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MEBI591C: Semantic Web in Biomedicine

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Schedule

MEBI 591C, Spring 2009
Semantic Web in Biomedicine

Instructor: Michal Galdzicki
Email: mgaldzic u washington edu

Meeting Times and Locations

Wednesdays 3:30-4:20pm
Health Sciences Building E-wing (HSE) Room# E212 Map showing E-wing ;Map of Campus
Dates: 4/1/2009 - 6/3/2009

Announcements

May 28 2009, 10:43 AM

6/3/2009 Ira Kalet

Please read: Pedersen, T. (2008). "Empiricism Is Not a Matter of Faith." Computational Linguistics 34(3): 465-470 (pdf). We will have a discussion with Dr. Kalet about this provocative article, followed by the course evaluations. There are two other papers Dr. Kalet suggested to be found on the schedule.

May 22 2009, 11:06 AM

5/27/2009 Marianne Shaw

Luciano, J. and R. Stevens (2007). "e-Science and biological pathway semantics." BMC bioinformatics 8(Suppl 3): S3. (pdf)

May 19 2009, 3:11 PM

RSC Publishing Journal: Integrative Biology offers basic semantic enhancement of articles

The evolution of chemotaxis assays from static models to physiologically relevant platforms Stephanie Toetsch, Peter Olwell, Adriele Prina-Mello and Yuri Volkov Integrative Biology 2009. DOI: 10.1039/b814567a

May 18 2009, 2:39 PM

5/20/2009 Blaine Reeder

Blaine will lead the seminar in discussion of literature and ontologies. Please read the following paper to prepare for the class:

Rajapakse, M., R. Kanagasabai, et al. (2008). "Ontology-centric integration and navigation of the dengue literature." Journal of Biomedical Informatics 41(5): 806-815. (pdf)

May 12 2009, 5:24 PM

5/13/2009 Max Neal

Max will lead the discussion about SWAN based on the article:

Ciccarese, P., E. Wu, et al. (2008). "The SWAN biomedical discourse ontology." Journal of Biomedical Informatics 41(5): 739-751. (pdf)

May 12 2009, 5:22 PM

5/6/2009 Jim Brinkley

Dr. Brinkley will present his update about Ontology Views.

April 28 2009, 10:51 AM

4/29/2009 CJ Inman

DiBernardo, M., R. Pottinger, et al. (2008). "Semi-automatic web service composition for the life sciences using the BioMoby semantic web framework." Journal of Biomedical Informatics 41(5): 837-847. (pdf)

April 18 2009, 5:33 PM

4/22/2009 Joseph Tennis

Dr. Tennis from the iSchool will lead the discussion on Versioning Concept Schemes (Tennis 2008).

April 9 2009, 3:50 PM

4/15/2009 Journal Club: Integration for Clinical and Translational Research

We will discuss the following paper:

Mirhaji, P., M. Zhu, et al. (2009). "Ontology driven integration platform for clinical and translational research." BMC Bioinformatics 10(Suppl 2): S2. (BMC link) (local pdf) Mirhaji, et al. present the generic architecture used in SAPPHIRE a PHI situational awareness effort applied to clinical and translational research.

April 6 2009, 3:04 PM

4/8/2009 John Gennari

Ontologies, Description Logics, Subsumption.

March 27 2009, 4:29 PM

4/1/2009 First Day

Michal Galdzicki will introduce the seminar and the Semantic Web (Feigenbaum2007_TheSemanticWebInAction.pdf).
We will also decide on the schedule for the journal club days.

March 13 2009, 9:56 AM

Description

The Semantic Web in Biomedicine Seminar will be organized as a journal club focused on semantic technology use in bioinformatics, medical and public health informatics. The journal club will be a discussion of articles using these technical methods as they apply across the disciplines. Each session will be led by one of the attendees in a discussions that will summarize the findings and critique the research. The goal is to get to know some of the many exciting examples of semantic web applications within biomedical and health literature. If you have questions or ideas for specific topics please e-mail me.