Mark A Musen

Mark A Musen

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Mark A Musen

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How Sustainable are Biomedical Ontologies?

AMIA Annu Symp Proc 2018 5;2018:470-479. Epub 2018 Dec 5.

Stanford University, Stanford, CA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371329PMC
September 2019

Enabling Web-scale data integration in biomedicine through Linked Open Data.

NPJ Digit Med 2019 10;2:90. Epub 2019 Sep 10.

1Center for Biomedical Informatics Research, Stanford University, Stanford, CA USA.

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http://dx.doi.org/10.1038/s41746-019-0162-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736878PMC
September 2019

Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations.

AMIA Annu Symp Proc 2017 16;2017:1272-1281. Epub 2018 Apr 16.

Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5977712PMC
April 2019

Mechanism-based Pharmacovigilance over the Life Sciences Linked Open Data Cloud.

AMIA Annu Symp Proc 2017 16;2017:1014-1023. Epub 2018 Apr 16.

Center for Biomedical Informatics Research, Stanford University, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5977627PMC
March 2019

The variable quality of metadata about biological samples used in biomedical experiments.

Sci Data 2019 02 19;6:190021. Epub 2019 Feb 19.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford CA, USA.

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http://dx.doi.org/10.1038/sdata.2019.21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380228PMC
February 2019

Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases.

Database (Oxford) 2019 01;2019

Stanford Center for Biomedical Informatics Research, 1265 Welch Road, Stanford University School of Medicine, Stanford, CA 94305-5479, USA.

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http://dx.doi.org/10.1093/database/baz059DOI Listing
January 2019

The New HIT: Human Health Information Technology.

Stud Health Technol Inform 2017 ;245:768-772

Center for Research, Prevention, and Treatment of Atherosclerosis Internal Medicine Department, Hadassah Hebrew University Medical Center, Jerusalem, Israel.

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June 2018

Analyzing user interactions with biomedical ontologies: A visual perspective.

Web Semant 2018 Mar 20;49:16-30. Epub 2017 Dec 20.

Stanford Center for Biomedical Informatics Research, Stanford University, USA.

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http://dx.doi.org/10.1016/j.websem.2017.12.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5895104PMC
March 2018

BiOnIC: A Catalog of User Interactions with Biomedical Ontologies.

Semant Web ISWC 2017 Oct 4;10588:130-138. Epub 2017 Oct 4.

Stanford Center for Biomedical Informatics Research, Stanford University.

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http://dx.doi.org/10.1007/978-3-319-68204-4_13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5889949PMC
October 2017

An ontology-driven tool for structured data acquisition using Web forms.

J Biomed Semantics 2017 Aug 1;8(1):26. Epub 2017 Aug 1.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1186/s13326-017-0133-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5540339PMC
August 2017

An empirical analysis of ontology reuse in BioPortal.

J Biomed Inform 2017 07 2;71:165-177. Epub 2017 Jun 2.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.jbi.2017.05.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557647PMC
July 2017

High-Risk Drug-Drug Interactions Between Clinical Practice Guidelines for Management of Chronic Conditions.

AMIA Jt Summits Transl Sci Proc 2017 26;2017:531-539. Epub 2017 Jul 26.

VA Palo Alto Health Care System, Palo Alto, CA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5543385PMC
July 2017

NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation.

J Biomed Semantics 2017 Jun 7;8(1):21. Epub 2017 Jun 7.

Stanford Center for Biomedical Informatics Research, 1265 Welch Road, Stanford University School of Medicine, Stanford, CA, 94305-5479, USA.

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http://dx.doi.org/10.1186/s13326-017-0128-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5463318PMC
June 2017

PhLeGrA: Graph Analytics in Pharmacology over the Web of Life Sciences Linked Open Data.

Proc Int World Wide Web Conf 2017 Apr;2017:321-329

Center for Biomedical Informatics Research, Stanford University, USA.

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http://dx.doi.org/10.1145/3038912.3052692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5824722PMC
April 2017

A Systematic Analysis of Term Reuse and Term Overlap across Biomedical Ontologies.

Semant Web 2017 ;8(6):853-871

Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5555235PMC
January 2017

A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies.

J Biomed Inform 2016 08 23;62:90-105. Epub 2016 Jun 23.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987206PMC
http://dx.doi.org/10.1016/j.jbi.2016.06.008DOI Listing
August 2016

Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies.

J Biomed Inform 2016 06 14;61:63-76. Epub 2016 Mar 14.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.jbi.2016.03.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4893909PMC
June 2016

Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology.

