ontoget Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Get ontology term(s) Description ontoget reads ontology terms matching a query. Optionally, the parents or children of the term, related to the term by 'is_a' (class/subclass) relationships, may also be returned. The information may be written to an output file in various formats. Usage Here is a sample session with ontoget % ontoget edam:1234 Get ontology term(s) Obo output file [1234.obo]: Go to the input files for this example Go to the output files for this example Example 2 % ontoget edam:0850 -subclasses Get ontology term(s) Obo output file [0850.obo]: Go to the input files for this example Go to the output files for this example Command line arguments Get ontology term(s) Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-oboterms] obo Obo term filename and optional format, or reference (input query) [-outfile] outobo [*.ontoget] Output ontology term file name Additional (Optional) qualifiers: -subclasses boolean [N] Extend the query matches to include all terms which are specialisations (sub-classes) of the matched terms. -obsolete boolean [N] The default behaviour is to not use or return obsolete terms. This option if set will include all terms. Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-oboterms" associated qualifiers -iformat1 string Input obo format -iquery1 string Input query fields or ID list -ioffset1 integer Input start position offset -idbname1 string User-provided database name "-outfile" associated qualifiers -odirectory2 string Output directory -oformat2 string Ontology term output format General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format Input files for usage example Database entry: edam:1234 [Term] id: EDAM_data:1234 name: Sequence set (nucleic acid) namespace: data def: Any collection of multiple nucleotide sequences and associated metadata tha t do not (typically) correspond to common sequence database records or database entries. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set is_a: EDAM_data:2977 ! Nucleic acid sequence Input files for usage example 2 Database entry: edam:0850 [Term] id: EDAM_data:0850 name: Sequence set namespace: data def: A collection of multiple molecular sequences and associated metadata that d o not (typically) correspond to molecular sequence database records or entries a nd which (typically) are derived from some analytical method. comment: This concept may be used for arbitrary sequence sets and associated dat a arising from processing. subset: bioinformatics subset: data subset: edam synonym: "SO:0001260" RELATED [] created_in: "beta12orEarlier" is_a: EDAM_data:2955 ! Sequence report Output file format The default behaviour is to report the entire OBO term statement from the ontology. Optionally, then only the the term id, name and namespace, or just the term id will be reported. The output file by default is in OBO plain text format as used by the ontologies in the EMBOSS data directory and explained at http://www.geneontology.org/GO.format.obo-1_2.shtml. Optionally, the output can be in HTML, OBO-XML or JSON format. Output files for usage example File: 1234.obo [Term] id: EDAM_data:1234 name: Sequence set (nucleic acid) namespace: data def: Any collection of multiple nucleotide sequences and associated metadata tha t do not (typically) correspond to common sequence database records or database entries. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set is_a: EDAM_data:2977 ! Nucleic acid sequence Output files for usage example 2 File: 0850.obo [Term] id: EDAM_data:0850 name: Sequence set namespace: data def: A collection of multiple molecular sequences and associated metadata that d o not (typically) correspond to molecular sequence database records or entries a nd which (typically) are derived from some analytical method. comment: This concept may be used for arbitrary sequence sets and associated dat a arising from processing. subset: bioinformatics subset: data subset: edam synonym: "SO:0001260" RELATED [] created_in: "beta12orEarlier" is_a: EDAM_data:2955 ! Sequence report [Term] id: EDAM_data:1233 name: Sequence set (protein) namespace: data def: Any collection of multiple protein sequences and associated metadata that d o not (typically) correspond to common sequence database records or database ent ries. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1245 name: Sequence cluster (protein) namespace: data def: A cluster of protein sequences. comment: The sequences are typically related, for example a family of sequences. subset: bioinformatics subset: data subset: edam synonym: "Protein sequence cluster" EXACT [] created_in: "beta12orEarlier" is_a: EDAM_data:1233 ! Sequence set (protein) is_a: EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:1262 name: Peptide molecular weight hits namespace: data def: A report on peptide fragments of certain molecular weight(s) in one or more protein sequences. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:1233 ! Sequence set (protein) [Term] [Part of this file has been deleted for brevity] id: EDAM_data:1246 name: Sequence cluster (nucleic acid) namespace: data def: A cluster of nucleotide sequences. comment: The sequences are typically related, for example a family of sequences. subset: bioinformatics subset: data subset: edam synonym: "Nucleotide sequence cluster" EXACT [] created_in: "beta12orEarlier" is_a: EDAM_data:1234 ! Sequence set (nucleic acid) is_a: EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:1239 name: Restriction digest namespace: data def: Restriction digest fragments from digesting a nucleotide sequence with rest riction sites using a restriction endonuclease. subset: bioinformatics subset: data subset: edam xref: SO:0000412 created_in: "beta12orEarlier" is_a: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] id: EDAM_data:2245 name: Sequence set (bootstrapped) namespace: data def: A collection of sequences output from a bootstrapping (resampling) procedur e. comment: Bootstrapping is often performed in phylogenetic analysis. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1235 name: Sequence cluster namespace: data def: A set of sequences that have been clustered or otherwise classified as belo nging to a group including (typically) sequence cluster information. comment: The cluster might include sequences identifiers, short descriptions, al ignment and summary information. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set relationship: has_topic EDAM_topic:0724 ! Protein families relationship: has_topic EDAM_topic:3052 ! Sequence clusters and classification Data files OBO-format ontologies must be installed in the EMBOSS data directory and indexed. This is done automatically for typical installations. Notes The default behaviour is to report a single term with the specified id. Optionally, it will also return the parent(s) or children of that term, i.e. terms which are related to the specified term id via an is_a (class/subclass) relationship. References Warnings None. Diagnostic Error Messages None. Exit status It exits with a status of 0. Known bugs None. See also Program name Description edamdef Find EDAM ontology terms by definition edamhasinput Find EDAM ontology terms by has_input relation edamhasoutput Find EDAM ontology terms by has_output relation edamisformat Find EDAM ontology terms by is_format_of relation edamisid Find EDAM ontology terms by is_identifier_of relation edamname Find EDAM ontology terms by name godef Find GO ontology terms by definition goname Find GO ontology terms by name ontocount Count ontology term(s) ontogetcommon Get common ancestor for terms ontogetdown Get ontology term(s) by parent id ontogetobsolete Get ontology ontology terms ontogetroot Get ontology root terms by child identifier ontogetsibs Get ontology term(s) by id with common parent ontogetup Get ontology term(s) by id of child ontoisobsolete Report whether an ontology term id is obsolete ontotext Get ontology term(s) original full text Author(s) Jon Ison European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. This application was modified by Jon Ison European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None