The NCBO OBOF to OWL Mapping (2009)
Dilvan A. Moreira, Christopher J. Mungall, Nigam H. Shah, Stuart Aitken, John-Day Richter, Timothy Redmond, ...
Two of the most significant formats for biomedical ontologies are the Open Biomedical Ontologies Format (OBOF) and the Web Ontology Language (OWL). To make it possible to translate ontologies between...
BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse (2009)
Patricia L. Whetzel, Nigam H. Shah, Natalya F. Noy, Benjamin Dai, Michael Dorf, Nicholas Griffith, ...
BioPortal ("http://bioportal.bioontology.org":http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides programmatic and web-based access to ontologies...
Comparison of concept recognizers for building the Open Biomedical Annotator (2009)
Shah, Nigam H, Bhatia, Nipun, Jonquet, Clement, Rubin, Daniel, Chiang, Annie P, Musen, Mark A
Abstract The National Center for Biomedical Ontology (NCBO) is developing a system for automated, ontology-based access to online biomedical resources (Shah NH, et al .: Ontology-driven indexing of...
Daniel L. Rubin, Yasser Bashir, David Grossman, Parvati Dev, Mark A. Musen
Abstract—Rapid diagnosis of penetrating injuries is essential to increased chance of survival. Geometric models representing anatomic structures could be useful, but such models generally contain...
BioPortal: A Web Repository for Biomedical Ontologies and Data Resources [Demonstration] (2009)
Natalya F. Noy, Nigam H. Shah, Benjamin Dai, Michael Dorf, Nicholas Griffith, Clement Jonquet, ...
Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, naturallanguage processing, and decision support. The National Center for...
Collaborative Protégé: Enabling Community-based Authoring of Ontologies [Demonstration] (2009)
Tania Tudorache, Natalya F. Noy, Mark A. Musen
Ontologies are becoming so large in their coverage that no single person or a small group of people can develop them effectively and ontology development becomes a community-based enterprise. We...
Yongqun He, Lindsay Cowell, Alexander D. Diehl, Harry Mobley, Bjoern Peters, Alan Ruttenberg, ...
Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein...
Yongqun He, Lindsay Cowell, Alexander D. Diehl, Harry Mobley, Bjoern Peters, Alan Ruttenberg, ...
The collaborative, community-based Vaccine Ontology (VO) was developed to promote vaccine data standardization, integration, and computer-assisted reasoning. Currently VO covers a variety of aspects...
Rubin, Daniel L, Talos, Ion-Florin, Halle, Michael, Musen, Mark A, Kikinis, Ron
Abstract Background A critical challenge in neuroscience is organizing, managing, and accessing the explosion in neuroscientific knowledge, particularly anatomic knowledge. We believe that explicit...
Ontology-driven indexing of public datasets for translational bioinformatics (2009)
Shah, Nigam H, Jonquet, Clement, Chiang, Annie P, Butte, Atul J, Chen, Rong, Musen, Mark A
Abstract The volume of publicly available genomic scale data is increasing. Genomic datasets in public repositories are annotated with free-text fields describing the pathological state of the...
Post-fielding Surveillance of a Guidelinebased Decision Support System (2009)
Albert S. Chan, Susana B. Martins, Robert W. Coleman, Hayden B, Mark A. Musen, ...
Quality assurance (QA) processes for new technologies are used to ensure safety. Clinical decision support systems (DSS), identified by the Institute of Medicine (IOM) as an important tool in...
BioPortal: ontologies and integrated data resources at the click of a mouse (2009)
Noy, Natalya F., Shah, Nigam H., Whetzel, Patricia L., Dai, Benjamin, Dorf, Michael, Griffith, Nicholas, ...
Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. BioPortal...
Harith Alani, Nigel Shadbolt, Natalya F. Noy, Mark A. Musen, Nigam Shah
As more ontologies become publicly available, finding the “right ” ontologies becomes much harder. In this paper, we address the problem of ontology search: finding a collection of ontologies...
UMLS-Query: A Perl Module for Querying the UMLS (2008)
The Metathesaurus from the Unified Medical Language System (UMLS) is a widely used ontology resource, which is mostly used in a relational database form for terminology research, mapping and...
The Semantic Web: A Brain (2008)
For Humankind, Dieter Fensel, Mark A. Musen
Originally, the computer was intended as a device for computation. Then, in the 1980s, the PC developed into a system for games, text processing, and PowerPoint pre-sentations. Eventually, the...
Which Annotation did you mean? (2008)
Ontologies are widely used to create biomedical annotations. Considerable effort goes into curation of publications to create annotations of genes and gene products as well as in the annotation of...
Making Biomedical Ontologies and Ontology Libraries Work (2008)
Natalya F. Noy, Daniel Rubin, Mark A. Musen
Today, it is impossible to contemplate successful biomedical research in the absence of canonical data structures. From primary databases (such as those found in GenBank 1 and MEDLINE) to meta-data...
Dilvan A. Moreira, Mark A. Musen, Dmitrij Frishman
The Open Biomedical Ontologies (OBO) format from the GO consortium is a very successful format for biomedical ontologies, including the Gene Ontology. But it lacks formal computational definitions...
Protégé: A Tool for Managing and Using Terminology in Radiology Applications (2008)
Daniel L. Rubin, Natalya F. Noy, Mark A. Musen
The development of standard terminologies such as RadLex is becoming important in radiology applications, such as structured reporting, teaching file authoring, report indexing, and text mining. The...
A Knowledge-Based Framework for Deploying Surveillance Problem Solvers (2008)
David L. Buckeridge, Martin J. O’connor, Haobo Xu, Mark A. Musen
Abstract — Increased concern about bioterrorism and emerging diseases is driving the development of systems for early epidemic detection. These systems have different requirements than traditional...
Using PROMPT Ontology-Comparison Tools in the EON Ontology Alignment Contest (2008)
Abstract. Objective evaluation and comparison of knowledge-based tools has so far been mostly an elusive goal for researchers and developers. Objective experiments are difficult to perform and...
Using ontologies linked with geometric models to reason about penetrating injuries (2008)
Daniel L. Rubin, Olivier Dameron, Yasser Bashir, David Grossman, Parvati Dev, Mark A. Musen
Medical assessment of penetrating injuries is a difficult and knowledge-intensive task. Physical examination and computed tomographic (CT) imaging data must be combined with detailed anatomic,...
Daniel L. Rubin, Olivier Dameron, Mark A. Musen
Anatomic reasoning tasks—such as inferring the consequences of penetrating injuries—is challenging because of the complexity and richness of anatomic knowledge. Applications that use ontologies...
EZPAL: Environment for Composing Constraint Axioms by Instantiating Templates (2008)
Abstract: Many ontology-development tools allow users to supplement frame-based representations with arbitrary logical sentences. However, few users actually take advantage of this opportunity. For...
07132 Report -- Towards Interoperability of Biomedical Ontologies (2008)
Musen, Mark A., Schroeder, Michael, Smith, Barry
The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of...