J Biomed Inform 2016 Apr 10;60:199-209. Epub 2016 Feb 10.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305-5479, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2016.02.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4836980PMC
April 2016

An empirically derived taxonomy of errors in SNOMED CT.

AMIA Annu Symp Proc 2014 14;2014:899-906. Epub 2014 Nov 14.

Stanford Center for Biomedical Informatics Research Stanford University, Stanford, CA 94305-5479 U.S.A.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4419962PMC
September 2015

Automating Identification of Multiple Chronic Conditions in Clinical Practice Guidelines.

AMIA Jt Summits Transl Sci Proc 2015 25;2015:456-60. Epub 2015 Mar 25.

Department of Veterans Affairs, VA Palo Alto Health Care System, Palo Alto, CA ; Center for Primary Care and Outcomes Research, Stanford University, Stanford, CA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4525235PMC
August 2015

Using ontologies to model human navigation behavior in information networks: A study based on Wikipedia.

Semant Web 2015;6(4):403-422. Epub 2015 Aug 7.

Stanford Center for Biomedical Informatics Research, Stanford University, USA.

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http://dx.doi.org/10.3233/SW-140143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4643321PMC
August 2015

Investigating Term Reuse and Overlap in Biomedical Ontologies.

CEUR Workshop Proc 2015 Jul 18;1515. Epub 2015 Nov 18.

Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5889951PMC
July 2015

Analysis and Prediction of User Editing Patterns in Ontology Development Projects.

J Data Semant 2015 Jun;4(2):117-132

Stanford Center for Biomedical Informatics Research, Stanford University, 1265 Welch Road, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1007/s13740-014-0047-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4454427PMC
June 2015

The Protégé Project: A Look Back and a Look Forward.

Authors:
Mark A Musen

AI Matters 2015 Jun;1(4):4-12

Stanford University.

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http://dx.doi.org/10.1145/2757001.2757003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4883684PMC
June 2015

Using the wisdom of the crowds to find critical errors in biomedical ontologies: a study of SNOMED CT.

J Am Med Inform Assoc 2015 May 23;22(3):640-8. Epub 2014 Oct 23.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA Biomedical Informatics Training Program, Stanford University, Stanford, California, USA.

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http://dx.doi.org/10.1136/amiajnl-2014-002901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5566196PMC
May 2015

Data breaches of protected health information in the United States.

JAMA 2015 Apr;313(14):1471-3

Department of Computer Science, Stanford University, Stanford, California.

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http://dx.doi.org/10.1001/jama.2015.2252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479128PMC
April 2015

Discovering beaten paths in collaborative ontology-engineering projects using Markov chains.

J Biomed Inform 2014 Oct 17;51:254-71. Epub 2014 Jun 17.

Stanford Center for Biomedical Informatics Research, Stanford University, USA.

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http://dx.doi.org/10.1016/j.jbi.2014.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194274PMC
October 2014

WebProtégé: a collaborative Web-based platform for editing biomedical ontologies.

Bioinformatics 2014 Aug 26;30(16):2384-5. Epub 2014 Apr 26.

Stanford Center for Biomedical Informatics Research, Stanford University, 1265 Welch Road, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4176057PMC
August 2014

Crowdsourcing the verification of relationships in biomedical ontologies.

AMIA Annu Symp Proc 2013 16;2013:1020-9. Epub 2013 Nov 16.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305-5479 U.S.A.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3900126PMC
May 2014

Applications of ontology design patterns in biomedical ontologies.

AMIA Annu Symp Proc 2012 3;2012:643-52. Epub 2012 Nov 3.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3540458PMC
July 2013

Chapter 9: Analyses using disease ontologies.

PLoS Comput Biol 2012 27;8(12):e1002827. Epub 2012 Dec 27.

Center for Biomedical Informatics Research, Stanford University, Stanford, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002827DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531278PMC
May 2013

How Ontologies are Made: Studying the Hidden Social Dynamics Behind Collaborative Ontology Engineering Projects.

Web Semant 2013 May;20

Knowledge Management Institute, Graz University of Technology, Austria ; Stanford Center for Biomedical Informatics Research, Stanford University, USA.

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http://dx.doi.org/10.1016/j.websem.2013.04.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3845806PMC
May 2013

BioPortal as a Dataset of Linked Biomedical Ontologies and Terminologies in RDF.

