Box 4.5Selected Information Extraction Successes in Biology

Besides the recognition of protein interactions from scientific text, natural language processing has been applied to a broad range of information extraction problems in biology.

Capturing of Specific Relations in Databases.

… We begin with systems that capture specific relations in databases. Hahn et al. (2002) used natural language techniques and nomenclatures of the Unified Medical Language System (UMLS) to learn ontological relations for a medical domain. Baclawski et al. (2000) is a diagrammatic knowledge representation method called keynets. The UMLS ontology was used to build keynets.

Using both domain-independent and domain-specific knowledge, keynets parsed texts and resolved references to build relationships between entities. Humphreys et al. (2000) described two information extraction applications in biology based on templates: EMPathIE extracted from journal articles details of enzyme and metabolic pathways; PASTA extracted the roles of amino acids and active sites in protein molecules. This work illustrated the importance of template matching, and applied the technique to terminology recognition. Rindflesch et al. (2000) described EDGAR, a system that extracted relationships between cancer-related drugs and genes from biomedical literature. EDGAR drew on a stochastic part-of-speech tagger, a syntactic parser able to produce partial parses, a rule-based system, and semantic information from the UMLS. The metathesaurus and lexicon in the knowledge base were used to identify the structure of noun phrases in MEDLINE texts. Thomas et al. (2000) customized an information extraction system called Highlight for the task of gathering data on protein interactions from MEDLINE abstracts. They developed and applied templates to every part of the texts and calculated the confidence for each match. The resulting system could provide a cost-effective means for populating a database of protein interactions.

Information Retrieval and Clustering.

The next papers [in this volume] focus on improving retrieval and clustering in searching large collections. Chang et al. (2001) modified PSI-BLAST to use literature similarity in each iteration of its search. They showed that supplementing sequence similarity with information from biomedical literature search could increase the accuracy of homology search result. Illiopoulos et al. (2001) gave a method for clustering MEDLINE abstracts based on a statistical treatment of terms, together with stemming, a “go-list,” and unsupervised machine learning. Despite the minimal semantic analysis, clusters built here gave a shallow description of the documents and supported concept discovery.

Wilbur (2002) formalized the idea of a “theme” in a set of documents as a subset of the documents and a subset of the indexing terms so that each element of the latter had a high probability of occurring in all elements of the former. An algorithm was given to produce themes and to cluster documents according to these themes.


… text processing has been used for classification. Stapley et al. (2002) used a support vector machine to classify terms derived by standard term weighting techniques to predict the cellular location of proteins from description in abstracts. The accuracy of the classifier on a benchmark of proteins with known cellular locations was better than that of a support vector machine trained on amino acid composition and was comparable to a handcrafted rule-based classifier (Eisenhaber and Bork, 1999).

SOURCE: Reprinted by permission from L. Hirschman, J.C. Park, J. Tsujii, L. Wong, and C.H. Wu, “Accomplishments and Challenges in Literature Data Mining for Biology, Bioinformatics Review 18(12):1553-1561, 2002, available at Copyright 2002 Oxford University Press.

From: 4, Computational Tools

Cover of Catalyzing Inquiry at the Interface of Computing and Biology
Catalyzing Inquiry at the Interface of Computing and Biology.
National Research Council (US) Committee on Frontiers at the Interface of Computing and Biology; Wooley JC, Lin HS, editors.
Washington (DC): National Academies Press (US); 2005.
Copyright © 2005, National Academy of Sciences.

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