucleic acid sequences, typically by scanning for known motifs, patterns and regular expressions. @@ -43127,9 +42871,7 @@ Assembly 1.6 - Reformatting XXX - Format conversion @@ -43538,7 +43280,7 @@ 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. @@ -43615,22 +43357,104 @@ + + + + Enrichment + + + + + + + + + Analyse a dataset with respect to concepts from an ontology. + 1.8 + Term enrichment + A relevant ontology will be used. The input is typically a set of identifiers or other data, and the output of the analysis is typically a ranked list of ontology terms, each associated with a p-value. + + + + + + + + + + Chemical class enrichment + + + + + + + + + Analyse a dataset with respect to concepts from an ontology of chemical structure. + 1.8 + + + + + + + + + + Incident curve plotting + + Plot an incident curve such as a survival curve, death curve, mortality curve. + 1.8 + + + + + + + + + + Variant pattern analysis + + 1.8 + Identify and map patterns of genomic variations. + Methods often utilise a database of aligned reads. + + + + + + + + + + Mathematical modelling + + beta12orEarlier + Model some biological system using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models. + + + + + + Topic - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality" + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method sumo:FieldOfStudy + http://www.ifomis.org/bfo/1.1/snap#Continuant beta12orEarlier - http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research" + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other. - http://www.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" + http://www.onto-med.de/ontologies/gfo.owl#Perpetuant + http://www.ifomis.org/bfo/1.1/snap#Quality + http://www.onto-med.de/ontologies/gfo.owl#Category + http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research + http://purl.org/biotop/biotop.owl#Quality @@ -43644,12 +43468,12 @@ Topic concerning the processing and analysis of nucleic acid sequence, structural and other data. beta12orEarlier + http://purl.bioontology.org/ontology/MSH/D017422 Nucleic acid physicochemistry - http://purl.bioontology.org/ontology/MSH/D017422" - http://purl.bioontology.org/ontology/MSH/D017423" Nucleic acid properties - Nucleic acid analysis + http://purl.bioontology.org/ontology/MSH/D017423 Nucleic acid informatics + Nucleic acid analysis Nucleic acid bioinformatics @@ -43663,11 +43487,11 @@ Proteins beta12orEarlier + http://purl.bioontology.org/ontology/MSH/D020539 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. @@ -43695,9 +43519,9 @@ 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 + http://purl.bioontology.org/ontology/MSH/D017421 Sequences Sequence databases beta12orEarlier @@ -43719,8 +43543,8 @@ Structure databases Structural bioinformatics Structure analysis + http://purl.bioontology.org/ontology/MSH/D015394 Topic concerning the curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules. - http://purl.bioontology.org/ontology/MSH/D015394" Computational structural biology @@ -43767,7 +43591,7 @@ 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 - http://purl.bioontology.org/ontology/MSH/D010802" + http://purl.bioontology.org/ontology/MSH/D010802 Topic concerning the study of evolutionary relationships amongst organisms. Phylogenetic clocks Phylogenetic dating @@ -43808,8 +43632,8 @@ Topic concerning the conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource. Ontology Applied ontology + http://purl.bioontology.org/ontology/MSH/D002965 beta12orEarlier - http://purl.bioontology.org/ontology/MSH/D002965" Terminology BioCatalogue:Ontology @@ -43849,7 +43673,7 @@ beta12orEarlier Topic concerning the archival, curation, processing and analysis of complex biological data. - http://purl.bioontology.org/ontology/MSH/D016247" + http://purl.bioontology.org/ontology/MSH/D016247 This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation. @@ -43940,13 +43764,14 @@ Mapping - + + This includes resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. It also includes resources for physical (sequence) maps of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. + beta12orEarlier + DNA mapping Synteny Linkage mapping - 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. @@ -44055,7 +43880,10 @@ Gene structure - Topic concerning resources that aim to identify, predict, model, analyse or curate gene structure in DNA sequences. This includes introns, exons, and gene fusion. + + Topic concerning gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc. + + Gene features beta12orEarlier This includes the study of promoters, coding regions etc. @@ -44072,10 +43900,10 @@ BioCatalogue:Proteomics Protein expression Topic concerning protein and peptide identification, especially in the study of whole proteomes of organisms. + http://purl.bioontology.org/ontology/MSH/D040901 Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein expression data, for example in