                                 ontogetsibs



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

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


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.

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 (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