Abstract Knowledge-Based Temporal Abstraction in Clinical Domains (2007)
We have defined a knowledge-based framework for the creation of abstract, interval-based concepts from time-stamped clinical dataÑthe knowledge-based temporal-abstraction (KBTA) method. The KBTA...
Evidence-Based Automation), a project at the VA Palo (2007)
Ravi D. Shankar, Samson W. Tu, Mary K. Goldstein, Mark A. Musen, A Hypertension Decision
Medical Informatics, consists of a set of general components that work together to provide decisionsupport to physicians for guideline-based medical therapy [1]. A clinical application based on the...
Ontology 1. Reuse in Knowledge-Based Systems (2007)
Protégé is a system that encompasses a suite of graphical tools and a methodology for applying them to the task of creating and maintaining knowledge-based systems. One of our key goals for...
The New World of Mechanisms (2007)
Angel R. Puerta, Samson W. Tu, Mark A. Musen
A goal of second-generation expert systems is to supply knowledge engineers with common frameworks to develop expert systems, thus, eliminating the need to build entirely new systems for each...
A Rational Reconstruction of INTERNIST-I Using PROTÉGÉ-II (2007)
Mark A. Musen, John H. Gennari, Wesley W. Wong
INTRODUCTION Despite substantial progress in the development of principled methodologies for the construction of knowledgebased systems, the vast majority of such systems continue to be built using...
Evaluation of a Temporal-Abstraction Knowledge-Acquisition Tool (2007)
ion Knowledge-Acquisition Tool Yuval Shahar and Mark A. Musen Stanford Medical Informatics 251 Campus Drive, Medical School Office Building X-215 Stanford University, Stanford, CA 94305-5479, USA...
THE NEED FOR CONTEXT IN INTEGRATING HETEROGENEOUS DATA (2007)
Zachary Pincus, Mark A Musen, Md Phd
Systems that attempt to integrate and analyze data from multiple data sources are greatly aided by the addition of specific semantic and metadata “context” that explicitly describes what a data...
1. REUSABLE COMPONENTS AND MAPPINGS IN KNOWLEDGE- BASED SYSTEMS (2007)
John Y. Park, John H. Gennari, Mark A. Musen
By dividing the world into domain knowledge and problem-solving methods that reason over that knowledge, knowledge-based systems seek to promote reusability and shareability of the given components....
We have defined a knowledge-based framework for solving the task of creating abstract, interval-based concepts from time-stamped clinical dataÑthe knowledge-based temporal-abstraction (KBTA) method....
Abstract EON: A Component-Based Approach to Automation of Protocol-Directed Therapy (2007)
Mark A. Musen, Samson W. Tu, Amar K. Das, Yuval Shahar
Provision of automated support for planning protocol-directed therapy requires a computer program to take as input clinical data stored in an electronic patient-record system, and to generate as...
This paper presents a set of patient-care tasks for which a computer-interpretable representation of clinical practice guideline can provide assistance, surveys the formalisms and computational...
Musen M. A formal method to resolve temporal mismatches in clinical databases (2007)
Amar K. Das, Mark A. Musen, Ph. D
Overcoming data heterogeneity is essential to the transfer of decision-support programs to legacy databases and to the integration of data in clinical repositories. Prior methods have focused...
Abstract: Reuse For Knowledge-Based Systems and CORBA Components (2007)
John H. Gennari, Adam R. Stein, Mark A. Musen
For many years, researchers in knowledge-based systems have worked toward the development of sharable and reusable problem-solving methods and knowledge bases. The aim is to reduce development and...
Martin J. O’connor, M. Sc, Ravi D. Shankar, Samson W. Tu, Aneel Advani, Mary K. Goldstein, ...
There is a conflict between the desire for increasingly complex and robust decision-support applications and the reality of deploying them in legacy systems in existing clinical settings. The...
Evaluation of a Temporal-Abstraction Knowledge-Acquisition Tool (2007)
We describe the design and evaluation of a graphical knowledge-acquisition (KA) tool for entering the knowledge required by the RÉSUMÉ system. RÉSUMÉ is an implementation of the knowledge-based...
The New World of Mechanisms (2007)
Angel R. Puerta, Samson W. Tu, Mark A. Musen
A goal of second-generation expert systems is to supply knowledge engineers with common frameworks to develop expert systems, thus, eliminating the need to build entirely new systems for each...
Abstract Modeling Data and Knowledge in the EON Guideline Architecture (2007)
Compared to guideline representation formalisms, data and knowledge modeling for clinical guidelines is a relatively neglected area. Yet it has enormous impact on the format and expressiveness of...
A typology for modeling processes in clinical guidelines and protocols (2007)
We analyzed the graphical representations that are used by various guideline-modeling methods to express process information embodied in clinical guidelines and protocols. From this analysis, we...
Samson W. Tu, Henrik Eriksson, John Gennari, Yuval Shahar, Mark A. Musen
PROTÉGÉ-II is a suite of tools and a methodology for building knowledge-based systems and domain-specific knowledge-acquisition tools. In this paper, we show how PROTÉGÉ-II can be applied to the...
ABSTRACT Episodic Refinement of Episodic Skeletal Plan Refinement (2007)
This paper describes the reformulation of the episodic skeletal-plan refinement (ESPR) problemsolving method (PSM) in a new framework that seeks to integrate knowledge-based applications with a...
Mark A. Musen, Martin J. O’connor, David L. Buckeridge, Justin Graham, Natalya Fridman Noy, Yuval Shahar, ...
Automated surveillance for disease detection requires the integration of many kinds of data. The clinical information systems in hospitals, clinics, and emergency rooms that record patient findings...
Use of Protégé with the EON Architecture (2007)
Domain ontologies are formal descriptions of the classes of concepts and the relationships among those concepts that describe an application area. The Protégé software-engineering methodology...
Annotation and query of tissue microarray data using the NCI Thesaurus (2007)
Shah, Nigam H, Rubin, Daniel L, Espinosa, Inigo, Montgomery, Kelli, Musen, Mark A
Abstract Background The Stanford Tissue Microarray Database (TMAD) is a repository of data serving a consortium of pathologists and biomedical researchers. The tissue samples in TMAD are annotated...
OBO to OWL: a protege OWL tab to read/save OBO ontologies (2007)
Moreira, Dilvan A., Musen, Mark A.
The Open Biomedical Ontologies (OBO) format from the GO consortium is a very successful format for biomedical ontologies, including the Gene Ontology. But it lacks formal computational definitions...
Rubin, Daniel L., Lewis, Suzanna E., Mungall, Chris J., Misra, Sima, Westerfield, Monte, Ashburner, Michael, ...
The National Center for Biomedical Ontology (http://bioontology.org) is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists funded by the NIH Roadmap to...
Musen M.: A Framework for Ontology Evolution in Collaborative Environments (2006)
Natalya F. Noy, Abhita Chugh, William Liu, Mark A. Musen
Abstract. With the wider use of ontologies in the Semantic Web and as part of production systems, multiple scenarios for ontology maintenance and evolution are emerging. For example, successive...
