[ome-devel] data grouping/searching, creating dataset

[Bernd Jagla]

Hi there again,

 

Please forward to user group if you think this group would be a better
target.

 

I was wondering a bit on how to actually use OME. To give you an idea of
what I am thinking of, let me describe to you our workflow:

 

We are screening chemical compounds using cell based assays. We want to
screen about 100,000 compounds per screen. The images coming from the INCell
Analyzer comprise the raw data and will usually be analyzed on the fly and
the resulting features (sometime a few dozen) will be written into text
files. "Somehow" those results and images will be imported into OME (see
e-mail from yesterday). 

Then we want to display a particular feature for all the wells/plates as a
heat map to identify by eye any biases or problems in the data set. For this
we envision right now using Partek's Screener Solution which could interface
with OME through ODBC. A simple (complex) select statement should bring all
the necessary information into the Screener Solution.

Then we have to select hits and analyze the screen: 

Display a particular feature for all wells and plates. (This is for quality
control). 

Select a relevant feature and a threshold.

Write back the results (somehow) to OME. Those results will eventually group
the results in different categories (hit, non-hit, not-known, positive
control, negative control, etc). This actually still has to be solved.

Then we want to see/ cross-link the results with other screens: of these
hits, which other assays where they active in? Which compounds where active
in a given set of screens? Give me a complete profile of all the compounds
and in which assays they where active, given a specified threshold etc.

Of course at some point we want to see the compounds with the results and
everything but this will wait a while and needs probably further discussions
on how to integrate all this.

Then we have to push some of the data to PubChem at the NIH. How could we do
this? A simple script with select statements could do the work, no? Maybe we
can write a chain module that automatically propagates the data to PubChem
(they use XML - their own format of course).

 

At the moment I believe that the most important part is to improve (or for
me to learn how to do) the grouping features of OME. I don't think it is
good that you have to know in advance that you want to add something to a
data set. From my experience I would rather play with the data and mark e.g.
bad wells along the way, select images that look interesting in one way or
the other and say: Wow they look cool lets make a new dataset and collect
them here, or lets add them to the list of interesting data. As far as I
know this is only possible once you know the name of the data set, and then
you have to search for them again.

 

Also for the sake of better understanding can you please point me to all the
relevant information concerning data sets: how to programmatically do it,
how to do it with ODBC, and the web interface?

 

I would be more than happy to explain in more detail or discuss our
strategies as we are just in the process of getting started.

 

Thanks a lot for all your kind help.

 

Happy Turkey day (for those of you who don't care about turkeys, happy
weekend. ;-)

 

Best

 

Bernd

 

 

 

Bernd Jagla, PhD
Associate Research Scientist
Columbia University
1150 St. Nicholas Avenue
Russ Berrie Medical Pavilion, Room 520
New York, NY 10032
Tel: 212 - 851 5560 x16
Fax: 212 - 851 5570
e-mail: baj2107 at columbia.edu
  

 

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