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[I3C-pathways] Re: Biochemical Pathways RFP

Eric Neumann ENeumann at
Wed Jun 26 12:23:33 PDT 2002


It was interesting to see OMG beginning to focus on pathways (I've had it on the LSR-OMG roadmap agenda since 1998!). We have been seeing general activity in this are picking up. In that regard, I wanted to bring attention to the I3C-pathways group of a review article Vincent and I wrote this last March (attached). It emphasizes the need for pathways models to go beyond the use of basic data and object models (i.e., not to rely solely on UML for capturing any pathway-related expressiveness, molecular as well as functional). The article suggests the use of symbolic methodologies that apply ontologies to a variety of different pathway models (metabolic, signal cascades, gene regulatory, protein interaction, disease-causal models, etc).

I also want to let folks know that there will be presentations of various pathways models and their applications at BioPathways02 ( at ISMB (Aug 1,2), which is being co-located with BOSC (Open Bio). In particular, the application of a molecular ontologies in conjunction pathways information as a model for data-interchange will be discussed (and hopefully a reference model demonstrated). In addition, there will also be talks on text-mining initiatives and pathway reconstruction algorithms. 

Looking forward to seeing you in Edmonton!



Eric K. Neumann PhD
VP Bioinformatics

Beyond Genomics
Discovery through Systems Biology

40 Bear Hill Road
Waltham, MA
tel: 781-434-0222
fax: 781-895-1119

> -----Original Message-----
> From: Eric Minch [mailto:eric.minch at]
> Sent: Saturday, June 22, 2002 10:35 AM
> To: i3c-pathways at; gofriends at;
> sysbio at
> Subject: [I3C-pathways] Re: Biochemical Pathways RFP - draft A
> [Apologies if this reaches you via multiple routes]
> I wish to call your attention to a Request for Proposals on 
> Biochemical Pathways
> submitted to the Object Management Group/Life Sciences 
> Research. A first draft
> can be found at
> This effort is of relevance to several ongoing projects, 
> including SBML and GO,
> both of which can greatly facilitate the specification of pathway and
> pathway-related data and objects.
> 	Best--
> 	--Eric
> ----------------------------------------------------------------
> Dr. Eric Minch
> Senior Science Fellow
> LION Bioscience AG, D-69120 Heidelberg, Germany
> tel: +49 (0) 6221/4038-313 fax: +49 (0) 6221/4038-480
> eric.minch at
> _______________________________________________
> I3c-pathways mailing list
> I3c-pathways at
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