Topic-Specific Trust and Open Rating Systems: An Approach for Ontology Evaluation (2006)
Holger Lewen, Kaustubh Supekar, Natalya F. Noy, Mark A. Musen
To achieve better interoperability among intelligent applications, and to relieve knowledge engineers from the burden of developing ontologies from scratch, it is critical to reuse ontologies....
User Ratings of Ontologies: Who will Rate the Raters (2005)
Natalya F. Noy, Ramanathan Guha, Mark A. Musen
The number of ontologies and knowledge bases covering different domains and available on the World-Wide Web is steadily growing. As more ontologies are available, it is becoming harder, and not...
Ontology-Centered Syndromic Surveillance for Bioterrorism (2005)
Monica Crubézy, David L. Buckeridge, Zachary Pincus, Mark A. Musen
Syndromic surveillance requires the acquisition and analysis of data that may be suggestive of early epidemics in a community, long before there is categorical evidence of unusual infection. These...
www.computer.org/intelligent Ontology-Centered (2005)
Syndromic Surveillance For, Monica Crubézy, David L. Buckeridge, Zachary Pincus, Mark A. Musen, Syndromic Surveillance, ...
This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying...
Knowledge Representation with Ontologies: The Present and Future (2004)
Brewster, Christopher, O'Hara, Kieron, Fuller, Steve, Wilks, Yorick, Franconi, Enrico, Musen, Mark A., ...
Debate on ontologies edited by Christopher Brewster & Kieron O'Hara.
Knowledge Representation with Ontologies: The Present and Future (2004)
Brewster, Christopher, O'Hara, Kieron, Fuller, Steve, Wilks, Yorick, Franconi, Enrico, Musen, Mark A., ...
Debate on ontologies edited by Christopher Brewster & Kieron O'Hara.
Knowledge Representation with Ontologies: The Present and Future (2004)
Brewster, Christopher, O'Hara, Kieron, Fuller, Steve, Wilks, Yorick, Franconi, Enrico, Musen, Mark A., ...
Debate on ontologies edited by Christopher Brewster & Kieron O'Hara.
Tracking Changes During Ontology Evolution (2004)
Natalya F. Noy, Hya Kunnatur, Michel Klein, Mark A. Musen
Abstract. As ontology development becomes a collaborative process, developers face the problem of maintaining versions of ontologies akin to maintaining versions of software code or versions of...
Editing description logic ontologies with the protégé OWL plugin (2004)
Holger Knublauch, Holger Knublauch, Ray W. Fergerson, Natalya F. Noy, Natalya F. Noy, Mark A. Musen, ...
We will demonstrate the OWL Plugin [1,2,3], a Semantic Web extension of the Protégé ontology development platform. The OWL Plugin can be used to edit ontologies in the Web Ontology Language (OWL),...
Ontology Versioning in an Ontology Management Framework (2004)
A uniform framework for managing ontology versions will help developers work more effectively with existing ontologies and create new ones. O n t o l o g i e s
AN ALGEBRAIC FRAMEWORK FOR THE INTEROPERATION OF ONTOLOGIES (2004)
ii I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a disser-tation for the degree of Doctor of Philosophy.
Editing Description Logic Ontologies with the Protégé OWL Plugin (2004)
Holger Knublauch, Mark A. Musen, Alan L. Rector
The growing interest in the Semantic Web and the Web Ontology Language (OWL) will reveal the potential of Description Logics in industrial projects. The rich semantics of OWL provide powerful...
Weaving the Biomedical Semantic Web with the Protégé OWL Plugin (2004)
Holger Knublauch, Olivier Dameron, Mark A. Musen
In this document we show how biomedical resources can be linked into a Semantic Web using Prot eg e. Prot eg e is a widely-used open-source ontology modeling environment with support for the Web...
Accessing and Manipulating Ontologies Using Web Services (2004)
Olivier Dameron, Natalya F. Noy, Holger Knublauch, Mark A. Musen
Abstract. Ontologies and Semantic Web Services are the two core technologies of the Semantic Web. The Semantic Web hinges on the ability of computer programs to perform some task involving the...
The Protégé OWL plugin: An open development environment for semantic web applications (2004)
Holger Knublauch, Ray W. Fergerson, Natalya F. Noy, Mark A. Musen
Abstract. We introduce the OWL Plugin, a Semantic Web extension of the Protégé ontology development platform. The OWL Plugin can be used to edit ontologies in the Web Ontology Language (OWL), to...
Editing description logic ontologies with the protégé OWL plugin (2004)
Holger Knublauch, Mark A. Musen, Alan L. Rector
The growing interest in the Semantic Web and the Web Ontology Language (OWL) will reveal the potential of Description Logics in industrial projects. The rich semantics of OWL provide powerful...
The prompt suite: Interactive tools for ontology merging and mapping (2003)
Researchers in the ontology-design field have developed the content for ontologies in many domain areas. This distributed nature of ontology development has led to a large number of ontologies...
Ontology versioning as an element of an ontology-management framework (2003)
As ontology development becomes a more ubiquitous and collaborative process, the developers face the problem of managing multiple ontologies: comparing, aligning, and merging them, maintaining...
Ontologies in Support of Problem Solving (2003)
Monica Crubézy, Monica Crubézy, Mark A. Musen, Mark A. Musen
Problem-solving methods are ready-made software components that can be assembled with domain knowledge bases to create application systems. Ontologies and problem-solving methods have a long history...
Mediating Knowledge between Application Components (2003)
Monica Crubezy, Zachary Pincus, Mark A. Musen
In such contexts as the Semantic Web, the components of an application increasingly rely on ontological models and content knowledge developed and maintained by independent contributors. These...
The Structure of Guideline Recommendations: A Synthesis (2003)
Samson Tu James, James Campbell, Mark A. Musen
We propose that recommendations in a clinical guideline can be structured either as collections of decisions that are to be applied in specific situations or as processes that specify activities that...
Mediating Knowledge between Application Components (2003)
Monica Crubezy, Zachary Pincus, Mark A. Musen
In such contexts as the Semantic Web, the components of an application increasingly rely on ontological models and content knowledge developed and maintained by independent contributors. These...
Meric, Funda, Bernstam, Elmer V, Mirza, Nadeem Q, Hunt, Kelly K, Ames, Frederick C, Ross, Merrick I, ...
OBJECTIVES: To determine the characteristics of popular breast cancer related websites and whether more popular sites are of higher quality. DESIGN: The search engine Google was used to generate a...
Pushing the envelope: Challenges in a frame-based representation of human anatomy (2002)
Natalya F. Noy, Mark A. Musen, Cornelius Rosse
One of the main threads in the history of knowledge-representation formalisms is the trade-off between the expressiveness of first-order logic on the one hand and the tractability and ease-of-use of...
PROMPTDIFF: A fixed-point algorithm for comparing ontology versions (2002)
As ontology development becomes a more ubiquitous and collaborative process, the developers face the problem of maintaining versions of ontologies akin to maintaining versions of software code in...
