Mark Musen

Administrative Appointments

• Principal Investigator, National Center for Biomedical Ontology , (2005– present )
• Co-Editor-in-Chief, Applied Ontology: An International Journal of Ontological Analysis and Conceptual Modeling , (2005– present )
• Chair, Health Informatics and Modeling Topic Advisory Group, ICD Revision Steering Group, World Health Organization , (2008– present )
• Head, Stanford Center for Biomedical Informatics Research , (1992– present )
• Deputy Director for Bioinformatics, Immune Tolerance Network , (2005– 2007 )
• Member, International Research Advisory Board, University Health Network, Toronto, Canada , (2002– 2005 )
• Biomedical Library Review Committee, National Library of Medicine , (1992– 1996 )

Honors and Awards

• Donald A. B. Lindberg Award for Innovation in Informatics, American Medical Informatics Association (2006)
• General Chair, International Semantic Web Conference (2005)
• Chair, Scientific Program Committee, American Medical Informatics Association Annual Symposium (2003)
• Elected Member, American Society for Clinical Investigation (1997)
• NSF Young Investigator Award, National Science Foundation (1992)
• Elected Fellow, American College of Medical Informatics (1989)
• Young Investigator Award for Research in Medical Knowledge Systems, American Association for Medical Systems and Informatics (1989)

Professional Education

• Ph.D., Stanford University Medical Information Sciences (1988)
• M.D., Brown University Medicine (1980)
• Sc.B., Brown University Biology (1977)

Postdoctoral Advisees

• Adrien Coulet, Clement Jonquet

Graduate & Fellowship Program Affiliations

• Biomedical Informatics
• Medicine

Web Site Links

• The National Center for Biomedical Ontology

Industry Relationships

Stanford is committed to ethical and transparent interactions with our industry partners. It is our policy to disclose payments of $5,000 or more, equity valued at $5,000 or more in a publicly traded company, or any equity in a privately held company, to physicians and scientists employed by Stanford University from companies or other commercial entities with which they interact as part of their professional activities. 

• Consulting: Skadden, Arps, Slate, Meagher, and Flom LLP

Research Interests

The construction of automated systems to assist biomedical decision making is impeded by difficulties in formalizing knowledge and in encoding that knowledge for use by the computer. Current work in our laboratory addresses mechanisms by which computers can assist in the development of large, electronic biomedical knowledge bases. Emphasis is placed on new methods for the automated generation of computer-based tools that end-users can use to enter knowledge of specific biomedical content. In particular, we are studying:

- Development of reusable domain descriptions (ontologies) and problem-solving methods

- Automated generation of knowledge-acquisition tools from domain ontologies

- Visual metaphors to facilitate knowledge entry by application specialists

- Decision-support systems for protocol-based care

- Representation of biomedical concepts and terminologies for development of intelligent systems

The Protégé system provides a uniform infrastructure for our work on knowledge modeling and representation.

The National Center for Biomedical Ontology, supported by the NIH Roadmap, develops a new generation of technology for storing, accessing, evaluating, and using online biomedical knowledge resources.

