An ontology-based approach to systems biology literature retrieval and processing

• Autor(es): Lourenço, Anália ; Simões, Alberto ; Almeida, J. J. ; Rocha, Miguel ; Rocha, I. ; Ferreira, E. C.
• Data: 2007
• Identificador Persistente: http://hdl.handle.net/1822/7697
• Origem: RepositóriUM - Universidade do Minho
• Tipo de Documento: Documento de conferência
• Idioma: Inglês

Descrição

This paper details the SysBio Explorer, a Systems Biology Literature Retrieval and Processing Framework, whose aim relies on the automatic inference of regulatory and metabolic networks based on biomedical literature. The SysBio Explorer does not focus on any organism or problem in particular and encompasses a number of processing and analysis techniques. It works over full-text documents, applying Natural Language Processing techniques and using biomedical dictionaries and ontologies together with hand-made rules. Besides biological entity recognition and relation extraction, document classification, relevance assessment and authoring networks are also within its present scope. The framework is described in terms of its design requirements and implementation decisions, exposing current achievements, but also highlighting present obstacles and future work. Experiments over realworld problems concerning the organisms E. coli, S. cerevisiae and H. pylori are used in its validation.