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Evaluation of linear classifiers on articles containing pharmacokinetic evidenc...
Kolchinsky, A.; Lourenço, Anália; Li, L.; Rocha, Luís M.Background. Drug-drug interaction (DDI) is a major cause of morbidity and mortality. DDI research includes the study of different aspects of drug interactions, from in vitro pharmacology, which deals with drug interaction mechanisms, to pharmaco-epidemiology, which investigates the effects of DDI on drug efficacy and adverse drug reactions. Biomedical literature mining can aid both kinds of approaches by extrac...
A linear classifier based on entity recognition tools and a statistical approac...
Lourenço, Anália; Conover, M.; Wong, A.; Nematzadeh, A.; Pan, F.; Shatkay, Hagit; Rocha, Luís M.Background We participated, as Team 81, in the Article Classification and the Interaction Method subtasks (ACT and IMT, respectively) of the Protein-Protein Interaction task of the BioCreative III Challenge. For the ACT, we pursued an extensive testing of available Named Entity Recognition and dictionary tools, and used the most promising ones to extend our Variable Trigonometric Threshold linear classifier. O...
BioDR : semantic indexing networks for biomedical document retrieval
Lourenço, Anália; Carreira, Rafael; Glez-Peña, Daniel; Méndez, José R.; Carneiro, S.; Rocha, Luís M.; Díaz, Fernando; Ferreira, E. C.; Rocha, I.In Biomedical research, retrieving documents that match an interesting query is a task performed quite frequently. Typically, the set of obtained results is extensive containing many non-interesting documents and consists in a flat list, i.e., not organized or indexed in any way. This work proposes BioDR, a novel approach that allows the semantic indexing of the results of a query, by identifying relevant terms...
Biomedical text mining applied to document retrieval and semantic indexing
Lourenço, Anália; Carneiro, S.; Ferreira, E. C.; Carreira, Rafael; Rocha, Luís M.; Peña, Daniel Glez; Méndez, José R.; Riverola, Florentino FdezIn Biomedical research, the ability to retrieve the adequate information from the ever growing literature is an extremely important asset. This work provides an enhanced and general purpose approach to the process of document retrieval that enables the filtering of PubMed query results. The system is based on semantic indexing providing, for each set of retrieved documents, a network that links documents and re...
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