drfindresource 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 resource Description drfindresource searches the Data Resource Catalogue to find entries with EDAM resource terms matching a query string. Algorithm The first search is of the EDAM ontology topic 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 'etpc' EDAM topic index. Usage Here is a sample session with drfindresource % drfindresource pathogens Find public databases by resource Data resource output file [drfindresource.drcat]: Go to the output files for this example Command line arguments Find public databases by resource Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-query] string List of EDAM data keywords (Any string) [-outfile] outresource [*.drfindresource] 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: drfindresource.drcat ID ApiDB_TrichDB IDalt TrichDB Name Trichomonas genome resources (TrichDB) Desc Genomic-scale datasets associated with the eukaryotic Trichomonas. URL http://trichdb.org/trichdb/ URLrest http://eupathdb.org/eupathdb/serviceList.jsp Cat Not available Taxon 5721 | Trichomonas EDAMtpc 2821 | Unicellular eukaryotes EDAMtpc 0783 | Pathogens EDAMdat 0916 | Gene annotation EDAMid 2295 | Gene ID EDAMfmt 2331 | HTML Xref SP_FT | None Query Gene annotation | HTML | Gene ID | http://trichdb.org/gene/%s Example Gene ID | TVAG_386080 ID ApiDB_GiardiaDB IDalt GiardiaDB Name Giardia genome resources (GiardiaDB) Desc Genomic-scale datasets for the eukaryotic pathogen Giardia. URL http://giardiadb.org/giardiadb/ URLrest http://eupathdb.org/eupathdb/serviceList.jsp Cat Not available Taxon 5740 | Giardia EDAMtpc 2821 | Unicellular eukaryotes EDAMtpc 0783 | Pathogens EDAMdat 0916 | Gene annotation EDAMid 2295 | Gene ID EDAMfmt 2331 | HTML Xref SP_FT | None Query Gene annotation | HTML | Gene ID | http://giardiadb.org/gene/%s Example Gene ID | GL50803_102438 ID GeneDB Name GeneDB database from Sanger Institute Pathogen Sequencing Units Desc Sequence data and annotation/curation for the whole range of organisms s equenced by the PSU (Sanger Institute Pathogen Sequencing Units). URL http://www.genedb.org/ Taxon 1 | all EDAMtpc 0783 | Pathogens EDAMdat 0916 | Gene annotation EDAMid 1026 | Gene symbol EDAMfmt 2331 | HTML Xref SP_FT | None Query Gene annotation | HTML | Gene symbol | http://www.genedb.org/gene/%s Example Gene symbol | ECA4014 ID EuPathDB IDalt ApiDB Acc DB-0153 [Part of this file has been deleted for brevity] Taxon 1 | all EDAMtpc 0783 | Pathogens EDAMdat 2399 | Gene annotation (transcript) EDAMdat 0895 | Peptide annotation EDAMdat 0916 | Gene annotation EDAMid 2759 | Gene ID (VectorBase) EDAMfmt 2331 | HTML Xref SP_explicit | Gene ID (VectorBase) Query Gene annotation {VectorBase entry} | HTML | Gene ID (VectorBase) | http ://www.vectorbase.org/Genome/BRCGene/?feature=%s Query Peptide annotation {VectorBase peptide page} | HTML | Gene ID (VectorBa se) | http://www.vectorbase.org/Genome/BRCGene/?feature=%s-PA Query Gene annotation (transcript) | HTML | Gene ID (VectorBase) | http://www .vectorbase.org/Genome/BRCGene/?feature=%s-RA Example Gene ID (VectorBase) | AGAP005025 ID ApiDB_TriTryPDB IDalt TritryPDB Name Kinetoplastid genome resources (TritryPDB) Desc Kinetoplastid genome resources. URL http://tritryPDB.org/tritryPDB/ URLrest http://eupathdb.org/eupathdb/serviceList.jsp Cat Not available Taxon 5653 | Kinetoplastida EDAMtpc 2821 | Unicellular eukaryotes EDAMtpc 0783 | Pathogens EDAMdat 0916 | Gene annotation EDAMid 2295 | Gene ID EDAMfmt 2331 | HTML Xref SP_FT | None Query Gene annotation | HTML | Gene ID | http://tritryPDB.org/gene/%s Example Gene ID | Tb927.8.620 ID NMPDR Acc DB-0125 Name National microbial pathogen Desc Curated annotations in an environment for comparative analysis of genome s and biological subsystems, with an emphasis on the food-borne pathogens Campyl obacter, Listeria, Staphylococcus, Streptococcus, and Vibrio as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Urea plasma. URL http://www.nmpdr.org URLlink http://www.nmpdr.org/FIG/wiki/view.cgi/FIG/LinkingToTheGenomeViewer Cat Genome annotation databases Taxon 2 | Bacteria EDAMtpc 0783 | Pathogens EDAMtpc 0797 | Comparative genomics EDAMdat 0916 | Gene annotation EDAMid 1179 | NCBI taxonomy ID EDAMid 2737 | FIG ID EDAMfmt 2331 | HTML Xref SP_explicit | FIG ID Query Gene annotation | HTML | NCBI taxonomy ID | http://www.nmpdr.org/linkin .cgi?genome=%s Query Gene annotation {Protein encoding gene or other feature} | HTML | FIG I D | http://www.nmpdr.org/linkin.cgi?id=%s Example NCBI taxonomy ID | 83333.1 Example FIG ID | 83333.1.peg.123 Example FIG ID | 83333.1.rna.1 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 drfinddata Find public databases by data type drfindformat Find public databases by format drfindid Find public databases by identifier 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 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