ontogetsibs

 

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Function

Get ontology term(s) by id with common parent

Description

ontogetsibs finds ontology terms matching a query. All siblings of the term (i.e. sharingh the same parent 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 ontogetsibs


% ontogetsibs edam:0575 
Get ontology term(s) by id with common parent
Obo output file [0575.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 with common parent
Version: EMBOSS:6.5.0.0

   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
   -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

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  
-iquery1
-iquery_oboterms
string Input query fields or ID list Any string  
-ioffset1
-ioffset_oboterms
integer Input start position offset Any integer value 0
-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

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:0575

[Term]
id: EDAM_operation:0575
name: Restriction map rendering
namespace: operation
def: Visualise restriction maps in DNA sequences.
subset: operations
is_a: EDAM_operation:0573 ! Map rendering
is_a: EDAM_operation:0431 ! Restriction site recognition
relationship: has_output EDAM_data:1289 ! Restriction map

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: 0575.obo

[Term]
id: EDAM_operation:0575
name: Restriction map rendering
namespace: operation
def: Visualise restriction maps in DNA sequences.
subset: operations
is_a: EDAM_operation:0573 ! Map rendering
is_a: EDAM_operation:0431 ! Restriction site recognition
relationship: has_output EDAM_data:1289 ! Restriction map

[Term]
id: EDAM_operation:0578
name: DNA circular map rendering
namespace: operation
def: Draw a circular maps of DNA, for example a plasmid map.
subset: operations
is_a: EDAM_operation:0573 ! Map rendering

[Term]
id: EDAM_operation:0579
name: Operon rendering
namespace: operation
def: Visualise operon structure etc.
subset: operations
is_a: EDAM_operation:0573 ! Map rendering
relationship: has_topic EDAM_topic:0109 ! Gene finding

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
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)

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 © 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