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...
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...
Editing Description Logic Ontologies (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...
Editing Description Logic Ontologies (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 Prot eg e 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...
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.
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.
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 PROMPT Suite: Interactive Tools For Ontology Merging And (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...
The Structure of Guideline Recommendations: A Synthesis (2003)
Samson W. Tu, 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...
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)
m-Solving Methods, because they provide reusable reasoning components that participate in the principled construction of knowledge-based applications. 1.1 Reasoning on Domain Knowledge There is a...
Contextualizing Heterogeneous Data for Integration and Inference (2003)
Zachary Pincus, Mark A Musen, Md Phd
this paper, we describe a systematic approach to constructing models' of data and their context. Our approach provides a generic "template" for constructing such models'. For each data source, a...
The Evolution of Protg: An Environment for (2002)
John H. Gennari, Mark A. Musen, Ray W. Fergerson, William E. Grosso, Monica Crubzy, Henrik Eriksson, ...
The Protg project has come a long way since Mark Musen first built the Protg metatool for knowledge-based systems in 1987. The original tool was a small application, aimed at building...
The appep0x-O of a large numb e of ontology tools may le ve ause looking for anappropriate tool ove-(qWx0" andunceOOWP on which tool to choose Thus e aluation and comparison oftheO tools is important...
Evaluating Ontology-Mapping Tools: Requirements and Experience (2002)
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 these tools is...
The knowledge model of Protege-2000: combining interoperability and flexibility (2002)
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...
From Guideline Modeling to Guideline Execution: Defining Guideline-Based (2002)
concepts can be derived from concrete entities through a classification hierarchy (e.g., angina is a kind of cardiovascular disease). The presence or absence of a clinical syndrome can be derived...
Knowledge-Based Temporal Abstraction in Clinical Domains (2002)
We have defined a knowledge-based framework for solving the task of creating abstract, intervalbased concepts from time-stamped clinical datathe knowledge-based temporal-abstraction (KBTA) method....
EON: A Component-Based Approach to Automation of Protocol-Directed Therapy (2002)
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...
Hierarchical Neural Networks for Partial Diagnosis in Medicine (2002)
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...
Medical Quality Assessment by Scoring Adherence to Guideline Intentions (2002)
Aneel Advani, Yuval Shahar, Mark A. Musen
this paper we describe an approach for evaluating and consistently scoring clinician adherence to medical guidelines using the intentions of guideline authors. We present the Quality Indicator...
A Formal Method to Resolve Temporal Mismatches in Clinical Databases (2002)
Amar K. Das, Mark A. Musen, Ph. D
this paper, we present a method to resolve temporal mismatches present in clinical databases. This method is based on a foundational model of time that can formalize various temporal representations....
Reuse For Knowledge-Based Systems and CORBA Components (2002)
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...
From Guideline Modeling to Guideline Execution: Defining Guideline-Based (2002)
concepts can be derived from concrete entities through a classification hierarchy (e.g., angina is a kind of cardiovascular disease). The presence or absence of a clinical syndrome can be derived...
When Knowledge Models Collide (How it Happens and What to Do) (2002)
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...
A Structure of Problem-Solving Methods for Real-time Decision Support: (2002)
Martin Molina, Yuval Shahar, Jose Cuena, Mark A. Musen
The paper presents a case study that compares two of the existing knowledge modeling platforms: PROTG-II and KSM. These two software environments allow a developer to build a knowledge level model...
PROMPT: Algorithm and Tool for Automated Ontology Merging and (2002)
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 WorldWide Web where they provide...
Beyond Data Models for Automated (2002)
Angel R. Puerta, Henrik Eriksson, John H. Gennari, Mark A. Musen
this paper, we present Mecano, a model-based interface development environment that extends the concept of generating interface specifications from data models. Mecano employs a domain model to...
The New World of Mechanisms (2002)
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...
Reuse, CORBA, and Knowledge-Based Systems (2002)
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...
A Typology for Modeling Processes in Clinical Guidelines and Protocols (2002)
Samson W. Tu, Mark A. Musen, Sowerby Centre, Health Informatics Newcastle
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...
A Template-Based Approach Toward Acquisition of Logical Sentences (2002)
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 ontologies...
Monica Crubzy, 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, nor to...
Configuring Online Problem-Solving Resources with the Internet Reasoning Service (2002)
Monica Crubzy, Wenjin Lu, Enrico Motta, Mark A. Musen
Key words: 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 underlying...
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...
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...
Medical Informatics: Searching for Underlying Components (2002)
ss customers by claiming that their products are based on "informatics techniques" and "informatics methods." The recent report of the Institute of Medicine on the problem of medical errors...
Integration of Textual Guideline Documents with Formal (2002)
Ravi D. Shankar, Samson W. Tu, Susana B. Martins, Lawrence M. Fagan, Mary K. Goldstein, Mark A. Musen
Numerous approaches have been proposed to integrate the text of guideline documents with guideline-based care systems. Current approaches range from serving marked up guideline text documents to...
A Knowledge-Based Approach To Temporal Abstraction Of Clinical Data For Disease Surveillance (2001)
Martin J. O'connor, Mark A. Musen, David L. Buckeridge, Natalya Fridman Noy, Yuval Shahar, ...
Introduction Disease surveillance---including surveillance for nascent epidemics that could reflect occult acts of bioterrorism---requires the continuous analysis, interpretation, and feedback of...
Researchers in the ontology-design field have developed the content for ontologies in many domain areas. Recently, ontologies have become increasingly common on the WorldWide Web where they provide...
