Managing knowledge in neuroscience.

Chiquito J. Crasto, Gordon M. Shepherd

Research output: Contribution to journalReview articlepeer-review

6 Scopus citations


Processing text from scientific literature has become a necessity due to the burgeoning amounts of information that are fast becoming available, stemming from advances in electronic information technology. We created a program, NeuroText ( ), designed specifically to extract information relevant to neuroscience-specific databases, NeuronDB and CellPropDB ( ), housed at the Yale University School of Medicine. NeuroText extracts relevant information from the Neuroscience literature in a two-step process: each step parses text at different levels of granularity. NeuroText uses an expert-mediated knowledge base and combines the techniques of indexing, contextual parsing, semantic and lexical parsing, and supervised and non-supervised learning to extract information. The constrains, metadata elements, and rules for information extraction are stored in the knowledge base. NeuroText was created as a pilot project to process 3 years of publications in Journal of Neuroscience and was subsequently tested for 40,000 PubMed abstracts. We also present here a template to create domain non-specific knowledge base that when linked to a text-processing tool like NeuroText can be used to extract knowledge in other fields of research.

Original languageEnglish
Pages (from-to)3-21
Number of pages19
JournalMethods in molecular biology (Clifton, N.J.)
StatePublished - 2007


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