EMBOSS: ontogetsibs manual

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:6.6.0.0

   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: bioinformatics
subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:0431 ! Restriction site recognition
is_a: EDAM_operation:0573 ! Map rendering
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: bioinformatics
subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:0431 ! Restriction site recognition
is_a: EDAM_operation:0573 ! Map rendering
relationship: has_output EDAM_data:1289 ! Restriction map

[Term]
id: EDAM_operation:0579
name: Operon rendering
namespace: operation
def: Visualise operon structure etc.
subset: bioinformatics
subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:0573 ! Map rendering
relationship: has_topic EDAM_topic:0109 ! Gene finding

[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: bioinformatics
subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:0573 ! Map rendering

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.

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

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None

Wiki

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

Database entry: edam:0575

Output file format

Output files for usage example

File: 0575.obo

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments