Mark A. Musen

According to our database1, Mark A. Musen authored at least 329 papers between 1987 and 2019.

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2019
Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases.
Database, 2019

WebProtégé: A Cloud-Based Ontology Editor.
Proceedings of the Companion of The 2019 World Wide Web Conference, 2019

HopRank: How Semantic Structure Influences Teleportation in PageRank (A Case Study on BioPortal).
Proceedings of the World Wide Web Conference, 2019

Aligning Biomedical Metadata with Ontologies Using Clustering and Embeddings.
Proceedings of the Semantic Web - 16th International Conference, 2019

2018
Analyzing user interactions with biomedical ontologies: A visual perspective.
J. Web Semant., 2018

AgroPortal: A vocabulary and ontology repository for agronomy.
Computers and Electronics in Agriculture, 2018

CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata.
BMC Bioinformatics, 2018

CEDAR: Semantic Web Technology to Support Open Science.
Proceedings of the Companion of the The Web Conference 2018 on The Web Conference 2018, 2018

Using semantic technologies to enhance metadata submissions to public repositories in biomedicine.
Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, 2018

A More Decentralized Vision for Linked Data.
Proceedings of the 2nd Workshop on Decentralizing the Semantic Web co-located with the 17th International Semantic Web Conference, 2018

WebProtégé 3.0 - Collaborative OWL Ontology Engineering in the Cloud.
Proceedings of the ISWC 2018 Posters & Demonstrations, 2018

Using Ontologies to Drive the Creation of High-Quality Metadata in CEDAR.
Proceedings of the ISWC 2018 Posters & Demonstrations, 2018

Protégé 5.5 - Improvements for Editing Biomedical Ontologies.
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

Quality Assurance of Ontology Content Reuse.
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

TOCSOC: A Temporal Ontology for Comparing the Survival Outcomes of Clinical Trials in Oncology.
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

How Sustainable are Biomedical Ontologies?
Proceedings of the AMIA 2018, 2018

2017
A systematic analysis of term reuse and term overlap across biomedical ontologies.
Semantic Web, 2017

An empirical analysis of ontology reuse in BioPortal.
Journal of Biomedical Informatics, 2017

Use of ontology structure and Bayesian models to aid the crowdsourcing of ICD-11 sanctioning rules.
Journal of Biomedical Informatics, 2017

NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation.
J. Biomedical Semantics, 2017

An ontology-driven tool for structured data acquisition using Web forms.
J. Biomedical Semantics, 2017

How Users Explore Ontologies on the Web: A Study of NCBO's BioPortal Usage Logs.
Proceedings of the 26th International Conference on World Wide Web, 2017

PhLeGrA: Graph Analytics in Pharmacology over the Web of Life Sciences Linked Open Data.
Proceedings of the 26th International Conference on World Wide Web, 2017

Embracing Semantic Technology for Better Metadata Authoring in Biomedicine.
Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017), 2017

Making Online Datasets More Searchable and Accessible: The CEDAR project.
Proceedings of the 4th Annual International Symposium on Information Management and Big Data, 2017

Real Time Summarization and Visualization of Ontology Change in Protégé.
Proceedings of the Third International Workshop on Visualization and Interaction for Ontologies and Linked Data co-located with the 16th International Semantic Web Conference (ISWC 2017), 2017

BiOnIC: A Catalog of User Interactions with Biomedical Ontologies.
Proceedings of the Semantic Web - ISWC 2017, 2017

Metadata in the BioSample Online Repository are Impaired by Numerous Anomalies.
Proceedings of the First Workshop on Enabling Open Semantic Science co-located with 16th International Semantic Web Conference (ISWC 2017), 2017

The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments.
Proceedings of the Semantic Web - ISWC 2017, 2017

The New HIT: Human Health Information Technology.
Proceedings of the MEDINFO 2017: Precision Healthcare through Informatics, 2017

Supporting Ontology-Based Standardization of Biomedical Metadata in the CEDAR Workbench.
Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017), Newcastle-upon-Tyne, United Kingdom, September 13th, 2017

High-Risk Drug-Drug Interactions Between Clinical Practice Guidelines for Management of Chronic Conditions.
Proceedings of the Summit on Clinical Research Informatics, 2017

Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations.
Proceedings of the AMIA 2017, 2017

Mechanism-based Pharmacovigilance over the Life Sciences Linked Open Data Cloud.
Proceedings of the AMIA 2017, 2017

Big Data to Knowledge (BD2K) and the Application of Metadata.
Proceedings of the AMIA 2017, 2017

2016
Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies.
Journal of Biomedical Informatics, 2016

A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies.
Journal of Biomedical Informatics, 2016

Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology.
Journal of Biomedical Informatics, 2016

Visualizing User Editing Behavior in Collaborative Ontology-engineering Projects.
Proceedings of the Second International Workshop on Visualization and Interaction for Ontologies and Linked Data co-located with the 15th International Semantic Web Conference, 2016

Reusing the NCBO BioPortal Technology for Agronomy to Build AgroPortal.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

An Open Repository Model for Acquiring Knowledge About Scientific Experiments.
Proceedings of the Knowledge Engineering and Knowledge Management, 2016

CEDAR: Better Data Sharing Through the Authoring of Better Metadata.
Proceedings of the AMIA 2016, 2016

2015
Using ontologies to model human navigation behavior in information networks: A study based on Wikipedia.
Semantic Web, 2015

