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drfindid |
Please help by correcting and extending the Wiki pages.
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.
% drfindid "uniprot accession" Find public databases by identifier Data resource output file [drfindid.drcat]: |
Go to the output files for this example
Find public databases by identifier
Version: EMBOSS:6.5.6.0
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
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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 | <*>.drfindid |
| 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 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 identifications.
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%20accession%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, which include curator-evaluated computational analysis, as well as, information extracted 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.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
[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-berlin.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 between animal species. Bgee first maps heterogeneous expression data (currently EST, Affymetrix, and in situ hybridization data) on anatomical and developmental ontologies. Then, in order to perform automated cross species comparisons, homology 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/bgee?uniprot_id=%s
Query Gene annotation | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=%s
Query Gene expression profile | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=%s
Query Gene annotation (expression) | HTML | Gene ID (Ensembl) | http://bgee.unil.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&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&display_type=tsv
Query Gene annotation (expressed gene list) {Bgee ID file with expression data} | 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&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&display_type=tsv&gene_information=2
Query Gene annotation (expressed gene list) {Bgee ID file with expression data count} | 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&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&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s
Query Gene annotation (expressed gene list) {Bgee ID file with expression data} | 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&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&gene_information=2
Query Gene annotation (expressed gene list) {Bgee ID file with expression data count} | 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&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&gene_information=1
Example Gene ID (Ensembl) | ENSG00000091831
Example UniProt accession | P32234
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| 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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.