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EMBOSS: drfindresource
drfindresource

 

Wiki

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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:6.4.0.0

   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_PlasmoDB
IDalt   PlasmoDB
Name    Plasmodium genome resources (PlasmoDB)
Desc    Genomic-scale dataset associated with the eukaryotic pathogens Plasmodium.
URL     http://plasmodb.org/plasmo/
URLrest http://eupathdb.org/eupathdb/serviceList.jsp
Cat     Not available
Taxon   5820 | Plasmodium
EDAMtpc 0002821 | Unicellular eukaryote
EDAMtpc 0000643 | Genomes
EDAMtpc 0000783 | Pathogen
EDAMdat 0000916 | Gene annotation
EDAMid  0002295 | Gene ID
EDAMfmt 0002331 | HTML
Xref    SP_FT | None
Query    Gene annotation | HTML | Gene ID | http://plasmodb.org/gene/%s
Example Gene ID | PF11_0344

ID      COGEME
Name    Phytopathogenic fungi and oomycete EST database (COGEME)
Desc    Phytopathogenic fungi and oomycete EST database.
URL     http://cogeme.ex.ac.uk/
Taxon   4751 | Fungi
EDAMtpc 0000655 | mRNA, EST or cDNA
EDAMtpc 0000783 | Pathogen
EDAMtpc 0000782 | Fungal
EDAMdat 0000849 | Sequence record
EDAMid  0002729 | COGEME EST ID
EDAMid  0002730 | COGEME unisequence ID
EDAMfmt 0002331 | HTML
Query    Sequence record {Unisequence} | HTML | COGEME unisequence ID | http://cogeme.ex.ac.uk/cgi-bin/uni.pl?uni=x
Query    Sequence record {EST} | HTML | COGEME EST ID | http://cogeme.ex.ac.uk/cgi-bin/est.pl?est=x
Example COGEME EST ID | Bg13901527
Example COGEME unisequence ID | BgCon[0123]

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 0002821 | Unicellular eukaryote
EDAMtpc 0000643 | Genomes
EDAMtpc 0000783 | Pathogen
EDAMdat 0000916 | Gene annotation
EDAMid  0002295 | Gene ID
EDAMfmt 0002331 | HTML
Xref    SP_FT | None


  [Part of this file has been deleted for brevity]

Name    Enteropathogen resource integration center (ERIC)
Desc    Annotated enterobacterial genome and associated information.
URL     http://www.ericbrc.org/portal/eric/
Cat     Not available
Taxon   543 | Enterobacteriaceae
EDAMtpc 0001811 | Prokaryote
EDAMtpc 0000643 | Genomes
EDAMtpc 0000783 | Pathogen
Xref    SP_FT | None

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 0000643 | Genomes
EDAMtpc 0000783 | Pathogen
EDAMtpc 0000797 | Comparative genomics
EDAMdat 0000916 | Gene annotation
EDAMid  0001179 | NCBI taxonomy ID
EDAMid  0002737 | FIG ID
EDAMfmt 0002331 | 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

ID      Pathema
Name    Pathema: a clade-specific bioinformatics resource
Desc    Genome database for six clades of Category A-C pathogens — Bacillus anthracis, Clostridium botulinum, Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens, Entamoeba histolytica.
URL     http://www.jcvi.org/cms/research/projects/pathema/overview/
Cat     Not available
Taxon   1 | all
EDAMtpc 0001811 | Prokaryote
EDAMtpc 0000643 | Genomes
EDAMtpc 0000783 | Pathogen
Xref    SP_FT | None

ID      PHI-base
Name    PHI-base pathogen host interactions database
Desc    Curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. Information is also given on the target sites of some anti-infective chemistries.
URL     http://www.phibase.org
Taxon   1 | all
EDAMtpc 0000623 | Gene family or system
EDAMtpc 0000783 | Pathogen

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 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

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