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Title@Note: a workbench for biomedical text mining
Author(s)Lourenço, Anália
Carreira, Rafael
Carneiro, S.
Maia, Paulo
Glez-Peña, Daniel
Fdez-Riverola, Florentino
Ferreira, E. C.
Rocha, I.
Rocha, Miguel
KeywordsBiomedical text mining
Named entity recognition
Information retrieval
Information extraction
Literature curation
Semantic annotation
Component-based software development
Issue dateAug-2009
JournalJournal of Biomedical Informatics
Citation"Journal of Biomedical Informatics". ISSN 1532-0464. 42:4 (Aug. 2009) 710-720.
Abstract(s)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.
AccessOpen access
Appears in Collections:CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series

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