IDClight: Tool for conversion of single IDs through URL

Purpose

IDClight or IDconverter light is an extension of IDconverter. It converts single IDs to multiple gene, protein and clone IDs. It also provides with the gene location and PubMed references to the gene in question. Its main purpose is to enrich the output from several of the applications developed at the Bioinformatics Unit of the CNIO. The information is taken from public available databases and the ID conversions are pregenerated to ensure a quick service. We would like to keep the informal promise to update the databases at least every two months.

Please let us know any suggestion or comment you want, or any bug you find.

Databases

This application makes extensive use of the following publicly available databases: Ensembl, UniGene, UCSC Genome Browser, PubMed, Reactome, and KEGG.

"API"

You are free to link to IDClight from you own applications, but we would appreciate if you could let us know and if you cite our program. The URL used has to be in the form:

 http://IDClight.bionfo.cnio.es/IDClight.prog?idtype=XXXXX&id=YYYYY&org=ZZ

idtype refers to the type of ID from which you want to obtain further information. Current options are: ug (UniGene cluster), entrez (EntrezGene ID), ensembl (Ensembl Gene), hugo (HUGO Gene Name), acc (GenBank accession), clone (Clone ID), affy (Affymetrix ID), rsdna (RefSeq_RNA), rspep (RefSeq_peptide), and swissp (SwissProt name).
id is the ID of the gene or clone for which more information is required.
org is the organism you are working with. Three different organisms are available Hs (Human - Homo sapiens), Mm (Mouse - Mus musculus), and Rn (Rat - Rattus norvegicus).

Examples

Human - GenBank accession: http://idclight.bioinfo.cnio.es/idclight.prog?id=BG618195&idtype=acc&org=Hs
Mouse - UniGene cluster: http://idclight.bioinfo.cnio.es/idclight.prog?id=Mm.10&idtype=ug&org=Mm
Rat - Ensembl Gene: http://idclight.bioinfo.cnio.es/idclight.prog?id=ENSRNOG00000016640&idtype=ensembl&org=Rn

Authors

Andreu Alibés developed this application based on the IDconverter tool originally developed by Patricio Yankilevich. Andrés Cañada added KEGG Pathway Ids as an output. This web application is running on an Apache server, it uses a MySQL database server and its code (both for the frontend and the backend parts) is written in Python. The mod_python module is used in the frontend.

Reference

Alibés, A, Yankilevich, P., Cañada, A., Díaz-Uriarte, R. IDconverter and IDClight: Conversion and annotation of gene and protein IDs (2007) BMC Bioinformatics, 8:9 link