EMBOSS: drfindresource manual

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 pathogens 
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:6.6.0.0

   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.

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

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: drfindresource.drcat

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments