drfinddata |
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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.
% drfinddata virus Find public databases by data type Data resource output file [drfinddata.drcat]: |
Go to the output files for this example
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 |
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 |
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.
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 |
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 |
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