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. 2011 Mar 29;12 Suppl 2(Suppl 2):S1.
doi: 10.1186/1471-2105-12-S2-S1.

A linguistic rule-based approach to extract drug-drug interactions from pharmacological documents

Isabel Segura-Bedmar  1 , Paloma Martínez, César de Pablo-Sánchez
Affiliations

A linguistic rule-based approach to extract drug-drug interactions from pharmacological documents

Isabel Segura-Bedmar et al. BMC Bioinformatics. .

Abstract

Background: A drug-drug interaction (DDI) occurs when one drug influences the level or activity of another drug. The increasing volume of the scientific literature overwhelms health care professionals trying to be kept up-to-date with all published studies on DDI.

Methods: This paper describes a hybrid linguistic approach to DDI extraction that combines shallow parsing and syntactic simplification with pattern matching. Appositions and coordinate structures are interpreted based on shallow syntactic parsing provided by the UMLS MetaMap tool (MMTx). Subsequently, complex and compound sentences are broken down into clauses from which simple sentences are generated by a set of simplification rules. A pharmacist defined a set of domain-specific lexical patterns to capture the most common expressions of DDI in texts. These lexical patterns are matched with the generated sentences in order to extract DDIs.

Results: We have performed different experiments to analyze the performance of the different processes. The lexical patterns achieve a reasonable precision (67.30%), but very low recall (14.07%). The inclusion of appositions and coordinate structures helps to improve the recall (25.70%), however, precision is lower (48.69%). The detection of clauses does not improve the performance.

Conclusions: Information Extraction (IE) techniques can provide an interesting way of reducing the time spent by health care professionals on reviewing the literature. Nevertheless, no approach has been carried out to extract DDI from texts. To the best of our knowledge, this work proposes the first integral solution for the automatic extraction of DDI from biomedical texts.

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Figures

Figure 1
Figure 1
Architecture for drug-drug interactions extraction. This figure shows the pipeline architecture of our drug-drug interaction prototype. Firstly, texts are processed by the MMTx program. This tool performs sentence splitting, tokenization, POS-tagging, chunking, and linking of phrases with UMLS concepts. Then, appositions and coordinate structures are interpreted based on shallow syntactic parsing provided by the UMLS MetaMap tool (MMTx). Subsequently, complex and compound sentences are broken down into clauses from which simple sentences are generated by a set of simplification rules. Finally, the lexical patterns are matched with the generated sentences in order to extract DDIs.
See this image and copyright information in PMC

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