Standards and identifiers
The provision and use of common and unambiguous identifiers for bio-molecules such as genes, proteins and bioactive compounds is key to supporting the information flow from basic science, model organism biology, bioinformatics and structural biology through to translational research and clinical care. This issue, which lies at the core of the BioMedBridges mission, is addressed through a wide variety of initiatives and resources, in particular the harmonisation of existing standards and identifiers and the identification of new identifiers where needed, the provision of a registry for users to be able to find suitable standards, and a registry of tools and data resources. In addition, the project has co-organised a series of workshops establishing longer-lasting important collaborations and contributing to the harmonisation of the life science data interoperability landscape.
European e-Infrastructure projects are increasingly turning to Semantic Web technologies to address data integration challenges. This approach is proving to be a solution to some of the emerging challenges in the life sciences. The BioMedBridges semantic web pilot in WP4 Technical integration spans deliverables 4.4, 4.6, 4.7, and 4.8; its goal is to test the suitability of a semantic web approach to the task of integrating research data and to report on our experience of running an RDF-based platform integrating multiple data resources.
Tools and resources
- Interoperability pilots demonstrating software bridges
- REPORT Online Dictionary of common molecular identifiers
- Julie McMurry et al.. (2015) 10 Simple rules for design, provision, and reuse of identifiers for web-based life science data. Zenodo.doi:10.5281/zenodo.31765
- Tools and data services registry
- Ontology tools
- Metadata Models and Mapping Registry
- REPORT Pilot integration using REST web services - part 1, part 2
- WP4 Technical integration