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):

MyGene.info is a web service that provides up to date annotations in several fields and is great for gene ID conversion. All species from NCBI and Ensembl are supported and annotations are updated weekly to ensure the latest annotations are available. Both python and R/Bioconductor clients are easy to use.

MyGene.info may not be able to solve your problem with Agilent IDs but several other IDs from Genebank, Uniprot, Ensembl, Refseq are all available. Also, from either client, you can query several thousand genes at once.

Here is some example syntax for ID conversion from the python module:

>>> import mygene
>>> mg = mygene.MyGeneInfo()
>>> mg.metadata['available_fields'] ## returns available query terms, pay special attention to "ensemblgene", "entrezgene", "symbol" and "uniprot"
[u'accession', u'alias', u'biocarta', u'chr', u'end', u'ensemblgene', u'ensemblprotein', u'ensembltranscript', u'entrezgene', u'exons', u'flybase', u'generif', u'go', u'hgnc', u'homologene', u'hprd', u'humancyc', u'interpro', u'ipi', u'kegg', u'mgi', u'mim', u'mirbase', u'mousecyc', u'name', u'netpath', u'pdb', u'pfam', u'pharmgkb', u'pid', u'pir', u'prosite', u'ratmap', u'reactome', u'reagent', u'refseq', u'reporter', u'retired', u'rgd', u'smpdb', u'start', u'strand', u'summary', u'symbol', u'tair', u'taxid', u'type_of_gene', u'unigene', u'uniprot', u'wikipathways', u'wormbase', u'xenbase', u'yeastcyc', u'zfin']

>>> xli = ['DDX26B','CCDC83', 'MAST3', 'RPL11', 'ZDHHC20', 'LUC7L3', 'SNORD49A', 'CTSH', 'ACOT8']
>>> mg.querymany(xli, scopes="symbol", fields=["uniprot", "ensembl.gene", "reporter"], species="human", as_dataframe=True)

A DataFrame is returned:

And now for the Bioconductor package:

library(mygene)
xli <-  c('DDX26B','CCDC83',  'MAST3', 'RPL11', 'ZDHHC20',  'LUC7L3',  'SNORD49A',  'CTSH', 'ACOT8')
queryMany(xli, scopes="symbol", fields=c("uniprot", "ensembl.gene", "reporter"), species="human")

This returns a DataFrame:

Finished
DataFrame with 9 rows and 5 columns
                     ensembl.gene         _id uniprot.Swiss-Prot uniprot.TrEMBL       query
                  <CharacterList> <character>        <character>         <List> <character>
1                 ENSG00000165359      203522             Q5JSJ4       ########      DDX26B
2                 ENSG00000150676      220047             Q8IWF9       ########      CCDC83
3                 ENSG00000099308       23031             O60307       ########       MAST3
4                 ENSG00000142676        6135             P62913       ########       RPL11
5                 ENSG00000180776      253832             Q5W0Z9       ########     ZDHHC20
6                 ENSG00000108848       51747             O95232       ########      LUC7L3
7 ENSG00000277370,ENSG00000175061       26800                 NA       ########    SNORD49A
8                 ENSG00000103811        1512             P09668       ########        CTSH
9                 ENSG00000101473       10005             O14734       ########       ACOT8

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.

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

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.

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.

The following link has a list of ID conversion tools:

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

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.

Try out: http://mygene.info/v2/api#MyGene.info-gene-query-service

It's Awesome!

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 did the trick for me:

# Test the new Ensemble REST API with an example gene
$ensemblID = "ENSG00000157764";
$url = "http://beta.rest.ensembl.org/xrefs/id/$ensemblID?content-type=application/json";
$ensemblResultJson = file_get_contents($url);
$ensemblResult = json_decode($ensemblResultJson, true);

# Print out each found Gene symbol on a separate row:
echo "<ul>";
foreach ($ensemblResult as $mapping) {
    if ( in_array( $mapping['dbname'], array("EntrezGene","HGNC"))) {
        echo "<li>Found Gene symbol: " . $mapping['display_id'] . "</li>\n";
    }
}
echo "</ul>";

The most easy way is as the follow:

http://www.genenames.org/cgi-bin/download

GeneID convert:

http://www.ensembl.org/biomart/martview

http://mygene.info/

https://biodbnet-abcc.ncifcrf.gov/

http://biodb.jp/

biobtree is also a strong alternative tool for simple or advanced identifiers mapping and data retrieval for small or large datasets with R/Python packages.

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.

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).

Share a R script to do it:

library("org.Hs.eg.db")
symbol <- as.list(org.Hs.egALIAS2EG)
symbol2geneid<-data.frame(names(symbol),as.character(symbol))

BioDBnet is a great tool for database do database id conversion. Link is https://biodbnet-abcc.ncifcrf.gov/db/db2db.php

You can convert the gene id to a different different database like Agilent ID, GO ID, Pathway ID. You can check the link to see all the databases available.

I have used it to convert the Gene ID to GO ID.