EMBOSS: ontogetcommon manual

ontogetcommon

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 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:{0097,0640}" 
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:6.6.0.0

   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
   -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

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
-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 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:{0097,0640}"

[Term]
id: EDAM_topic:0640
name: Nucleic acid sequence analysis
namespace: topic
def: Processing and analysis of nucleotide sequences and sequence-based entities such as alignments, motifs and profiles.
subset: bioinformatics
subset: edam
subset: topics
xref: BioCatalogue:Nucleotide Sequence Analysis
created_in: "beta12orEarlier"
is_a: EDAM_topic:0077 ! Nucleic acid analysis
is_a: EDAM_topic:0080 ! Sequence analysis

[Term]
id: EDAM_topic:0097
name: Nucleic acid structure analysis
namespace: topic
def: The processing and analysis of nucleic acid (secondary or tertiary) structural data.
subset: bioinformatics
subset: edam
subset: topics
created_in: "beta12orEarlier"
is_a: EDAM_topic:0077 ! Nucleic acid analysis
is_a: EDAM_topic:0081 ! Structure analysis

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_topic:0077
name: Nucleic acid analysis
namespace: topic
def: Processing and analysis of nucleic acid data, typically (but not exclusively) nucleic acid sequence analysis.
subset: bioinformatics
subset: edam
subset: topics
synonym: "http://purl.bioontology.org/ontology/MSH/D017422" NARROW []
synonym: "http://purl.bioontology.org/ontology/MSH/D017423" NARROW []
synonym: "Nucleic acid bioinformatics" EXACT []
synonym: "Nucleic acid informatics" EXACT []
synonym: "Nucleic acids" EXACT []
created_in: "beta12orEarlier"
is_a: EDAM_topic:0003 ! Topic

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

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

History

Target users

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

Comments

None

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Input files for usage example

Database entry: "edam:{0097,0640}"

Output file format

Output files for usage example

File: ontogetcommon.obo

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments