Thank you Nick, Tony:
To be clear, there are three distinct use cases:
(1) UI for complete LIMS management system
(2) API for reading existing microarray results and loading them into a DB
(3) Querying that database using webservices such as those supported by BioMoby
I am primarily interested in #2 -- you are probably not suprised to find that
harvard medical school has troves of unpublished array results (affy cel files,
etc) scattered across many desktops just waiting to be uploaded to locally
controlled repository (not GEO, unpublished results). Hence, the Base2 API
could be attractive if I dont have to rewrite the array file parsers for
CEL/MINIML/etc. I'm hoping that user intervention wouldn't really be required,
and that I could write an adapater for Base2 that would simply INSPECT a folder
of say, CGH results, and load it into a local Base2 instance on a scheduled
basis. (our investigators are always over stretched for time and will likely
not take the time to submit each sample individually).
As for #3, these locally controlled instances would (later) indeed need to be
queried and aggregated. We already have a query-aggregator technology (SPIN)
which we are extending for this purpose. That said, the serialized XML query
payload could be made very close to BIOMoby, if appropriate. We are open source
advocates so any upgrades/extensions would be of course donated back to this
community freely.
thoughts?
--andy
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of Tony Travis
Sent: Tue 12/11/2007 5:05 AM
To: BASE dev
Cc: Chris Evelo; Ted Liefeld
Subject: Re: [basedb-devel] Open Source utils for sharing array results
Nicklas Nordborg wrote:
> [...]
> I am not sure I understand what you mean. You say you want to use BASE 2
> to find the results... but then that you don't need the full-blown BASE
> 2. Can you clarify? BASE 2 stores it's data in a database already... Do
> you want to copy this data into a second database?
Hello, Nicklas.
Just to clarify our interest in this in NuGO: I would like to be able to
query multiple base2 instances from GenePattern and analyse the results
using R/Java modules. We are also interested in using Taverna/Kepler
workflows. In this respect, it would be useful to have a BioMOBY
compliant web service for base2.
We've done two proof of concept projects on base2/BioMOBY integration
here at RRI, and the work is now being followed up by Chris Evelo's
group at Maastrcht University. It seems useful to me that we try to
minimise duplication of effort in this work. My opinion is that while
base2 is appropriate to use as our microarray LIMS, it would be useful
to have a 'standard' BioMBY compliant query interface to make it easy to
analyse data outside of the base2/base2-plugin environment. For example,
in GenePattern. I'm realise that you support integration of base2 with
TIGR's MeV, but I believe that GenePattern represents a much 'broader'
and flexible microarray data analysis platform :-)
Best wishes,
Tony.
--
Dr. A.J.Travis, | mailto:[EMAIL PROTECTED]
Rowett Research Institute, | http://www.rri.sari.ac.uk/~ajt
Greenburn Road, Bucksburn, | phone:+44 (0)1224 712751
Aberdeen AB21 9SB, Scotland, UK. | fax:+44 (0)1224 716687
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