|   | edamhasinput | 
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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:6.6.0.0
   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:1780 name: Sequence submission namespace: operation def: Submit a molecular sequence to a database. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" is_a: EDAM_operation:2446 ! Sequence processing relationship: has_input EDAM_data:2044 ! Sequence relationship: has_topic EDAM_topic:3077 ! Data acquisition and deposition [Term] id: EDAM_operation:0564 name: Sequence rendering namespace: operation def: Visualise, format or render a molecular sequence, possibly with sequence features or properties shown. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2446 ! Sequence processing relationship: has_input EDAM_data:2044 ! Sequence relationship: has_output EDAM_data:2969 ! Sequence image [Term] id: EDAM_operation:2451 name: Sequence comparison namespace: operation def: Compare two or more molecular sequences. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2424 ! Comparison relationship: has_input EDAM_data:2044 ! Sequence relationship: has_output EDAM_data:2955 ! Sequence report relationship: has_topic EDAM_topic:0159 ! Sequence comparison [Term] id: EDAM_operation:0292 name: Sequence alignment construction namespace: operation def: Align (identify equivalent sites within) molecular sequences. subset: bioinformatics subset: edam subset: operations [Part of this file has been deleted for brevity] subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" is_a: EDAM_operation:0338 ! Sequence database search relationship: has_input EDAM_data:1267 ! Amino acid frequencies relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis [Term] id: EDAM_operation:0566 name: Sequence cluster rendering namespace: operation def: Visualise, format or render sequence clusters. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2452 ! Sequence cluster processing relationship: has_input EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_operation:2507 name: Sequence alignment analysis (nucleic acid) namespace: operation def: Analyse a protein sequence alignment, typically to detect features or make predictions. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" is_a: EDAM_operation:0258 ! Sequence alignment analysis is_a: EDAM_operation:2501 ! Nucleic acid data processing is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) relationship: has_input EDAM_data:1383 ! Sequence alignment (nucleic acid) relationship: has_topic EDAM_topic:0740 ! Nucleic acid sequence alignment [Term] id: EDAM_operation:2479 name: Protein sequence analysis namespace: operation def: Analyse a protein sequence (using methods that are only applicable to protein sequences). subset: bioinformatics subset: edam subset: operations synonym: "Sequence analysis (protein)" EXACT [] created_in: "beta12orEarlier" is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2447 ! Sequence processing (protein) relationship: has_input EDAM_data:2976 ! Protein sequence relationship: has_topic EDAM_topic:0639 ! Protein sequence analysis | 
| 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.