different cells or tissues. Peptide identification Protein and peptide identification - http://purl.bioontology.org/ontology/MSH/D040901" beta12orEarlier @@ -44174,7 +44002,7 @@ Mass spectrometry - + Topic concerning an analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase. beta12orEarlier @@ -44471,13 +44299,10 @@ HMMs Sequence sites Sequence profiles - Protein sequence features Topic concerning the archival, detection, prediction and analysis of positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. - Sequence feature detection Sequence motifs Functional sites - Protein functional sites Sequence features @@ -44513,7 +44338,6 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier This includes systems that generate, process and analyse sequence clusters. - @@ -44524,13 +44348,15 @@ positional features such as functional and other key sites, in molecular sequenc Protein structural motifs and surfaces + Protein surfaces Protein structural motifs - This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on. - 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. + Protein 3D motifs + Structural motifs + Protein structural features + This includes conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches, role and functions etc. @@ -44576,9 +44402,6 @@ positional features such as functional and other key sites, in molecular sequenc Topic concerning the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. Nucleic acid folding - BioCatalogue:Nucleotide Structure Prediction - BioCatalogue:Nucleotide Tertiary Structure - BioCatalogue:Nucleotide Secondary Structure beta12orEarlier RNA structure prediction Nucleic acid design @@ -44599,7 +44422,6 @@ positional features such as functional and other key sites, in molecular sequenc 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 - @@ -44706,7 +44528,6 @@ positional features such as functional and other key sites, in molecular sequenc 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. - @@ -44722,9 +44543,7 @@ positional features such as functional and other key sites, in molecular sequenc 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 - @@ -44784,8 +44603,8 @@ positional features such as functional and other key sites, in molecular sequenc Phylogenomics + - Topic concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction. beta12orEarlier @@ -44816,7 +44635,7 @@ positional features such as functional and other key sites, in molecular sequenc Sequence assembly - + This covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. beta12orEarlier Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence. @@ -44832,12 +44651,13 @@ positional features such as functional and other key sites, in molecular sequenc Genetic variation + + Topic concerning stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. beta12orEarlier Polymorphism Mutation - http://purl.bioontology.org/ontology/MSH/D014644" - Topic concerning DNA sequence variation (mutation and polymorphism) data. DNA variation + http://purl.bioontology.org/ontology/MSH/D014644 @@ -44853,7 +44673,7 @@ 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" + http://purl.bioontology.org/ontology/MSH/D046228 true BioCatalogue:Microarrays @@ -44886,6 +44706,7 @@ positional features such as functional and other key sites, in molecular sequenc Codon usage DNA microarrays Gene expression analysis + http://purl.bioontology.org/ontology/MSH/D015870 Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc. http://edamontology.org/topic_0197 Topic concerning the analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. @@ -44894,7 +44715,6 @@ 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" @@ -45028,16 +44848,12 @@ positional features such as functional and other key sites, in molecular sequenc Data mining - BioCatalogue:Document Clustering - BioCatalogue:Document Similarity - Text data mining - BioCatalogue:Text Mining - beta12orEarlier - Topic concerning the analysis of the biomedical and informatics literature. Literature mining Text mining Literature analysis - BioCatalogue:Named Entity Recognition + Text data mining + beta12orEarlier + Topic concerning the analysis of the biomedical and informatics literature. @@ -45048,16 +44864,11 @@ positional features such as functional and other key sites, in molecular sequenc - Data curation and annotation + Data deposition, annotation and curation - Annotation - Ontology annotation - Topic concerning the organisation and maintenance of a collection of biological database entries (or other such entities) and their annotation, typically with terms from a controlled vocabulary. - BioCatalogue:Ontology Annotation - BioCatalogue:Genome Annotation - Genome annotation beta12orEarlier - Curation + Database curation + Topic concerning the organisation and maintenance of a collection of biological database entries (or other such entities) including the annotation of entries, typically with terms from