diff --git a/releases/EDAM.owl b/releases/EDAM.owl index 10f0fe5..4941ab6 100644 --- a/releases/EDAM.owl +++ b/releases/EDAM.owl @@ -29,18 +29,18 @@ xmlns:edam="&oboOther;edam#"> EDAM_topic http://edamontology.org/topic_ "EDAM topics" + 08:02:2016 22:15GMT EDAM_operation http://edamontology.org/operation_ "EDAM operations" - 18:12:2015 formats "EDAM data formats" EDAM An ontology of bioinformatics topics, operations, types of data including identifiers, and data formats Jon Ison, Matus Kalas, Hervé Ménager identifiers "EDAM types of identifiers" data "EDAM types of data" - 3680 relations "EDAM relations" edam "EDAM" EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence. + 3702 operations "EDAM operations" EDAM http://edamontology.org/ "EDAM relations and concept properties" application/rdf+xml @@ -49,9 +49,9 @@ Jon Ison Matúš Kalaš EDAM_format http://edamontology.org/format_ "EDAM data formats" + 1.13 topics "EDAM topics" Hervé Ménager - 1.12 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. @@ -70,6 +70,20 @@ + + + + Citation + concept_properties + 1.13 + Publication reference + Publication + 'Citation' concept property ('citation' metadata tag) contains a dereferenceable URI, preferrably including a DOI, pointing to a citeable publication of the given data format. + true + + + + @@ -97,7 +111,43 @@ Example - 'Example' concept property ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. + 'Example' concept property ('example' metadata tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. + true + Separated by bar ('|'). + concept_properties + + + + + + + + File extension + 'File extension' concept property ('file_extension' metadata tag) lists examples of usual file extensions of formats. + Separated by bar ('|'), without a dot ('.') prefix, preferrably not all capital characters. + concept_properties + true + + + + + + + + isdebtag + When 'true', the term has been proposed or is supported within Debian Med as a tag. + concept_properties + true + + + + + + + + Media type + MIME type + 'Media type' trailing modifier (qualifier, 'media_type') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page specifying a media type of the given data format. true concept_properties @@ -368,8 +418,8 @@ - In very unusual cases. true + In very unusual cases. @@ -421,8 +471,8 @@ - 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. OBO_REL:has_participant + 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. @@ -519,8 +569,8 @@ - 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. @@ -548,12 +598,6 @@ - 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 - - - - true In very unusual cases. @@ -565,6 +609,12 @@ + + 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 + + + @@ -609,17 +659,17 @@ - OBO_REL:participates_in - 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments. - - - - 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 inputs or input arguments. + OBO_REL:participates_in + + + @@ -644,14 +694,14 @@ - true In very unusual cases. + true - 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. OBO_REL:participates_in + 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. @@ -685,16 +735,16 @@ - true - In very unusual cases. + 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. - + - 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 + true + In very unusual cases. - + @@ -714,11 +764,12 @@ Resource type - + beta12orEarlier beta12orEarlier A type of computational resource used in bioinformatics. true + @@ -749,6 +800,12 @@ + 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). + + + + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). Data set @@ -760,12 +817,6 @@ - - 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 - - - @@ -773,11 +824,12 @@ Tool - + beta12orEarlier A bioinformatics package or tool, e.g. a standalone application or web service. beta12orEarlier true + @@ -787,11 +839,12 @@ Database - + A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model. beta12orEarlier true beta12orEarlier + @@ -821,7 +874,7 @@ Directory metadata - + 1.5 A directory on disk from which files are read. beta12orEarlier @@ -836,7 +889,7 @@ MeSH vocabulary - + beta12orEarlier true Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases. @@ -851,7 +904,7 @@ HGNC vocabulary - + beta12orEarlier beta12orEarlier Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee. @@ -866,7 +919,7 @@ UMLS vocabulary - + Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System). beta12orEarlier beta12orEarlier @@ -914,7 +967,7 @@ Database entry - + beta12orEarlier beta12orEarlier An entry (retrievable via URL) from a biological database. @@ -1028,7 +1081,7 @@ Sequence mask character - + true beta12orEarlier 1.5 @@ -1043,7 +1096,7 @@ Sequence mask type - + A label (text token) describing the type of sequence masking to perform. Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits. beta12orEarlier @@ -1075,7 +1128,7 @@ Sequence length specification - + true A specification of sequence length(s). beta12orEarlier @@ -1090,7 +1143,7 @@ Sequence metadata - + beta12orEarlier Basic or general information concerning molecular sequences. This is used for such things as a report including the sequence identifier, type and length. @@ -1157,7 +1210,7 @@ Sequence signature model - + Data files used by motif or profile methods. beta12orEarlier beta12orEarlier @@ -1192,7 +1245,7 @@ Sequence alignment (words) - + 1.5 beta12orEarlier true @@ -1243,7 +1296,7 @@ Sequence alignment parameter - + Some simple value controlling a sequence alignment (or similar 'match') operation. true 1.5 @@ -1271,7 +1324,7 @@ Sequence alignment metadata - + Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score. beta12orEarlier true @@ -1400,13 +1453,13 @@ Protein topology - + beta12orEarlier beta12orEarlier Predicted or actual protein topology represented as a string of protein secondary structure elements. true The location and size of the secondary structure elements and intervening loop regions is usually indicated. - + @@ -1416,7 +1469,7 @@ Protein features report (secondary structure) - + beta12orEarlier 1.8 true @@ -1431,7 +1484,7 @@ Protein features report (super-secondary) - + 1.8 Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. true @@ -1461,12 +1514,12 @@ Secondary structure alignment metadata (protein) - + An informative report on protein secondary structure alignment-derived data or metadata. beta12orEarlier beta12orEarlier true - + @@ -1512,12 +1565,12 @@ Secondary structure alignment metadata (RNA) - + true beta12orEarlier An informative report of RNA secondary structure alignment-derived data or metadata. beta12orEarlier - + @@ -1550,7 +1603,7 @@ Tertiary structure record - + true beta12orEarlier beta12orEarlier @@ -1565,7 +1618,7 @@ Structure database search results - + 1.8 Results (hits) from searching a database of tertiary structure. beta12orEarlier @@ -1631,7 +1684,7 @@ - + beta12orEarlier @@ -1662,7 +1715,7 @@ Sequence-3D profile alignment - + Sequence-structural profile alignment 1.5 An alignment of a sequence to a 3D profile (representing structures or a structure alignment). @@ -1704,7 +1757,7 @@ Amino acid annotation - + An informative report about a specific amino acid. 1.4 true @@ -1719,7 +1772,7 @@ Peptide annotation - + 1.4 true An informative report about a specific peptide. @@ -1765,7 +1818,7 @@ Protein structural motifs and surfaces - + true 1.8 3D structural motifs in a protein. @@ -1780,7 +1833,7 @@ Protein domain classification - + true Data concerning the classification of the sequences and/or structures of protein structural domain(s). 1.5 @@ -1795,7 +1848,7 @@ Protein features report (domains) - + true structural domains or 3D folds in a protein or polypeptide chain. 1.8 @@ -1810,7 +1863,7 @@ Protein architecture report - + 1.4 An informative report on architecture (spatial arrangement of secondary structure) of a protein structure. Protein property (architecture) @@ -1827,7 +1880,7 @@ Protein folding report - + beta12orEarlier A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc. true @@ -1842,7 +1895,7 @@ Protein features (mutation) - + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Data on the effect of (typically point) mutation on protein folding, stability, structure and function. true @@ -1949,7 +2002,7 @@ Nucleotide base annotation - + beta12orEarlier true An informative report about a specific nucleotide base. @@ -2022,7 +2075,7 @@ Gene classification - + beta12orEarlier true A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products. @@ -2037,7 +2090,7 @@ DNA variation - + stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. true 1.8 @@ -2053,12 +2106,6 @@ Chromosome report - - - - - - beta12orEarlier An informative report on a specific chromosome. This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. @@ -2086,7 +2133,7 @@ Nucleic acid features report (primers) - + true 1.8 beta12orEarlier @@ -2101,7 +2148,7 @@ PCR experiment report - + true beta12orEarlier PCR experiments, e.g. quantitative real-time PCR. @@ -2143,8 +2190,8 @@ - SO:0001248 Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. + SO:0001248 @@ -2199,7 +2246,7 @@ Microarray experiment report - + true microarray experiments including conditions, protocol, sample:data relationships etc. 1.8 @@ -2214,7 +2261,7 @@ Oligonucleotide probe data - + beta12orEarlier beta13 true @@ -2229,7 +2276,7 @@ SAGE experimental data - + beta12orEarlier true Output from a serial analysis of gene expression (SAGE) experiment. @@ -2245,7 +2292,7 @@ MPSS experimental data - + beta12orEarlier Massively parallel signature sequencing (MPSS) data. beta12orEarlier @@ -2261,7 +2308,7 @@ SBS experimental data - + beta12orEarlier beta12orEarlier true @@ -2450,7 +2497,7 @@ Pathway or network annotation - + beta12orEarlier true An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway. @@ -2465,7 +2512,7 @@ Biological pathway map - + beta12orEarlier true A map (typically a diagram) of a biological pathway. @@ -2480,7 +2527,7 @@ Data resource definition - + beta12orEarlier true 1.5 @@ -2541,7 +2588,7 @@ EMBOSS database resource definition - + beta12orEarlier Resource definition for an EMBOSS database. true @@ -2556,7 +2603,7 @@ Version information - + "http://purl.obolibrary.org/obo/IAO_0000129" 1.5 Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. @@ -2655,7 +2702,7 @@ Job metadata - + beta12orEarlier true 1.5 @@ -2721,7 +2768,7 @@ Scent annotation - + beta12orEarlier An informative report about a specific scent. 1.4 @@ -2839,7 +2886,7 @@ Entity identifier - + beta12orEarlier true beta12orEarlier @@ -2854,7 +2901,7 @@ Data resource identifier - + true An identifier of a data resource. beta12orEarlier @@ -2898,7 +2945,7 @@ Discrete entity identifier - + beta12orEarlier true beta12orEarlier @@ -2913,7 +2960,7 @@ Entity feature identifier - + true beta12orEarlier Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing). @@ -2928,7 +2975,7 @@ Entity collection identifier - + beta12orEarlier true beta12orEarlier @@ -2943,7 +2990,7 @@ Phenomenon identifier - + beta12orEarlier true beta12orEarlier @@ -3002,7 +3049,7 @@ Molecule type - + For example, 'Protein', 'DNA', 'RNA' etc. true 1.5 @@ -3019,7 +3066,7 @@ Chemical identifier - + true beta12orEarlier beta12orEarlier @@ -3119,7 +3166,7 @@ Ligand identifier - + true beta12orEarlier Code word for a ligand, for example from a PDB file. @@ -3475,7 +3522,7 @@ Sequence position specification - + 1.5 A specification (partial or complete) of one or more positions or regions of a molecular sequence or map. beta12orEarlier @@ -3535,7 +3582,7 @@ Nucleic acid feature identifier - + beta12orEarlier beta12orEarlier Name or other identifier of an nucleic acid feature. @@ -3550,7 +3597,7 @@ Protein feature identifier - + Name or other identifier of a protein feature. true beta12orEarlier @@ -3625,7 +3672,7 @@ Codon name - + beta12orEarlier beta12orEarlier String of one or more ASCII characters representing a codon. @@ -3699,7 +3746,7 @@ Gene identifier (NCBI RefSeq) - + beta12orEarlier true beta12orEarlier @@ -3714,7 +3761,7 @@ Gene identifier (NCBI UniGene) - + beta12orEarlier An NCBI UniGene unique identifier of a gene. beta12orEarlier @@ -3729,7 +3776,7 @@ Gene identifier (Entrez) - + An Entrez unique identifier of a gene. beta12orEarlier true @@ -4143,7 +4190,7 @@ Sequence database name - + The name of a molecular sequence database. true beta13 @@ -4223,7 +4270,7 @@ Database entry identifier - + true This concept is required for completeness. It should never have child concepts. beta12orEarlier @@ -4280,7 +4327,7 @@ Sequence signature identifier - + beta12orEarlier beta12orEarlier true @@ -4317,7 +4364,7 @@ Phylogenetic distance matrix identifier - + beta12orEarlier Identifier of a phylogenetic distance matrix. true @@ -4814,7 +4861,7 @@ Sequence type - + 1.5 Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc). A label (text token) describing a type of molecular sequence. @@ -4904,7 +4951,7 @@ UniProt accession (extended) - + true Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number. [A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+ @@ -4943,7 +4990,7 @@ TREMBL accession - + beta12orEarlier Identifier of a TREMBL sequence database entry. true @@ -5036,7 +5083,7 @@ EMBOSS sequence type - + beta12orEarlier true See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. @@ -5052,7 +5099,7 @@ EMBOSS listfile - + 1.5 List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile). true @@ -5208,7 +5255,7 @@ Sequence alignment type - + beta12orEarlier 1.5 true @@ -5224,7 +5271,7 @@ BLAST sequence alignment type - + true beta12orEarlier beta12orEarlier @@ -5239,7 +5286,7 @@ Phylogenetic tree type - + For example 'nj', 'upgmp' etc. beta12orEarlier true @@ -5284,7 +5331,7 @@ Comparison matrix type - + 1.5 true beta12orEarlier @@ -5716,7 +5763,7 @@ HIVDB identifier - + true beta12orEarlier Identifier of an entry from the HIVDB database. @@ -5777,7 +5824,7 @@ Pathway ID (aMAZE) - + beta12orEarlier aMAZE ID true @@ -5948,8 +5995,8 @@ - A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. UniProt|Enzyme Nomenclature + A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. @@ -6499,7 +6546,7 @@ Psiblast checkpoint file - + beta12orEarlier A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. beta12orEarlier @@ -6515,7 +6562,7 @@ HMMER synthetic sequences set - + Sequences generated by HMMER package in FASTA-style format. beta12orEarlier beta12orEarlier @@ -6576,7 +6623,7 @@ vectorstrip cloning vector definition file - + beta12orEarlier true File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format. @@ -6591,7 +6638,7 @@ Primer3 internal oligo mishybridizing library - + true beta12orEarlier A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format. @@ -6606,7 +6653,7 @@ Primer3 mispriming library file - + true A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format. beta12orEarlier @@ -6621,7 +6668,7 @@ primersearch primer pairs sequence record - + true beta12orEarlier beta12orEarlier @@ -6681,7 +6728,7 @@ Word size - + Word size is used for example in word-based sequence database search methods. Word length 1.5 @@ -6698,7 +6745,7 @@ Window size - + 1.5 true A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring. @@ -6714,7 +6761,7 @@ Sequence length range - + true Specification of range(s) of length of sequences. beta12orEarlier @@ -6729,12 +6776,12 @@ Sequence information report - + Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc. beta12orEarlier beta12orEarlier true - + @@ -6778,7 +6825,7 @@ Sequence features (comparative) - + Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc. beta13 This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. @@ -6794,7 +6841,7 @@ Sequence property (protein) - + true A report of general sequence properties derived from protein sequence data. beta12orEarlier @@ -6809,7 +6856,7 @@ Sequence property (nucleic acid) - + A report of general sequence properties derived from nucleotide sequence data. beta12orEarlier true @@ -6892,7 +6939,7 @@ Sequence composition table - + A table of character or word composition / frequency of a molecular sequence. beta12orEarlier true @@ -6965,7 +7012,7 @@ DAS sequence feature annotation - + beta12orEarlier Annotation of a molecular sequence in DAS format. beta12orEarlier @@ -7094,12 +7141,12 @@ Sequence signature map - + true Image of a sequence with matches to signatures, motifs or profiles. beta12orEarlier beta12orEarlier - + @@ -7192,13 +7239,13 @@ InterPro compact match image - + beta12orEarlier Image showing matches between protein sequence(s) and InterPro Entries. The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches. beta12orEarlier true - + @@ -7208,13 +7255,13 @@ InterPro detailed match image - + beta12orEarlier beta12orEarlier Image showing detailed information on matches between protein sequence(s) and InterPro Entries. The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. true - + @@ -7224,13 +7271,13 @@ InterPro architecture image - + beta12orEarlier beta12orEarlier true The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein. Image showing the architecture of InterPro domains in a protein sequence. - + @@ -7240,12 +7287,12 @@ SMART protein schematic - + true beta12orEarlier beta12orEarlier SMART protein schematic in PNG format. - + @@ -7255,12 +7302,12 @@ GlobPlot domain image - + beta12orEarlier beta12orEarlier true Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences. - + @@ -7270,7 +7317,7 @@ Sequence motif matches - + beta12orEarlier Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences. 1.8 @@ -7285,15 +7332,14 @@ Sequence features (repeats) - + beta12orEarlier true 1.5 Repeat sequence map The report might include derived data map such as classification, annotation, organization, periodicity etc. Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. - - + @@ -7303,7 +7349,7 @@ Gene and transcript structure (report) - + 1.5 beta12orEarlier A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. @@ -7318,7 +7364,7 @@ Mobile genetic elements - + true beta12orEarlier regions of a nucleic acid sequence containing mobile genetic elements. @@ -7333,7 +7379,7 @@ Nucleic acid features report (PolyA signal or site) - + true regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. 1.8 @@ -7348,7 +7394,7 @@ Nucleic acid features (quadruplexes) - + true 1.5 A report on quadruplex-forming motifs in a nucleotide sequence. @@ -7363,7 +7409,7 @@ Nucleic acid features report (CpG island and isochore) - + 1.8 CpG rich regions (isochores) in a nucleotide sequence. beta12orEarlier @@ -7378,7 +7424,7 @@ Nucleic acid features report (restriction sites) - + beta12orEarlier true 1.8 @@ -7393,7 +7439,7 @@ Nucleosome exclusion sequences - + beta12orEarlier true Report on nucleosome formation potential or exclusion sequence(s). @@ -7408,7 +7454,7 @@ Nucleic acid features report (splice sites) - + splice sites in a nucleotide sequence or alternative RNA splicing events. beta12orEarlier true @@ -7423,7 +7469,7 @@ Nucleic acid features report (matrix/scaffold attachment sites) - + 1.8 matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. true @@ -7438,12 +7484,12 @@ Gene features (exonic splicing enhancer) - + beta12orEarlier beta13 true A report on exonic splicing enhancers (ESE) in an exon. - + @@ -7453,12 +7499,12 @@ Nucleic acid features (microRNA) - + true beta12orEarlier A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc. 1.5 - + @@ -7468,7 +7514,7 @@ Gene features report (operon) - + true operons (operators, promoters and genes) from a bacterial genome. 1.8 @@ -7483,7 +7529,7 @@ Nucleic acid features report (promoters) - + 1.8 whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. true @@ -7498,7 +7544,7 @@ Coding region - + beta12orEarlier protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. 1.8 @@ -7513,7 +7559,7 @@ Gene features (SECIS element) - + beta12orEarlier beta13 A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence. @@ -7528,7 +7574,7 @@ Transcription factor binding sites - + transcription factor binding sites (TFBS) in a DNA sequence. beta12orEarlier true @@ -7543,7 +7589,7 @@ Protein features (sites) - + true beta12orEarlier Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. @@ -7559,7 +7605,7 @@ Protein features report (signal peptides) - + true signal peptides or signal peptide cleavage sites in protein sequences. 1.8 @@ -7574,7 +7620,7 @@ Protein features report (cleavage sites) - + true 1.8 cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. @@ -7589,7 +7635,7 @@ Protein features (post-translation modifications) - + true beta12orEarlier post-translation modifications in a protein sequence, typically describing the specific sites involved. @@ -7604,7 +7650,7 @@ Protein features report (active sites) - + 1.8 true beta12orEarlier @@ -7619,7 +7665,7 @@ Protein features report (binding sites) - + beta12orEarlier ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. true @@ -7634,13 +7680,13 @@ Protein features (epitopes) - + A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data. beta13 beta12orEarlier Epitope mapping is commonly done during vaccine design. true - + @@ -7650,7 +7696,7 @@ Protein features report (nucleic acid binding sites) - + true beta12orEarlier 1.8 @@ -7665,12 +7711,12 @@ MHC Class I epitopes report - + beta12orEarlier beta12orEarlier true A report on epitopes that bind to MHC class I molecules. - + @@ -7680,12 +7726,12 @@ MHC Class II epitopes report - + beta12orEarlier beta12orEarlier true A report on predicted epitopes that bind to MHC class II molecules. - + @@ -7695,13 +7741,13 @@ Protein features (PEST sites) - + beta12orEarlier A report or plot of PEST sites in a protein sequence. true beta13 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. - + @@ -7711,7 +7757,7 @@ Sequence database hits scores list - + Scores from a sequence database search (for example a BLAST search). beta12orEarlier true @@ -7726,7 +7772,7 @@ Sequence database hits alignments list - + beta12orEarlier Alignments from a sequence database search (for example a BLAST search). beta12orEarlier @@ -7741,7 +7787,7 @@ Sequence database hits evaluation data - + beta12orEarlier A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search). beta12orEarlier @@ -7756,7 +7802,7 @@ MEME motif alphabet - + Alphabet for the motifs (patterns) that MEME will search for. beta12orEarlier beta12orEarlier @@ -7771,7 +7817,7 @@ MEME background frequencies file - + MEME background frequencies file. true beta12orEarlier @@ -7786,7 +7832,7 @@ MEME motifs directive file - + beta12orEarlier true File of directives for ordering and spacing of MEME motifs. @@ -7814,7 +7860,7 @@ HMM emission and transition counts - + Emission and transition counts of a hidden Markov model, generated once HMM has been determined, for example after residues/gaps have been assigned to match, delete and insert states. true 1.4 @@ -7901,7 +7947,7 @@ Prosite nucleotide pattern - + A nucleotide regular expression pattern from the Prosite database. beta12orEarlier true @@ -7916,7 +7962,7 @@ Prosite protein pattern - + A protein regular expression pattern from the Prosite database. beta12orEarlier beta12orEarlier @@ -8001,7 +8047,7 @@ Domainatrix signature - + A protein signature of the type used in the EMBASSY Signature package. true beta12orEarlier @@ -8016,7 +8062,7 @@ HMMER NULL hidden Markov model - + beta12orEarlier beta12orEarlier true @@ -8031,7 +8077,7 @@ Protein family signature - + Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures. beta12orEarlier true @@ -8047,7 +8093,7 @@ Protein domain signature - + beta12orEarlier 1.5 true @@ -8063,7 +8109,7 @@ Protein region signature - + A protein region signature (sequence classifier) from the InterPro database. true beta12orEarlier @@ -8079,7 +8125,7 @@ Protein repeat signature - + true 1.5 A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain. @@ -8095,7 +8141,7 @@ Protein site signature - + A protein site signature is a classifier for a specific site in a protein. beta12orEarlier A protein site signature (sequence classifier) from the InterPro database. @@ -8111,7 +8157,7 @@ Protein conserved site signature - + 1.4 true A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification. @@ -8127,7 +8173,7 @@ Protein active site signature - + A protein active site signature (sequence classifier) from the InterPro database. A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available. true @@ -8143,7 +8189,7 @@ Protein binding site signature - + 1.4 A protein binding site signature (sequence classifier) from the InterPro database. true @@ -8159,7 +8205,7 @@ Protein post-translational modification signature - + A protein post-translational modification signature (sequence classifier) from the InterPro database. A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible. 1.4 @@ -8189,7 +8235,7 @@ Sequence alignment (multiple) - + beta12orEarlier beta12orEarlier Alignment of more than two molecular sequences. @@ -8245,7 +8291,7 @@ Sequence alignment (nucleic acid pair) - + beta12orEarlier Alignment of exactly two nucleotide sequences. true @@ -8261,7 +8307,7 @@ Sequence alignment (protein pair) - + true 1.12 Alignment of exactly two protein sequences. @@ -8277,7 +8323,7 @@ Hybrid sequence alignment (pair) - + true beta12orEarlier beta12orEarlier @@ -8292,7 +8338,7 @@ Multiple nucleotide sequence alignment - + beta12orEarlier Alignment of more than two nucleotide sequences. true @@ -8307,7 +8353,7 @@ Multiple protein sequence alignment - + true beta12orEarlier beta12orEarlier @@ -8335,7 +8381,7 @@ Score end gaps control - + beta12orEarlier beta12orEarlier Whether end gaps are scored or not. @@ -8350,7 +8396,7 @@ Aligned sequence order - + beta12orEarlier beta12orEarlier true @@ -8404,7 +8450,7 @@ Terminal gap penalty - + beta12orEarlier A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. true @@ -8459,7 +8505,7 @@ Gap opening penalty (integer) - + beta12orEarlier true A simple floating point number defining the penalty for opening a gap in an alignment. @@ -8474,7 +8520,7 @@ Gap opening penalty (float) - + beta12orEarlier beta12orEarlier A simple floating point number defining the penalty for opening a gap in an alignment. @@ -8489,7 +8535,7 @@ Gap extension penalty (integer) - + true A simple floating point number defining the penalty for extending a gap in an alignment. beta12orEarlier @@ -8504,7 +8550,7 @@ Gap extension penalty (float) - + beta12orEarlier true A simple floating point number defining the penalty for extending a gap in an alignment. @@ -8519,7 +8565,7 @@ Gap separation penalty (integer) - + A simple floating point number defining the penalty for gaps that are close together in an alignment. beta12orEarlier true @@ -8534,7 +8580,7 @@ Gap separation penalty (float) - + beta12orEarlier true beta12orEarlier @@ -8602,7 +8648,7 @@ Sequence alignment metadata (quality report) - + beta12orEarlier true beta12orEarlier @@ -8617,7 +8663,7 @@ Sequence alignment report (site conservation) - + beta12orEarlier Data on character conservation in a molecular sequence alignment. 1.4 @@ -8633,7 +8679,7 @@ Sequence alignment report (site correlation) - + 1.4 beta12orEarlier Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures. @@ -8648,7 +8694,7 @@ Sequence-profile alignment (Domainatrix signature) - + beta12orEarlier Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment). beta12orEarlier @@ -8663,7 +8709,7 @@ Sequence-profile alignment (HMM) - + beta12orEarlier 1.5 true @@ -8678,7 +8724,7 @@ Sequence-profile alignment (fingerprint) - + Alignment of molecular sequences to a protein fingerprint from the PRINTS database. 