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% ontogetdown edam:0000850 Get ontology term(s) by parent id Obo output file [0000850.obo]:
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Get ontology term(s) by parent id Version: EMBOSS:220.127.116.11 Standard (Mandatory) qualifiers: [-oboterms] obo Obo term filename and optional format, or reference (input query) [-outfile] outobo [*.ontogetdown] 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
|Standard (Mandatory) qualifiers|
|obo||Obo term filename and optional format, or reference (input query)||OBO bio-ontology term(s)|
|outobo||Output ontology term file name||OBO ontology term(s)||<*>.ontogetdown|
|Additional (Optional) qualifiers|
|-obsolete||boolean||The default behaviour is to not use or return obsolete terms. This option if set will include all terms.||Boolean value Yes/No||No|
|Advanced (Unprompted) qualifiers|
|"-oboterms" associated obo qualifiers|
|string||Input obo format||Any string|
|string||User-provided database name||Any string|
|"-outfile" associated outobo qualifiers|
|string||Output directory||Any string|
|string||Ontology term output format||Any string|
|-auto||boolean||Turn off prompts||Boolean value Yes/No||N|
|-stdout||boolean||Write first file to standard output||Boolean value Yes/No||N|
|-filter||boolean||Read first file from standard input, write first file to standard output||Boolean value Yes/No||N|
|-options||boolean||Prompt for standard and additional values||Boolean value Yes/No||N|
|-debug||boolean||Write debug output to program.dbg||Boolean value Yes/No||N|
|-verbose||boolean||Report some/full command line options||Boolean value Yes/No||Y|
|-help||boolean||Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose||Boolean value Yes/No||N|
|-warning||boolean||Report warnings||Boolean value Yes/No||Y|
|-error||boolean||Report errors||Boolean value Yes/No||Y|
|-fatal||boolean||Report fatal errors||Boolean value Yes/No||Y|
|-die||boolean||Report dying program messages||Boolean value Yes/No||Y|
|-version||boolean||Report version number and exit||Boolean value Yes/No||N|
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.
[Term] id: EDAM:0000850 name: Sequence set namespace: data def: A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method. comment: This term may be used for arbitrary sequence sets and associated data arising from processing. subset: data is_a: EDAM:0002955 ! Sequence report
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.
[Term] id: EDAM:0001234 name: Sequence set (nucleic acid) namespace: data def: Any collection of multiple nucleotide sequences and associated metadata that 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:0001233 name: Sequence set (protein) namespace: data def: Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. subset: data is_a: EDAM:0000850 ! Sequence set [Term] id: EDAM:0001235 name: Sequence cluster namespace: data def: A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information. comment: The cluster might include sequences identifiers, short descriptions, alignment 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) procedure. comment: Bootstrapping is often performed in phylogenetic analysis. subset: data is_a: EDAM:0000850 ! Sequence set
|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|
|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|
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.