diff --git a/releases/EDAM.owl b/releases/EDAM.owl index 27b617d..d517bfc 100644 --- a/releases/EDAM.owl +++ b/releases/EDAM.owl @@ -32,15 +32,15 @@ EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries. Hervé Ménager topics "EDAM topics" - 14:11:2014 09:26 + 17:11:2014 23:35 EDAM_format http://edamontology.org/format_ "EDAM data formats" Jon Ison, Matus Kalas, Herve Menager Matúš Kalaš - 3429 1.5 Jon Ison concept_properties "EDAM concept properties" EDAM_data http://edamontology.org/data_ "EDAM types of data" + 3442 application/rdf+xml EDAM http://edamontology.org/ "EDAM relations and concept properties" operations "EDAM operations" @@ -379,17 +379,17 @@ - OBO_REL:bearer_of - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. - - - - true In very unusual cases. + + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. + OBO_REL:bearer_of + + + @@ -434,8 +434,14 @@ - '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. + In very unusual cases. + true + + + + OBO_REL:has_participant + 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. @@ -445,12 +451,6 @@ - - In very unusual cases. - true - - - @@ -475,18 +475,18 @@ - 'OBI:has_specified_output' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant). - - - - - OBO_REL:has_participant 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it. + 'OBI:has_specified_output' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant). + + + + + true In very unusual cases. @@ -524,12 +524,6 @@ - true - In very unusual cases. - - - - 'is about' is narrower in the sense that it only relates subjects that are information artifacts and the relation is not necessarily the one of having a topic. It is broader in the sense that it relates with any object. @@ -547,6 +541,12 @@ + + In very unusual cases. + true + + + @@ -601,18 +601,18 @@ - OBO_REL:inheres_in - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. - - - - In very unusual cases. true + OBO_REL:inheres_in + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. + + + + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. OBO_REL:function_of @@ -664,23 +664,23 @@ - true In very unusual cases. + true - 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. - - - - 'OBI:is_specified_input_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011). + + OBO_REL:participates_in + 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments. + + + @@ -718,8 +718,8 @@ - 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. + OBO_REL:participates_in @@ -820,16 +820,22 @@ - Data record - EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). + Data does theoretically not need to have a purpose, but in all regular cases it does. Remark: EDAM Data sub-ontology focuses on scientific data (SIO_000472), in particular the bioinformatics (SIO_010065) and biological (SIO_010019). - + + - Data does theoretically not need to have a purpose, but in all regular cases it does. Remark: EDAM Data sub-ontology focuses on scientific data (SIO_000472), in particular the bioinformatics (SIO_010065) and biological (SIO_010019). + GFO 'Perpetuant' is in general broader than data, but it may be seen narrower in the sense of being a concrete individual. - + + + + Data set + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + + IAO 'data item' is a closely related ontological category (concept) broader in the sense of being any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant), standing in relation of aboutness to some entity (http://purl.obolibrary.org/obo/IAO_0000030), and to data that is intended to be a truthful statement about something. @@ -838,6 +844,12 @@ + 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 + + + + IAO 'information content entity' is a closely related ontological category (concept) broader in the sense of covering any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant) and standing in relation of aboutness to some entity. @@ -850,20 +862,8 @@ - Data set EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - - - - - GFO 'Perpetuant' is in general broader than data, but it may be seen narrower in the sense of being a concrete individual. - - - - - Datum - EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). @@ -921,7 +921,7 @@ - DEP_Directory metadata + Directory metadata true beta12orEarlier @@ -1133,7 +1133,7 @@ - DEP_Sequence mask character + Sequence mask character A character used to replace (mask) other characters in a molecular sequence. 1.5 @@ -1142,13 +1142,11 @@ - - - DEP_Sequence mask type + Sequence mask type true 1.5 @@ -1181,7 +1179,7 @@ - DEP_Sequence length specification + Sequence length specification 1.5 beta12orEarlier @@ -1196,7 +1194,7 @@ - DEP_Sequence metadata + Sequence metadata true 1.5 @@ -1292,7 +1290,7 @@ - DEP_Sequence alignment (words) + Sequence alignment (words) Alignment of exact matches between subsequences (words) within two or more molecular sequences. Sequence word alignment @@ -1345,7 +1343,7 @@ - DEP_Sequence alignment parameter + Sequence alignment parameter beta12orEarlier 1.5 @@ -1374,7 +1372,7 @@ - DEP_Sequence alignment metadata + Sequence alignment metadata 1.5 true @@ -1790,7 +1788,7 @@ - DEP_Sequence-3D profile alignment + Sequence-3D profile alignment true beta12orEarlier @@ -1918,7 +1916,7 @@ - DEP_Protein domain classification + Protein domain classification beta12orEarlier 1.5 @@ -2676,7 +2674,7 @@ - DEP_Data resource definition + Data resource definition A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper. 1.5 @@ -2740,7 +2738,7 @@ - DEP_EMBOSS database resource definition + EMBOSS database resource definition 1.5 true @@ -2755,7 +2753,7 @@ - DEP_Version information + Version information true Information on a version of software or data, for example name, version number and release date. @@ -2865,7 +2863,7 @@ - DEP_Job metadata + Job metadata Textual metadata on a submitted or completed job. Moby:PDGJOB @@ -3222,7 +3220,7 @@ - DEP_Molecule type + Molecule type Protein|DNA|RNA A label (text token) describing the type a molecule. @@ -3721,7 +3719,7 @@ - DEP_Sequence position specification + Sequence position specification true beta12orEarlier @@ -5126,7 +5124,7 @@ - DEP_Sequence type + Sequence type beta12orEarlier true @@ -5374,7 +5372,7 @@ - DEP_EMBOSS listfile + EMBOSS listfile beta12orEarlier true @@ -5538,7 +5536,7 @@ - DEP_Sequence alignment type + Sequence alignment type A label (text token) describing the type of a sequence alignment. Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on. @@ -5569,7 +5567,7 @@ - DEP_Phylogenetic tree type + Phylogenetic tree type nj|upgmp 1.5 @@ -5616,7 +5614,7 @@ - DEP_Comparison matrix type + Comparison matrix type For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used. Substitution matrix type @@ -7104,7 +7102,7 @@ - DEP_Word size + Word size beta12orEarlier true @@ -7121,7 +7119,7 @@ - DEP_Window size + Window size Size of a sequence window. beta12orEarlier @@ -7137,7 +7135,7 @@ - DEP_Sequence length range + Sequence length range 1.5 beta12orEarlier @@ -7730,7 +7728,7 @@ - DEP_Sequence features (repeats) + Sequence features (repeats) Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. The report might include derived data map such as classification, annotation, organization, periodicity etc. @@ -7748,7 +7746,7 @@ - DEP_Gene and transcript structure (report) + Gene and transcript structure (report) true A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. @@ -7798,7 +7796,7 @@ - DEP_Nucleic acid features (quadruplexes) + Nucleic acid features (quadruplexes) beta12orEarlier A report on quadruplex-forming motifs in a nucleotide sequence. @@ -7906,7 +7904,7 @@ - DEP_Nucleic acid features (microRNA) + Nucleic acid features (microRNA) 1.5 A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc. @@ -8300,7 +8298,7 @@ - DEP_Regular expression + Regular expression beta12orEarlier true @@ -8511,7 +8509,7 @@ - DEP_Protein family signature + Protein family signature A protein family signature (sequence classifier) from the InterPro database. 1.5 @@ -8527,7 +8525,7 @@ - DEP_Protein domain signature + Protein domain signature Protein domain signatures identify structural or functional domains or other units with defined boundaries. A protein domain signature (sequence classifier) from the InterPro database. @@ -8543,7 +8541,7 @@ - DEP_Protein region signature + Protein region signature A protein region signature defines a region which cannot be described as a protein family or domain signature. 1.5 @@ -8559,7 +8557,7 @@ - DEP_Protein repeat signature + Protein repeat signature A protein repeat signature (sequence classifier) from the InterPro database. beta12orEarlier @@ -8575,7 +8573,7 @@ - DEP_Protein site signature + Protein site signature 1.5 true @@ -9156,7 +9154,7 @@ - DEP_Sequence-profile alignment (HMM) + Sequence-profile alignment (HMM) Alignment of molecular sequence(s) to a hidden Markov model(s). true @@ -9171,7 +9169,7 @@ - DEP_Sequence-profile alignment (fingerprint) + Sequence-profile alignment (fingerprint) true beta12orEarlier @@ -9255,7 +9253,7 @@ - DEP_Phylogenetic report + Phylogenetic report true This is a broad data type and is used for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis. @@ -9578,13 +9576,13 @@ - + - + 3D coordinate and associated data for a carbohydrate (3D) structure. @@ -9702,7 +9700,7 @@ - DEP_Protein structure (all atoms) + Protein structure (all atoms) 3D coordinate and associated data for a protein tertiary (3D) structure (all atoms). true @@ -9717,7 +9715,7 @@ - DEP_Protein structure (C-alpha atoms) + Protein structure (C-alpha atoms) 1.5 beta12orEarlier @@ -9887,7 +9885,7 @@ - DEP_Structure alignment (protein all atoms) + Structure alignment (protein all atoms) true beta12orEarlier @@ -9902,7 +9900,7 @@ - DEP_Structure alignment (protein C-alpha atoms) + Structure alignment (protein C-alpha atoms) beta12orEarlier true @@ -10221,7 +10219,7 @@ - DEP_Enzyme report + Enzyme report An informative report on a specific enzyme. Enzyme report @@ -10238,7 +10236,7 @@ - DEP_Restriction enzyme report + Restriction enzyme report true Restriction enzyme report @@ -10722,7 +10720,7 @@ - DEP_DEP_CATH node + CATH node CATH classification node report true @@ -10739,7 +10737,7 @@ - DEP_DEP_SCOP node + SCOP node beta12orEarlier 1.5 @@ -10769,7 +10767,7 @@ - DEP_CATH class + CATH class true Information on a protein 'class' node from the CATH database. @@ -10784,7 +10782,7 @@ - DEP_CATH architecture + CATH architecture true Information on a protein 'architecture' node from the CATH database. @@ -10799,7 +10797,7 @@ - DEP_CATH topology + CATH topology beta12orEarlier Information on a protein 'topology' node from the CATH database. @@ -10814,7 +10812,7 @@ - DEP_CATH homologous superfamily + CATH homologous superfamily Information on a protein 'homologous superfamily' node from the CATH database. beta12orEarlier @@ -10829,7 +10827,7 @@ - DEP_CATH structurally similar group + CATH structurally