LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes

Abstract

A considerable effort has been devoted to retrieve systematically information for genes and proteins as well as relationships between them. Despite the importance of chemical compounds and drugs as a central bio-entity in pharmacological and biological research, only a limited number of freely available chemical text-mining/search engine technologies are currently accessible. Here we present LimTox (Literature Mining for Toxicology), a web-based online biomedical search tool with special focus on adverse hepatobiliary reactions. It integrates a range of text mining, named entity recognition and information extraction components. LimTox relies on machine-learning, rule-based, pattern-based and term lookup strategies. This system processes scientific abstracts, a set of full text articles and medical agency assessment reports. Although the main focus of LimTox is on adverse liver events, it enables also basic searches for other organ level toxicity associations (nephrotoxicity, cardiotoxicity, thyrotoxicity and phospholipidosis). This tool supports specialized search queries for: chemical compounds/drugs, genes (with additional emphasis on key enzymes in drug metabolism, namely P450 cytochromes-CYPs) and biochemical liver markers. The LimTox website is free and open to all users and there is no login requirement. LimTox can be accessed at: http://limtox.bioinfo.cnio.es.

Figure 1.

Simplified schematic flow chart of the LimTox system pipeline. This figure shows the various tasks that are part of the LimTox processing pipeline, from the initial document pre-processing to the detection of chemical entities to the hepatotoxicity text scoring approaches and relation extraction tasks.

Figure 2.

Sildenafil search for CYPs relations using LimTox compound search interface. Example search output using as a query Sildenafil with the user restriction to return only those sentences that co-mention CYPs. The corresponding sentences returned by LimTox can be re-ranked by end users according to the various hepatotoxicity scoring criteria, that is using the SVM sentence classifier scores (SVM), the corresponding confidence scores of the SVM classifiers (conf.), the pattern-based approach (Pattern), the term-lookup method (Term) and the rule-based method (Rule). A simple mouse-over highlight allows the end user to get a short description of each method type, while clicking on the method generated a re-sorted output.