[DAS2] Re: BioCyc pathway database sharing

[Suzanna Lewis]

Hmm, too bad this is one of the specific aims we are dropping. But that 
doesn't mean we can't work on it if we have the chance.

-S

On Jul 18, 2005, at 6:36 PM, Chervitz, Steve wrote:

> 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
> annotation.
>
> 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?
>
> Steve
>
>
>> 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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>>> DAS2 at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/das2
>>
>