[MOBY-l] Queries in bioMOBY
mueller at acoma.stanford.edu
Fri Nov 8 19:09:07 EST 2002
The fun thing with their implementation is that they seem to treat
algorithms the same they treat simple services such as sequence
retrieval etc. So ncbi blast is treated like another sql table (as ncbi
sequence retrieval would be). I thought that was really cool (if I
really understood it correctly!-).
On Friday, November 8, 2002, at 02:26 , Chris Mungall wrote:
> On Fri, 8 Nov 2002, Lukas Mueller wrote:
>> I recently heard at talk at a bay area bioinformatics meeting about a
>> company that has implemented exactly what Chris is talking about. I was
>> a bit skeptical of their implentation. What they do is develop wrappers
>> around web-pages and query them as web-services, presenting to the user
>> what looks like a big sql database. The company is at
>> www.geneticXchange.com. Unfortunately, they don't have that much
>> information on the site than the (I think) CEO presented in the talk.
>> also gave a demo and the performance seemed quite good. It must be a
>> nightmare to maintain these wrappers.... as web-pages changes, these
>> wrappers have to be adapted. They have about 60 wrappers developed.
>> really seem to be a poor man's ad-hoc moby, so I think that such a
>> system would be better built on top of something like moby. Of course
>> the system on top of the wrappers must be pretty neat.
> I agree the wrappers must be tricky to maintain - the idea here would
> say, you could wrap Entrez in a bunch of crazy scripts that ultimately
> allow you to query genbank as if it were a relational db?
> Given that the native form of the data is often a relational db, it
> to me that it would be easier having a few SQL views or materialised
> to turn the native schema to an export schema...
> Of course, if the site in question refuses to provide that then some
> of wrapper is necessary. A lot of bioinformatics would be so much easier
> if NCBI provided external access to a relational db containing genbank,
> dbsnp, ....
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