Beyond interoperability-tracking and managing the results of computational applications

Molecular biology applications, like those of other scientific domains, need to store and view large amounts of specialized quantitative information. With the advent of high speed sequencing technology and considerable funding to "map" the genomes of key biological organisms, public databases such as GenBank, PDB, EMBL, JIPID, and SwissProt make millions of genetic sequences available to molecular biologists, and industry and university laboratories maintain large databases. The need for common interfaces and query languages to exploit these heterogeneous databases is well documented, and several such systems now exist or are under development. The authors' own work on database and program interoperability in this domain has shown, however, that providing an interface is but a first step towards making these databases fully useful. The system they are developing integrates and trades inputs and results from numerous computational biology programs. It helps researchers organize result items from sequence comparisons into "clusters" that can be marked, named, annotated, and manipulated. An alpha version is implemented in Smalltalk. The paper describes the scientific problem the system aims to solve, as well as current barriers to development and research opportunities suggested by those barriers. They present its conceptual data model, the current prototype, and future implementation plans.