Publications

• BioPortal: ontologies and integrated data resources at the click of a mouse. Noy NF,  Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA.  Nucleic Acids Res.  2009; 37 (Web Server issue): W170-3
• Technology for building intelligent systems: from psychology to engineering. Musen MA,  Nebr Symp Motiv.  2007; 52 145-84
• Medical informatics: searching for underlying components. Musen MA,  Methods Inf Med.  2002; 41 (1): 12-9
• Scalable software architectures for decision support. Musen MA,  Methods Inf Med.  1999; 38 (4-5): 229-38
• Development of large-scale functional brain networks in children. Supekar K,  Musen M, Menon V.  PLoS Biol.  2009; 7 (7): e1000157
• Comparison of concept recognizers for building the Open Biomedical Annotator. Shah NH,  Bhatia N, Jonquet C, Rubin D, Chiang AP, Musen MA.  BMC Bioinformatics.  2009; 10 Suppl 9 S14
• Ontology-driven indexing of public datasets for translational bioinformatics. Shah NH,  Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA.  BMC Bioinformatics.  2009; 10 Suppl 2 S1
• Computational neuroanatomy: ontology-based representation of neural components and connectivity. Rubin DL,  Talos IF, Halle M, Musen MA, Kikinis R.  BMC Bioinformatics.  2009; 10 Suppl 2 S3
• UMLS-Query: a perl module for querying the UMLS. Shah NH,  Shah N, Muse MA, Musen M.  AMIA Annu Symp Proc.  2008; 652-6
• BioPortal: ontologies and data resources with the click of a mouse. Musen MA,  Musen M, Shah NH, Shah N, Noy NF, Noy N, Dai BY, Dai B, Dorf M, Dorf M, Griffith N, Griffith N, Buntrok J, Buntrock JD, Jonquet C, Jonquet C, Montegut MJ, Montegut MJ, Rubin DL, Rubin DL.  AMIA Annu Symp Proc.  2008; 1223-4
• Comparison of ontology-based semantic-similarity measures. Lee WN,  Shah N, Sundlass K, Musen M.  AMIA Annu Symp Proc.  2008; 384-8
• Developing biomedical ontologies collaboratively. Noy NF,  Tudorache T, de Coronado S, Musen MA.  AMIA Annu Symp Proc.  2008; 520-4
• Network analysis of intrinsic functional brain connectivity in Alzheimer's disease. Supekar K,  Menon V, Rubin D, Musen M, Greicius MD.  PLoS Comput Biol.  2008; 4 (6): e1000100
• The SAGE Guideline Model: achievements and overview. Tu SW,  Campbell JR, Glasgow J, Nyman MA, McClure R, McClay J, Parker C, Hrabak KM, Berg D, Weida T, Mansfield JG, Musen MA, Abarbanel RM.  J Am Med Inform Assoc.  2007 Sep-Oct; 14 (5): 589-98
• Knowledge Zone: a public repository of peer-reviewed biomedical ontologies. Supekar K,  Rubin D, Noy N, Musen M.  Stud Health Technol Inform.  2007; 129 (Pt 1): 812-6
• Protégé: a tool for managing and using terminology in radiology applications. Rubin DL,  Noy NF, Musen MA.  J Digit Imaging.  2007; 20 Suppl 1 34-46
• OBO to OWL: a protege OWL tab to read/save OBO ontologies. Moreira DA,  Musen MA.  Bioinformatics.  2007; 23 (14): 1868-70
• Using semantic dependencies for consistency management of an ontology of brain-cortex anatomy. Dameron O,  Musen MA, Gibaud B.  Artif Intell Med.  2007; 39 (3): 217-25
• Annotation and query of tissue microarray data using the NCI Thesaurus. Shah NH,  Rubin DL, Espinosa I, Montgomery K, Musen MA.  BMC Bioinformatics.  2007; 8 296
• Interpretation errors related to the GO annotation file format. Moreira DA,  Shah NH, Musen MA.  AMIA Annu Symp Proc.  2007; 538-42
• Wrestling with SUMO and bio-ontologies. Stoeckert C,  Ball C, Brazma A, Brinkman R, Causton H, Fan L, Fostel J, Fragoso G, Heiskanen M, Holstege F, Morrison N, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Sarkans U, Sherlock G, Stevens R, Taylor C, Taylor R, Whetzel P, White J.  Nat Biotechnol.  2006; 24 (1): 21-2; author reply 23
