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edamisid |
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Optionally the search can be restricted to specified EDAM namespaces.
% edamisid sequence Find EDAM ontology terms by is_identifier_of relation Obo output file [edamisid.obo]: |
Go to the output files for this example
Find EDAM ontology terms by is_identifier_of relation
Version: EMBOSS:6.5.6.0
Standard (Mandatory) qualifiers:
[-identifier] string Identifier(s) to search for in ontology (Any
string)
[-outfile] outobo [*.edamisid] Output ontology term file name
Additional (Optional) qualifiers:
-namespace menu [*] By default all terms are returned.
Searches can be limited to one or a few
namespaces. (Values: data (Data entity);
entity (Biological entity); format (Data
format); identifier (Identifier); operation
(Bioinformatics operation); resource (Data
resource); topic (Field of bioinformatics
study))
Advanced (Unprompted) qualifiers:
-sensitive boolean [N] By default, the query keywords are
matched against the EDAM term names (and
synonyms) only. This option also matches the
keywords against the EDAM term definitions
and will therefore (typically) report more
matches.
-subclasses boolean [N] Extend the query matches to include all
terms which are specialisations (EDAM
sub-classes) of the matched type.
-obsolete boolean [N] The default behaviour is to not use or
return obsolete terms. This option if set
will include all terms.
Associated qualifiers:
"-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 | ||||||||||||||||||
| [-identifier] (Parameter 1) |
string | Identifier(s) to search for in ontology | Any string | |||||||||||||||
| [-outfile] (Parameter 2) |
outobo | Output ontology term file name | OBO ontology term(s) | <*>.edamisid | ||||||||||||||
| Additional (Optional) qualifiers | ||||||||||||||||||
| -namespace | list | By default all terms are returned. Searches can be limited to one or a few namespaces. |
|
* | ||||||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||||||||||
| -sensitive | boolean | By default, the query keywords are matched against the EDAM term names (and synonyms) only. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches. | Boolean value Yes/No | No | ||||||||||||||
| -subclasses | boolean | Extend the query matches to include all terms which are specialisations (EDAM sub-classes) of the matched type. | Boolean value Yes/No | No | ||||||||||||||
| -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 | ||||||||||||||
| Associated qualifiers | ||||||||||||||||||
| "-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 | ||||||||||||||
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_data:1063
name: Sequence identifier
namespace: identifier
def: An identifier of molecular sequence(s) or entries from a molecular sequence database.
subset: identifiers
subset: data
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:0855 ! Sequence metadata
relationship: is_identifier_of EDAM_data:2044 ! Sequence
[Term]
id: EDAM_data:1094
name: Sequence type
namespace: data
def: A label (text token) describing a type of molecular sequence.
comment: Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc).
subset: data
is_a: EDAM_data:2100 ! Type
is_a: EDAM_data:2534 ! Sequence parameter
relationship: is_identifier_of EDAM_data:2044 ! Sequence
relationship: is_identifier_of EDAM_data:0849 ! Sequence record
[Term]
id: EDAM_data:1114
name: Sequence motif identifier
namespace: identifier
def: Identifier of a sequence motif, for example an entry from a motif database.
subset: identifiers
subset: data
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:1353 ! Sequence motif
[Term]
id: EDAM_data:1096
name: Sequence accession (protein)
namespace: identifier
def: Accession number of a protein sequence database entry.
subset: identifiers
subset: data
synonym: "Protein sequence accession number" EXACT [http://edamontology.org]
is_a: EDAM_data:1093 ! Sequence accession
relationship: is_identifier_of EDAM_data:2976 ! Protein sequence
[Term]
id: EDAM_data:1112
name: Sequence cluster ID
namespace: identifier
def: An identifier of a cluster of molecular sequence(s).
subset: identifiers
[Part of this file has been deleted for brevity]
subset: data
is_a: EDAM_data:1093 ! Sequence accession
relationship: is_identifier_of EDAM_data:0849 ! Sequence record
[Term]
id: EDAM_data:2621
name: TAIR accession (protein)
namespace: identifier
def: Identifier of a protein sequence from the TAIR database.
subset: identifiers
subset: data
regex: "AASequence:[0-9]{10}"
is_a: EDAM_data:1096 ! Sequence accession (protein)
is_a: EDAM_data:2387 ! TAIR accession
relationship: is_identifier_of EDAM_data:0849 ! Sequence record
[Term]
id: EDAM_data:1101
name: TREMBL accession
namespace: identifier
def: Identifier of a TREMBL sequence database entry.
subset: identifiers
subset: data
is_a: EDAM_data:3021 ! UniProt accession
synonym: "TREMBL accession number" EXACT [http://edamontology.org]
synonym: "TREMBL ID" EXACT [http://edamontology.org]
relationship: is_identifier_of EDAM_data:0849 ! Sequence record
[Term]
id: EDAM_data:1100
name: PIR identifier
namespace: identifier
def: An identifier of PIR sequence database entry.
subset: identifiers
subset: data
synonym: "PIR accession number" EXACT [http://edamontology.org]
synonym: "PIR ID" EXACT [http://edamontology.org]
is_a: EDAM_data:1096 ! Sequence accession (protein)
relationship: is_identifier_of EDAM_data:0849 ! Sequence record
[Term]
id: EDAM_data:2291
name: UniProt ID
namespace: identifier
def: An identifier of a polypeptide in the UniProt database.
subset: identifiers
subset: data
synonym: "UniProt identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:1096 ! Sequence accession (protein)
relationship: is_identifier_of EDAM_data:0849 ! Sequence record
|
| Program name | Description |
|---|---|
| drfinddata | Find public databases by data type |
| drfindformat | Find public databases by format |
| drfindid | Find public databases by identifier |
| drfindresource | Find public databases by resource |
| 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 |
| edamname | Find EDAM ontology terms by name |
| godef | Find GO ontology terms by definition |
| goname | Find GO ontology terms by name |
| ontoget | Get ontology term(s) |
| ontogetcommon | Get common ancestor for terms |
| 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 |
| wossdata | Find programs by EDAM data |
| wossinput | Find programs by EDAM input data |
| wossoperation | Find programs by EDAM operation |
| wossoutput | Find programs by EDAM output data |
| wossparam | Find programs by EDAM parameter |
| wosstopic | Find programs by EDAM topic |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.