a controlled vocabulary. @@ -45068,17 +44879,13 @@ positional features such as functional and other key sites, in molecular sequenc - Data processing and validation + File management - beta12orEarlier - Data file handling - Report processing - Datatypes - Report handling - Data types + Utility software This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. + beta12orEarlier Topic concerning basic manipulations of files or reports of generic biological data. - File handling + Routine data management @@ -45208,7 +45015,7 @@ positional features such as functional and other key sites, in molecular sequenc Molecular interactions, pathways and networks - + BioCatalogue:Pathways http://edamontology.org/topic_3076 Topic concerning molecular interactions, biological pathways, networks and other models. @@ -45298,8 +45105,8 @@ positional features such as functional and other key sites, in molecular sequenc Ecoinformatics Computational ecology beta12orEarlier - http://purl.bioontology.org/ontology/MSH/D004777" Ecological informatics + http://purl.bioontology.org/ontology/MSH/D004777 Topic concerning the ecological and environmental sciences and especially the application of information technology (ecoinformatics). @@ -45456,9 +45263,9 @@ 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. + http://purl.bioontology.org/ontology/MSH/D023281 BioCatalogue:Genomics @@ -45471,10 +45278,9 @@ positional features such as functional and other key sites, in molecular sequenc Gene families - - Genes, gene family or system Gene and protein families + Genes, gene family or system Topic concerning particular gene(s), gene family or other gene group or system and their encoded proteins. Gene system Gene family @@ -45543,9 +45349,9 @@ positional features such as functional and other key sites, in molecular sequenc Topic concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR). Probe design Gene design + http://purl.bioontology.org/ontology/MSH/D015335 This includes the design of primers for PCR and DNA amplification or the design of molecular probes. Probes - http://purl.bioontology.org/ontology/MSH/D015335" @@ -45600,13 +45406,13 @@ positional features such as functional and other key sites, in molecular sequenc Protein sequence analysis - - Protein sequences + + true Topic concerning archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. - BioCatalogue:Protein Sequence Analysis + 1.8 beta12orEarlier - - + + @@ -45615,12 +45421,15 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid sequence analysis - + Topic concerning the archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles. + true + 1.8 BioCatalogue:Nucleotide Sequence Analysis beta12orEarlier + - + @@ -45689,11 +45498,12 @@ positional features such as functional and other key sites, in molecular sequenc Coding RNA - + beta12orEarlier + This includes expressed sequence tag (EST) or complementary DNA (cDNA) sequences. + Topic concerning protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames mRNA cDNA - Topic concerning messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences. EST @@ -45706,12 +45516,14 @@ positional features such as functional and other key sites, in molecular sequenc Functional, regulatory and non-coding RNA - Topic concerning non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA). + beta12orEarlier - Regulatory RNA + Topic concerning non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA). Non-coding RNA includes piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA). + Regulatory RNA Functional RNA Non-coding RNA + ncRNA @@ -45750,14 +45562,14 @@ positional features such as functional and other key sites, in molecular sequenc Protein secondary structure - + This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. - BioCatalogue:Protein Secondary Structure + 1.8 Topic concerning protein secondary structure or secondary structure alignments. beta12orEarlier - Protein secondary structure analysis - - + true + + @@ -45781,13 +45593,13 @@ positional features such as functional and other key sites, in molecular sequenc Protein tertiary structure - + beta12orEarlier - Protein tertiary structure analysis + true Topic concerning protein tertiary structures. - BioCatalogue:Protein Tertiary Structure - - + 1.8 + + @@ -45812,7 +45624,6 @@ positional features such as functional and other key sites, in molecular sequenc Protein families - A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. Protein secondary databases Protein sequence classification @@ -45909,11 +45720,13 @@ positional features such as functional sites in nucleotide sequences. Transcription factors and regulatory sites - + + Transcription factor binding sites beta12orEarlier Transcription factors + TFBS Transcriptional regulatory sites Topic concerning proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences. BioCatalogue:Transcription Factors @@ -45959,6 +45772,7 @@ positional features such as functional sites in nucleotide sequences.Signaling pathways beta12orEarlier + Signal transduction pathways Topic concerning signaling pathways. @@ -46074,6 +45888,7 @@ positional features such as functional sites in nucleotide sequences. Fungi + Yeast The resource may be specific to a fungus, a group of fungi or all fungi. Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation. beta12orEarlier @@ -46164,9 +45979,11 @@ positional features such as functional sites in nucleotide sequences. Mobile genetic elements - + + Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns. beta12orEarlier + Transposons @@ -46194,10 +46011,10 @@ positional features such as functional sites in nucleotide sequences.Immunology beta12orEarlier + http://purl.bioontology.org/ontology/MSH/D007125 + http://purl.bioontology.org/ontology/MSH/D007120 Computational immunology Immunoinformatics - 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. @@ -46236,6 +46053,136 @@ positional features such as functional sites in nucleotide sequences. + + + Primers + + Primer binding sites + beta12orEarlier + Topic concerning PCR primers and hybridization oligos in a nucleic acid sequence. + Nucleic acid features (primers) + + + + + + + + + + + PolyA signal or sites + + Topic concerning regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. + PolyA site + A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation. + PolyA signal + Nucleic acid features (PolyA signal or site) + beta12orEarlier + + + + + + + + + + + CpG island and isochores + + Topic concerning CpG rich regions (isochores) in a nucleotide sequence. + Nucleic acid features (CpG island and isochore) + beta12orEarlier + + + + + + + + + + + Restriction sites + + Nucleic acid restriction sites (report) + beta12orEarlier + Nucleic acid features (restriction sites) + Topic concerning restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. + + + + + + + + + + + Splice sites + + + Nucleic acid report (RNA splice model) + beta12orEarlier + Nucleic acid report (RNA splicing) + Nucleic acid features (splice sites) + Topic concerning splice sites in a nucleotide sequence or alternative RNA splicing events. + + + + + + + + + + + Matrix/scaffold attachment sites + + Topic concerning matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. + beta12orEarlier + Nucleic acid features (matrix/scaffold attachment sites) + + + + + + + + + + + Operon + + The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query. + Nucleic acid features (operon) + beta12orEarlier + Topic concerning operons (operators, promoters and genes) from a bacterial genome. + Gene features (operon) + + + + + + + + + + + Promoters + + Topic concerning whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. + Nucleic acid features (promoters) + beta12orEarlier + + + + + + + @@ -46255,6 +46202,26 @@ positional features such as functional sites in nucleotide sequences. + + + Protein membrane regions + + + Transmembrane regions + Protein transmembrane regions + Intramembrane regions + Topic concerning trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. + This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. + Protein features (membrane regions) + 1.8 + + + + + + + @@ -46416,16 +46383,16 @@ 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 + http://purl.bioontology.org/ontology/MSH/D049490 Biological models Topic concerning the holistic modelling and analysis of complex biological systems and the interactions therein. BioCatalogue:Model Creation - BioCatalogue:Model Execution This includes databases of models and methods to construct or analyse a model. + BioCatalogue:Model Execution + http://en.wikipedia.org/wiki/Systems_biology @@ -46438,11 +46405,11 @@ positional features such as functional sites in nucleotide sequences. Statistics + http://purl.bioontology.org/ontology/MSH/D056808 beta12orEarlier BioCatalogue:Biostatistics - http://purl.bioontology.org/ontology/MSH/D056808" + http://en.wikipedia.org/wiki/Biostatistics Biostatistics - http://en.wikipedia.org/wiki/Biostatistics" Topic concerning the application of statistical methods to biological problems. @@ -46504,10 +46471,11 @@ positional features such as functional sites in nucleotide sequences. - SNPs - + SNP + Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. + Single nucleotide polymorphism beta12orEarlier @@ -46548,6 +46516,63 @@ positional features such as functional sites in nucleotide sequences. + + + Exons + + beta12orEarlier + Topic concerning exons in a nucleotide sequences. + Gene features (exon) + + + + + + + + + + + Gene transcription features + + Attenuators (report) + TATA signals (report) + beta12orEarlier + Topic concerning transcription of DNA into RNA including the regulation of transcription. + -10 signals (report) + Ribosome binding sites (report) + Terminators (report) + Enhancers (report) + This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. + Gene transcriptional features + -35 signals (report) + CAAT signals (report) + GC signals (report) + + + + + + + + + + + DNA mutation + + + Topic concerning DNA mutation. + Nucleic acid features (mutation) + beta12orEarlier + Mutation annotation + + + + + + + @@ -46581,6 +46606,22 @@ positional features such as functional sites in nucleotide sequences. + + + Introns + + beta12orEarlier + Topic concerning introns in a nucleotide sequences. + Nucleic acid features (intron) + Gene features (intron) + + + + + + + @@ -46723,7 +46764,7 @@ positional features such as functional sites in nucleotide sequences. Invertebrates - + Topic concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation. beta12orEarlier The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates. @@ -46737,7 +46778,7 @@ positional features such as functional sites in nucleotide sequences. Vertebrates - + beta12orEarlier Topic concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates. @@ -46801,7 +46842,7 @@ 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" + http://purl.bioontology.org/ontology/MSH/D002965 1.3 true @@ -46891,7 +46932,6 @@ positional features such as functional sites in nucleotide sequences.Structure classification 1.7 - @@ -46926,6 +46966,75 @@ positional features such as functional sites in nucleotide sequences. + + + VNTR + + Topic concerning variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. + VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. + VNTR annotation + beta12orEarlier + Variable number of tandem repeat polymorphism + Nucleic acid features (VNTR) + + + + + + + + + + + Microsatellites + + Microsatellite annotation + A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine. + Topic concerning microsatellite polymorphism in a DNA sequence. + Nucleic acid features (microsatellite) + beta12orEarlier + + + + + + + + + + + RFLP + + Nucleic acid features (RFLP) + beta12orEarlier + RFLP annotation + An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. + Topic concerning restriction fragment length polymorphisms (RFLP) in a DNA sequence. + + + + + + + + + + + DNA polymorphism + + + Topic concerning DNA polymorphism. + beta12orEarlier + Polymorphism annotation + Nucleic acid features (polymorphism) + + + + + + + @@ -47083,8 +47192,8 @@ positional features such as functional sites in nucleotide sequences. Biodiversity + http://purl.bioontology.org/ontology/MSH/D044822 Topic concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet. - http://purl.bioontology.org/ontology/MSH/D044822" beta13 @@ -47119,7 +47228,7 @@ positional features such as functional sites in nucleotide sequences.Gene resource beta13 Genetics data resources - http://purl.bioontology.org/ontology/MSH/D005823" + http://purl.bioontology.org/ontology/MSH/D005823 Gene database Topic concerning the study of genes, genetic variation and heredity in living organisms. @@ -47271,7 +47380,7 @@ positional features such as functional sites in nucleotide sequences. Literature and reference - http://purl.bioontology.org/ontology/MSH/D011642" + http://purl.bioontology.org/ontology/MSH/D011642 Topic concerning the scientific literature, reference information and documentation. Literature sources beta13 @@ -47303,12 +47412,14 @@ positional features such as functional sites in nucleotide sequences. Data management - http://purl.bioontology.org/ontology/MSH/D030541" + Data processing Knowledge management Databases Information management Data handling + http://purl.bioontology.org/ontology/MSH/D030541 beta13 + Data acquisition Databases Topic concerning the general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources. @@ -47323,10 +47434,10 @@ positional features such as functional sites in nucleotide sequences. Sequence feature detection + http://purl.bioontology.org/ontology/MSH/D058977 beta13 true Topic concerning the detection of the positional features, such as functional and other key sites, in molecular sequences. - http://purl.bioontology.org/ontology/MSH/D058977" 1.3 @@ -47384,15 +47495,11 @@ positional features such as functional sites in nucleotide sequences. - Data acquisition and deposition + Data acquisition - Topic concerning the acquisition and deposition of biological data. - Data acquisition - Database submission beta13 - Data deposition - Deposition - + Topic concerning the acquisition of biological data. + @@ -47415,6 +47522,133 @@ positional features such as functional sites in nucleotide sequences. + + + Protein topological domains + + + 1.8 + Topic concerning topological domains such as cytoplasmic regions in a protein. + Protein features (topological domains) + + + + + + + + + + + Protein variants + + Topic concerning protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. + beta13 + + + + + + + + + + + Expression signals + + + Nucleic acid features (expression signal) + Topic concerning regions within a nucleic acid sequence containing a signal that alters a biological function. + beta13 + + + + + + + + + + + DNA binding sites + + + Nucleic acid features (binding) + Topic concerning nucleic acids binding to some other molecule. + beta13 + This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). + + + + + + + + + + + Nucleic acid repeats + + Topic concerning repetitive elements within a nucleic acid sequence. + This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. + beta13 + + + + + + + + + + + DNA replication and recombination + + Topic concerning DNA replication or recombination. + beta13 + Nucleic acid features (replication and recombination) + Nucleosome exclusion sequences + This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. + + + + + + + + + + + Signal or transit peptide + + A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. + Nucleic acid features (signal or transit peptide) + beta13 + Topic concerning coding sequences for a signal or transit peptide. + + + + + + + + + + + Sequence tagged sites + + Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs. + beta13 + Topic concerning sequence tagged sites (STS) in nucleic acid sequences. + Nucleic acid features (STS) + + + + + + + @@ -47422,8 +47656,9 @@ positional features such as functional sites in nucleotide sequences. Next gen sequencing Next generation sequencing + NGS 1.1 - http://purl.bioontology.org/ontology/MSH/D059014" + 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. @@ -47477,9 +47712,9 @@ positional features such as functional sites in nucleotide sequences.DNA methylation 1.1 + http://purl.bioontology.org/ontology/MSH/D019175 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. @@ -47493,7 +47728,7 @@ positional features such as functional sites in nucleotide sequences.Metabolomics 1.1 - http://purl.bioontology.org/ontology/MSH/D055432" + 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. @@ -47508,8 +47743,8 @@ 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. + http://purl.bioontology.org/ontology/MSH/D057890 1.1 Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. @@ -47525,12 +47760,12 @@ 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 + http://purl.bioontology.org/ontology/MSH/D056186 @@ -47543,6 +47778,7 @@ positional features such as functional sites in nucleotide sequences. Structural variation + Genomic structural variation Topic concerning variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations. 1.1 @@ -47557,8 +47793,8 @@ positional features such as functional sites in nucleotide sequences. DNA packaging + http://purl.bioontology.org/ontology/MSH/D042003 Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures. - http://purl.bioontology.org/ontology/MSH/D042003" beta12orEarlier @@ -47671,9 +47907,9 @@ positional features such as functional sites in nucleotide sequences.Phylogenetics + http://purl.bioontology.org/ontology/MSH/D010802 1.3 Topic concerning the study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences). - http://purl.bioontology.org/ontology/MSH/D010802" @@ -47685,9 +47921,9 @@ positional features such as functional sites in nucleotide sequences. Epigenetics - http://purl.bioontology.org/ontology/MSH/D019175" 1.3 Histone modification + http://purl.bioontology.org/ontology/MSH/D019175 This includes sub-topics such as histone modification and DNA methylation. DNA methylation Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence. @@ -49128,9 +49364,10 @@ positional features such as functional sites in nucleotide sequences. - Neutron diffraction experiment + Neutron diffraction + Neutron diffraction experiment Topic concerning the study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure. 1.7 Elastic neutron scattering @@ -49184,6 +49421,506 @@ positional features such as functional sites in nucleotide sequences. + + + Biological databases + + Topic concerning databases of biological information including the results of scientific experiments, the application of high-throughput technology, computational analysis and the the scientific literature. + 1.8 + + + + + + + + + + Animals + + Topic concerning animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation. + Metazoa + Animal + Zoology + Animal biology + 1.8 + The resource may be specific to a plant, a group of plants or all plants. + + + + + + + + + + Protein sites, features and motifs + + 1.8 + Protein functional sites + Protein sequence features + Topic concerning the biologiy, archival, detection, prediction and analysis of positional features such as functional and other key sites, in protein sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. + + + + + + + + + + Nucleic acid sites, features and motifs + + Topic concerning the biologiy, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. + Nucleic acid functional sites + 1.8 + Nucleic acid sequence features + + + + + + + + + + Gene transcript features + + + 1.8 + This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). + mRNA features + Nucleic acid features (mRNA