• Using ontologies linked with geometric models to reason about penetrating injuries. Rubin DL,  Dameron O, Bashir Y, Grossman D, Dev P, Musen MA.  Artif Intell Med.  2006; 37 (3): 167-76
• Use of declarative statements in creating and maintaining computer-interpretable knowledge bases for guideline-based care. Tu SW,  Hrabak KM, Campbell JR, Glasgow J, Nyman MA, McClure R, McClay J, Abarbanel R, Mansfield JG, Martins SM, Goldstein MK, Musen MA.  AMIA Annu Symp Proc.  2006; 784-8
• National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. Rubin DL,  Lewis SE, Mungall CJ, Misra S, Westerfield M, Ashburner M, Sim I, Chute CG, Solbrig H, Storey MA, Smith B, Day-Richter J, Noy NF, Musen MA.  OMICS.  2006; 10 (2): 185-98
• Ontology-based annotation and query of tissue microarray data. Shah NH,  Rubin DL, Supekar KS, Musen MA.  AMIA Annu Symp Proc.  2006; 709-13
• Ontology-based representation of simulation models of physiology. Rubin DL,  Grossman D, Neal M, Cook DL, Bassingthwaighte JB, Musen MA.  AMIA Annu Symp Proc.  2006; 664-8
• An evaluation model for syndromic surveillance: assessing the performance of a temporal algorithm. Buckeridge DL,  Switzer P, Owens D, Siegrist D, Pavlin J, Musen M.  MMWR Morb Mortal Wkly Rep.  2005; 54 Suppl 109-15
• Ontology metadata to support the building of a library of biomedical ontologies. Supekar K,  Musen M.  AMIA Annu Symp Proc.  2005; 1126
• Use of description logic classification to reason about consequences of penetrating injuries. Rubin DL,  Dameron O, Musen MA.  AMIA Annu Symp Proc.  2005; 649-53
• Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study. Dameron O,  Rubin DL, Musen MA.  AMIA Annu Symp Proc.  2005; 181-5
• Using an ontology of human anatomy to inform reasoning with geometric models. Rubin DL,  Bashir Y, Grossman D, Dev P, Musen MA.  Stud Health Technol Inform.  2005; 111 429-35
• Translating research into practice: organizational issues in implementing automated decision support for hypertension in three medical centers. Goldstein MK,  Coleman RW, Tu SW, Shankar RD, O'Connor MJ, Musen MA, Martins SB, Lavori PW, Shlipak MG, Oddone E, Advani AA, Gholami P, Hoffman BB.  J Am Med Inform Assoc.  2004 Sep-Oct; 11 (5): 368-76
• The SAGE guideline modeling: motivation and methodology. Tu SW,  Campbell J, Musen MA.  Stud Health Technol Inform.  2004; 101 167-71
• Linking ontologies with three-dimensional models of anatomy to predict the effects of penetrating injuries. Rubin DL,  Bashir Y, Grossman D, Dev P, Musen MA.  Conf Proc IEEE Eng Med Biol Soc.  2004; 5 3128-31
• Modeling guidelines for integration into clinical workflow. Tu SW,  Musen MA, Shankar R, Campbell J, Hrabak K, McClay J, Huff SM, McClure R, Parker C, Rocha R, Abarbanel R, Beard N, Glasgow J, Mansfield G, Ram P, Ye Q, Mays E, Weida T, Chute CG, McDonald K, Molu D, Nyman MA, Scheitel S, Solbrig H, Zill DA, Goldstein MK.  Stud Health Technol Inform.  2004; 107 (Pt 1): 174-8
• An intelligent case-adjustment algorithm for the automated design of population-based quality auditing protocols. Advani A,  Jones N, Shahar Y, Goldstein MK, Musen MA.  Stud Health Technol Inform.  2004; 107 (Pt 2): 1003-7
• Evaluating provider adherence in a trial of a guideline-based decision support system for hypertension. Chan AS,  Coleman RW, Martins SB, Advani A, Musen MA, Bosworth HB, Oddone EZ, Shlipak MG, Hoffman BB, Goldstein MK.  Stud Health Technol Inform.  2004; 107 (Pt 1): 125-9
• BioSTORM: a system for automated surveillance of diverse data sources. O'Connor MJ,  Buckeridge DL, Choy M, Crubezy M, Pincus Z, Musen MA.  AMIA Annu Symp Proc.  2003; 1071
• A knowledge-acquisition wizard to encode guidelines. Shankar RD,  Tu SW, Musen MA.  AMIA Annu Symp Proc.  2003; 1007
• Protégé-2000: an open-source ontology-development and knowledge-acquisition environment. Noy NF,  Crubezy M, Fergerson RW, Knublauch H, Tu SW, Vendetti J, Musen MA.  AMIA Annu Symp Proc.  2003; 953
• The structure of guideline recommendations: a synthesis. Tu SW,  Campbell J, Musen MA.  AMIA Annu Symp Proc.  2003; 679-83
• Developing quality indicators and auditing protocols from formal guideline models: knowledge representation and transformations. Advani A,  Goldstein M, Shahar Y, Musen MA.  AMIA Annu Symp Proc.  2003; 11-5
• Contextualizing heterogeneous data for integration and inference. Pincus Z,  Musen MA.  AMIA Annu Symp Proc.  2003; 514-8
• A framework for evidence-adaptive quality assessment that unifies guideline-based and performance-indicator approaches. Advani A,  Goldstein M, Musen MA.  Proc AMIA Symp.  2002; 2-6
• Knowledge-based bioterrorism surveillance. Buckeridge DL,  Graham J, O'Connor MJ, Choy MK, Tu SW, Musen MA.  Proc AMIA Symp.  2002; 76-80
• The Chronus II temporal database mediator. O'Connor MJ,  Tu SW, Musen MA.  Proc AMIA Symp.  2002; 567-71
• SYNCHRONUS: a reusable software module for temporal integration. Das AK,  Musen MA.  Proc AMIA Symp.  2002; 195-9
• Modeling data and knowledge in the EON guideline architecture. Tu SW,  Musen MA.  Stud Health Technol Inform.  2001; 84 (Pt 1): 280-4
• Integration of textual guideline documents with formal guideline knowledge bases. Shankar RD,  Tu SW, Martins SB, Fagan LM, Goldstein MK, Musen MA.  Proc AMIA Symp.  2001; 617-21
• A formal method to resolve temporal mismatches in clinical databases. Das AK,  Musen MA.  Proc AMIA Symp.  2001; 130-4
• Medical quality assessment by scoring adherence to guideline intentions. Advani A,  Shahar Y, Musen MA.  Proc AMIA Symp.  2001; 2-6
• Building an explanation function for a hypertension decision-support system. Shankar RD,  Martins SB, Tu SW, Goldstein MK, Musen MA.  Stud Health Technol Inform.  2001; 84 (Pt 1): 538-42
• RASTA: a distributed temporal abstraction system to facilitate knowledge-driven monitoring of clinical databases. O'Connor MJ,  Grosso WE, Tu SW, Musen MA.  Stud Health Technol Inform.  2001; 84 (Pt 1): 508-12
• Implementing clinical practice guidelines while taking account of changing evidence: ATHENA DSS, an easily modifiable decision-support system for managing hypertension in primary care. Goldstein MK,  Hoffman BB, Coleman RW, Musen MA, Tu SW, Advani A, Shankar R, O'Connor M.  Proc AMIA Symp.  2000; 300-4
• From guideline modeling to guideline execution: defining guideline-based decision-support services. Tu SW,  Musen MA.  Proc AMIA Symp.  2000; 863-7
• The impact of displayed awards on the credibility and retention of Web site information. Shon J,  Marshall J, Musen MA.  Proc AMIA Symp.  2000; 794-8
• Representation of temporal indeterminacy in clinical databases. O'Connor MJ,  Tu SW, Musen MA.  Proc AMIA Symp.  2000; 615-9
• Ontology acquisition from on-line knowledge sources. Li Q,  Shilane P, Noy NF, Musen MA.  Proc AMIA Symp.  2000; 497-501
• Design and use of clinical ontologies: curricular goals for the education of health-telematics professionals. Musen MA,  Stud Health Technol Inform.  2000; 72 40-7