Configuring Online Problem-Solving Resources with the Internet Reasoning Service (2002)
Monica Crubézy, Wenjin Lu, Enrico Motta, Mark A. Musen
Abstract: Existing services on the World-Wide Web tend to be “integral. ” For instance, online services for data analysis are available, but usually it is neither possible to modify the...
Medical informatics: searching for underlying components (2002)
“Yes, well, you may well ask, what is my theory?” — Anne Elk, in a skit by Monty Python, 1972 Objective: To discuss unifying principles that can provide a theory for the diverse aspects of work...
A template-based approach toward acquisition of logical sentences (2002)
Abstract: Ontology-development languages may allow users to supplement frame-based representations with arbitrary logical sentences. In the case of the Ontolingua ontology library, only 10 % of the...
Evaluating ontology-mapping tools: Requirements and experience (2002)
Abstract. The appearance of a large number of ontology tools may leave a user looking for an appropriate tool overwhelmed and uncertain on which tool to choose. Thus evaluation and comparison of...
The Evolution of Protégé: An Environment for Knowledge-Based Systems Development (2002)
John H. Gennari, Mark A. Musen, Ray W. Fergerson, William E. Grosso, Monica Crubézy, Henrik Eriksson, ...
The Protégé project has come a long way since Mark Musen first built the Protégé metatool for knowledge-based systems in 1987. The original tool was a small application, aimed at building...
Evaluating ontology-mapping tools: Requirements and experience (2002)
Abstract. The appearance of a large number of ontology tools may leave a user looking for an appropriate tool overwhelmed and uncertain on which tool to choose. Thus evaluation and comparison of...
Configuring Online Problem-Solving Resources with the Internet Reasoning Service (2002)
Monica Crubézy, Wenjin Lu, Enrico Motta, Mark A. Musen
Abstract: Existing services on the World-Wide Web tend to be “integral. ” For instance, online services for data analysis are available, but usually it is neither possible to modify the...
Creating semantic web contents with (2001)
Natalya F. Noy, Michael Sintek, Stefan Decker, Monica Crubézy, Ray W. Fergerson, Mark A. Musen
T h e S e m a n t i c W e b As researchers continue to create new languages in the hope of developing a Semantic Web, they still lack consensus on a standard. The authors describe how...
Abstract Modeling Data and Knowledge in the EON Guideline Architecture (2001)
Compared to guideline representation formalisms, data and knowledge modeling for clinical guidelines is a relatively neglected area. Yet it has enormous impact on the format and expressiveness of...
Creating semantic web contents with (2001)
Natalya F. Noy, Michael Sintek, Stefan Decker, Monica Crubézy, Ray W. Fergerson, Mark A. Musen
T h e S e m a n t i c W e b As researchers continue to create new languages in the hope of developing a Semantic Web, they still lack consensus on a standard. The authors describe how...
Monica Crubézy, Wenjin Lu, Enrico Motta, Mark A. Musen
Existing services on the Web tend to be ‘holistic’. For instance, online services for data analysis are available, but usually it is neither possible to modify the underlying reasoning system,...
Martin J. O’connor, M. Sc, William E. Grosso, Samson W. Tu, Mark A. Musen
The time dimension is very important when reasoning with clinical data. Unfortunately, the task of temporal reasoning is inherently computationally expensive. As the problems tackled by clinical...
Anchor-PROMPT: Using non-local context for semantic matching (2001)
Researchers in the ontology-design field have developed the content for ontologies in many domain areas. Recently, ontologies have become increasingly common on the World-Wide Web where they provide...
Creating semantic web contents with (2001)
Natalya F. Noy, Michael Sintek, Stefan Decker, Monica Crubézy, Ray W. Fergerson, Mark A. Musen
T h e S e m a n t i c W e b As researchers continue to create new languages in the hope of developing a Semantic Web, they still lack consensus on a standard. The authors describe how...
Knowledge Representation and Tool Support for Critiquing Clinical Trial Protocols (2000)
Daniel L. Rubin, John Gennari, Mark A. Musen
The increasing complexities of clinical trials have led to increasing costs for investigators and organizations that author and administer those trials. The process of authoring a clinical trial...
The knowledge model of protege-2000: Combining interoperability and flexibility (2000)
Natalya Fridman Noy, Ray W. Fergerson, Mark A. Musen
Knowledge-based systems have become ubiquitous in recent years. The World-Wide Web consortium is developing the Resource Description Framework (RDF)—a system for annotating even Web pages with...
We describe our task-based approach to defining the guideline-based decision-support services that the EON system provides. We categorize uses of guidelines in patient-specific decision support into...
In computer science, the notion of a domain ontology—a formal specification of the concepts and of the relationships among concepts that characterize an application area—has received considerable...
Component-Based Support for Building Knowledge-Acquisition Systems (2000)
Mark A. Musen, Ray W. Fergerson, William E. Grosso, Natalya F. Noy, Monica Crubézy, John H. Gennari
During the past decade, there has been increasing consensus within the knowledge-based–systems community on appropriate conceptual components for building intelligent computer programs. Intelligent...
Knowledge-acquisition interfaces for domain experts: An empirical evaluation of protege-2000 (2000)
Natalya Fridman Noy, William Grosso, Mark A. Musen
Application experts need to be able to maintain, populate, and verify existing knowledge bases in order to use knowledge-based tools to perform their daily tasks. Protégé-2000 is a tool that...
Knowledge Representation and Tool Support for Critiquing Clinical Trial Protocols (2000)
Daniel L. Rubin, John Gennari, Mark A. Musen
The increasing complexities of clinical trials have led to increasing costs for investigators and organizations that author and administer those trials. The process of authoring a clinical trial...
We describe the task-based approach we have taken to define guideline-based decision-support services that the EON system provides. We categorize uses of guidelines in patient-specific decision...
PROMPT: Algorithm and Tool for Automated Ontology Merging and Alignment (2000)
Natalya Fridman Noy, Mark A. Musen
Researchers in the ontology-design field have developed the content for ontologies in many domain areas. Recently, ontologies have become increasingly common on the World-Wide Web where they provide...
Ontology-oriented design and programming (2000)
Abstract: In the construction of both conventional software and intelligent systems, developers continue to seek higher level abstractions that both can aid in conceptual modeling and can assist in...
Ontology acquisition from on-line knowledge sources (2000)
Qi Li, Philip Shilane, Natalya Fridman Noy, Mark A. Musen
Electronic knowledge representation is becoming more and more pervasive both in the form of formal ontologies and less formal reference vocabularies, such as UMLS. The developers of clinical...
Representation of Temporal Indeterminacy in Clinical Databases (2000)
Martin J. O’connor, M. Sc, Samson W. Tu, Mark A. Musen, Ph. D
Temporal indeterminacy is common in clinical medicine because the time of many clinical events is frequently not precisely known. Decision support systems that reason with clinical data may need to...