Analysis and Prediction of User Editing Patterns in Ontology Development Projects.
J. Data Semantics, 2015

The center for expanded data annotation and retrieval.
JAMIA, 2015

Using the wisdom of the crowds to find critical errors in biomedical ontologies: a study of SNOMED CT.
JAMIA, 2015

Toward a science of learning systems: a research agenda for the high-functioning Learning Health System.
JAMIA, 2015

How to apply Markov chains for modeling sequential edit patterns in collaborative ontology-engineering projects.
Int. J. Hum.-Comput. Stud., 2015

Ten years of Applied Ontology.
Applied Ontology, 2015

Applied ontology: The next decade begins.
Applied Ontology, 2015

The protégé project: a look back and a look forward.
AI Matters, 2015

Understanding How Users Edit Ontologies: Comparing Hypotheses About Four Real-World Projects.
Proceedings of the Semantic Web - ISWC 2015, 2015

User Extensible System to Identify Problems in OWL Ontologies and SWRL Rules.
Proceedings of the Rule Technologies: Foundations, Tools, and Applications, 2015

Snap-SPARQL: A Java Framework for Working with SPARQL and OWL.
Proceedings of the Ontology Engineering, 2015

Modeling and tools for supporting post-coordination in ICD-11.
Proceedings of the International Conference on Biomedical Ontology, 2015

Investigating term reuse and overlap in biomedical ontologies.
Proceedings of the International Conference on Biomedical Ontology, 2015

Structured data acquisition with ontology-based web forms.
Proceedings of the International Conference on Biomedical Ontology, 2015

OWL-based form generation and structured data acquisition.
Proceedings of the International Conference on Biomedical Ontology, 2015

NCBO BioPortal version 4.
Proceedings of the International Conference on Biomedical Ontology, 2015

Roadmap for a Multilingual BioPortal.
Proceedings of the Fourth Workshop on the Multilingual Semantic Web (MSW4) co-located with 12th Extended Semantic Web Conference (ESWC 2015), 2015

Helping Users Bootstrap Ontologies: An Empirical Investigation.
Proceedings of the 33rd Annual ACM Conference on Human Factors in Computing Systems, 2015

Using aggregate taxonomies to summarize SNOMED CT evolution.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

A Method to Compare ICF and SNOMED CT for Coverage of U.S. Social Security Administration's Disability Listing Criteria.
Proceedings of the AMIA 2015, 2015

2014
Discovering Beaten Paths in Collaborative Ontology-Engineering Projects using Markov Chains.
Journal of Biomedical Informatics, 2014

Cross-domain targeted ontology subsets for annotation: The case of SNOMED CORE and RxNorm.
Journal of Biomedical Informatics, 2014

WebProtégé: a collaborative Web-based platform for editing biomedical ontologies.
Bioinformatics, 2014

A Study on the Atomic Decomposition of Ontologies.
Proceedings of the Semantic Web - ISWC 2014, 2014

WebProtégé: a Web-based Development Environment for OWL Ontologies.
Proceedings of the 11th International Workshop on OWL: Experiences and Directions (OWLED 2014) co-located with 13th International Semantic Web Conference on (ISWC 2014), 2014

Investigating Collaboration Dynamics in Different Ontology Development Environments.
Proceedings of the Knowledge Science, Engineering and Management, 2014

An empirically derived taxonomy of errors in SNOMED CT.
Proceedings of the AMIA 2014, 2014

Crowdsourcing ICD-11 Sanctioning Rules.
Proceedings of the AMIA 2014, 2014

Automating Identification of Multiple Chronic Conditions in Clinical Practice Guidelines.
Proceedings of the AMIA 2014, 2014

Reasoning Based Quality Assurance of Medical Ontologies: A Case Study.
Proceedings of the AMIA 2014, 2014

2013
How ontologies are made: Studying the hidden social dynamics behind collaborative ontology engineering projects.
J. Web Semant., 2013

WebProtégé: A collaborative ontology editor and knowledge acquisition tool for the Web.
Semantic Web, 2013

BioPortal as a dataset of linked biomedical ontologies and terminologies in RDF.
Semantic Web, 2013

PragmatiX: An Interactive Tool for Visualizing the Creation Process Behind Collaboratively Engineered Ontologies.
Int. J. Semantic Web Inf. Syst., 2013

The knowledge acquisition workshops: A remarkable convergence of ideas.
Int. J. Hum.-Comput. Stud., 2013

Mechanical turk as an ontology engineer?: using microtasks as a component of an ontology-engineering workflow.
Proceedings of the Web Science 2013 (co-located with ECRC), 2013

Using Semantic Web in ICD-11: Three Years Down the Road.
Proceedings of the Semantic Web - ISWC 2013, 2013

Boosting RDF Adoption in Ruby with Goo.
Proceedings of the Workshop on Semantic Web Enterprise Adoption and Best Practice Co-located with 12th International Semantic Web Conference (ISWC 2013), 2013

Getting Lucky in Ontology Search: A Data-Driven Evaluation Framework for Ontology Ranking.
Proceedings of the Semantic Web - ISWC 2013, 2013

Developing Crowdsourced Ontology Engineering Tasks: An iterative process.
Proceedings of the 1st International Workshop on Crowdsourcing the Semantic Web, 2013

