Thursday 26 March 2009

Linking to the Atlas!

Hello!

As the previous post says, we released Atlas 1.0.2. In addition to the memory usage fix discussed below, and to major autocompletion speed-ups (we switched from using Solr's prefix faceting to our own prefix tree-based implementation), we improved how you can link to the Atlas now.

To link to Atlas Gene Pages, you can use the following URL format:

http://www.ebi.ac.uk/microarray-as/atlas/gene?gid=IDENTIFIER

Valid identifiers are, at the moment, the following:
  • embl - EMBL IDs
  • ensgene - Ensembl Gene IDs
  • ensprotein - Ensembl Protein IDs
  • enstranscript - Ensembl Transcript IDs
  • goid - Gene Ontology IDs
  • interproid - InterPro IDs
  • locuslink - Entrez Gene IDs (formerly LocusLink)
  • omimid - OMIM IDs
  • refseq - RefSeq IDs
  • unigene - UniGene IDs
  • uniprot - UniProt Accessions
  • dbxref - A mixed bag of various external identifiers, primarily MGI IDs.
You can download a large file, listing all indexed gene identifiers, to help you link to Atlas:



This file is automatically generated with every data release. Where an identifier links to a single gene, e.g., UniProt accession Q8IZT6, the link http://www.ebi.ac.uk/microarray-as/atlas/gene?gid=Q8IZT6 goes directly to the respective gene page. If the chosen identifier is linked to a group of genes - an InterPro or a Gene Ontology ID, say, then the link will go to the gene expression summary Heatmap View, e.g., for "phosphopyruvate hydratase complex", GO:0000015, the link is http://www.ebi.ac.uk/microarray-as/atlas/gene?gid=GO:0000015

7 comments:

Ian said...

I just discovered ArrayExpress Atlas, and am in a state of awe that might not wear off. What a fantastic resource, thanks for your hard work and keep it up!

Misha Kapushesky said...

Hi Ian,

Thank you for the kind words. We try hard! :)

--Misha

Arjun said...

Hi,
First, the Atlas is, in one word, amazing! Thanks a lot for this resource and kudos to the team for making this possible.

I have a quick question about the results to a query: For every gene in the result, I'm able to see other names/identifiers/aliases when I mouse-over it. Can I get this mapping file for all the genes associating the IDs/aliases to each other?

Please let me know.
Thanks again!

Misha Kapushesky said...

Hi Arjun,

Thanks for your comment! There are a couple ways to get the various IDs for the genes in the Atlas:

1) REST APIs. Looking at at any page, e.g. http://www.ebi.ac.uk/gxa/gene/ENSG00000066279 you can get all the metadata for this gene by going to http://www.ebi.ac.uk/gxa/api?geneIs=ENSG00000066279 for example.

2) Download one of our data releases from the Atlas FTP site, ftp://ftp1.ebi.ac.uk/pub/databases/microarray/data/atlas and look in the tables dumping the gene attribute data.

Hope this helps. Let us know if you have any more questions!

--Misha

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Rajesh sharma said...

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