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
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?
2 answers
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.
And FWIW for the BioGPS users in the crowd, I wrapped Lars' MQL query into a BioGPS plugin for the Freebase gene pages.
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
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.
nice suggestion, thanks!
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How did you search for this page using the NCBI Gene ID in the first place?
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?