The protégé project: a look back and a look forward

Few funded research projects in computer science go on for decades. It’s even questionable whether any project should be sustained that long. Nevertheless, the Protege project at Stanford University began in the 1980s and is still going strong, helping developers to construct reusable ontologies and to build knowledge-based systems. The recognition of our work at the International Semantic Web Conference in October 2014 with the “Ten Years” Award was a great honor. The award has provided an opportunity f o r reflection—both on the Protege project itself and on the need for computational infrastructure in the AI community. Protege has become the most widely used software for building and maintaining ontologies. It is by no means the only solution, and there are known problems with Protege, but we appreciate that the system is extremely popular. Although his study is now a bit dated, Cardoso (2007) surveyed the Semantic Web community and found that two-thirds of his respondents used Protege. To date, more than 250,000 people have registered to use the software. Many Fortune 500 companies use Protege to build their ontologies. Important government projects, such as the development of the National Cancer Institute Thesaurus (Noy et al., 2008; Figure 1) and the World Health Organization’s International Classification of Diseases (ICD-11; Tudorache et al., 2010) depend on the software. Figure 1 The Protege 5 Desktop System. The figure shows the most recent version of the Protege system used to edit the National Cancer Institute Thesaurus. In the Figure, the user has selected the class Antigen Gene. The visualization ... Protege currently exists in a variety of frameworks. A desktop system (Protege 5) supports many advanced features to enable the construction and management of OWL ontologies (see Figure 1). A Web-based system (WebProtege) offers distributed access over the Internet using any Web browser and, by design, is much simpler to use for many ontology-engineering tasks (Figure 2). The Web-based version has become extremely popular, and it recently exceeded the desktop-client in its degree of usage. It is extremely handy to be able to point a Web browser to an appropriate server and to begin editing. Like a Google doc, a WebProtege ontology can be easily shared with a distributed group of users who can engage in collaborative authoring activities from wherever they happen to be logged in. The development environment used by the World Health Organization to manage ICD-11 is based on WebProtege (Tudorache et al., 2010). Figure 2 WebProtege. The Web-based version of Protege offers users and their collaborators the opportunity to share and edit ontologies online, much like a Google doc. Here we see the Ontology for Parasite Lifecycle (OPL), an ontology ... Older versions of the Protege desktop system have included support for editing ontologies represented in a frame language (namely, in the OKBC framework developed by the DARPA Knowledge Sharing Initiative in the 1990s; Neches et al., 1991). Comparable functionality has not yet been migrated to current versions of Protege, however. All versions of Protege may be downloaded from the project’s Web site (http://protege.stanford.edu). They are available under an open-source license. The paper for which the Protege team won the “Ten Years” Award (Knublauch et al., 2004) describes the first Protege system to support the World Wide Web Consortium’s recommended Web Ontology Language (OWL). We had been tracking the emerging OWL specification, and Holger Knublauch, then a post-doctoral fellow in our laboratory, worked with the rest of the team to extend Protege to create what was, at the time, the only ontology-development platform that could accommodate nearly the complete OWL specification. Protege’s support for OWL has been enhanced over the years, particularly through a very successful collaboration with Alan Rector’s CO-ODE project at the University of Manchester, and recent versions of Protege fully support the latest OWL 2.0 specification. When people think of Protege, they think of an editor for ontologies, and they think of OWL. Protege did not start out this way, however. Gennari et al. (2003) traced the history of the first 15 years of the Protege project, documenting the many shifts in perspective as Protege progressed from a student project for a Ph.D. dissertation that focused on problems of building knowledge-based systems (Musen, 1989) to a major open-source platform supported by a huge community of diverse users (Musen, 2005).