CDISC2RDF

I’m happy to announce that our pre-competitive CDISC2RDF work now is part of the newly launched FDA/PhUSE working group on Emerging Technolgies.

This is the outcome of a discussion with Wayne Kubick, CTO for CDISC, at the recent CDISC Interchange Europe conference. Wayne also appointed Landen Bain as the CDISC liaison for the Semantic Technology project, part of the Emergining Technologies working group.

As described in my previous blog post CDISC2RDF has been presented at the annual computational science symposium (CSS) arranged by the FDA and PhUSE (Pharmaceutical Users Software Exchange). At this event a number of working groups started, One of them a working group for Emerging Technologies that has sponsored a project on Semantic Technology.

This project came out of a proposal from Hoffman-La Roche and the high degree of interest expressed by FDA representatives in semantic web following a presentation from W3C at the FDA CDER meeting on Solutions for Study Data Exchange Standards in November 2012.

The Google code project for CDISC2RDF will remain active as the development repository for the FDA/PhUSE Semantic Technology project. Further details of publishing production versions will be provided on the FDA/PhUSE Semantic Technology page in the near future.

The precompetitive collaboration to publish CDISC standards in RDF, CDISC2RDF, has been described in two conferences recently.

• In the Emerging technologies panel at the FDA/PhUSE Annual Computational Science Symposium (CSS), 18 – 19 March, presented Frederik Malfait, IMOS Consulting working for Hoffmann-La Roche: ”Semantic Models for CDISC based Standards & Metadata Management“.
• In the Conference on Semantics in Healthcare and Life Sciences (CSHALS), 27 Febr – 1 March, did Charlie Mead and Eric Prud’hommeaux from W3C a presentation: “CDISC2RDF: What it is, What it’s done, Where it’s going…“

The first deliverable for the open source CDISC2RDF project is now published.

This contains OWL files for CDISC submission standards: SDTM 1.2, Implementation Guideline (IG) 3.1.2 and Controlled Terminology (CT), plus CT for data capture standards (CDASH) and analysis standards (ADaM). Files are available from https://code.google.com/p/cdisc2rdf. (Direkt link to source.) The best starting point for exploring these files is the Model class in the SDTMIG file. From there you can reach any piece of the model. (Please note that for CDASH and ADaM the CT versions are from 2011.)

We are happy to announce that the NCI EVS team providing the official version of CDISC CT:s have confirmed that they will publish a RDF/OWL version with the April 2013 publication (contact person: Erin Muhlbradt, muhlbradtee@mail.nih.gov). This will build on the CDISC2RDF deliverable and provide a linkable, computable and queryable version as option to the existing pdf, html and odm/xml versions of CDISC terminilogy on NCI EVS website.

The CDISC2RDF team members will continue with OWL representations for CDASH and ADaM data standards for demonstration and discussions together with representatives from CDISC, NCI EVS, TransCelerate BioPharma, FDA, from IMI (EHR4CR, eTRIKS, OpenPHACTS, DDMoRe), and other EU projects (e.g. SALUS, EURECA, Linked2Safety) and also representatives from pharma and CRO companies.

Kudos to Frederik Malfait (IMOS consulting, working for Roche) for a great work. And also to Charlie Mead and Eric Prud’hommeaux (W3C HCLS), Phil Ashworth (Top Quadrant), Sam Hume (Clinical Standard Governance Organisation, AstraZeneca, and CDISC ODM team) and also to Laura Hollink (Vrije Universiteit, Amsterdam) for review and comments.

The open source CDISC2RDF project is sponsored by Jonathan Chainey (Data Standard Office, Roche), Tom Plaster (Integrative Informatics Semantic Framework, AstraZeneca), Frank van Harmelen (Vrije Universiteit, Amsterdam) and Irene Polikoff (TopQuadrant).

Watch this space for upcoming results from the explorative work making standards from CDISC (Clinical Data Interchange Standards Consortium) available using generic standards from W3C (World Wide Web Consortium). That is, generic standards  from the  stack of standards for the Semantic Web (RDF triple based). This has been proposed by early adopters in AstraZeneca and Roche, see Semantic models for CDISC based standard and metadata management.

The results to be described in this blog will show in practice how this can been done using existing free and open source tools. The added value of making existing standards linkable, computable and queryable beyond today’s disconnected PDFs and Excels will also be described.