Managing Knowledge in Neuroscience

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 (http://senselab.med.yale.edu/textmine/neurotext.pl ), designed specifically to extract information relevant to neuroscience-specific databases, NeuronDB and CellPropDB (http://senselab.med.yale.edu/senselab/ ), 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 knowledgebase 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 knowledgebase. 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 knowledgebase that when linked to a text-processing tool like NeuroText can be used to extract knowledge in other fields of research.