ontogetcommon 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 common ancestor for terms Description ontogetcommon reads two or more terms from an ontology and traces their closest common ancestor. Algorithm ontogetcommon traces up through the hierarchy of terms for the first term it reads. Successive terms are similarly traced, saving any ancestral terms that are already in the saved list. The search fails if any term has no common ancestor with all previous terms. The match reported is the first match found when tracing back. There is no test for common ancestors in multiple paths. Usage Here is a sample session with ontogetcommon % ontogetcommon "edam:{0000108,0000110}" Get common ancestor for terms Obo output file [ontogetcommon.obo]: Go to the input files for this example Go to the output files for this example Command line arguments Get common ancestor for terms Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-oboterms] obo Obo term filename and optional format, or reference (input query) [-outfile] outobo [*.ontogetcommon] 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 ontogetcommon reads terms from an ontology database. Input files for usage example Database entry: "edam:{0000108,0000110}" [Term] id: EDAM:0000110 name: Transcription namespace: topic def: The study of the transcription of DNA into mRNA and transcription regulatio n including transcription factors and regulatory motifs, elements or regions in DNA sequences. comment: This includes promoters, enhancers, silencers and boundary elements / i nsulators. subset: topic xref: BioCatalogue:Transcription Factors is_a: EDAM:0000197 ! Gene expression and regulation [Term] id: EDAM:0000108 name: Translation namespace: topic def: The study of the translation of mRNA into protein. subset: topic is_a: EDAM:0000197 ! Gene expression and regulation 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: ontogetcommon.obo [Term] id: EDAM:0000197 name: Gene expression and regulation namespace: topic def: The study of gene expression and regulation (genetic information that is us ed in the synthesis of a protein). comment: This involves analysis of microarray data, northern blots, gene-indexed expression profiles etc. alt_id: EDAM:0000631 alt_id: EDAM:0000204 subset: topic is_a: EDAM:0002816 ! Genes Data files None. 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) 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) 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