BioPAX-Boston Google Group

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William Hayes is on vacation

william.ha...@biogenidec.com (William Hayes) — Sat, 22 Aug 2009 16:03:17 UT

I will be out of the office starting 08/21/2009 and will not return until
08/31/2009.
Please contact library.h...@biogenidec.com or call 617-679-3006 for urgent Library
requests.
For Library services - please email 'Library.h...@biogenidec.com' or call
+1-617-679-3006

Re: Meeting today

jluci...@predmed.com (Joanne Luciano) — Wed, 31 Oct 2007 00:29:47 UT

Hi,
I need a little more notice than this :-)
I dug around and before the "meeting today" message, the last message
I saw about meeting was from Jonathan on October 2 (and I hadn't seen
that message either until today :-).
How'd it go?
Joanne
Joanne Luciano, PhD
Predictive Medicine, Inc.
45 Orchard Street

Re: Meeting today + OBO and PWpool papers

d...@lexikos.com (Dan Corwin) — Tue, 30 Oct 2007 15:04:17 UT

Hi Oliver -
Somebody may have more recent updates, but this cites the principles:
[link]
Dan Corwin
PS - I once promised to send you a link on Pathway Pools, which is
below. I'd guess it overlaps with things that you envision -
[link]

Re: Meeting today

cur...@gmail.com (Oliver Ruebenacker) — Tue, 30 Oct 2007 14:40:19 UT

Dear friends,
Thank you! What are BFO papers?
Take care
Oliver
On 10/30/07, zuc...@research.dfci.harvard.e du

Re: Meeting today

zuc...@research.dfci.harvard.edu — Tue, 30 Oct 2007 11:59:51 UT

Hi Oliver,
We will meet on Tuesday Oct 30th from 3-5 in Stata 346. See a previous
message for directions.
Agenda:
Organization & goals
OWL exercises
BFO papers
LSW questions & demonstrations
Time permitting, convert Michel's ontology
Sincerely,
Jeremy

Meeting today

cur...@gmail.com (Oliver Ruebenacker) — Tue, 30 Oct 2007 11:18:35 UT

Dear friends,
Where are we meeting today? Same room as last time?
Anything particular on the agenda?
Take care
Oliver

SPARQL Query Over Distributed Heterogeneous Data - INVITATION TO PRODUCT LAUNCH

igolds...@insilicodiscovery.com (igoldsmid) — Thu, 25 Oct 2007 00:22:58 UT

Hi all
I believe some of you participating here will be interested in this..
The Semantic Discovery System V7 Releases 0 & 1
Providing Optimally Performing SPARQL Access Over Multiple Distributed
And Heterogeneous Data Sources
A web based copy of the intro email I would send is here:
[link]

Re: Unifying KEGG and BioCyc with InChI's

michel.dumont...@gmail.com (Michel Dumontier) — Tue, 16 Oct 2007 00:43:01 UT

Cool!
Grrr... now i wanna get out of my department meeting on Wed ;-)
Let me know what i can do to help.
-=Michel=-
On 10/15/07, zuc...@research.dfci.harvard.e du <

Unifying KEGG and BioCyc with InChI's

zuc...@research.dfci.harvard.edu — Mon, 15 Oct 2007 21:46:40 UT

Hey Michel,
I am inspired by your enthusiasm, and I think that unifying KEGG and
BioCyc compounds would be an excellent use case for us, enabling real
data integration to motivate our BioPAX representation. I spoke with
Peter Karp about this possibility on Friday, and I will be at SRI on
Thursday where we can discuss this further. He may be able to provide

BioPAX-Boston meeting Wed 17 October 2007

jonathan.r...@gmail.com (jonathan.rees@gmail.com) — Mon, 15 Oct 2007 17:13:12 UT

Wednesday, 3-5. Agenda: More about how one would recast BioPAX using
the methods of the OBO Foundry.
We'll be in Stata 346 this time. Why the change? Because it's closer
to my office than our room last week.
Location is directly below last week's room: 3rd floor, Gates (i.e.
east/Main St) tower. From the elevator go right, through doors, left,

What BioPAX communicates and how to extend OWL to help it (was: BioPAX Boston meeting, 11 October 2007)

cur...@gmail.com (Oliver Ruebenacker) — Fri, 12 Oct 2007 16:26:39 UT

Dear friends,
I think the paper accurately describes the tensions surrounding
BioPAX and I like the proposals to extend OWL with one caveat: I would
not propose them as extensions of OWL, but as a separate layer.
The extensions are very useful and easily implemented in principle,
but deeply clash with OWL principles. As the authors understand, they

Re: meeting today

michel.dumont...@gmail.com (Michel Dumontier) — Fri, 12 Oct 2007 13:40:37 UT

Alan, Jeremy
Thanks! What a great analysis! Well substantiated.
So, is it worthwhile to scan through the pathway/reaction databases and
enumerate which identifiers are being used?
-=Michel=-
On 10/12/07, zuc...@research.dfci.harvard.e du <

Re: meeting today

jluci...@predmed.com (Joanne Luciano) — Fri, 12 Oct 2007 11:22:34 UT

Are you in town now?
Joanne Luciano, PhD
Predictive Medicine, Inc.
45 Orchard Street
Belmont MA 02478-3008
Email: jluci...@predmed.com