similar group Information on a protein 'structurally similar group' node from the CATH database. beta12orEarlier @@ -10844,7 +10842,7 @@ - DEP_CATH functional category + CATH functional category beta12orEarlier 1.5 @@ -11465,7 +11463,7 @@ - DEP_MIRIAM datatype + MIRIAM datatype 1.5 true @@ -11527,7 +11525,7 @@ - DEP_Database version information + Database version information beta12orEarlier Information on a database (or ontology) version, for example name, version number and release date. @@ -11543,7 +11541,7 @@ - DEP_Tool version information + Tool version information 1.5 true @@ -11603,7 +11601,7 @@ - DEP_Job status + Job status Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed). true @@ -11633,7 +11631,7 @@ - DEP_Job type + Job type A label (text token) describing the type of job, for example interactive or non-interactive. beta12orEarlier @@ -11648,7 +11646,7 @@ - DEP_Tool log + Tool log beta12orEarlier true @@ -11877,7 +11875,7 @@ - DEP_Number of iterations + Number of iterations beta12orEarlier true @@ -11892,7 +11890,7 @@ - DEP_Number of output entities + Number of output entities true beta12orEarlier @@ -12303,7 +12301,7 @@ - DEP_Ontology relation type + Ontology relation type A relation type defined in an ontology. true @@ -13276,7 +13274,7 @@ - DEP_Map type + Map type beta12orEarlier true @@ -14109,7 +14107,7 @@ - DEP_Sequence mask parameter + Sequence mask parameter Data used to replace (mask) characters in a molecular sequence. true @@ -14186,7 +14184,7 @@ - DEP_Genome version information + Genome version information 1.5 Information on a genome version. @@ -14367,7 +14365,7 @@ - DEP_Search parameter + Search parameter Some simple value controlling a search operation, typically a search of a database. true @@ -14396,7 +14394,7 @@ - DEP_Secondary structure + Secondary structure The secondary structure assignment (predicted or real) of a nucleic acid or protein. beta12orEarlier @@ -14518,7 +14516,7 @@ - DEP_Database entry version information + Database entry version information Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on. 1.5 @@ -14623,7 +14621,7 @@ - DEP_Type + Type true beta12orEarlier @@ -14825,13 +14823,13 @@ - + - + beta12orEarlier @@ -15034,7 +15032,7 @@ - DEP_Sequence profile type + Sequence profile type beta12orEarlier A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc. @@ -15094,7 +15092,7 @@ - DEP_Results sort order + Results sort order A control of the order of data that is output, for example the order of sequences in an alignment. 1.5 @@ -15183,7 +15181,7 @@ - DEP_Window step size + Window step size Size of the incremental 'step' a sequence window is moved over a sequence. true @@ -15228,7 +15226,7 @@ - DEP_Sequence offset + Sequence offset An offset for a single-point sequence position. 1.5 @@ -15243,7 +15241,7 @@ - DEP_Threshold + Threshold A value that serves as a threshold for a tool (usually to control scoring or output). true @@ -15320,7 +15318,7 @@ - DEP_Rendering parameter + Rendering parameter Graphical parameter Graphics parameter @@ -15353,7 +15351,7 @@ - DEP_Date + Date true beta12orEarlier @@ -15517,7 +15515,7 @@ - DEP_Nucleic acid features (siRNA) + Nucleic acid features (siRNA) A report on siRNA duplexes in mRNA. beta12orEarlier @@ -15670,7 +15668,7 @@ - DEP_Error + Error true 1.5 @@ -15850,7 +15848,7 @@ - DEP_Server metadata + Server metadata true 1.5 @@ -15978,7 +15976,7 @@ - DEP_Sequence set (bootstrapped) + Sequence set (bootstrapped) A collection of sequences output from a bootstrapping (resampling) procedure. true @@ -16009,7 +16007,7 @@ - DEP_Schema + Schema 1.5 A data schema for organising or transforming data of some type. @@ -16024,7 +16022,7 @@ - DEP_DTD + DTD 1.5 beta12orEarlier @@ -16039,7 +16037,7 @@ - DEP_XML Schema + XML Schema 1.5 true @@ -16055,7 +16053,7 @@ - DEP_Relax-NG schema + Relax-NG schema true A relax-NG schema. @@ -16070,7 +16068,7 @@ - DEP_XSLT stylesheet + XSLT stylesheet true An XSLT stylesheet. @@ -16928,7 +16926,7 @@ - DEP_Protein signature type + Protein signature type 1.5 A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database. @@ -16943,7 +16941,7 @@ - DEP_Domain-nucleic acid interaction report + Domain-nucleic acid interaction report beta12orEarlier An informative report on protein domain-DNA/RNA interaction(s). @@ -17588,7 +17586,7 @@ - DEP_Protein-drug interaction report + Protein-drug interaction report beta12orEarlier 1.5 @@ -17727,7 +17725,7 @@ - DEP_Molecule report + Molecule report true 1.5 @@ -17981,7 +17979,7 @@ - DEP_Expressed gene list + Expressed gene list A simple summary of expressed genes. Gene annotation (expressed gene list) @@ -19265,13 +19263,13 @@ - + - + Identifier of a carbohydrate. @@ -20177,7 +20175,7 @@ - DEP_Embryo report + Embryo report 1.5 beta12orEarlier @@ -20785,7 +20783,7 @@ - DEP_Term ID list + Term ID list 1.5 The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included. @@ -21633,7 +21631,7 @@ - DEP_Article metadata + Article metadata 1.5 Bibliographic data concerning scientific article(s). @@ -21804,7 +21802,7 @@ - DEP_DRCAT resource + DRCAT resource true beta12orEarlier @@ -21876,7 +21874,7 @@ - DEP_Secondary structure report + Secondary structure report 1.5 An informative report on general information, properties or features of one or more molecular secondary structures. @@ -21907,7 +21905,7 @@ - DEP_RNA features report + RNA features report Nucleic acid features (RNA features) RNA features @@ -22500,7 +22498,7 @@ - DEP_Article report + Article report true Data derived from the analysis of a scientific text such as a full text article from a scientific journal. @@ -22657,7 +22655,7 @@ - DEP_Microarray image + Microarray image true An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data. @@ -22735,7 +22733,7 @@ - DEP_Workflow + Workflow A computational workflow. 1.5 @@ -22976,7 +22974,7 @@ - DEP_Classification report + Classification report 1.5 A report on a classification of molecular sequences, structures or other entities. @@ -23207,7 +23205,7 @@ - DEP_Core data + Core data beta13 true @@ -23317,7 +23315,7 @@ - DEP_Protein domain classification node + Protein domain classification node 1.5 true @@ -23379,7 +23377,7 @@ - DEP_Geotemporal metadata + Geotemporal metadata Basic information concerning geographical location or time. true @@ -23584,7 +23582,7 @@ - DEP_Sequence features (compositionally-biased regions) + Sequence features (compositionally-biased regions) A report of regions in a molecular sequence that are biased to certain characters. true @@ -23613,7 +23611,7 @@ - DEP_Nucleic acid features (difference and change) + Nucleic acid features (difference and change) true 1.5 @@ -23751,7 +23749,7 @@ - DEP_Nucleic acid features (d-loop) + Nucleic acid features (d-loop) A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. A report on displacement loops in a mitochondrial DNA sequence. @@ -23767,7 +23765,7 @@ - DEP_Nucleic acid features (stem loop) + Nucleic acid features (stem loop) A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs. 1.5 @@ -23844,7 +23842,7 @@ - DEP_Transcriptional features (report) + Transcriptional features (report) beta13 Features concerning transcription of DNA into RNA including the regulation of transcription. @@ -23876,7 +23874,7 @@ - DEP_Nucleic acid features (immunoglobulin gene structure) + Nucleic acid features (immunoglobulin gene structure) A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments. 1.5 @@ -23891,7 +23889,7 @@ - DEP_SCOP class + SCOP class Information on a 'class' node from the SCOP database. true @@ -23906,7 +23904,7 @@ - DEP_SCOP fold + SCOP fold true 1.5 @@ -23921,7 +23919,7 @@ - DEP_SCOP superfamily + SCOP superfamily true 1.5 @@ -23936,7 +23934,7 @@ - DEP_SCOP family + SCOP family beta13 Information on a 'family' node from the SCOP database. @@ -23951,7 +23949,7 @@ - DEP_SCOP protein + SCOP protein 1.5 beta13 @@ -23966,7 +23964,7 @@ - DEP_SCOP species + SCOP species Information on a 'species' node from the SCOP database. beta13 @@ -24217,7 +24215,7 @@ - DEP_Sequence feature type + Sequence feature type 1.5 1.3 @@ -24232,7 +24230,7 @@ - DEP_Gene homology (report) + Gene homology (report) 1.5 An informative report on gene homologues between species. @@ -27212,46 +27210,46 @@ - BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the data format. + GFO 'Perpetuant' is in general broader than format, but it may be seen narrower in the sense of being a concrete individual and in the way of exhibiting presentials. - - - - 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'.) - - + - GFO 'Perpetuant' is in general broader than format, but it may be seen narrower in the sense of being a concrete individual and in the way of exhibiting presentials. + Compression and encoding' defines additional 'formatting' and/or encoding on top of the primary format. + - - Format can be a quality of a data record. + Closely related concept focusing on the specification of a data format. + - - File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. File format + File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. - Closely related concept focusing on the specification of a data format. + Data model + A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) + + + + + Format can be a quality of a data record. - + - Compression and encoding' defines additional 'formatting' and/or encoding on top of the primary format. + BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the data format. - + @@ -30137,15 +30135,15 @@ - Tabular format - Many textual formats used in bioinformatics are tabular (tab-separated values, TSV). Typically with an additional header in their own format. + fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. + - fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats. + Tabular format + Many textual formats used in bioinformatics are tabular (tab-separated values, TSV). Typically with an additional header in their own format. - @@ -30280,7 +30278,7 @@ - + @@ -30292,7 +30290,7 @@ - + BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more). @@ -32256,70 +32254,70 @@ + However, one may think that an operation is not a process. + + + + + However, operation is not a GFO 'Concept' present only in someone's mind. - BFO 'function' is narrower in the sense that it is a 'realizable_entity' (snap:RealizableEntity) and a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it does not need to have input(s) and output(s). + Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. + Process - - However, one may think that an operation is not a process. + BFO 'function' is narrower in the sense that it is a 'realizable_entity' (snap:RealizableEntity) and a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it does not need to have input(s) and output(s). - + - Function - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. - - - - - GFO 'Perpetuant' is in general broader than operation, but it may be seen narrower in