BioDR: semantic indexing networks for biomedical document retrieval

• Main Author: Lourenço, Anália
• Publication Date: 2010
• Other Authors: Carreira, Rafael, Glez-Peña, Daniel, Méndez, José R., Carneiro, S., Rocha, Luís M., Díaz, Fernando, Ferreira, Eugénio C., Rocha, I., Fdez-Riverola, Florentino, Rocha, Miguel
• Format: Article
• Language: eng
• Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
• Download full: https://hdl.handle.net/1822/10213
• topic: Biomedical document retrieval; Document relevance; Enhanced Instance Retrieval Network; Named entity recognition; Semantic indexing document network; Science & Technology

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 in the documents. These terms emerge from a process of Named Entity Recognition that annotates occurrences of biological terms (e.g. genes or proteins) in abstracts or full-texts. The system is based on a learning process that builds an Enhanced Instance Retrieval Network (EIRN) from a set of manually classified documents, regarding their relevance to a given problem. The resulting EIRN implements the semantic indexing of documents and terms, allowing for enhanced navigation and visualization tools, as well as the assessment of relevance for new documents.