Semant Web 2013 ;4(3):277-284

Stanford Center for Biomedical Informatics Research Stanford University, US.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159173PMC
January 2013

WebProtégé: A Collaborative Ontology Editor and Knowledge Acquisition Tool for the Web.

Semant Web 2013 Jan;4(1):89-99

Stanford Center for Biomedical Informatics Research, Stanford University, 1265 Welch Road, Stanford, CA 94305, USA.

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http://dx.doi.org/10.3233/SW-2012-0057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691821PMC
January 2013

PragmatiX: An Interactive Tool for Visualizing the Creation Process Behind Collaboratively Engineered Ontologies.

Int J Semant Web Inf Syst 2013 ;9(1):45-78

Stanford Center for Biomedical Informatics Research, Stanford University, 1265 Welch Road, Stanford, CA 94305-5479, USA.

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http://dx.doi.org/10.4018/jswis.2013010103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901413PMC
January 2013

The National Center for Biomedical Ontology.

J Am Med Inform Assoc 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.

Center for Biomedical Informatics Research, Stanford University, Stanford, California 94305-5479, USA.

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http://dx.doi.org/10.1136/amiajnl-2011-000523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277625PMC
May 2012

Enabling enrichment analysis with the Human Disease Ontology.

J Biomed Inform 2011 Dec 29;44 Suppl 1:S31-8. Epub 2011 Apr 29.

Stanford Center for Biomedical Informatics Research, 251 Campus Drive, Medical School Office Building, Mail Code 5479, Stanford University, Stanford, CA 94305-5479, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3392036PMC
http://dx.doi.org/10.1016/j.jbi.2011.04.007DOI Listing
December 2011

NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources.

Web Semant 2011 Sep;9(3):316-324

Stanford Center for Biomedical Informatics Research, Stanford University, 251 Campus Drive, Stanford, CA 94305-5479, USA.

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http://dx.doi.org/10.1016/j.websem.2011.06.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170774PMC
September 2011

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

Nucleic Acids Res 2011 Jul 14;39(Web Server issue):W541-5. Epub 2011 Jun 14.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/nar/gkr469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125807PMC
July 2011

Integration and publication of heterogeneous text-mined relationships on the Semantic Web.

J Biomed Semantics 2011 May 17;2 Suppl 2:S10. Epub 2011 May 17.

LORIA - INRIA Nancy - Grand-Est, Campus Scientifique - BP 239 - 54506 Vandoeuvre-lès-Nancy Cedex, France.

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http://dx.doi.org/10.1186/2041-1480-2-S2-S10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102890PMC
May 2011

How orthogonal are the OBO Foundry ontologies?

J Biomed Semantics 2011 May 17;2 Suppl 2:S2. Epub 2011 May 17.

Stanford Center for Biomedical Informatics Research, Stanford University, 251 Campus Drive, Stanford, CA, USA.

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http://dx.doi.org/10.1186/2041-1480-2-S2-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102891PMC
May 2011

The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies.

AMIA Annu Symp Proc 2010 Nov 13;2010:587-91. Epub 2010 Nov 13.

Department of Computer Science.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041331PMC
November 2010

An ontology-neutral framework for enrichment analysis.

AMIA Annu Symp Proc 2010 Nov 13;2010:797-801. Epub 2010 Nov 13.

Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041299PMC
November 2010

Supporting the Collaborative Authoring of ICD-11 with WebProtégé.

AMIA Annu Symp Proc 2010 Nov 13;2010:802-6. Epub 2010 Nov 13.

Stanford Center for Biomedical Research, Stanford University, Stanford, CA;

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041458PMC
November 2010

A Comprehensive Analysis of Five Million UMLS Metathesaurus Terms Using Eighteen Million MEDLINE Citations.

AMIA Annu Symp Proc 2010 Nov 13;2010:907-11. Epub 2010 Nov 13.

Center for Biomedical Informatics Research, Stanford University School of Medicine Stanford, CA 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041393PMC
November 2010

Building a biomedical ontology recommender web service.

J Biomed Semantics 2010 Jun 22;1 Suppl 1:S1. Epub 2010 Jun 22.

Center for Biomedical Informatics Research, Stanford University, CA 94305, USA.

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http://dx.doi.org/10.1186/2041-1480-1-S1-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903720PMC
June 2010

Creating mappings for ontologies in biomedicine: simple methods work.

AMIA Annu Symp Proc 2009 Nov 14;2009:198-202. Epub 2009 Nov 14.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2815474PMC
November 2009

Software-engineering challenges of building and deploying reusable problem solvers.