the sense of being a concrete individual and exhibiting presentials. + Function, including an operation, can have a role of a quality/property in semantic annotation of e.g. a computational tool. - + - Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. - Process + However, one may think that an operation is not a process and not a physical entity. + - Function, including an operation, can have a role of a quality/property in semantic annotation of e.g. a computational tool. + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. In addition, one may think of 'biotop:Disposition' (parent of 'biotop:Function') being also a 'biotop:Quality'. - - + + - Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. + Method may in addition focus on how to achieve the result, not just on what to achieve as with operation. + - - Function, including an operation, can be a quality/property of e.g. a computational tool. + Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. - + - Computational tool provides one or more operations. Computational tool + Computational tool provides one or more operations. - However, one may think that an operation is not a process and not a physical entity. + Function + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. - - + Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. @@ -32328,22 +32326,22 @@ - Method may in addition focus on how to achieve the result, not just on what to achieve as with operation. + GFO 'Perpetuant' is in general broader than operation, but it may be seen narrower in the sense of being a concrete individual and exhibiting presentials. - + Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs. - + - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. In addition, one may think of 'biotop:Disposition' (parent of 'biotop:Function') being also a 'biotop:Quality'. + Function, including an operation, can be a quality/property of e.g. a computational tool. - - + + @@ -32351,22 +32349,25 @@ - Search and retrieval + Query and retrieval - - + + - - + + + Search Database retrieval Search or query a data resource and retrieve entries and / or annotation. + Retrieval + Query beta12orEarlier @@ -32394,7 +32395,7 @@ Annotation - + @@ -32420,8 +32421,8 @@ - Data indexing - + Indexing + @@ -32431,6 +32432,7 @@ Database indexing Generate an index of (typically a file of) biological data. beta12orEarlier + Data indexing @@ -32442,25 +32444,14 @@ Data index analysis - - - - - - - - - - - - - + beta12orEarlier Analyse an index of biological data. Database index analysis - - - + + 1.6 + true + @@ -32484,7 +32475,8 @@ Sequence generation - + + Generate a molecular sequence by some means. beta12orEarlier @@ -32498,7 +32490,7 @@ Sequence editing - + beta12orEarlier Edit or change a molecular sequence, either randomly or specifically. @@ -32529,6 +32521,7 @@ Sequence conversion + beta12orEarlier Convert a molecular sequence from one type to another. @@ -32571,14 +32564,14 @@ - - + + - - + + beta12orEarlier @@ -32595,16 +32588,17 @@ Sequence composition calculation + - - + + - - + + Calculate character or word composition or frequency of a molecular sequence. @@ -32642,7 +32636,12 @@ Sequence motif discovery - + + + + + + @@ -32665,17 +32664,16 @@ Sequence motif recognition - - - + + - - + + Sequence motif detection @@ -32694,10 +32692,15 @@ Sequence motif comparison - + + + + + + @@ -32731,8 +32734,8 @@ Conserved transcription regulatory sequence identification - + @@ -32798,7 +32801,8 @@ Protein structural motif recognition - + + @@ -32826,17 +32830,18 @@ Protein domain recognition - + + - - + + - - + + Identify structural domains in a protein structure from first principles (for example calculations on structural compactness). @@ -32922,6 +32927,7 @@ Protein property calculation + @@ -32930,14 +32936,14 @@ - - + + - - + + Protein property rendering @@ -32959,14 +32965,14 @@ - - + + - - + + Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins. @@ -32982,7 +32988,7 @@ - Feature prediction + Sequence feature detection @@ -32999,8 +33005,9 @@ SO:0000110 beta12orEarlier + Sequence feature recognition Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions. - Sequence feature detection + Sequence feature prediction @@ -33027,30 +33034,13 @@ Feature table query - - - - - - - - - - - - - - - - - - - + Query the features (in a feature table) of molecular sequence(s). beta12orEarlier - - - + + 1.6 + true + @@ -33058,9 +33048,9 @@ - Feature comparison + Sequence feature comparison + - @@ -33069,13 +33059,19 @@ + + + + + + Feature table comparison + Feature comparison Compare the feature tables of two or more molecular sequences. - Sequence feature comparison beta12orEarlier @@ -33103,8 +33099,13 @@ Sequence alignment analysis - - + + + + + + + @@ -33113,8 +33114,8 @@ - - + + beta12orEarlier @@ -33147,6 +33148,7 @@ Sequence alignment conversion + Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence). beta12orEarlier @@ -33176,6 +33178,7 @@ Nucleic acid property calculation + @@ -33252,25 +33255,25 @@ Protein secondary structure prediction - - + + - - + + - - + + - + beta12orEarlier @@ -33333,14 +33336,14 @@ - - + + - - + + Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods). @@ -33358,17 +33361,17 @@ Structure prediction - + - - + + - - + + beta12orEarlier @@ -33432,8 +33435,8 @@ Protein-protein interaction prediction (from protein sequence) + - Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences. beta12orEarlier @@ -33447,8 +33450,9 @@ Protein-protein interaction prediction (from protein structure) + - + Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures. beta12orEarlier @@ -33462,7 +33466,6 @@ Protein interaction network analysis - @@ -33473,6 +33476,12 @@ + + + + + + @@ -33511,23 +33520,24 @@ RNA secondary structure prediction + - - + + - - + + - Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). beta12orEarlier Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc). + Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). @@ -33538,19 +33548,20 @@ - Nucleic acid folding analysis + Nucleic acid folding prediction - + + - - + + - - + + Nucleic acid folding @@ -33601,6 +33612,7 @@ Genetic mapping + @@ -33608,6 +33620,7 @@ Functional mapping + Genetic map construction Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances. Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers. Genetic map generation @@ -33653,12 +33666,14 @@ Codon usage table generation + + Codon usage table construction beta12orEarlier Calculate codon usage statistics and create a codon usage table. @@ -33687,7 +33702,7 @@ Codon usage analysis - + @@ -33696,14 +33711,14 @@ - - + + - + @@ -33714,8 +33729,8 @@ - - + + synon: Codon usage table analysis @@ -33734,16 +33749,17 @@ Base position variability plotting + - - + + - - + + beta12orEarlier @@ -33774,6 +33790,7 @@ Sequence distance matrix generation + @@ -33787,6 +33804,7 @@ Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences. + Sequence distance matrix construction beta12orEarlier Phylogenetic distance matrix generation @@ -33800,19 +33818,13 @@ Sequence redundancy removal - + - - - - - - Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria. beta12orEarlier @@ -33827,8 +33839,14 @@ Sequence clustering - - + + + + + + + + @@ -33838,6 +33856,7 @@ Sequence cluster generation Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences. beta12orEarlier + Sequence cluster construction The clusters may be output or used internally for some other purpose. @@ -33849,27 +33868,33 @@ - Sequence alignment construction + Sequence alignment generation + - + + + + + + - - + + Sequence alignment computation Sequence alignment - Sequence alignment generation Align (identify equivalent sites within) molecular sequences. beta12orEarlier + Sequence alignment construction @@ -33882,6 +33907,7 @@ Hybrid sequence alignment construction + Hybrid sequence alignment generation Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA). beta12orEarlier beta13 @@ -33896,7 +33922,7 @@ - Structure-based sequence alignment construction + Structure-based sequence alignment @@ -33905,8 +33931,12 @@ Align molecular sequences using sequence and structural information. - beta12orEarlier + Structure-based sequence alignment generation Structure-based sequence alignment + Sequence alignment (structure-based) + beta12orEarlier + Structure-based sequence alignment construction + Sequence alignment generation (structure-based) @@ -33917,10 +33947,10 @@ - Structure alignment construction + Structure alignment generation + - @@ -33928,8 +33958,11 @@ Structure alignment - Align (superimpose) molecular tertiary structures. + Multiple structure alignment generation + Multiple structure alignment construction beta12orEarlier + Structure alignment construction + Align (superimpose) molecular tertiary structures. @@ -33941,8 +33974,14 @@ Sequence profile generation - - + + + + + + + + @@ -33955,8 +33994,9 @@ - Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment. beta12orEarlier + Sequence profile construction + Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment. @@ -33967,14 +34007,13 @@ - Structural (3D) profile generation - - - + 3D profile generation + + - - + + @@ -33985,11 +34024,12 @@ - - + + beta12orEarlier + Structural profile construction Generate some type of structural (3D) profile or template from a structure or structure alignment. Structural profile generation @@ -34002,9 +34042,8 @@ - Sequence profile alignment construction - - + Profile-to-profile alignment + @@ -34017,7 +34056,15 @@ + + + + + + Align sequence profiles (representing sequence alignments). + Sequence profile alignment generation + Sequence profile alignment construction See also 'Sequence alignment comparison'. beta12orEarlier Sequence profile alignment @@ -34031,13 +34078,13 @@ - Structural (3D) profile alignment construction - + 3D profile-to-3D profile alignment + - - + + @@ -34048,13 +34095,18 @@ - - + + - Structural (3D) profile alignment Align structural (3D) profiles or templates (representing structures or structure alignments). + Structural profile alignment construction + Structural profile alignment generation Structural profile alignment + Structural profile alignment construction (multiple) + Multiple 3D profile alignment construction + 3D profile alignment + 3D profile alignment (multiple) beta12orEarlier @@ -34066,10 +34118,14 @@ - Sequence-profile alignment construction - - - + Sequence-to-profile alignment + + + + + + + @@ -34078,14 +34134,16 @@ - - + + A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. Sequence-profile alignment Align molecular sequence(s) to sequence profile(s). beta12orEarlier + Sequence-profile alignment generation + Sequence-profile alignment construction @@ -34096,25 +34154,26 @@ - Sequence-3D profile alignment construction + Sequence-to-3D-profile alignment - - - + + - - + + Sequence-3D profile alignment Methods might perform one-to-one, one-to-many or many-to-many