1.5 beta12orEarlier @@ -8758,7 +8804,7 @@ Phylogenetic report - + Phylogenetic tree-derived report This is a broad data type and is used for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis. beta12orEarlier @@ -8792,7 +8838,7 @@ Phylogenetic tree report (tree shape) - + beta12orEarlier true 1.4 @@ -8807,7 +8853,7 @@ Phylogenetic tree report (tree evaluation) - + beta12orEarlier true 1.4 @@ -8836,7 +8882,7 @@ Phylogenetic tree report (tree stratigraphic) - + beta12orEarlier 1.4 true @@ -8865,7 +8911,7 @@ Comparison matrix (integers) - + beta12orEarlier Substitution matrix (integers) beta12orEarlier @@ -8881,7 +8927,7 @@ Comparison matrix (floats) - + beta12orEarlier beta12orEarlier true @@ -8927,7 +8973,7 @@ Nucleotide comparison matrix (integers) - + Nucleotide substitution matrix (integers) beta12orEarlier Matrix of integer numbers for nucleotide comparison. @@ -8943,7 +8989,7 @@ Nucleotide comparison matrix (floats) - + beta12orEarlier true Matrix of floating point numbers for nucleotide comparison. @@ -8959,7 +9005,7 @@ Amino acid comparison matrix (integers) - + beta12orEarlier Matrix of integer numbers for amino acid comparison. Amino acid substitution matrix (integers) @@ -8975,7 +9021,7 @@ Amino acid comparison matrix (floats) - + beta12orEarlier Amino acid substitution matrix (floats) beta12orEarlier @@ -8991,7 +9037,7 @@ Protein features report (membrane regions) - + true beta12orEarlier 1.8 @@ -9063,13 +9109,13 @@ - + - + beta12orEarlier @@ -9181,7 +9227,7 @@ Protein structure (all atoms) - + beta12orEarlier 1.5 true @@ -9211,7 +9257,7 @@ Protein chain (all atoms) - + 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms). beta12orEarlier beta12orEarlier @@ -9226,7 +9272,7 @@ Protein chain (C-alpha atoms) - + true 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only). beta12orEarlier @@ -9242,7 +9288,7 @@ Protein domain (all atoms) - + 3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms). beta12orEarlier true @@ -9257,7 +9303,7 @@ Protein domain (C-alpha atoms) - + C-beta atoms from amino acid side-chains may be included. true 3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only). @@ -9287,7 +9333,7 @@ Structure alignment (multiple) - + beta12orEarlier beta12orEarlier true @@ -9331,7 +9377,7 @@ Structure alignment (protein pair) - + 1.12 Protein pair structural alignment true @@ -9348,7 +9394,7 @@ Multiple protein tertiary structure alignment - + Alignment (superimposition) of more than two protein tertiary (3D) structures. beta12orEarlier true @@ -9363,7 +9409,7 @@ Structure alignment (protein all atoms) - + 1.5 Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered). beta12orEarlier @@ -9378,7 +9424,7 @@ Structure alignment (protein C-alpha atoms) - + Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered). C-beta atoms from amino acid side-chains may be considered. 1.5 @@ -9395,7 +9441,7 @@ Pairwise protein tertiary structure alignment (all atoms) - + Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). true beta12orEarlier @@ -9410,7 +9456,7 @@ Pairwise protein tertiary structure alignment (C-alpha atoms) - + C-beta atoms from amino acid side-chains may be included. true beta12orEarlier @@ -9426,7 +9472,7 @@ Multiple protein tertiary structure alignment (all atoms) - + beta12orEarlier true Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). @@ -9441,7 +9487,7 @@ Multiple protein tertiary structure alignment (C-alpha atoms) - + beta12orEarlier Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). true @@ -9457,7 +9503,7 @@ Structure alignment (nucleic acid pair) - + beta12orEarlier 1.12 true @@ -9474,7 +9520,7 @@ Multiple nucleic acid tertiary structure alignment - + beta12orEarlier Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures. true @@ -9515,7 +9561,7 @@ DaliLite hit table - + DaliLite hit table of protein chain tertiary structure alignment data. The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given. beta12orEarlier @@ -9531,7 +9577,7 @@ Molecular similarity score - + beta12orEarlier A score reflecting structural similarities of two molecules. true @@ -9685,7 +9731,7 @@ Enzyme report - + true 1.5 Protein report (enzyme) @@ -9701,7 +9747,7 @@ Restriction enzyme report - + An informative report on a specific restriction enzyme such as enzyme reference data. This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc. Restriction enzyme pattern data @@ -9909,7 +9955,7 @@ Protein subcellular localization - + Protein report (subcellular localization) An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins). beta12orEarlier @@ -9941,7 +9987,7 @@ MHC peptide immunogenicity report - + A report on the immunogenicity of MHC class I or class II binding peptides. beta13 true @@ -9994,7 +10040,7 @@ Protein non-covalent interactions report - + Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups. beta12orEarlier true @@ -10009,7 +10055,7 @@ Protein flexibility or motion 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 (flexibility or motion) Informative report on flexibility or motion of a protein structure. @@ -10042,7 +10088,7 @@ Protein surface 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 structure report (surface) 1.4 @@ -10138,7 +10184,7 @@ Protein non-canonical interactions - + Protein non-canonical interactions report true Non-canonical atomic interactions in protein structures. @@ -10154,7 +10200,7 @@ CATH node - + Information on a node from the CATH database. The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links. 1.5 @@ -10171,7 +10217,7 @@ SCOP node - + true SCOP classification node Information on a node from the SCOP database. @@ -10187,11 +10233,12 @@ EMBASSY domain classification - + beta12orEarlier beta12orEarlier true An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format. + @@ -10201,7 +10248,7 @@ CATH class - + beta12orEarlier 1.5 Information on a protein 'class' node from the CATH database. @@ -10216,7 +10263,7 @@ CATH architecture - + beta12orEarlier 1.5 Information on a protein 'architecture' node from the CATH database. @@ -10231,7 +10278,7 @@ CATH topology - + true 1.5 Information on a protein 'topology' node from the CATH database. @@ -10246,7 +10293,7 @@ CATH homologous superfamily - + 1.5 true beta12orEarlier @@ -10261,7 +10308,7 @@ CATH structurally similar group - + 1.5 true beta12orEarlier @@ -10276,7 +10323,7 @@ CATH functional category - + Information on a protein 'functional category' node from the CATH database. true 1.5 @@ -10291,13 +10338,13 @@ Protein fold recognition report - + Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. beta12orEarlier A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s). true beta12orEarlier - + @@ -10307,7 +10354,7 @@ Protein-protein interaction report - + protein-protein interaction(s), including interactions between protein domains. beta12orEarlier true @@ -10336,7 +10383,7 @@ Protein-nucleic acid interactions report - + true protein-DNA/RNA interaction(s). beta12orEarlier @@ -10392,7 +10439,7 @@ Nucleic acid melting temperature - + Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA). beta12orEarlier beta12orEarlier @@ -10460,7 +10507,7 @@ Vienna RNA parameters - + RNA parameters used by the Vienna package. true beta12orEarlier @@ -10475,7 +10522,7 @@ Vienna RNA structure constraints - + true Structure constraints used by the Vienna package. beta12orEarlier @@ -10490,7 +10537,7 @@ Vienna RNA concentration data - + RNA concentration data used by the Vienna package. beta12orEarlier true @@ -10505,7 +10552,7 @@ Vienna RNA calculated energy - + beta12orEarlier beta12orEarlier true @@ -10586,7 +10633,7 @@ Codon adaptation index - + true A simple measure of synonymous codon usage bias often used to predict gene expression levels. CAI @@ -10616,7 +10663,7 @@ Nc statistic - + true beta12orEarlier The effective number of codons used in a gene sequence. This reflects how far codon usage of a gene departs from equal usage of synonymous codons. @@ -10678,7 +10725,7 @@ Linkage disequilibrium (report) - + true A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). 1.8 @@ -10708,7 +10755,7 @@ Affymetrix probe sets library file - + true Affymetrix library file of information about which probes belong to which probe set. CDF file @@ -10724,7 +10771,7 @@ Affymetrix probe sets information library file - + true Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated. GIN file @@ -10740,7 +10787,7 @@ Molecular weights standard fingerprint - + beta12orEarlier true 1.12 @@ -10755,7 +10802,7 @@ Metabolic pathway report - + This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. beta12orEarlier A report typically including a map (diagram) of a metabolic pathway. @@ -10771,7 +10818,7 @@ Genetic information processing pathway report - + beta12orEarlier 1.8 true @@ -10786,7 +10833,7 @@ Environmental information processing pathway report - + true environmental information processing pathways. beta12orEarlier @@ -10801,7 +10848,7 @@ Signal transduction pathway report - + A report typically including a map (diagram) of a signal transduction pathway. 1.8 true @@ -10816,7 +10863,7 @@ Cellular process pathways report - + 1.8 Topic concernning cellular process pathways. true @@ -10831,7 +10878,7 @@ Disease pathway or network report - + true beta12orEarlier disease pathways, typically of human disease. @@ -10859,7 +10906,7 @@ Protein interaction networks - + 1.8 networks of protein interactions. true @@ -10874,7 +10921,7 @@ MIRIAM datatype - + A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types. An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources. beta12orEarlier @@ -10933,7 +10980,7 @@ Database version information - + true Ontology version information 1.5 @@ -10949,7 +10996,7 @@ Tool version information - + beta12orEarlier Information on an application version, for example name, version number and release date. true @@ -10964,7 +11011,7 @@ CATH version information - + beta12orEarlier beta12orEarlier true @@ -10979,7 +11026,7 @@ Swiss-Prot to PDB mapping - + Cross-mapping of Swiss-Prot codes to PDB identifiers. beta12orEarlier true @@ -10994,7 +11041,7 @@ Sequence database cross-references - + Cross-references from a sequence record to other databases. beta12orEarlier true @@ -11009,7 +11056,7 @@ Job status - + Metadata on the status of a submitted job. beta12orEarlier 1.5 @@ -11025,11 +11072,12 @@ Job ID - + 1.0 The (typically numeric) unique identifier of a submitted job. beta12orEarlier true + @@ -11039,7 +11087,7 @@ Job type - + 1.5 true beta12orEarlier @@ -11054,7 +11102,7 @@ Tool log - + 1.5 A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages. true @@ -11069,7 +11117,7 @@ DaliLite log file - + true beta12orEarlier DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures. @@ -11084,12 +11132,11 @@ STRIDE log file - + STRIDE log file. true beta12orEarlier beta12orEarlier - @@ -11100,12 +11147,11 @@ NACCESS log file - + beta12orEarlier beta12orEarlier true NACCESS log file. - @@ -11116,7 +11162,7 @@ EMBOSS wordfinder log file - + EMBOSS wordfinder log file. beta12orEarlier beta12orEarlier @@ -11131,7 +11177,7 @@ EMBOSS domainatrix log file - + beta12orEarlier EMBOSS (EMBASSY) domainatrix application log file. beta12orEarlier @@ -11146,7 +11192,7 @@ EMBOSS sites log file - + true beta12orEarlier beta12orEarlier @@ -11161,7 +11207,7 @@ EMBOSS supermatcher error file - + EMBOSS (EMBASSY) supermatcher error file. beta12orEarlier beta12orEarlier @@ -11176,7 +11222,7 @@ EMBOSS megamerger log file - + beta12orEarlier beta12orEarlier EMBOSS megamerger log file. @@ -11191,7 +11237,7 @@ EMBOSS whichdb log file - + beta12orEarlier true EMBOSS megamerger log file. @@ -11206,7 +11252,7 @@ EMBOSS vectorstrip log file - + true beta12orEarlier beta12orEarlier @@ -11279,7 +11325,7 @@ Number of iterations - + 1.5 Number of iterations of an algorithm. true @@ -11294,7 +11340,7 @@ Number of output entities - + Number of entities (for example database hits, sequences, alignments etc) to write to an output file. 1.5 beta12orEarlier @@ -11309,12 +11355,11 @@ Hit sort order - + Controls the order of hits (reported matches) in an output file from a database search. beta12orEarlier beta12orEarlier true - @@ -11461,7 +11506,7 @@ BioPax term - + beta12orEarlier A term from the BioPax ontology. beta12orEarlier @@ -11476,7 +11521,7 @@ GO - + beta12orEarlier Gene Ontology term Moby:Annotated_GO_Term @@ -11496,7 +11541,7 @@ MeSH - + true A term from the MeSH vocabulary. beta12orEarlier @@ -11511,7 +11556,7 @@ HGNC - + beta12orEarlier true A term from the HGNC controlled vocabulary. @@ -11526,7 +11571,7 @@ NCBI taxonomy vocabulary - + beta12orEarlier beta12orEarlier true @@ -11541,7 +11586,7 @@ Plant ontology term - + beta12orEarlier true beta12orEarlier @@ -11556,7 +11601,7 @@ UMLS - + beta12orEarlier beta12orEarlier A term from the UMLS vocabulary. @@ -11571,7 +11616,7 @@ FMA - + beta12orEarlier Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. beta12orEarlier @@ -11587,7 +11632,7 @@ EMAP - + A term from the EMAP mouse ontology. true beta12orEarlier @@ -11602,7 +11647,7 @@ ChEBI - + beta12orEarlier A term from the ChEBI ontology. true @@ -11617,7 +11662,7 @@ MGED - + beta12orEarlier true A term from the MGED ontology. @@ -11632,7 +11677,7 @@ myGrid - + The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. beta12orEarlier true @@ -11648,7 +11693,7 @@ GO (biological process) - + beta12orEarlier true beta12orEarlier @@ -11664,7 +11709,7 @@ GO (molecular function) - + A term definition for a molecular function from the Gene Ontology (GO). beta12orEarlier Data Type is an enumerated string. @@ -11680,7 +11725,7 @@ GO (cellular component) - + beta12orEarlier true A term definition for a cellular component from the Gene Ontology (GO). @@ -11696,7 +11741,7 @@ Ontology relation type - + 1.5 beta12orEarlier true @@ -11725,7 +11770,7 @@ Ontology concept comment - + beta12orEarlier 1.4 true @@ -11740,7 +11785,7 @@ Ontology concept reference - + beta12orEarlier true Reference for a concept from an ontology. @@ -11755,7 +11800,7 @@ doc2loc document information - + beta12orEarlier true The doc2loc output includes the url, format, type and availability code of a document for every service provider. @@ -11945,7 +11990,7 @@ CATH domain report - + beta12orEarlier true beta13 @@ -11961,7 +12006,7 @@ CATH representative domain sequences (ATOM) - + beta12orEarlier beta12orEarlier FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity). @@ -11976,7 +12021,7 @@ CATH representative domain sequences (COMBS) - + true FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity). beta12orEarlier @@ -11991,7 +12036,7 @@ CATH domain sequences (ATOM) - + true FASTA sequence database for all CATH domains (based on PDB ATOM records). beta12orEarlier @@ -12006,7 +12051,7 @@ CATH domain sequences (COMBS) - + FASTA sequence database for all CATH domains (based on COMBS sequence data). beta12orEarlier true @@ -12048,7 +12093,7 @@ Protein report (function) - + true For properties that can be mapped to a sequence, use 'Sequence report' instead. beta13 @@ -12064,7 +12109,7 @@ Gene name (ASPGD) - + 1.3 beta12orEarlier true @@ -12080,7 +12125,7 @@ Gene name (CGD) - + Name of a gene from Candida Genome Database. true http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS @@ -12096,7 +12141,7 @@ Gene name (dictyBase) - + http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase beta12orEarlier 1.3 @@ -12112,7 +12157,7 @@ Gene name (EcoGene primary) - + http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G Primary name of a gene from EcoGene Database. EcoGene primary gene name @@ -12129,7 +12174,7 @@ Gene name (MaizeGDB) - + http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus 1.3 Name of a gene from MaizeGDB (maize genes) database. @@ -12145,7 +12190,7 @@ Gene name (SGD) - + true 1.3 beta12orEarlier @@ -12161,7 +12206,7 @@ Gene name (TGD) - + beta12orEarlier 1.3 Name of a gene from Tetrahymena Genome Database. @@ -12177,7 +12222,7 @@ Gene name (CGSC) - + beta12orEarlier 1.3 true @@ -12193,7 +12238,7 @@ Gene name (HGNC) - + beta12orEarlier HUGO symbol 1.3 @@ -12218,7 +12263,7 @@ Gene name (MGD) - + MGI:[0-9]+ Symbol of a gene from the Mouse Genome Database. http://www.geneontology.org/doc/GO.xrf_abbs: MGD @@ -12235,7 +12280,7 @@ Gene name (Bacillus subtilis) - + http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG Symbol of a gene from Bacillus subtilis Genome Sequence Project. beta12orEarlier @@ -12298,7 +12343,7 @@ Gene ID (GeneDB Glossina morsitans) - + true http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans beta13 @@ -12314,7 +12359,7 @@ Gene ID (GeneDB Leishmania major) - + Gene identifier from Leishmania major GeneDB database. true http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor @@ -12330,7 +12375,7 @@ Gene ID (GeneDB Plasmodium falciparum) - + Gene identifier from Plasmodium falciparum GeneDB database. true http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum @@ -12346,7 +12391,7 @@ Gene ID (GeneDB Schizosaccharomyces pombe) - + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe beta12orEarlier true @@ -12362,7 +12407,7 @@ Gene ID (GeneDB Trypanosoma brucei) - + Gene identifier from Trypanosoma brucei GeneDB database. true beta13 @@ -12443,7 +12488,7 @@ Gene synonym - + Gene name synonym true Any name (other than the recommended one) for a gene. @@ -12474,7 +12519,7 @@ Sequence assembly component - + A component of a larger sequence assembly. true beta12orEarlier @@ -12489,7 +12534,7 @@ Chromosome annotation (aberration) - + beta12orEarlier beta12orEarlier true @@ -12620,7 +12665,7 @@ Map feature - + beta12orEarlier true A feature which may mapped (positioned) on a genetic or other type of map. @@ -12639,7 +12684,7 @@ Map type - + A designation of the type of map (genetic map, physical map, sequence map etc) or map set. Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. 1.5 @@ -12787,7 +12832,7 @@ Synonym - + beta12orEarlier Alternative name beta12orEarlier @@ -12803,7 +12848,7 @@ Misspelling - + A common misspelling of a word. beta12orEarlier true @@ -12818,7 +12863,7 @@ Acronym - + true An abbreviation of a phrase or word. beta12orEarlier @@ -12833,7 +12878,7 @@ Misnomer - + A term which is likely to be misleading of its meaning. beta12orEarlier beta12orEarlier @@ -12891,7 +12936,7 @@ UniProt keywords - + true beta12orEarlier beta12orEarlier @@ -12936,7 +12981,7 @@ Gene ID (MIPS Maize) - + MIPS genetic element identifier (Maize) Identifier for genetic elements in MIPS Maize database. beta12orEarlier @@ -12953,7 +12998,7 @@ Gene ID (MIPS Medicago) - + MIPS genetic element identifier (Medicago) beta12orEarlier beta13 @@ -12970,7 +13015,7 @@ Gene name (DragonDB) - + true The name of an Antirrhinum Gene from the DragonDB database. beta12orEarlier @@ -12986,7 +13031,7 @@ Gene name (Arabidopsis) - + Moby_namespace:ArabidopsisGeneSymbol true A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name. @@ -13019,7 +13064,7 @@ Gene name (GeneFarm) - + 1.3 true Name of a gene from the GeneFarm database. @@ -13240,7 +13285,7 @@ Quantitative trait locus - + QTL A QTL sometimes but does not necessarily correspond to a gene. true @@ -13330,7 +13375,7 @@ Ordered locus name - + beta12orEarlier true A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome. @@ -13387,7 +13432,7 @@ Annotation - + beta12orEarlier true beta13 @@ -13424,7 +13469,7 @@ Vienna RNA structural data - + true Data used by the Vienna RNA analysis package. beta12orEarlier @@ -13439,7 +13484,7 @@ Sequence mask parameter - + beta12orEarlier 1.5 true @@ -13495,7 +13540,7 @@ Experimental data - + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. true Raw data from or annotation on laboratory experiments. @@ -13513,7 +13558,7 @@ Genome version information - + beta12orEarlier true Information on a genome version. @@ -13541,7 +13586,7 @@ Sequence record lite - + beta12orEarlier A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment. true @@ -13579,7 +13624,7 @@ Nucleic acid sequence record (lite) - + beta12orEarlier 1.8 true @@ -13594,7 +13639,7 @@ Protein sequence record (lite) - + 1.8 Sequence record lite (protein) beta12orEarlier @@ -13640,7 +13685,7 @@ Structural data - + This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier true @@ -13687,7 +13732,7 @@ Search parameter - + beta12orEarlier 1.5 true @@ -13717,7 +13762,7 @@ Secondary structure - + 1.5 true beta12orEarlier @@ -13747,7 +13792,7 @@ Alignment data - + beta12orEarlier 1.8 true @@ -13835,7 +13880,7 @@ Database entry version information - + true beta12orEarlier 1.5 @@ -13866,7 +13911,7 @@ SNP - + single nucleotide polymorphism (SNP) in a DNA sequence. true beta12orEarlier @@ -13935,7 +13980,7 @@ Type - + A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values). http://purl.org/dc/elements/1.1/type 1.5 @@ -13980,7 +14025,7 @@ Gene name (KEGG GENES) - + beta12orEarlier KEGG GENES entry name [a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]* @@ -14194,7 +14239,7 @@ Nucleic acid features (codon) - + beta12orEarlier true An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon. @@ -14326,7 +14371,7 @@ Sequence profile type - + true 1.5 A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc. @@ -14355,7 +14400,7 @@ Mutation type - + beta12orEarlier true beta12orEarlier @@ -14384,7 +14429,7 @@ Results sort order - + Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on. beta12orEarlier true @@ -14400,7 +14445,7 @@ Toggle - + beta12orEarlier A simple parameter that is a toggle (boolean value), typically a control for a modal tool. true @@ -14415,7 +14460,7 @@ Sequence width - + true beta12orEarlier beta12orEarlier @@ -14470,7 +14515,7 @@ Window step size - + 1.5 beta12orEarlier true @@ -14485,7 +14530,7 @@ EMBOSS graph - + beta12orEarlier true beta12orEarlier @@ -14500,7 +14545,7 @@ EMBOSS report - + An application report generated by the EMBOSS suite. beta12orEarlier beta12orEarlier @@ -14515,7 +14560,7 @@ Sequence offset - + true beta12orEarlier 1.5 @@ -14530,7 +14575,7 @@ Threshold - + 1.5 beta12orEarlier true @@ -14545,7 +14590,7 @@ Protein report (transcription factor) - + beta13 true This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites. @@ -14562,7 +14607,7 @@ Database category name - + true The name of a category of biological or bioinformatics database. beta12orEarlier @@ -14577,7 +14622,7 @@ Sequence profile name - + beta12orEarlier Name of a sequence profile. true @@ -14592,7 +14637,7 @@ Color - + Specification of one or more colors. beta12orEarlier true @@ -14607,7 +14652,7 @@ Rendering parameter - + true beta12orEarlier 1.5 @@ -14639,7 +14684,7 @@ Date - + 1.5 A temporal date. beta12orEarlier @@ -14654,7 +14699,7 @@ Word composition - + beta12orEarlier Word composition data for a molecular sequence. true @@ -14726,7 +14771,7 @@ Protein sequence properties plot - + true beta12orEarlier beta12orEarlier @@ -14796,12 +14841,12 @@ Nucleic acid features (siRNA) - + true 1.5 beta12orEarlier A report on siRNA duplexes in mRNA. - + @@ -14811,7 +14856,7 @@ Sequence set (stream) - + beta12orEarlier true This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time. @@ -14842,7 +14887,7 @@ Cardinality - + The number of a certain thing. beta12orEarlier true @@ -14857,11 +14902,12 @@ Exactly 1 - + beta12orEarlier beta12orEarlier A single thing. true + @@ -14871,11 +14917,12 @@ 1 or more - + One or more things. beta12orEarlier true beta12orEarlier + @@ -14885,11 +14932,12 @@ Exactly 2 - + Exactly two things. beta12orEarlier true beta12orEarlier + @@ -14899,11 +14947,12 @@ 2 or more - + Two or more things. beta12orEarlier beta12orEarlier true + @@ -14930,7 +14979,7 @@ Protein features report (chemical modifications) - + 1.8 beta12orEarlier chemical modification of a protein. @@ -14945,7 +14994,7 @@ Error - + beta12orEarlier Data on an error generated by computer system or tool. 1.5 @@ -14973,7 +15022,7 @@ Gene cluster - + beta13 true beta12orEarlier @@ -14988,7 +15037,7 @@ Sequence record full - + true beta12orEarlier A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. @@ -15032,12 +15081,12 @@ Mutation annotation (basic) - + Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style. beta12orEarlier true beta12orEarlier - + @@ -15047,12 +15096,12 @@ Mutation annotation (prevalence) - + beta12orEarlier true An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).. beta12orEarlier - + @@ -15062,12 +15111,12 @@ Mutation annotation (prognostic) - + beta12orEarlier An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study. beta12orEarlier true - + @@ -15077,12 +15126,12 @@ Mutation annotation (functional) - + An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on. true beta12orEarlier beta12orEarlier - + @@ -15105,7 +15154,7 @@ Tumor annotation - + true 1.4 An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on. @@ -15120,7 +15169,7 @@ Server metadata - + Basic information about a server on the web, such as an SRS server. beta12orEarlier 1.5 @@ -15183,7 +15232,7 @@ Raw SCOP domain classification - + true beta12orEarlier Raw SCOP domain classification data files. @@ -15199,7 +15248,7 @@ Raw CATH domain classification - + Raw CATH domain classification data files. These are the parsable data files provided by CATH. true @@ -15215,7 +15264,7 @@ Heterogen annotation - + 1.4 true beta12orEarlier @@ -15230,7 +15279,7 @@ Phylogenetic property values - + beta12orEarlier Phylogenetic property values data. true @@ -15245,7 +15294,7 @@ Sequence set (bootstrapped) - + 1.5 beta12orEarlier Bootstrapping is often performed in phylogenetic analysis. @@ -15261,7 +15310,7 @@ Phylogenetic consensus tree - + true A consensus phylogenetic tree derived from comparison of multiple trees. beta12orEarlier @@ -15276,7 +15325,7 @@ Schema - + beta12orEarlier true A data schema for organising or transforming data of some type. @@ -15291,7 +15340,7 @@ DTD - + A DTD (document type definition). true beta12orEarlier @@ -15306,7 +15355,7 @@ XML Schema - + beta12orEarlier XSD An XML Schema. @@ -15322,7 +15371,7 @@ Relax-NG schema - + beta12orEarlier 1.5 A relax-NG schema. @@ -15337,11 +15386,12 @@ XSLT stylesheet - + 1.5 beta12orEarlier An XSLT stylesheet. true + @@ -15395,7 +15445,7 @@ Sequence identifier (protein) - + An identifier of protein sequence(s) or protein sequence database entries. beta12orEarlier beta12orEarlier @@ -15410,7 +15460,7 @@ Sequence identifier (nucleic acid) - + An identifier of nucleotide sequence(s) or nucleotide sequence database entries. beta12orEarlier true @@ -15532,7 +15582,7 @@ Gene name (AceView) - + AceView gene name 1.3 true @@ -15596,7 +15646,7 @@ Gene name (NCBI) - + beta12orEarlier 1.3 NCBI gene name @@ -15639,7 +15689,7 @@ Virus annotation - + An informative report on a specific virus. true 1.4 @@ -15654,7 +15704,7 @@ Virus annotation (taxonomy) - + An informative report on the taxonomy of a specific virus. beta12orEarlier true @@ -16150,7 +16200,7 @@ Protein signature type - + beta12orEarlier true A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database. @@ -16165,12 +16215,12 @@ Domain-nucleic acid interaction report - + 1.5 true An informative report on protein domain-DNA/RNA interaction(s). beta12orEarlier - + @@ -16180,7 +16230,7 @@ Domain-domain interactions - + 1.8 An informative report on protein domain-protein domain interaction(s). beta12orEarlier @@ -16195,12 +16245,12 @@ Domain-domain interaction (indirect) - + true beta12orEarlier beta12orEarlier Data on indirect protein domain-protein domain interaction(s). - + @@ -16230,13 +16280,13 @@ 2D PAGE data - + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. beta13 beta12orEarlier true Data concerning two-dimensional polygel electrophoresis. - + @@ -16246,7 +16296,7 @@ 2D PAGE report - + beta12orEarlier two-dimensional gel electrophoresis experiments, gels or spots in a gel. 1.8 @@ -16360,7 +16410,7 @@ 2D PAGE spot report - + 2D PAGE spot annotation beta12orEarlier An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel. @@ -16419,12 +16469,12 @@ Protein-motif interaction - + beta13 true Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs. beta12orEarlier - + @@ -16463,7 +16513,7 @@ Experiment report (genotyping) - + true Report of genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. 