diff --git a/#delete.me# b/#delete.me# new file mode 100644 index 0000000..1e82297 --- /dev/null +++ b/#delete.me# @@ -0,0 +1,2 @@ +Deprecated terms +Cleaning up synonyms \ No newline at end of file diff --git a/EDAM_dev.owl b/EDAM_dev.owl index 086d334..12483d9 100644 --- a/EDAM_dev.owl +++ b/EDAM_dev.owl @@ -418,14 +418,14 @@ - 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. + OBO_REL:bearer_of - In very unusual cases. true + In very unusual cases. @@ -471,14 +471,14 @@ - '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. 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. - true In very unusual cases. + true @@ -511,8 +511,8 @@ - OBO_REL:has_participant 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it. + OBO_REL:has_participant @@ -547,8 +547,8 @@ - true In very unusual cases. + true @@ -575,8 +575,8 @@ - OBO_REL:quality_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. + OBO_REL:quality_of @@ -604,20 +604,20 @@ - OBO_REL:function_of - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. - - - - 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. - true + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. + OBO_REL:function_of + + + + In very unusual cases. + true @@ -665,16 +665,16 @@ - 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. + In very unusual cases. + true - + - true - In very unusual cases. + 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments. + OBO_REL:participates_in - + @@ -700,14 +700,14 @@ - 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 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 @@ -741,16 +741,16 @@ - true - In very unusual cases. + OBO_REL:quality_of + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. - + - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. - OBO_REL:quality_of + In very unusual cases. + true - + @@ -806,10 +806,10 @@ - EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - Datum + Data record + EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). - + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). @@ -818,10 +818,10 @@ - Data record - EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + Datum - + @@ -2190,8 +2190,8 @@ - SO:0001248 Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. + SO:0001248 @@ -5989,8 +5989,8 @@ - A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. UniProt|Enzyme Nomenclature + A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. @@ -26567,16 +26567,16 @@ - File format - File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. + Data model + A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) - + - A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) - Data model + File format + File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. - + @@ -29416,7 +29416,7 @@ - + @@ -29428,7 +29428,7 @@ - + BioXSD XML format @@ -33220,8 +33220,8 @@ experiments employing a combination of technologies. - Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. Process + Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. @@ -33283,14 +33283,14 @@ experiments employing a combination of technologies. - - + + - - + + Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. @@ -33420,14 +33420,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -33545,14 +33545,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -33580,14 +33580,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -33637,14 +33637,14 @@ experiments employing a combination of technologies. - - + + - - + + This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. @@ -33806,14 +33806,14 @@ experiments employing a combination of technologies. - - + + - - + + Immunogenicity prediction @@ -34468,19 +34468,19 @@ experiments employing a combination of technologies. - + - - + + - - + + @@ -34507,14 +34507,14 @@ experiments employing a combination of technologies. - - + + - - + + Identify and plot third base position variability in a nucleotide sequence. @@ -34546,14 +34546,14 @@ experiments employing a combination of technologies. - - + + - - + + Sequence distance matrix construction @@ -34626,7 +34626,7 @@ experiments employing a combination of technologies. beta12orEarlier Align (identify equivalent sites within) molecular sequences. Sequence alignment generation - Sequence alignment computation + Consensus-based sequence alignment @@ -34678,12 +34678,8 @@ experiments employing a combination of technologies. - Align (superimpose) molecular tertiary structures. - Structure alignment generation - Structure alignment construction beta12orEarlier - Multiple structure alignment construction - Multiple structure alignment generation + Align (superimpose) molecular tertiary structures. @@ -34704,14 +34700,14 @@ experiments employing a combination of technologies. - - + + - - + + Sequence profile construction @@ -34732,7 +34728,7 @@ experiments employing a combination of technologies. - + @@ -34744,7 +34740,7 @@ experiments employing a combination of technologies. - + Structural profile generation @@ -34760,12 +34756,12 @@ experiments employing a combination of technologies. - Profile-to-profile alignment + Profile-profile alignment - - + + @@ -34776,16 +34772,15 @@ experiments employing a combination of technologies. - - + + Sequence profile alignment + Profile-to-profile alignment + Methods might perform one-to-one, one-to-many or many-to-many comparisons. See also 'Sequence alignment comparison'. beta12orEarlier - See also 'Sequence alignment comparison'. - Sequence profile alignment construction Align sequence profiles (representing sequence alignments). - Sequence profile