comparisons. + Sequence-3D profile alignment generation Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment). + Sequence-3D profile alignment construction beta12orEarlier @@ -34137,14 +34196,14 @@ - - + + - - + + Sequence-structure alignment @@ -34162,9 +34221,10 @@ Protein fold recognition - - + + + @@ -34192,7 +34252,7 @@ - Data retrieval (metadata and documentation) + Metadata retrieval @@ -34242,17 +34302,17 @@ Text mining - + - - + + - - + + @@ -34304,14 +34364,14 @@ - - + + - - + + Design or predict oligonucleotide primers for PCR and DNA amplification etc. @@ -34330,29 +34390,29 @@ Microarray probe design - + - + - - + + - - + + - + Microarray probe prediction @@ -34369,9 +34429,8 @@ Sequence assembly - - + @@ -34398,17 +34457,17 @@ Microarray data standardization and normalization - + - + - + @@ -34442,6 +34501,7 @@ Gene expression profile clustering + @@ -34460,18 +34520,21 @@ - Gene expression profile generation - + Gene expression profiling + + - Gene expression profiling + Gene expression profile generation beta12orEarlier - Expression profiling Generate a gene expression profile or pattern, for example from microarray data. + Functional profiling + Gene expression profile construction + Expression profiling @@ -34483,7 +34546,7 @@ Gene expression profile comparison - + @@ -34551,11 +34614,16 @@ Protein secondary structure assignment - + + + + + + @@ -34578,11 +34646,12 @@ Protein structure assignment - + + - - + + @@ -34591,6 +34660,12 @@ + + + + + + Assign a protein tertiary structure (3D coordinates) from raw experimental data. beta12orEarlier @@ -34603,31 +34678,31 @@ - Protein model evaluation + Protein model validation - + - + - + - + @@ -34651,12 +34726,11 @@ Protein model refinement - The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc. + Refine (after evaluation) a model of protein structure to reduce steric clashes, volume irregularities etc. beta12orEarlier WHATIF: CorrectedPDBasXML - Refine (after evlauation) a model of protein structure to reduce steric clashes, volume irregularities etc. @@ -34667,22 +34741,21 @@ - Phylogenetic tree construction + Phylogenetic tree generation - + - - + + - - + + - Phylogenetic tree generation beta12orEarlier Construct a phylogenetic tree. Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. @@ -34701,14 +34774,14 @@ - - + + - - + + Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions. @@ -34724,8 +34797,8 @@ Phylogenetic tree comparison - + For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc. Compare two or more phylogenetic trees. beta12orEarlier @@ -34744,13 +34817,13 @@ - + - + @@ -34818,6 +34891,7 @@ Protein SNP mapping + @@ -34872,6 +34946,7 @@ Immunogen design + beta12orEarlier beta12orEarlier @@ -34886,19 +34961,18 @@ - Zinc finger protein domain prediction and optimisation + Zinc finger prediction - - - + + - - + + beta12orEarlier @@ -34939,11 +35013,15 @@ - File format conversion + Formatting + File format conversion File reformatting + File formatting + Format conversion Reformat a file of data (or equivalent entity in memory). beta12orEarlier + Reformatting @@ -34954,10 +35032,11 @@ - File validation + Format validation beta12orEarlier + File format validation Test and validate the format and content of a data file. @@ -34969,28 +35048,28 @@ - Plotting and rendering + Visualisation - - + + - - + + - - + + + Rendering Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures. - Visualisation beta12orEarlier @@ -35032,17 +35111,16 @@ Structure database search - - - + + - - + + Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data. @@ -35059,17 +35137,17 @@ Protein secondary database search - + - - + + - - + + Sequence profile database search @@ -35090,7 +35168,6 @@ Motif database search - @@ -35140,12 +35217,13 @@ Sequence retrieval (by code) - + beta12orEarlier Query a database and retrieve sequences with a given entry code or accession number. - - - + + 1.6 + true + @@ -35154,12 +35232,13 @@ Sequence retrieval (by keyword) - + beta12orEarlier Query a database and retrieve sequences containing a given keyword. - - - + + 1.6 + true + @@ -35169,8 +35248,6 @@ Sequence database search (by sequence) - - Search a sequence database and retrieve sequences that are similar to a query sequence. beta12orEarlier Sequence similarity search @@ -35206,24 +35283,13 @@ Sequence database search (by amino acid composition) - - - - - - - - - - - - - + beta12orEarlier Search a sequence database and retrieve sequences of a given amino acid composition. - - - + + 1.6 + true + @@ -35231,10 +35297,10 @@ - Sequence database search (by physicochemical property) + Sequence database search (by property) beta12orEarlier - Search a sequence database and retrieve sequences with a specified physicochemical property. + Search a sequence database and retrieve sequences with a specified property, typically a physicochemical or compositional property. @@ -35246,15 +35312,15 @@ Sequence database search (by sequence using word-based methods) - - + Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method. Sequence similarity search (word-based methods) Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps. beta12orEarlier - - - + + 1.6 + true + @@ -35263,15 +35329,15 @@ Sequence database search (by sequence using profile-based methods) - - + This includes tools based on PSI-BLAST. beta12orEarlier Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query. Sequence similarity search (profile-based methods) - - - + + 1.6 + true + @@ -35280,21 +35346,15 @@ Sequence database search (by sequence using local alignment-based methods) - - - - - - - - + This includes tools based on the Smith-Waterman algorithm or FASTA. Sequence similarity search (local alignment-based methods) beta12orEarlier Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method. - - - + + 1.6 + true + @@ -35303,21 +35363,15 @@ Sequence database search (by sequence using global alignment-based methods) - - - - - - - - + beta12orEarlier Sequence similarity search (global alignment-based methods) Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method. This includes tools based on the Needleman and Wunsch algorithm. - - - + + 1.6 + true + @@ -35326,20 +35380,15 @@ Sequence database search (by sequence for primer sequences) - - - - - - - + Sequence similarity search (primer sequences) STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences. beta12orEarlier - - - + + 1.6 + true + @@ -35348,32 +35397,15 @@ Sequence database search (by molecular weight) - - - - - - - - - - - - - - - - - - - - beta12orEarlier + Peptide mass fingerprinting - 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. + beta12orEarlier Protein fingerprinting - - - + Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry. + + 1.6 + true + @@ -35382,18 +35414,13 @@ Sequence database search (by isoelectric point) - - - - - - - + Search sequence(s) or a sequence database for sequences of a given isoelectric point. beta12orEarlier - - - + + 1.6 + true + @@ -35402,12 +35429,13 @@ Structure retrieval (by code) - + beta12orEarlier Query a tertiary structure database and retrieve entries with a given entry code or accession number. - - - + + 1.6 + true + @@ -35416,12 +35444,13 @@ Structure retrieval (by keyword) - + beta12orEarlier Query a tertiary structure database and retrieve entries containing a given keyword. - - - + + 1.6 + true + @@ -35432,7 +35461,6 @@ Structure database search (by sequence) - Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence. Structure retrieval by sequence beta12orEarlier @@ -35541,14 +35569,14 @@ - - + + - - + + Generate digest fragments for a nucleotide sequence containing restriction sites. @@ -36031,21 +36059,21 @@ - Ramachandran plot evaluation + Ramachandran plot validation - - + + - - + + - Analyse (typically to validate) a Ramachandran plot of a protein structure. + Validate a Ramachandran plot of a protein structure. beta12orEarlier @@ -36145,6 +36173,7 @@ Protein titration curve plotting + @@ -36239,6 +36268,7 @@ Protein hydrophobic moment plotting + @@ -36361,15 +36391,15 @@ Protein feature prediction (from sequence) - - + Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure. Sequence feature detection (protein) beta12orEarlier Methods typically involve scanning for known motifs, patterns and regular expressions. - - - + + 1.6 + true + @@ -36377,23 +36407,23 @@ - Nucleic acid feature prediction - - + Nucleic acid feature detection - - + + - - + + + Nucleic acid feature prediction + Nucleic acid feature recognition beta12orEarlier Methods typically involve scanning for known motifs, patterns and regular expressions. Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions. @@ -36413,14 +36443,14 @@ - - + + - - + + Epitope mapping is commonly done during vaccine design. @@ -36468,14 +36498,14 @@ - - + + - - + + Detect or predict signal peptides and signal peptide cleavage sites in protein sequences. @@ -36491,12 +36521,13 @@ - Binding site prediction (from sequence) + Protein binding site detection beta12orEarlier Ligand-binding and active site prediction (from sequence) Predict catalytic residues, active sites or other ligand-binding sites in protein sequences. + Binding site prediction (from sequence) @@ -36552,14 +36583,14 @@ - - + + - - + + Detect or predict cleavage sites (enzymatic or chemical) in protein sequences. @@ -36632,7 +36663,7 @@ Transposon prediction - + @@ -36652,7 +36683,7 @@ PolyA signal detection - + @@ -36672,7 +36703,7 @@ Quadruplex formation site detection - + @@ -36700,7 +36731,7 @@ CpG island and isochore detection - + @@ -36729,7 +36760,7 @@ Restriction site recognition - + @@ -36761,7 +36792,7 @@ Nucleosome formation or exclusion sequence prediction - + @@ -36781,17 +36812,17 @@ Splice site prediction - + - - + + - - + + Methods might require a pre-mRNA or genomic DNA sequence. @@ -37058,11 +37089,12 @@ - Sequence alignment quality evaluation + Sequence alignment validation beta12orEarlier Evaluate molecular sequence alignment accuracy. + Sequence alignment quality evaluation Evaluation might be purely sequence-based or use structural information. @@ -37105,8 +37137,9 @@ - Sequence alignment analysis (chimeric sequence detection) + Chimeric sequence detection + Sequence alignment analysis (chimeric sequence detection) Detects chimeric sequences (chimeras) from a sequence alignment. A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles. beta12orEarlier @@ -37120,11 +37153,12 @@ - Sequence alignment analysis (recombination detection) + Recombination detection Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment. beta12orEarlier + Sequence alignment analysis (recombination detection) @@ -37135,10 +37169,11 @@ - Sequence alignment analysis (indel detection) + Indel detection Identify insertion, deletion and duplication events from a sequence alignment. Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. + Sequence alignment analysis (indel detection) beta12orEarlier @@ -37187,6 +37222,7 @@ Nucleic acid melting profile plotting + @@ -37464,14 +37500,14 @@ - - + + - - + + G protein-coupled receptor (GPCR) analysis @@ -37489,13 +37525,13 @@ Protein structure prediction - + - - + + @@ -37506,8 +37542,8 @@ - - + + Predict tertiary structure (backbone and side-chain conformation) of protein sequences. @@ -37525,18 +37561,17 @@ Nucleic acid structure prediction - - - + + - - + + Methods might identify thermodynamically stable or evolutionarily conserved structures. @@ -37604,20 +37639,20 @@ - - + + - - + + - + This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on. @@ -37706,7 +37741,6 @@ Structured RNA prediction and optimisation - @@ -37735,9 +37769,9 @@ SNP detection - - + + @@ -37808,6 +37842,7 @@ beta12orEarlier Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. Haplotype inference + Haplotype map generation @@ -37863,6 +37898,7 @@ Dotplot plotting + @@ -37881,8 +37917,8 @@ - Pairwise sequence alignment construction - + Pairwise sequence alignment + @@ -37890,9 +37926,11 @@ beta12orEarlier - Align exactly two molecular sequences. + Pairwise sequence alignment construction Methods might perform one-to-one, one-to-many or many-to-many comparisons. Pairwise sequence alignment + Align exactly two molecular sequences. + Pairwise sequence alignment generation @@ -37903,12 +37941,14 @@ - Multiple sequence alignment construction + Multiple sequence alignment + Multiple sequence alignment generation beta12orEarlier Multiple sequence alignment This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment. Align two or more molecular sequences. + Multiple sequence alignment construction @@ -37919,16 +37959,19 @@ - Pairwise sequence alignment construction (local) - + Pairwise sequence alignment generation (local) + + Pairwise sequence alignment construction (local) Local alignment methods identify regions of local similarity. Local pairwise sequence alignment construction beta12orEarlier Pairwise sequence alignment (local) Locally align exactly two molecular sequences. - - - + + + 1.6 + true + @@ -37936,16 +37979,19 @@ - Pairwise sequence alignment construction (global) - + Pairwise sequence alignment generation (global) + beta12orEarlier Global alignment methods identify similarity across the entire length of the sequences. Globally align exactly two molecular sequences. Pairwise sequence alignment (global) + Pairwise sequence alignment construction (global) Global pairwise sequence alignment construction - - - + + + 1.6 + true + @@ -37953,9 +37999,12 @@ - Multiple sequence alignment construction (local) - + Local sequence alignment + Locally align two or more molecular sequences. + Sequence alignment (local) + Sequence alignment generation (local) + Multiple sequence alignment construction (local) Local alignment methods identify regions of local similarity. beta12orEarlier Local multiple sequence alignment construction @@ -37970,13 +38019,16 @@ - Multiple sequence alignment construction (global) - - beta12orEarlier + Global sequence alignment + Global alignment methods identify similarity across the entire length of the sequences. + Sequence alignment generation (global) + Globally align two or more molecular sequences. + Multiple sequence alignment construction (global) + Sequence alignment (global) + beta12orEarlier Multiple sequence alignment (global) Global multiple sequence alignment construction - Globally align two or more molecular sequences. @@ -37987,12 +38039,15 @@ - Multiple sequence alignment construction (constrained) - + Constrained sequence alignment + Constrained multiple sequence alignment construction Multiple sequence alignment (constrained) + Multiple sequence alignment construction (constrained) + Sequence alignment generation (constrained) Align two or more molecular sequences with user-defined constraints. beta12orEarlier + Sequence alignment (constrained) @@ -38003,12 +38058,15 @@ - Multiple sequence alignment construction (consensus) - - Multiple sequence alignment (consensus) + Consensus-based sequence alignment + Align two or more molecular sequences using multiple methods to achieve higher quality. - beta12orEarlier + Sequence alignment generation (consensus) Consensus multiple sequence alignment construction + Multiple sequence alignment (consensus) + Multiple sequence alignment construction (consensus) + beta12orEarlier + Sequence alignment (consensus) @@ -38019,19 +38077,22 @@ - Multiple sequence alignment construction (phylogenetic tree-based) - + Tree-based sequence alignment + + Multiple sequence alignment (phylogenetic tree-based) + Multiple sequence alignment construction (phylogenetic tree-based) + Sequence alignment (phylogenetic tree-based) + Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree. Phylogenetic tree-based multiple sequence alignment construction beta12orEarlier This is supposed to give a more biologically meaningful alignment than standard alignments. - Multiple sequence alignment (phylogenetic tree-based) - Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree. + Sequence alignment generation (phylogenetic tree-based) @@ -38042,28 +38103,16 @@ - Secondary structure alignment construction - - - - - - - - - - - - - - - + Secondary structure alignment generation + Align molecular secondary structure (represented as a 1D string). - beta12orEarlier Secondary structure alignment - - - + Secondary structure alignment construction + beta12orEarlier + + 1.6 + true + @@ -38071,19 +38120,26 @@ - Protein secondary structure alignment construction - + Protein secondary structure alignment generation + + + + + + + - Protein secondary structure alignment Secondary structure alignment (protein) - beta12orEarlier Align protein secondary structures. + Protein secondary structure alignment + beta12orEarlier + Protein secondary structure alignment construction @@ -38094,13 +38150,13 @@ - RNA secondary structure alignment construction - + RNA secondary structure alignment + - - + + @@ -38109,10 +38165,18 @@ + + + + + + beta12orEarlier Secondary structure alignment (RNA) + RNA secondary structure alignment construction Align RNA secondary structures. RNA secondary structure alignment + RNA secondary structure alignment generation @@ -38123,9 +38187,10 @@ - Pairwise structure alignment construction + Pairwise structure alignment generation Align (superimpose) exactly two molecular tertiary structures. + Pairwise structure alignment construction Pairwise structure alignment beta12orEarlier @@ -38139,14 +38204,15 @@ Multiple structure alignment construction - + beta12orEarlier Multiple structure alignment This includes methods that use an existing alignment. Align (superimpose) two or more molecular tertiary structures. - - - + + 1.6 + true + @@ -38184,16 +38250,19 @@ - Pairwise structure alignment construction (local) - + Pairwise structure alignment generation (local) + + Pairwise structure alignment construction (local) Local alignment methods identify regions of local similarity, common substructures etc. Pairwise structure alignment (local) beta12orEarlier Local pairwise structure alignment construction Locally align (superimpose) exactly two molecular tertiary structures. - - - + + + 1.6 + true + @@ -38201,16 +38270,19 @@ - Pairwise structure alignment construction (global) - + Pairwise structure alignment generation (global) + beta12orEarlier Pairwise structure alignment (global) Global alignment methods identify similarity across the entire structures. Globally align (superimpose) exactly two molecular tertiary structures. Global pairwise structure alignment construction - - - + Pairwise structure alignment construction (global) + + + 1.6 + true + @@ -38218,12 +38290,15 @@ - Multiple structure alignment construction (local) - - beta12orEarlier + Local structure alignment + + Structure alignment generation (local) + Multiple structure alignment construction (local) Multiple structure alignment (local) - Local alignment methods identify regions of local similarity, common substructures etc. Locally align (superimpose) two or more molecular tertiary structures. + beta12orEarlier + Structure alignment construction (local) + Local alignment methods identify regions of local similarity, common substructures etc. Local multiple structure alignment construction @@ -38235,13 +38310,16 @@ - Multiple structure alignment construction (global) - - beta12orEarlier - Global multiple structure alignment construction + Global structure alignment + Globally align (superimpose) two or more molecular tertiary structures. - Multiple structure alignment (global) + Global multiple structure alignment construction Global alignment methods identify similarity across the entire structures. + beta12orEarlier + Multiple structure alignment construction (global) + Structure alignment generation (global) + Multiple structure alignment (global) + Structure alignment construction (global) @@ -38252,13 +38330,16 @@ - Sequence profile alignment construction (pairwise) + Profile-to-profile alignment (pairwise) + Sequence profile alignment generation (pairwise) Align exactly two molecular profiles. - Pairwise sequence profile alignment construction beta12orEarlier Sequence profile alignment (pairwise) + Sequence profile alignment construction (pairwise) + Pairwise sequence profile alignment construction Methods might perform one-to-one, one-to-many or many-to-many comparisons. + Sequence alignment generation (pairwise profile) @@ -38269,15 +38350,18 @@ - Sequence profile alignment construction (multiple) - + Sequence alignment generation (multiple profile) + Sequence profile alignment (multiple) + Sequence profile alignment construction (multiple) Multiple sequence profile alignment construction + Sequence profile alignment generation (multiple) beta12orEarlier Align two or more molecular profiles. - - - + + 1.6 + true + @@ -38285,13 +38369,15 @@ - Structural (3D) profile alignment construction (pairwise) + 3D profile-to-3D profile alignment (pairwise) beta12orEarlier - Align exactly two molecular Structural (3D) profiles. + Structural profile alignment construction (pairwise) Structural (3D) profile alignment (pairwise) - Pairwise structural (3D) profile alignment construction Methods might perform one-to-one, one-to-many or many-to-many comparisons. + Structural profile alignment generation (pairwise) + Align exactly two molecular Structural (3D) profiles. + Pairwise structural (3D) profile alignment construction @@ -38302,15 +38388,17 @@ - Structural (3D) profile alignment construction (multiple) - + Structural profile alignment generation (multiple) + Structural (3D) profile alignment (multiple) beta12orEarlier Multiple structural (3D) profile alignment construction Align two or more molecular 3D profiles. - - - + Structural profile alignment construction (multiple) + + 1.6 + true + @@ -38319,20 +38407,15 @@ Data retrieval (tool metadata) - - - - - - - + Tool information retrieval