                                drfindformat



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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