Simplified OWL Ontology Editing for the Web: Is WebProtégé Enough?
Proceedings of the Semantic Web - ISWC 2013, 2013

Binary OWL.
Proceedings of the 10th International Workshop on OWL: Experiences and Directions (OWLED 2013) co-located with 10th Extended Semantic Web Conference (ESWC 2013), 2013

Analysis of User Editing Patterns in Ontology Development Projects.
Proceedings of the On the Move to Meaningful Internet Systems: OTM 2013 Conferences, 2013

Crowdsourcing Ontology Verification.
Proceedings of the 4th International Conference on Biomedical Ontology, 2013

Introducing WebProtégé 2 as a Collaborative Platform for Editing Biomedical Ontologies.
Proceedings of the 4th International Conference on Biomedical Ontology, 2013

Ontology Quality Assurance with the Crowd.
Proceedings of the Human Computation and Crowdsourcing: Works in Progress and Demonstration Abstracts, 2013

Crowdsourcing the Verification of Relationships in Biomedical Ontologies.
Proceedings of the AMIA 2013, 2013

2012
Chapter 9: Analyses Using Disease Ontologies.
PLoS Computational Biology, 2012

Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis.
JAMIA, 2012

The National Center for Biomedical Ontology.
JAMIA, 2012

AMIA Board white paper: definition of biomedical informatics and specification of core competencies for graduate education in the discipline.
JAMIA, 2012

Using SPARQL to Query BioPortal Ontologies and Metadata.
Proceedings of the Semantic Web - ISWC 2012, 2012

Experiences with Multilingual Modeling in the Development of the International Classification of Traditional Medicine Ontology.
Proceedings of the 3rd Workshop on the Multilingual Semantic Web, 2012

Modest Use of Ontology Design Patterns in a Repository of Biomedical Ontologies.
Proceedings of the 3rd Workshop on Ontology Patterns, Boston, USA, November 12, 2012, 2012

Ontology Design Pattern Language Expressivity Requirements.
Proceedings of the 3rd Workshop on Ontology Patterns, Boston, USA, November 12, 2012, 2012

Recommending Concepts to Experts: An Exploration of Recommender Techniques for Collaborative Ontology Engineering Platforms in the Biomedical Domain.
Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

Deriving an Abstraction Network to Support Quality Assurance in OCRe.
Proceedings of the AMIA 2012, 2012

Applications of Ontology Design Patterns in Biomedical Ontologies.
Proceedings of the AMIA 2012, 2012

Opportunities to Support Complex Medical Decisions Through Informatics.
Proceedings of the AMIA 2012, 2012

Application of Preference-Oriented Decision Making to Multimorbidity for Computerized Decision Support: Decision Analysis and Analytic Hierarchy.
Proceedings of the AMIA 2012, 2012

Pragmatic Analysis of Crowd-Based Knowledge Production Systems with iCAT Analytics: Visualizing Changes to the ICD-11 Ontology.
Proceedings of the Wisdom of the Crowd, 2012

2011
NCBO Resource Index: Ontology-based search and mining of biomedical resources.
J. Web Semant., 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 Research, 2011

The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research.
Journal of Biomedical Informatics, 2011

Enabling enrichment analysis with the Human Disease Ontology.
Journal of Biomedical Informatics, 2011

How orthogonal are the OBO Foundry ontologies?
J. Biomedical Semantics, 2011

Integration and publication of heterogeneous text-mined relationships on the Semantic Web.
J. Biomedical Semantics, 2011

SWRL-F: a fuzzy logic extension of the semantic web rule language.
Proceedings of the International Conference on Web Intelligence, Mining and Semantics, 2011

From mappings to modules: using mappings to identify domain-specific modules in large ontologies.
Proceedings of the 6th International Conference on Knowledge Capture (K-CAP 2011), 2011

A knowledge base driven user interface for collaborative ontology development.
Proceedings of the 16th International Conference on Intelligent User Interfaces, 2011

Bioportal: Ontologies and Integrated Data Resources at the Click of a Mouse.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

The NCBO Annotator: Ontology-Based Annotation as a Web Service.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

The BioPortal Import Plugin for Protégé.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

The Age of Data-Driven Medicine: Mining the Electronic Health Record.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Semantic infrastructure to enable collaboration in ontology development.
Proceedings of the 2011 International Conference on Collaboration Technologies and Systems, 2011

Proposed SKOS Extensions for BioPortal Terminology Services.
Proceedings of the Semantic Web - Joint International Semantic Technology Conference, 2011

2010
Using text to build semantic networks for pharmacogenomics.
Journal of Biomedical Informatics, 2010

Building a biomedical ontology recommender web service.
J. Biomedical Semantics, 2010

A Typology for Modeling Processes in Clinical Guidelines and Protocols.
Proceedings of the Security-Enriched Urban Computing and Smart Grid, 2010

DataStorm.
Proceedings of the 6th World Congress on Services, 2010

SWRL-F - A Fuzzy Logic Extension of the Semantic Web Rule Language.
Proceedings of the 6th International Workshop on Uncertainty Reasoning for the Semantic Web (URSW 2010), 2010

Will Semantic Web Technologies Work for the Development of ICD-11?
Proceedings of the Semantic Web - ISWC 2010 - 9th International Semantic Web Conference, 2010

Lost in translation? Empirical analysis of mapping compositions for large ontologies.
Proceedings of the 5th International Workshop on Ontology Matching (OM-2010), 2010

