                               drfindresource



Wiki

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   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:6.5.6.0

   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
