|
|
edamisformat |
Please help by correcting and extending the Wiki pages.
Optionally the search can be restricted to specified EDAM namespaces.
% edamisformat sequence Find EDAM ontology terms by is_format_of relation Obo output file [edamisformat.obo]: |
Go to the output files for this example
Find EDAM ontology terms by is_format_of relation
Version: EMBOSS:6.5.6.0
Standard (Mandatory) qualifiers:
[-identifier] string Identifier(s) to search for in ontology (Any
string)
[-outfile] outobo [*.edamisformat] 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) | <*>.edamisformat | ||||||||||||||
| 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_format:2352
name: BioXSD
namespace: format
def: BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more).
subset: formats
synonym: "BioXSD XML format" EXACT [http://edamontology.org]
xref: http://bioxsd.org {documentation=true}
is_a: EDAM_format:2571 ! Raw sequence format
is_a: EDAM_format:1919 ! Sequence record format
is_a: EDAM_format:1920 ! Sequence feature annotation format
is_a: EDAM_format:2555 ! Alignment format (XML)
is_a: EDAM_format:2332 ! XML
relationship: is_format_of EDAM_data:2044 ! Sequence
relationship: is_format_of EDAM_data:1255 ! Feature record
relationship: is_format_of EDAM_data:0863 ! Sequence alignment
[Term]
id: EDAM_format:2202
name: Sequence record full format
namespace: format
def: Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database.
subset: formats
is_a: EDAM_format:1919 ! Sequence record format
relationship: is_format_of EDAM_data:2201 ! Sequence record full
[Term]
id: EDAM_format:2068
name: Sequence motif format
namespace: format
def: Format of a sequence motif.
subset: formats
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:1353 ! Sequence motif
[Term]
id: EDAM_format:2067
name: Sequence distance matrix format
namespace: format
def: Format of a matrix of genetic distances between molecular sequences.
subset: formats
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0870 ! Sequence distance matrix
[Term]
id: EDAM_format:2203
name: Sequence record lite format
namespace: format
def: Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment.
subset: formats
[Part of this file has been deleted for brevity]
namespace: format
def: Format of a sequence annotation track.
subset: formats
is_a: EDAM_format:1920 ! Sequence feature annotation format
relationship: is_format_of EDAM_data:3002 ! Sequence annotation track
[Term]
id: EDAM_format:2920
name: Alignment format (pair only)
namespace: format
def: Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences.
subset: formats
is_a: EDAM_format:1921 ! Alignment format
relationship: is_format_of EDAM_data:1381 ! Sequence alignment (pair)
[Term]
id: EDAM_format:2155
name: Sequence features (repeats) format
namespace: format
def: Format used for map of repeats in molecular (typically nucleotide) sequences.
subset: formats
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:1299 ! Sequence features (repeats)
[Term]
id: EDAM_format:2921
name: Sequence variation annotation format
namespace: format
def: Format of sequence variation annotation.
subset: formats
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0918 ! Nucleic acid features (variation)
[Term]
id: EDAM_format:2055
name: Sequence assembly format
namespace: format
def: Format for sequence assembly data.
subset: formats
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0925 ! Sequence assembly
[Term]
id: EDAM_format:2057
name: Sequence trace format
namespace: format
def: Format for sequence trace data (i.e. including base call information).
subset: formats
is_a: EDAM_format:1919 ! Sequence record format
relationship: is_format_of EDAM_data:0924 ! Sequence trace
|
| 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 |
| 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 |
| 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.