                                   ontoget



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)

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