beta12orEarlier Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function. Data retrieval (tool annotation) - - - + + 1.6 + true + @@ -38341,20 +38424,15 @@ Data retrieval (database metadata) - - - - - - - + Database information retrieval Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword. Data retrieval (database annotation) beta12orEarlier - - - + + 1.6 + true + @@ -38467,8 +38545,8 @@ Sequence assembly (mapping assembly) The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. - Sequence assembly by combining fragments using an existing backbone sequence. beta12orEarlier + Sequence assembly by combining fragments using an existing backbone sequence, typically a reference genome. @@ -38483,7 +38561,7 @@ beta12orEarlier De-novo assemblers are much slower and more memory intensive than mapping assemblers. - Sequence assembly by combining fragments into a new, previously unknown sequence. + Sequence assembly by combining fragments without the aid of a reference sequence or genome. @@ -38596,6 +38674,7 @@ Heat map generation + @@ -38603,6 +38682,7 @@ Generate a heat map of gene expression from microarray data. + Heat map construction The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions. beta12orEarlier @@ -38616,19 +38696,14 @@ Gene expression profile analysis - - - - - - - + Analyse one or more gene expression profiles, typically to interpret them in functional terms. beta12orEarlier Functional profiling - - - + + 1.6 + true + @@ -38637,7 +38712,8 @@ Gene expression profile pathway mapping - + + @@ -38659,7 +38735,7 @@ Protein secondary structure assignment (from coordinate data) - + Assign secondary structure from protein coordinate data. beta12orEarlier @@ -38732,10 +38808,11 @@ - Phylogenetic tree construction (data centric) + Phylogenetic tree generation (data centric) Construct a phylogenetic tree from a specific type of data. beta12orEarlier + Phylogenetic tree construction (data centric) @@ -38746,10 +38823,11 @@ - Phylogenetic tree construction (method centric) + Phylogenetic tree generation (method centric) beta12orEarlier Construct a phylogenetic tree using a specific method. + Phylogenetic tree construction (method centric) @@ -38764,6 +38842,7 @@ Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. + Phylogenetic tree generation (from molecular sequences) beta12orEarlier Phylogenetic tree construction from molecular sequences. @@ -38786,6 +38865,7 @@ Phylogenetic tree construction from continuous quantitative character data. beta12orEarlier + Phylogenetic tree generation (from continuous quantitative characters) @@ -38810,6 +38890,7 @@ + Phylogenetic tree generation (from gene frequencies) beta12orEarlier Phylogenetic tree construction from gene frequency data. @@ -38831,6 +38912,7 @@ beta12orEarlier + Phylogenetic tree generation (from polymorphism data) Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data. @@ -38845,6 +38927,7 @@ Phylogenetic species tree construction beta12orEarlier + Phylogenetic species tree generation Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison. @@ -38856,11 +38939,12 @@ - Phylogenetic tree construction (parsimony methods) + Phylogenetic tree generation (parsimony methods) beta12orEarlier This includes evolutionary parsimony (invariants) methods. Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment. + Phylogenetic tree construction (parsimony methods) @@ -38871,9 +38955,10 @@ - Phylogenetic tree construction (minimum distance methods) + Phylogenetic tree generation (minimum distance methods) Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances. + Phylogenetic tree construction (minimum distance methods) beta12orEarlier This includes neighbor joining (NJ) clustering method. @@ -38886,11 +38971,12 @@ - Phylogenetic tree construction (maximum likelihood and Bayesian methods) + Phylogenetic tree generation (maximum likelihood and Bayesian methods) beta12orEarlier Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm. Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution. + Phylogenetic tree construction (maximum likelihood and Bayesian methods) @@ -38901,9 +38987,10 @@ - Phylogenetic tree construction (quartet methods) + Phylogenetic tree generation (quartet methods) Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely. + Phylogenetic tree construction (quartet methods) beta12orEarlier @@ -38915,9 +39002,10 @@ - Phylogenetic tree construction (AI methods) + Phylogenetic tree generation (AI methods) beta12orEarlier + Phylogenetic tree construction (AI methods) Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms. @@ -38929,7 +39017,7 @@ - Sequence alignment analysis (phylogenetic modelling) + DNA substitution modelling @@ -38946,6 +39034,7 @@ Identify a plausible model of DNA substitution that explains a DNA sequence alignment. beta12orEarlier + Sequence alignment analysis (phylogenetic modelling) @@ -39027,9 +39116,10 @@ - Phylogenetic tree construction (consensus) + Phylogenetic tree generation (consensus) + Phylogenetic tree construction (consensus) beta12orEarlier Methods typically test for topological similarity between trees using for example a congruence index. Compare two or more phylogenetic trees to produce a consensus tree. @@ -39079,7 +39169,6 @@ Phylogenetic tree annotation - Annotate a phylogenetic tree with terms from a controlled vocabulary. beta12orEarlier @@ -39093,9 +39182,8 @@ - Peptide immunogen prediction and optimisation + Immunogenicity prediction - @@ -39104,17 +39192,18 @@ - - + + - - + + Predict and optimise peptide ligands that elicit an immunological response. + Peptide immunogen prediction beta12orEarlier @@ -39126,8 +39215,8 @@ - DNA vaccine prediction and optimisation - + DNA vaccine design + @@ -39153,18 +39242,17 @@ - Sequence reformatting + Sequence formatting - - + - + @@ -39181,9 +39269,8 @@ - Sequence alignment reformatting + Sequence alignment formatting - @@ -39208,7 +39295,7 @@ - Codon usage table reformatting + Codon usage table formatting @@ -39237,17 +39324,17 @@ Sequence rendering - + - - + + - - + + Visualise, format or render a molecular sequence, possibly with sequence features or properties shown. @@ -39264,7 +39351,13 @@ Sequence alignment rendering - + + + + + + + @@ -39291,7 +39384,12 @@ Sequence cluster rendering - + + + + + + @@ -39320,7 +39418,7 @@ beta12orEarlier - Visualise or plot a phylogenetic tree. + Render or visualise a phylogenetic tree. @@ -39354,13 +39452,18 @@ Protein secondary structure rendering - + + + + + + beta12orEarlier Render and visualise protein secondary structure. @@ -39375,17 +39478,17 @@ Structure rendering - + - - + + - - + + beta12orEarlier @@ -39402,7 +39505,8 @@ Microarray data rendering - + + @@ -39422,7 +39526,6 @@ Protein interaction network rendering - @@ -39430,6 +39533,12 @@ + + + + + + Identify and analyse networks of protein interactions. beta12orEarlier @@ -39443,8 +39552,7 @@ Map rendering - - + @@ -39638,24 +39746,13 @@ Sequence submission - - - - - - - - - - - - - + beta12orEarlier Submit a molecular sequence to a database. - - - + + 1.6 + true + @@ -39664,7 +39761,6 @@ Gene regulatory network analysis - @@ -39672,8 +39768,15 @@ + + + + + + Analyse a known network of gene regulation. beta12orEarlier + @@ -39684,7 +39787,7 @@ - Data loading + Loading @@ -39694,9 +39797,8 @@ beta12orEarlier Prepare or load a user-specified data file so that it is available for use. - Data submission - Database submission WHATIF:UploadPDB + Data loading @@ -39708,21 +39810,15 @@ Sequence retrieval - - - - - - - - + beta12orEarlier Query a sequence data resource (typically a database) and retrieve sequences and / or annotation. Data retrieval (sequences) This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. - - - + + 1.6 + true + @@ -39731,22 +39827,16 @@ Structure retrieval - - - - - - - - + Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation. - WHATIF:EchoPDB This includes direct retrieval methods but not those that perform calculations on the sequence or structure. WHATIF:DownloadPDB beta12orEarlier - - - + WHATIF:EchoPDB + + 1.6 + true + @@ -40244,9 +40334,8 @@ - Structure reformatting + Structure formatting - WHATIF: PDBasXML beta12orEarlier Reformat (a file or other report of) tertiary structure data. @@ -40297,13 +40386,14 @@ Structure retrieval (water) - + Query a tertiary structure database and retrieve water molecules. WHATIF:MovedWaterPDB beta12orEarlier - - - + + 1.6 + true + @@ -40347,12 +40437,13 @@ Listfile processing - + beta12orEarlier Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses). - - - + + 1.6 + true + @@ -40360,9 +40451,9 @@ - Sequence file processing - - + Sequence file editing + + beta12orEarlier Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, or create a file of sequences. @@ -40376,13 +40467,13 @@ Sequence alignment file processing - - + Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences. beta12orEarlier - - - + + 1.6 + true + @@ -40438,7 +40529,7 @@ Representative sequence identification - + @@ -40458,13 +40549,13 @@ Structure file processing - - + beta12orEarlier Perform basic (non-analytical) operations on a file of molecular tertiary structural data. - - - + + 1.6 + true + @@ -40489,12 +40580,12 @@ Statistical calculation - + beta12orEarlier Perform a statistical data operation of some type, e.g. calibration or validation. - - - + 1.6 + true + @@ -40505,6 +40596,7 @@ 3D-1D scoring matrix generation + @@ -40517,8 +40609,9 @@ - A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data. + A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. + 3D-1D scoring matrix construction beta12orEarlier @@ -40603,6 +40696,7 @@ Nucleic acid density plotting + Calculate a density plot (of base composition) for a nucleotide sequence. beta12orEarlier @@ -40616,23 +40710,23 @@ Sequence analysis - + - - + + - - + + - - + + Sequence analysis (general) @@ -40649,18 +40743,13 @@ Sequence motif processing - - - - - - - + beta12orEarlier Process (read and / or write) molecular sequence motifs. - - - + + 1.6 + true + @@ -40669,18 +40758,13 @@ Protein interaction data processing - - - - - - - + beta12orEarlier Process (read and / or write) protein interaction data. - - - + + 1.6 + true + @@ -40689,8 +40773,8 @@ Protein structure analysis - + @@ -40703,9 +40787,15 @@ - Analyse protein tertiary structural data. + + + + + + beta12orEarlier Structure analysis (protein) + Analyse protein tertiary structural data. @@ -40746,8 +40836,8 @@ - File processing - + Utility operaration + @@ -40755,10 +40845,11 @@ Data file processing + Basic (non-analytical) operations of some data, either a file or equivalent entity in memory. File handling Report handling + File processing beta12orEarlier - Process (read and / or write) a data file (or equivalent entity in memory). Processing is limited to basic (non-analytical) operations. @@ -40784,19 +40875,15 @@ - Structural (3D) profile processing - - - - - - - + Structural profile processing + + 3D profile