DOE Human Genome Program Contractor-Grantee Workshop VIII
February 27-March 2, 2000  Santa Fe, NM

89. BiSyCLES: Biological System for Cross-Linked Entries Search

Michael Brudno, Igor Dralyuk, Sylvia Spengler, Manfred Zorn, and Inna Dubchak

Center for Bioinformatics and Computational Genomics, National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

ildubchak@lbl.gov

We have developed a prototype of an Object Oriented search system, which would allow researchers in biological sciences and medicine to combine the information found in diverse databases. The information a researcher needs in most cases is not to be found in any single source, but is divided among several. Further, these sources are often cross-linked, either by the curators of the databases or by the contributing authors. The vast amount of information available to the researcher make manual searches extremely time-consuming, so biologists require the assistance of bioinformatics specialists to process and retrieve the relevant information. The number of projects addressing similar concerns, of which the TAMBIS and the K2 are just two examples, underscores the importance of this problem.

BiSyCLES possesses features, which should be both of immediate use to biomedical researchers and of interest to the bioinformatics community: it is easy-to-use, flexible, and extendable. We built an intuitive user interface, accessible through the World Wide Web. BiSyCLES allows user-defined queries to be executed across all of the recognized databases. Simple query syntax, similar to AltaVistaT, makes our program easy to learn and use. Furthermore, the set of databases is easily extendable because of our use of inheritance and other object-oriented techniques. This prototype works with the two databases most often used in biological research, Genbank and Medline, and it will be further extended in the near future to include others.