drfinddata 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 public databases by data type Description drfinddata searches the Data Resource Catalogue to find entries with EDAM data terms matching a query string. Algorithm The first search is of the EDAM ontology data namespace, using the term names and their synonynms. All child terms are automatically included in the set of matches inless the -nosubclasses qualifier is used. The -sensitive qualifier also searches the definition strings. The set of EDAM terms are then compared to entries in the Data Resource Catalogue, searching the 'edat' EDAM data index. Usage Here is a sample session with drfinddata % drfinddata virus Find public databases by data type Data resource output file [drfinddata.drcat]: Go to the output files for this example Command line arguments Find public databases by data type Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-query] string List of EDAM data keywords (Any string) [-outfile] outresource [*.drfinddata] Output data resource file name Additional (Optional) qualifiers: (none) 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. -[no]subclasses boolean [Y] Extend the query matches to include all terms which are specialisations (EDAM sub-classes) of the matched type. Associated qualifiers: "-outfile" associated qualifiers -odirectory2 string Output directory -oformat2 string Data resource 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 None. Output file format The output is a standard EMBOSS resource 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: drcat, basic, wsbasic, list. See: http://emboss.sf.net/docs/themes/ResourceFormats.html for further information on resource formats. Output files for usage example File: drfinddata.drcat ID DPVweb Name DPVweb database of plant viruses Desc Information about viruses, viroids and satellites of plants, fungi and p rotozoa, with some additional data on related animal viruses. URL http://www.dpvweb.net/ Taxon 10239 | Viruses EDAMtpc 0000781 | Virus EDAMtpc 0000780 | Plant EDAMdat 0002307 | Virus annotation EDAMdat 0002308 | Virus annotation (taxonomy) EDAMid 0002733 | Genus name (virus) EDAMid 0002734 | Family name (virus) EDAMid 0002836 | DPVweb ID EDAMfmt 0002331 | HTML Query Virus annotation | HTML | DPVweb ID | http://www.dpvweb.net/dpv/showdpv .php?dpvno=%s Query Virus annotation (taxonomy) | HTML | Family name (virus) | http://www.d pvweb.net/notes/showfamily.php?family=%s Query Virus annotation (taxonomy) | HTML | Genus name (virus) | http://www.dp vweb.net/notes/showgenus.php?genus=%s Example DPVweb ID | 1 Example Family name (virus) | Alphaflexiviridae Example Genus name (virus) | Alfamovirus ID RNAVirusDB Name RNA virus genome database (RNAVirusDB) Desc RNA virus genome database. URL http://tree.bio.ed.ac.uk/rnavirusdb Taxon 10239 | Viruses EDAMtpc 0000781 | Virus EDAMtpc 0000643 | Genomes EDAMdat 0002307 | Virus annotation EDAMid 0002784 | RNAVirusDB ID EDAMfmt 0002331 | HTML Query Virus annotation | HTML | RNAVirusDB ID | http://tree.bio.ed.ac.uk/rnav irusdb/virus.php?id=%s Example RNAVirusDB ID | 56486 Data files The Data Resource Catalogue is included in EMBOSS as local database drcat. 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 drfindformat Find public databases by format drfindid Find public databases by identifier drfindresource Find public databases by resource drget Get data resource entries drtext Get data resource entries complete text 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 edamname Find EDAM ontology terms by name wossdata Finds programs by EDAM data wossinput Finds programs by EDAM input data wossoperation Finds programs by EDAM operation wossoutput Finds programs by EDAM output data wossparam Finds programs by EDAM parameter wosstopic Finds 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