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edamhasoutput |
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Optionally the search can be restricted to specified EDAM namespaces.
% edamhasoutput sequence Find EDAM ontology terms by has_output relation Obo output file [edamhasoutput.obo]: |
Go to the output files for this example
Find EDAM ontology terms by has_output relation
Version: EMBOSS:6.5.6.0
Standard (Mandatory) qualifiers:
[-identifier] string Identifier(s) to search for in ontology (Any
string)
[-outfile] outobo [*.edamhasoutput] 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) | <*>.edamhasoutput | ||||||||||||||
| 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_operation:0290
name: Sequence redundancy removal
namespace: operation
def: Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria.
subset: operations
is_a: EDAM_operation:0291 ! Sequence clustering
relationship: has_output EDAM_data:2044 {min_cardinality=0} ! Sequence
relationship: has_topic EDAM_topic:0164 ! Sequence clustering
[Term]
id: EDAM_operation:2446
name: Sequence processing
namespace: operation
def: Process (read and / or write) one or more molecular sequences and associated annotation.
subset: operations
synonym: "Sequence processing (general)" EXACT [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:2044 {min_cardinality=0} ! Sequence
relationship: has_output EDAM_data:2044 {min_cardinality=0} ! Sequence
relationship: has_topic EDAM_topic:0080 ! Sequence analysis
[Term]
id: EDAM_operation:1813
name: Sequence retrieval
namespace: operation
def: Query a sequence data resource (typically a database) and retrieve sequences and / or annotation.
comment: This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence.
subset: operations
synonym: "Data retrieval (sequences)" EXACT [http://edamontology.org]
is_a: EDAM_operation:2422 ! Data retrieval
is_a: EDAM_operation:2446 ! Sequence processing
relationship: has_output EDAM_data:2044 {min_cardinality=0} ! Sequence
[Term]
id: EDAM_operation:2404
name: Sequence motif processing
namespace: operation
def: Process (read and / or write) molecular sequence motifs.
subset: operations
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:1353 {min_cardinality=0} ! Sequence motif
relationship: has_output EDAM_data:1353 {min_cardinality=0} ! Sequence motif
relationship: has_topic EDAM_topic:0158 ! Sequence motifs
[Term]
id: EDAM_operation:0239
name: Sequence motif recognition
namespace: operation
def: Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s).
[Part of this file has been deleted for brevity]
relationship: has_topic EDAM_topic:0080 ! Sequence analysis
[Term]
id: EDAM_operation:2451
name: Sequence comparison
namespace: operation
def: Compare two or more molecular sequences.
subset: operations
is_a: EDAM_operation:2403 ! Sequence analysis
is_a: EDAM_operation:2424 ! Comparison
relationship: has_input EDAM_data:2044 {min_cardinality=2} ! Sequence
relationship: has_output EDAM_data:2955 ! Sequence report
relationship: has_topic EDAM_topic:0159 ! Sequence comparison
[Term]
id: EDAM_operation:3197
name: Genetic variation analysis
namespace: operation
def: Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model.
comment: Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript.
subset: operations
synonym: "Sequence variation analysis" EXACT [http://edamontology.org]
synonym: "Genetic variation annotation" EXACT [http://edamontology.org]
is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison
relationship: has_output EDAM_data:0918 ! Nucleic acid features (variation)
[Term]
id: EDAM_operation:0310
name: Sequence assembly
namespace: operation
def: Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence.
comment: For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps.
subset: operations
is_a: EDAM_operation:2429 ! Mapping and assembly
is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid)
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis
relationship: has_output EDAM_data:0925 ! Sequence assembly
relationship: has_topic EDAM_topic:0196 ! Sequence assembly
[Term]
id: EDAM_operation:0258
name: Sequence alignment analysis
namespace: operation
def: Analyse a molecular sequence alignment.
subset: operations
is_a: EDAM_operation:2463 ! Sequence alignment processing
is_a: EDAM_operation:2946 ! Alignment analysis
relationship: has_input EDAM_data:0863 {min_cardinality=1} ! Sequence alignment ! Extends cardinality constraint on parent.
relationship: has_output EDAM_data:0867 {min_cardinality=1} ! Sequence alignment report
relationship: has_topic EDAM_topic:0182 ! Sequence alignment
|
| 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 |
| 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 |
| 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 |
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