[MOBY-l] Queries in bioMOBY

[Chris Mungall]

On Fri, 8 Nov 2002, Lukas Mueller wrote:

> Hi,
> 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. He
> 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. They
> 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 be,
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 seems
to me that it would be easier having a few SQL views or materialised views
to turn the native schema to an export schema...

Of course, if the site in question refuses to provide that then some kind
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, ....

> Cheers
> Lukas