• Semi-automated entry of clinical temporal-abstraction knowledge. Shahar Y,  Chen H, Stites DP, Basso LV, Kaizer H, Wilson DM, Musen MA.  J Am Med Inform Assoc.  1999 Nov-Dec; 6 (6): 494-511
• Representation of change in controlled medical terminologies. Oliver DE,  Shahar Y, Shortliffe EH, Musen MA.  Artif Intell Med.  1999; 15 (1): 53-76
• Integrating a modern knowledge-based system architecture with a legacy VA database: the ATHENA and EON projects at Stanford. Advani A,  Tu S, O'Connor M, Coleman R, Goldstein MK, Musen M.  Proc AMIA Symp.  1999; 653-7
• The low availability of metadata elements for evaluating the quality of medical information on the World Wide Web. Shon J,  Musen MA.  Proc AMIA Symp.  1999; 945-9
• Justification of automated decision-making: medical explanations as medical arguments. Shankar RD,  Musen MA.  Proc AMIA Symp.  1999; 395-9
• Applying temporal joins to clinical databases. O'Connor MJ,  Tu SW, Musen MA.  Proc AMIA Symp.  1999; 335-9
• A flexible approach to guideline modeling. Tu SW,  Musen MA.  Proc AMIA Symp.  1999; 420-4
• VM-in-Protégé: a study of software reuse. Park JY,  Musen MA.  Stud Health Technol Inform.  1998; 52 Pt 1 644-8
• Therapy planning as constraint satisfaction: a computer-based antiretroviral therapy advisor for the management of HIV. Smith DS,  Park JY, Musen MA.  Proc AMIA Symp.  1998; 627-31
• Domain ontologies in software engineering: use of Protégé with the EON architecture. Musen MA,  Methods Inf Med.  1998; 37 (4-5): 540-50
• Modern architectures for intelligent systems: reusable ontologies and problem-solving methods. Musen MA,  Proc AMIA Symp.  1998; 46-52
• A declarative explanation framework that uses a collection of visualization agents. Shankar RD,  Tu SW, Musen MA.  Proc AMIA Symp.  1998; 602-6
• A temporal database mediator for protocol-based decision support. Nguyen JH,  Shahar Y, Tu SW, Das AK, Musen MA.  Proc AMIA Annu Fall Symp.  1997; 298-302
• A foundational model of time for heterogeneous clinical databases. Das AK,  Musen MA.  Proc AMIA Annu Fall Symp.  1997; 106-10
• The EON model of intervention protocols and guidelines. Tu SW,  Musen MA.  Proc AMIA Annu Fall Symp.  1996; 587-91
• Making generic guidelines site-specific. Fridsma DB,  Gennari JH, Musen MA.  Proc AMIA Annu Fall Symp.  1996; 597-601
• Knowledge-based temporal abstraction in clinical domains. Shahar Y,  Musen MA.  Artif Intell Med.  1996; 8 (3): 267-98
• Knowledge acquisition for temporal abstraction. Stein A,  Musen MA, Shahar Y.  Proc AMIA Annu Fall Symp.  1996; 204-8
• PROTEGE-II: computer support for development of intelligent systems from libraries of components. Musen MA,  Gennari JH, Eriksson H, Tu SW, Puerta AR.  Medinfo.  1995; 8 Pt 1 766-70
• Hierarchical neural networks for survival analysis. Ohno-Machado L,  Walker MG, Musen MA.  Medinfo.  1995; 8 Pt 1 828-32
• Knowledge-based temporal abstraction in diabetes therapy. Shahar Y,  Das AK, Tu SW, Kraemer FB, Basso LV, Musen MA.  Medinfo.  1995; 8 Pt 1 852-6
• Computer-based screening of patients with HIV/AIDS for clinical-trial eligibility. Carlson RW,  Tu SW, Lane NM, Lai TL, Kemper CA, Musen MA, Shortliffe EH.  Online J Curr Clin Trials.  1995; Doc No 179 [3347 words; 32 paragraphs]
• The development of a controlled medical terminology: identification, collaboration, and customization. Miller ET,  Wieckert KE, Fagan LM, Musen MA.  Medinfo.  1995; 8 Pt 1 148-52
• A web-based architecture for a medical vocabulary server. Gennari JH,  Oliver DE, Pratt W, Rice J, Musen MA.  Proc Annu Symp Comput Appl Med Care.  1995; 275-9