Mapping Master: A Flexible Approach for Mapping Spreadsheets to OWL.
Proceedings of the Semantic Web - ISWC 2010 - 9th International Semantic Web Conference, 2010

Optimize First, Buy Later: Analyzing Metrics to Ramp-Up Very Large Knowledge Bases.
Proceedings of the Semantic Web - ISWC 2010 - 9th International Semantic Web Conference, 2010

From mappings to modules: using mappings to identify domain-specific modules in large ontologies.
Proceedings of the 5th International Workshop on Ontology Matching (OM-2010), 2010

WebProtégé: Supporting the Creation of ICD-11.
Proceedings of the ISWC 2010 Posters & Demonstrations Track: Collected Abstracts, 2010

M2: A Language for Mapping Spreadsheets to OWL.
Proceedings of the 7th International Workshop on OWL: Experiences and Directions (OWLED 2010), 2010

An efficient approach to intelligent real-time monitoring using ontologies and Hadoop.
Proceedings of the 2010 International Conference on High Performance Computing & Simulation, 2010

Indexation et intégration de ressources textuelles à l'aide d'ontologies : application au domaine biomédical.
Proceedings of the IC 2010 : 21es Journées Ingénierie des Connaissances 2010 (Proceedings of the 21st French Knowledge Engineering Conference), 2010

Ontology Development for the Masses: Creating ICD-11 in WebProtégé.
Proceedings of the Knowledge Engineering and Management by the Masses, 2010

2009
Traversing Ontologies to Extract Views.
Proceedings of the Modular Ontologies: Concepts, 2009

Ontologies for Formal Representation of Biological Systems.
Proceedings of the Handbook on Ontologies, 2009

BioPortal: ontologies and integrated data resources at the click of a mouse.
Nucleic Acids Research, 2009

Ontology-driven indexing of public datasets for translational bioinformatics.
BMC Bioinformatics, 2009

Comparison of concept recognizers for building the Open Biomedical Annotator.
BMC Bioinformatics, 2009

Computational neuroanatomy: ontology-based representation of neural components and connectivity.
BMC Bioinformatics, 2009

Software-engineering challenges of building and deploying reusable problem solvers.
AI EDAM, 2009

What Four Million Mappings Can Tell You about Two Hundred Ontologies.
Proceedings of the Semantic Web - ISWC 2009, 8th International Semantic Web Conference, 2009

Semantic Wiki Search.
Proceedings of the Semantic Web: Research and Applications, 2009

A Bayesian Network Model for Analysis of Detection Performance in Surveillance Systems.
Proceedings of the AMIA 2009, 2009

Creating Mappings For Ontologies in Biomedicine: Simple Methods Work.
Proceedings of the AMIA 2009, 2009

2008
Network Analysis of Intrinsic Functional Brain Connectivity in Alzheimer's Disease.
PLoS Computational Biology, 2008

A prototype symbolic model of canonical functional neuroanatomy of the motor system.
Journal of Biomedical Informatics, 2008

Model Formulation: Understanding Detection Performance in Public Health Surveillance: Modeling Aberrancy-detection Algorithms.
JAMIA, 2008

Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages.
Applied Ontology, 2008

AAAI 2008 Spring Symposia Reports.
AI Magazine, 2008

Supporting Collaborative Ontology Development in Protégé.
Proceedings of the Semantic Web - ISWC 2008, 7th International Semantic Web Conference, 2008

Collaborative Protege: Enabling Community-based Authoring of Ontologies.
Proceedings of the Poster and Demonstration Session at the 7th International Semantic Web Conference (ISWC2008), 2008

BioPortal: A Web Repository for Biomedical Ontologies and Data Resources.
Proceedings of the Poster and Demonstration Session at the 7th International Semantic Web Conference (ISWC2008), 2008

Collecting Community-Based Mappings in an Ontology Repository.
Proceedings of the Semantic Web - ISWC 2008, 7th International Semantic Web Conference, 2008

The SWRLAPI: A Development Environment for Working with SWRL Rules.
Proceedings of the Fifth OWLED Workshop on OWL: Experiences and Directions, 2008

An Ontology-Driven Framework for Deploying JADE Agent Systems.
Proceedings of the 2008 IEEE/WIC/ACM International Conference on Intelligent Agent Technology, 2008

A Generic Ontology for Collaborative Ontology-Development Workflows.
Proceedings of the Knowledge Engineering: Practice and Patterns, 2008

A System for Ontology-Based Annotation of Biomedical Data.
Proceedings of the Data Integration in the Life Sciences, 5th International Workshop, 2008

UMLS-Query: A Perl Module for Querying the UMLS.
Proceedings of the AMIA 2008, 2008

Developing Biomedical Ontologies Collaboratively.
Proceedings of the AMIA 2008, 2008

Comparison of Ontology-based Semantic-Similarity Measures.
Proceedings of the AMIA 2008, 2008

Predicting Outbreak Detection in Public Health Surveillance: Quantitative Analysis to Enable Evidence-Based Method Selection.
Proceedings of the AMIA 2008, 2008

Preface.
Proceedings of the Symbiotic Relationships between Semantic Web and Knowledge Engineering, 2008

Organizing Committee.
Proceedings of the Symbiotic Relationships between Semantic Web and Knowledge Engineering, 2008

