ontoisobsolete



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Function

   Report whether an ontology term id is obsolete

Description

   ontoisobsolete tests and ontology term retrieved by a query and returns
   "Obsolete" if the term is obsoleted in the ontology.

   Ontologies from the EMBOSS data directory are used.

Usage

   Here is a sample session with ontoisobsolete


% ontoisobsolete edam:0195
Report whether an ontology term id is obsolete
Output file [stdout]:

Obsolete


   Go to the input files for this example

   Example 2


% ontoisobsolete edam:0575
Report whether an ontology term id is obsolete
Output file [stdout]:

EDAM_operation:0575 OK


   Go to the input files for this example

Command line arguments

Report whether an ontology term id is obsolete
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-oboterms]          obo        Obo term filename and optional format, or
                                  reference (input query)
  [-outfile]           outfile    [stdout] Output file name

   Additional (Optional) qualifiers: (none)
   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

   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:0195

[Term]
id: EDAM_topic:0195
name: Virtual PCR
namespace: topic
def: Topic concerning simulated polymerase chain reaction (PCR).
subset: bioinformatics
subset: edam
subset: topics
synonym: "PCR" EXACT []
synonym: "Polymerase chain reaction" EXACT []
created_in: "beta12orEarlier"
obsolete_since: "beta13"
is_obsolete: true
consider: EDAM_topic:0077 ! Nucleic acid analysis


  Input files for usage example 2

  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

   A single line per term is is given, including the term id, namespace
   and name, and whether it is obsolete or not.

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
   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
                    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.

History

Target users

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

Comments

                    None