SMART: Automated support for ontology merging and alignment (1999)
Natalya Fridman Noy, Mark A. Musen
As researchers in the ontology-design field develop the content of a growing number of ontologies, the need for sharing and reusing this body of knowledge becomes increasingly critical. Aligning and...
Justification of Automated Decision-Making: Medical Explanation or Medical Argument (1999)
Ravi D. Shankar, Mark A. Musen
People use arguments to justify their causes. Computer systems use explanations to justify their claims. The WOZ explanation framework adopts an argumentation methodology for generating explanations...
Tool support for authoring eligibility criteria for cancer trials (1999)
Daniel L. Rubin, John H. Gennari, Ra Srinivas, Allen Yuen, Herbert Kaizer, Mark A. Musen, ...
A critical component of authoring new clinical trial protocols is assembling a set of eligibility criteria for patient enrollment. We found that clinical protocols in three different cancer domains...
Representation of change in controlled medical terminologies (1999)
Diane E. Oliver, Edward H. Shortliffe, Mark A. Musen, Ph. D, Ph. D
Computer-based systems that support health care require large controlled terminologies to manage names and meanings of data elements. These terminologies are not static, because change in health care...
John H. Nguyen, Yuval Shahar, Yuval Shahar, Samson W. Tu, Samson W. Tu, ...
The ability to reason with time-oriented data is central to the practice of medicine. Monitoring clinical variables over time often provides information that drives medical decision making (e.g.,...
A Specification for a Temporal Query System (1999)
Martin J. O’connor, Samson W. Tu, Mark A. Musen
This document outlines a specification for a temporal query system called Chronus II. The design of Chronus II has been influenced by the original Chronus system, which was written in Stanford...
A Flexible Approach to Guideline Modeling (1999)
We describe a task-oriented approach to guideline modeling that we have been developing in the EON project. We argue that guidelines seek to change behaviors by making statements involving some or...
Knowledge modeling at the millennium (the design and evolution of protege-2000 (1999)
William E. Grosso, Henrik Eriksson, Ray W. Fergerson, John H. Gennari, Samson W. Tu, Mark A. Musen
It has been 13 years since the first version of Protégé was run. The original tool was a small application, aimed mainly at building knowledge-acquisition tools for a few very specialized programs...
Knowledge modeling at the millennium (the design and evolution of protege-2000 (1999)
William E. Grosso, Henrik Eriksson, Ray W. Fergerson, John H. Gennari, Samson W. Tu, Mark A. Musen
It has been 13 years since the first version of Protégé was run. The original tool was a small application, aimed mainly at building knowledge-acquisition tools for a few very specialized programs...
An Algorithm for Merging and Aligning Ontologies: Automation and Tool Support (1999)
Natalya Fridman Noy, Mark A. Musen
As researchers in the ontology-design field develop the content of a growing number of ontologies, the need for sharing and reusing this body of knowledge becomes increasingly critical. Aligning and...
SMART: Automated Support for Ontology Merging and Alignment (1999)
Natalya Fridman Noy, Mark A. Musen
As researchers in the ontology-design field develop the content of a growing number of ontologies, the need for sharing and reusing this body of knowledge becomes increasingly critical. Aligning and...
Automatic Generation of Ontology Editors (1999)
Henrik Eriksson, Raymond W. Fergerson, Yuval Shahar, Mark A. Musen
Metalevel tools can support the knowledge-engineering process by assisting developers in the design and implementation of domain-oriented knowledge-acquisition tools. The use of ontologies as a basis...
Post-Fielding Surveillance of a Guideline-Based Decision Support System (1998)
Chan, Albert S., Martins, Susana B., Coleman, Robert W., Bosworth, Hayden B., Oddone, Eugene Z., Shlipak, Michael G., ...
Quality assurance (QA) processes for new technologies are used to ensure safety. Clinical decision support systems (DSS), identified by the Institute of Medicine (IOM) as an important tool in...
Modern architectures for intelligent systems: reusable ontologies and problem-solving methods (1998)
When interest in intelligent systems for clinical medicine soared in the 1970s, workers in medical informatics became particularly attracted to rule-based systems. Although many successful rule-based...
D. Scott Smith, John Y. Park, Mark A. Musen, Ph. D
We applied the Protégé methodology for building knowledge-based systems to the domain of antiretroviral therapy. We modeled the task of prescribing drug therapy for HIV, abstracting the essential...
When Knowledge Models Collide (How it Happens and What to Do (1998)
William E. Grosso, John H. Gennari, Ray W. Fergerson, Mark A. Musen
Interoperability and reuse of components and declarative knowledge are crucial to the further development of knowledge-based software. Unfortunately, it is hard to get components to interoperate and...
Reuse, corba, and knowledge-based systems (1998)
John H. Gennari, Heyning Cheng, Russ B. Altman, Mark A. Musen
By applying recent advances in the standards for distributed computing, we have developed an architecture for a CORBA implementation of a library of platform-independent, sharable problem-solving...
Modern architectures for intelligent systems: reusable ontologies and problem-solving methods (1998)
When interest in intelligent systems for clinical medicine soared in the 1970s, workers in medical informatics became particularly attracted to rule-based systems. Although many successful rule-based...
A temporal database mediator for protocol-based decision support (1997)
John H. Nguyen, Yuval Shahar, Samson W. Tu, Amar K. Das, Mark A. Musen
To meet the data-processing requirements for protocol-based decision support, a clinical datamanagement system must be capable of creating high-level summaries of time-oriented patient data, and of...
Lucila Ohno-machado, Mark A. Musen
This paper describes a medical application of modular neural networks for temporal pattern recognition. In order to increase the reliability of prognostic indices for patients living with the...
Musen M. Making generic guidelines site-specific (1996)
Douglas B. Fridsma, John H. Gennari, Mark A. Musen, Ph. D, Ph. D
Health care providers are more likely to follow a clinical guideline if the guideline’s recommendations are consistent with the way in which their organization does its work. Unfortunately,...
Thomas E. Rothenfluh, John H. Gennari, Henrik Eriksson, Angel R. Puerta, Samson W. Tu, Mark A. Musen
Abstract: This paper describes how we applied the PROTÉGÉ-II architecture to build a knowledgebased system that configures elevators. The elevator-configuration task was solved originally with a...
Peter D. Johnson, Mark A. Musen
Clinical guidelines are now commonly available, and their benefits have been demonstrated. However, they will not be widely used until they can be freely disseminated in a form that can be applied in...
Conceptual and Formal Specifications of Problem-Solving Methods (1996)
Dieter Fensel, Henrik Eriksson, Mark A. Musen, Rudi Studer
Reusable problem-solving methods as provided by the PROTÉGÉ-II improve knowledge engineering by allowing developers to design reasoners quickly from pre-existing components. The PROTÉGÉ-II...
Reuse with Protégé-II: From Elevators to Ribosomes (1995)
John H. Gennari, Russ B. Altman, Mark A. Musen
This paper describes the PROTEGE-II environment which supports the construction of knowledge-base systems from reusable compo-nents. To assist developers with reuse, the terminologies of both...
