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Health Pilot

Pilot for Health, demographic change and well-being societal challenge

Health-06op_logo_300dpi

Open PHACTS provides a reliable, large scale source of data relating to biological and medical questions at the early stages of drug discovery idea generation and target validation. Data comes from a variety of well known and trusted sources including ChEBI, ChEMBL, the Gene Ontology and UniProt. The pilot explores the benefits of using the BDE Platform compared with the existing solution which has evolved from the original research project and has become something of a victim of its own success. It further serves to initiate an integrated provenance approach across the seven pilots. This follows on from the major contributions made by the original Open PHACTS project to the domain of provenance. The current Open PHACTS methodology includes steps to track the provenance of data in various ways, most importantly through the VoID headers for each of the datasets used in Open PHACTS and the work on Nanopublications.

BDE components used

Open PHACTS makes extensive use of Linked Data to match and reconcile multiple datasets. The matching is done at ingestion time so that the stored data is ready for querying through a SPARQL endpoint. This is not publicly accessible, rather, a (developer-friendly) RESTful API is provided that handles requests and converts them into SPARQL queries using a set of templates.

The pilot uses the following components of the BDE platform:

  • 4Store triple store.
  • Data connector and transformation modules created by Open PHACTS based on SWAGGER descriptions to select the appropriate transformer.
  • Query endpoint that uses SWAGGER descriptions to rewrite queries dynamically.
  • Scientific Lenses query expansion module if no suitable online service can be found.

Webinars and Presentations

The Open PHACTS foundation, Manchester University and the VU Amsterdam are working on the Open PHACTS docker and its integration with the Big Data Europe infrastructure.

The webinar provides

  • a general overview of the infrastructure and the status of the generic components that are being developed;
  • an outline of the Societal Challenge and the rationale for the pilot a demonstration of the pilot;
  • a look into the future pilot options.

The intended audience are people acquainted with basic development tools like Docker and GitHub with an interest in Big Data and Drug Discovery.

Presenters:

  • Ronald Siebes (VU University Amsterdam)
  • Bryn Williams-Jones (Open PHACTS Foundation)
  • Stian Soiland-Reyes (BioExcel and University of Manchester)
  • Erika Pauwels (TenForce)
  • Aad Versteden (TenForce)

Installation Instructions

Full instructions for installing the OpenPHACTS pilot locally are available on GitHub along with all the Docker images used.