1.8 @@ -16660,7 +16710,7 @@ Fungi annotation - + true beta12orEarlier 1.4 @@ -16675,7 +16725,7 @@ Fungi annotation (anamorph) - + beta12orEarlier An informative report on a specific fungus anamorph. 1.4 @@ -16690,7 +16740,7 @@ Gene features report (exon) - + true exons in a nucleotide sequences. 1.8 @@ -16722,12 +16772,12 @@ Gene transcriptional features report - + 1.8 beta12orEarlier transcription of DNA into RNA including the regulation of transcription. true - + @@ -16737,7 +16787,7 @@ Toxin annotation - + beta12orEarlier An informative report on a specific toxin. 1.4 @@ -16752,12 +16802,12 @@ Protein report (membrane protein) - + beta12orEarlier true An informative report on a membrane protein. beta12orEarlier - + @@ -16767,7 +16817,7 @@ Protein-drug interaction report - + true An informative report on tentative or known protein-drug interaction(s). 1.12 @@ -16782,7 +16832,7 @@ Map data - + beta12orEarlier This is a broad data type and is used a placeholder for other, more specific types. true @@ -16813,7 +16863,7 @@ Protein data - + This is a broad data type and is used a placeholder for other, more specific types. beta13 Data concerning one or more protein molecules. @@ -16829,7 +16879,7 @@ Nucleic acid data - + true Data concerning one or more nucleic acid molecules. beta13 @@ -16879,7 +16929,7 @@ Molecular data - + Molecule-specific data true Data concerning a specific type of molecule. @@ -16896,7 +16946,7 @@ Molecule report - + An informative report on a specific molecule. beta12orEarlier Molecular report @@ -16942,7 +16992,7 @@ Nucleic acid features report (mutation) - + DNA mutation. 1.8 true @@ -17027,7 +17077,7 @@ Alignment data - + This is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles. true beta13 @@ -17044,7 +17094,7 @@ Data index data - + true Data concerning an index of data. beta12orEarlier @@ -17137,7 +17187,7 @@ Expressed gene list - + beta12orEarlier true 1.5 @@ -17167,7 +17217,7 @@ GO concept name - + true beta12orEarlier beta12orEarlier @@ -17212,7 +17262,7 @@ GO concept name (cellular component) - + The name of a concept for a cellular component from the GO ontology. true beta12orEarlier @@ -17283,7 +17333,7 @@ Hierarchy identifier - + Identifier of an entry from a database of biological hierarchies. beta12orEarlier beta12orEarlier @@ -17312,12 +17362,12 @@ Cancer type - + true A type (represented as a string) of cancer. beta12orEarlier beta12orEarlier - + @@ -17400,12 +17450,12 @@ Secondary structure alignment metadata - + An informative report on protein secondary structure alignment-derived data or metadata. beta12orEarlier beta12orEarlier true - + @@ -17415,7 +17465,7 @@ Molecule interaction report - + An informative report on the physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules). beta12orEarlier Molecular interaction report @@ -17450,7 +17500,7 @@ Small molecule data - + true This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier @@ -17466,7 +17516,7 @@ Genotype and phenotype data - + beta12orEarlier true beta13 @@ -17816,7 +17866,7 @@ Molecular interaction ID - + Identifier of a report of molecular interactions from a database (typically). true beta12orEarlier @@ -18347,13 +18397,13 @@ - + - + beta12orEarlier @@ -18475,7 +18525,7 @@ Ensembl ID (Homo sapiens) - + beta12orEarlier true beta12orEarlier @@ -18491,7 +18541,7 @@ Ensembl ID ('Bos taurus') - + beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division). true @@ -18507,7 +18557,7 @@ Ensembl ID ('Canis familiaris') - + beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division). true @@ -18523,7 +18573,7 @@ Ensembl ID ('Cavia porcellus') - + ENSCPO([EGTP])[0-9]{11} true beta12orEarlier @@ -18539,7 +18589,7 @@ Ensembl ID ('Ciona intestinalis') - + true Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division). beta12orEarlier @@ -18555,7 +18605,7 @@ Ensembl ID ('Ciona savignyi') - + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division). ENSCSAV([EGTP])[0-9]{11} beta12orEarlier @@ -18571,7 +18621,7 @@ Ensembl ID ('Danio rerio') - + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division). true beta12orEarlier @@ -18587,7 +18637,7 @@ Ensembl ID ('Dasypus novemcinctus') - + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division). beta12orEarlier beta12orEarlier @@ -18603,7 +18653,7 @@ Ensembl ID ('Echinops telfairi') - + ENSETE([EGTP])[0-9]{11} true beta12orEarlier @@ -18619,7 +18669,7 @@ Ensembl ID ('Erinaceus europaeus') - + true ENSEEU([EGTP])[0-9]{11} beta12orEarlier @@ -18635,7 +18685,7 @@ Ensembl ID ('Felis catus') - + beta12orEarlier true ENSFCA([EGTP])[0-9]{11} @@ -18651,7 +18701,7 @@ Ensembl ID ('Gallus gallus') - + ENSGAL([EGTP])[0-9]{11} Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division). beta12orEarlier @@ -18667,7 +18717,7 @@ Ensembl ID ('Gasterosteus aculeatus') - + beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division). true @@ -18683,7 +18733,7 @@ Ensembl ID ('Homo sapiens') - + ENSHUM([EGTP])[0-9]{11} beta12orEarlier beta12orEarlier @@ -18699,7 +18749,7 @@ Ensembl ID ('Loxodonta africana') - + beta12orEarlier true Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division). @@ -18715,7 +18765,7 @@ Ensembl ID ('Macaca mulatta') - + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division). beta12orEarlier ENSMMU([EGTP])[0-9]{11} @@ -18731,7 +18781,7 @@ Ensembl ID ('Monodelphis domestica') - + beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division). true @@ -18747,7 +18797,7 @@ Ensembl ID ('Mus musculus') - + ENSMUS([EGTP])[0-9]{11} true Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division). @@ -18763,7 +18813,7 @@ Ensembl ID ('Myotis lucifugus') - + beta12orEarlier ENSMLU([EGTP])[0-9]{11} true @@ -18779,7 +18829,7 @@ Ensembl ID ("Ornithorhynchus anatinus") - + beta12orEarlier true Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division). @@ -18795,7 +18845,7 @@ Ensembl ID ('Oryctolagus cuniculus') - + beta12orEarlier ENSOCU([EGTP])[0-9]{11} true @@ -18811,7 +18861,7 @@ Ensembl ID ('Oryzias latipes') - + ENSORL([EGTP])[0-9]{11} true beta12orEarlier @@ -18827,7 +18877,7 @@ Ensembl ID ('Otolemur garnettii') - + beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division). true @@ -18843,7 +18893,7 @@ Ensembl ID ('Pan troglodytes') - + beta12orEarlier beta12orEarlier ENSPTR([EGTP])[0-9]{11} @@ -18859,7 +18909,7 @@ Ensembl ID ('Rattus norvegicus') - + beta12orEarlier true Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division). @@ -18875,7 +18925,7 @@ Ensembl ID ('Spermophilus tridecemlineatus') - + true beta12orEarlier ENSSTO([EGTP])[0-9]{11} @@ -18891,7 +18941,7 @@ Ensembl ID ('Takifugu rubripes') - + beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division). @@ -18907,7 +18957,7 @@ Ensembl ID ('Tupaia belangeri') - + beta12orEarlier beta12orEarlier Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division). @@ -18923,7 +18973,7 @@ Ensembl ID ('Xenopus tropicalis') - + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division). beta12orEarlier beta12orEarlier @@ -19203,7 +19253,7 @@ Protein features report (disordered structure) - + 1.8 true beta12orEarlier @@ -19233,7 +19283,7 @@ Embryo report - + Annotation on an embryo or concerning embryological development. true Embryo annotation @@ -19265,7 +19315,7 @@ Inhibitor annotation - + 1.4 beta12orEarlier An informative report on one or more small molecules that are enzyme inhibitors. @@ -19368,7 +19418,7 @@ Genus name (virus) - + true The name of a genus of viruses. beta13 @@ -19383,7 +19433,7 @@ Family name (virus) - + beta13 The name of a family of viruses. true @@ -19398,7 +19448,7 @@ Database name (SwissRegulon) - + true beta13 The name of a SwissRegulon database. @@ -19471,7 +19521,7 @@ Gene name (Genolist) - + beta12orEarlier true Genolist gene name @@ -19516,12 +19566,12 @@ Gene name (HUGO) - + beta12orEarlier beta12orEarlier true Name of an entry (gene) from the HUGO database. - + @@ -19573,7 +19623,7 @@ Database name (CMD) - + beta12orEarlier true The name of a subdivision of the Collagen Mutation Database (CMD) database. @@ -19588,7 +19638,7 @@ Database name (Osteogenesis) - + beta12orEarlier true beta13 @@ -19659,7 +19709,7 @@ Gene features report (intron) - + introns in a nucleotide sequences. true beta12orEarlier @@ -19783,7 +19833,7 @@ Locus annotation - + Locus report true beta12orEarlier @@ -19813,7 +19863,7 @@ Term ID list - + One or more terms from one or more controlled vocabularies which are annotations on an entity. beta12orEarlier true @@ -19843,7 +19893,7 @@ Identifier with metadata - + Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance. beta12orEarlier true @@ -19858,12 +19908,12 @@ Gene symbol annotation - + true beta12orEarlier Annotation about a gene symbol. beta12orEarlier - + @@ -20152,7 +20202,7 @@ Sequence profile data - + 1.8 Data concerning, extracted from, or derived from the analysis of a sequence profile, such as its name, length, technical details about the profile or it's construction, the biological role or annotation, and so on. true @@ -20430,11 +20480,12 @@ Databank - + true beta12orEarlier A flat-file (textual) data archive. beta12orEarlier + @@ -20444,11 +20495,12 @@ Web portal - + A web site providing data (web pages) on a common theme to a HTTP client. beta12orEarlier true beta12orEarlier + @@ -20503,12 +20555,12 @@ Experimental data (proteomics) - + true Data concerning a proteomics experiment. beta12orEarlier beta12orEarlier - + @@ -20611,7 +20663,7 @@ Article metadata - + true beta12orEarlier Bibliographic data concerning scientific article(s). @@ -20653,7 +20705,7 @@ Northern blot report - + true beta12orEarlier 1.8 @@ -20668,7 +20720,7 @@ Nucleic acid features report (VNTR) - + 1.8 beta12orEarlier true @@ -20683,7 +20735,7 @@ Nucleic acid features report (microsatellite) - + true microsatellite polymorphism in a DNA sequence. 1.8 @@ -20699,7 +20751,7 @@ Nucleic acid features report (RFLP) - + beta12orEarlier true 1.8 @@ -20755,7 +20807,7 @@ Sequence set (polymorphic) - + beta13 beta12orEarlier true @@ -20770,7 +20822,7 @@ DRCAT resource - + 1.5 An entry (resource) from the DRCAT bioinformatics resource catalogue. beta12orEarlier @@ -20824,7 +20876,7 @@ Secondary structure image - + 1.4 beta12orEarlier Image of one or more molecular secondary structures. @@ -20839,7 +20891,7 @@ Secondary structure report - + Secondary structure-derived report beta12orEarlier true @@ -20855,7 +20907,7 @@ DNA features - + beta12orEarlier DNA sequence-specific feature annotation (not in a feature table). true @@ -20870,7 +20922,7 @@ RNA features report - + true beta12orEarlier 1.5 @@ -20888,8 +20940,6 @@ Plot - beta12orEarlier - true beta12orEarlier Biological data that has been plotted as a graph of some type. @@ -20902,7 +20952,7 @@ Nucleic acid features report (polymorphism) - + true DNA polymorphism. beta12orEarlier @@ -20949,7 +20999,7 @@ Protein sequence record (full) - + A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. 1.8 beta12orEarlier @@ -20964,7 +21014,7 @@ Nucleic acid sequence record (full) - + true A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. beta12orEarlier @@ -21399,7 +21449,7 @@ Sequence data - + This is a broad data type and is used a placeholder for other, more specific types. 1.8 beta12orEarlier @@ -21415,7 +21465,7 @@ Codon usage - + beta12orEarlier true beta13 @@ -21431,7 +21481,7 @@ Article report - + beta12orEarlier 1.5 Data derived from the analysis of a scientific text such as a full text article from a scientific journal. @@ -21531,7 +21581,7 @@ Gene regulatory network report - + 1.8 A report typically including a map (diagram) of a gene regulatory network. true @@ -21546,7 +21596,7 @@ 2D PAGE gel report - + An informative report on a two-dimensional (2D PAGE) gel. 2D PAGE image report 1.8 @@ -21577,7 +21627,7 @@ Microarray image - + 1.5 beta12orEarlier Gene expression image @@ -21637,7 +21687,7 @@ Workflow data - + beta12orEarlier beta13 Data concerning a computational workflow. @@ -21652,7 +21702,7 @@ Workflow - + true beta12orEarlier 1.5 @@ -21667,7 +21717,7 @@ Secondary structure data - + beta13 true beta12orEarlier @@ -21778,7 +21828,7 @@ Protein classification - + This is a broad data type and is used a placeholder for other, more specific types. Protein classification data An informative report concerning the classification of protein sequences or structures. @@ -21792,7 +21842,7 @@ Sequence motif data - + true 1.8 Data concerning specific or conserved pattern in molecular sequences. @@ -21808,7 +21858,7 @@ Sequence profile data - + beta12orEarlier true This is a broad data type and is used a placeholder for other, more specific types. @@ -21824,7 +21874,7 @@ Pathway or network data - + Data concerning a specific biological pathway or network. beta13 true @@ -21874,7 +21924,7 @@ Nucleic acid classification - + This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier Data concerning the classification of nucleic acid sequences or structures. @@ -21888,7 +21938,7 @@ Classification report - + This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. beta12orEarlier true @@ -21905,7 +21955,7 @@ Protein features report (key folding sites) - + beta12orEarlier key residues involved in protein folding. 1.8 @@ -22045,7 +22095,7 @@ GO concept name (biological process) - + true The name of a concept for a biological process from the GO ontology. beta12orEarlier @@ -22060,7 +22110,7 @@ GO concept name (molecular function) - + true beta12orEarlier The name of a concept for a molecular function from the GO ontology. @@ -22111,7 +22161,7 @@ Core data - + Core data entities typically have a format and may be identified by an accession number. A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation. 1.5 @@ -22187,7 +22237,7 @@ Protein sequence composition - + beta13 1.8 true @@ -22202,7 +22252,7 @@ Nucleic acid sequence composition (report) - + 1.8 A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s). true @@ -22217,7 +22267,7 @@ Protein domain classification node - + beta13 A node from a classification of protein structural domain(s). true @@ -22276,7 +22326,7 @@ Geotemporal metadata - + 1.5 beta13 true @@ -22423,7 +22473,7 @@ Microarray protocol annotation - + true This might describe e.g. the normalisation methods used to process the raw data. beta13 @@ -22452,7 +22502,7 @@ Protein features report (topological domains) - + 1.8 beta13 topological domains such as cytoplasmic regions in a protein. @@ -22467,7 +22517,7 @@ Sequence features (compositionally-biased regions) - + 1.5 beta13 true @@ -22482,12 +22532,12 @@ Nucleic acid features (difference and change) - + beta13 A report on features in a nucleic acid sequence that indicate changes to or differences between sequences. 1.5 true - + @@ -22497,7 +22547,7 @@ Nucleic acid features report (expression signal) - + true beta13 regions within a nucleic acid sequence containing a signal that alters a biological function. @@ -22512,7 +22562,7 @@ Nucleic acid features report (binding) - + nucleic acids binding to some other molecule. 1.8 true @@ -22528,7 +22578,7 @@ Nucleic acid repeats (report) - + true repetitive elements within a nucleic acid sequence. 1.8 @@ -22543,7 +22593,7 @@ Nucleic acid features report (replication and recombination) - + beta13 true 1.8 @@ -22576,7 +22626,7 @@ Protein features report (repeats) - + 1.8 short repetitive subsequences (repeat sequences) in a protein sequence. beta13 @@ -22591,12 +22641,12 @@ Sequence motif matches (protein) - + Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences. 1.8 beta13 true - + @@ -22606,12 +22656,12 @@ Sequence motif matches (nucleic acid) - + Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences. beta13 true 1.8 - + @@ -22621,7 +22671,7 @@ Nucleic acid features (d-loop) - + beta13 true 1.5 @@ -22637,7 +22687,7 @@ Nucleic acid features (stem loop) - + beta13 true A report on stem loops in a DNA sequence. @@ -22674,7 +22724,7 @@ Nucleic acid features report (signal or transit peptide) - + true coding sequences for a signal or transit peptide. 1.8 @@ -22689,7 +22739,7 @@ Non-coding RNA - + beta13 true features of non-coding or functional RNA molecules, including tRNA and rRNA. @@ -22704,13 +22754,13 @@ Transcriptional features (report) - + 1.5 true This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. Features concerning transcription of DNA into RNA including the regulation of transcription. beta13 - + @@ -22720,7 +22770,7 @@ Nucleic acid features report (STS) - + sequence tagged sites (STS) in nucleic acid sequences. 1.8 true @@ -22735,7 +22785,7 @@ Nucleic acid features (immunoglobulin gene structure) - + true beta13 1.5 @@ -22750,7 +22800,7 @@ SCOP class - + 1.5 beta13 true @@ -22765,7 +22815,7 @@ SCOP fold - + beta13 Information on a 'fold' node from the SCOP database. 1.5 @@ -22780,7 +22830,7 @@ SCOP superfamily - + beta13 Information on a 'superfamily' node from the SCOP database. 1.5 @@ -22795,7 +22845,7 @@ SCOP family - + 1.5 true Information on a 'family' node from the SCOP database. @@ -22810,7 +22860,7 @@ SCOP protein - + Information on a 'protein' node from the SCOP database. true beta13 @@ -22825,7 +22875,7 @@ SCOP species - + 1.5 true beta13 @@ -22840,7 +22890,7 @@ Mass spectrometry experiment - + 1.8 true mass spectrometry experiments. @@ -22901,7 +22951,7 @@ NGS experiment - + 1.8 1.0 sequencing experiment, including samples, sampling, preparation, sequencing, and analysis. @@ -22945,7 +22995,7 @@ GWAS report - + 1.8 1.1 Report concerning genome-wide association study experiments. @@ -23057,7 +23107,7 @@ Sequence feature type - + true A label (text token) describing a type of sequence feature such as gene, transcript, cds, exon, repeat, simple, misc, variation, somatic variation, structural variation, somatic structural variation, constrained or regulatory. 1.3 @@ -23072,7 +23122,7 @@ Gene homology (report) - + beta12orEarlier true An informative report on gene homologues between species. @@ -23267,7 +23317,7 @@ Proteomics experiment report - + true 1.8 Report concerning proteomics experiments. @@ -23282,7 +23332,7 @@ RNAi report - + 1.5 RNAi experiments. true @@ -23297,7 +23347,7 @@ Simulation experiment report - + 1.5 biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. true @@ -23972,7 +24022,7 @@ UniGene entry format - + beta12orEarlier Format of an entry from UniGene. A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. @@ -23988,7 +24038,7 @@ COG sequence cluster format - + beta12orEarlier true beta12orEarlier @@ -24529,7 +24579,7 @@ Phylogenetic property values format - + Format of phylogenetic property data. beta12orEarlier beta12orEarlier @@ -24766,11 +24816,12 @@ Domainatrix 3D-1D scoring matrix format - + beta12orEarlier true beta12orEarlier Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications. + @@ -24794,7 +24845,7 @@ IntEnz enzyme report format - + beta12orEarlier beta12orEarlier Format of an entry from IntEnz (The Integrated Relational Enzyme Database). @@ -24810,7 +24861,7 @@ BRENDA enzyme report format - + true Format of an entry from the BRENDA enzyme database. beta12orEarlier @@ -24825,7 +24876,7 @@ KEGG REACTION enzyme report format - + true beta12orEarlier Format of an entry from the KEGG REACTION database of biochemical reactions. @@ -24840,7 +24891,7 @@ KEGG ENZYME enzyme report format - + beta12orEarlier true Format of an entry from the KEGG ENZYME database. @@ -24855,7 +24906,7 @@ REBASE proto enzyme report format - + Format of an entry from the proto section of the REBASE enzyme database. true beta12orEarlier @@ -24870,7 +24921,7 @@ REBASE withrefm enzyme report format - + beta12orEarlier true beta12orEarlier @@ -24915,7 +24966,7 @@ SMART domain assignment report format - + beta12orEarlier true Format of SMART domain assignment data. @@ -24931,7 +24982,7 @@ BIND entry format - + Entry format for the BIND database of protein interaction. beta12orEarlier true @@ -24946,7 +24997,7 @@ IntAct entry format - + beta12orEarlier beta12orEarlier Entry format for the IntAct database of protein interaction. @@ -24961,7 +25012,7 @@ InterPro entry format - + Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences. true beta12orEarlier @@ -24977,7 +25028,7 @@ InterPro entry abstract format - + true beta12orEarlier References are included and a functional inference is made where possible. @@ -24993,7 +25044,7 @@ Gene3D entry format - + Entry format for the Gene3D protein secondary database. true beta12orEarlier @@ -25008,7 +25059,7 @@ PIRSF entry format - + beta12orEarlier Entry format for the PIRSF protein secondary database. true @@ -25023,7 +25074,7 @@ PRINTS entry format - + beta12orEarlier beta12orEarlier true @@ -25038,7 +25089,7 @@ Panther Families and HMMs entry format - + beta12orEarlier beta12orEarlier Entry format for the Panther library of protein families and subfamilies. @@ -25053,7 +25104,7 @@ Pfam entry format - + Entry format for the Pfam protein secondary database. true beta12orEarlier @@ -25068,7 +25119,7 @@ SMART entry format - + true beta12orEarlier Entry format for the SMART protein secondary database. @@ -25083,7 +25134,7 @@ Superfamily entry format - + Entry format for the Superfamily protein secondary database. beta12orEarlier beta12orEarlier @@ -25098,7 +25149,7 @@ TIGRFam entry format - + beta12orEarlier true Entry format for the TIGRFam protein secondary database. @@ -25113,7 +25164,7 @@ ProDom entry format - + Entry format for the ProDom protein domain classification database. beta12orEarlier beta12orEarlier @@ -25128,7 +25179,7 @@ FSSP entry format - + Entry format for the FSSP database. beta12orEarlier true @@ -25157,7 +25208,7 @@ Ensembl gene report format - + beta12orEarlier Entry format of Ensembl genome database. beta12orEarlier @@ -25172,7 +25223,7 @@ DictyBase gene report format - + true beta12orEarlier Entry format of DictyBase genome database. @@ -25187,7 +25238,7 @@ CGD gene report format - + beta12orEarlier true beta12orEarlier @@ -25202,7 +25253,7 @@ DragonDB gene report format - + beta12orEarlier Entry format of DragonDB genome database. beta12orEarlier @@ -25217,7 +25268,7 @@ EcoCyc gene report format - + Entry format of EcoCyc genome database. beta12orEarlier beta12orEarlier @@ -25232,7 +25283,7 @@ FlyBase gene report format - + true beta12orEarlier beta12orEarlier @@ -25247,7 +25298,7 @@ Gramene gene report format - + beta12orEarlier beta12orEarlier Entry format of Gramene genome database. @@ -25262,7 +25313,7 @@ KEGG GENES gene report format - + true beta12orEarlier Entry format of KEGG GENES genome database. @@ -25277,7 +25328,7 @@ MaizeGDB gene report format - + beta12orEarlier beta12orEarlier true @@ -25292,7 +25343,7 @@ MGD gene report format - + Entry format of the Mouse Genome Database (MGD). beta12orEarlier beta12orEarlier @@ -25307,7 +25358,7 @@ RGD gene report format - + true beta12orEarlier Entry format of the Rat Genome Database (RGD). @@ -25322,7 +25373,7 @@ SGD gene report format - + true beta12orEarlier beta12orEarlier @@ -25337,7 +25388,7 @@ GeneDB gene report format - + Entry format of the Sanger GeneDB genome database. true beta12orEarlier @@ -25352,7 +25403,7 @@ TAIR gene report format - + beta12orEarlier beta12orEarlier Entry format of The Arabidopsis Information Resource (TAIR) genome database. @@ -25367,7 +25418,7 @@ WormBase gene report format - + Entry format of the WormBase genomes database. beta12orEarlier beta12orEarlier @@ -25382,7 +25433,7 @@ ZFIN gene report format - + beta12orEarlier beta12orEarlier true @@ -25397,7 +25448,7 @@ TIGR gene report format - + true Entry format of the TIGR genome database. beta12orEarlier @@ -25412,7 +25463,7 @@ dbSNP polymorphism report format - + beta12orEarlier Entry format for the dbSNP database. true @@ -25427,7 +25478,7 @@ OMIM entry format - + beta12orEarlier true beta12orEarlier @@ -25442,7 +25493,7 @@ HGVbase entry format - + true Format of a record from the HGVbase database of genotypes and phenotypes. beta12orEarlier @@ -25457,7 +25508,7 @@ HIVDB entry format - + beta12orEarlier beta12orEarlier true @@ -25472,7 +25523,7 @@ KEGG DISEASE entry format - + beta12orEarlier Format of an entry from the KEGG DISEASE database. true @@ -25647,7 +25698,7 @@ ArrayExpress entry format - + beta12orEarlier true Entry format for the ArrayExpress microarrays database. @@ -25698,7 +25749,7 @@ EMDB entry format - + beta12orEarlier Format of an entry from the Electron Microscopy DataBase (EMDB). true @@ -25713,7 +25764,7 @@ KEGG PATHWAY entry format - + beta12orEarlier beta12orEarlier The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks. @@ -25728,7 +25779,7 @@ MetaCyc entry format - + true beta12orEarlier The format of an entry from the MetaCyc metabolic pathways database. @@ -25743,7 +25794,7 @@ HumanCyc entry format - + The format of a report from the HumanCyc metabolic pathways database. true beta12orEarlier @@ -25758,7 +25809,7 @@ INOH entry format - + beta12orEarlier true The format of an entry from the INOH signal transduction pathways database. @@ -25773,7 +25824,7 @@ PATIKA entry format - + beta12orEarlier The format of an entry from the PATIKA biological pathways database. beta12orEarlier @@ -25788,7 +25839,7 @@ Reactome entry format - + beta12orEarlier The format of an entry from the reactome biological pathways database. true @@ -25803,7 +25854,7 @@ aMAZE entry format - + beta12orEarlier true The format of an entry from the aMAZE biological pathways and molecular interactions database. @@ -25818,7 +25869,7 @@ CPDB entry format - + The format of an entry from the CPDB database. beta12orEarlier true @@ -25833,7 +25884,7 @@ Panther Pathways entry format - + beta12orEarlier true beta12orEarlier @@ -25862,7 +25913,7 @@ BioModel mathematical model format - + beta12orEarlier beta12orEarlier Format of mathematical models from the BioModel database. @@ -25878,7 +25929,7 @@ KEGG LIGAND entry format - + The format of an entry from the KEGG LIGAND chemical database. beta12orEarlier beta12orEarlier @@ -25893,7 +25944,7 @@ KEGG COMPOUND entry format - + beta12orEarlier The format of an entry from the KEGG COMPOUND database. true @@ -25908,7 +25959,7 @@ KEGG PLANT entry format - + beta12orEarlier beta12orEarlier The format of an entry from the KEGG PLANT database. @@ -25923,7 +25974,7 @@ KEGG GLYCAN entry format - + true beta12orEarlier The format of an entry from the KEGG GLYCAN database. @@ -25938,7 +25989,7 @@ PubChem entry format - + beta12orEarlier The format of an entry from PubChem. true @@ -25953,7 +26004,7 @@ ChemSpider entry format - + beta12orEarlier The format of an entry from a database of chemical structures and property predictions. beta12orEarlier @@ -25968,7 +26019,7 @@ ChEBI entry format - + beta12orEarlier beta12orEarlier The format of an entry from Chemical Entities of Biological Interest (ChEBI). @@ -25984,7 +26035,7 @@ MSDchem ligand dictionary entry format - + The format of an entry from the MSDchem ligand dictionary. beta12orEarlier true @@ -26013,7 +26064,7 @@ KEGG DRUG entry format - + The format of an entry from the KEGG DRUG database. true beta12orEarlier @@ -26128,7 +26179,7 @@ PDB atom record format - + true beta13 beta12orEarlier @@ -26143,7 +26194,7 @@ CATH chain report format - + The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain. beta12orEarlier Format of CATH domain classification information for a polypeptide chain. @@ -26159,7 +26210,7 @@ CATH PDB report format - + beta12orEarlier beta12orEarlier true @@ -26175,7 +26226,7 @@ NCBI gene report format - + true Entry (gene) format of the NCBI database. beta12orEarlier @@ -26190,7 +26241,7 @@ GeneIlluminator gene report format - + Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service. This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation. beta12orEarlier @@ -26207,7 +26258,7 @@ BacMap gene card format - + Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database. true