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drfindresource |
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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 'etpc' EDAM topic index.
% drfindresource pathogen Find public databases by resource Data resource output file [drfindresource.drcat]: |
Go to the output files for this example
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 |
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 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
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| 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 |
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