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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
Benjamin Dai, M.S.
Chief Software Architect, NCBO
Michael V. Dorf, M.S.
Chief Software Architect
Ray Fergerson, Ph.D.
NCBO Project Director
Paea LePendu, Ph.D., M.S., B.A.
Post Doctoral Scholar
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)
Ravi D. Shankar, M.S.
(formerly in BMIR)
Alex Skrenchuk
IT Manager
Samson W. Tu, M.S.
Sr. Research Engineer
Tania Tudorache, Ph.D.
Engineering Research Associate
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-2011-1482
Proposed SKOS Extensions for BioPortal Terminology Services
C. Tao, N. F. Noy, H. Solbrig, N. H. Shah, M. A. Musen, C. G. Chute
Joint International Semantic Technology Conference (JIST 2011), Hangzhou, China. Published in 2011
BMIR-2011-1481
How orthogonal are the OBO Foundry ontologies?
A. Ghazvinian, N. F. Noy, M. A. Musen
Journal of Biomedical Semantics, 2(Suppl 2), S2. Published in 2011
BMIR-2011-1480
NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources,information retrieval, biomedical data and ontologies
C. Jonquet, P. LePendu, S. M. Falconer, A. Coulet, N. F. Noy, M. A. Musen, N. H. Shah
Journal of Web Semantics: Science, Services and Agents on the World Wide Web, 9, 3. Published in 2011
BMIR-2011-1479
From Mappings to Modules: Using Mappings to Identify Domain-Specific Modules in Large Ontologies
A. Ghazvinian, N. F. Noy, M. A. Musen
The Sixth International Conference on Knowledge Capture, Banff, Canada, ACM. Published in 2011
BMIR-2011-1478
Document Annotation Support Using Biomedical Ontologies
T. Thanh, Y. Ma, N. F. Noy
Workshop on Web Scale Knowledge Extraction at ISWC 2011, Bonn, Germany. Published in 2011

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