[DAS2] Re: BioCyc pathway database sharing

Chervitz, Steve Steve_Chervitz at affymetrix.com
Tue Jul 19 01:36:39 UTC 2005

Cool. And speaking of interactions, I interacted with some of the
biopathways folks at the ISMB in Detroit and mentioned our vision of the
pathways extension to DAS for the continuation grant. They seemed very
interested and eager to have some way to enable distributed pathway

They also were interested in helping contribute ideas/verbiage for the
pathways section of the continuation grant. They recommended that we post a
blurb about what we are doing to the Biopax wiki, then send a message to
their discussion list with a pointer to this wiki entry. Sound reasonable?


> From: Suzanna Lewis <suzi at fruitfly.org>
> Date: Sun, 17 Jul 2005 13:53:20 -0700
> To: "Chervitz, Steve" <Steve_Chervitz at affymetrix.com>
> Cc: DAS/2 <das2 at portal.open-bio.org>
> Subject: Re: [DAS2] Re: BioCyc pathway database sharing
> Here is a little bit of additional information. Lincoln has just
> submitted a renewal application for the Reactome grant and it includes
> a collaboration with Peter K and Paul Thomas (ABI) to regularly
> exchange pathways. The plan is to use bioPax and I would guess that
> this can be DAS-ified without too much difficulty.
> It is interesting to see the migration of interaction sets (as this
> data gets refined) transmogrified into full-out pathway data, and all
> the intermediate forms in between.
> -S
> On Jul 13, 2005, at 2:22 PM, Chervitz, Steve wrote:
>> My earlier message got sent prematurely. Here's the link to the
>> BioInform
>> article:
>> http://www.bioinform.com/articles/view-sl.asp?Article=200578124042
>> The reason I mention it is that it would be instructive to look into
>> BioCyc's pathway tools in light of the pathway DAS extension being
>> proposed
>> in the DAS/2 continuation grant. This community may also be ideal
>> candidate
>> beta testers of pathway DAS prototypes.
>> Steve
>>> From: <Chervitz>, Steve <Steve_Chervitz at affymetrix.com>
>>> Date: Wed, 13 Jul 2005 14:09:43 -0700
>>> To: DAS/2 <das2 at portal.open-bio.org>
>>> Subject: BioCyc pathway database sharing
>>> The current BioInform has an article about SRI's database adoption
>>> program for
>>> the computationally generated pathway databases. He says they are
>>> making
>>> available "peer-to-peer database sharing techniques":
>>> http://biocyc.org/intro.shtml#adopt
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