beta12orEarlier @@ -26223,7 +26274,7 @@ ColiCard report format - + Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB). true beta12orEarlier @@ -26324,17 +26375,17 @@ - Data model - A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) - - - - File format File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. + + Data model + A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) + + + @@ -26342,7 +26393,7 @@ Atomic data format - + beta12orEarlier beta13 Data format for an individual atom. @@ -26427,7 +26478,7 @@ clustal sequence format - + true beta12orEarlier Clustalw output format. @@ -26603,6 +26654,7 @@ beta12orEarlier Genbank entry format. + GenBank @@ -26873,7 +26925,7 @@ phylip sequence format - + beta12orEarlier Phylip interleaved sequence format. true @@ -26888,7 +26940,7 @@ phylipnon sequence format - + true Phylip non-interleaved sequence format. beta12orEarlier @@ -26932,7 +26984,7 @@ selex sequence format - + beta12orEarlier true beta12orEarlier @@ -27023,7 +27075,7 @@ treecon sequence format - + true beta12orEarlier beta12orEarlier @@ -27110,7 +27162,7 @@ meganon sequence format - + beta12orEarlier beta12orEarlier Mega non-interleaved output sequence format. @@ -27184,7 +27236,7 @@ pir - + true 1.7 PIR feature format. @@ -27199,7 +27251,7 @@ swiss feature - + true Swiss-Prot feature format. beta12orEarlier @@ -27244,7 +27296,7 @@ EMBL feature - + beta12orEarlier EMBL feature format. true @@ -27259,7 +27311,7 @@ GenBank feature - + beta12orEarlier Genbank feature format. beta12orEarlier @@ -27422,7 +27474,7 @@ msf alignment format - + true beta12orEarlier beta12orEarlier @@ -27437,7 +27489,7 @@ nexus alignment format - + Nexus/paup format for (aligned) sequences. beta12orEarlier beta12orEarlier @@ -27452,7 +27504,7 @@ nexusnon alignment format - + beta12orEarlier true Nexus/paup non-interleaved format for (aligned) sequences. @@ -27669,7 +27721,7 @@ Sequence-profile alignment (HMM) format - + beta12orEarlier beta12orEarlier true @@ -27827,7 +27879,7 @@ Biological model format - + Data format for a biological model. beta12orEarlier 1.2 @@ -27956,7 +28008,7 @@ Electron microscopy model format - + beta12orEarlier true beta12orEarlier @@ -27990,11 +28042,12 @@ Polymorphism report format - + beta12orEarlier true 1.0 Format for sequence polymorphism data. + @@ -28114,7 +28167,7 @@ Genotype and phenotype annotation format - + beta12orEarlier true Format of a report on genotype / phenotype information. @@ -28180,7 +28233,7 @@ Protein report (enzyme) format - + Format of a report of general information about a specific enzyme. beta12orEarlier true @@ -28351,13 +28404,13 @@ - + - + Data format for the emission and transition counts of a hidden Markov model. @@ -28505,7 +28558,7 @@ Gene features (coding region) format - + beta12orEarlier Format used for report on coding regions in nucleotide sequences. true @@ -28565,7 +28618,7 @@ Gene cluster format - + true beta13 beta12orEarlier @@ -28676,7 +28729,7 @@ UniProt format - + beta12orEarlier true UniProt entry sequence format. @@ -28691,7 +28744,7 @@ ipi - + 1.8 beta12orEarlier ipi sequence format. @@ -28752,7 +28805,6 @@ OWL format - A serialisation format conforming to the Web Ontology Language (OWL) model. beta12orEarlier @@ -28782,7 +28834,7 @@ Sequence record full format - + 1.8 beta12orEarlier Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database. @@ -28797,7 +28849,7 @@ Sequence record lite format - + true 1.8 beta12orEarlier @@ -28854,11 +28906,12 @@ Strain data format - + Format of a report on organism strain data / cell line. beta12orEarlier true 1.0 + @@ -28868,7 +28921,7 @@ CIP strain data format - + Format for a report of strain data as used for CIP database entries. true beta12orEarlier @@ -28883,7 +28936,7 @@ phylip property values - + true PHYLIP file format for phylogenetic property data. beta12orEarlier @@ -28898,7 +28951,7 @@ STRING entry format (HTML) - + beta12orEarlier true beta12orEarlier @@ -28985,7 +29038,7 @@ BioCyc enzyme report format - + true beta12orEarlier beta12orEarlier @@ -29000,7 +29053,7 @@ ENZYME enzyme report format - + Format of an entry from the Enzyme nomenclature database (ENZYME). beta12orEarlier beta12orEarlier @@ -29015,7 +29068,7 @@ PseudoCAP gene report format - + true beta12orEarlier beta12orEarlier @@ -29030,7 +29083,7 @@ GeneCards gene report format - + Format of a report on a gene from the GeneCards database. beta12orEarlier beta12orEarlier @@ -29088,12 +29141,16 @@ XML Data in XML format can be serialised into text, or binary format. - eXtensible Markup Language (XML) format. beta12orEarlier - http://filext.com/file-extension/XML + eXtensible Markup Language (XML) format. + xml + Extensible Markup Language + + + @@ -29116,7 +29173,7 @@ URI format - + beta13 true Typical textual representation of a URI. @@ -29131,7 +29188,7 @@ NCI-Nature pathway entry format - + beta12orEarlier true The format of an entry from the NCI-Nature pathways database. @@ -29168,13 +29225,13 @@ - + - + @@ -29226,7 +29283,7 @@ Protein features (domains) format - + beta12orEarlier true beta12orEarlier @@ -29464,7 +29521,7 @@ STRING entry format - + beta12orEarlier Entry format for the STRING database of protein interaction. beta12orEarlier @@ -29492,7 +29549,7 @@ Amino acid identifier format - + beta13 Text format (representation) of amino acid residues. true @@ -29666,13 +29723,13 @@ - + - + Format of a bibliographic reference. @@ -30451,6 +30508,8 @@ + + @@ -31022,7 +31081,7 @@ EPS - + Encapsulated PostScript format 1.7 @@ -31081,7 +31140,7 @@ Gene expression data format - + true 1.10 1.7 @@ -31230,11 +31289,8 @@ Document format - Portable Document Format - Microsoft Word format Format of documents including word processor, spreadsheet and presentation. 1.8 - doc @@ -31454,8 +31510,8 @@ afg - + 1.11 AFG is a single text-based file assembly format that holds read and consensus information together @@ -31797,10 +31853,11 @@ - png + PNG 1.11 + png PNG is a file format for image compression. It iis expected to replace the Graphics Interchange Format (GIF). @@ -31814,11 +31871,13 @@ - svg + SVG The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999. Scalable Vector Graphics (SVG) is an XML-based vector image format for two-dimensional graphics with support for interactivity and animation. + svg + Scalable Vector Graphics 1.11 @@ -32248,6 +32307,7 @@ GPML + 1.12 Graphical Pathway Markup Language (GPML) is an XML format used for exchanging biological pathways. @@ -32264,7 +32324,7 @@ 1.12 - File extension for this format is .oxlicg + oxlicg http://www.iana.org/assignments/media-types/application/vnd.oxli.countgraph A list of k-mers and their occurences in a dataset. Can also be used as an implicit De Bruijn graph. @@ -32274,6 +32334,310 @@ + + + + mzTab + + + 1.13 + mzTab is a tab-delimited format for mass spectrometry-based proteomics and metabolomics results. + + + + + + + + + + + + + imzML + + + + imzML is a data format for mass spectrometry imaging data. NB.: See comment. + 1.13 + imzML|ibd + Data is recorded in 2 files: '.imzXML' is a metadata XML file based on mzML by HUPO-PSI, and '.ibd' is a binary file containing the mass spectra. + + + + + + + + + + + + + qcML + + + + The focus of qcML is towards mass spectrometry based proteomics, but the format is suitable for metabolomics and sequencing as well. + qcML is an XML format for quality-related data of mass spectrometry and other high-throughput measurements. + 1.13 + + + + + + + + + + + + PRIDE XML + + + + 1.13 + PRIDE XML is an XML format for mass spectra, peptide and protein identifications, and metadata about a corresponding measurement, sample, experiment. + + + + + + + + + + + + SED-ML + + + Simulation Experiment Description Markup Language (SED-ML) is an XML format for encoding simulation setups, according to the MIASE (Minimum Information About a Simulation Experiment) requirements. + 1.13 + + + + + + + + + + + + + + COMBINE OMEX + + + + 1.13 + An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. OMEX is one of the standardised formats within COMBINE (Computational Modeling in Biology Network). + Open Modeling EXchange format (OMEX) is a ZIPped format for encapsulating all information necessary for a modeling and simulation project in systems biology. + + + + + + + + + + + + + ISA-TAB + + + + ISA-TAB is based on MAGE-TAB. Other than tabular, the ISA model can also be represented in RDF, and in JSON (compliable with a set of defined JSON Schemata). + The Investigation / Study / Assay (ISA) tab-delimited (TAB) format incorporates metadata from +experiments employing a combination of technologies. + 1.13 + ISA-Tab + + + + + + + + + + + + SBtab + + + 1.13 + SBtab is a tabular format for biochemical network models. + + + + + + + + + + + + + BCML + + + 1.13 + Biological Connection Markup Language (BCML) is an XML format for biological pathways. + + + + + + + + + + + + BDML + + Biological Dynamics Markup Language (BDML) is an XML format for quantitative data describing biological dynamics. + 1.13 + + + + + + + + + + + + + BEL + + 1.13 + Biological Expression Language (BEL) is a textual format for representing scientific findings in life sciences in a computable form. + + + + + + + + + + + + SBGN-ML + + + SBGN-ML is an XML format for Systems Biology Graphical Notation (SBGN) diagrams of biological pathways or networks. + 1.13 + + + + + + + + + + + + AGP + + + 1.13 + AGP is a tabular format for a sequence assembly (a contig, a scaffold/supercontig, or a chromosome). + + + + + + + + + + + + PS + + PostScript + PostScript format + 1.13 + + + + + + + + + + SRA format + + SRA archive format (SRA) is the archive format used for input to the NCBI Sequence Read Archive. + SRA archive format + 1.13 + SRA + + + + + + + + + + + VDB + + VDB ('vertical database') is the format (SRA) is the native format used for export from the NCBI Sequence Read Archive. + SRA native format + 1.13 + SRA + + + + + + + + + + + Tabix index file format + + + + + + + + 1.3 + Index file format used by the samtools package to index TAB-delimited genome position files. + + + + + + + + + + + sequin + + A five-column, tab-delimited table of feature locations and qualifiers for importing annotation into an existing Sequin submission (an NCBI tool for submitting and updating GenBank entries). + 1.13 + + + + + + @@ -32317,14 +32681,14 @@ - Computational tool - Computational tool provides one or more operations. + Process + Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. - Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. - Process + Computational tool + Computational tool provides one or more operations. @@ -32356,10 +32720,8 @@ beta12orEarlier Query - Retrieval Search or query a data resource and retrieve entries and / or annotation. Database retrieval - Search @@ -32370,7 +32732,7 @@ Data retrieval (database cross-reference) - + beta12orEarlier Search database to retrieve all relevant references to a particular entity or entry. true @@ -32388,14 +32750,14 @@ - - + + - - + + Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. @@ -32432,7 +32794,7 @@ Data index analysis - + Database index analysis Analyse an index of biological data. beta12orEarlier @@ -32448,12 +32810,12 @@ Annotation retrieval (sequence) - + true beta12orEarlier Retrieve basic information about a molecular sequence. beta12orEarlier - + @@ -32522,14 +32884,14 @@ - - + + - - + + beta12orEarlier @@ -32616,6 +32978,7 @@ Sequence motif discovery + @@ -32643,6 +33006,7 @@ Sequence motif recognition + @@ -32677,6 +33041,7 @@ Sequence motif comparison + @@ -32702,7 +33067,7 @@ Transcription regulatory sequence analysis - + beta12orEarlier beta13 Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences. @@ -32737,14 +33102,14 @@ - - + + - - + + This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. @@ -32964,7 +33329,7 @@ Data retrieval (feature table) - + beta13 Extract a sequence feature table from a sequence database entry. true @@ -32979,7 +33344,7 @@ Feature table query - + 1.6 beta12orEarlier true @@ -33028,7 +33393,7 @@ Data retrieval (sequence alignment) - + beta12orEarlier true beta13 @@ -33091,7 +33456,7 @@ Nucleic acid property processing - + beta12orEarlier true Process (read and / or write) physicochemical property data of nucleic acids. @@ -33256,14 +33621,14 @@ - - + + - - + + Predict tertiary structure of a molecular (biopolymer) sequence. @@ -33302,14 +33667,14 @@ - - + + - - + + Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. @@ -33324,7 +33689,7 @@ Protein-protein interaction prediction (from protein sequence) - + beta12orEarlier 1.12 true @@ -33339,7 +33704,7 @@ Protein-protein interaction prediction (from protein structure) - + true 1.12 beta12orEarlier @@ -33358,14 +33723,14 @@ - - + + - - + + beta12orEarlier @@ -33440,7 +33805,7 @@ Data retrieval (restriction enzyme annotation) - + beta13 Restriction enzyme information retrieval true @@ -33456,7 +33821,7 @@ Genetic marker identification - + true beta12orEarlier beta13 @@ -33564,31 +33929,31 @@ - + - - + + - + - - + + - - + + beta12orEarlier @@ -33739,7 +34104,7 @@ Hybrid sequence alignment construction - + Hybrid sequence alignment true beta13 @@ -33868,14 +34233,14 @@ - - + + - - + + @@ -33935,14 +34300,14 @@ - - + + - - + + @@ -34069,14 +34434,14 @@ - - + + - - + + beta12orEarlier @@ -34100,14 +34465,14 @@ - - + + - - + + Text data mining @@ -34145,26 +34510,33 @@ - - + + - - + + - - + + + This includes predicting primers based on gene structure, promoters, exon-exon junctions, predicting primers that are conserved across multiple genomes or species, primers for for gene transcription profiling, for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs), for large scale sequencing, or for methylation PCRs. + PCR primer design (based on gene structure) + PCR primer design (for methylation PCRs) + beta12orEarlier + PCR primer design (for large scale sequencing) PCR primer prediction Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set. + PCR primer design (for conserved primers) Design or predict oligonucleotide primers for PCR and DNA amplification etc. - beta12orEarlier + PCR primer design (for gene transcription profiling) + PCR primer design (for genotyping polymorphisms) @@ -34179,14 +34551,14 @@ - - + + - - + + @@ -34197,8 +34569,8 @@ - - + + Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families. @@ -34218,14 +34590,14 @@ - - + + - - + + beta12orEarlier @@ -34245,13 +34617,13 @@ - + - + @@ -34268,7 +34640,7 @@ Sequencing-based expression profile data processing - + Process (read and / or write) SAGE, MPSS or SBS experimental data. true beta12orEarlier @@ -34347,12 +34719,12 @@ Functional profiling - + true beta12orEarlier Interpret (in functional terms) and annotate gene expression data. beta12orEarlier - + @@ -34362,7 +34734,7 @@ EST and cDNA sequence analysis - + Analyse EST or cDNA sequences. For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. beta12orEarlier @@ -34378,7 +34750,7 @@ Structural genomics target selection - + beta12orEarlier Identify and select targets for protein structural determination. beta12orEarlier @@ -34398,13 +34770,13 @@ - + - + beta12orEarlier @@ -34499,14 +34871,14 @@ - - + + - - + + Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. @@ -34630,7 +35002,7 @@ Protein SNP mapping - + true beta12orEarlier Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). @@ -34675,12 +35047,12 @@ Immunogen design - + true Design molecules that elicit an immune response (immunogens). beta12orEarlier beta12orEarlier - + @@ -34718,14 +35090,14 @@ - - + + - - + + beta12orEarlier @@ -34847,7 +35219,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein secondary database search - + 1.8 beta12orEarlier true @@ -34862,7 +35234,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Motif database search - + beta12orEarlier Screen a sequence against a motif or pattern database. true @@ -34877,7 +35249,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence profile database search - + true beta12orEarlier Search a database of sequence profiles with a query sequence. @@ -34892,7 +35264,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Transmembrane protein database search - + true beta12orEarlier Search a database of transmembrane proteins, for example for sequence or structural similarities. @@ -34907,7 +35279,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence retrieval (by code) - + Query a database and retrieve sequences with a given entry code or accession number. true 1.6 @@ -34922,7 +35294,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence retrieval (by keyword) - + true Query a database and retrieve sequences containing a given keyword. beta12orEarlier @@ -34953,7 +35325,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by motif or pattern) - + 1.8 Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. beta12orEarlier @@ -34968,7 +35340,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by amino acid composition) - + true Search a sequence database and retrieve sequences of a given amino acid composition. 1.6 @@ -34996,7 +35368,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by sequence using word-based methods) - + beta12orEarlier Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps. 1.6 @@ -35013,7 +35385,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by sequence using profile-based methods) - + true Sequence similarity search (profile-based methods) Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query. @@ -35030,7 +35402,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by sequence using local alignment-based methods) - + Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method. 1.6 beta12orEarlier @@ -35047,7 +35419,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by sequence using global alignment-based methods) - + This includes tools based on the Needleman and Wunsch algorithm. Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method. 1.6 @@ -35064,7 +35436,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by sequence for primer sequences) - + true beta12orEarlier Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences. @@ -35081,7 +35453,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by molecular weight) - + Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry. 1.6 Protein fingerprinting @@ -35098,7 +35470,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence database search (by isoelectric point) - + 1.6 beta12orEarlier Search sequence(s) or a sequence database for sequences of a given isoelectric point. @@ -35113,7 +35485,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure retrieval (by code) - + Query a tertiary structure database and retrieve entries with a given entry code or accession number. 1.6 beta12orEarlier @@ -35128,7 +35500,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure retrieval (by keyword) - + true 1.6 Query a tertiary structure database and retrieve entries containing a given keyword. @@ -35143,7 +35515,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure database search (by sequence) - + beta12orEarlier true Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence. @@ -35160,12 +35532,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structural similarity search - - - - - - beta12orEarlier Search a database of molecular structure and retrieve structures that are similar to a query structure. Structure database search (by structure) @@ -35269,14 +35635,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -35382,7 +35748,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence composition calculation (nucleic acid) - + true Calculate base frequency or word composition of a nucleotide sequence. 1.8 @@ -35397,7 +35763,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence composition calculation (protein) - + 1.8 Calculate amino acid frequency or word composition of a protein sequence. beta12orEarlier @@ -35440,7 +35806,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein hydropathy calculation (from structure) - + true Analyse the hydrophobic, hydrophilic or charge properties of a protein structure. 1.12 @@ -35478,7 +35844,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein hydropathy cluster calculation - + true 1.12 beta12orEarlier @@ -35537,7 +35903,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein binding site prediction (from structure) - + Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures. beta12orEarlier 1.12 @@ -35665,7 +36031,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue non-canonical interaction detection - + beta12orEarlier 1.12 Calculate non-canonical atomic interactions in protein structures. @@ -35793,7 +36159,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein hydropathy calculation (from sequence) - + 1.12 Hydropathy calculation on a protein sequence. beta12orEarlier @@ -36002,7 +36368,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern MHC peptide immunogenicity prediction - + true Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc. @@ -36018,7 +36384,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein feature prediction (from sequence) - + Methods typically involve scanning for known motifs, patterns and regular expressions. beta12orEarlier true @@ -36127,7 +36493,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein binding site prediction (from sequence) - + 1.12 Predict catalytic residues, active sites or other ligand-binding sites in protein sequences. true @@ -36188,7 +36554,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Epitope mapping (MHC Class I) - + 1.8 true beta12orEarlier @@ -36203,7 +36569,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Epitope mapping (MHC Class II) - + Predict epitopes that bind to MHC class II molecules. 1.8 true @@ -36219,7 +36585,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Whole gene prediction - + beta12orEarlier 1.12 true @@ -36234,7 +36600,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene component prediction - + true Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. beta12orEarlier @@ -36660,6 +37026,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Indel detection + beta12orEarlier Sequence alignment analysis (indel detection) Indel discovery @@ -36675,7 +37042,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleosome formation potential prediction - + true beta12orEarlier Predict nucleosome formation potential of DNA sequences. @@ -37218,7 +37585,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Functional mapping - + beta12orEarlier true This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). @@ -37357,7 +37724,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pairwise sequence alignment generation (local) - + beta12orEarlier Local pairwise sequence alignment construction Locally align exactly two molecular sequences. @@ -37377,7 +37744,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pairwise sequence alignment generation (global) - + Pairwise sequence alignment construction (global) Global pairwise sequence alignment construction 1.6 @@ -37497,7 +37864,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Secondary structure alignment generation - + beta12orEarlier 1.6 Secondary structure alignment construction @@ -37541,14 +37908,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + RNA secondary structure alignment generation @@ -37581,7 +37948,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Multiple structure alignment construction - + Align (superimpose) two or more molecular tertiary structures. This includes methods that use an existing alignment. 1.6 @@ -37598,7 +37965,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure alignment (protein) - + beta13 true beta12orEarlier @@ -37613,7 +37980,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure alignment (RNA) - + beta13 true Align RNA tertiary structures. @@ -37628,7 +37995,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pairwise structure alignment generation (local) - + Locally align (superimpose) exactly two molecular tertiary structures. Pairwise structure alignment (local) Local alignment methods identify regions of local similarity, common substructures etc. @@ -37648,7 +38015,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pairwise structure alignment generation (global) - + Global pairwise structure alignment construction Global alignment methods identify similarity across the entire structures. true @@ -37725,7 +38092,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence alignment generation (multiple profile) - + Align two or more molecular profiles. 1.6 true @@ -37762,7 +38129,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structural profile alignment generation (multiple) - + true Structural profile alignment construction (multiple) Align two or more molecular 3D profiles. @@ -37780,7 +38147,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (tool metadata) - + Data retrieval (tool annotation) 1.6 Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function. @@ -37797,7 +38164,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (database metadata) - + beta12orEarlier true Data retrieval (database annotation) @@ -37814,17 +38181,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern PCR primer design (for large scale sequencing) - - - - - - - + + 1.13 Predict primers for large scale sequencing. beta12orEarlier - - + true + + @@ -37833,11 +38196,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern PCR primer design (for genotyping polymorphisms) - + + true beta12orEarlier Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs). - - + 1.13 + + @@ -37846,17 +38211,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern PCR primer design (for gene transcription profiling) - - - - - - - + Predict primers for gene transcription profiling. beta12orEarlier - - + true + 1.13 + + @@ -37865,11 +38226,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern PCR primer design (for conserved primers) - + + 1.13 Predict primers that are conserved across multiple genomes or species. beta12orEarlier - - + true + + @@ -37878,17 +38241,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern PCR primer design (based on gene structure) - - - - - - - - Predict primers based on gene structure, promoters, exon-exon junctions etc. + + 1.13 + true beta12orEarlier - - + + @@ -37897,11 +38255,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern PCR primer design (for methylation PCRs) - + + true beta12orEarlier Predict primers for methylation PCRs. - - + 1.13 + + @@ -37992,7 +38352,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern SAGE data processing - + beta12orEarlier Serial analysis of gene expression data processing beta12orEarlier @@ -38008,7 +38368,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern MPSS data processing - + beta12orEarlier Process (read and / or write) massively parallel signature sequencing (MPSS) data. true @@ -38024,7 +38384,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern SBS data processing - + beta12orEarlier Sequencing by synthesis data processing beta12orEarlier @@ -38062,7 +38422,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene expression profile analysis - + true Functional profiling beta12orEarlier @@ -38132,7 +38492,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein structure assignment (from X-ray crystallographic data) - + true 1.7 Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data. @@ -38147,7 +38507,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein structure assignment (from NMR data) - + beta12orEarlier Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data. true @@ -38417,14 +38777,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict families of genes and gene function based on their position in a phylogenetic tree. @@ -38515,7 +38875,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Immunogenicity prediction - + true 1.12 beta12orEarlier @@ -38550,7 +38910,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence formatting - + 1.12 beta12orEarlier Reformat (a file or other report of) molecular sequence(s). @@ -38565,7 +38925,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence alignment formatting - + Reformat (a file or other report of) molecular sequence alignment(s). beta12orEarlier true @@ -38580,7 +38940,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Codon usage table formatting - + Reformat a codon usage table. true beta12orEarlier @@ -38821,7 +39181,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence motif rendering - + Render a sequence with motifs. true beta12orEarlier @@ -38856,7 +39216,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern DNA linear map rendering - + beta12orEarlier beta12orEarlier true @@ -38905,7 +39265,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid folding family identification - + true beta12orEarlier Identify folding families of related RNAs. @@ -38933,7 +39293,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Annotation retrieval - + beta12orEarlier Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations. Retrieve existing annotation (or documentation), typically annotation on a database entity. @@ -38990,7 +39350,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence submission - + Submit a molecular sequence to a database. beta12orEarlier 1.6 @@ -39046,7 +39406,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence retrieval - + This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. Data retrieval (sequences) 1.6 @@ -39063,7 +39423,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure retrieval - + true WHATIF:EchoPDB beta12orEarlier @@ -39097,7 +39457,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein atom surface calculation (accessible) - + beta12orEarlier 1.12 true @@ -39113,7 +39473,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein atom surface calculation (accessible molecular) - + beta12orEarlier 1.12 Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure. @@ -39129,7 +39489,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue surface calculation (accessible) - + true 1.12 beta12orEarlier @@ -39145,7 +39505,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue surface calculation (vacuum accessible) - + Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. 