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[protege-discussion] REMINDER: NCBO Seminar Series - Michel Dumontier, Wed April 1

Trish Whetzel plwhetzel at
Tue Mar 31 23:03:05 PDT 2009

Hi all!

The next NCBO Seminar Series will be held TOMORROW Wednesday, April 1st, at
10am PST. Please note there will not be a VOIP option, and attendees must
call into the teleconference.

Below is Information on how to join the online meeting and accompanying
teleconference. The seminar will be presented by Michel Dumontier, Assistant
Professor of Bioinformatics at Carleton University in Ottawa, Canada. The
title of the presentation will be “Precise biochemical knowledge starting
with structure-based criteria for molecular identity”.

For this talk, please send any questions to Trish Whetzel, at
whetzel at For a schedule of 2009 presentations through June, or
for more information about the series, please visit the Seminar Series home
page: **.

Title: Precise biochemical knowledge starting with structure-based criteria
for molecular identity

Abstract: Biochemical ontologies aim to capture and represent biochemical
entities and the relations that exist between them in an accurate and
precise manner. A fundamental starting point is the use of identifiers that
precisely and uniquely identify some biochemical entity, whether it be a
substance, a quality or some biological process. Yet, our current approach
for generating identifiers doing so is often haphazard and incomplete. This
prevents us from accurately integrating knowledge and also leads to under
specification of our knowledge. This talk aims to initiate a discussion on
plausible structure-based strategies for biochemical identity, ultimately to
generate identifiers in an automatic and curator/database independent
fashion, whether it be at molecular level or some part thereof (e.g.
residues, collection of residues, atoms, collection of atoms, functional
groups). With structure-based identifiers in hand, we will be in a position
to accurately capture specific biochemical knowledge, such as how a set of
residues in a binding site are involved in a chemical reaction including the
fact that a key nitrogen atom must first be de-protonated. Thus, this will
enhance our current representation of biochemical knowledge and make it
fundamentally more useful.

Topic: NCBO Seminar Series
Date: The 1st & 3rd Wednesday of every 1 months
Time: 10:00 am, Pacific Daylight Time (GMT -07:00, San Francisco)
*Meeting Number: 926 719 478
Meeting Password: ncbomeeting*

Please click the link below to see more information about the meeting,
including its agenda, or to join the meeting.

To join the online meeting
1. Go to
2. Enter your name and email address.
3. Enter the meeting password: ncbomeeting
4. Click "Join Now".
5. Follow the instructions that appear on your screen.

To join the meeting on iPhone
Go to

Don't have the iPhone WebEx application yet?
Go to

To join the teleconference
*Call-in toll number (US/Canada): 1-650-429-3300 *
Global call-in numbers:

For assistance
1. Go to
2. On the left navigation bar, click "Support".

You can contact me at:
whetzel at

To update this meeting to your calendar program (for example Microsoft
Outlook), click this link:

WebEx will automatically setup Meeting Manager for Windows the first time
you join a meeting. To save time, you can setup prior to the meeting by
clicking this link:
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