The technology for building large knowledge bases (KBs) is yet to witness a breakthrough so that a KB can be constructed by the assembly of prefabricated knowledge components. Knowledge components include both pieces of domain knowledge (for example, theories of economics or fault diagnosis) and KB tools (for example, editors and theorem provers). Most of the current KB development tools can only manipulate knowledge residing in the knowledge representation system (KRS) for which the tools were originally developed. Open Knowledge Base Connectivity (OKBC) is an application programming interface for accessing KRSs, and was developed to enable the construction of reusable KB tools. OKBC improves upon its predecessor, the Generic Frame Protocol (GFP), in several signi cant ways. OKBC can be used with a much larger range of systems because its knowledge model supports an assertional view of a KRS. OKBC provides an explicit treatment ofentities that are not frames, and it has a much better way of controlling inference and specifying default values. OKBC can be used on practically any platform because it supports network transparency and has implementations for multiple programming languages. In this paper, we discuss technical design issues faced in the development of OKBC, highlight how OKBC improves upon GFP, and report on practical experiences in using it.

Motivations: A number of important bioinformatics computations involve computing with function: executing computational operations whose inputs or outputs are descriptions of the functions of biomolecules. Examples include performing functional queries to sequence and pathway databases, and determining functional equality to evaluate algorithms that predict function from sequence. A prerequisite to computing with function is the existence of an ontology that provides a structured semantic encoding of function. Functional bioinformatics is an emerging subfield of bioinformatics that is concerned with developing ontologies and algorithms for computing with biological function. Results: The article explores the notion of computing with function, and explains the importance of ontologies of function to bioinformatics. The functional ontology developed for the EcoCyc database is presented. This ontology can encode a diverse array of biochemical processes, including enzymatic reactions invo...

The Generic Frame Protocol (GFP) is an application program interface for accessing knowledge bases stored in frame knowledge representation systems (FRSs). GFP provides a uniform model of FRSs based on a common conceptualization of frames, slots, facets, and inheritance. GFP consists of a set of Common Lisp functions that provide a generic interface to underlying FRSs. This interface isolates an application from many of the idiosyncrasies of specific FRS software and enables the development of generic tools (e.g., graphical browsers, frame editors) that operate on many FRSs. To date, GFP has been used as an interface to LOOM, Ontolingua, THEO, and SIPE-2. 1

A new architecture for the World Wide Web is emerging, known as the Semantic Web. In broad terms, it encompasses efforts to populate the Web with content which has formal semantics; this will enable automated agents to reason about Web content, and produce an intelligent response to unforeseen situations. We believe that to build the Semantic Web, the sharing of ontological information is required. This allows agents to reach partial shared understanding and thus interoperate. We are proposing frame-based representation as a suitable paradigm for building ontologies as well as the World Wide Web Consortium's RDF-formalism (and its extensions, such as the DARPA Agent Markup Language) as a manifestation of frame-based representation for the Web. The paper will discuss required and desirable features of ontological languages, giving examples of the possible usage of frame-based representation and ontologies on the Semantic Web. Introduction: Frame-based Representation Systems The term “Semantic Web ” encompasses efforts to build a new WWW architecture to support content with formal semantics; that is, content suitable for automated systems to consume, as opposed to content intended for human consumption. The Semantic Web will allow us to use more automated functions

Abstract. Collaborative knowledge base (KB) authoring environments are critical for the construction of high-performance KBs. Such environments must support rapid construction of KBs by a collaborative e ort of teams of knowledge engineers through reuse of existing knowledge and software components. They should support the manipulation of knowledge by diverse problem-solving engines even if that knowledge is encoded in di erent languages and by di erent researchers. They should support large KBs and provide a scalable and interoperable development infrastructure. In this paper, we present anenvironment that satis es many of these goals. We present an architecture for scalable frame representation systems (FRSs). The Generic Frame Protocol (GFP) provides infrastructure for reuse of software components. It is a procedural interface to frame representation systems that provides a common means of accessing and modifying frame KBs. The Generic KB Editor (Gkb-Editor) provides graphical KB browsing, editing, and comprehension services for large KBs. Scalability of loading and saving time is provided by a storage system (PERK) which submerges a database management system in an FRS. Multi-user access is controlled through a collaboration subsystem that uses a novel optimistic concurrency control algorithm. All the results have been implemented and tested in the development of several real KBs.

Motivation: Acritical element of the computational infrastructure required for functional genomics is a shared language for communicating biological data and knowledge. The Gene Ontology (GO; http://www.geneontology.org) provides a taxonomy of concepts and their attributes for annotating gene products. As GO increases in size, its ongoing construction and maintenance becomes more challenging. In this paper, we assess the applicability of a Knowledge Base Management System (KBMS), Prot eg e-2000, to the maintenance and development of GO.

. Ontologies are becoming increasingly prevalent and important in a wide range of e-commerce applications. E-commerce applications are using ontologies to support parametric searches, enhanced navigation and browsing, interoperable heterogeneous information systems, supplier enablement, configuration management, and transaction discovery. Applications such as information and service discovery and autonomous agents that are built on top of the emerging Semantic Web for the WWW also require extensive use of ontologies. Ontology-enhanced commercial applications, such as these and others require ontology management that is scalable (supporting thousands of simultaneous distributed users), available (running 365x24x7), fast, and reliable. This level of ontology management is necessary not only for the initial development and maintenance of ontologies, but is essential during deployment, when scalability, availability, reliability and performance are absolutely critical. VerticalNet's Ontology Builder and Ontology Server products are specifically designed to provide the ontology management infrastructure needed for e-commerce applications. These tools bring the best ontology and knowledge representation practices together with the best enterprise solutions architecture to provide a robust and scalable ontology management solution. 1

1 The GKB Editor is a generic editor and browser of knowledge bases (KBs) and ontologies --- generic in the sense that it is portable across several frame knowledge representation systems (FRSs). This generality is possible because the GKB Editor performs all KB access operations using a generic application programming interface to FRSs called the Generic Frame Protocol (GFP). To adapt the GKB Editor to a new FRS, we need only to create a GFP implementation for that FRS --- a task that is usually considerably simpler than implementing a complete KB editor. The GKB Editor also contains several relatively advanced features, including three di#erent viewers of KB relationships, incremental browsing of large graphs, KB analysis tools, extensive customizability, complex selection operations, cut-and-paste operations, and both user- and KB-specific profiles. The GKB Editor is in active use in the development of several ontologies and KBs. This paper discusses the design of the GKB Editor fr...

The world wide web (WWW) has become critical for storing and disseminating biological data. It offers an additional opportunity, however, to support distributed computation and sharing of results. Currently, computational analysis tools are often separated from the data in a manner that makes iterative hypothesis testing cumbersome. We hypothesize that the cycle of scientific reasoning (using data to build models, and evaluating models in light of data) can be facilitated with resources that link computations with semantic models of the data.

Ontologies are specifications of the concepts in a given field, and of the relationships among those concepts. The development of ontologies for molecular-biology information and the sharing of those ontologies within the bioinformatics community are central problems in bioinformatics. If the bioinformatics community is to share ontologies effectively, ontologies must be exchanged in a form that uses standardized syntax and semantics. This paper reports on an effort among the authors to evaluate alternative ontology-exchange languages, and to recommend one or more languages for use within the larger 1 bioinformatics community. The study selected a set of candidate languages, and defined a set of capabilities that the ideal ontology-exchange language should satisfy. The study scored the languages according to the degree to which they satisfied each capability. In addition, the authors performed several ontology-exchange experiments with the two languages that received ...