|   | edamname | 
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Optionally the search can be restricted to specified EDAM namespaces.
| % edamname "*sequence_set*" Find EDAM ontology terms by name Obo output file [edamname.obo]: | 
Go to the output files for this example
Example 2
| % edamname "*sequence_set*" -subclasses Find EDAM ontology terms by name Obo output file [edamname.obo]: | 
Go to the output files for this example
| 
Find EDAM ontology terms by name
Version: EMBOSS:6.6.0.0
   Standard (Mandatory) qualifiers:
  [-query]             string     Name(s) to search for in ontology (Any
                                  string)
  [-outfile]           outobo     [*.edamname] 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 | Name(s) to search for in ontology | Any string | |||||||||||||||
| [-outfile] (Parameter 2) | outobo | Output ontology term file name | OBO ontology term(s) | <*>.edamname | ||||||||||||||
| 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_data:1233 name: Sequence set (protein) namespace: data def: Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1064 name: Sequence set ID namespace: identifier def: An identifier of a set of molecular sequence(s). subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:0850 name: Sequence set namespace: data def: A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method. comment: This concept may be used for arbitrary sequence sets and associated data arising from processing. subset: bioinformatics subset: data subset: edam synonym: "SO:0001260" RELATED [] created_in: "beta12orEarlier" is_a: EDAM_data:2955 ! Sequence report [Term] id: EDAM_data:1234 name: Sequence set (nucleic acid) namespace: data def: Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set is_a: EDAM_data:2977 ! Nucleic acid sequence [Term] id: EDAM_data:2245 name: Sequence set (bootstrapped) namespace: data def: A collection of sequences output from a bootstrapping (resampling) procedure. comment: Bootstrapping is often performed in phylogenetic analysis. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set | 
| [Term] id: EDAM_data:1233 name: Sequence set (protein) namespace: data def: Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1245 name: Sequence cluster (protein) namespace: data def: A cluster of protein sequences. comment: The sequences are typically related, for example a family of sequences. subset: bioinformatics subset: data subset: edam synonym: "Protein sequence cluster" EXACT [] created_in: "beta12orEarlier" is_a: EDAM_data:1233 ! Sequence set (protein) is_a: EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:1262 name: Peptide molecular weight hits namespace: data def: A report on peptide fragments of certain molecular weight(s) in one or more protein sequences. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:1233 ! Sequence set (protein) [Term] id: EDAM_data:1238 name: Proteolytic digest namespace: data def: A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:1233 ! Sequence set (protein) relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_data:1064 [Part of this file has been deleted for brevity] id: EDAM_data:1246 name: Sequence cluster (nucleic acid) namespace: data def: A cluster of nucleotide sequences. comment: The sequences are typically related, for example a family of sequences. subset: bioinformatics subset: data subset: edam synonym: "Nucleotide sequence cluster" EXACT [] created_in: "beta12orEarlier" is_a: EDAM_data:1234 ! Sequence set (nucleic acid) is_a: EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:1239 name: Restriction digest namespace: data def: Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease. subset: bioinformatics subset: data subset: edam xref: SO:0000412 created_in: "beta12orEarlier" is_a: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] id: EDAM_data:2245 name: Sequence set (bootstrapped) namespace: data def: A collection of sequences output from a bootstrapping (resampling) procedure. comment: Bootstrapping is often performed in phylogenetic analysis. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1235 name: Sequence cluster namespace: data def: A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information. comment: The cluster might include sequences identifiers, short descriptions, alignment and summary information. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set relationship: has_topic EDAM_topic:0724 ! Protein families relationship: has_topic EDAM_topic:3052 ! Sequence clusters and classification | 
| 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 | 
| edamisformat | Find EDAM ontology terms by is_format_of relation | 
| edamisid | Find EDAM ontology terms by is_identifier_of relation | 
| 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.