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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:6.6.0.0
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
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
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