María Poveda-Villalón

Andrea Álvarez Pérez, Ana Iglesias-Molina, Lucía Prieto Santamaría et al.

There is a large number of online documents data sources available nowadays. The lack of structure and the differences between formats are the main difficulties to automatically extract information from them, which also has a negative impact on its use and reuse. In the biomedical domain, the DISNET platform emerged to provide researchers with a resource to obtain information in the scope of human disease networks by means of large-scale heterogeneous sources. Specifically in this domain, it is critical to offer not only the information extracted from different sources, but also the evidence that supports it. This paper proposes EBOCA, an ontology that describes (i) biomedical domain concepts and associations between them, and (ii) evidences supporting these associations; with the objective of providing an schema to improve the publication and description of evidences and biomedical associations in this domain. The ontology has been successfully evaluated to ensure there are no errors, modelling pitfalls and that it meets the previously defined functional requirements. Test data coming from a subset of DISNET and automatic association extractions from texts has been transformed according to the proposed ontology to create a Knowledge Graph that can be used in real scenarios, and which has also been used for the evaluation of the presented ontology.

Sheyla Leyva-Sánchez, Fabian Linde, Meem Arafat Manab et al.

The EU Data Act establishes comprehensive rules governing data access and sharing across business-to-consumer (B2C), business-to-business (B2B), and business-to-government (B2G) contexts. This paper presents a comprehensive ontology for the EU Data Act, enabling reasoning over data sharing agreements through machine-readable representations. The DAOnt ontology reuses elements from three established ontologies, LKIF-Core, ODRL, and DPV, to capture the normative structure of the Data Act. The ontology captures the main concepts and relationships in the Regulation, and it also operationalises three articles to facilitate compliance checking: Article 4(1) (B2C user access rights), Article 8(6) (B2B trade secret exceptions) and Article 19(2)(a) (B2G competitive use prohibitions). The ontology supports compliance checking through SPARQL queries that return obligations, permissions, and prohibitions, allowing organisations to verify whether data-sharing agreements meet the requirements of the EU Data Act and to assess conditions such as FRAND obligations. By representing key legal concepts in RDF, our work helps bridge the gap between the legal provisions of the Data Act and their computational interpretation. The complete ontology, along with example instances and queries, is available online.

Carlos Badenes-Olmedo, David Chaves-Fraga, MarÍa Poveda-VillalÓn et al.

In the absence of sufficient medication for COVID patients due to the increased demand, disused drugs have been employed or the doses of those available were modified by hospital pharmacists. Some evidences for the use of alternative drugs can be found in the existing scientific literature that could assist in such decisions. However, exploiting large corpus of documents in an efficient manner is not easy, since drugs may not appear explicitly related in the texts and could be mentioned under different brand names. Drugs4Covid combines word embedding techniques and semantic web technologies to enable a drug-oriented exploration of large medical literature. Drugs and diseases are identified according to the ATC classification and MeSH categories respectively. More than 60K articles and 2M paragraphs have been processed from the CORD-19 corpus with information of COVID-19, SARS, and other related coronaviruses. An open catalogue of drugs has been created and results are publicly available through a drug browser, a keyword-guided text explorer, and a knowledge graph.

Daniel Garijo, María Poveda-Villalón

With the adoption of Semantic Web technologies, an increasing number of vocabularies and ontologies have been developed in different domains, ranging from Biology to Agronomy or Geosciences. However, many of these ontologies are still difficult to find, access and understand by researchers due to a lack of documentation, URI resolving issues, versioning problems, etc. In this chapter we describe guidelines and best practices for creating accessible, understandable and reusable ontologies on the Web, using standard practices and pointing to existing tools and frameworks developed by the Semantic Web community. We illustrate our guidelines with concrete examples, in order to help researchers implement these practices in their future vocabularies.