[Top] [All Lists]

[ontolog-forum] REMINDER: NCBO Webinar Series - Nathan Baker, May 12 - I

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Trish Whetzel <plwhetzel@xxxxxxxxx>
Date: Tue, 11 May 2010 12:54:02 -0700
Message-id: <AANLkTikJxvMq6DokQxJleHaNHdakiLdjiYqu6RnEm8QK@xxxxxxxxxxxxxx>
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 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: http://www.bioontology.org/seminar-series.

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!) 
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 

Access code:928 155 525 

For assistance 
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

Message Archives: http://ontolog.cim3.net/forum/ontolog-forum/  
Config Subscr: http://ontolog.cim3.net/mailman/listinfo/ontolog-forum/  
Unsubscribe: mailto:ontolog-forum-leave@xxxxxxxxxxxxxxxx
Shared Files: http://ontolog.cim3.net/file/
Community Wiki: http://ontolog.cim3.net/wiki/ 
To join: http://ontolog.cim3.net/cgi-bin/wiki.pl?WikiHomePage#nid1J
To Post: mailto:ontolog-forum@xxxxxxxxxxxxxxxx    (01)

<Prev in Thread] Current Thread [Next in Thread>
  • [ontolog-forum] REMINDER: NCBO Webinar Series - Nathan Baker, May 12 - Indexing nano medicine resources with caOBR, Trish Whetzel <=