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[protege-discussion] NCBO Webinar: Hilmar Lapp, Nov. 17 at 10:00am PT

Trish Whetzel plwhetzel at
Sat Nov 13 19:37:17 PST 2010

The next NCBO Webinar will be presented by Dr. Hilmar Lapp, Assistant
Director for Informatics at the National Evolutionary Synthesis Center
(NESCent) on "Bringing reason to phenotype diversity, character change, and
common descent" at 10:00am PST, Wednesday, November 17. Below is information
on how to join the online meeting via WebEx and accompanying teleconference.
For the full schedule of the NCBO Webinar presentations see:

For more than a century, systematic biologists have meticulously documented
the stunning biodiversity of phenotypes across the tree of life in the
comparative systematics literature. This vast store of often complex
character and character state descriptions informs our understanding of the
evolutionary transitions that gave rise to the present diversity of life on
earth. Yet, as free text in natural language, these descriptive data are not
amenable to even simple computational processing, such as comparison of
organisms by phenotype similarity, much less large-scale data integration
and knowledge mining. I will present the approach that we have adopted
within the Phenoscape project ( to expose these data
to machine reasoning.  Phenoscape uses the Entity-Quality (EQ) model to
transform characters and character states into formal phenotype assertions.
Data transformed in this way from the systematics literature are integrated
with mutant phenotype data from model organisms in a large knowledge base (, in order to generate hypotheses about the genetic
causes of evolutionary character transitions. I will discuss both successes
and challenges in blending formal knowledge representation methods with
descriptive biology and hypotheses of descent.  An important remaining
challenge is a logic framework for reasoning over homology, i.e. descent
from a common ancestor, which is required for many forms of evolutionary

Hilmar Lapp is the Assistant Director for Informatics at the National
Evolutionary Synthesis Center (NESCent). His research interests are in
reusable and interoperable software and data, large-scale data integration,
and building sustainable cyberinfrastructure. A biologist by training, he
has also been programming for more than two decades, ranging from commercial
applications to real-time data acquisition to bioinformatics data
integration and standards. In his role at NESCent, he is involved in many of
the Center’s cyberinfrastructure initiatives, and serves as senior personnel
in the NSF-funded Phenoscape project (, as well as the
Dryad digital repository for data supporting scientific publications ( Before joining NESCent in 2006, he worked for almost
10 years in functional genome informatics in the biopharmaceutical sector.
At the Genomics Institute of the Novartis Research Foundation (GNF) in San
Diego, CA, he built SymAtlas, one of the first decidedly gene-centric
database integrating genome annotation databases with gene function data.

Topic: NCBO Webinar Series
Date: Wednesday, November 17, 2010
Time: 10:00 am, Pacific Standard Time (San Francisco, GMT-08:00)
Meeting Number: 929 613 752
Meeting Password: ncbomeeting

To join the online meeting (Now from the Apple iPhone (R) and other
1. Go to
2. If requested, enter your name and email address.
3. If a password is required, enter the meeting password: ncbomeeting
4. Click "Join".
5. Follow the instructions that appear on your screen.

To view in other time zones or languages, please click the link:

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

Access code:929 613 752

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:

The playback of UCF (Universal Communications Format) rich media files
requires appropriate players. To view this type of rich media files in the
meeting, please check whether you have the players installed on your
computer by going to


IMPORTANT NOTICE: This WebEx service includes a feature that allows audio
and any documents and other materials exchanged or viewed during the session
to be recorded. By joining this session, you automatically consent to such
recordings. If you do not consent to the recording, discuss your concerns
with the meeting host prior to the start of the recording or do not join the
session. Please note that any such recordings may be subject to discovery in
the event of litigation.
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