Question

Hey,

I was using DAVID (http://david.abcc.ncifcrf.gov/conversion.jsp) to do the gene ID conversion, e.g.conversion between Agilent ID, Genebank accession id and Entrez gene ID, but I found the DAVID database is not updated. Does anyone know a better updataed conversion tool to do this job? Thanks!

Answer 1

BioMart has already been mentioned. It can do much more than ID conversion but it is very useful for conversion purposes, it is regularly updated and you can select different genome builds and all kinds of genomic features. It seems to me that you wish to retrieve GeneIDs linked to Affymetrix IDs. To select these attributes in BioMart: go to the Martview page to start a new BioMart query.

Select attributes on the attribute page: The Ensembl GeneIDs and Transcript IDs are default. Ensembl GeneID and Affy IDs are under the "External" tab. Select your chip there. To limit to those genes which are on the chip, use the Filters->Gene menue. You can limit the genes to those present on various platforms or your favourite set.

There is an URL button in biomart that allows to retrieve a URL for your query and to pass it on to others. Try this example:

BioMart URL URL, that should be a good starting point.

If you are interested in KEGG identifiers (Pathways, Genes), EC-numbers, etc. the

KEGG Identifier page could be handy, because the KEGG ids are not in BioMart as far as I know.

Answer 2

The following link has a list of ID conversion tools:

http://hum-molgen.org/NewsGen/08-2009/000020.html

Answer 3

You can also do it with the following services:

• uniprot - Click on 'Id Mapping' from the home page.
• biomart - choose a database and a version, then put the ids you want to convert under Filters->Id List limit (select the proper input id in the menu), and then the output ids under 'Attributes'. Biomart is a general tool that enables you to extract a lot of different informations from databases - sequences, ontologies, transcripts, homologues - but maybe for converting gene ids is a bit too complex.
• galaxy - I can't help too much about this here but I am sure it has a function for doing that - and many other things.

Answer 4

BridgeDB provides a nice API and REST interface, so you can put ID mapping queries in your scripts.

Answer 5

http://idconverter.bioinfo.cnio.es/

Is another possible solution to this, although you might find this is not as up to date as you might like either.

Answer 6

If you have just a few, I just saw someone use the R package BioIDMapper and it seemed kind of neat. But it's slow.

Answer 7

I don't know of a direct solution myself, but this is a topic that may be of interest for the biological data analysis class that I am teaching.

If you specify the organism/genomic builds that you are interested in we may be able to generate a full translation list as an in class example or a homework. I was planning on covering an Affymetrix ID to Genebank example anyhow.