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 displays on-screen for a named ontology whether term statement(s) with the supplied IDs are obsolete or not. 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 ontoget % ontoget edam:0001234 Get ontology term(s) Obo output file [0001234.obo]: Go to the input files for this example Go to the output files for this example Example 2 % ontoget edam:0000850 -subclasses Get ontology term(s) Obo output file [0000850.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:6.4.0.0 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 -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: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 Input files for usage example 2 Database entry: edam:0000850 [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 Output file format A single line per term is is given, including the term id, namespace and name, and whether it is obsolete or not. Output files for usage example File: 0001234.obo [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 files for usage example 2 File: 0000850.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: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 [Term] id: EDAM:0001240 name: PCR primers namespace: data def: Oligonucleotide primer(s) for PCR and DNA amplification, for example a mini mal primer set. subset: data is_a: EDAM:0001234 ! Sequence set (nucleic acid) [Term] id: EDAM:0001246 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: data synonym: "Nucleotide sequence cluster" EXACT [] is_a: EDAM:0001234 ! Sequence set (nucleic acid) is_a: EDAM:0001235 ! Sequence cluster [Term] id: EDAM:0002198 name: Gene cluster namespace: data def: A cluster of similar genes. subset: data is_a: EDAM:0001246 ! Sequence cluster (nucleic acid) [Term] id: EDAM:0002874 name: Sequence set (polymorphic) namespace: data def: A set of sub-sequences displaying some type of polymorphism, typically indi cating the sequence in which they occur, their position and other metadata. [Part of this file has been deleted for brevity] 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: data is_a: EDAM:0000850 ! Sequence set [Term] id: EDAM:0001245 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: data synonym: "Protein sequence cluster" EXACT [] is_a: EDAM:0001233 ! Sequence set (protein) is_a: EDAM:0001235 ! Sequence cluster [Term] id: EDAM:0001238 name: Proteolytic digest namespace: data def: A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses. subset: data is_a: EDAM:0001233 ! Sequence set (protein) [Term] id: EDAM:0001262 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: data is_a: EDAM:0001233 ! Sequence set (protein) [Term] id: EDAM:0001235 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: data is_a: EDAM:0000850 ! Sequence set relationship: in_topic EDAM:0000164 ! Sequence clustering relationship: in_topic EDAM:0000724 ! Protein families [Term] id: EDAM:0002245 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: data is_a: EDAM:0000850 ! Sequence set 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) 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