ontogetup
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Function
Get ontology term(s) by id of child
Description
ontogetup finds ontology terms matching a query. All parents of the
term, related to the term by 'is_a' (class/subclass) relationships, are
returned. The information may be written to an output file in various
formats.
Usage
Here is a sample session with ontogetup
% ontogetup edam:1234
Get ontology term(s) by id of child
Obo output file [1234.obo]:
Go to the input files for this example
Go to the output files for this example
Command line arguments
Get ontology term(s) by id of child
Version: EMBOSS:6.5.6.0
Standard (Mandatory) qualifiers:
[-oboterms] obo Obo term filename and optional format, or
reference (input query)
[-outfile] outobo [*.ontogetup] 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
-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
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.
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: data
is_a: EDAM_data:0850 ! Sequence set
is_a: EDAM_data:2977 ! Nucleic acid sequence
Output file format
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.
Output files for usage example
File: 1234.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: data
synonym: "sequence_collection" EXACT [SO:0001260]
is_a: EDAM_data:2955 ! Sequence report
[Term]
id: EDAM_data:2977
name: Nucleic acid sequence
namespace: data
def: One or more nucleic acid sequences, possibly with associated annotation.
subset: data
synonym: "nucleotide sequence information" RELATED [http://purl.org/biotop/bioto
p.owl#NucleotideSequenceInformation]
is_a: EDAM_data:2044 ! Sequence
Data files
The EDAM Ontology is included in EMBOSS as local database edam.
Notes
None.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with status 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)
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
ontogetsibs Get ontology term(s) by id with common parent
ontoisobsolete Report whether an ontology term id is obsolete
ontotext Get ontology term(s) original full text
Author(s)
Peter Rice
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