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Research Labs

The Musen Lab

Lab Overview

Mark Musen’s laboratory studies methods for building intelligent computer systems that support the work of clinicians and basic scientists. The overall goal is to support e-science and clinical decision making using systems that store encoded knowledge. The laboratory investigates the use of components for building knowledge-based systems, controlled terminologies and ontologies, and technology for the Semantic Web.

For more than two decades, Musen’s group has worked to elucidate reusable building blocks for constructing intelligent systems, and to develop scalable computational architectures for systems that can address significant application tasks in biomedicine. An important element of that work has led to the development of the Protégé system, an open-source platform used around the world for the construction and maintenance of electronic knowledge bases, ontologies, and Semantic Web applications. Protégé provides a platform from which to study problems in knowledge modeling, ontology integration and alignment, and the construction of large-scale and distributed intelligent systems.

Related People

Paul R. Alexander
Web / UI Developer
Michael V. Dorf, M.S.
Chief Software Architect
Ray Fergerson, Ph.D.
NCBO Project Director
Paea LePendu, Ph.D., M.S., B.A
Research Scientist
Chris MacIntosh, M.B.A.
Office Manager
Mark A. Musen, M.D., Ph.D
Professor of Medicine (Biomedical Informatics); Division Head (BMIR); Co-Director, Biomedical Informatics Training Program
Natasha F. Noy, Ph.D.
Senior Research Engineer
Martin J. O'Connor, M.Sc.
System Software Developer
Stephen A. Racunas, Ph.D.
Bioinformatics Researcher
Daniel L. Rubin, M.D., M.S.
Assistant Professor of Radiology, and of Medicine (BMIR)
Manuel Salvadores, Ph.D.
Senior Software Engineer
Nigam H. Shah, MBBS, PhD
Assistant Professor of Medicine (Biomedical Informatics)
Alex Skrenchuk
IT Manager
Samson W. Tu, M.S.
Sr. Research Engineer
Tania Tudorache, Ph.D.
Research Scientist
Mike Uehara-Bingen
Software Developer
Jennifer L. Vendetti
Software Developer
Darren Weber, PhD
Software Engineer
Trish Whetzel, PhD, MS
Outreach Coordinator

Related Publications Only the 5 most recent displayed

BMIR-2013-1492
PragmatiX: An Interactive Tool for Visualizing the Creation Process Behind Collaboratively Engineered Ontologies
S. Walk, J. Pöschko, M. Strohmaier, K. Andrews, T. Tudorache, N. F. Noy, C. I. Nyulas, M. A. Musen
International Journal on Semantic Web and Information Systems, IJSWIS, Special Issue on Visualization of and Interaction with Semantic Web Data. In Press in 2013
BMIR-2012-1491
The Template Instance Pattern
C. I. Nyulas, T. Tudorache, S. W. Tu
3rd Workshop on Ontology Patterns in conjunction with the 11th International Semantic Web Conference 2012 (ISWC 2012), Boston, USA, CEUR-WS, 929. Published in 2012
BMIR-2012-1490
Experiences with Multilingual Modeling in the Development of the International Classification of Traditional Medicine Ontology
C. I. Nyulas, T. Tudorache, S. W. Tu, M. A. Musen
3rd Workshop on the Multilingual Semantic Web (MSW3), Boston, CEUR-WS, 936. Published in 2012
BMIR-2012-1489
Pragmatic Analysis of Crowd-Based Knowledge Production Systems with iCAT Analytics: Visualizing Changes to the ICD-11 Ontology
J. Pöschko, M. Strohmaier, T. Tudorache, N. F. Noy, M. A. Musen
AAAI Spring Symposium, Stanford, CA, USA. Published in 2012
BMIR-2012-1484
Recommending Concepts to Experts: An Exploration of Recommender Techniques for Collaborative Ontology Engineering Platforms in the Biomedical Domain
S. Walk, M. Strohmaier, T. Tudorache, N. F. Noy, C. I. Nyulas, M. A. Musen
International Conference on Biomedical Ontology (ICBO), Graz, Austria. Published in 2012

Projects

BioSTORM
View Project
Protégé
View Project
SGER: Hypothesis Based Query and Verification of Pathway Models
View Project

Related Events Only the 5 most recent displayed

Protégé Short Course
Protégé Short Course
Date:
Wed, Mar 23 2011 to Fri, Mar 25 2011
Location:
LKSC
Project:
Protégé
Special Colloquium
Sean Falconer
Date:
Fri, Sep 11 2009
Time:
12:00pm
Location:
MSOB X275
Speaker:
Sean Flaconer
Project:
NCBO
Special Colloquium
11th Protege Conference
Date:
Tue, Jun 23 2009 to Fri, Jun 26 2009
Time:
3:30pm
Location:
Stanford University
Project:
Protégé
Colloquium
Seminar Series - Larry Hunter
Date:
Wed, Jun 17 2009
Time:
10-11am
Location:
online
Speaker:
Larry Hunter
Project:
NCBO
Colloquium
SPECIAL Seminar Series - Mark Wilkinson
Date:
Wed, Jun 10 2009
Time:
11am-12pm
Location:
online
Speaker:
Mark Wilkinson
Project:
NCBO

Stanford School of Medicine