|
|
edamhasinput |
Please help by correcting and extending the Wiki pages.
Optionally the search can be restricted to specified EDAM namespaces.
% edamhasinput sequence Find EDAM ontology terms by has_input relation Obo output file [edamhasinput.obo]: |
Go to the output files for this example
Find EDAM ontology terms by has_input relation
Version: EMBOSS:6.5.6.0
Standard (Mandatory) qualifiers:
[-identifier] string Identifier(s) to search for in ontology (Any
string)
[-outfile] outobo [*.edamhasinput] 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) | <*>.edamhasinput | ||||||||||||||
| 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:2403
name: Sequence analysis
namespace: operation
def: Analyse one or more known molecular sequences.
subset: operations
synonym: "Sequence analysis (general)" EXACT [http://edamontology.org]
is_a: EDAM_operation:2446 ! Sequence processing
relationship: has_input EDAM_data:2044 {min_cardinality=1} ! Sequence
relationship: has_output EDAM_data:2955 {min_cardinality=1} ! Sequence report
relationship: has_topic EDAM_topic:0080 ! Sequence analysis
[Term]
id: EDAM_operation:0292
name: Sequence alignment construction
namespace: operation
def: Align (identify equivalent sites within) molecular sequences.
subset: operations
synonym: "Sequence alignment" EXACT [http://edamontology.org]
synonym: "Sequence alignment computation" EXACT [http://edamontology.org]
synonym: "Sequence alignment generation" EXACT [http://edamontology.org]
is_a: EDAM_operation:2463 ! Sequence alignment processing !(?)
is_a: EDAM_operation:2451 ! Sequence comparison
is_a: EDAM_operation:2928 ! Alignment construction
relationship: has_input EDAM_data:2044 {minCardinality=2, note="Applies to both pure/raw sequences and sequence records. Indirectly also to sequence sets or IDs (?)"} ! Sequence
relationship: has_output EDAM_data:0863 {min_cardinality=1} ! Sequence alignment
relationship: has_topic EDAM_topic:0182 ! Sequence alignment
[Term]
id: EDAM_operation:1780
name: Sequence submission
namespace: operation
def: Submit a molecular sequence to a database.
subset: operations
is_a: EDAM_operation:2446 ! Sequence processing
relationship: has_input EDAM_data:2044 {min_cardinality=1} ! Sequence
relationship: has_topic EDAM_topic:3077 ! Data acquisition and deposition
[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
[Part of this file has been deleted for brevity]
synonym: "PCR primer prediction" EXACT [http://edamontology.org]
is_a: EDAM_operation:2419 ! Primer and probe design
relationship: has_input EDAM_data:2977 ! Nucleic acid sequence
relationship: has_output EDAM_data:1240 {min_cardinality=0} ! PCR primers
relationship: has_topic EDAM_topic:3032 ! Primer or probe design
[Term]
id: EDAM_operation:2506
name: Sequence alignment analysis (protein)
namespace: operation
def: Analyse a protein sequence alignment, typically to detect features or make predictions.
subset: operations
is_a: EDAM_operation:0258 ! Sequence alignment analysis
is_a: EDAM_operation:2502 ! Protein data processing
is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein)
relationship: has_input EDAM_data:1384 {min_cardinality=1} ! Sequence alignment (protein)
relationship: has_topic EDAM_topic:0741 ! Protein sequence alignment
[Term]
id: EDAM_operation:0361
name: Sequence annotation
namespace: operation
def: Annotate a molecular sequence record with terms from a controlled vocabulary.
subset: operations
is_a: EDAM_operation:0226 ! Annotation
relationship: has_input EDAM_data:0849 {min_cardinality=1} ! Sequence record
relationship: has_output EDAM_data:0849 {min_cardinality=1} ! Sequence record
[Term]
id: EDAM_operation:0368
name: Sequence masking
namespace: operation
def: Mask characters in a molecular sequence (replacing those characters with a mask character).
comment: For example, SNPs or repeats in a DNA sequence might be masked.
subset: operations
is_a: EDAM_operation:0231 ! Sequence editing
relationship: has_input EDAM_data:0851 {min_cardinality=1} ! Sequence mask character
[Term]
id: EDAM_operation:3180
name: Sequence assembly evaluation
namespace: operation
def: Evaluate a DNA sequence assembly, typically for purposes of quality control.
subset: operations
is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid)
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis
is_a: EDAM_operation:2425 ! Optimisation and refinement
relationship: has_input EDAM_data:0925 ! Sequence assembly
relationship: has_output EDAM_data:3181 ! Sequence assembly report
relationship: has_topic EDAM_topic:0196 ! Sequence assembly
|
| 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 |
| 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 |
| 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.