ontoget
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Function
Get ontology term(s)
Description
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.
Usage
Here is a sample session with ontoget
% ontoget edam:1234
Get ontology term(s)
Obo output file [1234.obo]:
Go to the input files for this example
Go to the output files for this example
Example 2
% ontoget edam:0850 -subclasses
Get ontology term(s)
Obo output file [0850.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:6.6.0.0
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
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-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:1234
[Term]
id: EDAM_data:1234
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: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
is_a: EDAM_data:0850 ! Sequence set
is_a: EDAM_data:2977 ! Nucleic acid sequence
Input files for usage example 2
Database entry: edam:0850
[Term]
id: EDAM_data:0850
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 concept may be used for arbitrary sequence sets and associated dat
a arising from processing.
subset: bioinformatics
subset: data
subset: edam
synonym: "SO:0001260" RELATED []
created_in: "beta12orEarlier"
is_a: EDAM_data:2955 ! Sequence report
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: 1234.obo
[Term]
id: EDAM_data:1234
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: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
is_a: EDAM_data:0850 ! Sequence set
is_a: EDAM_data:2977 ! Nucleic acid sequence
Output files for usage example 2
File: 0850.obo
[Term]
id: EDAM_data:0850
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 concept may be used for arbitrary sequence sets and associated dat
a arising from processing.
subset: bioinformatics
subset: data
subset: edam
synonym: "SO:0001260" RELATED []
created_in: "beta12orEarlier"
is_a: EDAM_data:2955 ! Sequence report
[Term]
id: EDAM_data:1233
name: Sequence set (protein)
namespace: data
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: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
is_a: EDAM_data:0850 ! Sequence set
[Term]
id: EDAM_data:1245
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: bioinformatics
subset: data
subset: edam
synonym: "Protein sequence cluster" EXACT []
created_in: "beta12orEarlier"
is_a: EDAM_data:1233 ! Sequence set (protein)
is_a: EDAM_data:1235 ! Sequence cluster
[Term]
id: EDAM_data:1262
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: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
is_a: EDAM_data:1233 ! Sequence set (protein)
[Term]
[Part of this file has been deleted for brevity]
id: EDAM_data:1246
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: bioinformatics
subset: data
subset: edam
synonym: "Nucleotide sequence cluster" EXACT []
created_in: "beta12orEarlier"
is_a: EDAM_data:1234 ! Sequence set (nucleic acid)
is_a: EDAM_data:1235 ! Sequence cluster
[Term]
id: EDAM_data:1239
name: Restriction digest
namespace: data
def: Restriction digest fragments from digesting a nucleotide sequence with rest
riction sites using a restriction endonuclease.
subset: bioinformatics
subset: data
subset: edam
xref: SO:0000412
created_in: "beta12orEarlier"
is_a: EDAM_data:1234 ! Sequence set (nucleic acid)
[Term]
id: EDAM_data:2245
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: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
is_a: EDAM_data:0850 ! Sequence set
[Term]
id: EDAM_data:1235
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: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
is_a: EDAM_data:0850 ! Sequence set
relationship: has_topic EDAM_topic:0724 ! Protein families
relationship: has_topic EDAM_topic:3052 ! Sequence clusters and classification
Data files
OBO-format ontologies must be installed in the EMBOSS data directory
and indexed. This is done automatically for typical installations.
Notes
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.
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