Biotea: semantics for Pubmed Central

Authors : Alexander Garcia​, Federico Lopez, Leyla Garcia, Olga Giraldo, Victor Bucheli, Michel Dumontier

A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies.

In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology.

We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language.

We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at

URL : Biotea: semantics for Pubmed Central


Semantic representation and enrichment of information retrieval experimental data

Authors : Gianmaria Silvello, Georgeta Bordea, Nicola Ferro, Paul Buitelaar, Toine Bogers

Experimental evaluation carried out in international large-scale campaigns is a fundamental pillar of the scientific and technological advancement of information retrieval (IR) systems.

Such evaluation activities produce a large quantity of scientific and experimental data, which are the foundation for all the subsequent scientific production and development of new systems.

In this work, we discuss how to semantically annotate and interlink this data, with the goal of enhancing their interpretation, sharing, and reuse. We discuss the underlying evaluation workflow and propose a resource description framework model for those workflow parts.

We use expertise retrieval as a case study to demonstrate the benefits of our semantic representation approach. We employ this model as a means for exposing experimental data as linked open data (LOD) on the Web and as a basis for enriching and automatically connecting this data with expertise topics and expert profiles.

In this context, a topic-centric approach for expert search is proposed, addressing the extraction of expertise topics, their semantic grounding with the LOD cloud, and their connection to IR experimental data.

Several methods for expert profiling and expert finding are analysed and evaluated. Our results show that it is possible to construct expert profiles starting from automatically extracted expertise topics and that topic-centric approaches outperform state-of-the-art language modelling approaches for expert finding.