BioPortal: A Web Portal to Biomedical Ontologies.
Proceedings of the Symbiotic Relationships between Semantic Web and Knowledge Engineering, 2008

2007
Synthesis of Research Paper: The SAGE Guideline Model: Achievements and Overview.
JAMIA, 2007

Annotation and query of tissue microarray data using the NCI Thesaurus.
BMC Bioinformatics, 2007

OBO to OWL: a protégé OWL tab to read/save OBO ontologies.
Bioinformatics, 2007

Using semantic dependencies for consistency management of an ontology of brain-cortex anatomy.
Artificial Intelligence in Medicine, 2007

Querying the Semantic Web with SWRL.
Proceedings of the Advances in Rule Interchange and Applications, International Symposium, 2007

Efficiently Querying Relational Databases Using OWL and SWRL.
Proceedings of the Web Reasoning and Rule Systems, First International Conference, 2007

Knowledge Zone: A Public Repository of Peer-Reviewed Biomedical Ontologies.
Proceedings of the MEDINFO 2007 - Proceedings of the 12th World Congress on Health (Medical) Informatics, 2007

Searching ontologies based on content: experiments in the biomedical domain.
Proceedings of the 4th International Conference on Knowledge Capture (K-CAP 2007), 2007

07132 Report - Towards Interoperability of Biomedical Ontologies.
Proceedings of the Towards Interoperability of Biomedical Ontologies, 27.03. - 30.03.2007, 2007

Interpretation Errors related to the GO Annotation File Format.
Proceedings of the AMIA 2007, 2007

Document-Oriented Views of Guideline Knowledge Bases.
Proceedings of the Artificial Intelligence in Medicine, 2007

Using Semantic Web Technologies for Knowledge-Driven Querying of Biomedical Data.
Proceedings of the Artificial Intelligence in Medicine, 2007

2006
Using ontologies linked with geometric models to reason about penetrating injuries.
Artificial Intelligence in Medicine, 2006

Topic-Specific Trust and Open Rating Systems: An Approach for Ontology Evaluation.
Proceedings of 4th International EON Workshop 2006 Evaluation of Ontologies for the Web Co-located with the WWW2006 Edinburgh, 2006

A Framework for Ontology Evolution in Collaborative Environments.
Proceedings of the Semantic Web - ISWC 2006, 5th International Semantic Web Conference, 2006

Use of Declarative Statements in Creating and Maintaining Computer-Interpretable Knowledge Bases for Guideline-Based Care.
Proceedings of the AMIA 2006, 2006

Ontology-based Annotation and Query of Tissue Microarray Data.
Proceedings of the AMIA 2006, 2006

Ontology-Based Representation of Simulation Models of Physiology.
Proceedings of the AMIA 2006, 2006

Identifying Barriers to Hypertension Guideline Adherence Using Clinician Feedback at the Point of Care.
Proceedings of the AMIA 2006, 2006

Medical Arguments in an Automated Health Care System.
Proceedings of the Argumentation for Consumers of Healthcare, 2006

2005
Protégé: Community is Everything.
Int. J. Hum.-Comput. Stud., 2005

EZPAL: Environment for composing constraint axioms by instantiating templates.
Int. J. Hum.-Comput. Stud., 2005

Ontology-Centered Syndromic Surveillance for Bioterrorism.
IEEE Intelligent Systems, 2005

Applied Ontology: Focusing on content.
Applied Ontology, 2005

Supporting Rule System Interoperability on the Semantic Web with SWRL.
Proceedings of the Semantic Web, 2005

The Protege OWL Experience.
Proceedings of the OWLED*05 Workshop on OWL: Experiences and Directions, 2005

Ontology Metadata to Support the Building of a Library of Biomedical Ontologies.
Proceedings of the AMIA 2005, 2005

Protégé-OWL: Creating Ontology-Driven Reasoning Applications with the Web Ontology Language.
Proceedings of the AMIA 2005, 2005

Use of Description Logic Classification to Reason about Consequences of Penetrating Injuries.
Proceedings of the AMIA 2005, 2005

Semantic Clinical Guideline Documents.
Proceedings of the AMIA 2005, 2005

Challenges in Converting Frame-Based Ontology into OWL: the Foundational Model of Anatomy Case-Study.
Proceedings of the AMIA 2005, 2005

User Ratings of Ontologies: Who Will Rate the Raters?
Proceedings of the Knowledge Collection from Volunteer Contributors, 2005

Knowledge-Based Syndromic Surveillance for Bioterrorism.
Proceedings of the AI Technologies for Homeland Security, 2005

2004
Application of Information Technology: Translating Research into Practice: Organizational Issues in Implementing Automated Decision Support for Hypertension in Three Medical Centers.
JAMIA, 2004

Making Biomedical Ontologies and Ontology Repositories Work.
IEEE Intelligent Systems, 2004

Ontology Versioning in an Ontology Management Framework.
IEEE Intelligent Systems, 2004

Knowledge Representation with Ontologies: The Present and Future.
IEEE Intelligent Systems, 2004

Pushing the envelope: challenges in a frame-based representation of human anatomy.
Data Knowl. Eng., 2004

Specifying Ontology Views by Traversal.
Proceedings of the Semantic Web, 2004

Tracking Changes During Ontology Evolution.
Proceedings of the Semantic Web, 2004