processing Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type. beta12orEarlier - - - + + 1.6 + true + @@ -40805,13 +40892,14 @@ Data index processing - + beta12orEarlier Process (read and / or write) an index of (typically a file of) biological data. Database index processing - - - + + 1.6 + true + @@ -40820,18 +40908,13 @@ Sequence profile processing - - - - - - - + Process (read and / or write) some type of sequence profile. beta12orEarlier - - - + + 1.6 + true + @@ -40865,14 +40948,14 @@ - - + + - - + + beta12orEarlier @@ -40890,17 +40973,23 @@ Protein secondary structure analysis - + - - + + - - + + + + + + + + Secondary structure analysis (protein) @@ -40953,10 +41042,11 @@ - Analysis and processing + Operation (typed) beta12orEarlier Process (read and / or write) data of a specific type, for example applying analytical methods. + Processing Calculation Computation @@ -40971,7 +41061,6 @@ Database search - @@ -41012,9 +41101,12 @@ - Prediction, detection and recognition - + Prediction and recognition + + Detection Predict, recognise, detect or identify some properties of a biomolecule. + Prediction + Recognition beta12orEarlier @@ -41027,7 +41119,7 @@ Comparison - + Compare two or more things to identify similarities. beta12orEarlier @@ -41041,7 +41133,7 @@ Optimisation and refinement - + Refine or optimise some data model. beta12orEarlier @@ -41055,7 +41147,7 @@ Modelling and simulation - + @@ -41089,9 +41181,9 @@ - Evaluation and validation - - Validate or standardise some data. + Validation + + Validate some data. Validation and standardisation beta12orEarlier @@ -41104,8 +41196,8 @@ - Mapping and assembly - + Mapping + @@ -41132,13 +41224,13 @@ Design - + true - beta13 Design a biological entity (typically a molecular sequence or structure) with specific properties. beta12orEarlier - - + + + @@ -41191,12 +41283,13 @@ Gene expression profile processing - + beta12orEarlier Process (read and / or write) a gene expression profile. - - - + + 1.6 + true + @@ -41204,17 +41297,18 @@ - Gene expression profile annotation + Functional enrichment - + - Annotate a gene expression profile with concepts from an ontology of gene functions. + Gene expression profile annotation beta12orEarlier + Annotate a set of genes, e.g. an expression profile, with concepts from an ontology of gene functions. @@ -41226,8 +41320,14 @@ Gene regulatory network prediction - + + + + + + + @@ -41266,9 +41366,8 @@ - RNA secondary structure processing - - + RNA secondary structure analysis + @@ -41363,19 +41462,13 @@ Protein secondary structure processing - - - - - - - - + beta12orEarlier Process (read and / or write) protein secondary structure data. - - - + + 1.6 + true + @@ -41384,19 +41477,13 @@ Protein interaction network processing - - - - - - - - + Process (read and / or write) a network of protein interactions. beta12orEarlier - - - + + 1.6 + true + @@ -41405,13 +41492,14 @@ Sequence processing - + beta12orEarlier Process (read and / or write) one or more molecular sequences and associated annotation. Sequence processing (general) - - - + + 1.6 + true + @@ -41420,13 +41508,13 @@ Sequence processing (protein) - - + beta12orEarlier Process (read and / or write) a protein sequence and associated annotation. - - - + + 1.6 + true + @@ -41435,13 +41523,13 @@ Sequence processing (nucleic acid) - - + Process (read and / or write) a nucleotide sequence and associated annotation. beta12orEarlier - - - + + 1.6 + true + @@ -41454,8 +41542,8 @@ - - + + @@ -41466,8 +41554,8 @@ - - + + beta12orEarlier @@ -41483,18 +41571,13 @@ Sequence cluster processing - - - - - - - + beta12orEarlier Process (read and / or write) a sequence cluster. - - - + + 1.6 + true + @@ -41503,36 +41586,13 @@ Feature table processing - - - - - - - - - - - - - - - - - - - - - - - - - + beta12orEarlier Process (read and / or write) a sequence feature table. - - - + + 1.6 + true + @@ -41541,17 +41601,17 @@ Gene and gene component prediction - + - - + + - - + + Gene finding @@ -41612,19 +41672,13 @@ Structure processing (protein) - - - - - - - - + Process (read and / or write) a protein tertiary structure. beta12orEarlier - - - + + 1.6 + true + @@ -41676,18 +41730,13 @@ Sequence alignment processing - - - - - - - + Process (read and / or write) a molecular sequence alignment. beta12orEarlier - - - + + 1.6 + true + @@ -41722,12 +41771,13 @@ Structure processing - + beta12orEarlier Process (read and / or write) a molecular tertiary structure. - - - + + 1.6 + true + @@ -41736,25 +41786,13 @@ Map annotation - - - - - - - - - - - - - - + beta12orEarlier Annotate a DNA map of some type with terms from a controlled vocabulary. - - - + + 1.6 + true + @@ -41910,14 +41948,14 @@ - - + + - - + + @@ -41940,7 +41978,7 @@ Nucleic acid sequence analysis - + @@ -41950,6 +41988,12 @@ + + + + + + @@ -41968,7 +42012,7 @@ Protein sequence analysis - + @@ -41995,13 +42039,7 @@ Structure analysis - - - - - - - + @@ -42014,6 +42052,12 @@ + + + + + + Analyse known molecular tertiary structures. beta12orEarlier @@ -42028,7 +42072,13 @@ Nucleic acid structure analysis - + + + + + + + @@ -42054,18 +42104,13 @@ Secondary structure processing - - - - - - - + beta12orEarlier Process (read and / or write) a molecular secondary structure. - - - + + 1.6 + true + @@ -42135,19 +42180,19 @@ Protein structure comparison - + - - + + - - + + Compare protein tertiary structures. @@ -42189,8 +42234,8 @@ Protein subcellular localization prediction + - @@ -42241,7 +42286,7 @@ Protein interaction prediction - + @@ -42249,6 +42294,12 @@ + + + + + + beta12orEarlier Predict the interactions of proteins with other molecules. @@ -42276,7 +42327,7 @@ - Gene expression data processing + Gene expression data analysis @@ -42284,10 +42335,12 @@ - Process (read and / or write) gene expression (typically microarray) data. + Process (read and / or write) gene expression (typically microarray) data, including analysis of one or more gene expression profiles, typically to interpret them in functional terms. + Gene expression data processing Microarray data processing - Gene expression (microarray) data processing beta12orEarlier + Gene expression profile analysis + Gene expression (microarray) data processing @@ -42299,18 +42352,12 @@ Gene regulatory network processing - - - - - - - + Process (read and / or write) a network of gene regulation. beta12orEarlier - - - + 1.6 + true + @@ -42361,7 +42408,7 @@ - Splicing analysis + Splicing model analysis @@ -42377,9 +42424,9 @@ - Analyse (e.g. characterize and model) alternative splicing events from comparing multiple nucleic acid sequences. beta12orEarlier - Splicing modelling + Splicing analysis + Analyse, characterize and model alternative splicing events from comparing multiple nucleic acid sequences. @@ -42405,7 +42452,7 @@ - Nucleic acid data processing + Nucleic acid analysis @@ -42414,6 +42461,7 @@ beta12orEarlier + Nucleic acid data processing Process (read and / or write) nucleic acid sequence or structural data. @@ -42425,7 +42473,7 @@ - Protein data processing + Protein analysis @@ -42434,6 +42482,7 @@ Process (read and / or write) protein sequence or structural data. + Protein data processing beta12orEarlier @@ -42475,12 +42524,13 @@ Text processing - + Process (read and / or write) text. beta12orEarlier - - - + + 1.6 + true + @@ -42488,7 +42538,7 @@ - Sequence alignment analysis (protein) + Protein sequence alignment analysis @@ -42505,6 +42555,7 @@ beta12orEarlier + Sequence alignment analysis (protein) Analyse a protein sequence alignment, typically to detect features or make predictions. @@ -42516,23 +42567,24 @@ - Sequence alignment analysis (nucleic acid) + Nucleic acid sequence alignment analysis - - + + - - + + Analyse a protein sequence alignment, typically to detect features or make predictions. + Sequence alignment analysis (nucleic acid) beta12orEarlier @@ -42600,7 +42652,12 @@ Sequence editing (nucleic acid) - + + + + + + beta12orEarlier Edit or change a nucleic acid sequence, either randomly or specifically. @@ -42615,7 +42672,13 @@ Sequence editing (protein) - + + + + + + + beta12orEarlier Edit or change a protein sequence, either randomly or specifically. @@ -42630,7 +42693,6 @@ Sequence generation (nucleic acid) - @@ -42651,7 +42713,7 @@ Sequence generation (protein) - + @@ -42672,7 +42734,6 @@ Sequence rendering (nucleic acid) - @@ -42694,12 +42755,18 @@ Sequence rendering (protein) - - Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. + + + + + + + Protein sequence visualisation + beta12orEarlier + Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. Protein sequence rendering Visualise, format or render a protein sequence. - beta12orEarlier @@ -42728,19 +42795,13 @@ Structure processing (nucleic acid) - - - - - - - - + Process (read and / or write) nucleic acid tertiary structure data. beta12orEarlier - - - + + 1.6 + true + @@ -42750,7 +42811,6 @@ DNA mapping - @@ -42770,19 +42830,14 @@ Map data processing - - - - - - - + beta12orEarlier Process (read and / or write) a DNA map of some type. DNA map data processing - - - + + 1.6 + true + @@ -42794,14 +42849,14 @@ - - + + - - + + Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information). @@ -42821,19 +42876,19 @@ - + - - + + - - + + Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures. @@ -42871,14 +42926,15 @@ - Alignment construction - + Alignment generation + + Alignment construction beta12orEarlier Alignment Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits. @@ -42949,6 +43005,7 @@ Hopp and Woods plotting + Generate a Hopp and Woods plot of antigenicity of a protein. beta12orEarlier @@ -43135,14 +43192,14 @@ Analysis - + beta12orEarlier - true - beta12orEarlier For non-analytical operations, see the 'Processing' branch. Apply analytical methods to existing data of a specific type. - + + + @@ -43151,24 +43208,13 @@ Alignment analysis - - - - - - - - - - - - - + Analyse an existing alignment of two or more molecular sequences, structures or derived data. beta12orEarlier - - - + + 1.6 + true + @@ -43177,7 +43223,7 @@ Article analysis - + @@ -43196,6 +43242,7 @@ + Article analysis beta12orEarlier Analyse a body of scientific text (typically a full text article from a scientific journal.) @@ -43223,7 +43270,13 @@ Protein interaction analysis - + + + + + + + @@ -43257,12 +43310,14 @@ Alignment processing - + beta12orEarlier Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data. - - - + + + 1.6 + true + @@ -43271,18 +43326,13 @@ Structure alignment processing - - - - - - - + beta12orEarlier Process (read and / or write) a molecular tertiary (3D) structure alignment. - - - + + 1.6 + true + @@ -43312,6 +43362,7 @@ Codon usage bias plotting + @@ -43351,7 +43402,7 @@ Classification - + Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category. beta12orEarlier @@ -43436,7 +43487,7 @@ - Prediction, detection and recognition (protein) + Prediction and recognition (protein) Predict, recognise, detect or identify some properties