Pauline Kra

GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data

The immense growth in the volume of research literature and experimental data in the field of molecular biology calls for efficient automatic methods to capture and store information. In recent years, several groups have worked on specific problems in this area, such as automated selection of articles pertinent to molecular biology, or automated extraction of information using natural-language processing, information visualization, and generation of specialized knowledge bases for molecular biology. GeneWays is an integrated system that combines several such subtasks. It analyzes interactions between molecular substances, drawing on multiple sources of information to infer a consensus view of molecular networks. GeneWays is designed as an open platform, allowing researchers to query, review, and critique stored information.

Automated Terminology Networks for the Integration of Heterogeneous Databases

As cross-disciplinary research escalates, researchers are facing the challenge of linking disparate biomedical databases that have been developed without common indexes. Manually indexing these large-scale databases is laborious and often impractical. Solutions involving mediating terminologies have been proposed, but coordination of terms from the databases of interest to these mediating terminologies is also laborious, and regular synchronization between indexes is an additional problem. In this study we describe a novel method of linking heterogeneous databases using terminology networks constructed with automated mapping methods. Linkage was established between two disparate biomedical databases (SNOMED-CT and HDG), using two relevant intermediating databases (UMLS and OMIM). One gold standard of 514 distinct matches is used as proof-of-principle. In conclusion, as hypothesized, 1) Manually curated pathways provide high precision, but offer low recall, 2) the automated terminology pathways can significantly increase recall at acceptable precision. Taken together, our conclusion may suggest the combined manual and automated terminology networks could offer recall and precision in an incremental manner.