The Protégé OWL Plugin: An Open Development Environment for Semantic Web Applications.
Proceedings of the Semantic Web, 2004

Accessing and Manipulating Ontologies Using Web Services.
Proceedings of the ISWC 2004 Workshop on Semantic Web Services: Preparing to Meet the World of Business Applications, 2004


Evaluating Provider Adherence in a Trial of a Guideline-Based Decision Support System for Hypertension.
Proceedings of the MEDINFO 2004, 2004

An Intelligent Case-Adjustment Algorithm for the Automated Design of Population-based Quality Auditing Protocols.
Proceedings of the MEDINFO 2004, 2004

Weaving the biomedical Semantic Web with the Prote'ge' OWL Plugin.
Proceedings of the KR-MED 2004, 2004

Using semantic dependencies for consistency management of an ontology of brain-cortex anatomy.
Proceedings of the KR-MED 2004, 2004

A Knowledge-Based Framework for Deploying Surveillance Problem Solvers.
Proceedings of the International Conference on Information and Knowledge Engineering. IKE'04, 2004

Using Prompt Ontology-Comparison Tools in the EON Ontology Alignment Contest.
Proceedings of the EON 2004, 2004

Editing Description Logic Ontologies with the Protégé OWL Plugin.
Proceedings of the 2004 International Workshop on Description Logics (DL2004), 2004

The SAGE Guideline Modeling: Motivation and Methodology.
Proceedings of the Computer-based Support for Clinical Guidelines and Protocols, 2004

Ontologies in Support of Problem Solving.
Proceedings of the Handbook on Ontologies, 2004

2003
The Unified Problem-Solving Method Development Language UPML.
Knowl. Inf. Syst., 2003

The PROMPT suite: interactive tools for ontology merging and mapping.
Int. J. Hum.-Comput. Stud., 2003

The evolution of Protégé: an environment for knowledge-based systems development.
Int. J. Hum.-Comput. Stud., 2003

IFIP Conference on Intelligent Information Processing.
IEEE Intelligent Systems, 2003

Configuring Online Problem-Solving Resources with the Internet Reasoning Service.
IEEE Intelligent Systems, 2003

UPML: The Language and Tool Support for Making the Semantic Web Alive.
Proceedings of the Spinning the Semantic Web: Bringing the World Wide Web to Its Full Potential [outcome of a Dagstuhl seminar], 2003

The Structure of Guideline Recommendations: A Synthesis.
Proceedings of the AMIA 2003, 2003

A Knowledge-Acquisition Wizard to Encode Guidelines.
Proceedings of the AMIA 2003, 2003

Contextualizing Heterogeneous Data for Integration and Inference.
Proceedings of the AMIA 2003, 2003

BioSTORM: A System for Automated Surveillance of Diverse Data Sources.
Proceedings of the AMIA 2003, 2003

Protégé-2000: An Open-Source Ontology-Development and Knowledge-Acquisition Environment: AMIA 2003 Open Source Expo.
Proceedings of the AMIA 2003, 2003

An Analytic Framework for Space-Time Aberrancy Detection in Public Health Surveillance Data.
Proceedings of the AMIA 2003, 2003

Developing Quality Indicators and Auditing Protocols from Formal Guideline Models: Knowledge Representation and Transformations.
Proceedings of the AMIA 2003, 2003

2002
Report on the First International Conference on Knowledge Capture (K-CAP).
AI Magazine, 2002

Jambalaya: an interactive environment for exploring ontologies.
Proceedings of the 7th International Conference on Intelligent User Interfaces, 2002

A Template-Based Approach Toward Acquisition of Logical Sentences.
Proceedings of the Intelligent Information Processing, 2002

Configuring Online Problem-Solving Resources with the Internet Reasoning Service.
Proceedings of the Intelligent Information Processing, 2002

Evaluating Ontology-Mapping Tools: Requirements and Experience.
Proceedings of the EON2002, 2002

SHriMP views: an interactive environment for information visualization and navigation.
Proceedings of the Extended abstracts of the 2002 Conference on Human Factors in Computing Systems, 2002

A Typology for Modeling Processes in Clinical Guidelines and Protocols.
Proceedings of the AMIA 2002, 2002

Use of Protégé-2000 to Encode Clinical Guidelines.
Proceedings of the AMIA 2002, 2002

The Chronus II temporal database mediator.
Proceedings of the AMIA 2002, 2002

Protocol Design Patterns: Domain-oriented Abstractions to Support the Authoring of Computer-executable Clinical Trials.
Proceedings of the AMIA 2002, 2002

Conceptual Heterogeneity Complicates Automated Syndromic Surveillance for Bioterrorism.
Proceedings of the AMIA 2002, 2002

SYNCHRONUS: a reusable software module for temporal integration.
Proceedings of the AMIA 2002, 2002

Knowledge-based bioterrorism surveillance.
Proceedings of the AMIA 2002, 2002

Standards-based Sharable Active Guideline Environment (SAGE): A Project to Develop a Universal Framework for Encoding and Disseminating Electronic Clinical Practice Guidelines.
Proceedings of the AMIA 2002, 2002

A framework for evidence-adaptive quality assessment that unifies guideline-based and performance-indicator approaches.
Proceedings of the AMIA 2002, 2002

PROMPTDIFF: A Fixed-Point Algorithm for Comparing Ontology Versions.
Proceedings of the Eighteenth National Conference on Artificial Intelligence and Fourteenth Conference on Innovative Applications of Artificial Intelligence, July 28, 2002

