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drfindformat
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 format
Description
drfindformat searches the Data Resource Catalogue to find entries with
EDAM format terms matching a query string.
Algorithm
The first search is of the EDAM ontology format 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 'efmt' EDAM format index.
Usage
Here is a sample session with drfindformat
% drfindformat fasta
Find public databases by format
Data resource output file [drfindformat.drcat]:
Go to the output files for this example
Command line arguments
Find public databases by format
Version: EMBOSS:6.6.0.0
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
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: drfindformat.drcat
ID UniProtKB_Swiss-Prot
IDalt SwissProt
Name Universal protein resource knowledge base / Swiss-Prot
Desc Section of the UniProt knowledgebase, containing annotated records, whic
h include curator-evaluated computational analysis, as well as, information extr
acted from the literature
URL http://www.uniprot.org
Taxon 1 | all
EDAMtpc 0639 | Protein sequence analysis
EDAMdat 2201 | Sequence record full
EDAMid 3021 | UniProt accession
EDAMfmt 1929 | FASTA format
EDAMfmt 2376 | RDF
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref EMBL_explicit | UniProt accession
Query Sequence record full | HTML | UniProt accession | http://www.uniprot.or
g/uniprot/%s
Query Sequence record full | Text | UniProt accession | http://www.uniprot.or
g/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.un
iprot.org/uniprot/%s.fasta
Example UniProt accession | P12345
ID UniProtKB_TrEMBL
IDalt TrEMBL
Name Universal protein resource knowledge base / Swiss-Prot
Desc Section of the UniProt knowledgebase, containing computationally analyse
d records waiting for full manual annotation
URL http://www.uniprot.org/
Taxon 1 | all
EDAMtpc 0639 | Protein sequence analysis
EDAMdat 2201 | Sequence record full
EDAMid 3021 | UniProt accession
EDAMfmt 1929 | FASTA format
EDAMfmt 2376 | RDF
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref SP_FT | None
Query Sequence record full | HTML | UniProt accession | http://www.uniprot.or
g/uniprot/%s
Query Sequence record full | Text | UniProt accession | http://www.uniprot.or
g/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.un
iprot.org/uniprot/%s.fasta
Example UniProt accession | Q00177
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 2818 | Eukaryotes
[Part of this file has been deleted for brevity]
Query Sequence record full | HTML | UniProt accession | http://www.uniprot.or
g/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.un
iprot.org/uniprot/%s.fasta
Example UniProt accession | P12345
ID dbEST
Name dbEST database of EST sequences
Desc dbEST is a division of GenBank that contains sequence data and other inf
ormation on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a n
umber of organisms.
URL http://www.ncbi.nlm.nih.gov/dbEST/
Cat Not available
Taxon 1 | all
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMdat 0849 | Sequence record
EDAMid 2314 | GI number
EDAMid 1105 | dbEST accession
EDAMfmt 2310 | FASTA-HTML
EDAMfmt 2532 | GenBank-HTML
EDAMfmt 2331 | 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.ni
h.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.ni
h.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.go
v/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.g
ov/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.go
v/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 da
tabases and literature. All editing information such as substitutions, insertion
s and deletions occurring in a wide range of organisms is stored.
URL http://biologia.unical.it/py_script/overview.html
Taxon 1 | all
EDAMtpc 0114 | Gene structure and RNA splicing
EDAMdat 2043 | Sequence record lite
EDAMdat 1383 | Sequence alignment (nucleic acid)
EDAMid 2781 | REDIdb ID
EDAMfmt 2310 | FASTA-HTML
EDAMfmt 2331 | HTML
Query Sequence record lite {REDIdb entry} | HTML | REDIdb ID | http://biologi
a.unical.it/py_script/cgi-bin/retrieve.py?query=%s
Query Sequence record lite {REDIdb fasta} | FASTA-HTML | REDIdb ID | http://b
iologia.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
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
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
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 (c) 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
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