Experiences from CancerGrid and caBIG

1. what are the real issues in international interoperability? Peter Maccallum CancerGrid Project Manager Department of Oncology University of Cambridge Experiences from CancerGrid and caBIG

2. Overview • Some National Grids for Cancer Research • UK CancerGrid • US caBIG • Technical interoperability • Security infrastructure • Data integration infrastructure • Semantic interoperability • Shared terminologies and standards • Shared models

3. CancerGrid • CancerGrid is a consortium of leading researchers from the UK cancer and computing science communities developing open standards for clinical cancer informatics. Department of Oncology, University of Cambridge Weatherall Institute of Molecular Medicine, University of Oxford Division of Cancer Studies, University of Birmingham Department of Oncology, University College London Centre for Cancer Research and Cell Biology, Queen’s University Belfast Oxford University Computing Laboratory Cambridge e-Science Centre Midlands e-Science Centre Belfast e-Science Centre

4. NEAT tAnGo Eligibility Criteria (i)Operable breast cancer (ii)Clear resection margins (iii)Any nodal status (iv)Any hormone receptor status Eligibility Criteria (i)Early stage breast cancer (ii)Tumour completely excised (iii)Certain indication for chemotherapy SURGERY SURGERY Randomisation for Sequence ArmA1 4xEC 4x PTx ArmA2 4x Tx 4xEC ArmB1 4xEC 4x PTxG ArmB2 PTxG 4x  4x EC Randomisation Randomisation Arm A 4 cycles x EC 4x Paclitaxel (PTx) Arm B 4 x EC  4x PTx + Gemcitabine(G) SURGERY Phase III breast cancer trials Neo-tAnGo Eligibility Criteria (i)Histologically confirmed invasive breast cancer (ii)T2 tumour and above (iii)Diameter >20mm Arm A CMF Classical x 6 cycles Arm B E x 4 cycles / CMF x 4 cycles SAMPLE OF BLOOD TO BE COLLECTED ON ONE OCCASION ONLY FROM THE ABOVE TRIALS AT FOLLOW-UP OR DURING CHEMOTHERAPY SNP PROFILE GENOTYPE ANALYSIS CORRELATION WITH CLINICAL TOXICITIES AND OUTCOME

5. caBIG • cancer Biomedical Informatics Grid • An initiative of the NCI in the USA, linking hundreds of cancer reserarchers with a shared technology stack. • Key technologies • The Enterprise Vocabulary Service (EVS) • The Cancer Data Standards Repository (caDSR) • Grid technology (caGRID) • Biomedical object models (caBIO) • Clinical trials object models (BRIDG)

6. Certificates issued by caBIG CA. No recognition of other CAs (e.g. UK eScience). Overall access to the Grid is under US control. Fine-grained access control must be added by providers. US UK caBIG security CancerGrid security Technical issues

7. A peer-to-peer trust network. Role-based access control to provide access to some shared resources. Clear, legally enforced agreements on role membership criteria US UK caBIG security CancerGrid security Trust Technical solutions

8. Current status • Adding UK nodes to caGRID • caGRID 0.5 is based on GT 3 • We’ve added 4 nodes to the caGRID 0.5 network • The nodes trust each other, and share services with the US • Future technical developments • caGRID 1.0 will allow us to register web services directly via GT4

9. Data sources are wrapped (using hibernate). Resources conform to caBIO models. Models are registered in the caBIG data standards repository. Data standards reference NCI vocabularies. Data integration issues caBIG Vocabulary caBIG Data Standards caBIG Models US UK

10. Data sources conform to models. Resources conform to standard models where available. Models are registered in local data standards repositories. Data standards reference validated vocabularies Knowldge Standards Models Data integration solutions Vocabulary Vocabulary Data Standards Data Standards Models Models US UK

11. Current status • Working with caBIG • We currently use the caDSR as our data standards repository via web services • We’ve evaluated some caBIG software and models directly (caTissue, caArray) • Building a compatible infrastructure • We’re deploying vocabulary services based on caBIG technology (LexGrid from the Mayo clinic) • We’ve built a lightweight, caDSR compatible data standards repository

12. …towards interoperable Grids? Knowldge Knowldge caBIG Semantics CancerGrid Semantics Standards Standards Models Models US UK caBIG Technology CancerGrid Technology Trust

13. Overview • Linking Software Grids • Linking with caGRID is technically feasible • True interoperability will depend on shared security infrastructures • Linking Semantic Grids • Linking models and messages is where the real long term interoperability will be found • If we can prove the benefits, many more cancer research networks could be linked through shared models.

14. Acknowledgements • Technical interoperability • PV Jithesh (QUB), Ioannis Daskalopoulos (Cambridge) • Oxford eSC, Cambridge eSC, Midlands eSC • George Komatsoulis (NCICB) • Semantic interoperability • Steve Harris (Oxford), Igor Toujilov (UCL), Maria Lin (Birmingham), Andrew Tsui (Oxford) • Harold Solbrig (Mayo), James Buntrock (Mayo)

15. Funding The Medical Research Council provides support through grant G0300648 (2005/06 to 2008/06) for 12 full time staff, 1 graduate student, travel and equipment. The EPSRC provides support through grant EP/C531272/1 (2005/05 to 2008/05) for travel and meetings. Microsoft Research provides support for 2 graduate students, software and equipment.