Going Translational with Linked Data

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Project Overview

This project builds on previous successful modeling of the SDMT domains DM, VS, EX, TS, and AE and conversion instance data to Linked Data as Resource Description Framework (RDF). The original follow-on project was approved to extend the concept to additional domains. At the CSS 2019 conference, the team recognised that the project goals should change to focus on smaller, modular projects that can be released over time to demonstrate incremental value in a shorter time frame (instead of merely extending to additional SDTM domains). The proposed new focus increases cooperation with the Food and Drug Administration and the Maintenance and Support Services Organisation (MSSO, for MedDRA).

This new proposal includes (but is not limited to) the following sub-projects:

a) MedDRA as RDF Development and release of R and SAS scripts that convert MedDRA ASCII files to RDF. Due to licensing limitations, only the MedDRA RDF instance data that supports a subset of the test project (CDISCPILOT01) will be released online. The conversion scripts will be available publicly from a dedicated Github repository that will include documentation and usage instructions. The project team has the interest of and permission from the MSSO for this subject.

b) Automating Conformance Checks for DM and TS domains in SEND and SDTM The team will update existing SDTM ontology for the TS and DM domains to accommodate SEND. SPIN, SHEX, and SHACL will be evaluated for their potential to model conformance checks for both SEND and SDTM, working in cooperation with the Centre for Drug Evaluation and Research, with Dr. Lilliam Rosario as FDA sponsor. The project will evaluate the efficiency of replacing manual conformance checks using an automated Linked Data approach, with potential efficiencies for both FDA and industry.

c) Unique Identifiers for Pharma A sub-group was formed after the PHUSE EUConnect18 to further develop the concept of "Study URI" presented by Kersin Forsberg and Daniel Goude from AstraZeneca. The group will develop methods and guidance for unique, universal, persistent identifiers for the pharmaceutical industry based on the RDF URI concept. Work is already underway (https://github.com/phuse-org/LinkedDataEducation/blob/master/doc/URIsForPharma.md) and a poster is planned for EUConnect19.

d) Study Ontology & Data Conversion Work on Study ontology development may continue as time allows, with primary focus on deliverables for sub-projects a) , b) and c).

Project Leads

Tim Williams Co-lead UCB Biosciences tim.williams@phuse.eu
Armando Oliva Co-lead Semantica LLC aoliva@semanticallc.com

Project Members

Abdul Kadir Member Industry
Amit Jain Member GSK
Andy Iverson Member Medtronic
Dave Iberson-Hurst Member Assero
Erick Antezana Member Bayer
Gaspare Mellino Member Roche
Giuseppe Di Monaco Member UCB
Hanming Tu Member Frontagelab
Ilaria Maresi Member TheHyve
Iraj Mohebalian Member Bayer
Jeremy Teoh Member Industry
Johannes Ulander Member S-cubed
Katja Glass Member Industry
Kerstin Forsberg Member Astrazeneca
Kurt Dauth Member Boehringer-Ingelheim
Lutz Weber Member Ontochem
Mike Hamidi Member CDISC
Marc Andersen Member StatGroup
Matthew Travell Member GSK
Naouel Karam Member Fraunhofer
Nolan Nichols Member Gene
Rashedul Hasan Member FDA
Siddharth Arthi Member Zifornd
Suhas Sanjee Member Merck.com
Sujit Khune Member Novonordisk
Susheel Arkala Member MMSHoldings
Todor Primov Member Ontotext.com
Tom Van der Spiegel Member JNJ
Vishnu Kollisetti Member PPDI

Project Updates

Provide project updates in this section.
Date: Description of Update

Objectives and Timelines

Objective Timeline
Project Initiation/Restart February 2019/July 2019
MedDRA as RDF PhUSE CSS 2020
Automating Conformance Checks PHUSE CSS 2020
Unique IDs for Pharma PhUSE CSS 2020
Conclusion PHUSE CSS 2020

Project Activities

This section can document project activities or serve as a jumping off point to other pages in the project.

Meeting Minutes


Archived Content