ontogetsibs |
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% ontogetsibs edam:0000575 Get ontology term(s) by id with common parent Obo output file [0000575.obo]: |
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Get ontology term(s) by id with common parent Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-oboterms] obo Obo term filename and optional format, or reference (input query) [-outfile] outobo [*.ontogetsibs] 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 |
Qualifier | Type | Description | Allowed values | Default |
---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||
[-oboterms] (Parameter 1) |
obo | Obo term filename and optional format, or reference (input query) | OBO bio-ontology term(s) | |
[-outfile] (Parameter 2) |
outobo | Output ontology term file name | OBO ontology term(s) | <*>.ontogetsibs |
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 | ||||
(none) | ||||
Associated qualifiers | ||||
"-oboterms" associated obo qualifiers | ||||
-iformat1 -iformat_oboterms |
string | Input obo format | Any string | |
-idbname1 -idbname_oboterms |
string | User-provided database name | Any string | |
"-outfile" associated outobo qualifiers | ||||
-odirectory2 -odirectory_outfile |
string | Output directory | Any string | |
-oformat2 -oformat_outfile |
string | Ontology term output format | Any string | |
General qualifiers | ||||
-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:0000575 name: Restriction map rendering namespace: operation def: Visualise restriction maps in DNA sequences. subset: operation is_a: EDAM:0000573 ! DNA map rendering is_a: EDAM:0000431 ! Restriction site recognition relationship: has_output EDAM:0001289 ! Restriction map |
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:0000578 name: DNA circular map rendering namespace: operation def: Draw a circular maps of DNA, for example a plasmid map. subset: operation is_a: EDAM:0000573 ! DNA map rendering [Term] id: EDAM:0000575 name: Restriction map rendering namespace: operation def: Visualise restriction maps in DNA sequences. subset: operation is_a: EDAM:0000573 ! DNA map rendering is_a: EDAM:0000431 ! Restriction site recognition relationship: has_output EDAM:0001289 ! Restriction map [Term] id: EDAM:0000579 name: Operon rendering namespace: operation def: Visualise operon structure etc. subset: operation is_a: EDAM:0000573 ! DNA map rendering relationship: in_topic EDAM:0000109 ! Gene finding |
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 |
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.