Knowledge Discovery in Medline and Other Databases.

Abstract

All neuroscientists are in the business of discovering knowledge about how the brain works. However, only a portion of time is spent in making new discoveries in the laboratory or clinic. An increasingly large task is to learn what has already been reported in the literature: either to assess an hypothesis and to plan out the best way to test it, or to keep abreast of new research trends, or simply to avoid rediscovering something already known. The days are gone when a person could keep up in neuroscience simply by scanning the pages of a few leading journals, or even by using alerting services such as Current Contents. Investigators not only need to become sophisticated users of Medline, the primary repository of published biomedical literature -- more than that, they need to go beyond simple queries. Think of getting information in Genbank: A simple query will retrieve the nucleotide sequence for “reelin”, but one cannot directly look up the most probable transcription factor binding sites within its promoter region. Rather, specialized algorithms are needed to process the raw data and make plausible inferences (and these still need to be confirmed in the laboratory). Similarly, you can look up lots of findings in the biomedical literature, but to find knowledge that is implicit (not explicitly stated) and to make inferences, specialized approaches are needed. The purpose of this chapter is to guide neuroscientists in using informatics tools for making inferences in Medline as well as other public and private research databases.