                                 drfinddata



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 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:6.5.6.0

   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 0781 | Viruses
EDAMtpc 0780 | Plants
EDAMdat 2307 | Virus annotation
EDAMdat 2308 | Virus annotation (taxonomy)
EDAMid  2733 | Genus name (virus)
EDAMid  2734 | Family name (virus)
EDAMid  2836 | DPVweb ID
EDAMfmt 2331 | 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 0781 | Viruses
EDAMdat 2307 | Virus annotation
EDAMid  2784 | RNAVirusDB ID
EDAMfmt 2331 | 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       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
