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drfindformat |
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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 'efmt' EDAM format index.
% drfindformat fasta Find public databases by format Data resource output file [drfindformat.drcat]: |
Go to the output files for this example
Find public databases by format
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-query] string List of EDAM data keywords (Any string)
[-outfile] outresource [*.drfindformat] 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
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| 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 | <*>.drfindformat |
| 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 dbEST
Name dbEST database of EST sequences
Desc dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
URL http://www.ncbi.nlm.nih.gov/dbEST/
Cat Not available
Taxon 1 | all
EDAMtpc 0000655 | mRNA, EST or cDNA
EDAMdat 0000849 | Sequence record
EDAMid 0002314 | GI number
EDAMid 0001105 | dbEST accession
EDAMfmt 0002310 | FASTA-HTML
EDAMfmt 0002532 | GenBank-HTML
EDAMfmt 0002331 | HTML
Xref SP_FT | None
Query Sequence record | GenBank-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Query Sequence record | HTML {est} | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=est
Query Sequence record | HTML {docsum} | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=docsum
Query Sequence record | FASTA-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=fasta
Query Sequence record | GenBank-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Query Sequence record | GenBank-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Query Sequence record | HTML {est} | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=est
Query Sequence record | HTML {docsum} | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=docsum
Query Sequence record | FASTA-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=fasta
Query Sequence record | GenBank-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Example dbEST accession | f12345
Example GI number | 706694
ID REDIdb
Name RNA editing database (REDIdb)
Desc Sequences post-transcriptionally modified by RNA editing from primary databases and literature. All editing information such as substitutions, insertions and deletions occurring in a wide range of organisms is stored.
URL http://biologia.unical.it/py_script/overview.html
Taxon 1 | all
EDAMtpc 0000630 | Gene structure
EDAMdat 0002043 | Sequence record lite
EDAMdat 0001383 | Sequence alignment (nucleic acid)
EDAMid 0002781 | REDIdb ID
EDAMfmt 0002310 | FASTA-HTML
EDAMfmt 0002331 | HTML
Query Sequence record lite {REDIdb entry} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/retrieve.py?query=%s
Query Sequence record lite {REDIdb fasta} | FASTA-HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/fasta.py?query=%s
Query Sequence alignment (nucleic acid) {REDIdb overview} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/display.py?query=%s
Query Sequence alignment (nucleic acid) {REDIdb alignment} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/align.py?query=%s
Example REDIdb ID | EDI_000000002
ID UniRef
Name Non-redundant reference (UniRef) databases
Desc Clustered sets of sequences from UniProt Knowledgebase (including splice variants and isoforms) and selected UniParc records, in order to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.
URL http://www.uniprot.org/help/uniref
Cat Other
Taxon 1 | all
[Part of this file has been deleted for brevity]
Xref SP_FT | None
Query Sequence record full | HTML | UniProt accession | http://www.uniprot.org/uniprot/%s
Query Sequence record full | uniprot | UniProt accession | http://www.uniprot.org/uniprot/%s.txt
Query Sequence record full | XML | UniProt accession | http://www.uniprot.org/uniprot/%s.xml
Query Sequence record full | RDF | UniProt accession | http://www.uniprot.org/uniprot/%s.rdf
Query Sequence record full | FASTA format | UniProt accession | http://www.uniprot.org/uniprot/%s.fasta
Example UniProt accession | P12345
ID Ensembl
Acc DB-0023
Name Ensembl eukaryotic genome annotation project
Desc Genome databases for vertebrates and other eukaryotic species.
URL http://www.ensembl.org/
Cat Genome annotation databases
Taxon 33208 | Metazoa
EDAMtpc 0000643 | Genomes
EDAMtpc 0002818 | Eukaryote
EDAMtpc 0000643 | Genomes
EDAMdat 0000849 | Sequence record
EDAMdat 0000916 | Gene annotation
EDAMid 0001033 | Gene ID (Ensembl)
EDAMid 0002725 | Transcript ID (Ensembl)
EDAMfmt 0001929 | FASTA format
EDAMfmt 0002331 | HTML
Xref SP_explicit | Transcript ID (Ensembl);Protein ID (Ensembl);Gene ID (Ensembl)
Xref SP_FT | None
Query Gene annotation | HTML | Gene ID (Ensembl) | http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=%s
Query Sequence record | FASTA format | Gene ID (Ensembl);Transcript ID (Ensembl) | http://www.ensembl.org/Homo_sapiens/Gene/Export?db=core;g=%s1;output=fasta;r=13:31787617-31871809;strand=feature;t=%s2;time=1244110856.85314;st=cdna;st=coding;st=peptide;st=utr5;st=utr3;st=exons;st=introns;genomic=unmasked;_format=Text
Example Gene ID (Ensembl);Transcript ID (Ensembl) | ENSG00000139618;ENST00000380152
ID UniProtKB/Swiss-Prot
IDalt SwissProt
Name Universal protein resource knowledge base / Swiss-Prot
Desc Section of the UniProt knowledgebase, containing annotated records, which include curator-evaluated computational analysis, as well as, information extracted from the literature
URL http://www.uniprot.org
Taxon 1 | all
EDAMtpc 0000639 | Protein sequences
EDAMdat 0002201 | Sequence record full
EDAMid 0003021 | UniProt accession
EDAMfmt 0001929 | FASTA format
EDAMfmt 0002376 | RDF
EDAMfmt 0002331 | HTML
EDAMfmt 0002332 | XML
Xref EMBL_explicit | UniProt accession
Query Sequence record full | HTML | UniProt accession | http://www.uniprot.org/uniprot/%s
Query Sequence record full | Text | UniProt accession | http://www.uniprot.org/uniprot/%s.txt
Query Sequence record full | XML | UniProt accession | http://www.uniprot.org/uniprot/%s.xml
Query Sequence record full | RDF | UniProt accession | http://www.uniprot.org/uniprot/%s.rdf
Query Sequence record full | FASTA format | UniProt accession | http://www.uniprot.org/uniprot/%s.fasta
Example UniProt accession | P12345
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| Program name | Description |
|---|---|
| drfinddata | Find public databases by data type |
| 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 | 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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