Abstract
Biomedical Text Mining (BioTM) is providing valuable approaches to the automated curation of scientific literature. However, most efforts have addressed the benchmarking of new algorithms rather than user operational needs. Bridging the gap between BioTM researchers and biologists’ needs is crucial to solve real-world problems and promote further research. We present @Note, a platform for BioTM that aims at the effective translation of the advances between three distinct classes of users: biologists, text miners and software developers. Its main functional contributions are the ability to process abstracts and full-texts; an information retrieval module enabling PubMed search and journal crawling; a pre-processing module with PDF-to-text conversion, tokenisation and stopword removal; a semantic annotation schema; a lexicon-based annotator; a user-friendly annotation view that allows to correct annotations and a Text Mining Module supporting dataset preparation and algorithm evaluation. @Note improves the interoperability, modularity and flexibility when integrating in-home and open-source third-party components. Its component-based architecture allows the rapid development of new applications, emphasizing the principles of transparency and simplicity of use. Although it is still on-going, it has already allowed the development of applications that are currently being used.

Keywords:
Biomedical text mining Named entity recognition Information retrieval Information extraction Literature curation Semantic annotation Component-based software development

Publication Type: Papers

PubMed: 19393341 http://www.ncbi.nlm.nih.gov/pubmed/19393341

DOI: 10.1016/j.jbi.2009.04.002 http://dx.doi.org/10.1016/j.jbi.2009.04.002

RepositoriUM: http://hdl.handle.net/1822/9416 http://hdl.handle.net/1822/9416

Thomson Reuters WOS: 000267846800014 http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&&rft_id=info:ut/000267846800014

ISI JCR Impact Factor: 1,719 in 2010
Computer Science, Interdisciplinary Applications Medical Informatics

SJR (SCImago Journal Rank): 0,148 in 2011
Catalysis Computer Science Applications Computer Science (miscellaneous) Health Informatics

ISO 690

LOURENÇO, A.; CARREIRA, R.; CARNEIRO, S.; MAIA, P.; GLEZ-PEÑA, D.; FDEZ-RIVEROLA, F.; FERREIRA, E.C.; ROCHA, I.; ROCHA, M.. @Note: a workbench for biomedical text mining Journal of Biomedical Informatics : Academic Press. 2009, 42:4 710-720.. ISSN 1532-0480

NP 405

Lourenço, A.; Carreira, R.; Carneiro, S.; Maia, P.; Glez-Peña, D.; Fdez-Riverola, F.; Ferreira, E.C.; Rocha, I.; Rocha, M. - @Note: a workbench for biomedical text mining. Journal of Biomedical Informatics. ISSN 1532-0480. 42:4 (2009) 710-720.

SIEEUM

Lourenço, A.; Carreira, R.; Carneiro, S.; Maia, P.; Glez-Peña, D.; Fdez-Riverola, F.; Ferreira, E.C.; Rocha, I.; Rocha, M. @Note: a workbench for biomedical text mining Journal of Biomedical Informatics 42(4) 710-720, 2009.