This document is licensed under a Creative Commons License.

1. Introduction and purpose
2. Usage
   • Input
   • Output
3. Authors
4. Terms of use
5. Privacy and Security
6. References
7. Acknowledgements

Introduction and purpose

IDconverter is a tool that converts gene, clone or protein IDs to other IDs. It can be used for small queries or for tens of thousands of IDs (typically from a micro array experiment). Most of the conversions are pregenerated every time that the databases are updated, in order to get a fast answer for each query. Previous versions did not have pregenerated tables, so by using queries of offline pre-generated database we are able to increase speed of response by a factor of up to 20 (most noticeable in queries with many identifiers)

The relations among identifiers is shown in the following Figure:

Regardless of the caveats, please enjoy and let us know your suggestions, comments and complaints.

Usage

Input

The input data can be from a single identifiers to several tenths of thousands, and the accepted types of identifiers are Gene Name (HUGO), GenBank accession, UniGene cluster, Ensembl gene, Clone Id, Affymetrix Id, RefSeq_DNA, RefSeq_peptide, EntrezGene, and SwissProt name.

Note: Affymetrix Ids have to be [array] probeset, (i.e., [HG_U133A] 206797_at)

Output

Three different output formats are available:

• Web page, including links for each identifier to external websites.
• Spreadsheet file
• Text file (tab separated)

Authors

Patricio Yankilevich created the original version, designed the UI using PHP and the necessary queries to the Ensembl and UniGene databases.

Andreu Alibés upgraded it by adding information on PubMed references, GO terms, several protein identifiers and the UCSC Gene Location. Andreu also created a Python script that pregenerate the conversions to speed up the performance.

Andrés Cañada included Kegg and Reactome to the list of available outputs.

This application is running on a cluster of machines using Debian GNU/Linux as operating system, Apache as web server and MySQL as database server.

NOTE: Due to recent changes on the Ensembl database, Affymetrix IDs for mouse and rat are not available.

Terms of use

• You acknowledge that this Software is experimental in nature and is supplied "AS IS", without obligation by the authors, the CNIO's Bioinformatics Unit or the CNIO to provide accompanying services or support. The entire risk as to the quality and performance of the Software is with you. The CNIO and the authors expressly disclaim any and all warranties regarding the software, whether express or implied, including but not limited to warranties pertaining to merchantability or fitness for a particular purpose.
• If you use IDconverter for any publication, we would appreciate if you could let us know and if you cite our program (you know, "credit where credit is due") as:
  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
• We appreciate if you give us feedback concerning bugs, errors or misconfigurations. Complaints or suggestions are welcome.

Privacy and Security

Uploaded data set are saved in temporary directories in the server and are accessible through the web until they are erased after some time. Anybody can access those directories, nevertheless the name of the files are not trivial, thus it is not easy for a third person to access your data.

In any case, you should keep in mind that communications between the client (your computer) and the server are not encripted at all, thus it is also possible for somebody else to look at your data while you are uploading or dowloading them.

References

IDconverter: Alibés, A, et al. (2007) IDconverter and IDClight: Conversion and annotation of gene and protein IDs, BMC Bioinformatics, 8:9 link

Ensembl: E. Birney, et al. (2006) Ensembl 2006, Nucleic Acids Research 34:D556 link

UCSC: A.S. Hinrichs, et al (2006) The UCSC Genome Browser Database: update 2006, Nucleic Acids Research 34:D590 link

NCBI: D.L. Wheeler, et al (2006) Database resources of the National Center for Biotechnology Information, Nucleic Acids Research 34:D173 link

KEGG: M. Kanehisa, et al (2006) From genomics to chemical genomics: new developments in KEGG, Nucleic Acids Research 34:D354 link

Reactome: G. Joshi-Tope, et al (2005) Reactome: a knowledgebase of biological pathways, Nucleic Acids Research 33:D428 link

iHOP: R. Hoffmann, A. Valencia (2004) A gene network for navigating the literature, Nature Genetics 36:664 (2004) link

Acknowledgements

We thank Robert Hoffmann for helping us link with iHOP.

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