Research Article: Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature

Date Published: November 21, 2004

Publisher: Public Library of Science

Author(s): Hans-Michael Müller, Eimear E Kenny, Paul W Sternberg

Abstract: We have developed Textpresso, a new text-mining system for scientific literature whose capabilities go far beyond those of a simple keyword search engine. Textpresso’s two major elements are a collection of the full text of scientific articles split into individual sentences, and the implementation of categories of terms for which a database of articles and individual sentences can be searched. The categories are classes of biological concepts (e.g., gene, allele, cell or cell group, phenotype, etc.) and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., biological process, etc.). Together they form a catalog of types of objects and concepts called an ontology. After this ontology is populated with terms, the whole corpus of articles and abstracts is marked up to identify terms of these categories. The current ontology comprises 33 categories of terms. A search engine enables the user to search for one or a combination of these tags and/or keywords within a sentence or document, and as the ontology allows word meaning to be queried, it is possible to formulate semantic queries. Full text access increases recall of biological data types from 45% to 95%. Extraction of particular biological facts, such as gene-gene interactions, can be accelerated significantly by ontologies, with Textpresso automatically performing nearly as well as expert curators to identify sentences; in searches for two uniquely named genes and an interaction term, the ontology confers a 3-fold increase of search efficiency. Textpresso currently focuses on Caenorhabditis elegans literature, with 3,800 full text articles and 16,000 abstracts. The lexicon of the ontology contains 14,500 entries, each of which includes all versions of a specific word or phrase, and it includes all categories of the Gene Ontology database. Textpresso is a useful curation tool, as well as search engine for researchers, and can readily be extended to other organism-specific corpora of text. Textpresso can be accessed at or via WormBase at

Partial Text: Text-mining tools have become indispensable for the biomedical sciences. The increasing wealth of literature in biology and medicine makes it difficult for the researcher to keep up to date with ongoing research. This problem is worsened by the fact that researchers in the biomedical sciences are turning their attention from small-scale projects involving only a few genes or proteins to large-scale projects including genome-wide analyses, making it necessary to capture extended biological networks from literature. Most information of biological discovery is stored in descriptive, full text. Distilling this information from scientific papers manually is expensive and slow, if the full text is available to the researcher at all. We therefore wanted to develop a useful text-mining tool for full-text articles that allows an individual biologist to locate efficiently information of interest.

We have developed a text processing system, Textpresso, that splits papers into sentences, and sentences into words or phrases. Each word or phrase is then labeled using the eXtensible Markup Language (XML) according to the lexicon of our ontology (described below). We then index all sentences with respect to labels and words to allow a rapid search for sentences that have a desired label and/or keyword. The labels fall into 33 categories that comprise the Textpresso ontology. We built a database of 3,800 C. elegans papers, bibliographic information from WormBase, abstracts of C. elegans meetings and the Worm Breeder’s Gazette, and some additional links and WormBase entities. See Materials and Methods for details on the database preparation.



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