Task modeling with reusable problem-solving methods (1995)
Henrik Eriksson, Yuval Shahar, Samson W. Tu, Angel R. Puerta, Mark A. Musen
Problem-solving methods for knowledge-based systems establish the behavior of such systems by de�ning the roles in which domain knowledge is used and the ordering of inferences. Developers can...
Plan Recognition and Revision in Support of Guideline-Based Care (1995)
We consider the problem of providing automated support for guideline-based clinical care. Clinical guidelines are a common format in medical domains for prescribing a set of rules and policies that...
Toward ontology-based frameworks for knowledge-acquisition tools (1994)
Angel R. Puerta, Robert Neches, Henrik Eriksson, Pedro Szekely, Ping Luo, Mark A. Musen
One of the strongest limitations of knowledge-acquisition metatools—tools that automate the development of knowledge-acquisition tools—is that the interface-design knowledge employed by such...
Hierarchical Neural Networks for Partial Diagnosis in Medicine (1994)
Lucila Ohno-machado, Mark A. Musen
Various domains require hierarchical classification. In medicine, learning partial diagnoses can be helpful when time and information constraints are present. Hierarchical neural networks provide a...
Mapping domains to methods in support of reuse (1994)
John H. Gennari, Samson W. Tu, Thomas E. Rothenfluh, Mark A. Musen
In this paper, we characterize the relationship between abstract problem-solving methods and the domain-oriented knowledge bases that they use. We argue that, to reuse methods and knowledge bases, we...
Generation of knowledge-acquisition tools from domain ontologies (1994)
Henrik Eriksson, Angel R. Puerta, Mark A. Musen
Metalevel tools can support the software development process by automating the design of task- and application-speci�c tools. Dash is a metalevel tool that allows developers to generate...
Beyond Data Models for Automated User Interface Generation (1994)
Angel R. Puerta, Henrik Eriksson, John H. Gennari, Mark A. Musen
Researchers in the area of automated design of user interfaces have shown that the layout of an interface can, in many cases, be generated from the application’s data model using an intelligent...
Model-Based Automated Generation of User Interfaces (1994)
Angel R. Puerta, Henrik Eriksson, John H. Gennari, Mark A. Musen
ABSTRACT 1 User interface design and development for knowledgebased systems and most other types of applications is a resource-consuming activity. Thus, many attempts have been made to automate, to...
Modeling tasks with mechanisms (1993)
Angel R. Puerta, Samson W. Tu, Mark A. Musen
All of the buildings and all of the cars were once just a dream in somebody’s head
An Extended SQL for Temporal Data Management in Clinical Decision-Support Systems (1992)
Amar K. Das, Samson W. Tu, Gretchen P. Purcell, Mark A. Musen
We are developing a database implementation to support temporal data management for the T-HELPER physician workstation, an advice system for protocol-based care of patients who have HIV disease. To...
Eckart Walther, Henrik Eriksson, Mark A. Musen
Previous approaches to the reuse of problem-solving methods have relied on the existence of a global data model to serve as the mediator among the individual methods. This hard-coded approach limits...
Generation of Knowledge-Acquisition Tools from Reusable Domain Ontologies (1992)
Angel R. Puerta, Henrik Eriksson, John W. Egar, Mark A. Musen
We present Mecano, a development environment that automates the design of knowledge-acquisition software tools for knowledge-based systems. Mecano is a component of PROTG-II---a development...
Modeling Tasks with Mechanisms (1992)
Angel R. Puerta, Samson W. Tu, Mark A. Musen
Building a problem solver and acquiring the knowledge needed to operate it are the two central goals of knowledge engineering. To achieve these goals, knowledge engineers construct models of the...
A Problem-Solving Architecture for Managing Temporal Data and their Abstractions (1992)
Yuval Shahar, Samson W. Tu, Amar K. Das, Mark A. Musen
ions Yuval Shahar, Samson W. Tu, Amar K. Das, Mark A. Musen Section on Medical Informatics Stanford University School of Medicine Stanford, CA 94305-5479 1. Introduction Representing and reasoning...
Eckart Walther, Henrik Eriksson, Mark A. Musen
Previous approaches to the reuse of problem-solving methods have relied on the existence of a global data model to serve as the mediator among the individual methods. This hard-coded approach limits...
Episodic Monitoring of Time-Oriented Data for Heuristic SkeletalPlan Refinement (1989)
Samson W. Tu, Michael G. Kahn, Mark A. Musen, Jay C. Ferguson, Edward H. Shortliffe, Lawrence M. Fagan
ONCOCIN is a medical expert system that extends the skeletal-planning technique to an application area where the history of past events and the duration of actions are important. The system's...
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How Should We Organize to Do Informatics?: Report of the ACMI Debate at the 1997 AMIA Fall Symposium
Friedman, Charles P., Frisse, Mark E., Musen, Mark A., Slack, Warner V., Stead, William W.
Semi-automated Entry of Clinical Temporal-abstraction Knowledge
Shahar, Yuval, Chen, Hai, Stites, Daniel P., Basso, Lawrence V., Kaizer, Herbert, Wilson, Darrell M., ...
Objectives: The authors discuss the usability of an automated tool that supports entry, by clinical experts, of the knowledge necessary for forming high-level concepts and patterns from raw...
Integration and Beyond: Linking Information from Disparate Sources and into Workflow
Stead, William W., Miller, Randolph A., Musen, Mark A., Hersh, William R.
The vision of integrating information—from a variety of sources, into the way people work, to improve decisions and process—is one of the cornerstones of biomedical informatics. Thoughts on how...
Integration and Beyond: Panel Discussion
Stead, William W., Miller, Randolph A., Musen, Mark A., Hersh, William R.
Meric, Funda, Bernstam, Elmer V, Mirza, Nadeem Q, Hunt, Kelly K, Ames, Frederick C, Ross, Merrick I, ...
Medical Quality Assessment by Scoring Adherence to Guideline Intentions
Advani, Aneel, Shahar, Yuval, Musen, Mark A.
Quality assessment of clinician actions and patient outcomes is a central problem in guideline- or standards-based medical care. In this paper we describe an approach for evaluating and consistently...
Goldstein, Mary K., Coleman, Robert W., Tu, Samson W., Shankar, Ravi D., O'Connor, Martin J., Musen, Mark A., ...
Information technology can support the implementation of clinical research findings in practice settings. Technology can address the quality gap in health care by providing automated decision support...
Contextualizing Heterogeneous Data for Integration and Inference
Pincus, Zachary, Musen, Mark A
Systems that attempt to integrate and analyze data from multiple data sources are greatly aided by the addition of specific semantic and metadata “context” that explicitly describes what a data...
An Analytic Framework for Space–Time Aberrancy Detection in Public Health Surveillance Data
Buckeridge, David L, Musen, Mark A, Switzer, Paul, Crubézy, Monica
Public health surveillance is changing in response to concerns about bioterrorism, which have increased the pressure for early detection of epidemics. Rapid detection necessitates following multiple...
