How To Link To Freebase Gene Pages Using A Gene/Protein Identifier?

Question

[Andrew Su]

Freebase has a page for the gene CDK2, which clearly indicates that its NCBI Entrez Gene ID is 1017. How can I link directly to this page using this identifier (or any other common gene/protein identifier)? Ideally it would be something like this:

http://freebase.com/query?NCBI_ID=1017

but of course that doesn't work. Can't find any info on this in a quick scan of the documentation, but it seems like this would be an essential feature for any semantic web application... Thoughts?

[Science_Robot]

How did you search for this page using the NCBI Gene ID in the first place?

[Andrew Su]

I didn't use the Gene ID... I searched for the symbol "cdk2", and then selected the "right" entry. So I'm wondering if I do know the Gene ID, can I get to that right entry directly?

Answer 1

[Lars Juhl Jensen]

I haven't been able to produce a link that will get you to the actual page. However, I have managed to figure out how to construct a URL that queries their MSQL interface for NCBI ID 1017:

http://www.freebase.com/api/service/mqlread?query={"query":{"/type/object/id":[],"/biology/gene/ncbi_id":"1017"}}

It correctly returns (in JSON format) that this corresponds to the Freebase concept /en/cyclin_dependent_kinase_2:

{
  "code": "/api/status/ok",
  "result": {
    "/biology/gene/ncbi_id": "1017",
    "/type/object/id": [
      "/en/cyclin_dependent_kinase_2"
    ]
  },
  "status": "200 OK",
  "transaction_id": "cache;cache02.p01.sjc1:8101;2010-08-18T18:36:48Z;0038"
}

I hope it is possible to make some clever little Javascript uses this JSON as input to direct you to the correct web page, but I fear that you may run into the dreaded cross-domain security problems.

[Andrew Su]

And FWIW for the BioGPS users in the crowd, I wrapped Lars' MQL query into a BioGPS plugin for the Freebase gene pages. And the CGI can be accessed directly here

[Andrew Su]

Brilliant! I'm not a smart enough programmer to write the javascript wrapper, but I can write a perl CGI wrapper that queries freebase, parses JSON, and issues an HTTP redirect to the right page. Perfect... For others and future reference, more about MQL documentation is here: http://wiki.freebase.com/wiki/MQL

[Andrew Su]

And FWIW for the BioGPS users in the crowd, I wrapped Lars' MQL query into a BioGPS plugin for the Freebase gene pages.

Answer 2

[Philip Kendall]

At the moment, there is no direct way to link to a gene via its NCBI identifier.

However, it would be possible to modify the Freebase schema to make the NCBI identifier act as a "key" to the topic, rather than its current behaviour of being "just" a property. You'd then be able to access it as something like

http://www.freebase.com/view/biology/ncbi_gene/1017

(but that's not possible yet).

If this is something you're interested in doing, I'd suggest joining the freebase-discuss list and floating the idea there - it seems sensible to me.

Hope this helps.

[Andrew Su]

nice suggestion, thanks!