                               ontogetobsolete



Wiki

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   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Get ontology ontology terms

Description

   ontogetobsolete displays on-screen for a named ontology all term
   statement(s) that are obsolete. The information may be written to an
   output file in various formats.

   Ontologies from the EMBOSS data directory are used.

Usage

   Here is a sample session with ontogetobsolete


% ontogetobsolete edam:alignment -subclasses
Get ontology ontology terms
Obo output file [0083.obo]:


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

Get ontology ontology terms
Version: EMBOSS:6.5.6.0

   Standard (Mandatory) qualifiers:
  [-oboterms]          obo        Obo term filename and optional format, or
                                  reference (input query)
  [-outfile]           outobo     [*.ontogetobsolete] 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.

   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:alignment

[Term]
id: EDAM_topic:0083
name: Alignment
namespace: topic
def: Topic concerning the alignment (equivalence between sites) of molecular seq
uences, structures or profiles (representing a sequence or structure alignment).
subset: topics
is_obsolete: true ! {since=beta12orEarlier}
consider: EDAM_topic:0182 ! Sequence alignment
consider: EDAM_topic:0183 ! Structure alignment
consider: EDAM_topic:0184 ! Threading

[Term]
id: EDAM_data:1916
name: Alignment
namespace: data
def: An alignment of molecular sequences, structures or profiles derived from th
em.
subset: data
is_a: EDAM_data:3031 ! Core data


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: 0083.obo

[Term]
id: EDAM_topic:0083
name: Alignment
namespace: topic
def: Topic concerning the alignment (equivalence between sites) of molecular seq
uences, structures or profiles (representing a sequence or structure alignment).
subset: topics
is_obsolete: true ! {since=beta12orEarlier}
consider: EDAM_topic:0182 ! Sequence alignment
consider: EDAM_topic:0183 ! Structure alignment
consider: EDAM_topic:0184 ! Threading


Data files

   OBO-format ontologies must be installed in the EMBOSS data directory
   and indexed. This is done automatically for typical installations.

Notes

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)
                    ontoget        Get ontology term(s)
                    ontogetcommon  Get common ancestor for terms
                    ontogetdown    Get ontology term(s) by parent id
                    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
