i2b2 grid integration with health ontology mapper ctsa informatics all hands meeting october 24,...
TRANSCRIPT
![Page 1: I2b2 grid integration with Health Ontology Mapper CTSA Informatics All Hands Meeting October 24, 2009 Rob Wynden (UCSF)](https://reader036.vdocuments.us/reader036/viewer/2022062515/56649c985503460f94954e1a/html5/thumbnails/1.jpg)
I2b2 grid integration with Health Ontology MapperCTSA Informatics All Hands MeetingOctober 24, 2009Rob Wynden (UCSF)
![Page 2: I2b2 grid integration with Health Ontology Mapper CTSA Informatics All Hands Meeting October 24, 2009 Rob Wynden (UCSF)](https://reader036.vdocuments.us/reader036/viewer/2022062515/56649c985503460f94954e1a/html5/thumbnails/2.jpg)
Interrelated Teams
• Ontology Mapper: UCSF, UCD, Rochest, UPenn
• caGrid and TRIAD: OSU
• I2b2 and SHRINE: Harvard
• CICTR: UW, UCSF, UCD (SHRINE grid evaluation)
• HSDB: UCSF, WUSTL, Stanford, UCD, Columbia, Duke, Emory, Johns H, Mayo, OSU, Rockefeller, UW, UTSW, UTHSC (a caGrid based Network)
• Other grid launching with OntoMapper: DBRD (Dist Biobank for Rare Disease), HOMERUN (Hospital Reengineering) etc.
![Page 3: I2b2 grid integration with Health Ontology Mapper CTSA Informatics All Hands Meeting October 24, 2009 Rob Wynden (UCSF)](https://reader036.vdocuments.us/reader036/viewer/2022062515/56649c985503460f94954e1a/html5/thumbnails/3.jpg)
Project Objectives
• To create a general purpose instance mapper that can provide a best-fit translation of locally encoded data into multiple standard formats
• To allow the just-in-time translation of locally encoded data (not handled during ETL)
• To allow researchers to request data in any standard format that they require
• To enable the inter-institutional sharing of data encoded in standard formats
![Page 4: I2b2 grid integration with Health Ontology Mapper CTSA Informatics All Hands Meeting October 24, 2009 Rob Wynden (UCSF)](https://reader036.vdocuments.us/reader036/viewer/2022062515/56649c985503460f94954e1a/html5/thumbnails/4.jpg)
I2b2 based initial deployment
• Many CTSA sites are already using i2b2.org as their integrated data repository (IDR) platform
• By integrating i2b2 with grid computing environments we can rapidly connect a large number of CTSA sites
• Integration with sites NOT based on i2b2 is also essential
![Page 5: I2b2 grid integration with Health Ontology Mapper CTSA Informatics All Hands Meeting October 24, 2009 Rob Wynden (UCSF)](https://reader036.vdocuments.us/reader036/viewer/2022062515/56649c985503460f94954e1a/html5/thumbnails/5.jpg)
Ontology Translation
• The ontology used in the HSDB project is OCRe (the ontology of clinical research) using OWL
• The OWL ontology must first be translated into ISO 111-79 format
• ISO 111-79 elements that can carry a data payload are then annotated with Common Data Element (CDE) IDs and checked into either caDSR or OpenMDR
![Page 6: I2b2 grid integration with Health Ontology Mapper CTSA Informatics All Hands Meeting October 24, 2009 Rob Wynden (UCSF)](https://reader036.vdocuments.us/reader036/viewer/2022062515/56649c985503460f94954e1a/html5/thumbnails/6.jpg)
Semantic Interoperabilityontology check-in to a
Data Standards Repository (DSR)
![Page 7: I2b2 grid integration with Health Ontology Mapper CTSA Informatics All Hands Meeting October 24, 2009 Rob Wynden (UCSF)](https://reader036.vdocuments.us/reader036/viewer/2022062515/56649c985503460f94954e1a/html5/thumbnails/7.jpg)
Instance Mapping
• The caGrid and TRIAD environments provide semantic interoperability
• The data exposed on the grid must have the same value-set ranges for query to be possible (we also need syntactic interoperability)
• Ontology Mapper provides the best-fit instance mapping of that local data for query over caGrid
![Page 8: I2b2 grid integration with Health Ontology Mapper CTSA Informatics All Hands Meeting October 24, 2009 Rob Wynden (UCSF)](https://reader036.vdocuments.us/reader036/viewer/2022062515/56649c985503460f94954e1a/html5/thumbnails/8.jpg)
Syntactic Interoperabilityinstance mapping of local data
![Page 9: I2b2 grid integration with Health Ontology Mapper CTSA Informatics All Hands Meeting October 24, 2009 Rob Wynden (UCSF)](https://reader036.vdocuments.us/reader036/viewer/2022062515/56649c985503460f94954e1a/html5/thumbnails/9.jpg)
Two i2b2 based grid projects
• SHRINE – a Harvard based project to create a new grid platform (Andy McMurray at Harvard leads that team). The CICTR project is based on this technology
• I2b2 caGrid connectivity – the existing caBIG grid augmented with the TRIAD platform (Shannon Hastings at OSU leads that team). The initial pilot of the TRIAD project is the HSDB (Human Studies Database) project
• (Health Ontology Mapper will support both grids)
![Page 10: I2b2 grid integration with Health Ontology Mapper CTSA Informatics All Hands Meeting October 24, 2009 Rob Wynden (UCSF)](https://reader036.vdocuments.us/reader036/viewer/2022062515/56649c985503460f94954e1a/html5/thumbnails/10.jpg)
OntoMapper Encoding Tables
• Health Ontology Mapper extends the i2b2 Concept Dimension by adding keys to new tables called encoding tables.
• The Encoding Tables associate caGrid Common Data Elements (CDE’s) with i2b2 Concept Dimension entries.
• OntoMapper therefore integrates i2b2 with the semantic interoperability components of caBIG for both SHRINE and caGrid.
![Page 11: I2b2 grid integration with Health Ontology Mapper CTSA Informatics All Hands Meeting October 24, 2009 Rob Wynden (UCSF)](https://reader036.vdocuments.us/reader036/viewer/2022062515/56649c985503460f94954e1a/html5/thumbnails/11.jpg)
SHRINE Layered Integration
![Page 12: I2b2 grid integration with Health Ontology Mapper CTSA Informatics All Hands Meeting October 24, 2009 Rob Wynden (UCSF)](https://reader036.vdocuments.us/reader036/viewer/2022062515/56649c985503460f94954e1a/html5/thumbnails/12.jpg)
caGrid “Introduce” based Integration
![Page 13: I2b2 grid integration with Health Ontology Mapper CTSA Informatics All Hands Meeting October 24, 2009 Rob Wynden (UCSF)](https://reader036.vdocuments.us/reader036/viewer/2022062515/56649c985503460f94954e1a/html5/thumbnails/13.jpg)
System Architecture
![Page 14: I2b2 grid integration with Health Ontology Mapper CTSA Informatics All Hands Meeting October 24, 2009 Rob Wynden (UCSF)](https://reader036.vdocuments.us/reader036/viewer/2022062515/56649c985503460f94954e1a/html5/thumbnails/14.jpg)
Summary• The Health Ontology Mapper extends i2b2 so that it
can contain and reference formally encoded information in a semantically interoperable way.
• Our initial pilot for the HSDB project has been successful. We have initiated HSDB queries from caGrid of an i2b2 based integrated data repository.
• We will now seek to integrate OntoMapper more closely with the SHRINE grid and it’s SHRIMP association mapper.
• We will also now create deployment and user documentation for more wide-spread usage.
• Contact: Rob Wynden ([email protected])
![Page 15: I2b2 grid integration with Health Ontology Mapper CTSA Informatics All Hands Meeting October 24, 2009 Rob Wynden (UCSF)](https://reader036.vdocuments.us/reader036/viewer/2022062515/56649c985503460f94954e1a/html5/thumbnails/15.jpg)
Thanks!
Questions?