                                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:{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:6.5.6.0

   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


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: topics
xref: BioCatalogue:Nucleotide Sequence Analysis
is_a: EDAM_topic:0080 ! Sequence analysis
is_a: EDAM_topic:0077 ! Nucleic acid analysis

[Term]
id: EDAM_topic:0097
name: Nucleic acid structure analysis
namespace: topic
def: The processing and analysis of nucleic acid (secondary or tertiary) structu
ral data.
subset: topics
is_a: EDAM_topic:0081 ! Structure analysis
is_a: EDAM_topic:0077 ! Nucleic acid 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 exclusivel
y) nucleic acid sequence analysis.
subset: topics
synonym: "Nucleic acids" EXACT [http://edamontology.org]
synonym: "Nucleic acid informatics" EXACT [http://edamontology.org]
synonym: "Nucleic acid bioinformatics" EXACT [http://edamontology.org]
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.

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 (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