features) + Topic concerning features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. + + + + + + + + + + Protein-ligand interactions + + 1.8 + Topic concerning protein-ligand (small molecule) interaction(s). + + + + + + + + + + Protein-drug interactions + + 1.8 + Topic concerning protein-drug interaction(s). + + + + + + + + + + Genotyping experiment + + Topic concerning genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. + 1.8 + + + + + + + + + + GWAS study + + Topic concerning genome-wide association study experiments. + Genome-wide association study + 1.8 + + + + + + + + + + Microarray experiment + + This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates. + 1.8 + Topic concerning microarray experiments including conditions, protocol, sample:data relationships etc. + + + + + + + + + + PCR experiment + + Topic concerning PCR experiments, e.g. quantitative real-time PCR. + 1.8 + + + + + + + + + + Proteomics experiment + + Topic concerning proteomics experiments. + 1.8 + + + + + + + + + + 2D PAGE experiment + + 1.8 + Topic concerning two-dimensional gel electrophoresis experiments, gels or spots in a gel. + + + + + + + + + + Northern blot experiment + + 1.8 + Topic concerning Northern Blot experiments. + + + + + + + + + + RNAi experiment + + Topic concerning RNAi experiments. + 1.8 + + + + + + + + + + Simulation experiment + + Topic concerning biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. + 1.8 + + + + + + + + + + Protein-nucleic acid interactions + + Topic concerning protein-DNA/RNA interaction(s). + 1.8 + + + + + + + + + + Protein-protein interactions + + Protein interaction networks + 1.8 + Domain-domain interactions + Topic concerning protein-protein interaction(s), including interactions between protein domains. + + + + + + + + + + Cellular process pathways + + Topic concernning cellular process pathways. + 1.8 + + + + + + + + + + Disease pathways + + 1.8 + Pathway or network (disease) + Topic concerning disease pathways, typically of human disease. + + + + + + + + + + Environmental information processing pathways + + Pathway or network (environmental information processing) + 1.8 + Topic concerning environmental information processing pathways. + + + + + + + + + + Genetic information processing pathways + + 1.8 + Pathway or network (genetic information processing) + Topic concerning genetic information processing pathways. + + + + + + + + + + Protein super-secondary structure + + Topic concerning super-secondary structure of protein sequence(s). + Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. + 1.8 + Protein features (super-secondary) + + + + + + + + + + Protein active sites + + Protein features (active sites) + Topic concerning catalytic residues (active site) of an enzyme. + 1.8 + Enzyme active site + + + + + + + + + + Protein binding sites + + Protein features (binding sites) + Topic concerning ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. + 1.8 + + + + + + + + + + Protein-nucleic acid binding sites + + Protein features (nucleic acid binding sites) + 1.8 + Topic concerning RNA and DNA-binding proteins and binding sites in protein sequences. + + + + + + + + + + Protein cleavage sites + + 1.8 + Protein features (cleavage sites) + Topic concerning cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. + + + + + + + + + + Protein chemical modifications + + GO:0006464 + 1.8 + MOD:00000 + Protein features (chemical modifications) + Topic concerning chemical modification of a protein. + + + + + + + + + + Protein disordered structure + + Protein features (disordered structure) + 1.8 + Topic concerning disordered structure in a protein. + + + + + + + + + + Protein domains + + + Protein features (domains) + Protein structural domains + Topic concerning structural domains or 3D folds in a protein or polypeptide chain. + 1.8 + The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc. + + + + + + + + + + Protein key folding sites + + + Topic concerning key residues involved in protein folding. + 1.8 + Protein features (key folding sites) + + + + + + + + + + Protein post-translational modifications + + 1.8 + Topic concerning post-translation modifications in a protein sequence, typically describing the specific sites involved. + Post-translation modifications + Protein features (post-translation modifications) + + + + + + + + + + Protein secondary structure + + + 1.8 + Topic concerning secondary structure (predicted or real) of a protein. + Protein features (secondary structure) + The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks). + + + + + + + + + + Protein sequence repeats + + Protein repeats + Protein features (repeats) + Topic concerning short repetitive subsequences (repeat sequences) in a protein sequence. + 1.8 + + + + + + + + + + Protein signal peptides + + Topic concerning signal peptides or signal peptide cleavage sites in protein sequences. + 1.8 + Protein features (signal peptides) + + + + + +