MOTIVATION The development of experimental methods for genome scale analysis of molecular interaction networks has made possible new approaches to inferring protein function. This paper describes a method of assigning functions based on a probabilistic analysis of graph neighborhoods in a protein-protein interaction network. The method exploits the fact… (More)
Conceptual representation methods play a significant role in facilitating the software process. Recent studies explore and clarify the use of these representations and their impact on progress.
Version 6.0 of the Human Genome Data Base introduces a number of significant improvements over previous releases of GDB. The most important of these are revised data representations for genes and genomic maps and a new curatorial model for the database. GDB 6.0 is the first major genomic database to provide read/write access directly to the scientific… (More)
A maintainer's understanding can go awry when it is based on purely local clues. How can we spell out the intentions behind a piece of code?
The Genome Database (GDB, http://www.gdb.org ) is a public repository of data on human genes, clones, STSs, polymorphisms and maps. GDB entries are highly cross-linked to each other, to literature citations and to entries in other databases, including the sequence databases, OMIM, and the Mouse Genome Database. Mapping data from large genome centers and… (More)
Current explanation-based generalization (EBG) techniques can perform badly when the problem being solved involves recursion. Often an infinite series of learned concepts are generated that correspond to the expansion of recursive solutions over every finite depth. Previous attempts to address the problem, such as Shavlik's generalization-toN EBG method,… (More)
A prerequisite of any attempt to build intelligent tools to assist in the programming process is a representation language for encoding programming knowledge. Languages that have been used for this purpose include the predicate calculus  and various program-schema languages [1,4]. This paper advocates a new candidate which is as expressive as the… (More)
COMBREX (http://combrex.bu.edu) is a project to increase the speed of the functional annotation of new bacterial and archaeal genomes. It consists of a database of functional predictions produced by computational biologists and a mechanism for experimental biochemists to bid for the validation of those predictions. Small grants are available to support… (More)