alignment generation @@ -34799,24 +34794,21 @@ experiments employing a combination of technologies. - - + + - - + + - beta12orEarlier - 3D profile alignment (multiple) - 3D profile alignment - Multiple 3D profile alignment construction - Structural profile alignment construction (multiple) Structural profile alignment Align structural (3D) profiles or templates (representing structures or structure alignments). - Structural profile alignment generation + beta12orEarlier + 3D profile alignment + Methods might perform one-to-one, one-to-many or many-to-many comparisons. @@ -34836,18 +34828,16 @@ experiments employing a combination of technologies. - - + + - - + + - Sequence-profile alignment construction - Sequence-profile alignment generation beta12orEarlier Align molecular sequence(s) to sequence profile(s). Sequence-profile alignment @@ -34877,9 +34867,7 @@ experiments employing a combination of technologies. beta12orEarlier - Sequence-3D profile alignment construction Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment). - Sequence-3D profile alignment generation Methods might perform one-to-one, one-to-many or many-to-many comparisons. Sequence-3D profile alignment @@ -34896,14 +34884,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34964,14 +34952,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34989,14 +34977,14 @@ experiments employing a combination of technologies. - - + + - - + + @@ -35040,14 +35028,14 @@ experiments employing a combination of technologies. - - + + - - + + @@ -35081,26 +35069,26 @@ experiments employing a combination of technologies. - - + + - + - - + + - - + + Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families. @@ -35303,13 +35291,13 @@ experiments employing a combination of technologies. - + - + beta12orEarlier @@ -35354,14 +35342,14 @@ experiments employing a combination of technologies. - - + + - - + + WHATIF: UseResidueDB @@ -35598,14 +35586,14 @@ experiments employing a combination of technologies. - - + + - - + + Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). @@ -35680,20 +35668,20 @@ experiments employing a combination of technologies. - + - - + + - - + + Visualization @@ -36161,14 +36149,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -36594,14 +36582,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -36663,14 +36651,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Calculate pH-dependent properties from pKa calculations of a protein sequence. @@ -36930,14 +36918,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Sequence feature detection (nucleic acid) @@ -37959,13 +37947,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + - + Model the structure of a protein in complex with a small molecule or another macromolecule. @@ -38211,17 +38199,16 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pairwise sequence alignment - + - Pairwise sequence alignment generation Methods might perform one-to-one, one-to-many or many-to-many comparisons. Align exactly two molecular sequences. - Pairwise sequence alignment construction + Pairwise alignment beta12orEarlier @@ -38234,11 +38221,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Multiple sequence alignment - Multiple sequence alignment construction - Align two or more molecular sequences. + Multiple 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 more than two molecular sequences. beta12orEarlier - Multiple sequence alignment generation @@ -38282,16 +38268,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Local sequence alignment + Local alignment - Multiple sequence alignment (local) - Local multiple sequence alignment construction beta12orEarlier - Local alignment methods identify regions of local similarity. - Multiple sequence alignment construction (local) - Sequence alignment generation (local) Sequence alignment (local) + Local alignment methods identify regions of local similarity. Locally align two or more molecular sequences. + Local sequence alignment Smith-Waterman @@ -38302,16 +38285,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Global sequence alignment + Global alignment - Global multiple sequence alignment construction - Multiple sequence alignment (global) - beta12orEarlier Sequence alignment (global) - Multiple sequence alignment construction (global) + Global sequence alignment Globally align two or more molecular sequences. - Sequence alignment generation (global) Global alignment methods identify similarity across the entire length of the sequences. + beta12orEarlier @@ -38325,11 +38305,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier Align two or more molecular sequences with user-defined constraints. - Multiple sequence alignment construction (constrained) - Sequence alignment generation (constrained) Multiple sequence alignment (constrained) Sequence alignment (constrained) - Constrained multiple sequence alignment construction @@ -38340,16 +38317,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Consensus-based sequence alignment - - Consensus multiple sequence alignment construction - Sequence alignment (consensus) + beta12orEarlier Align two or more molecular sequences using multiple methods to achieve higher quality. - Sequence alignment generation (consensus) - Multiple sequence alignment construction (consensus) - Multiple sequence alignment (consensus) - - + 1.16 + true + + @@ -38452,8 +38426,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pairwise structure alignment beta12orEarlier - Pairwise structure alignment generation - Pairwise structure alignment construction + Structure alignment (pairwise) Align (superimpose) exactly two molecular tertiary structures. @@ -38464,15 +38437,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Multiple structure alignment construction - - Align (superimpose) two or more molecular tertiary structures. + Multiple structure alignment + + Align (superimpose) more than two molecular tertiary structures. This includes methods that use an existing alignment. - 1.6 - true + Structure alignment (multiple) beta12orEarlier - - + + @@ -38546,14 +38518,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Local structure alignment - Local multiple structure alignment construction + Locally align (superimpose) two or more molecular tertiary structures. + Structure alignment (local) Local alignment methods identify regions of local similarity, common substructures etc. - Structure alignment construction (local) beta12orEarlier - Locally align (superimpose) two or more molecular tertiary structures. - Multiple structure alignment construction (local) - Multiple structure alignment (local) - Structure alignment generation (local) @@ -38565,14 +38533,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Global structure alignment - Structure alignment construction (global) - Multiple structure alignment (global) - Structure alignment generation (global) - Multiple structure alignment construction (global) - beta12orEarlier Global alignment methods identify similarity across the entire structures. - Global multiple structure alignment construction + Structure alignment (global) Globally align (superimpose) two or more molecular tertiary structures. + beta12orEarlier @@ -38582,18 +38546,15 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Profile-to-profile alignment (pairwise) - - Sequence alignment generation (pairwise profile) + Profile-profile alignment (pairwise) + Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Pairwise sequence profile alignment construction - Sequence profile alignment construction (pairwise) - Sequence profile alignment (pairwise) beta12orEarlier + true + 1.16 Align exactly two molecular profiles. - Sequence profile alignment generation (pairwise) - - + + @@ -38617,16 +38578,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 3D profile-to-3D profile alignment (pairwise) - - Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Pairwise structural (3D) profile alignment construction - Structural (3D) profile alignment (pairwise) - Structural profile alignment construction (pairwise) + + 1.16 + true Align exactly two molecular Structural (3D) profiles. beta12orEarlier - Structural profile alignment generation (pairwise) - - + + @@ -39078,14 +39036,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Phylogenetic tree construction (from gene frequencies) @@ -39212,14 +39170,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Identify a plausible model of DNA substitution that explains a molecular (DNA or protein) sequence alignment. @@ -39561,14 +39519,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -40634,14 +40592,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -40791,14 +40749,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Structure analysis (protein) @@ -40952,14 +40910,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + This is a broad concept and is used a placeholder for other, more specific concepts. @@ -40979,14 +40937,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Analyse known protein secondary structure data. @@ -41298,14 +41256,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict a network of gene regulation. @@ -41501,14 +41459,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Compare two or more molecular sequences. @@ -41584,19 +41542,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern GPCR classification - - - - - - - - + beta12orEarlier - G protein-coupled receptor (GPCR) classification + 1.16 Classify G-protein coupled receptors (GPCRs) into families and subfamilies. - - + true + + @@ -41706,14 +41658,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Identify or predict protein-protein interactions, interfaces, binding sites etc. @@ -41899,7 +41851,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + @@ -41911,7 +41863,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation. @@ -41930,14 +41882,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences). @@ -41997,14 +41949,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Analyse nucleic acid tertiary structural data. @@ -42190,14 +42142,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict the interactions of proteins with other molecules. @@ -42644,13 +42596,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + - + @@ -42689,14 +42641,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -43048,8 +43000,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + @@ -43060,8 +43012,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + Analyse a body of scientific text (typically a full text article from a scientific journal.) @@ -43510,14 +43462,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta13 @@ -44398,14 +44350,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + Infer a transcriptome sequence by analysis of short sequence reads. @@ -44689,14 +44641,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + Recognition of which format the given data is in. @@ -45568,8 +45520,8 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + @@ -45580,8 +45532,8 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + 1.12 @@ -45698,14 +45650,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + 1.12