1.12 @@ -39161,7 +39521,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue surface calculation (accessible molecular) - + Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure. true Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). @@ -39177,7 +39537,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue surface calculation (vacuum molecular) - + Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). true beta12orEarlier @@ -39193,7 +39553,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein surface calculation (accessible molecular) - + true 1.12 beta12orEarlier @@ -39208,7 +39568,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein surface calculation (accessible) - + Calculate the solvent accessibility ('accessible surface') for a structure as a whole. beta12orEarlier 1.12 @@ -39223,7 +39583,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Backbone torsion angle calculation - + 1.12 beta12orEarlier true @@ -39238,7 +39598,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Full torsion angle calculation - + 1.12 beta12orEarlier Calculate for each residue in a protein structure all its torsion angles. @@ -39253,7 +39613,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Cysteine torsion angle calculation - + beta12orEarlier Calculate for each cysteine (bridge) all its torsion angles. 1.12 @@ -39268,7 +39628,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Tau angle calculation - + beta12orEarlier Tau is the backbone angle N-Calpha-C (angle over the C-alpha). 1.12 @@ -39328,7 +39688,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue contact calculation (residue-nucleic acid) - + beta12orEarlier 1.12 true @@ -39357,7 +39717,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue contact calculation (residue-negative ion) - + Calculate ion contacts in a structure (all ions for all side chain atoms). beta12orEarlier true @@ -39386,7 +39746,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue symmetry contact calculation - + Calculate the number of symmetry contacts made by residues in a protein structure. true 1.12 @@ -39403,7 +39763,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue contact calculation (residue-ligand) - + true beta12orEarlier 1.12 @@ -39436,7 +39796,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Rotamer likelihood prediction - + WHATIF:ShowLikelyRotamers WHATIF:ShowLikelyRotamers500 1.12 @@ -39462,7 +39822,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Proline mutation value calculation - + true 1.12 Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein. @@ -39507,13 +39867,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern PDB file sequence retrieval - + Extract a molecular sequence from a PDB file. beta12orEarlier WHATIF: PDB_sequence true beta12orEarlier - + @@ -39523,7 +39883,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern HET group detection - + true Identify HET groups in PDB files. beta12orEarlier @@ -39539,7 +39899,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern DSSP secondary structure assignment - + Determine for residue the DSSP determined secondary structure in three-state (HSC). beta12orEarlier WHATIF: ResidueDSSP @@ -39555,7 +39915,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure formatting - + 1.12 true Reformat (a file or other report of) tertiary structure data. @@ -39590,7 +39950,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue validation - + 1.12 Identify poor quality amino acid positions in protein structures. beta12orEarlier @@ -39605,7 +39965,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure retrieval (water) - + beta12orEarlier 1.6 WHATIF:MovedWaterPDB @@ -39654,7 +40014,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Listfile processing - + 1.6 Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses). true @@ -39683,7 +40043,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence alignment file processing - + beta12orEarlier Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences. 1.6 @@ -39698,12 +40058,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Small molecule data processing - + beta13 true beta12orEarlier Process (read and / or write) physicochemical property data for small molecules. - + @@ -39713,7 +40073,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (ontology annotation) - + beta13 Ontology information retrieval true @@ -39729,7 +40089,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (ontology concept) - + Query an ontology and retrieve concepts or relations. true beta13 @@ -39758,7 +40118,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure file processing - + Perform basic (non-analytical) operations on a file of molecular tertiary structural data. 1.6 beta12orEarlier @@ -39773,7 +40133,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (sequence profile) - + Query a profile data resource and retrieve one or more profile(s) and / or associated annotation. true This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. @@ -39812,7 +40172,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + @@ -39856,11 +40216,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Demonstration - + beta12orEarlier true An operation performing purely illustrative (pedagogical) purposes. beta13 + @@ -39870,7 +40231,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (pathway or network) - + beta12orEarlier true Query a biological pathways database and retrieve annotation on one or more pathways. @@ -39885,7 +40246,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (identifier) - + beta12orEarlier Query a database and retrieve one or more data identifiers. beta13 @@ -39933,14 +40294,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Sequence motif processing - - true - 1.6 - Process (read and / or write) molecular sequence motifs. + Sequence motif analysis + + Analyse molecular sequence motifs. beta12orEarlier - - + Sequence motif processing + + @@ -39949,7 +40309,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein interaction data processing - + 1.6 Process (read and / or write) protein interaction data. true @@ -39968,14 +40328,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Structure analysis (protein) @@ -39991,7 +40351,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Annotation processing - + true beta12orEarlier beta12orEarlier @@ -40006,7 +40366,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence feature analysis - + beta12orEarlier true Analyse features in molecular sequences. @@ -40021,7 +40381,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern File handling - + @@ -40032,7 +40392,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern File processing beta12orEarlier Report handling - Data file processing + Data handling Utility operation @@ -40044,7 +40404,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene expression analysis - + Analyse gene expression and regulation data. beta12orEarlier true @@ -40059,13 +40419,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structural profile processing - + beta12orEarlier 1.6 Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type. 3D profile processing true - + @@ -40075,7 +40435,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data index processing - + Database index processing true Process (read and / or write) an index of (typically a file of) biological data. @@ -40091,12 +40451,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence profile processing - + true beta12orEarlier Process (read and / or write) some type of sequence profile. 1.6 - + @@ -40130,14 +40490,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + This is a broad concept and is used a placeholder for other, more specific concepts. @@ -40180,12 +40540,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Physicochemical property data processing - + beta13 true Process (read and / or write) data on the physicochemical property of a molecule. beta12orEarlier - + @@ -40216,7 +40576,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Operation (typed) - + true Process (read and / or write) data of a specific type, for example applying analytical methods. beta12orEarlier @@ -40241,6 +40601,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database. Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query. + Search @@ -40261,6 +40622,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Information retrieval beta12orEarlier Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords. + Retrieval @@ -40333,12 +40695,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data handling - + true beta12orEarlier Perform basic operations on some data or a database. beta12orEarlier - + @@ -40380,7 +40742,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier Design a biological entity (typically a molecular sequence or structure) with specific properties. - true @@ -40391,7 +40752,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Microarray data processing - + beta12orEarlier Process (read and / or write) microarray data. beta12orEarlier @@ -40419,7 +40780,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (codon usage table) - + Retrieve a codon usage table and / or associated annotation. beta12orEarlier true @@ -40434,7 +40795,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene expression profile processing - + 1.6 Process (read and / or write) a gene expression profile. true @@ -40497,7 +40858,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pathway or network processing - + Generate, analyse or handle a biological pathway or network. beta12orEarlier true @@ -40531,12 +40892,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure processing (RNA) - + Process (read and / or write) RNA tertiary structure data. beta12orEarlier beta13 true - + @@ -40584,7 +40945,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic tree processing - + beta12orEarlier 1.12 true @@ -40599,7 +40960,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein secondary structure processing - + Process (read and / or write) protein secondary structure data. 1.6 true @@ -40614,7 +40975,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein interaction network processing - + true beta12orEarlier Process (read and / or write) a network of protein interactions. @@ -40629,7 +40990,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence processing - + Sequence processing (general) Process (read and / or write) one or more molecular sequences and associated annotation. true @@ -40645,12 +41006,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence processing (protein) - + Process (read and / or write) a protein sequence and associated annotation. beta12orEarlier true 1.6 - + @@ -40660,12 +41021,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence processing (nucleic acid) - + 1.6 true beta12orEarlier Process (read and / or write) a nucleotide sequence and associated annotation. - + @@ -40701,7 +41062,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence cluster processing - + Process (read and / or write) a sequence cluster. true beta12orEarlier @@ -40716,12 +41077,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Feature table processing - + Process (read and / or write) a sequence feature table. 1.6 true beta12orEarlier - + @@ -40803,12 +41164,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure processing (protein) - + true 1.6 beta12orEarlier Process (read and / or write) a protein tertiary structure. - + @@ -40818,7 +41179,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein atom surface calculation - + Waters are not considered. Calculate the solvent accessibility for each atom in a structure. beta12orEarlier @@ -40834,7 +41195,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue surface calculation - + beta12orEarlier true Calculate the solvent accessibility for each residue in a structure. @@ -40849,7 +41210,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein surface calculation - + beta12orEarlier Calculate the solvent accessibility of a structure as a whole. 1.12 @@ -40864,7 +41225,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence alignment processing - + beta12orEarlier true Process (read and / or write) a molecular sequence alignment. @@ -40905,7 +41266,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure processing - + true 1.6 Process (read and / or write) a molecular tertiary structure. @@ -40920,7 +41281,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Map annotation - + Annotate a DNA map of some type with terms from a controlled vocabulary. true beta12orEarlier @@ -40935,7 +41296,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (protein annotation) - + Retrieve information on a protein. beta13 true @@ -40951,7 +41312,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (phylogenetic tree) - + beta12orEarlier beta13 Retrieve a phylogenetic tree from a data resource. @@ -40966,7 +41327,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (protein interaction annotation) - + Retrieve information on a protein interaction. true beta13 @@ -40981,7 +41342,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (protein family annotation) - + beta12orEarlier Protein family information retrieval beta13 @@ -40997,7 +41358,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (RNA family annotation) - + true Retrieve information on an RNA family. RNA family information retrieval @@ -41013,7 +41374,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (gene annotation) - + beta12orEarlier Gene information retrieval Retrieve information on a specific gene. @@ -41029,7 +41390,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data retrieval (genotype and phenotype annotation) - + Retrieve information on a specific genotype or phenotype. Genotype and phenotype information retrieval beta12orEarlier @@ -41086,14 +41447,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation. @@ -41201,12 +41562,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Secondary structure processing - + 1.6 Process (read and / or write) a molecular secondary structure. true beta12orEarlier - + @@ -41221,7 +41582,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + beta12orEarlier @@ -41338,7 +41699,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue contact calculation (residue-residue) - + true beta12orEarlier Calculate contacts between residues in a protein structure. @@ -41353,7 +41714,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Hydrogen bond calculation (inter-residue) - + Identify potential hydrogen bonds between amino acid residues. 1.12 true @@ -41372,14 +41733,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict the interactions of proteins with other molecules. @@ -41394,7 +41755,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Codon usage data processing - + beta12orEarlier beta13 Process (read and / or write) codon usage data. @@ -41433,11 +41794,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene regulatory network processing - + 1.6 beta12orEarlier Process (read and / or write) a network of gene regulation. true + @@ -41468,7 +41830,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequencing-based expression profile data analysis - + Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts. beta12orEarlier beta12orEarlier @@ -41505,7 +41867,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Microarray raw data analysis - + beta12orEarlier beta12orEarlier true @@ -41560,11 +41922,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence data processing - + beta12orEarlier Process (read and / or write) molecular sequence data. beta13 true + @@ -41574,12 +41937,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structural data processing - + Process (read and / or write) molecular structural data. beta13 true beta12orEarlier - + @@ -41589,7 +41952,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Text processing - + true beta12orEarlier Process (read and / or write) text. @@ -41699,7 +42062,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence editing (nucleic acid) - + 1.8 true Edit or change a nucleic acid sequence, either randomly or specifically. @@ -41714,7 +42077,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence editing (protein) - + Edit or change a protein sequence, either randomly or specifically. beta12orEarlier true @@ -41756,7 +42119,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid sequence visualisation - + Visualise, format or render a nucleic acid sequence. true Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. @@ -41772,7 +42135,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein sequence visualisation - + true beta12orEarlier Visualise, format or render a protein sequence. @@ -41804,11 +42167,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure processing (nucleic acid) - + 1.6 beta12orEarlier true Process (read and / or write) nucleic acid tertiary structure data. + @@ -41823,7 +42187,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + @@ -41835,7 +42199,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + beta12orEarlier @@ -41850,7 +42214,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Map data processing - + DNA map data processing Process (read and / or write) a DNA map of some type. beta12orEarlier @@ -41869,14 +42233,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -41995,7 +42359,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + Compare two or more molecular secondary structures. @@ -42010,7 +42374,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Hopp and Woods plotting - + beta12orEarlier 1.12 Generate a Hopp and Woods plot of antigenicity of a protein. @@ -42207,7 +42571,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Alignment analysis - + Process or analyse an alignment of molecular sequences or structures. true beta12orEarlier @@ -42225,20 +42589,20 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - - + + Analyse a body of scientific text (typically a full text article from a scientific journal.) @@ -42253,11 +42617,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Molecular interaction analysis - + Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact. beta12orEarlier beta13 true + @@ -42270,14 +42635,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -42322,13 +42687,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Alignment processing - + true Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data. 1.6 beta12orEarlier - - + + @@ -42338,7 +42703,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure alignment processing - + Process (read and / or write) a molecular tertiary (3D) structure alignment. 1.6 beta12orEarlier @@ -42424,11 +42789,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Molecular interaction data processing - + beta13 true beta12orEarlier Process (read and / or write) molecular interaction data. + @@ -42571,7 +42937,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein function prediction (from sequence) - + beta13 true Predict general (non-positional) functional properties of a protein from analysing its sequence. @@ -42622,7 +42988,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein feature prediction (from structure) - + beta13 1.6 true @@ -42667,7 +43033,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Database search (by sequence) - + Sequence screening true 1.6 @@ -42686,14 +43052,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta13 @@ -42745,14 +43111,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Assembly quality evaluation @@ -42871,7 +43237,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Trim ends - + 1.1 Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. 1.12 @@ -42887,7 +43253,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Trim vector - + true Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences. 1.12 @@ -42902,7 +43268,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Trim to reference - + true 1.1 1.12 @@ -42919,11 +43285,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence trimming 1.1 - Trim to reference Cut (remove) the end from a molecular sequence. + Barcode sequence removal Trim vector Trimming Trim ends + Trim to reference This includes ennd trimming @@ -43048,10 +43415,12 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - DNA barcoding + Community profiling + - Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms. + Analyse DNA sequences in order to identify a DNA 'barcode'; marker genes or any short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms. 1.1 + DNA barcoding Sample barcoding @@ -43076,11 +43445,12 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - Mutation detection + Polymorphism detection Polymorphism detection Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware. 1.1 + Mutation detection @@ -43217,7 +43587,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Genome indexing (Burrows-Wheeler) - + The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. 1.12 true @@ -43233,7 +43603,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Genome indexing (suffix arrays) - + 1.1 Generate an index of a genome sequence using a suffix arrays algorithm. A suffix array consists of the lexicographically sorted list of suffixes of a genome. @@ -43257,7 +43627,6 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - Spectrum analysis 1.1 Analyse one or more spectra from mass spectrometry (or other) experiments. Spectrum analysis @@ -43333,7 +43702,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Raw sequence data quality control. - Analyse raw sequence data from a sequencing pipeline and identify problems. + Analyse raw sequence data from a sequencing pipeline and identify (and possiby fix) problems. Sequencing QC 1.1 @@ -43571,14 +43940,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + Infer a transcriptome sequence by analysis of short sequence reads. @@ -43593,7 +43962,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Transcriptome assembly (de novo) - + de novo transcriptome assembly true 1.6 @@ -43609,7 +43978,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Transcriptome assembly (mapping) - + Infer a transcriptome sequence by mapping short reads to a reference genome. 1.6 1.2 @@ -43752,14 +44121,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + Generate a checksum of a molecular sequence. @@ -43845,7 +44214,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Ontology comparison - + 1.4 Compare two or more ontologies, e.g. identify differences. 1.9 @@ -43862,14 +44231,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + Recognition of which format the given data is in. @@ -44067,7 +44436,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Genome assembly - + 1.12 1.6 The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated. @@ -44294,8 +44663,9 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Taxonomic classification + Taxonomy assignment + Classifiication (typically of molecular sequences) by assignment to some taxonomic hierarchy. 1.7 - Classifiication of molecular sequences by assignment to some taxonomic hierarchy. @@ -44559,7 +44929,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Mathematical modelling - + 1.12 Model some biological system using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models. true @@ -44685,7 +45055,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp RNA-seq read count analysis - + Analyze read counts from RNA-seq experiments. 