Textpresso for oro-pharyngeal anatomy: a system for searching the full text of anatomy literatures

Abstract

Biological databases are a useful resource for parlaying existing data into new experimental hypotheses. Populating such databases with information from the published literature, however, can be labor intensive and thus is aided greatly by text mining tools capable of retrieving key facts from full text. The Textpresso information retrieval system (http://www.textpresso.org) is used by several Model Organism Database (MOD) communities to assist in curation [Müller HM, Kenny EE, Sternberg PW. 2004. PLoS Biol. Nov;2(11):e309; Van Auken KM, Fey P, Berardini TZ, et al. 2012. Database (Oxford). Nov 17;2012:bas040.] Textpresso searches the full text of literature using keywords and/or categories, groups of semantically related words, to identify sentences within a paper that describe specific aspects of biology. Using the anatomy ontology of oro-pharyngeal structures developed in the FEED project [Druzinsky R, et al., in prep ], we are constructing a Textpresso site to aid in curation of the oro-pharyngeal muscle literature. At this time, we have amassed a database of over 2000 searchable references. We will present a demonstration of Textpresso for Oro-Pharyngeal Anatomy and show how it can be used to construct meaningful queries on the full text of the literature.

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