ontogetup 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) by id of child Description ontogetup finds ontology terms matching a query. All parents of the term, related to the term by 'is_a' (class/subclass) relationships, are returned. The information may be written to an output file in various formats. Usage Here is a sample session with ontogetup % ontogetup edam:0001234 Get ontology term(s) by id of child Obo output file [0001234.obo]: Go to the input files for this example Go to the output files for this example Command line arguments Get ontology term(s) by id of child Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-oboterms] obo Obo term filename and optional format, or reference (input query) [-outfile] outobo [*.ontogetup] Output ontology term file name Additional (Optional) qualifiers: -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 -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 The input is a standard EMBOSS ontology query. The major ontology sources defined as standard in EMBOSS installations are EDAM, GO (gene Ontology) and SO (Sequence Ontology). Data can also be read from ontology output in "obo" format written by an EMBOSS application. Input files for usage example Database entry: edam:0001234 [Term] id: EDAM:0001234 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: data is_a: EDAM:0000850 ! Sequence set is_a: EDAM:0002977 ! Nucleic acid sequence Output file format The output is a standard EMBOSS ontology term file. The results can be output in one of several styles by using the command-line qualifier -oformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: obo, brief, list, html, xml, json, excel. See: http://emboss.sf.net/docs/themes/OntologyFormats.html for further information on ontology formats. Output files for usage example File: 0001234.obo [Term] id: EDAM:0000850 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 term may be used for arbitrary sequence sets and associated data a rising from processing. subset: data is_a: EDAM:0002955 ! Sequence report [Term] id: EDAM:0002977 name: Nucleic acid sequence namespace: data def: One or more nucleic acid sequences, possibly with associated annotation. subset: data is_a: EDAM:0002044 ! Sequence is_a: EDAM:0002525 ! Nucleic acid data Data files The EDAM Ontology is included in EMBOSS as local database edam. Notes None. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 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) ontoget Get 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 ontoisobsolete Report whether an ontology term id is obsolete ontotext Get ontology term(s) original full text Author(s) Peter Rice 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