The Structure of Guideline Recommendations: A Synthesis
Tu, Samson W., Campbell, James, Musen, Mark A.
We propose that recommendations in a clinical guideline can be structured either as collections of decisions that are to be applied in specific situations or as processes that specify activities that...
Advani, Aneel, Goldstein, Mary, Shahar, Yuval, Musen, Mark A.
Automated quality assessment of clinician actions and patient outcomes is a central problem in guideline- or standards-based medical care. In this paper we describe a model representation and...
Noy, Natalya F., Crubézy, Monica, Fergerson, Ray W., Knublauch, Holger, Tu, Samson W., Vendetti, Jennifer, ...
Protégé-2000 is an open-source tool that assists users in the construction of large electronic knowledge bases. It has an intuitive user interface that enables developers to create and edit domain...
BioSTORM: A System for Automated Surveillance of Diverse Data Sources
O’Connor, Martin J., Buckeridge, David L., Choy, Michael, Crubezy, Monica, Pincus, Zachary, Musen, Mark A.
How Should We Organize to Do Informatics?: Report of the ACMI Debate at the 1997 AMIA Fall Symposium
Friedman, Charles P., Frisse, Mark E., Musen, Mark A., Slack, Warner V., Stead, William W.
Semi-automated Entry of Clinical Temporal-abstraction Knowledge
Shahar, Yuval, Chen, Hai, Stites, Daniel P., Basso, Lawrence V., Kaizer, Herbert, Wilson, Darrell M., ...
Objectives: The authors discuss the usability of an automated tool that supports entry, by clinical experts, of the knowledge necessary for forming high-level concepts and patterns from raw...
Integration and Beyond: Linking Information from Disparate Sources and into Workflow
Stead, William W., Miller, Randolph A., Musen, Mark A., Hersh, William R.
The vision of integrating information—from a variety of sources, into the way people work, to improve decisions and process—is one of the cornerstones of biomedical informatics. Thoughts on how...
Integration and Beyond: Panel Discussion
Stead, William W., Miller, Randolph A., Musen, Mark A., Hersh, William R.
Meric, Funda, Bernstam, Elmer V, Mirza, Nadeem Q, Hunt, Kelly K, Ames, Frederick C, Ross, Merrick I, ...
Medical Quality Assessment by Scoring Adherence to Guideline Intentions
Advani, Aneel, Shahar, Yuval, Musen, Mark A.
Quality assessment of clinician actions and patient outcomes is a central problem in guideline- or standards-based medical care. In this paper we describe an approach for evaluating and consistently...
Goldstein, Mary K., Coleman, Robert W., Tu, Samson W., Shankar, Ravi D., O'Connor, Martin J., Musen, Mark A., ...
Information technology can support the implementation of clinical research findings in practice settings. Technology can address the quality gap in health care by providing automated decision support...
Contextualizing Heterogeneous Data for Integration and Inference
Pincus, Zachary, Musen, Mark A
Systems that attempt to integrate and analyze data from multiple data sources are greatly aided by the addition of specific semantic and metadata “context” that explicitly describes what a data...
An Analytic Framework for Space–Time Aberrancy Detection in Public Health Surveillance Data
Buckeridge, David L, Musen, Mark A, Switzer, Paul, Crubézy, Monica
Public health surveillance is changing in response to concerns about bioterrorism, which have increased the pressure for early detection of epidemics. Rapid detection necessitates following multiple...
The Structure of Guideline Recommendations: A Synthesis
Tu, Samson W., Campbell, James, Musen, Mark A.
We propose that recommendations in a clinical guideline can be structured either as collections of decisions that are to be applied in specific situations or as processes that specify activities that...
Advani, Aneel, Goldstein, Mary, Shahar, Yuval, Musen, Mark A.
Automated quality assessment of clinician actions and patient outcomes is a central problem in guideline- or standards-based medical care. In this paper we describe a model representation and...
Noy, Natalya F., Crubézy, Monica, Fergerson, Ray W., Knublauch, Holger, Tu, Samson W., Vendetti, Jennifer, ...
Protégé-2000 is an open-source tool that assists users in the construction of large electronic knowledge bases. It has an intuitive user interface that enables developers to create and edit domain...
BioSTORM: A System for Automated Surveillance of Diverse Data Sources
O’Connor, Martin J., Buckeridge, David L., Choy, Michael, Crubezy, Monica, Pincus, Zachary, Musen, Mark A.
Ontology-based Annotation and Query of Tissue Microarray Data
Shah, Nigam H., Rubin, Daniel L., Supekar, Kaustubh S., Musen, Mark A.
The Stanford Tissue Microarray Database (TMAD) is a repository of data amassed by a consortium of pathologists and biomedical researchers. The TMAD data are annotated with multiple free-text fields,...
Ontology-Based Representation of Simulation Models of Physiology
Rubin, Daniel L., Grossman, David, Neal, Maxwell, Cook, Daniel L., Bassingthwaighte, James B., Musen, Mark A.
Dynamic simulation models of physiology are often represented as a set of mathematical equations. Such models are very useful for studying and understanding the dynamic behavior of physiological...
Tu, Samson W., Hrabak, Karen M., Campbell, James R., Glasgow, Julie, Nyman, Mark A, McClure, Robert, ...
Developing computer-interpretable clinical practice guidelines (CPGs) to provide decision support for guideline-based care is an extremely labor-intensive task. In the EON/ATHENA and SAGE projects,...
Protégé-OWL: Creating Ontology-Driven Reasoning Applications with the Web Ontology Language
Rubin, Daniel L., Knublauch, Holger, Fergerson, Ray W., Dameron, Olivier, Musen, Mark A.
Protégé OWL1 is an open source tool created to support ontology development for the Semantic Web. It is a plug-in extension to the Protégé ontology development platform. Protégé OWL allows...
Use of Description Logic Classification to Reason about Consequences of Penetrating Injuries
Rubin, Daniel L., Dameron, Olivier, Musen, Mark A.
The consequences of penetrating injuries can be complex, including abnormal blood flow through the injury channel and functional impairment of organs if arteries supplying them have been severed....
Challenges in Converting Frame-Based Ontology into OWL: the Foundational Model of Anatomy Case-Study
Dameron, Olivier, Rubin, Daniel L., Musen, Mark A.
A description logics representation of the Foundational Model of Anatomy (FMA) in the Web Ontology Language (OWL-DL) would allow developers to combine it with other OWL ontologies, and would provide...
Annotation and query of tissue microarray data using the NCI Thesaurus
Shah, Nigam H, Rubin, Daniel L, Espinosa, Inigo, Montgomery, Kelli, Musen, Mark A
Protégé: A Tool for Managing and Using Terminology in Radiology Applications
Rubin, Daniel L., Noy, Natalya F., Musen, Mark A.
The development of standard terminologies such as RadLex is becoming important in radiology applications, such as structured reporting, teaching file authoring, report indexing, and text mining. The...
