Question: Gene Id Conversion Tool
23
gravatar for Renee
4.5 years ago by
Renee230
Renee230 wrote:

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!

ADD COMMENTlink modified 4 months ago by aheinzel50 • written 4.5 years ago by Renee230

How frequently do you need things updated? DAVID does have yearly releases so far, but their latest release is this month (March 2010). See the release announcement here: http://david.abcc.ncifcrf.gov/forum/cgi-bin/ikonboard.cgi?act=ST;f=10;t=25 This does suggest the underlying mapping framework will be updated along with it in the 6.7 beta, and hence should include more recent information for the conversion tool

ADD REPLYlink modified 18 months ago by Istvan Albert ♦♦ 39k • written 4.1 years ago by Daniel Swan10k
19
gravatar for Casey Bergman
3.0 years ago by
Casey Bergman15k
Manchester, UK
Casey Bergman15k wrote:

The bioDBnet and Hyperlink Management System (HMS) systems convert multiple ID sets to each other.

HMS is limited to three species (human, mouse ciona) and has fewer data sources (Agilent - no, GenBank and Entrez - yes).

The bioDBnet system appears to be species-neutral and the network of linked databases is shown here, (includes Agilent, GenBank and Entrez, so it should fit your requirements): alt text

ADD COMMENTlink written 3.0 years ago by Casey Bergman15k
14
gravatar for Michael Dondrup
4.1 years ago by
Bergen
Michael Dondrup27k wrote:

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.

ADD COMMENTlink written 4.1 years ago by Michael Dondrup27k
7
gravatar for Perry
4.1 years ago by
Perry280
philadelphia
Perry280 wrote:

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

ADD COMMENTlink written 4.1 years ago by Perry280

BridgeDB is really a software framework that you can use in our own code; either directly (currently only in Java) or through calling it as a webservice. It can use different and even multiple stacked mappings. By default these come from ENSEMBL (for gene products) and HMDB (for metabolites). Ongoing projects extend the available mappings with ChemSPider and SNP info. There is a short introduction available at Nature Precedings: http://precedings.nature.com/documents/5023/version/1 and a paper in BMC Bioinformatics: http://dx.doi.org/10.1186/1471-2105-11-5

ADD REPLYlink written 3.2 years ago by Chris Evelo8.8k
6
gravatar for Giovanni M Dall'Olio
4.2 years ago by
London, UK
Giovanni M Dall'Olio18k wrote:

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.
ADD COMMENTlink written 4.2 years ago by Giovanni M Dall'Olio18k
5
gravatar for Madelaine Gogol
4.1 years ago by
Madelaine Gogol3.3k
Kansas City
Madelaine Gogol3.3k wrote:

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.

ADD COMMENTlink written 4.1 years ago by Madelaine Gogol3.3k

Unfortunately, this link is now broken :/ ...

ADD REPLYlink written 29 days ago by Samuel Lampa790

There is a more recent version at: http://sourceforge.net/projects/bioidmapper/

ADD REPLYlink written 19 days ago by Daniel Swan10k
4
gravatar for Mohammed Islaih
4.4 years ago by
Mohammed Islaih40 wrote:

The following link has a list of ID conversion tools:

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

ADD COMMENTlink modified 18 months ago by Istvan Albert ♦♦ 39k • written 4.4 years ago by Mohammed Islaih40
3
gravatar for Daniel Swan
4.1 years ago by
Daniel Swan10k
Oxford, UK
Daniel Swan10k wrote:

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.

ADD COMMENTlink written 4.1 years ago by Daniel Swan10k
1
gravatar for Samuel Lampa
10 months ago by
Samuel Lampa790
Uppsala
Samuel Lampa790 wrote:

Have a look at the (BETA stage) Ensembl REST API

For example, for converting from Ensembl Gene ids to Gene symbols, you could use a query like this one:

http://beta.rest.ensembl.org/xrefs/id/ENSG00000059804?content-type=application/json

... and then programmatically (some python parsing should be rather straight forward) extract the "display_id" for the items that have "dbname" = "HGNC", or "EntrezGene".

For example, the following PHP code does the trick for me:

http://beta.rest.ensembl.org/xrefs/id/$ensemblID?content-type=application/json");
$ensemblResult = json_decode($ensemblResultJson, true);

// Print out each found Gene symbol on a separate row:
echo "
";
foreach ($ensemblResult as $mapping) {
    if ( in_array( $mapping['dbname'], array("EntrezGene","HGNC"))) {
        echo "Found Gene symbol: " . $mapping['display_id'] . "\n";
    }
}
echo "
"; ?>
ADD COMMENTlink modified 10 months ago • written 10 months ago by Samuel Lampa790
0
gravatar for Istvan Albert
4.5 years ago by
Istvan Albert ♦♦ 39k
University Park, USA
Istvan Albert ♦♦ 39k wrote:

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.

ADD COMMENTlink written 4.5 years ago by Istvan Albert ♦♦ 39k

Thanks! That's great! But I'm not student there...Can I access to that anyway? I am using Human whole genome Agilent array. Thank you so much.

ADD REPLYlink written 4.5 years ago by Renee230

missed this comment, sorry about it!

ADD REPLYlink written 4.2 years ago by Istvan Albert ♦♦ 39k
0
gravatar for aheinzel
4 months ago by
aheinzel50
aheinzel50 wrote:

Not sure what your background is, however, we recently started to develop an id mapper / converter for experimentalists who prefer organizing their data in Excel. Therefore, the client directly integrates into MS Excel.

Currently, we provide the possibility to map from various IDs to ensembl and back. The mapping data were extracted from Ensembl 73 (released on the 4.9.2013). If you need mappings for any additional ID types availalble from the ensembl database we will be happy to add them (please just tell us via our feedback form).

ADD COMMENTlink written 4 months ago by aheinzel50
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