Artif Intell Eng Des Anal Manuf 2009 Nov;23(Spec Iss 4):339-356

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA.

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http://www.journals.cambridge.org/abstract_S0890060409990047
Publisher Site
http://dx.doi.org/10.1017/S0890060409990047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3615443PMC
November 2009

Comparison of concept recognizers for building the Open Biomedical Annotator.

BMC Bioinformatics 2009 Sep 17;10 Suppl 9:S14. Epub 2009 Sep 17.

Centre for Biomedical Informatics, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1186/1471-2105-10-S9-S14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745685PMC
September 2009

BioPortal: ontologies and integrated data resources at the click of a mouse.

Nucleic Acids Res 2009 Jul 29;37(Web Server issue):W170-3. Epub 2009 May 29.

Stanford Center for Biomedical Informatics Research, Stanford University.

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http://dx.doi.org/10.1093/nar/gkp440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703982PMC
July 2009

The open biomedical annotator.

Summit Transl Bioinform 2009 Mar 1;2009:56-60. Epub 2009 Mar 1.

Stanford Center for Biomedical Informatics Research and the National Center for Biomedical Ontology, Stanford University, Stanford, CA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041576PMC
March 2009

Ontology-driven indexing of public datasets for translational bioinformatics.

BMC Bioinformatics 2009 Feb 5;10 Suppl 2:S1. Epub 2009 Feb 5.

Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA 94305, USA.

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http://www.biomedcentral.com/1471-2105/10/S2/S1
Publisher Site
http://dx.doi.org/10.1186/1471-2105-10-S2-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2646250PMC
February 2009

Computational neuroanatomy: ontology-based representation of neural components and connectivity.

BMC Bioinformatics 2009 Feb 5;10 Suppl 2:S3. Epub 2009 Feb 5.

Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.

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http://dx.doi.org/10.1186/1471-2105-10-S2-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2646240PMC
February 2009

Understanding detection performance in public health surveillance: modeling aberrancy-detection algorithms.

J Am Med Inform Assoc 2008 Nov-Dec;15(6):760-9. Epub 2008 Aug 28.

Department of Epidemiology and Biostatistics, McGill University, Montreal, Canada.

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http://dx.doi.org/10.1197/jamia.M2799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2585528PMC
December 2008

Developing biomedical ontologies collaboratively.

AMIA Annu Symp Proc 2008 Nov 6:520-4. Epub 2008 Nov 6.

Stanford Center for Biomedical Research, Stanford University, Stanford, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656043PMC
November 2008

Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages.

Appl Ontol 2008 Jan;3(3):173-190

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, United States, ,

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http://dx.doi.org/10.3233/AO-2008-0051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753293PMC
January 2008

Protégé: a tool for managing and using terminology in radiology applications.

J Digit Imaging 2007 Nov 9;20 Suppl 1:34-46. Epub 2007 Aug 9.

Section of Medical Informatics, Stanford University, MSOB X-215, 251 Campus Drive, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1007/s10278-007-9065-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2039856PMC
November 2007

The SAGE Guideline Model: achievements and overview.

J Am Med Inform Assoc 2007 Sep-Oct;14(5):589-98. Epub 2007 Jun 28.

Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305-5479, USA.

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http://dx.doi.org/10.1197/jamia.M2399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1975799PMC
October 2007

Interpretation errors related to the GO annotation file format.

AMIA Annu Symp Proc 2007 Oct 11:538-42. Epub 2007 Oct 11.

Stanford University, Stanford, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655813PMC
October 2007

Ontology-based representation of simulation models of physiology.

AMIA Annu Symp Proc 2006 :664-8

Stanford Medical Informatics, Stanford University School of Medicine, Stanford, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839612PMC
September 2007

Ontology-based annotation and query of tissue microarray data.

AMIA Annu Symp Proc 2006 :709-13

Stanford Medical Informatics, Stanford University School of Medicine and the National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839511PMC
September 2007

Technology for building intelligent systems: from psychology to engineering.

Authors:
Mark A Musen

Nebr Symp Motiv 2007 ;52:145-84

Stanford University, Stanford Center for Biomedical Informatics Research, USA.

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September 2007

Annotation and query of tissue microarray data using the NCI Thesaurus.

BMC Bioinformatics 2007 Aug 8;8:296. Epub 2007 Aug 8.

Stanford Medical Informatics, School of Medicine, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1186/1471-2105-8-296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1988837PMC
August 2007

OBO to OWL: a protege OWL tab to read/save OBO ontologies.

