ontoget |
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ontoget reads ontology terms matching a query. Optionally, the parents or children of the term, related to the term by 'is_a' (class/subclass) relationships, may also be returned. The information may be written to an output file in various formats.
% ontoget edam:0001234 Get ontology term(s) Obo output file [0001234.obo]: |
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Example 2
% ontoget edam:0000850 -subclasses Get ontology term(s) Obo output file [0000850.obo]: |
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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 |
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) | <*>.ontoget |
Additional (Optional) qualifiers | ||||
-subclasses | boolean | Extend the query matches to include all terms which are specialisations (sub-classes) of the matched terms. | Boolean value Yes/No | No |
-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 |
[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: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 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.
[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: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 [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:0001240 name: PCR primers namespace: data def: Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal 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 indicating 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 do not (typically) correspond to common sequence database records or database entries. 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 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 |
OBO-format ontologies must be installed in the EMBOSS data directory and indexed. This is done automatically for typical installations.
The default behaviour is to report a single term with the specified id. Optionally, it will also return the parent(s) or children of that term, i.e. terms which are related to the specified term id via an is_a (class/subclass) relationship.
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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © 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 © emboss.open-bio.org) not to the original author.