Bioinformatics publications

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…

This article provides an overview of the DB-interoperation problem, and offers several solutions. It discusses how links are used in molecular biology DBs, and describes the potential stumbling blocks when…

We describe the design and implementation of visual presentations that closely mimic those found in the biology literature, and employ a frame knowledge representation system (FRS) called HyperTHEO to manage…

The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways.

We propose a network protocol whereby a database administrator can provide information about changes to the identifiers of objects in their database via Internet, to allow other databases to maintain…

We present a methodology for predicting the metabolic pathways of an organism from its genomic sequence.

We have developed a Web server tool, written in Common Lisp, that allows existing graphical user interface applications written using the Common Lisp Interface Manager (CLIM) to hook easily into…

We describe the design and implementation of a storage subsystem that submerges a database management system (DBMS) within a knowledge representation system.

We have developed a Web server tool, written in Common Lisp, that allows any existing graphical user interface application written using the Common Lisp Interface Manager (CLIM) to hook easily…

The Generic Frame Protocol (GFP) is an application program interface for accessing knowledge bases stored in frame knowledge representation systems (FRSs).

Our research investigates the hypothesis that one can employ an existing database management system (DBMS) as a storage subsystem for an FRS, to provide high-speed access to large, shared KBs.