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 pathogen 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:6.4.0.0 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_PlasmoDB IDalt PlasmoDB Name Plasmodium genome resources (PlasmoDB) Desc Genomic-scale dataset associated with the eukaryotic pathogens Plasmodiu m. URL http://plasmodb.org/plasmo/ URLrest http://eupathdb.org/eupathdb/serviceList.jsp Cat Not available Taxon 5820 | Plasmodium EDAMtpc 0002821 | Unicellular eukaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000783 | Pathogen EDAMdat 0000916 | Gene annotation EDAMid 0002295 | Gene ID EDAMfmt 0002331 | HTML Xref SP_FT | None Query Gene annotation | HTML | Gene ID | http://plasmodb.org/gene/%s Example Gene ID | PF11_0344 ID COGEME Name Phytopathogenic fungi and oomycete EST database (COGEME) Desc Phytopathogenic fungi and oomycete EST database. URL http://cogeme.ex.ac.uk/ Taxon 4751 | Fungi EDAMtpc 0000655 | mRNA, EST or cDNA EDAMtpc 0000783 | Pathogen EDAMtpc 0000782 | Fungal EDAMdat 0000849 | Sequence record EDAMid 0002729 | COGEME EST ID EDAMid 0002730 | COGEME unisequence ID EDAMfmt 0002331 | HTML Query Sequence record {Unisequence} | HTML | COGEME unisequence ID | http://c ogeme.ex.ac.uk/cgi-bin/uni.pl?uni=x Query Sequence record {EST} | HTML | COGEME EST ID | http://cogeme.ex.ac.uk/c gi-bin/est.pl?est=x Example COGEME EST ID | Bg13901527 Example COGEME unisequence ID | BgCon[0123] 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 0002821 | Unicellular eukaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000783 | Pathogen EDAMdat 0000916 | Gene annotation EDAMid 0002295 | Gene ID EDAMfmt 0002331 | HTML Xref SP_FT | None [Part of this file has been deleted for brevity] Name Enteropathogen resource integration center (ERIC) Desc Annotated enterobacterial genome and associated information. URL http://www.ericbrc.org/portal/eric/ Cat Not available Taxon 543 | Enterobacteriaceae EDAMtpc 0001811 | Prokaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000783 | Pathogen Xref SP_FT | None 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 0000643 | Genomes EDAMtpc 0000783 | Pathogen EDAMtpc 0000797 | Comparative genomics EDAMdat 0000916 | Gene annotation EDAMid 0001179 | NCBI taxonomy ID EDAMid 0002737 | FIG ID EDAMfmt 0002331 | 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 ID Pathema Name Pathema: a clade-specific bioinformatics resource Desc Genome database for six clades of Category A-C pathogens aEUR" Bacillus anthracis, Clostridium botulinum, Burkholderia mallei, Burkholderia pseudomallei , Clostridium perfringens, Entamoeba histolytica. URL http://www.jcvi.org/cms/research/projects/pathema/overview/ Cat Not available Taxon 1 | all EDAMtpc 0001811 | Prokaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000783 | Pathogen Xref SP_FT | None ID PHI-base Name PHI-base pathogen host interactions database Desc Curated molecular and biological information on genes proven to affect t he outcome of pathogen-host interactions. Information is also given on the targe t sites of some anti-infective chemistries. URL http://www.phibase.org Taxon 1 | all EDAMtpc 0000623 | Gene family or system EDAMtpc 0000783 | Pathogen 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 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