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[ontolog-forum] REMINDER: NCBO Seminar Series - Michel Dumontier, Wed Ap

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Trish Whetzel <plwhetzel@xxxxxxxxx>
Date: Tue, 31 Mar 2009 23:01:24 -0700
Message-id: <139835960903312301n29fbf959oe518277e81a0977@xxxxxxxxxxxxxx>

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@xxxxxxxxxxxx. For a schedule of 2009 presentations through June, or for more information about the series, please visit the Seminar Series home page: http://www.bioontology.org/seminar_series.html.

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 https://stanford.webex.com/stanford/j.php?ED=107799137&UID=0&PW=acc85e345a3d3d2a1559595c27
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 wbx://stanford.webex.com/stanford?MK=926719478&MPW=fa80f225f0bacb57916395a9454864fe09cdcc184b1d352d317ec99949d4d080

Don't have the iPhone WebEx application yet?
Go to http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=298844386

To join the teleconference
Call-in toll number (US/Canada): 1-650-429-3300
Global call-in numbers: https://stanford.webex.com/stanford/globalcallin.php?serviceType=MC&ED=107799137&tollFree=0

For assistance
1. Go to https://stanford.webex.com/stanford/mc
2. On the left navigation bar, click "Support".

You can contact me 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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