EMBOSS: drfindresource

| 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:6.5.6.0

       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

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 | <*>.drfindresource
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: 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 sequenced 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 (VectorBase) | 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 genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.
    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 ID | 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 © 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