• A rational reconstruction of INTERNIST-I using PROTEGE-II. Musen MA,  Gennari JH, Wong WW.  Proc Annu Symp Comput Appl Med Care.  1995; 289-93
• A comparison of the temporal expressiveness of three database query methods. Das AK,  Musen MA.  Proc Annu Symp Comput Appl Med Care.  1995; 331-7
• A comparison of two computer-based prognostic systems for AIDS. Ohno-Machado L,  Musen MA.  Proc Annu Symp Comput Appl Med Care.  1995; 737-41
• A logical foundation for representation of clinical data. Campbell KE,  Das AK, Musen MA.  J Am Med Inform Assoc.  1994 May-Jun; 1 (3): 218-32
• Knowledge-based temporal abstraction for diabetic monitoring. Shahar Y,  Das AK, Tu SW, Kraemer FB, Musen MA.  Proc Annu Symp Comput Appl Med Care.  1994; 697-701
• A temporal query system for protocol-directed decision support. Das AK,  Musen MA.  Methods Inf Med.  1994; 33 (4): 358-70
• A temporal-abstraction mediator for protocol-based decision-support systems. Das AK,  Shahar Y, Tu SW, Musen MA.  Proc Annu Symp Comput Appl Med Care.  1994; 320-4
• PROTEGE-II: a suite of tools for development of intelligent systems from reusable components. Musen MA,  Eriksson H, Gennari JH, Tu SW, Puerta AR.  Proc Annu Symp Comput Appl Med Care.  1994; 1065
• Patient care applications on Internet. Barnett O,  Shortliffe E, Chueh H, Piggins J, Greenes R, Cimino J, Musen M, Clayton P, Humphreys B, Kingsland L.  Proc Annu Symp Comput Appl Med Care.  1994; 1060
• Knowledge reuse: temporal-abstraction mechanisms for the assessment of children's growth. Kuilboer MM,  Shahar Y, Wilson DM, Musen MA.  Proc Annu Symp Comput Appl Med Care.  1993; 449-53
• RESUME: a temporal-abstraction system for patient monitoring. Shahar Y,  Musen MA.  Comput Biomed Res.  1993; 26 (3): 255-73
• A methodology for determining patients' eligibility for clinical trials. Tu SW,  Kemper CA, Lane NM, Carlson RW, Musen MA.  Methods Inf Med.  1993; 32 (4): 317-25
• AIDS2: a decision-support tool for decreasing physicians' uncertainty regarding patient eligibility for HIV treatment protocols. Ohno-Machado L,  Parra E, Henry SB, Tu SW, Musen MA.  Proc Annu Symp Comput Appl Med Care.  1993; 429-33
• A computer-based tool for generation of progress notes. Campbell KE,  Wieckert K, Fagan LM, Musen MA.  Proc Annu Symp Comput Appl Med Care.  1993; 284-8
• Automated modeling of medical decisions. Egar JW,  Musen MA.  Proc Annu Symp Comput Appl Med Care.  1993; 424-8
• T-HELPER: automated support for community-based clinical research. Musen MA,  Carlson RW, Fagan LM, Deresinski SC, Shortliffe EH.  Proc Annu Symp Comput Appl Med Care.  1992; 719-23
• A needs analysis for computer-based telephone triage in a community AIDS clinic. Henry SB,  Schreiner JG, Borchelt D, Musen MA.  Proc Annu Symp Comput Appl Med Care.  1992; 59-63
• A temporal-abstraction system for patient monitoring. Shahar Y,  Musen MA.  Proc Annu Symp Comput Appl Med Care.  1992; 121-7
• An extended SQL for temporal data management in clinical decision-support systems. Das AK,  Tu SW, Purcell GP, Musen MA.  Proc Annu Symp Comput Appl Med Care.  1992; 128-32
• Representation of clinical data using SNOMED III and conceptual graphs. Campbell KE,  Musen MA.  Proc Annu Symp Comput Appl Med Care.  1992; 354-8
• Graph-grammar productions for the modeling of medical dilemmas. Egar JW,  Musen MA.  Proc Annu Symp Comput Appl Med Care.  1992; 349-53
• Temporal-abstraction mechanisms in management of clinical protocols. Shahar Y,  Tu SW, Musen MA.  Proc Annu Symp Comput Appl Med Care.  1991; 629-33