|   | edamdef | 
Please help by correcting and extending the Wiki pages.
Optionally the search can be restricted to specified EDAM namespaces.
| % edamdef multiple Find EDAM ontology terms by definition Obo output file [edamdef.obo]: | 
Go to the output files for this example
Example 2
| % edamdef multiple -subclasses Find EDAM ontology terms by definition Obo output file [edamdef.obo]: | 
Go to the output files for this example
| 
Find EDAM ontology terms by definition
Version: EMBOSS:6.6.0.0
   Standard (Mandatory) qualifiers:
  [-query]             string     Definition word(s) to search for in ontology
                                  (Any string)
  [-outfile]           outobo     [*.edamdef] 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:
   -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 | ||||||||||||||||||
| [-query] (Parameter 1) | string | Definition word(s) to search for in ontology | Any string | |||||||||||||||
| [-outfile] (Parameter 2) | outobo | Output ontology term file name | OBO ontology term(s) | <*>.edamdef | ||||||||||||||
| Additional (Optional) qualifiers | ||||||||||||||||||
| -namespace | list | By default all terms are returned. Searches can be limited to one or a few namespaces. | 
 | * | ||||||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||||||||||
| -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:1391 name: HMMER-aln namespace: format def: FASTA-style format for multiple sequences aligned by HMMER package to an HMM. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" is_a: EDAM_format:2200 ! FASTA-like (text) is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_data:1383 name: Sequence alignment (nucleic acid) namespace: data def: Alignment of multiple nucleotide sequences. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0863 ! Sequence alignment is_a: EDAM_data:2084 ! Nucleic acid report [Term] id: EDAM_topic:0797 name: Comparative genomics namespace: topic def: Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes. subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Comparative Genomics created_in: "beta12orEarlier" is_a: EDAM_topic:0622 ! Genomics [Term] id: EDAM_format:2001 name: EMBOSS simple format namespace: format def: EMBOSS simple multiple alignment format. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) [Term] [Part of this file has been deleted for brevity] subset: operations synonym: "Multiple sequence alignment (phylogenetic tree-based)" EXACT [] synonym: "Phylogenetic tree-based multiple sequence alignment construction" EXACT [] created_in: "beta12orEarlier" is_a: EDAM_operation:0492 ! Multiple sequence alignment construction relationship: has_topic EDAM_topic:0084 ! Phylogenetics [Term] id: EDAM_operation:0498 name: Multiple sequence alignment construction (consensus) namespace: operation def: Align two or more molecular sequences using multiple methods to achieve higher quality. subset: bioinformatics subset: edam subset: operations synonym: "Consensus multiple sequence alignment construction" EXACT [] synonym: "Multiple sequence alignment (consensus)" EXACT [] created_in: "beta12orEarlier" is_a: EDAM_operation:0492 ! Multiple sequence alignment construction [Term] id: EDAM_operation:0434 name: Integrated gene prediction namespace: operation def: Predict whole gene structure using a combination of multiple methods to achieve better predictions. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" is_a: EDAM_operation:0425 ! Whole gene prediction [Term] id: EDAM_data:0842 name: Identifier namespace: identifier def: A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things). subset: bioinformatics subset: data subset: edam subset: identifiers synonym: "WSIO_data:005" EXACT [] synonym: "http://purl.org/dc/elements/1.1/identifier" NARROW [] synonym: "ID" EXACT [] synonym: "SIO:000115" EXACT [] created_in: "beta12orEarlier" is_a: EDAM_data:0006 ! Data disjoint_from: EDAM_data:2048 ! Report disjoint_from: EDAM_data:2527 ! Parameter disjoint_from: EDAM_data:3031 ! Core data relationship: is_identifier_of EDAM_data:0006 ! Data | 
| [Term] id: EDAM_format:1391 name: HMMER-aln namespace: format def: FASTA-style format for multiple sequences aligned by HMMER package to an HMM. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" is_a: EDAM_format:2200 ! FASTA-like (text) is_a: EDAM_format:2330 ! Textual format is_a: EDAM_format:2554 ! Alignment format (text) [Term] id: EDAM_data:1383 name: Sequence alignment (nucleic acid) namespace: data def: Alignment of multiple nucleotide sequences. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0863 ! Sequence alignment is_a: EDAM_data:2084 ! Nucleic acid report [Term] id: EDAM_data:1386 name: Sequence alignment (nucleic acid pair) namespace: data def: Alignment of exactly two nucleotide sequences. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:1381 ! Sequence alignment (pair) is_a: EDAM_data:1383 ! Sequence alignment (nucleic acid) [Term] id: EDAM_topic:0797 name: Comparative genomics namespace: topic def: Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes. subset: bioinformatics subset: edam subset: topics xref: BioCatalogue:Comparative Genomics created_in: "beta12orEarlier" is_a: EDAM_topic:0622 ! Genomics [Term] [Part of this file has been deleted for brevity] regex: "[0-9]+" is_a: EDAM_data:2091 ! Accession [Term] id: EDAM_data:1047 name: URI namespace: data def: A string of characters that name or otherwise identify a resource on the Internet. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0842 ! Identifier [Term] id: EDAM_data:1052 name: URL namespace: data def: A Uniform Resource Locator (URL). subset: bioinformatics subset: data subset: edam xref: Moby:Link xref: Moby:URL created_in: "beta12orEarlier" is_a: EDAM_data:1047 ! URI [Term] id: EDAM_data:1053 name: URN namespace: data def: A Uniform Resource Name (URN). subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:1047 ! URI [Term] id: EDAM_data:1055 name: LSID namespace: data def: A Life Science Identifier (LSID) - a unique identifier of some data. comment: LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following EDAM_format: URN:LSID:<Authority>:<Namespace>:<ObjectID>[:<Version>] subset: bioinformatics subset: data subset: edam synonym: "Life Science Identifier" EXACT [] created_in: "beta12orEarlier" is_a: EDAM_data:1053 ! URN | 
| 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 | 
| 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 | 
| 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.