The OBiBa Project. Update. Luxembourg 2009

Transcription

1 The OBiBa Project Update Luxembourg 2009

2 What is OBiBa? P3G Core o Shares P3G's mission; focused on delivering IT solutions to biobanks OBiBa's Objectives o Foster collaboration in software development among IT biobank teams o Provide free and open source software for existing and emerging biobanks

3 OBiBa's Approach Several independent software development projects o Each focused on supporting different biobank activities (e.g.: recruitment, baseline interviews, etc.) Software applications o built collaboratively by different teams using a common software development infrastructure o compatible and meant to be integrated together o free and open source o implement P3G methodologies and principles (e.g. DataShaPER)

4 OBiBa's end goal Provide a common IT infrastructure for any biobank o o o to collect and manage data locally to share harmonized data among biobanks to implement control mechanisms on data access

5 1 A New OBiBa Team The Australian Informatics Resource (AIR) Jointly funded by the Australian National Health & Medical Research Council and the University of Western Australia (UWA) Established in 2004 by Lyle Palmer as a resource to support Australian researchers Currently supports more than 60 research studies across Australia as well as several international collaborations

6 2 AIR s first software application for OBiBa ETA: Enrollment and Tracking Application A web-based application that manages the enrollment process and participant status, and tracks all staff - participant interactions Six AIR software developers are or will be working on this software Led by Paul White, new OBiBa Principal Investigator

7 ETA: Some features Study and registry definitions Participant contact details Participant consent status and document storage Correspondence Staff & resources calendars & appointments Planned for release in March 2010

8 Other OBiBa software coming from the AIR team AIR developed a number of integrated applications Study and participant management Phenotypic, genotypic and pedigree data management Laboratory Information Management System (LIMS) Currently use proprietary technologies The AIR Portal Some will be migrated and integrated into the OBiBa software suite

9 Onyx 1.5 released Onyx is a web-based application that manages participant baseline interviews at assessment centers or clinics Developed for the Canadian Partnership for Tomorrow project o A network of five prospective cohorts in Canada o participants by 2012 Developer team: 10 people in Montreal and Toronto Onyx is now used in 10 assessment centers across Canada 3

10 Onyx manages Participant appointments & walk-ins Participant interview flow Electronic Consent Questionnaires Two modes of administration Assisted Self-administered using touch screen Physical Measurements Tube (sample) registration Data encryption for export Cryptographic keys (PKI) Onyx stores data centrally and makes it available to all workstations

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12 Onyx: Electronic Consent Custom consent form in any language o Electronic signature: cryptographically bound to the document o Uses PDF now an ISO standard

13 Onyx: Questionnaires Many features Multiple languages, answer validation rules, skip patterns, timestamps Two interfaces Nurse-assisted Self administered using touch screen

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16 Onyx: Physical Measurements Integrates proprietary software Allows any number of measurement types Validation of measurement values Repeated measurements (quality control) 6 different electronic instruments available Any other instrument can be easily integrated

17 A new OBiBa project Opal: Study Coordinating Center Application Developed by the Onyx team for the CPT cohorts The central data repository application of a biobank Meant for data integration and management Integrate multiple sources of data Rich semantics for variable description Manage participant identifiers or keys for privac Manage, browse, query and export the cohort variable dictionary Produce aggregated reports for administrative and scientific purposes (e.g QC report, HTF reports) Ultimate purpose: to achieve seamless data sharing among biobanks 4

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19 Opal: Study Center Application Currently in analysis and prototyping phase Able to load data from Onyx data, manage keys, create Marts and produce QC reports from the database Source code available

20 Conclusion: You can join OBiBa As a Software Development Team, if you have open source projects relevant to biobanks share OBiBa and P3G vision of scientific collaboration and biobank harmonization As a User/Partner, if you wish to use OBiBa software in your biobank and help us to improve our software with your feedback Contact us: [email protected]

21 Acknowledgments Principal Investigators Vincent Ferretti, OICR Philippe Laflamme, GQ Paul White, UWA Onyx & Opal Development Teams Martin Boulanger Alice Carey Tony Debat Dwain Elson Nathalie Emond Vincent Ferretti Philippe Laflamme Nancy Lambert Yannick Marcon Julie Ncoq Dennis Spathis Patricia Watt P3G Isabel Fortier Francois L'Heureux ETA Development Team Paul White Chris Williams Eric Lam Chris Ellis Kristian Menendez Nivedan Nadaraj Canadian Partnerships for Tomorrow Marilyn Borugian Rachel Farrall Isabel Fortier Rick Gallagher Bartha Knoppers Vivek Kurup Genevieve Lachance Tim Lee John McLaughlin Louise Parker Paula Robson Ontario Health Study Kelly McDonald John McLaughlin Caitlin Mills Joan Antal Sandra Sinclair Cartagene Serge mani Mohammed ElMabrouk Funders Ontario Institute for Cancer Research Cancer Care Ontario Genome Quebec National Health and Medical Research Council University of Western Australia