of proteins. beta12orEarlier @@ -43450,7 +43501,7 @@ - Prediction, detection and recognition (nucleic acid) + Prediction and recognition (nucleic acid) Predict, recognise, detect or identify some properties of nucleic acids. beta12orEarlier @@ -43465,7 +43516,6 @@ Structure editing - @@ -43486,7 +43536,6 @@ Sequence alignment editing - beta13 Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically. @@ -43522,21 +43571,14 @@ Protein function prediction (from sequence) - - - - - - - - - + + For functional properties that are positional, use 'Protein site detection' instead. Predict general (non-positional) functional properties of a protein from analysing its sequence. - For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. beta13 - - - + + 1.6 + true + @@ -43545,11 +43587,15 @@ Protein site detection - - + + + beta13 - name: Sequence motif recognition (protein) + Sequence feature detection (protein) + Protein sequence feature detection + Protein site prediction Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions. + Protein site recognition @@ -43576,13 +43622,13 @@ Protein feature prediction (from structure) - - + Predict, recognise and identify positional features in proteins from analysing protein structure. beta13 - - - + + 1.6 + true + @@ -43590,14 +43636,13 @@ - Protein feature prediction - + Protein feature detection - + @@ -43609,9 +43654,12 @@ - + + Features includes functional sites or regions and secondary structure. Sequence-based methods typically involve scanning for known motifs, patterns and regular expressions. + Protein feature prediction + Protein feature recognition beta13 Predict, recognise and identify positional features in proteins from analysing protein sequences or structures. @@ -43624,13 +43672,15 @@ - Sequence screening - + Database search (by sequence) + beta13 Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries. - - - + Sequence screening + + 1.6 + true + @@ -43639,13 +43689,19 @@ Protein interaction network prediction - + + + + + + + Predict a network of protein interactions. beta13 @@ -43659,6 +43715,7 @@ Nucleic acid design + Design (or predict) nucleic acid sequences with specific chemical or physical properties. beta13 @@ -43673,7 +43730,7 @@ Editing - + Edit, convert or otherwise change a data entity, either randomly or specifically. beta13 @@ -43686,9 +43743,8 @@ - Sequence assembly evaluation - - + Sequence assembly validation + @@ -43698,18 +43754,18 @@ - - + + - - + + - 1.1 Evaluate a DNA sequence assembly, typically for purposes of quality control. + 1.1 @@ -43720,10 +43776,11 @@ - Genome alignment construction + Genome alignment Genome alignment 1.1 + Genome alignment construction Align two or more (tpyically huge) molecular sequences that represent genomes. @@ -43767,7 +43824,7 @@ Base-calling - + @@ -43937,17 +43994,18 @@ Genetic variation analysis + - Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model. Genetic variation annotation + 1.1 + Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model. Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript. Sequence variation analysis - 1.1 @@ -43970,6 +44028,7 @@ The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. Oligonucleotide alignment construction Short read mapping + Oligonucleotide alignment generation Oligonucleotide mapping Short oligonucleotide alignment @@ -43997,7 +44056,7 @@ DNA barcoding - + Sample barcoding 1.1 Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms. @@ -44057,7 +44116,7 @@ Methylation analysis - + Determine cytosine methylation states in nucleic acid sequences. 1.1 @@ -44071,6 +44130,7 @@ Methylation calling + Determine cytosine methylation status of specific positions in a nucleic acid sequences. 1.1 @@ -44200,10 +44260,11 @@ - Spectrum analysis - + Spectral analysis + Mass spectrum analysis Analyse a spectrum from a mass spectrometry (or other) experiment. + Spectrum analysis 1.1 Spectral analysis @@ -44238,11 +44299,17 @@ Scaffolding - - - + + + + + + + + Scaffold may be positioned along a chromosome physical map to create a "golden path". 1.1 + Scaffold generation Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps. Scaffold construction @@ -44256,9 +44323,7 @@ Scaffold gap completion - - - + 1.1 Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced. Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences. @@ -44275,9 +44340,9 @@ Sequencing quality control - Analyse raw sequence data from a sequencing pipeline and identify problems. 1.1 Sequencing QC + Analyse raw sequence data from a sequencing pipeline and identify problems. Raw sequence data quality control. @@ -44290,6 +44355,7 @@ Read pre-processing + 1.1 Pre-process sequence reads to ensure (or improve) quality and reliability. @@ -44326,7 +44392,7 @@ Peak calling - + 1.1 Protein binding peak detection Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data. @@ -44358,7 +44424,7 @@ Gene set testing - + Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc. Gene sets can be defined beforehand by biological function, chromosome locations and so on. 1.1 @@ -44403,12 +44469,12 @@ - Variant mapping + Variant calling - Variant calling Methods often utilise a database of aligned reads. Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence. 1.1 + Variant mapping @@ -44466,7 +44532,7 @@ Gene expression QTL analysis - + @@ -44520,19 +44586,17 @@ Transcriptome assembly - - - + - - + + - - + + 1.2 @@ -44548,13 +44612,14 @@ Transcriptome assembly (de novo) - + Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other. 1.2 de novo transcriptome assembly - - - + + 1.6 + true + @@ -44563,12 +44628,13 @@ Transcriptome assembly (mapping) - + 1.2 Infer a transcriptome sequence by mapping short reads to a reference genome. - - - + + 1.6 + true + @@ -44577,7 +44643,7 @@ Sequence coordinate conversion - + @@ -44603,7 +44669,7 @@ Document similarity calculation - + 1.3 Calculate similarity between 2 or more documents. @@ -44617,7 +44683,8 @@ Document clustering - + + 1.3 Cluster (group) documents on the basis of their calculated similarity. @@ -44631,9 +44698,13 @@ Named entity recognition - + + 1.3 Recognise named entities (text tokens) within documents. + Entity extraction + Entity chunking + Entity identification @@ -44645,7 +44716,8 @@ ID mapping - + + Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration. Accession mapping 1.3 @@ -44660,10 +44732,10 @@ - Data anonymisation + Anonymisation + Data anonymisation 1.3 - Data anonymization Process data in such a way that makes it hard to trace to the person which the data concerns. @@ -44701,8 +44773,8 @@ - Sequence checksum generation - + Checksum generation + @@ -44715,6 +44787,7 @@ + Sequence checksum generation 1.4 Generate a checksum of a molecular sequence. @@ -44727,10 +44800,11 @@ - Bibliography construction - + Bibliography generation + 1.4 Construct a bibliography from the scientific literature. + Bibliography construction @@ -44783,9 +44857,8 @@ - Semantic analysis - - Analyse set(s) of terms from a controlled vocabulary to make scientific inferences. + Ontology comparison + Compare two or more ontologies, e.g. identify differences. 1.4 @@ -44802,14 +44875,14 @@ - - + + - - + + Format inference @@ -44835,11 +44908,208 @@ - File splitting + Splitting 1.4 - split a file containing multiple data items into many files, each -containing one item + Split a file containing multiple data items into many files, each containing one item + File splitting + + + + + + + + + + + Generation + + Construct some data entity. + For non-analytical operations, see the 'Processing' branch. + beta12orEarlier + Construction + + + + + + + + + + + Nucleic acid site detection + + + + 1.6 + Nucleic acid site recognition + Predict, recognise and identify functional or other key sites within nucleic acid sequences, typically by scanning for known motifs, patterns and regular expressions. + Nucleic acid site prediction + + + + + + + + + + + Deposition + + For non-analytical operations, see the 'Processing' branch. + Database deposition + Data deposition + Data submission + Submission + Database submission + 1.6 + Deposit some data in a database. + + + + + + + + + + + Clustering + + Group together some data entities on the basis of similarities such that entities in the same group (cluster) are more similar to each other than to those in other groups (clusters). + 1.6 + + + + + + + + + + + Assembly + + 1.6 + Reformatting + XXX + Format conversion + + + + + + + + + + + Conversion + + Non-analytical data conversion. + 1.6 + + + + + + + + + + + Standardization and normalization + + Standardize or normalize data. + 1.6 + + + + + + + + + + + Aggregation + + 1.6 + Combine multiple files or data items into a single file or object. + + + + + + + + + + + Article comparison + + 1.6 + Compare two or more scientific articles. + + + + + + + + + + + Calculation + + 1.6 + Mathemetical determination of the value of something, typically a properly of a molecule. + + + + + + + + + + + Pathway or network prediction + + + Predict a molecular pathway or network. + 1.6 + + + + + + + + + + + Genome assembly + + The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated. + 1.6 + + + + + + + + + + + Plotting + + 1.6 + Generate a graph, or other visual representation, of data, showing the relationship between two or more variables. @@ -44868,12 +45138,6 @@ containing one item - GFO 'Perpetuant' is in general broader than topic, but depending on metaphysical (non-)beliefs it may be seen narrower in the sense of being a concrete individual and exhibiting presentials. - - - - - Topic can be a quality of an entity. @@ -44886,6 +45150,12 @@ containing one item + GFO 'Perpetuant' is in general broader than topic, but depending on metaphysical (non-)beliefs it may be seen narrower in the sense of being a concrete individual and exhibiting presentials. + + + + + BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the topic. @@ -45135,9 +45405,8 @@ containing one item beta12orEarlier Data rendering and visualisation + Topic for the rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data. Data rendering - Data plotting - Topic for the plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data. @@ -45793,6 +46062,7 @@ positional features such as functional and other key sites, in molecular sequenc Sequence clustering + Sequence clusters Topic concerning the comparison and grouping together of molecular sequences on the basis of their similarities. @@ -47588,6 +47858,7 @@ positional features such as functional sites in nucleotide sequences. Structure comparison + beta12orEarlier Topic concerning the comparison of two or more molecular structures. This might involve comparison of secondary or tertiary (3D) structural information. @@ -48228,6 +48499,7 @@ positional features such as functional sites in nucleotide sequences. Structural clustering + beta12orEarlier Topic concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters.