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Methods and tools for the development of computer-interpretable guidelines

Protégé
 logo
Ontology Editor and Knowledge Acquisition System
Open Source ontology development and knowledge acquisition environment
keywords Ontology development, knowledge acquisition, open source, knowledge-based tools, knowledge-based systems development, Semantic Web, description logic, Java, RDF(S), OWL, XML
developed by (Originally) Stanford Medical Informatics.
introduced Protégé: 1989; Protégé2000: 2000.
status Available for use / under continued development. New versions released quite regularly.
support USA: Defense Advanced Research Projects Agency; National Cancer Institute; National Institute of Standards and Technology; National Institutes of Health's National Centers for Biomedical Computing; National Library of Medicine; National Science Foundation.
in use In use in the development of clinical applications (among many other uses).
tools  bullet  Protégé is available for download subject to registration and under an open source licence
description
"Protégé is a free, open source ontology editor and knowledge-base framework."

"The Protégé platform supports two main ways of modeling ontologies via the Protégé-Frames and Protégé-OWL editors. Protégé ontologies can be exported into a variety of formats including RDF(S), OWL, and XML Schema." ...

"Protégé is based on Java, is extensible, and provides a plug-and-play environment that makes it a flexible base for rapid prototyping and application development." ...
description 2
A number of methods for computerising clinical guidelines have been implemented in the Protégé environment. Some of these are illustrated below.

Click on the each of the screens to view full-size images:

View of Protégé being used to author a guideline for managing hypertension. The guideline model being used in this application is Dharma, part of the EON framework.

Guideline for hypertension written in the GLIF format and shown in the Protégé environment.
Protégé screen showing the development of a primary care guideline for cough using the PRODIGY model.
PROforma guideline modelled in Protégé.
plans
 
references

Gennari JH, Musen MA, Fergerson, RW et al. The evolution of Protégé: an environment for knowledge-based systems development. Int J Hum Comput Stud 2003 58(1): 89-123.

[]   [paper - SMI]

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 knowledge-acquisition tools for a few specialized programs in medical planning. From this initial tool, the Protégé system has evolved into a durable, ex-tensible platform for knowledge-based systems development and research. The current version, Protégé-2000, can be run on a variety of platforms, supports customized user-interface extensions, incorporates the Open Knowledge Base Connectivity (OKBC) knowledge model, interacts with standard storage formats such as relational databases, XML, and RDF, and has been used by hundreds of individuals and research groups. In this paper, we follow the evolution of the Protégé project through 3 distinct re-implementations. We describe our overall methodology, our design decisions, and the lessons we have learned over the duration of the project. We believe that our success is one of infra-structure: Protégé is a flexible, well-supported, and robust development environment. Using Protégé, developers and domain experts can easily build effective knowledge-based systems, and researchers can explore ideas in a variety of knowledge-based domains.
Noy NF, Crubezy M, Fergerson RW et al. Protégé-2000: An Open-source Ontology-development and Knowledge-acquisition Environment. Proc AMIA Symp. 2003;:953.

[PubMed]   []

" 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 ontologies. Numerous plugins provide alternative visualization mechanisms, enable management of multiple ontologies, allow the use of interference engines and problem spolvers with Protégé ontologies, and provide other functionality. The Protégé user community has more than 7000 members. "
Shankar RD, Tu SW, Musen MA. A Knowledge-acquisition Wizard to Encode Guidelines. Proc AMIA Symp. 2003;:1007.

[PubMed]   []

" An important step in building guideline-based clinical care systems is encoding guidelines. Protégé-2000, developed in our laboratory, is a general-purpose knowledge-acquisition tool that facilitates domain experts and developers to record, browse and maintain domain knowledge in knowledge bases. In this poster we illustrate a knowledge-acquisition wizard that we built around Protégé-2000. The wizard provides an environment that is more intuitive to domain specialists to enter knowledge, and domain specialists and practitioners to review the knowledge entered. "
R. D. Shankar, S. W. Tu, M. A. Musen. Use of Protégé-2000 to Encode Clinical Guidelines. AMIA Annual Symposium 2002.

[Abstract - SMI] []

" 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 encapsulate guideline knowledge. Developers who are familiar with the guideline model and domain experts who have relevant medical knowledge work as a team to encode guidelines using knowledge acquisition tools. Protégé-2000, developed in our laboratory, is an environment for building knowledge bases. It facilitates knowledge acquisition and maintenance. We have used Protégé-2000 to encode clinical guidelines such as the JNC6 hypertension guidelines and cancer trial protocols. Many other modeling groups are also using it in their work. In this paper, we show that Protégé-2000’s general-purpose knowledge-acquisition framework can provide a rich environment to encode clinical guidelines. "

Abu-Hanna A, Cornet R, de Keizer N et al. Protégé as a Vehicle for Developing Medical Terminological Systems. International Journal of Human-Computer Studies 62(5): 639-663, 2005.