Bioinformatics 2007 Jul 12;23(14):1868-70. Epub 2007 May 12.

Stanford Medical Informatics, Stanford University School of Medicine, Stanford, CA 94002, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm258DOI Listing
July 2007

Linking ontologies with three-dimensional models of anatomy to predict the effects of penetrating injuries.

Conf Proc IEEE Eng Med Biol Soc 2004 ;5:3128-31

Stanford Medical Informatics, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1109/IEMBS.2004.1403883DOI Listing
June 2007

Using semantic dependencies for consistency management of an ontology of brain-cortex anatomy.

Artif Intell Med 2007 Mar 24;39(3):217-25. Epub 2007 Jan 24.

EA 3888, Université de Rennes 1, 2 Rue Henri Le Guilloux, F-35033 Rennes, France.

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http://dx.doi.org/10.1016/j.artmed.2006.09.004DOI Listing
March 2007

Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study.

AMIA Annu Symp Proc 2005 :181-5

Stanford Medical Informatics, Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1560487PMC
February 2007

Use of description logic classification to reason about consequences of penetrating injuries.

AMIA Annu Symp Proc 2005 :649-53

Stanford Medical Informatics, Stanford University School of Medicine, CA 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1560440PMC
February 2007

Evaluating detection of an inhalational anthrax outbreak.

Emerg Infect Dis 2006 Dec;12(12):1942-9

McGill University, Montreal, Quebec, Canada.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3291344PMC
http://dx.doi.org/10.3201/eid1212.060331DOI Listing
December 2006

Using ontologies linked with geometric models to reason about penetrating injuries.

Artif Intell Med 2006 Jul 30;37(3):167-76. Epub 2006 May 30.

Stanford Medical Informatics, MSOB X-215, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.artmed.2006.03.006DOI Listing
July 2006

Wrestling with SUMO and bio-ontologies.

Nat Biotechnol 2006 Jan;24(1):21; author reply 23

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http://dx.doi.org/10.1038/nbt0106-21bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768033PMC
January 2006

Using an ontology of human anatomy to inform reasoning with geometric models.

Stud Health Technol Inform 2005 ;111:429-35

Stanford Medical Informatics, Stanford, California 94305-5479, USA.

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August 2005

An intelligent case-adjustment algorithm for the automated design of population-based quality auditing protocols.

Stud Health Technol Inform 2004 ;107(Pt 2):1003-7

Stanford Medical Informatics, Stanford University, CA 94025, USA.

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June 2005

Developing quality indicators and auditing protocols from formal guideline models: knowledge representation and transformations.

AMIA Annu Symp Proc 2003 :11-5

Stanford Medical Informatics, Stanford University School of Medicine, California, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1480136PMC
December 2004

Contextualizing heterogeneous data for integration and inference.

AMIA Annu Symp Proc 2003 :514-8

Stanford Medical Informatics, Stanford University School of Medicine, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1479915PMC
December 2004

The structure of guideline recommendations: a synthesis.

AMIA Annu Symp Proc 2003 :679-83

Stanford Medical Information, Stanford University School of Medicine, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1480008PMC
December 2004

Protégé-2000: an open-source ontology-development and knowledge-acquisition environment.

AMIA Annu Symp Proc 2003 :953

Standford Medical Informatics, Stanford University School Medicine, CA 94305, USA. http://protege.stanford.edu

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1480139PMC
December 2004

A knowledge-acquisition wizard to encode guidelines.

AMIA Annu Symp Proc 2003 :1007

Stanford Medical Informatics, Stanford University School of Medicine, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1479958PMC
December 2004

BioSTORM: a system for automated surveillance of diverse data sources.

AMIA Annu Symp Proc 2003 :1071

Stanford Medical Informatics, Stanford University School of Medicine, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1480334PMC
December 2004

The SAGE guideline modeling: motivation and methodology.

Stud Health Technol Inform 2004 ;101:167-71

Stanford Medical Informatics, Stanford University, Stanford, CA, USA.

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December 2004

SYNCHRONUS: a reusable software module for temporal integration.

Proc AMIA Symp 2002 :195-9

Stanford Medical Informatics, Stanford University, Stanford, CA 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244421PMC
April 2003

The Chronus II temporal database mediator.

Proc AMIA Symp 2002 :567-71

Stanford Medical Informatics, Stanford University School of Medicine, Stanfroed, CA 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244583PMC
April 2003