1.9 @@ -44711,7 +45081,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp RNA-seq time series data analysis - + 1.9 Analyze time series data from an RNA-seq experiment. @@ -44746,14 +45116,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + 1.12 @@ -44870,14 +45240,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + Peptide-spectrum-matching @@ -45273,6 +45643,46 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp + + + + RNA-Seq analysis + + Analyze data from RNA-seq experiments. + 1.13 + + + + + + + + + + Mass spectrum visualisation + + 1.1 + Visualise, format or render a mass spectrum. + + + + + + + + + + Filtering + + Filter a set of files or data items according to some property. + 1.13 + Sequence filtering + + + + + + @@ -45298,16 +45708,17 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - Nucleic acids - + Nucleic acid analysis + The processing and analysis of nucleic acid sequence, structural and other data. Nucleic acid bioinformatics - Nucleic acid analysis + Nucleic acids Nucleic acid informatics http://purl.bioontology.org/ontology/MSH/D017423 Nucleic acid properties Nucleic acid physicochemistry http://purl.bioontology.org/ontology/MSH/D017422 + true beta12orEarlier @@ -45318,15 +45729,16 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - Proteins - - Protein bioinformatics + Protein analysis + Protein informatics - Protein databases - Protein analysis + Proteins http://purl.bioontology.org/ontology/MSH/D020539 - Archival, processing and analysis of protein data, typically molecular sequence and structural data. + Protein bioinformatics + Protein databases + true beta12orEarlier + Archival, processing and analysis of protein data, typically molecular sequence and structural data. @@ -45337,13 +45749,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Metabolites - - Metabolite structures - This concept excludes macromolecules such as proteins and nucleic acids. + + 1.13 + true The structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. beta12orEarlier - - + + @@ -45353,6 +45765,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Sequence analysis + true beta12orEarlier Sequence databases Sequences @@ -45371,6 +45784,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Structure analysis Computational structural biology + true 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 Structural bioinformatics @@ -45397,6 +45811,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Nucleic acid structure prediction beta12orEarlier Protein structure prediction + true DNA structure prediction Nucleic acid design Nucleic acid folding @@ -45412,13 +45827,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Alignment - + beta12orEarlier true The alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment). beta12orEarlier - - + + @@ -45429,11 +45844,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Phylogeny + Phylogeny reconstruction Phylogenetic stratigraphy beta12orEarlier Phylogenetic dating Phylogenetic clocks + true http://purl.bioontology.org/ontology/MSH/D010802 The study of evolutionary relationships amongst organisms. Phylogenetic simulation @@ -45452,6 +45869,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp beta12orEarlier + true The study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc. @@ -45465,6 +45883,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Ontology and terminology + true Terminology beta12orEarlier http://purl.bioontology.org/ontology/MSH/D002965 @@ -45483,16 +45902,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Information retrieval - + beta12orEarlier - Data retrieval + 1.13 + true The search and query of data sources (typically databases or ontologies) in order to retrieve entries or other information. - This includes, for example, search, query and retrieval of molecular sequences and associated data. - Data search VT 1.3.3 Information retrieval - Data query - - + + @@ -45507,6 +45924,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp The archival, curation, processing and analysis of complex biological data. http://purl.bioontology.org/ontology/MSH/D016247 beta12orEarlier + true @@ -45521,6 +45939,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Data rendering Rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data. + true VT 1.2.5 Computer graphics beta12orEarlier Computer graphics @@ -45534,7 +45953,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Nucleic acid thermodynamics - + true The study of the thermodynamic properties of a nucleic acid. 1.3 @@ -45548,14 +45967,15 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Nucleic acid structure analysis + Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc. DNA melting Nucleic acid denaturation RNA alignment The archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation. - RNA structure alignment beta12orEarlier + RNA structure alignment Nucleic acid structure Nucleic acid thermodynamics RNA structure @@ -45583,12 +46003,12 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Nucleic acid restriction - + 1.3 beta12orEarlier Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids. true - + @@ -45599,14 +46019,15 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp 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. It also covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. - DNA mapping - beta12orEarlier The mapping of complete (typically nucleotide) sequences. Mapping (in the sense of short read alignment, or more generally, just alignment) has application in RNA-Seq analysis (mapping of transcriptomics reads), variant discovery (e.g. mapping of exome capture), and re-sequencing (mapping of WGS reads). Genetic linkage Linkage Linkage mapping + true Synteny + 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. It also covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. + DNA mapping + beta12orEarlier @@ -45616,7 +46037,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Genetic codes and codon usage - + beta12orEarlier true 1.3 @@ -45647,7 +46068,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Gene finding - + 1.3 This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. Gene discovery @@ -45665,7 +46086,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Transcription - + 1.3 The transcription of DNA into mRNA. beta12orEarlier @@ -45680,7 +46101,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Promoters - + true beta12orEarlier Promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins). @@ -45695,12 +46116,12 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Nucleic acid folding - + beta12orEarlier The folding (in 3D space) of nucleic acid molecules. true beta12orEarlier - + @@ -45711,13 +46132,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Gene structure - This includes the study of promoters, coding regions etc. beta12orEarlier Fusion genes Gene features + true Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc. + This incudes operons (operators, promoters and genes) from a bacterial genome. For example the operon leader and trailer gene, gene composition of the operon and associated information. @@ -45734,6 +46156,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Protein and peptide identification Peptide identification Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein expression data, for example in different cells or tissues. + true http://purl.bioontology.org/ontology/MSH/D040901 Protein expression @@ -45749,6 +46172,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Structural genomics + true beta12orEarlier The elucidation of the three dimensional structure for all (available) proteins in a given organism. @@ -45765,6 +46189,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp The study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein. Protein hydropathy + true Protein physicochemistry beta12orEarlier @@ -45782,11 +46207,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions. Protein-nucleic acid interactions Protein-RNA interaction + Protein interaction networks This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. Protein-protein interactions Protein-ligand interactions beta12orEarlier Protein-DNA interaction + true @@ -45798,12 +46225,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Protein folding, stability and design - Protein folding - Protein stability beta12orEarlier - Protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. Protein residue interactions Protein design + true + Protein folding + Protein stability + Protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. Rational protein design @@ -45815,7 +46243,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Two-dimensional gel electrophoresis - + Two-dimensional gel electrophoresis image and related data. beta13 beta12orEarlier @@ -45830,12 +46258,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Mass spectrometry - + beta12orEarlier + true + 1.13 An analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase. - - - + + @@ -45844,7 +46273,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Protein microarrays - + Protein microarray data. true beta12orEarlier @@ -45859,7 +46288,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Protein hydropathy - + beta12orEarlier true The study of the hydrophobic, hydrophilic and charge properties of a protein. @@ -45890,12 +46319,12 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Protein cleavage sites and proteolysis - + true beta12orEarlier 1.3 Enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence. - + @@ -45905,14 +46334,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Protein structure comparison - + The comparison of two or more protein structures. beta12orEarlier true Use this concept for methods that are exclusively for protein structure. beta12orEarlier - - + @@ -45922,7 +46350,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Protein residue interactions - + The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures. true 1.3 @@ -45937,7 +46365,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Protein-protein interactions - + Protein interaction networks true Protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc. @@ -45953,7 +46381,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Protein-ligand interactions - + beta12orEarlier true 1.3 @@ -45968,7 +46396,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Protein-nucleic acid interactions - + beta12orEarlier 1.3 Protein-DNA/RNA interactions. @@ -45983,7 +46411,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Protein design - + 1.3 beta12orEarlier The design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. @@ -45998,7 +46426,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp G protein-coupled receptors (GPCR) - + G-protein coupled receptors (GPCRs). true beta12orEarlier @@ -46013,9 +46441,10 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Carbohydrates - + beta12orEarlier Carbohydrates, typically including structural information. + true @@ -46026,8 +46455,9 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Lipids - + beta12orEarlier + true Lipidomics Lipids and their structures. @@ -46040,12 +46470,27 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Small molecules - + + Drugs and target structures + Amino acids + Targets + Drug structures + Metabolite structures + Target structures Small molecules of biological significance, typically archival, curation, processing and analysis of structural information. Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. + true + This concept excludes macromolecules such as proteins and nucleic acids. + Toxins and targets CHEBI:23367 + Toxins + Metabolites + Drug targets + Peptides and amino acids beta12orEarlier Chemical structures + This includes the structures of drugs, drug target, their interactions and binding affinities. Also the structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. Also the physicochemical, biochemical or structural properties of amino acids or peptides. Also structural and associated data for toxic chemical substances. + Peptides @@ -46056,7 +46501,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Sequence editing - + beta12orEarlier true beta12orEarlier @@ -46073,13 +46518,20 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Sequence composition, complexity and repeats - Sequence complexity Repeat sequences + This includes short repetitive subsequences (repeat sequences) in a protein sequence. + true The archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences. beta12orEarlier - Sequence repeats + Protein sequence repeats + Nucleic acid repeats + This includes repetitive elements within a nucleic acid sequence, e.g. +long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a sequence and other types of repeating unit. + Sequence complexity Low complexity sequences + Sequence repeats Sequence composition + Protein repeats @@ -46090,7 +46542,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Sequence motifs - + beta12orEarlier Motifs true @@ -46106,13 +46558,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Sequence comparison - + true The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. beta12orEarlier 1.12 The comparison of two or more molecular sequences, for example sequence alignment and clustering. - + @@ -46124,9 +46576,9 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Sequence sites, features and motifs Sequence features - 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. + true Functional sites + The archival, detection, prediction and analysis of positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. Sequence motifs Sequence profiles Sequence sites @@ -46142,13 +46594,13 @@ positional features such as functional and other key sites, in molecular sequenc Sequence database search - + beta12orEarlier Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence). beta12orEarlier true The query is a sequence-based entity such as another sequence, a motif or profile. - + @@ -46158,14 +46610,14 @@ positional features such as functional and other key sites, in molecular sequenc Sequence clustering - + This includes systems that generate, process and analyse sequence clusters. beta12orEarlier true 1.7 The comparison and grouping together of molecular sequences on the basis of their similarities. Sequence clusters - + @@ -46176,11 +46628,11 @@ positional features such as functional and other key sites, in molecular sequenc Protein structural motifs and surfaces - This includes conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches, role and functions etc. Protein structural features Structural motifs Protein 3D motifs + true beta12orEarlier Protein structural motifs Structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules. @@ -46195,13 +46647,13 @@ positional features such as functional and other key sites, in molecular sequenc Structural (3D) profiles - + The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment. true beta12orEarlier 1.3 Structural profiles - + @@ -46211,7 +46663,7 @@ positional features such as functional and other key sites, in molecular sequenc Protein structure prediction - + true beta12orEarlier The prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features. @@ -46226,12 +46678,12 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid structure prediction - + The folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. 1.12 true beta12orEarlier - + @@ -46241,7 +46693,7 @@ positional features such as functional and other key sites, in molecular sequenc Ab initio structure prediction - + 1.7 The prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates. true @@ -46256,7 +46708,7 @@ positional features such as functional and other key sites, in molecular sequenc Homology modelling - + 1.4 The modelling of the three-dimensional structure of a protein using known sequence and structural data. true @@ -46274,6 +46726,7 @@ positional features such as functional and other key sites, in molecular sequenc This includes resources concerning flexibility and motion in protein and other molecular structures. Protein dynamics + true Molecular flexibility Molecular motions beta12orEarlier @@ -46288,10 +46741,11 @@ positional features such as functional and other key sites, in molecular sequenc Molecular docking - + beta12orEarlier true The modelling the structure of proteins in complex with small molecules or other macromolecules. + true 1.12 @@ -46303,13 +46757,12 @@ positional features such as functional and other key sites, in molecular sequenc Protein secondary structure prediction - + beta12orEarlier 1.3 The prediction of secondary or supersecondary structure of protein sequences. true - - + @@ -46319,13 +46772,12 @@ positional features such as functional and other key sites, in molecular sequenc Protein tertiary structure prediction - + 1.3 true The prediction of tertiary structure of protein sequences. beta12orEarlier - - + @@ -46335,7 +46787,7 @@ positional features such as functional and other key sites, in molecular sequenc Protein fold recognition - + 1.12 The recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s). true @@ -46350,13 +46802,13 @@ positional features such as functional and other key sites, in molecular sequenc Sequence alignment - + This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on. beta12orEarlier 1.7 The alignment of molecular sequences or sequence profiles (representing sequence alignments). true - + @@ -46366,13 +46818,13 @@ positional features such as functional and other key sites, in molecular sequenc Structure alignment - + The superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment). This includes the generation, storage, analysis, rendering etc. of structure alignments. true 1.7 beta12orEarlier - + @@ -46382,13 +46834,13 @@ positional features such as functional and other key sites, in molecular sequenc Threading - + Sequence-structure alignment 1.3 beta12orEarlier The alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). true - + @@ -46398,7 +46850,7 @@ positional features such as functional and other key sites, in molecular sequenc Sequence profiles and HMMs - + true Sequence profiles; typically a positional, numerical matrix representing a sequence alignment. beta12orEarlier @@ -46414,7 +46866,7 @@ positional features such as functional and other key sites, in molecular sequenc Phylogeny reconstruction - + The reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree. 1.3 true @@ -46434,6 +46886,7 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier The integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction. + true @@ -46445,7 +46898,7 @@ positional features such as functional and other key sites, in molecular sequenc Virtual PCR - + beta13 Polymerase chain reaction beta12orEarlier @@ -46463,6 +46916,7 @@ positional features such as functional and other key sites, in molecular sequenc Sequence assembly + true Assembly The assembly of fragments of a DNA sequence to reconstruct the original sequence. beta12orEarlier @@ -46477,8 +46931,7 @@ positional features such as functional and other key sites, in molecular sequenc Genetic variation - - + Mutation beta12orEarlier Polymorphism @@ -46486,6 +46939,7 @@ positional features such as functional and other key sites, in molecular sequenc 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. http://purl.bioontology.org/ontology/MSH/D014644 DNA variation + true @@ -46496,7 +46950,7 @@ positional features such as functional and other key sites, in molecular sequenc Microarrays - + true http://purl.bioontology.org/ontology/MSH/D046228 Microarrays, for example, to process microarray data or design probes and experiments. @@ -46519,6 +46973,7 @@ positional features such as functional and other key sites, in molecular sequenc Pharmacoinformatics The study of drugs and their effects or responses in living systems. VT 3.1.7 Pharmacology and pharmacy + true @@ -46530,7 +46985,7 @@ positional features such as functional and other key sites, in molecular sequenc Gene expression - + This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on. Transcription Gene expression profiling @@ -46543,6 +46998,7 @@ positional features such as functional and other key sites, in molecular sequenc DNA microarrays The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. Codon usage + true @@ -46555,6 +47011,7 @@ positional features such as functional and other key sites, in molecular sequenc Gene regulation + true Regulatory genomics beta12orEarlier The regulation of gene expression. @@ -46570,6 +47027,7 @@ positional features such as functional and other key sites, in molecular sequenc Pharmacogenomics + true beta12orEarlier Pharmacogenetics The influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. @@ -46589,6 +47047,7 @@ positional features such as functional and other key sites, in molecular sequenc VT 3.1.4 Medicinal chemistry The design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes. This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. + true Drug design beta12orEarlier @@ -46602,7 +47061,7 @@ positional features such as functional and other key sites, in molecular sequenc Fish - + beta12orEarlier true 1.3 @@ -46617,7 +47076,7 @@ positional features such as functional and other key sites, in molecular sequenc Flies - + 1.3 true beta12orEarlier @@ -46646,7 +47105,7 @@ positional features such as functional and other key sites, in molecular sequenc Worms - + true 1.3 beta12orEarlier @@ -46661,7 +47120,7 @@ positional features such as functional and other key sites, in molecular sequenc Literature analysis - + beta12orEarlier 1.3 The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query. @@ -46708,17 +47167,14 @@ positional features such as functional and other key sites, in molecular sequenc Document, record and content management - - Document management - File management - This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. - Content management + + true The management and manipulation of digital documents, including database records, files and reports. VT 1.3.6 Multimedia, hypermedia - Record management + 1.13 beta12orEarlier - - + + @@ -46727,7 +47183,7 @@ positional features such as functional and other key sites, in molecular sequenc Sequence annotation - + beta12orEarlier beta12orEarlier true @@ -46742,7 +47198,7 @@ positional features such as functional and other key sites, in molecular sequenc Genome annotation - + Annotation of a genome. beta12orEarlier true @@ -46782,13 +47238,13 @@ positional features such as functional and other key sites, in molecular sequenc Sequence classification - + 1.12 true beta12orEarlier The classification of molecular sequences based on some measure of their similarity. Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences. - + @@ -46798,7 +47254,7 @@ positional features such as functional and other key sites, in molecular sequenc Protein classification - + 1.3 true beta12orEarlier @@ -46813,14 +47269,13 @@ positional features such as functional and other key sites, in molecular sequenc Sequence motif or profile - + beta12orEarlier true Sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type. This includes comparison, discovery, recognition etc. of sequence motifs. beta12orEarlier - - + @@ -46832,10 +47287,14 @@ positional features such as functional and other key sites, in molecular sequenc Protein modifications GO:0006464 - Protein chemical modifications, e.g. post-translational modifications. + Protein chemical modifications Protein post-translational modification - MOD:00000 + Protein chemical modifications, e.g. post-translational modifications. + true EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000) + Protein post-translational modifications + Post-translation modifications + MOD:00000 beta12orEarlier @@ -46847,17 +47306,24 @@ positional features such as functional and other key sites, in molecular sequenc Molecular interactions, pathways and networks - + Networks + Environmental information processing pathways Pathways Biological networks - Network or pathway analysis + Disease pathways + true + Signal transduction pathways beta13 - Molecular interactions Biological models + Cellular process pathways + Molecular interactions + Gene regulatory networks Molecular interactions, biological pathways, networks and other models. Biological pathways Interactions + Genetic information processing pathways + Signaling pathways http://edamontology.org/topic_3076 @@ -46871,6 +47337,7 @@ positional features such as functional and other key sites, in molecular sequenc Informatics + true The study and practice of information processing and use of computer information systems. VT 1.3.99 Other Knowledge management @@ -46890,7 +47357,7 @@ positional features such as functional and other key sites, in molecular sequenc Literature data resources - + Data resources for the biological or biomedical literature, either a primary source of literature or some derivative. true 1.3 @@ -46906,6 +47373,7 @@ positional features such as functional and other key sites, in molecular sequenc Laboratory information management + true Laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on. beta12orEarlier Laboratory resources @@ -46921,7 +47389,7 @@ positional features such as functional and other key sites, in molecular sequenc Cell and tissue culture - + Tissue culture 1.3 true @@ -46939,6 +47407,7 @@ positional features such as functional and other key sites, in molecular sequenc Ecology + true The ecological and environmental sciences and especially the application of information technology (ecoinformatics). http://purl.bioontology.org/ontology/MSH/D004777 Ecological informatics @@ -46981,7 +47450,7 @@ positional features such as functional and other key sites, in molecular sequenc Cell cycle - + beta13 beta12orEarlier true @@ -46996,13 +47465,13 @@ positional features such as functional and other key sites, in molecular sequenc Peptides and amino acids - + beta12orEarlier The physicochemical, biochemical or structural properties of amino acids or peptides. - Amino acids - Peptides - - + 1.13 + true + + @@ -47011,7 +47480,7 @@ positional features such as functional and other key sites, in molecular sequenc Organelles - + Cell membrane Cytoplasm Organelle genes and proteins @@ -47037,13 +47506,13 @@ positional features such as functional and other key sites, in molecular sequenc Ribosomes - + beta12orEarlier Ribosomes, typically of ribosome-related genes and proteins. Ribosome genes and proteins 1.3 true - + @@ -47053,7 +47522,7 @@ positional features such as functional and other key sites, in molecular sequenc Scents - + A database about scents. beta12orEarlier beta13 @@ -47068,16 +47537,13 @@ positional features such as functional and other key sites, in molecular sequenc Drugs and target structures - - - Drug structures + beta12orEarlier The structures of drugs, drug target, their interactions and binding affinities. - Drug targets - Target structures - - - + true + 1.13 + + @@ -47090,6 +47556,7 @@ positional features such as functional and other key sites, in molecular sequenc This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism. beta12orEarlier A specific organism, or group of organisms, used to study a particular aspect of biology. + true Organisms @@ -47107,6 +47574,7 @@ positional features such as functional and other key sites, in molecular sequenc Personal genomics beta12orEarlier Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. + true @@ -47118,13 +47586,14 @@ positional features such as functional and other key sites, in molecular sequenc Gene families - - Particular gene(s), gene family or other gene group or system and their encoded proteins. + beta12orEarlier Gene family Gene system - Genes, gene family or system Gene and protein families + Particular gene(s), gene family or other gene group or system and their encoded proteins. + Genes, gene family or system + true @@ -47136,11 +47605,13 @@ positional features such as functional and other key sites, in molecular sequenc Chromosomes - + beta12orEarlier Study of chromosomes. - - + 1.13 + true + + @@ -47154,6 +47625,7 @@ positional features such as functional and other key sites, in molecular sequenc The study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on. Genotyping Phenotyping + true beta12orEarlier @@ -47166,12 +47638,11 @@ positional features such as functional and other key sites, in molecular sequenc Gene expression and microarray - + true beta12orEarlier beta12orEarlier Gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc. - @@ -47186,9 +47657,11 @@ positional features such as functional and other key sites, in molecular sequenc Probes This includes the design of primers for PCR and DNA amplification or the design of molecular probes. http://purl.bioontology.org/ontology/MSH/D015335 - Molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR). Primers + true beta12orEarlier + Molecular probes (e.g. a peptide probe or DNA microarray probe) or PCR primers and hybridization oligos in a nucleic acid sequence. + @@ -47202,8 +47675,8 @@ positional features such as functional and other key sites, in molecular sequenc Disease Diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases. + true beta12orEarlier - Diseases VT 3.1.6 Pathology @@ -47216,7 +47689,7 @@ positional features such as functional and other key sites, in molecular sequenc Specific protein resources - + 1.3 A particular protein, protein family or other group of proteins. true @@ -47233,6 +47706,7 @@ positional features such as functional and other key sites, in molecular sequenc Taxonomy + true beta12orEarlier VT 1.5.25 Taxonomy Organism classification, identification and naming. @@ -47246,7 +47720,7 @@ positional features such as functional and other key sites, in molecular sequenc Protein sequence analysis - + beta12orEarlier Archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. 