[]   [SMI]

" A medical terminological system (TS) is essentially an ontology consisting of concepts, attributes and relationships pertaining to medical terms. There are many TSs around today, most of which are essentially frame-based. Various efforts have been made to get a better understanding of the requirements and the conceptual and formal structures of TSs. However, the actual implementation of a TS consisted so far of ad hoc approaches starting from scratch and, due to ad hoc semantics of the representation, the interoperability with external applications of the knowledge represented is diminished. In recent years, Protégé has been gaining in popularity as a software environment for the development of knowledge-based systems. It provides an architecture for integrating frame-based ontologies with knowledge acquisition and other applications operating on these ontologies. In its recent version, Protégé provides the ability to specify meta-classes and -slots. This contributes to an explicit separability of knowledge levels and allows for an increased modeling flexibility. These properties, and the fact that it complies with a standard knowledge model, enable Protégé to be an attractive candidate for the implementation of frame-based TSs. This paper investigates how to specify a TS in Protégé and demonstrates this in a specific application in the domain of intensive care. Our approach is characterized by the utilization of a conceptual framework for understanding TSs and mapping its components onto Protégé constructs. This results in specifications of knowledge components for the implementation of terminological systems. The significance of our work stems from the generality of these specifications. This facilitates their reuse, leading to a principled process for the development of terminological systems for a broad spectrum of medical domains. "

N. F. Noy, W. Grosso, & M. A. Musen. Knowledge-Acquisition Interfaces for Domain Experts: An Empirical Evaluation of Protégé-2000. Twelfth International Conference on Software Engineering and Knowledge Engineering (SEKE2000), Chicago, IL, 2000.

[Paper - SMI]

"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 enables experts to perform the knowledge-acquisition and maintenance process. In this paper, we describe a controlled study that we performed to measure both the efficiency and quality of knowledge acquisition by domain experts and to evaluate how well the domain experts can retain their proficiency in using a knowledge-acquisition tool. We adopted the techniques that are used to evaluate usability of traditional software products to evaluating knowledge-acquisition process. Using Protégé-2000 and its domain-specific extensions, the domain experts with no previous experience with knowledge-based systems were able to perform complex knowledge-acquisition tasks efficiently and correctly. Our data show that subject-matter experts were able to use both tools after only 1-2 hours of training, and entered knowledge correctly overall 94% of the time. The custom-developed user interface greatly enhanced the ability of experts to identify known errors in a knowledge base (93% vs. 48% detection). The experts also were able to retain their skills over 1-2 week period of time without using the system. "
M. A. Musen, R. W. Fergerson, W. E. Grosso, N. F. Noy, M. Crubezy, & J. H. Gennari. Component-Based Support for Building Knowledge-Acquisition Systems. Conference on Intelligent Information Processing (IIP 2000) of the International Federation for Information Processing World Computer Congress (WCC 2000), Beijing, 2000.

[Paper]

"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 systems are now generally construed in terms of both domain ontologies and abstract problemsolving methods that operate on knowledge bases defined in terms of those ontologies. There has been less consensus, however, regarding how to optimize the operational components and the user interfaces of tools that assist developers in the construction of knowledge-based systems. For the most part, such lack of consensus is to be expected, given the way in which domain considerations often dominate the way in which knowledge can best be entered, browsed, and updated in any computerbased tool. In our research group at Stanford University, we acknowledge both the central importance and the great variability of domain-specific idioms that can enhance the functionality of knowledgeacquisition tools. Our work seeks specific ways to harness this variability and to allow developers to take advantage of alternative approaches. ... "
N. F. Noy, R. W. Fergerson, & M. A. Musen. The knowledge model of Protégé-2000: Combining interoperability and flexibility. 12th International Conference on Knowledge Engineering and Knowledge Management (EKAW'2000), Juan-les-Pins, France, 2000.

[SMI]   []

" 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 knowledge elements. Knowledge-base developers need to be able to share and reuse knowledge bases that they build. Therefore, interoperability among different knowledge-representation systems is essential. The Open Knowledge-Base Connectivity protocol (OKBC) is a common query and construction interface for frame-based systems that facilitates this interoperability. Protege-2000 is an OKBC-compatible knowledge-base–editing environment developed in our laboratory. Protege-2000 has an easy-to-use and configurable interface. We describe its OKBC-compatible knowledge model that makes the import and export of knowledge bases from and to other knowledge-base servers easy. We discuss how the requirements of being usable and configurable knowledge-acquisition tool affected our decisions in the knowledge-model design. Protege-2000 also has a flexible metaclass architecture which provides configurable templates for new classes in the knowledge base. The use of metaclasses makes Protege-2000 easily extensible and enables its use with other knowledge models. For example, we demonstrate that we can resolve many of the differences between the knowledge models of Protege-2000 and RDF by defining a new metaclass set. Resolving the differences between the knowledge models in declarative way enables easy adaptation of Protege-2000 as an editor for other knowledge-representation systems. "
G. Schreiber, M. Crubezy, & M. A. Musen. A Case Study in Using Protégé-2000 as a Tool for CommonKADS 12th International Conference on Knowledge Engineering and Knowledge Management (EKAW'2000), Juan-les-Pins, France, 200

[SMI]   []

" This article describes a case study in which Protege-2000 was used to build a tool for constructing CommonKADS knowledge models. The case study tries to capitalize on the strong points of both approaches in the tool-support and modeling areas. We specify the CommonKADS knowledge model as an ontology in the Protege specification formalism, and define a number of visualizations for the resulting types. The study shows that this type of usage of Protege-2000 as a metaCASE tool is to a large extent feasible. In particular, the flexible class/instance distinction in Protege is a feature that is needed for undertaking such a metamodeling exercise. The case study revealed a number of problems, such as the representation of rule types. The study also led to a set of new tool requirements, such as extended expressivity of the Protege forms. Finally, this experience shows how the concrete, operational approach of Protege and the highly methodological approach of CommonKADS can be combined successfully to provide the middle-ground tool that reduces the gap between a conceptual model. "
contact
links  bullet  Protégé  bullet  Projects that use Protégé  bullet  Stanford Medical Informatics  bullet  Protégé Ontologies Library  bullet  Protégé-based tool for encoding, viewing, and testing clinical practice guideline applications developed using the SAGE Guideline Model
acknowledgements
Protégé website
page history
Entry on OpenClinical: 2002
Last main update: 01 March 2006
Design - template v0.3: 25 June 2005.

 

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