Protégé - Decision Support System



    What is Protégé?:


    Click here to download Protégé 3.1.1
    Click here to run an applet of Protégé showing information for cancer patients.
    Click to see a screen capture of Protégé explaining its windows.

    Protégé was developed by Stanford Medical Informatics at the Stanford University School of Medicine with support from the following agencies:1
    * 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
    With additional support from:
    * DaimlerChrysler
    * iSOCO: Intelligent Software for the Networked Economy

    Currently, Protégé is a free open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies.1 An ontology in general is the hierarchical structuring of knowledge about things by subcategorising them according to their essential/relevant qualities. At its core, Protégé implements a rich set of knowledge-modeling structures and actions that support the creation, visualization, and manipulation of ontologies in various representation formats. Protégé can be customized to provide domain-friendly support for creating knowledge models and entering data. Protégé can also be extended by way of a plug-in architecture and a Java-based Application Programming Interface for building knowledge-based tools and applications.
    An ontology describes the concepts and relationships that are important in a particular domain, providing a vocabulary for that domain as well as a computerized specification of the meaning of terms used in the vocabulary. Ontologies range from taxonomies and classifications, to database schemas. In recent years, ontologies have been adopted in many business and scientific communities as a way to share, reuse and process domain knowledge. Ontologies are now central to many applications such as scientific knowledge portals, information management and integration systems, electronic commerce, and semantic web services.1

    The Protégé platform supports two main ways of modeling ontologies:
    * The Protégé-Frames editor enables users to build and populate ontologies that are frame-based. In this model, an ontology consists of a set of classes organized in a hierarchy to represent a domain's concepts, a set of slots associated to classes to describe their properties and relationships, and a set of instances of those classes.
    * The Protégé-OWL editor enables users to build ontologies for the Semantic Web, in particular in the W3C's Web Ontology Language (OWL). An OWL ontology may include descriptions of classes, properties and their instances. Given such an ontology, the OWL formal semantics specifies how to derive its logical consequences. These entailments may be based on a single document or multiple distributed documents that have been combined using defined OWL mechanisms.

    Building an ontology with Protégé is similar to starting a database project. Once you have decided on the information you want to put into it and get back from it, the next step is to design the formal data structures that will hold your information. Since Protégé describes information in a hierarchical manner that is familiar to anyone who knows an Object-Oriented programming language such as Java, Python, or Ruby, it is a system that is potentially easy to learn. An Protégé ontology consists of a number of classes, each of which can contain sub-classes that inherit the attributes of their parents. Every unique data item is an individual or instance of one or more classes, and every instance has one or more properties. Properties can take either scalar values or references to other instances. An ontology about a given domain can contain every thing about that domain. Protégé is concerned with representing information, making it easy to model real-world data. Protégé is very flexible for modeling information, and allows a knowledge base to grow and change in response to new data and needs. You can change the class definitions, hierarchy relationships, and property assignments on the fly, with Protégé taking care of the resulting changes to the instance data. While these features alone are enough to make it a useful tool, Protégé OWL is a lot more than an object-oriented data editor. Generally Protégé works by allowing you to declare logical constraints on classes and properties, which Protégé can then use to modulate the flow of information into and out of the knowlege base.

    History of Protégé:


    *ONCOCIN was developed in the early 1980's as a clinical decision support system for management of patients enrolled in cancer clinical trials.
    *OPAL was developed in 1985 as a graphical user interface to encode cancer clinical trials for ONCOCIN based on a model of cancer trials.
    *Protégé was created by Mark Musen for his dissertation as a system to define a model of trials for any domain, to generate OPAL for ONCOCIN.
    *Protégé-II implemented in the early 1990's as a knowledge engineering environment to define a model or trials and generate GUI editor for any domain.
    *ProtegeWin this version in the mid 1990's was a Windows version that emphasized usability and external user groups.
    *Protégé-2000 used from late 1990's to 2003 it was the java-based version that emphasized the formal knowledge model and began the development of a plugin architecture.
    *Protégé v2.0 was released Feburary 4, 2004. It supports multi-user development, built-in support for XML, and web support.
    *Protégé 3.1.1 was released August 10, 2005.
    *Protégé 3.2 beta was released March 22, 2006.


    Projects Currently Using Protégé?


    Protégé is very versatile and therefore it is being used for many different types of projects, ranging from medical uses to inventory to wine matching. Click here for a list of projects using Protégé. A few of them are:
    *AnimeManga: For cataloging their fictional series.
    *CellFrame: For expierimental results of cell biology.
    *Computational Modeling of Genes, Proteins, and Brain Functions.
    *GeoLexDe: Used to place geographic entities with their German names.
    *And many more.


    Other Ontology Editors:


    Protégé is an ontology editor, which is an application that helps to create and then manipulate an ontology. Each one has its own special features, but some examples of other ontology editors are3:
    * Java Ontology Editor
    * Ontolingua
    * Chimaera
    * OntoEdit
    * OilEd
    * Protege
    * ScholOnto
    * WebODE
    * KAON





    References:

    1 http://protege.stanford.edu
    2 http://protege.cim3.net/cgi-bin/wiki.pl?
    3 http://en.wikipedia.org/wiki/Ontology_Editors_%28computer_science%29