A Client-Server Framework for Deploying a (2001)
Martin J. O'connor, M. Sc, Ravi D. Shankar, Samson W. Tu, Mary K. Goldstein, ...
This paper presents a framework for designing a decision-support system that addresses these issues. The primary goal of this framework is to allow rapid deployment of complex decision-support...
Ontology Acquisition from On-line Knowledge Sources (2001)
Qi Li, Philip Shilane, Natalya Fridman Noy, Mark A. Musen
this paper, bridge the gap between the disparate large existing knowledge sources with poor semantics and the "Semantic Web" envisioned by the Web creators ---the Web that not only is useful for...
AVirtual Medical Record for Guideline-Based Decision Support (2001)
Peter D. Johnson, Mark A. Musen, Md Phd, Ian Purves, Mb Bs, ...
This paper reports an approach, developed jointly by researchers at Newcastle and Stanford, where guideline models are encoded assuming a uniform virtual electronic medical record and...
Building an Explanation Function for a Hypertension Decision-Support System (2001)
Ravi D. Shankar, Susana B. Martins, Samson W. Tu, Mary K. Goldstein, Mark A. Musen
ATHENA DSS is a decision-support system that provides recommendations for managing hypertension in primary care. ATHENA DSS is built on a component-based architecture called EON. User acceptance of a...
RASTA: A Distributed Temporal Abstraction System to facilitate (2001)
Martin J. O'connor, M. Sc, William E. Grosso, Samson W. Tu, Mark A. Musen, Ph. D
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...
Representation of Temporal Indeterminacy in Clinical Databases (2001)
Martin J. O'connor, M. Sc, Samson W. Tu, Mark A. Musen, Ph. D
This paper describes an approach for representing uncertain temporal information and reasoning with it, and has shown that this approach can be integrated with a temporal abstraction mechanism....
Modeling Data and Knowledge in the EON Guideline Architecture (2000)
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...
Knowledge-Based Temporal Abstraction in Clinical Domains (2000)
We have defined a knowledge-based framework for the creation of abstract, interval-based concepts from time-stamped clinical datathe knowledge-based temporal-abstraction (KBTA) method. The KBTA...
Representation Formalisms and Computational Methods for Modeling Guideline-Based Patient Care (2000)
Survey of Methods Given this task-oriented framework for conceptualizing the assistance that guidelines and protocols provide to their users, we will survey a sample of formalisms and computational...
Ontology-Oriented Design and Programming (2000)
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...
Explanations for a Hypertension Decision-Support System (2000)
Ravi D. Shankar, Samson W. Tu, Mary K. Goldstein, Mark A. Musen, A Hypertension Decisionsupport
ferences made by the EON guideline interpreter such as what to assume when patient data are missing, and (4) the guideline document, which includes the JNC6 hypertension guideline report as well as...
Knowledge Representation and Tool Support for Critiquing (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...
Component-Based Support for Building (2000)
Mark A. Musen, Ray W. Fergerson, William E. Grosso, Natalya F. Noy, Monica Crubzy, John H. Gennari
sumes that, as with Web browsers, users will want to enhance and custom tailor the system's behavior by means of a variety of "plugins. " These plug-ins are modular pieces of program code that add...
A Flexible Approach to Guideline Modeling (2000)
this paper, we analyze the dimensions along which guidelines may vary, and describe a task-oriented approach to guideline modeling that we have been developing in the EON project
Knowledge-Acquisition Interfaces for Domain Experts: (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. Protg-2000 is a tool that enables...
Conceptual and Formal Specifications of Problem-Solving Methods (1999)
Dieter Fensel, Henrik Eriksson, Mark A. Musen
Reusable problem-solving methods as provided by the PROTG-II improve knowledge engineering by allowing developers to design reasoners quickly from pre-existing components. The PROTG-II approach...
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...
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...
Domain Ontologies in Software Engineering: Use of Protégé with the EON Architecture (1999)
this paper, when we combine a domain ontology with an enumeration of the instances intended by that ontology for a particular application, the resulting set of classes and instances is what we call a...
Evaluation of a Temporal-Abstraction Knowledge-Acquisition Tool (1999)
We describe the design and evaluation of a graphical knowledge-acquisition (KA) tool for entering the knowledge required by the RSUM system. RSUM is an implementation of the knowledge-based...
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...
Knowledge Modeling at the Millennium (The Design and Evolution of Protégé-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 Protg was run. The original tool was a small application, aimed mainly at building knowledge-acquisition tools for a few very specialized programs (it...
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...
Evaluation of a Temporal-Abstraction Knowledge-Acquisition Tool (1999)
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...
Tool Support for Authoring Eligibility Criteria for Cancer Trials (1999)
Daniel L. Rubin, John H. Gennari, Sandra 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...
Knowledge Modeling at the Millennium (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 Protg was run. The original tool was a small application, aimed mainly at building knowledge-acquisition tools for a few very specialized programs (it...
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...
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...
Design and Use of Clinical Ontologies: (1999)
ng specific medical information. It is not simply because of the successes of health telematics, but rather because of the infusion of the Internet and the World-Wide Web into the culture at large,...
VM-in-Protg: A Study of Software Reuse (1998)
Protg 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 Protg is to...
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...
D. Scott Smith, John Y. Park, Mark A. Musen, Ph. D
this paper, we take a formal approach to modeling the planning task for antiretroviral therapy. We follow a prescribed series of steps, to abstract the general form and properties of the task....
Modern Architectures for Intelligent Systems: Reusable Ontologies and Problem-Solving Methods (1998)
This paper will highlight how intelligent systems for diverse tasks can be efficiently automated using these kinds of building blocks. The creation of domain ontologies and problem-solving methods is...