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ontogetobsolete |
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ontogetobsolete displays on-screen for a named ontology all term statement(s) that are obsolete. The information may be written to an output file in various formats.
Ontologies from the EMBOSS data directory are used.
% ontogetobsolete edam:alignment -subclasses Get ontology ontology terms Obo output file [0000083.obo]: |
Go to the input files for this example
Go to the output files for this example
Get ontology ontology terms
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-oboterms] obo Obo term filename and optional format, or
reference (input query)
[-outfile] outobo [*.ontogetobsolete] Output ontology term
file name
Additional (Optional) qualifiers:
-subclasses boolean [N] Extend the query matches to include all
terms which are specialisations
(sub-classes) of the matched 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
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| 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) | <*>.ontogetobsolete |
| Additional (Optional) qualifiers | ||||
| -subclasses | boolean | Extend the query matches to include all terms which are specialisations (sub-classes) of the matched 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 |
[Term]
id: EDAM:0000083
name: Alignment
namespace: topic
def: Study concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment).
subset: topic
is_obsolete: true
consider: EDAM:0000182 ! Sequence alignment
consider: EDAM:0000183 ! Structure alignment
consider: EDAM:0000184 ! Threading
[Term]
id: EDAM:0002928
name: Alignment
namespace: operation
def: Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits.
subset: operation
is_a: EDAM:0000004 ! Operation
is_a: EDAM:0002951 ! Alignment processing
relationship: has_output EDAM:0001916 ! Alignment {minCardinality=1}
[Term]
id: EDAM:0001916
name: Alignment
namespace: data
def: An alignment of molecular sequences, structures or profiles derived from them.
subset: data
is_a: EDAM:0002539 ! Alignment data
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The default behaviour is to report the entire OBO term statement from the ontology. Optionally, then only the the term id, name and namespace, or just the term id will be reported.
The output file by default is in OBO plain text format as used by the ontologies in the EMBOSS data directory and explained at http://www.geneontology.org/GO.format.obo-1_2.shtml.
Optionally, the output can be in HTML, OBO-XML or JSON format.
[Term] id: EDAM:0000083 name: Alignment namespace: topic def: Study concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment). subset: topic is_obsolete: true consider: EDAM:0000182 ! Sequence alignment consider: EDAM:0000183 ! Structure alignment consider: EDAM:0000184 ! Threading |
OBO-format ontologies must be installed in the EMBOSS data directory and indexed. This is done automatically for typical installations.
| 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 |
| 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.
This application was modified by
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.