2001
Creating Semantic Web Contents with Protégé-2000.
IEEE Intelligent Systems, 2001

Guest Editors' Introduction: A Brain for Humankind.
IEEE Intelligent Systems, 2001

Modeling Data and Knowledge in the EON Guideline Architecture.
Proceedings of the MEDINFO 2001, 2001

Building an Explanation Function for a Hypertension Decision-Support System.
Proceedings of the MEDINFO 2001, 2001

RASTA: A Distributed Temporal Abstraction System to Facilitate Knowledge-Driven Monitoring of Clinical Databases.
Proceedings of the MEDINFO 2001, 2001

Creating and Using Ontologies: What Informatics is All About.
Proceedings of the MEDINFO 2001, 2001

Workshop on the Future of Academic Research on Electronic Patient Records IMIA Working Group 17 on Electronic Patient Records.
Proceedings of the MEDINFO 2001, 2001

Anchor-PROMPT: Using Non-Local Context for Semantic Matching.
Proceedings of the IJCAI-01 Workshop on Ontologies and Information Sharing Seattle, 2001

Integration of textual guideline documents with formal guideline knowledge bases.
Proceedings of the AMIA 2001, 2001

A Client-Server Framework for Deploying a Decision-support System in a Resource-constrained Environment.
Proceedings of the AMIA 2001, 2001

Protege-2000: A Plug-in Architecture to Support Knowledge Acquisition, Knowledge Visualization, and the Semantic Web.
Proceedings of the AMIA 2001, 2001

Representation of Structural Relationships in the Foundational Model of Anatomy.
Proceedings of the AMIA 2001, 2001

A virtual medical record for guideline-based decision support.
Proceedings of the AMIA 2001, 2001

Patient safety in guideline-based decision support for hypertension management: ATHENA DSS.
Proceedings of the AMIA 2001, 2001

A formal method to resolve temporal mismatches in clinical databases.
Proceedings of the AMIA 2001, 2001

Medical quality assessment by scoring adherence to guideline intentions.
Proceedings of the AMIA 2001, 2001

2000
Discussion Forum: Integration and Beyond: Panel Discussion.
JAMIA, 2000

Review Paper: Integration and Beyond: Linking Information from Disparate Sources and into Workflow.
JAMIA, 2000

A Case Study in Using Protégé-2000 as a Tool for CommonKADS.
Proceedings of the Knowledge Acquisition, 2000

The Knowledge Model of Protégé-2000: Combining Interoperability and Flexibility.
Proceedings of the Knowledge Acquisition, 2000

Representation Formalisms and Computational Methods for Modeling Guideline-Based Patient Care.
Proceedings of the Computer-Based Support for Clinical Guidelines and Protocols, 2000

From guideline modeling to guideline execution: defining guideline-based decision-support services.
Proceedings of the AMIA 2000, 2000

The impact of displayed awards on the credibility and retention of Web site information.
Proceedings of the AMIA 2000, 2000

Explanations for a Hypertension Decision Support System.
Proceedings of the AMIA 2000, 2000

Knowledge representation and tool support for critiquing clinical trial protocols.
Proceedings of the AMIA 2000, 2000

Representation of temporal indeterminacy in clinical databases.
Proceedings of the AMIA 2000, 2000

Representation of Nursing Guidelines Using the EON Guideline Model.
Proceedings of the AMIA 2000, 2000

Ontology acquisition from on-line knowledge sources.
Proceedings of the AMIA 2000, 2000

Implementing clinical practice guidelines while taking account of changing evidence: ATHENA DSS, an easily modifiable decision-support system for managing hypertension in primary care.
Proceedings of the AMIA 2000, 2000

Quality Assessment of Guideline-oriented Medical Care Using Recognition of Clinician Intentions.
Proceedings of the AMIA 2000, 2000

PROMPT: Algorithm and Tool for Automated Ontology Merging and Alignment.
Proceedings of the Seventeenth National Conference on Artificial Intelligence and Twelfth Conference on on Innovative Applications of Artificial Intelligence, July 30, 2000

1999
Integration of Temporal Reasoning and Temporal-Data Maintenance into a Reusable Database Mediator to Answer Abstract, Time-Oriented Queries: The Tzolkin System.
J. Intell. Inf. Syst., 1999

Original Investigation: Semi-automated Entry of Clinical Temporal-abstraction Knowledge.
JAMIA, 1999

Use of a domain model to drive an interactive knowledge-editing tool.
Int. J. Hum.-Comput. Stud., 1999

Representation of change in controlled medical terminologies.
Artificial Intelligence in Medicine, 1999

A flexible approach to guideline modeling.
Proceedings of the AMIA 1999, 1999

Effects of Evidence-Based Explanations of Clinical Guideline Recommendations on Clinical Decision-Making.
Proceedings of the AMIA 1999, 1999

The low availability of metadata elements for evaluating the quality of medical information on the World Wide Web.
Proceedings of the AMIA 1999, 1999

Justification of automated decision-making: medical explanations as medical arguments.
Proceedings of the AMIA 1999, 1999

Tool support for authoring eligibility criteria for cancer trials.
Proceedings of the AMIA 1999, 1999

Applying temporal joins to clinical databases.
Proceedings of the AMIA 1999, 1999

