ontogetcommon

 

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Function

Get common ancestor for terms

Description

ontogetcommon reads two or more terms from an ontology and traces their closest common ancestor.

Algorithm

ontogetcommon traces up through the hierarchy of terms for the first term it reads. Successive terms are similarly traced, saving any ancestral terms that are already in the saved list.

The search fails if any term has no common ancestor with all previous terms.

The match reported is the first match found when tracing back.

There is no test for common ancestors in multiple paths.

Usage

Here is a sample session with ontogetcommon 


% ontogetcommon "edam:{0000108,0000110}" 
Get common ancestor for terms
Obo output file [ontogetcommon.obo]:

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

Command line arguments 

Get common ancestor for terms
Version: EMBOSS:6.4.0.0

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

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)		 outobo Output ontology term file name OBO ontology term(s) <*>.ontogetcommon
Additional (Optional) qualifiers
-obsolete boolean The default behaviour is to not use or return obsolete terms. This option if set will include all terms. Boolean value Yes/No No
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-oboterms" associated obo qualifiers
-iformat1
-iformat_oboterms		 string Input obo format Any string  
-idbname1
-idbname_oboterms		 string User-provided database name Any string  
"-outfile" associated outobo qualifiers
-odirectory2
-odirectory_outfile		 string Output directory Any string  
-oformat2
-oformat_outfile		 string Ontology term output format 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

ontogetcommon reads terms from an ontology database.

Input files for usage example

Database entry: "edam:{0000108,0000110}"

[Term]
id: EDAM:0000110
name: Transcription
namespace: topic
def: The study of the transcription of DNA into mRNA and transcription regulation including transcription factors and regulatory motifs, elements or regions in DNA sequences.
comment: This includes promoters, enhancers, silencers and boundary elements / insulators.
subset: topic
xref: BioCatalogue:Transcription Factors
is_a: EDAM:0000197 ! Gene expression and regulation

[Term]
id: EDAM:0000108
name: Translation
namespace: topic
def: The study of the translation of mRNA into protein.
subset: topic
is_a: EDAM:0000197 ! Gene expression and regulation

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: ontogetcommon.obo

[Term]
id: EDAM:0000197
name: Gene expression and regulation
namespace: topic
def: The study of gene expression and regulation (genetic information that is used in the synthesis of a protein).
comment: This involves analysis of microarray data, northern blots, gene-indexed expression profiles etc.
alt_id: EDAM:0000631
alt_id: EDAM:0000204
subset: topic
is_a: EDAM:0002816 ! Genes

Data files

None.

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)
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)

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 © 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