                                  drfindid



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Function

   Find public databases by identifier

Description

   drfindid searches the Data Resource Catalogue to find entries with EDAM
   data identifier terms matching a query string.

Algorithm

   The first search is of the EDAM ontology data 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 'eid' EDAM identifier index.

Usage

   Here is a sample session with drfindid


% drfindid "uniprot accession"
Find public databases by identifier
Data resource output file [drfindid.drcat]:


   Go to the output files for this example

Command line arguments

Find public databases by identifier
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-query]             string     List of EDAM data keywords (Any string)
  [-outfile]           outresource [*.drfindid] 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: drfindid.drcat

ID      PRIDE
Acc     DB-0130
Name    PRIDE proteomics identifications database
Desc    Standards compliant, public data repository for proteomics data, protein
 and peptide identifications together with the evidence supporting these identif
ications.
URL     http://www.ebi.ac.uk/pride
URLrest http://www.ebi.ac.uk/pride/prideMartWebService.do
Cat     Proteomic databases
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification
EDAMtpc 0121 | Proteomics
EDAMdat 2536 | Mass spectrometry data
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query    Mass spectrometry data {PRIDE entry} | HTML | UniProt accession | http:
//www.ebi.ac.uk/pride/searchSummary.do?queryTypeSelected=identification%20access
ion%20number&identificationAccessionNumber=%s
Example UniProt accession | P29375

ID      PhosSite
Acc     DB-0076
Name    Phosphorylation site database for Archaea and Bacteria
Desc    Phosphorylation site database for Archaea and Bacteria
URL     http://www.phosphorylation.biochem.vt.edu/
Cat     PTM databases
Taxon   2 | Bacteria
Taxon   2157 | Archaea
EDAMtpc 0751 | Phosphorylation sites
EDAMdat 2071 | Sequence motif (protein)
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query    Sequence motif (protein) {PhosSite entry} | HTML | UniProt accession |
http://www.phosphorylation.biochem.vt.edu/xpd2.cfm?extf=uniprot&extref=%s
Example UniProt accession | P36683

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


  [Part of this file has been deleted for brevity]

EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query    2D PAGE spot annotation | HTML | UniProt accession | http://www.mpiib-b
erlin.mpg.de/mpiib-cgi/RAT-HEART/get-2d-entry?%s
Example UniProt accession | P62738

ID      PHCI-2DPAGE
Acc     DB-0075
Name    Parasite host cell interaction 2D-PAGE database (PHCI-2DPAGE)
Desc    Two-dimensional polyacrylamide gel electrophoresis database.
URL     http://www.gram.au.dk/2d/2d.html
Cat     2D gel databases
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query    Experiment annotation (2D PAGE) | HTML | UniProt accession | http://www
.gram.au.dk/cgi-bin/get-2d-entry?%s
Example UniProt accession | P17821

ID      Bgee
Acc     DB-0133
Name    Bgee database for gene expression evolution
Desc    Bgee is a database to retrieve and compare gene expression patterns betw
een animal species.  Bgee first maps heterogeneous expression data (currently ES
T, Affymetrix, and in situ hybridization data) on anatomical and developmental o
ntologies.  Then, in order to perform automated cross species comparisons, homol
ogy relationships across anatomical ontologies, and comparison criteria between
developmental ontologies, are designed.
URL     http://bgee.unil.ch
Cat     Gene expression databases
Taxon   1 | all
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0203 | Transcriptomics
EDAMdat 0929 | Gene annotation (expression)
EDAMdat 0928 | Gene expression profile
EDAMdat 0916 | Gene annotation
EDAMdat 2579 | Gene annotation (expressed gene list)
EDAMid  3021 | UniProt accession
EDAMid  1033 | Gene ID (Ensembl)
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query    Gene annotation | HTML | UniProt accession | http://bgee.unil.ch/bgee/b
gee?uniprot_id=%s
Query    Gene annotation | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/b
gee?page=gene&action=expression&gene_id=%s
Query    Gene expression profile | HTML | Gene ID (Ensembl) | http://bgee.unil.c
h/bgee/bgee?page=gene&action=expression&gene_id=%s
Query    Gene annotation (expression) | HTML | Gene ID (Ensembl) | http://bgee.u
nil.ch/bgee/bgee?page=expression&action=data&gene_id=%s
Query    Gene annotation (expressed gene list) {Bgee ID file} | Text | Gene ID (
Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=
1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&a
ttribut_list=gene_name&attribut_list=gene_id&gene_id=%s&display_type=tsv
Query    Gene annotation (expressed gene list) {Bgee ID file with expression dat
a} | Text | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&ac
tion=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribu
t_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&dis
play_type=tsv&gene_information=2
Query    Gene annotation (expressed gene list) {Bgee ID file with expression dat
a count} | Text | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=express
ion&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&a
ttribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=
%s&display_type=tsv&gene_information=1
Query    Gene annotation (expressed gene list) {Bgee ID file} | HTML | Gene ID (
Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=
1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&a
ttribut_list=gene_name&attribut_list=gene_id&gene_id=%s
Query    Gene annotation (expressed gene list) {Bgee ID file with expression dat
a} | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&ac
tion=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribu
t_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&gen
e_information=2
Query    Gene annotation (expressed gene list) {Bgee ID file with expression dat
a count} | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=express
ion&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&a
ttribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=
%s&gene_information=1
Example Gene ID (Ensembl) | ENSG00000091831
Example UniProt accession | P32234


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
   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
