diff --git a/#delete.me# b/#delete.me# deleted file mode 100644 index 1e82297..0000000 --- a/#delete.me# +++ /dev/null @@ -1,2 +0,0 @@ -Deprecated terms -Cleaning up synonyms \ No newline at end of file diff --git a/EDAM_dev.owl b/EDAM_dev.owl index 12483d9..9446832 100644 --- a/EDAM_dev.owl +++ b/EDAM_dev.owl @@ -418,14 +418,14 @@ - 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 + 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. + true @@ -471,16 +471,16 @@ - 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. - + - In very unusual cases. - true + 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. + OBO_REL:has_participant - + @@ -604,22 +604,22 @@ - 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 + In very unusual cases. - + - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. OBO_REL:function_of + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL: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. - 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. - + @@ -665,17 +665,17 @@ - In very unusual cases. - true - - - - 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments. OBO_REL:participates_in + + true + In very unusual cases. + + + @@ -700,17 +700,17 @@ - In very unusual cases. - true - - - - 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. OBO_REL:participates_in + + true + In very unusual cases. + + + @@ -741,14 +741,14 @@ - 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 - In very unusual cases. true + In very unusual cases. @@ -806,12 +806,6 @@ - Data record - EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). - - - - EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). Data set @@ -823,6 +817,12 @@ + + Data record + EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). + + + @@ -2190,8 +2190,8 @@ - Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. SO:0001248 + Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. @@ -2477,6 +2477,7 @@ Peptide identification + @@ -2484,7 +2485,8 @@ - Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database. + 'Protein identification' + Protein or peptide identifications with evidence supporting the identifications, for example from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database, or the set of typical spectra one obtains when running a protein through a mass spectrometer. beta12orEarlier @@ -4543,13 +4545,13 @@ - + - + Unique name of a codon usage table. @@ -5989,8 +5991,8 @@ - UniProt|Enzyme Nomenclature A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. + UniProt|Enzyme Nomenclature @@ -26567,17 +26569,17 @@ - Data model - A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) - - - - File format File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. + + 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 + + + @@ -28596,13 +28598,13 @@ - + - + Data format for the emission and transition counts of a hidden Markov model. @@ -29921,13 +29923,13 @@ - + - + Format of a bibliographic reference. @@ -31326,19 +31328,11 @@ TSV - + tsv|tab - Delimiter-separated values - DSV - http://www.iana.org/assignments/media-types/text/csv - Tabular format - Tab-separated values - http://filext.com/file-extension/CSV - CSV Tabular data represented as tab-separated values in a text file. - Comma-separated values 1.7 - https://en.wikipedia.org/wiki/Delimiter-separated_values + Tab-separated values @@ -33171,6 +33165,38 @@ experiments employing a combination of technologies. + + + + DSV + + 1.16 + Tabular data represented as values in a text file delimited by some character. + Tabular format + Delimiter-separated values + https://en.wikipedia.org/wiki/Delimiter-separated_values + + + + + + + + + + CSV + + Comma-separated values + http://filext.com/file-extension/CSV + 1.16 + http://www.iana.org/assignments/media-types/text/csv + Tabular data represented as comma-separated values in a text file. + + + + + + @@ -33214,23 +33240,23 @@ experiments employing a combination of technologies. - Function - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. - - - - - Process Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. + Process - Computational tool provides one or more operations. Computational tool + Computational tool provides one or more operations. + + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. + Function + + + @@ -33283,14 +33309,14 @@ experiments employing a combination of technologies. - - + + - - + + Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. @@ -33517,14 +33543,14 @@ experiments employing a combination of technologies. - - + + - - + + Motifs and patterns might be conserved or over-represented (occur with improbable frequency). @@ -33637,14 +33663,14 @@ 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. @@ -33904,13 +33930,13 @@ experiments employing a combination of technologies. - + - + beta12orEarlier @@ -34155,14 +34181,14 @@ experiments employing a combination of technologies. - - + + - - + + Predict tertiary structure of a molecular (biopolymer) sequence. @@ -34257,14 +34283,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34400,14 +34426,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34461,32 +34487,32 @@ experiments employing a combination of technologies. - - + + - + - - + + - - + + - - + + beta12orEarlier @@ -34507,14 +34533,14 @@ experiments employing a combination of technologies. - - + + - - + + Identify and plot third base position variability in a nucleotide sequence. @@ -34694,14 +34720,14 @@ experiments employing a combination of technologies. - - + + - - + + @@ -34728,7 +34754,7 @@ experiments employing a combination of technologies. - + @@ -34740,7 +34766,7 @@ experiments employing a combination of technologies. - + Structural profile generation @@ -34760,14 +34786,14 @@ experiments employing a combination of technologies. - - + + - - + + @@ -34794,14 +34820,14 @@ experiments employing a combination of technologies. - - + + - - + + Structural profile alignment @@ -34856,14 +34882,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34884,14 +34910,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34952,14 +34978,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -35028,14 +35054,14 @@ experiments employing a combination of technologies. - - + + - - + + @@ -35069,6 +35095,12 @@ experiments employing a combination of technologies. + + + + + + @@ -35085,12 +35117,6 @@ 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. beta12orEarlier Microarray probe prediction @@ -35108,14 +35134,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -35291,13 +35317,13 @@ experiments employing a combination of technologies. - + - + beta12orEarlier @@ -35586,14 +35612,14 @@ experiments employing a combination of technologies. - - + + - - + + Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). @@ -35611,14 +35637,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -35668,19 +35694,19 @@ experiments employing a combination of technologies. - - + + - - + + - + @@ -36063,13 +36089,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + - + @@ -36582,14 +36608,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -36607,14 +36633,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Calculate the molecular weight of a protein sequence or fragments. @@ -36918,14 +36944,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Sequence feature detection (nucleic acid) @@ -39036,14 +39062,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Phylogenetic tree construction (from gene frequencies) @@ -39224,14 +39250,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict families of genes and gene function based on their position in a phylogenetic tree. @@ -39405,14 +39431,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Visualise, format or render a molecular sequence or sequences such as a sequence alignment, possibly with sequence features or properties shown. @@ -41256,14 +41282,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict a network of gene regulation. @@ -41459,14 +41485,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Compare two or more molecular sequences. @@ -41514,14 +41540,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Gene component prediction @@ -41850,14 +41876,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + @@ -41949,14 +41975,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Analyse nucleic acid tertiary structural data. @@ -42142,14 +42168,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict the interactions of proteins with other molecules. @@ -42595,20 +42621,20 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - + - - + + beta12orEarlier @@ -42946,14 +42972,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -43000,20 +43026,20 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - - + + Analyse a body of scientific text (typically a full text article from a scientific journal.) @@ -43046,14 +43072,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -43515,8 +43541,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + @@ -43527,8 +43553,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + Assembly quality evaluation @@ -44590,13 +44616,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - + - + 1.4 @@ -44663,8 +44689,8 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp The has_input "Data" (data_0006) may cause visualisation or other problems although ontologically correct. But on the other hand it may be useful to distinguish from nullary operations without inputs. - + @@ -45520,20 +45546,20 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + - - + + 1.12 @@ -45650,14 +45676,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + 1.12 @@ -50632,14 +50658,17 @@ positional features such as functional sites in nucleotide sequences.Metagenomics - http://purl.bioontology.org/ontology/MSH/D056186 Ecogenomics + http://purl.bioontology.org/ontology/MSH/D056186 Community genomics Environmental genomics + Environmental omics true 1.1 + Environmental sequencing Shotgun metagenomics The study of genetic material recovered from environmental samples, and associated environmental data. + Biome sequencing