BioMedBridges pilot life science data integration using rest web services

The report describes six pilot integration studies which span the BioMedBridges domains and which will act as drivers for future data integration activities:

Pilot 1 (Biosample information integration and discovery) integrated two pivotal resources by transferring data from the BBMRI.eu catalogue to the BioSamples Database (BioSD).  This fulfils the urgent requirement for integrated searches over larger sample collections in support of increasingly complex scientific questions, including query by relevant disease ontologies.  Future developments will ensure that all other biobanks in the BBMRI catalogue, which agree to publish their data, will be seamlessly reflected into the BioSD.

Pilot 2 (Federating biobank queries for translational research) achieves a seamless federated search of two biobank catalogues via new RESTful services and demonstrates the feasibility of a search across two biobank catalogues created for different purposes. Future developments will federate searches across ELIXIR, BBMRI, and EATRIS databases, resulting in the first instance with an integrated search across 6 countries.

Pilot 3 (Leveraging the utility of compound screening functional assays) implemented a new vocabulary for functional assays, focusing on animal models of diabesity, and a RESTful Web service allowing external users to utilize these data in powerful new ways. Future developments will ensure new terms are included into the official public release of BioAssay Ontology, and that tables of the terms are accessible via downloads and the ChEMBL interface.  

Pilot 4 (Sharing protein engineering knowledge) developed a new RESTful interface over PiMS; a laboratory information management system that is widely used in recombinant protein production laboratories. This pilot was motivated by the need to support more complex and flexible queries than are currently possible, and to interpret and analyse data in light of other datasets. Planned integration of PiMS with UniProt will enable scientists using the PiMS system to seamlessly traverse between PiMS data and UniProt data and deliver a major enhancement in the usability of the whole experimental pipeline.

Pilot 5 (Integrating mouse phenotype data for diabetes research) developed new RESTful Web services providing a gene-based integration of the Gene Expression Atlas with systemic phenotyped mice data, focussing on the relevant diseases for WP7 (diabetes and obesity). These developments are the groundwork for further integration, which will be enriched by RDF transformation of the mice data (D4.4/4.6) as well as by the outcomes of the PhenoBridge use case for interspecies data mapping (WP7).

Pilot 6 (Integrating gene and drug information with a clinical trials registry) implemented a clinical trials portal which links publications and information about genes and drugs to data from clinical trials registries.  The pilot addresses the dearth of scientifically relevant annotations on clinical phenotypes and aims to provide more insight into the effect of drugs or genes on patients. In future developments, the Web service will be enhanced with additional information relevant to a clinical trials query.

These services and the underlying data lay the foundations for the integration strategy of BioMedBridges: the developments are extensible in the future and will act as drivers for future WP4 activities and will be built upon in subsequent deliverables. The developments are also sustainable in the context of BioMedBridges and beyond.