EON 2.0: Enhanced Middleware for Automation of Protocol-Directed Therapy.
Proceedings of the AMIA 1999, 1999

Representing the Digital Anatomist Foundational Model as a Protege Ontology.
Proceedings of the AMIA 1999, 1999

Integrating a modern knowledge-based system architecture with a legacy VA database: the ATHENA and EON projects at Stanford.
Proceedings of the AMIA 1999, 1999

1998
Forum Paper: How Should We Organize to Do Informatics?: Report of the ACMI Debate at the 1997 AMIA Fall Symposium.
JAMIA, 1998

Episodic refinement of episodic skeletal-plan refinement.
Int. J. Hum.-Comput. Stud., 1998

Reuse, CORBA, and knowledge-based systems.
Int. J. Hum.-Comput. Stud., 1998

VM-in-Protégé: A Study of Software Reuse.
Proceedings of the MEDINFO '98, 1998

Therapy planning as constraint satisfaction: a computer-based antiretroviral therapy advisor for the management of HIV.
Proceedings of the AMIA 1998, 1998

A declarative explanation framework that uses a collection of visualization agents.
Proceedings of the AMIA 1998, 1998

Modern architectures for intelligent systems: reusable ontologies and problem-solving methods.
Proceedings of the AMIA 1998, 1998

1997
Modular Neural Networks for Medical Prognosis: Quantifying the Benefits of Combining Neural Networks for Survival Prediction.
Connect. Sci., 1997

A temporal database mediator for protocol-based decision support.
Proceedings of the AMIA 1997, 1997

Theater-Style Demonstration: EON: CORBA-Based Middleware for Automation of Protocol-Directed Therapy.
Proceedings of the AMIA 1997, 1997

A foundational model of time for heterogeneous clinical databases.
Proceedings of the AMIA 1997, 1997

Domain Modeling with Integrated Ontologies: Principles for Reconciliation and Reuse.
Proceedings of the AMIA 1997, 1997

1996
Synthesis of Research: EON: A Component-Based Approach to Automation of Protocol-Directed Therapy.
JAMIA, 1996

Reusable ontologies, knowledge-acquisition tools, and performance systems: PROTÉGÉ-II solutions to Sisyphus-2.
Int. J. Hum.-Comput. Stud., 1996

Knowledge-based temporal abstraction in clinical domains.
Artificial Intelligence in Medicine, 1996

1995
Ontology-based configuration of problem-solving methods and generation of knowledge-acquisition tools: application of PROTEGE-II to protocol-based decision support.
Artificial Intelligence in Medicine, 1995

Architectures for intelligent systems based on reusable components.
Artificial Intelligence in Medicine, 1995

Task Modeling with Reusable Problem-Solving Methods.
Artif. Intell., 1995

Reuse with PROTÉgÉ-II: From Elevators to Ribosomes.
Proceedings of the ACM SIGSOFT Symposium on Software Reusability, 1995

Learning Rare Categories in Backpropagation.
Proceedings of the Advances in Artificial Intelligence, 1995

A Component-Based Architecture for Automation of Protocol-Directed Therapy.
Proceedings of the Artificial Intelligence Medicine, 1995

1994
Research Paper: A Logical Foundation for Representation of Clinical Data.
JAMIA, 1994

Mapping domains to methods in support of reuse.
Int. J. Hum.-Comput. Stud., 1994

Generation of knowledge-acquisition tools from domain ontologies.
Int. J. Hum.-Comput. Stud., 1994

Beyond Data Models for Automated User Interface Generation.
Proceedings of the People and Computers IX, 1994

Model-Based Automated Generation of User Interfaces.
Proceedings of the 12th National Conference on Artificial Intelligence, Seattle, WA, USA, July 31, 1994

1993
Metatools for Knowledge Acquisition.
IEEE Software, 1993

There's no theory better than that of a practical tool.
Knowledge Eng. Review, 1993

Modeling tasks with mechanisms.
Int. J. Intell. Syst., 1993

Graph-Grammar Assistance for Automated Generation of Influence Diagrams.
Proceedings of the UAI '93: Proceedings of the Ninth Annual Conference on Uncertainty in Artificial Intelligence, 1993

1992
Conceptual Models for Automatic Generation of Knowledge-Acquisition Tools.
Proceedings of the Current Developments in Knowledge Acquisition, 1992

Problem-Solving Models for Generation of Task-Specific Knowledge-Acquisition Tools.
Proceedings of the Knowledge Oriented Software Design, Extended Papers from the IFIP TC12 Workshop on Artificial Intelligence from the Information Processing Perspective, 1992

1990
Die Suche nach der Wissensebene.
KI, 1990

The 1990 AAAI Spring Symposium on Artificial Intelligence in Medicine.
Artificial Intelligence in Medicine, 1990

1989
Knowledge acquisition at the metalevel: creation of custom-tailored knowledge-acquisition tools.
SIGART Newsletter, 1989

Automated Support for Building and Extending Expert Models.
Machine Learning, 1989

An Editor for the Conceptual Models of Interactive Knowledge-Acquisition Tools.
International Journal of Man-Machine Studies, 1989

Episodic Skeletal-Plan Refinement Based on Temporal Data.
Commun. ACM, 1989

1987
Use of a Domain Model to Drive an Interactive Knowledge-Editing Tool.
International Journal of Man-Machine Studies, 1987


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