EMBOSS: drfinddata

drfinddata

Wiki

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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:6.4.0.0

   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

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 0000781 | Virus
EDAMtpc 0000780 | Plant
EDAMdat 0002307 | Virus annotation
EDAMdat 0002308 | Virus annotation (taxonomy)
EDAMid  0002733 | Genus name (virus)
EDAMid  0002734 | Family name (virus)
EDAMid  0002836 | DPVweb ID
EDAMfmt 0002331 | 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 0000781 | Virus
EDAMtpc 0000643 | Genomes
EDAMdat 0002307 | Virus annotation
EDAMid  0002784 | RNAVirusDB ID
EDAMfmt 0002331 | 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.

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	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

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Output file format

Output files for usage example

File: drfinddata.drcat

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments