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[ncbo-publictalks] NCBO Webinar Series - Nathan Baker, May 12 - Indexing nano medicine resources with caOBR

Trish Whetzel whetzel at
Mon May 10 11:20:58 PDT 2010

The next NCBO Webinar will be held Wednesday, May 12 at 10am PT.  
Please note there will not be a VOIP option and attendees must call  
into the teleconference.

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
2. On the left navigation bar, click "Support".

You can contact me at:
whetzel 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
whetzel at

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