|   | ontogetcommon | 
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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.
| 
% 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
| 
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 | 
| [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 | 
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.
| [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 | 
| 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 | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.