edamdef Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Find EDAM ontology terms by definition Description edamdef searches the definition of EDAM terms and returns matching terms. The input is read from the installed EDAM database. The ontology term output can be written to screen, to file, or passed to another program. A wide range of standard ontology term formats may be specified for input and output. Optionally the search can be restricted to specified EDAM namespaces. Usage Here is a sample session with edamdef % 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 Command line arguments 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 Input file format edamdef queries the EDAM ontology. Output file format 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. Output files for usage example File: edamdef.obo [Term] id: EDAM_format:1391 name: HMMER-aln namespace: format def: FASTA-style format for multiple sequences aligned by HMMER package to an HM M. 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, structur e 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" EXAC T [] 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 hig her 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 ach ieve 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 whic h may not be persistent (stable) or unique (the same identifier may identify mul tiple 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 Output files for usage example 2 File: edamdef.obo [Term] id: EDAM_format:1391 name: HMMER-aln namespace: format def: FASTA-style format for multiple sequences aligned by HMMER package to an HM M. 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, structur e 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 In ternet. 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 re presented as a Uniform Resource Name (URN) with the following EDAM_format: URN:L SID:::[:] subset: bioinformatics subset: data subset: edam synonym: "Life Science Identifier" EXACT [] created_in: "beta12orEarlier" is_a: EDAM_data:1053 ! URN Data files The EDAM Ontology is included in EMBOSS as local database edam. Notes None. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also 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 Author(s) Peter Rice European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None