edamisformat 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 is_format_of relation Description edamisformat searches the is_format_of relations 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 edamisformat % edamisformat sequence Find EDAM ontology terms by is_format_of relation Obo output file [edamisformat.obo]: Go to the output files for this example Command line arguments Find EDAM ontology terms by is_format_of relation Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-identifier] string Identifier(s) to search for in ontology (Any string) [-outfile] outobo [*.edamisformat] 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 Input file format edamisformat 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: edamisformat.obo [Term] id: EDAM_format:2352 name: BioXSD namespace: format def: BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more). subset: bioinformatics subset: edam subset: formats synonym: "BioXSD XML format" EXACT [] xref: http://bioxsd.org created_in: "beta12orEarlier" documentation: http://bioxsd.org is_a: EDAM_format:1919 ! Sequence record format is_a: EDAM_format:1920 ! Sequence feature annotation format is_a: EDAM_format:2332 ! XML is_a: EDAM_format:2555 ! Alignment format (XML) is_a: EDAM_format:2571 ! Raw sequence format relationship: is_format_of EDAM_data:0863 ! Sequence alignment relationship: is_format_of EDAM_data:1255 ! Feature record relationship: is_format_of EDAM_data:2044 ! Sequence [Term] id: EDAM_format:2055 name: Sequence assembly format namespace: format def: Format for sequence assembly data. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0925 ! Sequence assembly [Term] id: EDAM_format:2014 name: Sequence-profile alignment format namespace: format def: Data format for a sequence-profile alignment. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0869 ! Sequence-profile alignment [Term] id: EDAM_format:2068 name: Sequence motif format namespace: format def: Format of a sequence motif. [Part of this file has been deleted for brevity] relationship: is_format_of EDAM_data:1255 ! Feature record [Term] id: EDAM_format:2057 name: Sequence trace format namespace: format def: Format for sequence trace data (i.e. including base call information). subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" is_a: EDAM_format:1919 ! Sequence record format relationship: is_format_of EDAM_data:0924 ! Sequence trace [Term] id: EDAM_format:2159 name: Gene features (coding region) format namespace: format def: Format used for report on coding regions in nucleotide sequences. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" is_a: EDAM_format:2031 ! Gene annotation format relationship: is_format_of EDAM_data:1313 ! Nucleic acid features (coding sequen ce) [Term] id: EDAM_format:2571 name: Raw sequence format namespace: format def: Format of a raw molecular sequence (i.e. the alphabet used). subset: bioinformatics subset: edam subset: formats synonym: "Symbol_sequence" RELATED [] created_in: "beta12orEarlier" is_a: EDAM_format:2350 ! Format (typed) relationship: is_format_of EDAM_data:0848 ! Raw sequence [Term] id: EDAM_format:2920 name: Alignment format (pair only) namespace: format def: Data format for molecular sequence alignment information that can hold sequ ence alignment(s) of only 2 sequences. subset: bioinformatics subset: edam subset: formats created_in: "beta12orEarlier" is_a: EDAM_format:1921 ! Alignment format relationship: is_format_of EDAM_data:1381 ! Sequence alignment (pair) 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 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 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