A semantic-based workflow for biomedical literature annotation

Pedro Sernadela, José Luís Oliveira
2017 Database: The Journal of Biological Databases and Curation  
Citation details: Sernadela,P and Oliveira,J.L. A semantic-based workflow for biomedical literature annotation. Abstract Computational annotation of textual information has taken on an important role in knowledge extraction from the biomedical literature, since most of the relevant information from scientific findings is still maintained in text format. In this endeavour, annotation tools can assist in the identification of biomedical concepts and their relationships, providing faster reading
more » ... d curation processes, with reduced costs. However, the separate usage of distinct annotation systems results in highly heterogeneous data, as it is difficult to efficiently combine and exchange this valuable asset. Moreover, despite the existence of several annotation formats, there is no unified way to integrate miscellaneous annotation outcomes into a reusable, sharable and searchable structure. Taking up this challenge, we present a modular architecture for textual information integration using semantic web features and services. The solution described allows the migration of curation data into a common model, providing a suitable transition process in which multiple annotation data can be integrated and enriched, with the possibility of being shared, compared and reused across semantic knowledge bases.
doi:10.1093/database/bax088 pmid:29220478 pmcid:PMC5691355 fatcat:tbt65j3vwfbefhhhpdx6lvapu4