1.8 @@ -47261,7 +47735,7 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid sequence analysis - + beta12orEarlier 1.8 true @@ -47277,7 +47751,7 @@ positional features such as functional and other key sites, in molecular sequenc Repeat sequences - + true The repetitive nature of molecular sequences. beta12orEarlier @@ -47292,7 +47766,7 @@ positional features such as functional and other key sites, in molecular sequenc Low complexity sequences - + true The (character) complexity of molecular sequences, particularly regions of low complexity. 1.3 @@ -47307,7 +47781,7 @@ positional features such as functional and other key sites, in molecular sequenc Proteome - + A specific proteome including protein sequences and annotation. beta12orEarlier beta13 @@ -47326,6 +47800,7 @@ positional features such as functional and other key sites, in molecular sequenc DNA analysis beta12orEarlier Ancient DNA + Chromosomes DNA sequences and structure, including processes such as methylation and replication. The DNA sequences might be coding or non-coding sequences. @@ -47338,15 +47813,13 @@ positional features such as functional and other key sites, in molecular sequenc Coding RNA - - EST - cDNA - mRNA - This includes expressed sequence tag (EST) or complementary DNA (cDNA) sequences. + Protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames + 1.13 beta12orEarlier - - + true + + @@ -47357,6 +47830,7 @@ positional features such as functional and other key sites, in molecular sequenc Functional, regulatory and non-coding RNA + true small interfering RNA small nucleolar RNA ncRNA @@ -47384,7 +47858,7 @@ positional features such as functional and other key sites, in molecular sequenc rRNA - + 1.3 One or more ribosomal RNA (rRNA) sequences. true @@ -47398,7 +47872,7 @@ positional features such as functional and other key sites, in molecular sequenc tRNA - + 1.3 true One or more transfer RNA (tRNA) sequences. @@ -47412,7 +47886,7 @@ positional features such as functional and other key sites, in molecular sequenc Protein secondary structure - + true beta12orEarlier 1.8 @@ -47428,7 +47902,7 @@ positional features such as functional and other key sites, in molecular sequenc RNA structure - + 1.3 RNA secondary or tertiary structure and alignments. beta12orEarlier @@ -47443,7 +47917,7 @@ positional features such as functional and other key sites, in molecular sequenc Protein tertiary structure - + 1.8 true Protein tertiary structures. @@ -47458,7 +47932,7 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid classification - + Classification of nucleic acid sequences and structures. 1.3 true @@ -47474,6 +47948,7 @@ positional features such as functional and other key sites, in molecular sequenc Protein families + true beta12orEarlier Protein sequence classification Protein secondary databases @@ -47489,12 +47964,21 @@ positional features such as functional and other key sites, in molecular sequenc - Protein domains and folds + Protein folds and structural domains + Protein tertiary structural domains and folds in a protein or polypeptide chain. + This includes topological domains such as cytoplasmic regions in a protein. + Protein transmembrane regions + Protein domains + Protein membrane regions + Intramembrane regions beta12orEarlier + Protein topological domains + true + This includes trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. For example, 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 folds - Protein tertiary structural domains and folds. - Protein domains + Transmembrane regions + Protein structural domains @@ -47505,12 +47989,12 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid sequence alignment - + beta12orEarlier true 1.3 Nucleotide sequence alignments. - + @@ -47520,13 +48004,13 @@ positional features such as functional and other key sites, in molecular sequenc Protein sequence alignment - + 1.3 Protein sequence alignments. beta12orEarlier true A sequence profile typically represents a sequence alignment. - + @@ -47536,7 +48020,7 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid sites and features - + beta12orEarlier 1.3 true @@ -47553,7 +48037,7 @@ positional features such as functional sites in nucleotide sequences. Protein sites and features - + beta12orEarlier The detection, identification and analysis of positional features in proteins, such as functional sites. 1.3 @@ -47569,14 +48053,29 @@ positional features such as functional sites in nucleotide sequences. Transcription factors and regulatory sites + - - Transcription factor proteins either promote (as an activator) or block (as a repressor) the binding to DNA of RNA polymerase. Regulatory sites including transcription factor binding site as well as promoters, enhancers, silencers and boundary elements / insulators. + CpG islands 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. + Attenuators + Enhancers + CAAT signals Transcriptional regulatory sites TFBS + CAT box + CCAAT box + This includes CpG rich regions (isochores) in a nucleotide sequence. + 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. + -10 signals + Transcription factor proteins either promote (as an activator) or block (as a repressor) the binding to DNA of RNA polymerase. Regulatory sites including transcription factor binding site as well as promoters, enhancers, silencers and boundary elements / insulators. + Terminators + TATA signals + GC signals + Promoters + -35 signals Transcription factors + Isochores beta12orEarlier Transcription factor binding sites @@ -47589,7 +48088,7 @@ positional features such as functional sites in nucleotide sequences. Phosphorylation sites - + 1.0 Protein phosphorylation and phosphorylation sites in protein sequences. true @@ -47605,11 +48104,13 @@ positional features such as functional sites in nucleotide sequences. Metabolic pathways - + beta12orEarlier + 1.13 + true Metabolic pathways. - - + + @@ -47618,12 +48119,13 @@ positional features such as functional sites in nucleotide sequences. Signaling pathways - + + true Signaling pathways. - Signal transduction pathways + 1.13 beta12orEarlier - - + + @@ -47632,7 +48134,7 @@ positional features such as functional sites in nucleotide sequences. Protein and peptide identification - + 1.3 beta12orEarlier true @@ -47659,7 +48161,7 @@ positional features such as functional sites in nucleotide sequences. Data types and objects - + Structuring data into basic types and (computational) objects. beta12orEarlier 1.0 @@ -47674,7 +48176,7 @@ positional features such as functional sites in nucleotide sequences. Theoretical biology - + 1.3 true @@ -47687,12 +48189,12 @@ positional features such as functional sites in nucleotide sequences. Mitochondria - + beta12orEarlier true Mitochondria, typically of mitochondrial genes and proteins. 1.3 - + @@ -47769,7 +48271,7 @@ positional features such as functional sites in nucleotide sequences. Arabidopsis - + beta12orEarlier Arabidopsis-specific data. 1.3 @@ -47784,7 +48286,7 @@ positional features such as functional sites in nucleotide sequences. Rice - + Rice-specific data. true 1.3 @@ -47799,7 +48301,7 @@ positional features such as functional sites in nucleotide sequences. Genetic mapping and linkage - + Linkage mapping beta12orEarlier 1.3 @@ -47818,6 +48320,7 @@ positional features such as functional sites in nucleotide sequences.Comparative genomics The study (typically comparison) of the sequence, structure or function of multiple genomes. + true beta12orEarlier @@ -47830,8 +48333,7 @@ positional features such as functional sites in nucleotide sequences. Mobile genetic elements - - + Transposons beta12orEarlier Mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns. @@ -47845,7 +48347,7 @@ positional features such as functional sites in nucleotide sequences. Human disease - + Human diseases, typically describing the genes, mutations and proteins implicated in disease. beta13 true @@ -47866,6 +48368,7 @@ positional features such as functional sites in nucleotide sequences.http://purl.bioontology.org/ontology/MSH/D007120 http://purl.bioontology.org/ontology/MSH/D007125 beta12orEarlier + true Computational immunology The application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on. @@ -47878,9 +48381,10 @@ positional features such as functional sites in nucleotide sequences. - Membrane and lipoproteins + Membrane and lipoproteins Lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane. + true beta12orEarlier Membrane proteins Lipoproteins @@ -47899,6 +48403,7 @@ positional features such as functional sites in nucleotide sequences.Proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. beta12orEarlier Enzymology + true @@ -47909,14 +48414,13 @@ positional features such as functional sites in nucleotide sequences. Primers - + + true + 1.13 PCR primers and hybridization oligos in a nucleic acid sequence. - Nucleic acid features (primers) beta12orEarlier - Primer binding sites - - - + + @@ -47925,16 +48429,13 @@ positional features such as functional sites in nucleotide sequences. PolyA signal or sites - + beta12orEarlier - Nucleic acid features (PolyA signal or site) - PolyA signal - A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation. - PolyA site + 1.13 + true Regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. - - - + + @@ -47943,13 +48444,13 @@ positional features such as functional sites in nucleotide sequences. CpG island and isochores - + beta12orEarlier - Nucleic acid features (CpG island and isochore) + 1.13 + true CpG rich regions (isochores) in a nucleotide sequence. - - - + + @@ -47958,14 +48459,13 @@ positional features such as functional sites in nucleotide sequences. Restriction sites - + Restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. - Nucleic acid features (restriction sites) beta12orEarlier - Nucleic acid restriction sites (report) - - - + 1.13 + true + + @@ -47974,16 +48474,14 @@ positional features such as functional sites in nucleotide sequences. Splice sites - - - Nucleic acid features (splice sites) - Nucleic acid report (RNA splicing) + beta12orEarlier Splice sites in a nucleotide sequence or alternative RNA splicing events. - Nucleic acid report (RNA splice model) - - - + 1.13 + true + + + @@ -47992,13 +48490,13 @@ positional features such as functional sites in nucleotide sequences. Matrix/scaffold attachment sites - - Nucleic acid features (matrix/scaffold attachment sites) + + 1.13 + true beta12orEarlier Matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. - - - + + @@ -48007,15 +48505,13 @@ positional features such as functional sites in nucleotide sequences. Operon - - Gene features (operon) + beta12orEarlier - Nucleic acid features (operon) - The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query. + 1.13 + true Operons (operators, promoters and genes) from a bacterial genome. - - - + + @@ -48024,13 +48520,13 @@ positional features such as functional sites in nucleotide sequences. Promoters - + + true + 1.13 Whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. beta12orEarlier - Nucleic acid features (promoters) - - - + + @@ -48046,6 +48542,7 @@ positional features such as functional sites in nucleotide sequences.1.3 This includes Informatics concerning data generated from the use of microscopes, including optical, electron and scanning probe microscopy. Includes methods for digitizing microscope images and viewing the produced virtual slides and associated data on a computer screen. The molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids. + true VT 1.5.24 Structural biology Structural determination @@ -48059,18 +48556,13 @@ positional features such as functional sites in nucleotide sequences. Protein membrane regions - - + 1.8 - Protein features (membrane regions) - This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. - Intramembrane regions + 1.13 + true Trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. - Protein transmembrane regions - Transmembrane regions - - - + + @@ -48079,13 +48571,14 @@ positional features such as functional sites in nucleotide sequences. Structure comparison - + This might involve comparison of secondary or tertiary (3D) structural information. + true The comparison of two or more molecular structures, for example structure alignment and clustering. + 1.13 beta12orEarlier - - - + + @@ -48095,6 +48588,7 @@ positional features such as functional sites in nucleotide sequences. Function analysis + true Protein function prediction The study of gene and protein function including the prediction of functional properties of a protein. Protein function analysis @@ -48126,7 +48620,7 @@ positional features such as functional sites in nucleotide sequences. Protein databases - + true 1.3 Protein data resources. @@ -48142,7 +48636,7 @@ positional features such as functional sites in nucleotide sequences. Structure determination - + Experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. beta12orEarlier true @@ -48159,7 +48653,9 @@ positional features such as functional sites in nucleotide sequences.Cell biology beta12orEarlier + true VT 1.5.11 Cell biology + Cellular processes Cells, such as key genes and proteins involved in the cell cycle. @@ -48171,7 +48667,7 @@ positional features such as functional sites in nucleotide sequences. Classification - + beta13 beta12orEarlier Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships. @@ -48186,7 +48682,7 @@ positional features such as functional sites in nucleotide sequences. Lipoproteins - + true 1.3 beta12orEarlier @@ -48201,7 +48697,7 @@ positional features such as functional sites in nucleotide sequences. Phylogeny visualisation - + true Visualise a phylogeny, for example, render a phylogenetic tree. beta12orEarlier @@ -48221,6 +48717,7 @@ positional features such as functional sites in nucleotide sequences.Chemical informatics beta12orEarlier Chemoinformatics + true @@ -48237,6 +48734,7 @@ positional features such as functional sites in nucleotide sequences.This includes databases of models and methods to construct or analyse a model. Biological models http://purl.bioontology.org/ontology/MSH/D049490 + true beta12orEarlier Biological modelling Biological system modelling @@ -48254,9 +48752,11 @@ positional features such as functional sites in nucleotide sequences.Statistics and probability Biostatistics - The application of statistical methods to biological problems. + Probability http://en.wikipedia.org/wiki/Biostatistics beta12orEarlier + The application of statistical methods to biological problems. + Statistics http://purl.bioontology.org/ontology/MSH/D056808 @@ -48269,13 +48769,13 @@ positional features such as functional sites in nucleotide sequences. Structure database search - + The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template. beta12orEarlier Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure). beta12orEarlier true - + @@ -48293,6 +48793,7 @@ positional features such as functional sites in nucleotide sequences.Homology modelling Molecular modeling Comparative modeling + true The construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour, including the modelling the structure of proteins in complex with small molecules or other macromolecules (docking). @@ -48304,7 +48805,7 @@ positional features such as functional sites in nucleotide sequences. Protein function prediction - + 1.2 beta12orEarlier true @@ -48319,13 +48820,13 @@ positional features such as functional sites in nucleotide sequences. SNP - + + true Single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. beta12orEarlier - Single nucleotide polymorphism - A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. - - + 1.13 + + @@ -48334,12 +48835,12 @@ positional features such as functional sites in nucleotide sequences. Transmembrane protein prediction - + Predict transmembrane domains and topology in protein sequences. beta12orEarlier beta12orEarlier true - + @@ -48350,7 +48851,7 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid structure comparison - + The comparison two or more nucleic acid (typically RNA) secondary or tertiary structures. beta12orEarlier true @@ -48367,13 +48868,13 @@ positional features such as functional sites in nucleotide sequences. Exons - - Gene features (exon) + beta12orEarlier + true Exons in a nucleotide sequences. - - - + 1.13 + + @@ -48381,24 +48882,14 @@ positional features such as functional sites in nucleotide sequences. - Gene transcription features - - GC signals (report) - CAAT signals (report) - -35 signals (report) - Gene transcriptional features - This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. - Enhancers (report) - Terminators (report) + Gene transcription + Transcription of DNA into RNA including the regulation of transcription. - Ribosome binding sites (report) - -10 signals (report) + true + 1.13 beta12orEarlier - TATA signals (report) - Attenuators (report) - - - + + @@ -48409,11 +48900,8 @@ positional features such as functional sites in nucleotide sequences.DNA mutation - Mutation annotation beta12orEarlier DNA mutation. - Nucleic acid features (mutation) - @@ -48428,6 +48916,7 @@ positional features such as functional sites in nucleotide sequences.beta12orEarlier VT 3.2.16 Oncology Cancer + true The study of cancer, for example, genes and proteins implicated in cancer. Cancer biology @@ -48441,15 +48930,13 @@ positional features such as functional sites in nucleotide sequences. Toxins and targets - - - Toxins - Targets + + 1.13 beta12orEarlier + true Structural and associated data for toxic chemical substances. - - - + + @@ -48458,14 +48945,13 @@ positional features such as functional sites in nucleotide sequences. Introns - - Gene features (intron) - Nucleic acid features (intron) + + 1.13 Introns in a nucleotide sequences. beta12orEarlier - - - + true + + @@ -48474,7 +48960,7 @@ positional features such as functional sites in nucleotide sequences. Tool topic - + beta12orEarlier A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool. true @@ -48489,7 +48975,7 @@ positional features such as functional sites in nucleotide sequences. Study topic - + A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding. beta12orEarlier true @@ -48504,7 +48990,7 @@ positional features such as functional sites in nucleotide sequences. Nomenclature - + true 1.3 beta12orEarlier @@ -48519,7 +49005,7 @@ positional features such as functional sites in nucleotide sequences. Disease genes and proteins - + 1.3 true beta12orEarlier @@ -48534,8 +49020,10 @@ positional features such as functional sites in nucleotide sequences. Protein structure analysis + Protein structure + true Protein secondary or tertiary structural data and/or associated annotation. http://edamontology.org/topic_3040 beta12orEarlier @@ -48552,7 +49040,6 @@ positional features such as functional sites in nucleotide sequences.Humans beta12orEarlier - true The human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general. @@ -48564,7 +49051,7 @@ positional features such as functional sites in nucleotide sequences. Gene resources - + Gene resource beta12orEarlier 1.3 @@ -48581,7 +49068,7 @@ positional features such as functional sites in nucleotide sequences. Yeast - + beta12orEarlier Yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation. true @@ -48653,12 +49140,12 @@ positional features such as functional sites in nucleotide sequences. Protein structure alignment - + Protein secondary or tertiary structure alignments. beta12orEarlier true 1.3 - + @@ -48686,7 +49173,7 @@ positional features such as functional sites in nucleotide sequences. Ontologies, nomenclature and classification - + true Conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics. 1.3 @@ -48722,7 +49209,7 @@ positional features such as functional sites in nucleotide sequences. Molecules - + CHEBI:23367 beta12orEarlier beta12orEarlier @@ -48743,6 +49230,7 @@ positional features such as functional sites in nucleotide sequences.Toxins and the adverse effects of these chemical substances on living organisms. VT 3.1.9 Toxicology Toxicoinformatics + true beta12orEarlier Computational toxicology @@ -48756,7 +49244,7 @@ positional features such as functional sites in nucleotide sequences. High-throughput sequencing - + Next-generation sequencing beta13 true @@ -48772,13 +49260,13 @@ positional features such as functional sites in nucleotide sequences. Structural clustering - + The comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters. 1.7 Structure classification true beta12orEarlier - + @@ -48788,12 +49276,13 @@ positional features such as functional sites in nucleotide sequences. Gene regulatory networks - - + Gene regulatory networks. + true + 1.13 beta12orEarlier - - + + @@ -48802,7 +49291,7 @@ positional features such as functional sites in nucleotide sequences. Disease (specific) - + Informatics resources dedicated to one or more specific diseases (not diseases in general). beta12orEarlier true @@ -48817,15 +49306,13 @@ positional features such as functional sites in nucleotide sequences. VNTR - - Nucleic acid features (VNTR) - Variable number of tandem repeat polymorphism + Variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. beta12orEarlier - VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. - - - + 1.13 + true + + @@ -48834,13 +49321,14 @@ positional features such as functional sites in nucleotide sequences. Microsatellites - + + true + 1.13 beta12orEarlier - 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 polymorphism in a DNA sequence. - - + + @@ -48849,13 +49337,14 @@ positional features such as functional sites in nucleotide sequences. RFLP - + 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. + true + 1.13 beta12orEarlier - - + + @@ -48866,10 +49355,19 @@ positional features such as functional sites in nucleotide sequences.DNA polymorphism - Nucleic acid features (polymorphism) + Includes 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. + true + RFLP + Single nucleotide polymorphism + Microsatellites + VNTR + SNP + Includes microsatellite polymorphism in a DNA sequence. A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine. DNA polymorphism. + Variable number of tandem repeat polymorphism + Includes single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. beta12orEarlier - + Includes 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. @@ -48880,12 +49378,12 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid design - + Topic for the design of nucleic acid sequences with specific conformations. 1.3 beta12orEarlier true - + @@ -48895,7 +49393,7 @@ positional features such as functional sites in nucleotide sequences. Primer or probe design - + 1.3 true beta13 @@ -48910,7 +49408,7 @@ positional features such as functional sites in nucleotide sequences. Structure databases - + beta13 true 1.2 @@ -48926,7 +49424,7 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid structure - + true beta13 Nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation. @@ -48941,7 +49439,7 @@ positional features such as functional sites in nucleotide sequences. Sequence databases - + Molecular sequence data resources, including sequence sites, alignments, motifs and profiles. true beta13 @@ -48959,13 +49457,13 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid sequences - + Nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles. beta13 1.3 true Nucleotide sequences - + @@ -48975,12 +49473,12 @@ positional features such as functional sites in nucleotide sequences. Protein sequences - + Protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles. beta13 1.3 true - + @@ -48990,10 +49488,10 @@ positional features such as functional sites in nucleotide sequences. Protein interaction networks - + 1.3 true - + @@ -49004,6 +49502,7 @@ positional features such as functional sites in nucleotide sequences. Molecular biology + true VT 1.5.4 Biochemistry and molecular biology beta13 The molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life. @@ -49018,7 +49517,7 @@ positional features such as functional sites in nucleotide sequences. Mammals - + true beta13 1.3 @@ -49037,6 +49536,7 @@ positional features such as functional sites in nucleotide sequences.The degree of variation of life forms within a given ecosystem, biome or an entire planet. beta13 VT 1.5.5 Biodiversity conservation + true http://purl.bioontology.org/ontology/MSH/D044822 @@ -49049,7 +49549,7 @@ positional features such as functional sites in nucleotide sequences. Sequence clusters and classification - + This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. The comparison, grouping together and classification of macromolecules on the basis of sequence similarity. Sequence families @@ -49057,7 +49557,7 @@ positional features such as functional sites in nucleotide sequences.true Sequence clusters beta13 - + @@ -49069,6 +49569,7 @@ positional features such as functional sites in nucleotide sequences.Genetics http://purl.bioontology.org/ontology/MSH/D005823 + true The study of genes, genetic variation and heredity in living organisms. beta13 Heredity @@ -49086,6 +49587,7 @@ positional features such as functional sites in nucleotide sequences. beta13 The genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight). + true @@ -49098,6 +49600,7 @@ positional features such as functional sites in nucleotide sequences.Population genetics The distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow. + true beta13 @@ -49110,7 +49613,7 @@ positional features such as functional sites in nucleotide sequences. Regulatory RNA - + 1.3 Regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA). true @@ -49125,14 +49628,13 @@ positional features such as functional sites in nucleotide sequences. Documentation and help - + The documentation of resources such as tools, services and databases and how to get help. - Help + true beta13 - Documentation - - - + 1.13 + + @@ -49141,7 +49643,7 @@ positional features such as functional sites in nucleotide sequences. Genetic organisation - + The structural and functional organisation of genes and other genetic elements. 