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Pharmaceutical Analysis Workflows and IP

From: John Wilbanks <wilbanks@w3.org>
Date: Mon, 12 Jul 2004 11:40:05 -0400
Message-ID: <40F2B0D5.2060206@w3.org>
To: public-semweb-lifesci@w3.org

One of the points of discussion at the pharmagrid retreat last week 
pricked my ears and I wanted to throw it out here for discussion.  It 
revolved around workflows, and how intellectual property theory is 
starting to gel around them.

The concept of a "workflow" in the pharma community is not a new one.  
Here's an example...a very basic one.

1.  After running gene expression analysis, get 54,000 data points 
representing 18,000 genes (three spots per gene for significance 
testing) back from robot.
2.  Test significance and toss out genes with too much variation amongst 
the three.
3.  Normalize the data according to your preferences (or prejudices, as 
it were)
4.  Choose algorithm and distance metric for clustering.

Now, the impact of semantics on life sciences means that a second 
workflow could be applied to the clusters coming out of step 4 above.  
Such as.

1.  Represent list of clusters as text list of gene aliases with 
semantic associations to activity:  "on/off" (and if "on" then 
"upregulated/downregulated" associations attached)
2.  Filter for genes that make proteins that are nuclear proteins
3.  Filter again for genes that make proteins that are involved in cell 
death
4.  Filter yet again for genes that make proteins that have a molecular 
signature similar to my candidate drug compound
5.  Filter yet again for genes that make proteins that have a "minimal" 
representation in literature (i.e., less likely to have restrictive 
intellectual property around them)
6.  Rank according to my ontology of the subclasses of semantic 
constraints in 2-5 and the on/off, upregulated/downregulated 
relationships, because some nuclear proteins are more equal than others 
in pharma.  Ones that create the biological activity you want when they 
are turned "off" are ideal, since it's easier to silence a gene without 
side effect than it is to activate one without side effect.  And so forth.

On two different occasions at the conference I heard mention of  
"protecting" this second type of workflow as a business process 
representative of the skill of the designer of the workflow.  In one 
case it's already happened, though the office action is not known.

This strikes me as a place where the concept of a precompetitive 
repository of workflows might make a lot of sense.  Anyone out there 
have an opinion?

jtw
Received on Monday, 12 July 2004 11:41:09 GMT

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