drfindid 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 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