ontogetobsolete 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 ontology terms Description ontogetobsolete displays on-screen for a named ontology all term statement(s) that are obsolete. The information may be written to an output file in various formats. Ontologies from the EMBOSS data directory are used. Usage Here is a sample session with ontogetobsolete % ontogetobsolete edam:alignment -subclasses Get ontology ontology terms Obo output file [0000083.obo]: Go to the input files for this example Go to the output files for this example Command line arguments Get ontology ontology terms Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-oboterms] obo Obo term filename and optional format, or reference (input query) [-outfile] outobo [*.ontogetobsolete] 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. 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 Input files for usage example Database entry: edam:alignment [Term] id: EDAM:0000083 name: Alignment namespace: topic def: Study concerning the alignment (equivalence between sites) of molecular seq uences, structures or profiles (representing a sequence or structure alignment). subset: topic is_obsolete: true consider: EDAM:0000182 ! Sequence alignment consider: EDAM:0000183 ! Structure alignment consider: EDAM:0000184 ! Threading [Term] id: EDAM:0002928 name: Alignment namespace: operation def: Compare two or more entities, typically the sequence or structure (or deriv atives) of macromolecules, to identify equivalent subunits. subset: operation is_a: EDAM:0000004 ! Operation is_a: EDAM:0002951 ! Alignment processing relationship: has_output EDAM:0001916 ! Alignment {minCardinality=1} [Term] id: EDAM:0001916 name: Alignment namespace: data def: An alignment of molecular sequences, structures or profiles derived from th em. subset: data is_a: EDAM:0002539 ! Alignment data 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: 0000083.obo [Term] id: EDAM:0000083 name: Alignment namespace: topic def: Study concerning the alignment (equivalence between sites) of molecular seq uences, structures or profiles (representing a sequence or structure alignment). subset: topic is_obsolete: true consider: EDAM:0000182 ! Sequence alignment consider: EDAM:0000183 ! Structure alignment consider: EDAM:0000184 ! Threading Data files OBO-format ontologies must be installed in the EMBOSS data directory and indexed. This is done automatically for typical installations. Notes 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) ontoget Get ontology term(s) ontogetcommon Get common ancestor for terms ontogetdown Get ontology term(s) by parent id 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