A Day in the Life of an RDF Curator Josephine Anne Gough Information Architect Team Lead F. Hoffmann-La Roche Ltd Switzerland

About Work on the Roche Global Data Standards Repository

Who am I ?

•  My name is Amy, Didier, Robin, Ivan

•  I am an Information Architect working in the Roche Data Standards Office

•  I used to work in Data Management / Statistical Programming

•  I found out about RDF and Semantic technology from the GDSR

•  I took a leap of faith and changed my career direction to work in RDF

What is RDF ?

•  RDF is a really cool technology

•  It’s been around for 15 years

•  Resource Description framework means we can describe all of our Data Standards in abstract models and then fill those models with content

•  RDF means we can really describe our standards in a machine readable format

•  RDF means we can uniquely identify things

•  RDF means that we can link pieces of information and even whole models together

•  RDF….is just really cool when you get to know it…you get hooked.

Demo of RDF

•  Short demo of RDF in TopBraid to show linking of information through an RDF network.

What is the GDSR?

•  The GDSR is Roche’s RDF Dataset where all Data Standards are defined

•  GDSR stands for Global Data Standards Repository

•  The GDSR holds CDISC, Roche and other standards such as Questionnaires, Biomarkers, Lab data.

•  It has a browser and web services….but I’ll get onto that later

•  It is accessed by anyone in Roche who needs information or download products about Clinical Data Standards

•  It is available 365/24/7 to the business

•  Our job is basically to look after the content and exports from the GDSR

Roche GDSR

GDSR Menu

Data Collection homepage

SDTM VS Domain

CDISC Controlled Terminology

Labs filtering for Albumin

Asthma Questionnaire

GDSR Search

Today

•  My boss “Cheffe” keeps me really busy

•  But she’s nice

She makes sure that training is part of the job

and boy is there a lot to learn !

TRAINING

Technical Training

SPARQL SPARQL Protocol and RDF Query Language

RDF Resource Description Framework

HTTP REST Representational State Transfer XML Extensible Markup Language

URIs Uniform Resource Identifier

RDFS RDF Schema

XSLT Extensible Stylesheet Language

OWL Web Ontology Language

SKOS Simple Knowledge organisation System

Tools Training

TopBraid RDF development

Graph Validation

oXygen XML editor XSLT development

Graph Adminsitration

GDSR Browser

GDSR

Administering GDSR Search

GDSR UI Models

Content Training…so glad I knew some of these already !

Roche Data Collection

SDTM

Roche extensions to CT Roche EDC

ISO 11179

Roche extensions to SDTM

Questionnaires ePRO

CDISC Controlled Terminology

ADaM

Roche Data Analysis

Biomedial Concepts

Other skills

User Requirements

Documentation UAT

Customer Facing

Validation and Testing

GDSR Overall Architecture

W3C Semantic Standards RDF - OWL - SKOS

ISO 11179 for Metadata Registries

CDISC Foundational Standards

Sponsor Extensions

Protocol Submission DC DT DA �

HTTP REST Application Services

Overwhelming at first!

•  A lot to learn

•  Business needs to be aware of the learning curve

•  Continuous reading/training program

•  Simple steps

•  Progression to more complex parts

•  Each step is absorbing and interesting

•  Keep the training wheel turning

My job broadly splits into three

•  Day to day changes to the GDSR metadata

•  Product development

•  Modeling

CHANGES TO METADATA

Daily content changes - Jira requests

•  A user sends us a request to change metadata via a JIRA ticket system.

•  Today I’ve got a bunch of changes for example:

•  They want to change the CRF label on one of the Medical History Forms

•  The SDTM group have some new annotations

•  There is a new Questionnaire to be uploaded.

Example Jira request to IA team

Which graph do I change ?

Changing the CRF field label for Medical History in TopBraid

Admin Panel to load content into the GDSR

Medical History Form in GDSR browser

Adding new standards: bulk uploads example CRF

PRODUCT DEVELOPMENT

Product development

1.  Web Services give XML

2.  Transform XML into other formats using XSLT

Product development oXygen

Product for SAS programmers: Lab unit conversions in csv

GDSR Export Products in Production Today

•  Operational CRFs in pdf

•  SDTM and Codelists in Excel

•  Lab Analytes in excel and csv

•  Questionnaires in excel and csv

•  RAVE Medidata ALS (EDC build)

•  PK test codes in csv and excel format

Operational CRF

Product downloads from the GDSR

•  Demo of SDTM spreadsheet export if time

GDSR Export Products in progress

•  Non-CRF contracts with standard specifications

•  Conformance checks

•  Data Analysis TLGs

•  Data Analysis VAD specifications

•  eSubmission

eSubmission CRF

MODELING

RDF Modelling

•  Currently Models separated logically by domain but all Linked Data

•  40+ existing models in GDSR

•  New content can require new models and/or extensions

•  Team has learnt from scratch

How to learn to modeling in RDF ?

RDF Apprenticeship

Know the domain

Explore existing models

Make extensions to

existing models.

Experiment designing new

models

Guidance and review from experienced

modelers

Iterate, review with peers, try

out

Modeling: Case history in apprenticeship

1.  Make changes to existing Data Collection models via jira

2.  Create a whole new CRF for a new TA

3.  Learn and explore CDISC SDTM models and code lists

4.  See if same model could be applied to non-CRF data

5.  Do gap analysis of use cases between SDTM and non CRF

6.  Propose any new Classes or Predicates for the model

7.  Present ideas to team – “Live” modeling workshops

8.  Finalise and fill

RDF at the heart of….

RDF gives us the reality (finally) that we can really link together:

•  Standards to Standards (Via Models and Linked Data)

•  Standards to Governance (in an MDR with Admin and Validation)

•  Standards to User Interface (configurable Browser and Search)

•  Standards to Web Services (configurable schema downloads in XML)

•  Standards to exports (word, PDF, Excel etc)

Thanks go to the Roche IA Team:

•  Amy Klopman (SDTM Models, SOA Models)

•  Robin Köger (our XSLT and Web Service goto, Data Analysis Models)

•  Didier Clement (Data Collection Models, non CRF and Biomarker Models)

•  Ivan Robinson (UI Models, Controlled Terminology Models)

Special thanks for our most interesting jobs goes to:

Frederik Malfait creator of the GDSR

Doing now what patients need next