Towards standardisation of named-entity annotations in the life science literature

The main aim of this proposal is to revisit and in the best case re-launch an initiative that would provide harmonised ways for representing and tagging named entities in the life science literature. We are proposing to establish common document formats that facilitate the exchange of annotation results contained in the literature as a complementary approach to the development of interoperable tools. We want to work towards (a) recommendations for a common syntax to embody entity mentions in publishers' document formats (e.g., into PMC), and (b) provision of a common way to reference semantic types. The main stakeholders (text mining users, researchers, service providers and publishers) would need to build an infrastructure that integrates literature resources with entity databases. The main benefits result from better integration of literature resources and text-mining results with data from other biomedical research groups and from the identification of the next generation challenges for novel text mining research.