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REMINDER: NCBO Webinar Series - Nathan Baker, May 12 - Indexing nano medicine resources with caOBR

From: Trish Whetzel <plwhetzel@gmail.com>
Date: Tue, 11 May 2010 17:09:20 -0700
Message-ID: <AANLkTik86r4fbSsEz102N--rJq8pH70zG5ZZ_kFuEKwW@mail.gmail.com>
To: HCLS <public-semweb-lifesci@w3.org>
The next NCBO Webinar will be held TOMORROW, Wednesday, May 12 at 10am PT.
Please note there will not be a VOIP option and attendees must call into the

The Webinar will be presented by Dr. Nathan Baker, from Washington
University. The title of the presentation will be “Indexing nano medicine
resources with caOBR”. Below is information on how to join the online
meeting and accompanying teleconference. For a schedule of the 2010
presentations or for more information about the NCBO Seminar series, see:

Indexing nano medicine resources with caOBR

caOBR has been developed to provide an interface between caBIG cancer
informatics resources and the NCBO ontology-based annotation tools.   In the
past, caGRID resources have not been accessible for annotating and indexing
data using the NCBO Annotator/resource tools.  This has posed a problem for
annotating caNanoLab data using NPO or other relevant ontologies.  At the
same time, the caBIG community can benefit from access to OBR annotations
from data resources relevant to cancer research (eg., MICAD) but are outside
of the caBIG resource. Therefore, we have developed a middleware software
tool called caOBR that 1) provides BioPortal NCBO Resource Index access to
caGRID resources for annotating data in caGRID resources, and 2) provides
caGRID access to the NCBO Resource Index to access annotations.  In both
cases, the caOBR offers the ability to annotate and search a wide range of
biomedical data resources with a large number of ontologies.

Our initial development work on caOBR has focused on the caNanoLab caGrid
resource and the NanoParticle Ontology. caOBR uses the NCBO Annotator
workflow to make caNanoLab to be accessible through the NCBO Resource Index.
 This has enabled the annotation and indexing of caNanoLab data using NPO.
 The caOBR has enhanced the use of caNanoLab in several ways.  First,
semantic integration and searching of data is now feasible by data
annotation with ontology terms.  Second, caNanoLab data is now accessible by
semantically-enabled tools and for searching and analyses outside caGRID.
 Finally, the problem of synonymy can be addressed through the availability
of semantically-aware searching of the caNanoLab resource.  Synonymy is a
problem for any interdisciplinary field, such as nanomedicine, where
different terms are used by researchers from different backgrounds for the
same concept.  Semantically-aware search resources such as caOBR resolves
this problem by implicitly incorporating synonyms into the annotation and
search of the data.

Nathan A. Baker, Ph.D. received his B.S. degree in Chemistry from the
University of Iowa in 1997.  In 2001, he received his Ph.D. in Physical
Chemistry at the University of California San Diego under the joint guidance
of Profs. J. Andrew McCammon (Chemistry) and Michael Holst (Mathematics).
 After a brief period of postdoctoral work in the McCammon lab, he joined
the Department of Biochemistry and Molecular Biophysics at Washington
University in St. Louis in 2002 and was promoted to Associate Professor with
tenure in 2006.  Prof. Baker is also Director of the Computational and
Molecular Biophysics graduate program, Director of the Biocomputing Core for
the Siteman Center for Cancer Nanotechnology Excellence, Lead for the
National Cancer Institute caBIG Nanotechnology Working Group, and Chair for
the ASTM E56.01 Subcommittee on Nanotechnology Informatics.  Prof. Baker's
research is in the area of computational biophysics with projects on
continuum models of biomolecular solvation, simulation of lipid bilayers and
monolayers in biological membranes and nanoemulsions, modeling of protein
allostery, and development of informatics methods for the rational design of
nanomaterials.  The Baker group is actively involved in the development of
new algorithms and software for biomolecular simulations and modeling in
support of these research projects.  Prof. Baker is the author of 40
peer-reviewed articles as well as several reviews and book chapters.  He has
been awarded the Hewlett-Packard Junior Faculty Excellence Award by the
American Chemical Society and was an Alfred P. Sloan Research Fellow.

Topic: NCBO Webinar
Date: Wednesday, May 12, 2010
Time: 10:00 am, Pacific Daylight Time (San Francisco, GMT-07:00)
Meeting Number: 928 155 525
Meeting Password: ncbo

To join the online meeting (Now from iPhones too!)
1. Go to

2. Enter your name and email address.
3. Enter the meeting password: ncbo
4. Click "Join Now".

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

To join the audio conference only
To receive a call back, provide your phone number when you join the meeting,
or call the number below and enter the access code.
Call-in toll number (US/Canada): 1-650-429-3300
Global call-in numbers:

Access code:928 155 525

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

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378

NCBO-PublicTalks mailing list
Received on Wednesday, 12 May 2010 00:09:53 UTC

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