1.3 beta13 @@ -49157,6 +49659,7 @@ positional features such as functional sites in nucleotide sequences. Medical informatics + true Health informatics Clinical informatics Biomedical informatics @@ -49179,6 +49682,7 @@ positional features such as functional sites in nucleotide sequences.Developmental biology VT 1.5.14 Developmental biology + true beta13 How organisms grow and develop. @@ -49193,6 +49697,7 @@ positional features such as functional sites in nucleotide sequences. Embryology + true beta13 The development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. @@ -49210,6 +49715,7 @@ positional features such as functional sites in nucleotide sequences.VT 3.1.1 Anatomy and morphology beta13 The form and function of the structures of living organisms. + true @@ -49223,10 +49729,13 @@ positional features such as functional sites in nucleotide sequences.Literature and reference beta13 + true + http://purl.bioontology.org/ontology/MSH/D011642 The scientific literature, reference information and documentation. Literature sources Bibliography - http://purl.bioontology.org/ontology/MSH/D011642 + This includes the documentation of resources such as tools, services and databases, user support, how to get help etc. + Documentation @@ -49251,6 +49760,7 @@ positional features such as functional sites in nucleotide sequences.Aerobiology VT 1.5.99 Other Chronobiology + true VT 1.5.13 Cryobiology VT 1.5.1 Aerobiology @@ -49270,6 +49780,7 @@ positional features such as functional sites in nucleotide sequences.Data management The development and use of architectures, policies, practices and procedures for management of data. + true beta13 Data handling http://purl.bioontology.org/ontology/MSH/D030541 @@ -49285,7 +49796,7 @@ positional features such as functional sites in nucleotide sequences. Sequence feature detection - + 1.3 true beta13 @@ -49301,7 +49812,7 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid feature detection - + The detection of positional features such as functional sites in nucleotide sequences. true beta13 @@ -49316,7 +49827,7 @@ positional features such as functional sites in nucleotide sequences. Protein feature detection - + The detection, identification and analysis of positional protein sequence features, such as functional sites. beta13 1.3 @@ -49331,7 +49842,7 @@ positional features such as functional sites in nucleotide sequences. Biological system modelling - + 1.2 true beta13 @@ -49359,7 +49870,7 @@ positional features such as functional sites in nucleotide sequences. Genes and proteins resources - + 1.3 Gene family beta13 @@ -49376,14 +49887,13 @@ positional features such as functional sites in nucleotide sequences. Protein topological domains - - + + 1.13 Topological domains such as cytoplasmic regions in a protein. - Protein features (topological domains) + true 1.8 - - - + + @@ -49392,9 +49902,10 @@ positional features such as functional sites in nucleotide sequences. Protein variants - - protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. + beta13 + true + Protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. @@ -49406,7 +49917,7 @@ positional features such as functional sites in nucleotide sequences. Expression signals - + beta13 true 1.12 @@ -49423,10 +49934,16 @@ positional features such as functional sites in nucleotide sequences.DNA binding sites - This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). + Matrix-attachment region beta13 - Nucleic acid features (binding) + Nucleosome exclusion sequences + This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes), restriction enzyme recognition sites (restriction sites) etc. + Restriction sites + Ribosome binding sites + Scaffold-attachment region + This includes sites involved with DNA replication and recombination. 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. Also nucleosome exclusion regions, i.e. specific patterns or regions which exclude nucleosomes (the basic structural units of eukaryotic chromatin which play a significant role in regulating gene expression). Nucleic acids binding to some other molecule. + Matrix/scaffold attachment region @@ -49438,13 +49955,14 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid repeats - + + true beta13 This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. Repetitive elements within a nucleic acid sequence. - - - + 1,13 + + @@ -49453,13 +49971,10 @@ positional features such as functional sites in nucleotide sequences. DNA replication and recombination - + DNA replication or recombination. - This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. - Nucleosome exclusion sequences - Nucleic acid features (replication and recombination) beta13 - + true @@ -49470,14 +49985,13 @@ positional features such as functional sites in nucleotide sequences. 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. + 1.13 + true Coding sequences for a signal or transit peptide. - - - + + @@ -49486,14 +50000,13 @@ positional features such as functional sites in nucleotide sequences. Sequence tagged sites - - Nucleic acid features (STS) + beta13 - Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs. + 1.13 Sequence tagged sites (STS) in nucleic acid sequences. - - - + true + + @@ -49504,6 +50017,7 @@ positional features such as functional sites in nucleotide sequences.Sequencing Resequencing + true http://purl.bioontology.org/ontology/MSH/D059014 Chromosome walking NGS @@ -49560,7 +50074,7 @@ positional features such as functional sites in nucleotide sequences. DNA methylation - + true DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc. 1.3 @@ -49578,6 +50092,7 @@ positional features such as functional sites in nucleotide sequences.Metabolomics 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. + true http://purl.bioontology.org/ontology/MSH/D055432 1.1 @@ -49597,6 +50112,7 @@ positional features such as functional sites in nucleotide sequences.1.1 http://purl.bioontology.org/ontology/MSH/D057890 The study of the epigenetic modifications of a whole cell, tissue, organism etc. + true @@ -49614,6 +50130,7 @@ positional features such as functional sites in nucleotide sequences.Ecogenomics Community genomics Environmental genomics + true 1.1 The study of genetic material recovered from environmental samples, and associated environmental data. @@ -49628,7 +50145,7 @@ positional features such as functional sites in nucleotide sequences. DNA structural variation - + 1.1 Variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations. Structural variation @@ -49658,7 +50175,7 @@ positional features such as functional sites in nucleotide sequences. DNA-Seq - + 1.1 A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements. 1.3 @@ -49674,7 +50191,7 @@ positional features such as functional sites in nucleotide sequences. RNA-Seq alignment - + true 1.3 RNA-seq alignment @@ -49691,7 +50208,6 @@ positional features such as functional sites in nucleotide sequences. ChIP-on-chip - ChiP ChIP-Chip 1.1 @@ -49744,6 +50260,7 @@ positional features such as functional sites in nucleotide sequences.Chemical biology 1.3 Biological chemistry + true Chemical substances and physico-chemical processes and that occur within living organisms. @@ -49761,6 +50278,7 @@ positional features such as functional sites in nucleotide sequences.The study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences). 1.3 http://purl.bioontology.org/ontology/MSH/D010802 + true @@ -49771,13 +50289,14 @@ positional features such as functional sites in nucleotide sequences. Epigenetics - + Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence. This includes sub-topics such as histone modification and DNA methylation. DNA methylation includes bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc. http://purl.bioontology.org/ontology/MSH/D019175 DNA methylation Bisulfite sequencing Histone modification + true 1.3 @@ -49791,6 +50310,7 @@ positional features such as functional sites in nucleotide sequences. Biotechnology + true 1.3 The exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production. @@ -49809,6 +50329,7 @@ positional features such as functional sites in nucleotide sequences. Phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. 1.3 + true @@ -49822,6 +50343,7 @@ positional features such as functional sites in nucleotide sequences.Evolutionary biology VT 1.5.16 Evolutionary biology + true 1.3 The evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity. @@ -49839,6 +50361,7 @@ positional features such as functional sites in nucleotide sequences.The functions of living organisms and their constituent parts. 1.3 VT 3.1.8 Physiology + true @@ -49851,6 +50374,7 @@ positional features such as functional sites in nucleotide sequences. Microbiology + true The biology of microorganisms. 1.3 VT 1.5.20 Microbiology @@ -49866,6 +50390,7 @@ positional features such as functional sites in nucleotide sequences. Parasitology + true 1.3 The biology of parasites. @@ -49882,6 +50407,7 @@ positional features such as functional sites in nucleotide sequences. General medicine Research in support of healing by diagnosis, treatment, and prevention of disease. + true 1.3 VT 3.1 Basic medicine VT 3.2.9 General and internal medicine @@ -49904,6 +50430,7 @@ positional features such as functional sites in nucleotide sequences. Neuroscience 1.3 + true The study of the nervous system and brain; its anatomy, physiology and function. VT 3.1.5 Neuroscience @@ -49920,6 +50447,7 @@ positional features such as functional sites in nucleotide sequences. VT 3.3.1 Epidemiology Topic concerning the the patterns, cause, and effect of disease within populations. + true 1.3 Public health Epidemiology @@ -49937,6 +50465,7 @@ positional features such as functional sites in nucleotide sequences. 1.3 + true VT 1.5.9 Biophysics The use of physics to study biological system. @@ -49959,6 +50488,7 @@ positional features such as functional sites in nucleotide sequences.Theoretical biology 1.3 The development and application of theory, analytical methods, mathematical models and computational simulation of biological systems. + true Biomathematics @@ -49973,11 +50503,12 @@ positional features such as functional sites in nucleotide sequences.Transcriptomics + Comparative transcriptomics Metatranscriptomics The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. Transcriptome 1.3 - Comparative transcriptomics + true @@ -50067,11 +50598,13 @@ positional features such as functional sites in nucleotide sequences. RNA splicing - + + This includes the study of splice sites, splicing patterns, alternative splicing events and variants, isoforms, etc.. + Splice sites RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons. - This includes the study of splice sites, splicing patterns, splice alternatives or variants, isoforms, etc. 1.3 Alternative splicing + true @@ -50083,8 +50616,10 @@ positional features such as functional sites in nucleotide sequences. Molecular genetics + 1.3 The structure and function of genes at a molecular level. + true @@ -50097,6 +50632,7 @@ positional features such as functional sites in nucleotide sequences. Respiratory medicine + true VT 3.2.25 Respiratory systems Pulmonology The study of respiratory system. @@ -50115,7 +50651,7 @@ positional features such as functional sites in nucleotide sequences. Metabolic disease - + The study of metabolic diseases. 1.4 1.3 @@ -50165,6 +50701,7 @@ positional features such as functional sites in nucleotide sequences. 1.3 VT 1.7.4 Computational chemistry + true Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems. @@ -50179,6 +50716,7 @@ positional features such as functional sites in nucleotide sequences.Neurology Neurological disorders + true 1.3 The branch of medicine that deals with the anatomy, functions and disorders of the nervous system. @@ -50193,6 +50731,7 @@ positional features such as functional sites in nucleotide sequences. Cardiology + true Cardiovascular disease VT 3.2.4 Cardiac and Cardiovascular systems 1.3 @@ -50216,6 +50755,7 @@ positional features such as functional sites in nucleotide sequences.The discovery and design of drugs or potential drug compounds. This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. 1.3 + true @@ -50228,6 +50768,7 @@ positional features such as functional sites in nucleotide sequences. Biobank + true biobanking 1.3 Repositories of biological samples, typically human, for basic biological and clinical research. @@ -50301,6 +50842,7 @@ positional features such as functional sites in nucleotide sequences.Translational medicine 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice. + true 1.3 @@ -50333,6 +50875,7 @@ positional features such as functional sites in nucleotide sequences.Biomedical science Topic concerning biological science that is (typically) performed in the context of medicine. + true VT 3.3 Health sciences Health science 1.3 @@ -50361,13 +50904,13 @@ positional features such as functional sites in nucleotide sequences. Sequence search - + 1.3 Sequence database search true 1.12 The search and retrieval from a database on the basis of molecular sequence similarity. - + @@ -50381,6 +50924,7 @@ positional features such as functional sites in nucleotide sequences.Diagnostic markers 1.4 Objective indicators of biological state often used to assess health, and determinate treatment. + true @@ -50458,6 +51002,7 @@ positional features such as functional sites in nucleotide sequences.Chemical biology + true 1.4 The use of synthetic chemistry to study and manipulate biological systems. @@ -50531,6 +51076,7 @@ positional features such as functional sites in nucleotide sequences.The process of bringing a new drug to market once a lead compounds has been identified through drug discovery. Drug development science Medicines development + true @@ -50562,6 +51108,7 @@ positional features such as functional sites in nucleotide sequences.Pharmacodynamics Pharmacokinetics Drug distribution + true 1.4 Drug excretion The study of how a drug interacts with the body. @@ -50648,12 +51195,13 @@ positional features such as functional sites in nucleotide sequences. Imaging - This includes diffraction experiments that are based upon the interference of waves, typically electromagnetic waves such as X-rays or visible light, by some object being studied, typical in order to produce an image of the object or determine its structure. + true Microscopy imaging - 1.4 Microscopy Diffraction experiment The visual representation of an object. + This includes diffraction experiments that are based upon the interference of waves, typically electromagnetic waves such as X-rays or visible light, by some object being studied, typical in order to produce an image of the object or determine its structure. + 1.4 @@ -50729,6 +51277,7 @@ positional features such as functional sites in nucleotide sequences. 1.4 VT 1.5.18 Marine and Freshwater biology + true The study of organisms in the ocean or brackish waters. @@ -50744,6 +51293,7 @@ positional features such as functional sites in nucleotide sequences. The identification of molecular and genetic causes of disease and the development of interventions to correct them. 1.4 + true @@ -50773,6 +51323,7 @@ positional features such as functional sites in nucleotide sequences. Omics + true The collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms. 1.4 @@ -50821,6 +51372,7 @@ positional features such as functional sites in nucleotide sequences. Stem cell research Biomedical approaches to clinical interventions that involve the use of stem cells. + true 1.4 @@ -50834,6 +51386,7 @@ positional features such as functional sites in nucleotide sequences. Systems medicine + true 1.4 An interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life. @@ -50879,6 +51432,7 @@ positional features such as functional sites in nucleotide sequences. The branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging. VT 3.2.10 Geriatrics and gerontology + true Ageing Gerontology Aging @@ -50899,6 +51453,7 @@ positional features such as functional sites in nucleotide sequences.VT 3.2.1 Allergy Health issues related to the immune system and their prevention, diagnosis and mangement. 1.4 + true Immune disorders Clinical immunology Immunomodulators @@ -50916,9 +51471,9 @@ positional features such as functional sites in nucleotide sequences. Pain medicine - Ageing 1.4 Algiatry + true The prevention of pain and the evaluation, treatment and rehabilitation of persons in pain. @@ -50949,7 +51504,6 @@ positional features such as functional sites in nucleotide sequences.Critical care medicine Acute medicine - Geriatrics VT 3.2.5 Critical care/Emergency medicine Emergency medicine 1.4 @@ -51017,9 +51571,10 @@ positional features such as functional sites in nucleotide sequences. 1.4 Metabolic disorders + true + The branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism. Metabolism Endocrinology - The branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism. Endocrine disorders @@ -51034,6 +51589,7 @@ positional features such as functional sites in nucleotide sequences.Haematology VT 3.2.11 Hematology + true The branch of medicine that deals with the blood, blood-forming organs and blood diseases. Haematological disorders 1.4 @@ -51050,6 +51606,7 @@ positional features such as functional sites in nucleotide sequences. Gastroenterology + true The branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum. Gastrointestinal disorders VT 3.2.8 Gastroenterology and hepatology @@ -51080,10 +51637,11 @@ positional features such as functional sites in nucleotide sequences. Gynaecology and obstetrics - VT 3.2.15 Obstetrics and gynaecology + The branch of medicine that deals with the health of the female reproductive system, pregnancy and birth. + true 1.4 + VT 3.2.15 Obstetrics and gynaecology Gynaecology - The branch of medicine that deals with the health of the female reproductive system, pregnancy and birth. Gynaecological disorders Obstetrics @@ -51101,6 +51659,7 @@ positional features such as functional sites in nucleotide sequences.Hepatobiliary medicine Liver disorders 1.4 + true The branch of medicine that deals with the liver, gallbladder, bile ducts and bile. @@ -51113,12 +51672,13 @@ positional features such as functional sites in nucleotide sequences. Infectious tropical disease - + The branch of medicine that deals with the infectious diseases of the tropics. + 1.13 + true 1.4 - - - + + @@ -51142,6 +51702,7 @@ positional features such as functional sites in nucleotide sequences. Medical toxicology + true The branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents. 1.4 @@ -51354,6 +51915,7 @@ positional features such as functional sites in nucleotide sequences.1.7 VT 1.3.2 Data mining The discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format. + true KDD Knowledge discovery in databases @@ -51382,13 +51944,18 @@ positional features such as functional sites in nucleotide sequences. Database management + File management + Document, record and content management + Database administration + This includes databases for the results of scientific experiments, the application of high-throughput technology, computational analysis and the scientific literature. It covers the management and manipulation of digital documents, including database records, files and reports. + Document management + Content management 1.8 - Data maintenance Databases - Database administration + Data maintenance The general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources. - This includes databases for the results of scientific experiments, the application of high-throughput technology, computational analysis and the scientific literature. + Record management Biological databases @@ -51419,11 +51986,13 @@ positional features such as functional sites in nucleotide sequences. Protein sites, features and motifs + + 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. Protein sequence features - Protein functional sites 1.8 The biology, 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. + Signal peptide cleavage sites @@ -51434,11 +52003,15 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid sites, features and motifs + + Primer binding sites + Nucleic acid functional sites + Sequence tagged sites Nucleic acid sequence features 1.8 - Nucleic acid functional sites The biology, 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. + 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. @@ -51448,15 +52021,29 @@ positional features such as functional sites in nucleotide sequences. - Gene transcript features + Gene transcripts - Nucleic acid features (mRNA features) - Fusion transcripts - Features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. + EST + This includes Introns, and protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. Also expressed sequence tag (EST) or complementary DNA (cDNA) sequences. + Transcription mRNA features - This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). + This includes regions or sites 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. + cDNA + Introns + PolyA site + Fusion transcripts + Exons + Signal peptide coding sequence + This includes coding sequences for a 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. + Transcription of DNA into RNA and features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. 1.8 + PolyA signal + mRNA + Transit peptide coding sequence + This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). + Coding RNA + Gene transcript features @@ -51467,11 +52054,14 @@ positional features such as functional sites in nucleotide sequences. Protein-ligand interactions - + + true 1.8 Protein-ligand (small molecule) interaction(s). - - + 1.13 + Protein-drug interactions + + @@ -51480,11 +52070,13 @@ positional features such as functional sites in nucleotide sequences. Protein-drug interactions - + + 1.13 1.8 + true Protein-drug interaction(s). - - + + @@ -51563,7 +52155,11 @@ positional features such as functional sites in nucleotide sequences.Proteomics experiment Proteomics experiments. + Northern blot experiment + 2D PAGE experiment 1.8 + This includes two-dimensional gel electrophoresis (2D PAGE) experiments, gels or spots in a gel. Also mass spectrometry - an analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase. Also Northern blot experiments. + Mass spectrometry @@ -51574,11 +52170,13 @@ positional features such as functional sites in nucleotide sequences. 2D PAGE experiment - + + true Two-dimensional gel electrophoresis experiments, gels or spots in a gel. 1.8 - - + 1.13 + + @@ -51587,11 +52185,13 @@ positional features such as functional sites in nucleotide sequences. Northern blot experiment - + Northern Blot experiments. + true + 1.13 1.8 - - + + @@ -51626,11 +52226,13 @@ positional features such as functional sites in nucleotide sequences. Protein-nucleic acid interactions - + + true 1.8 Protein-DNA/RNA interaction(s). - - + 1.13 + + @@ -51639,13 +52241,13 @@ positional features such as functional sites in nucleotide sequences. Protein-protein interactions - - Domain-domain interactions + + 1.13 Protein-protein interaction(s), including interactions between protein domains. 1.8 - Protein interaction networks - - + true + + @@ -51654,11 +52256,13 @@ positional features such as functional sites in nucleotide sequences. Cellular process pathways - + 1.8 Cellular process pathways. - - + true + 1.13 + + @@ -51667,12 +52271,13 @@ positional features such as functional sites in nucleotide sequences. Disease pathways - + + 1.13 Disease pathways, typically of human disease. - Pathway or network (disease) + true 1.8 - - + + @@ -51681,12 +52286,13 @@ positional features such as functional sites in nucleotide sequences. Environmental information processing pathways - + + true Environmental information processing pathways. 1.8 - Pathway or network (environmental information processing) - - + 1.13 + + @@ -51695,12 +52301,13 @@ positional features such as functional sites in nucleotide sequences. Genetic information processing pathways - - Pathway or network (genetic information processing) + + true 1.8 Genetic information processing pathways. - - + 1.13 + + @@ -51709,13 +52316,13 @@ positional features such as functional sites in nucleotide sequences. Protein super-secondary structure - + Super-secondary structure of protein sequence(s). - Protein features (super-secondary) + true 1.8 - Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. - - + 1.13 + + @@ -51724,13 +52331,13 @@ positional features such as functional sites in nucleotide sequences. Protein active sites - - Enzyme active site + 1.8 - Protein features (active sites) + 1.13 + true Catalytic residues (active site) of an enzyme. - - + + @@ -51739,10 +52346,14 @@ positional features such as functional sites in nucleotide sequences. Protein binding sites - - Ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. + + Protein functional sites + Enzyme active site + Binding sites in proteins, including cleavage sites (for a proteolytic enzyme or agent), key residues involved in protein folding, catalytic residues (active site) of an enzyme, ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids, RNA and DNA-binding proteins and binding sites etc. + Protein-nucleic acid binding sites 1.8 - Protein features (binding sites) + Protein cleavage sites + Protein key folding sites @@ -51753,12 +52364,13 @@ positional features such as functional sites in nucleotide sequences. Protein-nucleic acid binding sites - + RNA and DNA-binding proteins and binding sites in protein sequences. + 1.13 1.8 - Protein features (nucleic acid binding sites) - - + true + + @@ -51767,12 +52379,13 @@ positional features such as functional sites in nucleotide sequences. Protein cleavage sites - + Cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. - Protein features (cleavage sites) + true 1.8 - - + 1.13 + + @@ -51781,14 +52394,13 @@ positional features such as functional sites in nucleotide sequences. Protein chemical modifications - + + true Chemical modification of a protein. - Protein features (chemical modifications) - MOD:00000 + 1.13 1.8 - GO:0006464 - - + + @@ -51797,7 +52409,7 @@ positional features such as functional sites in nucleotide sequences. Protein disordered structure - + Disordered structure in a protein. 1.8 Protein features (disordered structure) @@ -51811,15 +52423,13 @@ positional features such as functional sites in nucleotide sequences. Protein 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. + + true + 1.13 Structural domains or 3D folds in a protein or polypeptide chain. 1.8 - Protein structural domains - Protein features (domains) - - + + @@ -51828,13 +52438,13 @@ positional features such as functional sites in nucleotide sequences. Protein key folding sites - - - Protein features (key folding sites) + 1.8 + 1.13 + true Key residues involved in protein folding. - - + + @@ -51843,13 +52453,13 @@ positional features such as functional sites in nucleotide sequences. Protein post-translational modifications - - Protein features (post-translation modifications) - Post-translation modifications + + true + 1.13 Post-translation modifications in a protein sequence, typically describing the specific sites involved. 1.8 - - + + @@ -51859,9 +52469,10 @@ positional features such as functional sites in nucleotide sequences. Protein 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). - Secondary structure (predicted or real) of a protein. + Secondary structure (predicted or real) of a protein, including super-secondary structure. + Protein super-secondary structure + Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. Protein features (secondary structure) 1.8 @@ -51874,13 +52485,13 @@ positional features such as functional sites in nucleotide sequences. Protein sequence repeats - + + true 1.8 - Protein features (repeats) Short repetitive subsequences (repeat sequences) in a protein sequence. - Protein repeats - - + 1.13 + + @@ -51889,12 +52500,13 @@ positional features such as functional sites in nucleotide sequences. Protein signal peptides - - Protein features (signal peptides) + + 1.13 Signal peptides or signal peptide cleavage sites in protein sequences. + true 1.8 - - + + @@ -51998,6 +52610,7 @@ positional features such as functional sites in nucleotide sequences. Human genetics + true The study of inheritatnce in human beings. VT 3.1.2 Human genetics 1.10 @@ -52028,8 +52641,9 @@ positional features such as functional sites in nucleotide sequences. Medical biotechnology - 1.10 VT 3.4.1 Biomedical devices + 1.10 + true VT 3.4.2 Health-related biotechnology VT 3.4 Medical biotechnology VT 3.3.14 Tropical medicine @@ -52050,6 +52664,7 @@ positional features such as functional sites in nucleotide sequences.1.10 Health problems that are prevalent in tropical and subtropical regions. Molecular diagnostics + true VT 3.4.5 Molecular diagnostics @@ -52138,6 +52753,7 @@ positional features such as functional sites in nucleotide sequences.Experimental design Studies The design of an experiment intended to test a hypothesis, and describe or explain empirical data obtained under various experimental conditions. + true @@ -52160,16 +52776,33 @@ positional features such as functional sites in nucleotide sequences. + + + Microbial ecology + + + 1.13 + The ecology of microorganisms including their relationship with one another and their environment. + Microbiome + true + Environmental microbiology + + + + + + Obsolete concept (EDAM) - 1.2 Needed for conversion to the OBO format. An obsolete concept (redefined in EDAM). true +