The SAGE Guideline Model: Achievements and Overview
Tu, Samson W., Campbell, James R., Glasgow, Julie, Nyman, Mark A., McClure, Robert, McClay, James, ...
The SAGE (Standards-Based Active Guideline Environment) project was formed to create a methodology and infrastructure required to demonstrate integration of decision-support technology for...
Representing the Digital Anatomist Foundational Model as a Protege Ontology
Hahn, Jin S., Burnside, Elizabeth, Brinkley, James F., Rosse, Cornelius, Musen, Mark A.
EON 2.0: Enhanced Middleware for Automation of Protocol-Directed Therapy
Musen, Mark A., Tu, Samson W., Shankar, Ravi D., O'Connor, Martin J., Advani, Aneel
Theater-Style Demonstration: EON: CORBA-Based Middleware for Automation of Protocol-Directed Therapy
Musen, Mark A., Tu, Samson W., Advani, Aneel, Das, Amar K., Hasan, Zaki, Nguyen, John, ...
O'Connor, Martin J., Shankar, Ravi D., Tu, Samson W., Advani, Aneel, Goldstein, Mary K., Coleman, Robert W., ...
Representation of Structural Relationships in the Foundational Model of Anatomy
Mejino, José L.V., Noy, Natalya F., Musen, Mark A., Brinkley, James F., Rosse, Cornelius
We propose an ontology of anatomical relationships in the Digital Anatomist Foundational Model. Our purpose is to generate a sharable resource that can support inference about the structural...
Explanations for a Hypertension Decision Support System
Shankar, Ravi D., Tu, Samson W., Goldstein, Mary K., Musen, Mark A.
Beard, Nick, Campbell, James R., Huff, Stanley M., Leon, Mauricio, Mansfield, James G., Mays, Eric, ...
A collaborative project has been initiated to develop a standards-based, comprehensive technology infrastructure that will enable encoding and dissemination of interoperable, electronic clinical...
Advani, Aneel, Goldstein, Mary, Musen, Mark A.
Automated quality assessment of clinician actions and patient outcomes is a central problem in guideline- or standards-based medical care. In this paper we describe a unified model representation and...
Knowledge-based bioterrorism surveillance.
Buckeridge, David L., Graham, Justin, O'Connor, Martin J., Choy, Michael K., Tu, Samson W., Musen, Mark A.
An epidemic resulting from an act of bioterrorism could be catastrophic. However, if an epidemic can be detected and characterized early on, prompt public health intervention may mitigate its impact....
SYNCHRONUS: a reusable software module for temporal integration.
Querying time-stamped data in clinical databases is an essential step in the actuation of many decision-support rules. Since previous methods of temporal data management are not readily transferable...
Use of Protégé-2000 to Encode Clinical Guidelines
Shankar, Ravi D., Tu, Samson W., Musen, Mark A.
A major step in building guideline-based clinical care systems is encoding medical knowledge in guideline documents for interpretation by the computer. Guideline models provide the structure to...
The Chronus II temporal database mediator.
O'Connor, Martin J., Tu, Samson W., Musen, Mark A.
Clinical databases typically contain a significant amount of temporal information. This information is often crucial in medical decision-support systems. Although temporal queries are common in...
OPAL: Toward the Computer-Aided Design of Oncology Advice Systems
Musen, Mark A., Combs, David M., Walton, Joan D., Shortliffe, Edward H., Fagan, Lawrence M.
Tools that allow physicians to enter knowledge directly into computers will greatly facilitate the creation of medical expert systems. OPAL is the knowledge entry program for ONCOCIN, an expert...
Van Der Lei, Johan, Musen, Mark A., Van Der Does, Emiel, Manintveld, Arie J.
This paper describes the evaluation of a critiquing system, HYPERCRITIC, that relies on automated medical records for its data input. The purpose of HYPERCRITIC is to offer comments to general...
Protégé-II: A Suite of Tools for Development of Intelligent Systems from Reusable Components
Musen, Mark A., Eriksson, Henrik, Gennari, John H., Tu, Samson W., Puerta, Angel R.
PROTÉGÉ-II comprises a set of tools that developers use to build intelligent software systems. One tool, called MAÎTRE, allows developers to browse through and edit domain models (ontologies)....
Plan Recognition and Revision in Protocol-Based Care
Automated support for protocol-based care can be viewed as a collaborative effort of two planning agents: the physician and an automated planner. Achieving this collaboration with sufficient...
Intermed: An Internet-based Medical Collaboratory
Oliver, Diane E., Barnes, Michael R., Barnett, G. Octo, Chueh, Henry C., Cimino, James J., Clayton, Paul D., ...
Buckeridge, David L., Okhmatovskaia, Anna, Tu, Samson, O'Connor, Martin, Nyulas, Csongor, Musen, Mark A.
Computational neuroanatomy: ontology-based representation of neural components and connectivity
Rubin, Daniel L, Talos, Ion-Florin, Halle, Michael, Musen, Mark A, Kikinis, Ron
Ontology-driven indexing of public datasets for translational bioinformatics
Shah, Nigam H, Jonquet, Clement, Chiang, Annie P, Butte, Atul J, Chen, Rong, Musen, Mark A
The volume of publicly available genomic scale data is increasing. Genomic datasets in public repositories are annotated with free-text fields describing the pathological state of the studied sample....
Interpretation Errors related to the GO Annotation File Format
Moreira, Dilvan A., Shah, Nigam H., Musen, Mark A.
The Gene Ontology (GO) is the most widely used ontology for creating biomedical annotations. GO annotations are statements associating a biological entity with a GO term. These statements comprise a...
UMLS-Query: A Perl Module for Querying the UMLS
Shah, Nigam H., Musen, Mark A.
The Metathesaurus from the Unified Medical Language System (UMLS) is a widely used ontology resource, which is mostly used in a relational database form for terminology research, mapping and...
Developing Biomedical Ontologies Collaboratively
Noy, Natalya F., Tudorache, Tania, De Coronado, Sherri, Musen, Mark A.
The development of ontologies that define entities and relationships among them has become essential for modern work in biomedicine. Ontologies are becoming so large in their coverage that no single...
Buckeridge, David L., Okhmatovskaia, Anna, Tu, Samson, O’Connor, Martin, Nyulas, Csongor, Musen, Mark A.
Public health surveillance is critical for accurate and timely outbreak detection and effective epidemic control. A wide range of statistical algorithms is used for surveillance, and important...
BioPortal: ontologies and integrated data resources at the click of a mouse
Noy, Natalya F., Shah, Nigam H., Whetzel, Patricia L., Dai, Benjamin, Dorf, Michael, Griffith, Nicholas, ...
Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. BioPortal...
Comparison of concept recognizers for building the Open Biomedical Annotator
Shah, Nigam H, Bhatia, Nipun, Jonquet, Clement, Rubin, Daniel, Chiang, Annie P, Musen, Mark A
The National Center for Biomedical Ontology (NCBO) is developing a system for automated, ontology-based access to online biomedical resources (Shah NH, et al.: Ontology-driven indexing of public...