The FlyBase Drosophila genetics database and the public interfaces of the Berkeley Drosophila Genome Project (BDGP) and European Drosophila Genome Project (EDGP) are in the process of integrating. At present, the data of these projects are available from independent, but hyperlinked, WWW sites (FlyBase URL, http://flybase. bio.indiana.edu/; BDGP URL,… (More)
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? A maintainer must develop an understanding of a pro-ways people talk about programs. Rich4 has developed a formal-gram if he is to carry out maintenance on it; the more ism for notating plans suitable for synthesis and… (More)
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)
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)