ontoisobsolete

 

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

Report whether an ontology term id is obsolete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Report whether an ontology term id is obsolete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Report whether an ontology term id is obsolete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Report whether an ontology term id is obsolete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

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)
outfile Output file name Output file stdout
Additional (Optional) qualifiers
(none)
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 outfile qualifiers
-odirectory2
-odirectory_outfile
string Output directory 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

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 © 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