Textpresso for neuroscience: searching the full text of thousands of neuroscience research papers

Abstract

Textpresso is a text-mining system for scientific literature. Its two major features are access to the full text of research papers and the development and use of categories of biological concepts as well as categories that describe or relate objects. A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. Here we describe Textpresso for Neuroscience, part of the core Neuroscience Information Framework (NIF). The Textpresso site currently consists of 67,500 full text papers and 131,300 abstracts. We show that using categories in literature can make a pure keyword query more refined and meaningful. We also show how semantic queries can be formulated with categories only. We explain the build and content of the database and describe the main features of the web pages and the advanced search options. We also give detailed illustrations of the web service developed to provide programmatic access to Textpresso. This web service is used by the NIF interface to access Textpresso. The standalone website of Textpresso for Neuroscience can be accessed at http://www.textpresso.org/neuroscience/.

Fig. 1

Example of complex query without any keywords: What TRP channels are associated with particular neural cell types in specific brain areas? No keywords are used but three categories. 18 sentences are identified in 8 papers from 67,500 papers. Note that this query returns more hits than when replacing the category ‘TRP channel’ with the keyword ‘TRPC1’ as the category comprises more terms than just one keyword

Fig. 2

Example of a more complex query: Are any drugs of abuse other than nicotine associated with nicotinic receptors? Keywords nicotinic receptor but excluding nicotine, and category Prescription Drugs of Abuse returns 150 matches in 79 documents from 67,500 papers

Fig. 3

Example search results. Bibliography and matching sentences are displayed

Fig. 4

Advanced search options are available to refine queries

Fig. 5

The web service ‘search’ is available for automated queries

Fig. 6

After an automated search has been performed, bibliographies and matching sentences can be retrieved with the web service ‘retrieve’