brisskit: biomedical research made easy - jisc digital festival 2015
TRANSCRIPT
BRISSKit: Biomedical research software as a serviceDr Jonathan Tedds (PI BRISSKit, Senior Research Fellow, Health and Research Data Informatics, University of Leicester)
Saj Issa (BRISSKit Technical Lead)
Andrew Burnham (UoL / BRISSKit Information Governance Lead / NHS-HE Forum IG Working Group)
Daniela Duca (Senior Co-Design Manager, Jisc)
Catherine Grout (Head of Change, e-Research, Jisc)
brisskit.le.ac.uk
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 3
Example BRISSkit implementation
BRISSKit CiviCRM: patient cohort management
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 4
» Manages studies: enables end-to-end contact management for volunteers and research participants
» Track approaches, contact, responses, recruitment, exclusions
» Object model that reflects community building and non-profit relationships
BRISSKit CiviCRM: patient cohort management
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 5
Example BRISSkit implementation
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 6
brisskit.le.ac.uk
BRISSKit OpenSpecimen: sample management
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 7
» Holds data on primary, derived and aliquot specimen, including linear and 2d barcodes
» Storage inventory, order tracking e.g. 30,000+ NIHR UHL Cardiovascular Biomedical Research Unit samples stored and recorded
BRISSKit OpenSpecimen: sample management
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 8
brisskit.le.ac.uk
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 9
Example BRISSkit implementation
BRISSKit RedCap: survey management
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 10
» Web-based, secure questionnaire data entry by research or nursing staff
› E.g. used for all patient recruits in NIHR UHL Respiratory Biomedical Research Unit – mobile computing on wards and outpatient clinic
BRISSKit RedCap: survey management
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 11
brisskit.le.ac.uk
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 12
Example BRISSkit implementation
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 13
Data from multiple data sources combined into multiple ontologies for flexible and sophisticated searching, cohort discovery and research
BRISSKit i2b2: data warehousing & querying
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 14
Survey dataRecords participant consent, questionnaire data and primary specimen IDs
I2b2 data queryCohort selection and data querying
Research: the semantic bridge
?
Research: the semantic bridge
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 15
Bio-ontology!
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 16
» Information Governance Toolkit - analysis of Department of Health (DoH/NHS) IGT requirements vs. BRISSKit organisation/project and services/tools› a) Hosted Secondary Use Team/project (Hosted IGT)
› b) Acute Trust (Acute Trust IGT)
» IG Training Tool (NHS – University is registered)
» Pseudonymisation requirements
BRISSKit Information governance and security management work stream - Dr Andrew Burnham leading
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 17
» Data Management Plan
» IT Security and standards – Penetration testing and Security testing
» Other NHS Standards/Requirements:- Care Records Guarantee- NHS Constitution- NHS Records Management- Patient Safety DSCN 14/2009, 18/2009
BRISSKit Information governance and security management work stream - Dr Andrew Burnham leading
» Integrated support for core research processes
» Well-established mature open source applications as protoyped in e.g. Cardiovascular, Respiratory, Cancer: fully UK customised
» A cloud based platform for seamless management and integration between applications
» A BRISSKit API allows integration with existing clinical systems
BRISSKit USPs
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 18
» Easy set up, use and administration through browser (including on mobile devices)
» Capability of being hosted in any compliant cloud provider including UHL (NHS information governance)
» Direct secure links through Jisc via Janet network under consideration (Shared Data Centre)
BRISSKit USPs
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 19
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 20
» ALSPAC Birth Cohort Studies
» DataShield: simultaneous remote, secure access to multiple large international cohorts
» SAIL-Farr secure NHS data hosting (Swansea)
University of Bristol
BRISSKit highlighted collaborations
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 21
» Case Study Module Development
» UoL Health Sciences Longitudinal Studies
» NIHR BRUs: Cardiovascular, Respiratory, Lifestyle (Loughborough-Leicester)
» Leicester Diabetes Centre
» UoL Data to Knowledge for Practice strategic theme
› UoL Genomics, UHL NHS Trust – IBM IT Partnership
University Hospitals Leicester NHS Trust
BRISSKit highlighted collaborations
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 22
» BRISSKit Community event and Health research hack: Public cloud i2b2, 23-24 Feb 2015, College Court, Leicester
» Co-located european i2b2 community user group meeting + BRISSKit hack event, Leicester 5-7 October 2015!
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 23
» Launched Sept 2014 –supporting 6 of UK’s most successful scientific and academic organisations
» First shared data centre for medical and academic research in the UK
» First large scale example of HPCenvironments being placed in anoutsourced co-location facility
Jisc shared data centre
In this phase of funding Jisc is working with University of Leicester to determine:
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 24
» How BRISSkit might operate as a Jisc Service (there may be other options)
» What the “market” for the service is
» How it might be sustained
BRISSkit and Jisc
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 25
» Market research
› First survey this year: bit.ly/1z5vVgq
» Cost modelling and test out fit with existing infrastructure and services
Our current focus:
BRISSkit and Jisc
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 26
» Exciting and innovative (based on a successful project(s))
» Has real potential to improve quality and efficiency of research
» Could fit well with Jisc’s offer of software as a service
» Could fit well with existing and emerging Infrastructure and projects
» Shared Data centre arrangements, framework agreements, work to support access to sensitive data
» And fit with ongoing operations to reach customers (service delivery - help desk, market research, customer engagement etc.)
Opportunities
BRISSkit and Jisc
» Users can now get free servers from public clouds, e.g. Amazon, Azure for Research etc
» In March 2015 BRISSKit users will be able to:
› deploy their own i2b2 virtual app onto their own cloud server
› upload their data through .csv files – default nominal ontology created
› modify/align this ontology to standardised BioPortal codesets– e.g. SNOMED
› perform queries on their data using the revised ontology through i2b2
March 2015: i2b2 via public cloud (anon data)
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 27
» With datasets uploaded into a range of i2b2 instances
» Users will be able to publish their i2b2 datasets
» A community of public cloud i2b2 users will emerge, within which users can publish, exchange and augment data and ontologies
» These merged datasets can then be used to service NHS-wide cohort search, selection and quality management
» Re-identification of cohorts will remain with original sources of i2b2 data
Towards an i2b2 NHS community
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 28
Sign up to jiscmail.ac.uk/brisskit-announce
10/03/2015 Jisc Digital Festival, 9-10 March 2015, ICC Birmingham 29
Example BRISSkit implementation