EMBOSS: drfinddata

| 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:6.5.6.0

       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

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-query] (Parameter 1) | string | List of EDAM data keywords | Any string |
[-outfile] (Parameter 2) | outresource | Output data resource file name | Data resource entry | <*>.drfinddata
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-sensitive | boolean | 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. | Boolean value Yes/No | No
-[no]subclasses | boolean | Extend the query matches to include all terms which are specialisations (EDAM sub-classes) of the matched type. | Boolean value Yes/No | Yes
Associated qualifiers
"-outfile" associated outresource qualifiers
-odirectory2 -odirectory_outfile | string | Output directory | Any string |
-oformat2 -oformat_outfile | string | Data resource output format | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## 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 protozoa, 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.dpvweb.net/notes/showfamily.php?family=%s
    Query    Virus annotation (taxonomy) | HTML | Genus name (virus) | http://www.dpvweb.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/rnavirusdb/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 © 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