caBIG Semantic Infrastructure 2.0: Supporting TBPT Needs Dave Hau, M.D., M.S. Acting Director, Semantic Infrastructure NCI Center for Biomedical Informatics and Information Technology

Key Extensions from 1.0 Infrastructure Lower barrier of entry - “Make easy things easy” Linear value proposition Vs. all or none Immediate return upon initial investment Tools guide user to increase semantics for more “return” Support all levels of participation based on user needs Support non-NCI semantic representation strategies Legacy support for 1.0 users Leverage existing open-source technologies and standards from the community 2

Semantic Infrastructure 2.0 Knowledge Management Service (SAIF / ECCF Registry) Informational (Static) Semantics Layered (~ upper ontology) – promote reuse ; enhance interoperability ; avoid data element “explosion” Contextual – all elements have a model context ; vs. individual element curation RIM-based semantics and ISO healthcare datatypes Ability to transform between different formats based on use case Behavioral (Dynamic) Semantics Support semantic workflow composition on caGrid 2.0 Analytical and transactional services Artifact Management – SAIF metamodel (UML profile) ; DITA Form templates – HL7 CDA, CDISC ODM, Xform Governance Service Conformance checking – design time and run time 3

Leverage Open-Source Technologies Informational (Static) Semantics Eclipse Modeling Framework (EMF) Transformation between model formats 4 HL7 MIF HL7 Static Model Designer UML MDT (Model Development Tools) Ontology Protégé?

Linear Value Proposition “Just enough semantics” for different deployment contexts (Lab-wide vs. Institution-wide vs. Global) 5 Innovation Path Transition Enterprise Path “VALUE”

Linear Value Proposition – Static Semantics Value – Data integration across caGrid Any community ontology (e.g. Gene Ontology) Mapping (e.g. ISA-TAB -> LSDAM mapping) caBIG Domain Analysis Model (e.g. BRIDG, LSDAM)

Linear Value Proposition – Behavioral Semantics Value – Semantic Workflow Composition 7 WSDL / WADL WSDL / WADL + pre,post- conditions SAIF Behavioral Framework (Service Contract – roles, interactions)

SI 2.0 is federated 8 StandardInstitutionalLab InstitutionalLab

SI 2.0 Supports Multiple Platforms 9 Semantic Infrastructure 2.0

SI 2.0 -> Service Registry -> Service Instance 10 Semantic Infrastructure Service Registry Service Instances

Dynamic Extensions 11 Semantic Infrastructure (NCI instance or local instance) Service Registry Service Instances DEs CDA template / xform Version bump - resync LexEVS Value sets, pick lists

Dynamic Extensions - Details SI 2.0 will provide portlet and service capabilities for caTissue to create Dynamic Extensions (DEs) directly on an SI 2.0 instance. SI 2.0 will provide capabilities for querying and reuse existing models and attributes. Newly created DEs are available for sharing from SI 2.0 instance at owner’s preferred timing. LexEVS will provide value set querying, creation and management capabilities for the DEs. Forms will be created on SI 2.0, and retrievable by caTissue as a CDA template, xform etc., with validation mechanisms (e.g. schematrons associated with CDA template). 12

Dynamic Extensions - Details For defining DEs, SI 2.0 will support use of NCIt concepts, and also non-NCI semantic representations such as community ontologies (NCBO Bioportal ontologies, OBO Foundry etc.) Upon creation of DEs, the version of a user's model will be incremented. SI 2.0 will prompt the runtime registry to reload the new version of the model, so discovery can be based on the new extended model. (Possibly) Entity-Attribute-Value(EAV) or RDF triple representation to avoid building and deploying new data service. 13

AIM v3 Sample Annotations … 14

AIM v3 Sample Annotations 15

AIM v3 Sample Annotations 16

AIM – Radiology / Pathology Imaging The metadata is in the data. We are annotating each data instance, instead of each class and attributes. “One annotation per object” Entity-Attribute-Value representation RDF triples / SPARQL endpoint 17

Semantic Infrastructure 2.0 Timeline (Tentative) Nov 2010 – Jan 2011: “Inception Activities” – Risk Mitigation: Data Migration Semantic Workflow Composition Summer 2011: SI 2.0 repository initial release ; data migration starts Fall 2011: Knowledge Management Service Winter 2011: Governance Service Spring 2012: Tools Summer 2012: Decision Support / Analysis Service 18

Use Case – Reuse Metadata (Interim Strategy) I'm a Prostate SPORE Group, and we have a list of new data elements that we want to add to caTissue (or other caBIG tools). I'd like to know what are the data elements and query from caTissue as I'm filling out a dynamic extension form in caTissue. - how can we a) use a vocabulary service - to send "prostate cancer " (or similar term) and get a drop down list of values that are in caDSR and thus registered in NCI Thesaurus. So, in this very simple example - they would have "prostate carcinoma". “CDE Curation Tool” (Querying now open to public) 19

Use Case – Reuse Metadata 20

Use Case – Reuse Metadata 21

Use Case – Reuse Metadata 22

Use Case – Reuse Metadata 23

Use Case – Reuse Metadata 24

Semantic Infrastructure 2.0 Roadmap SI 2.0 Roadmap public website: SI 2.0 Roadmap, Sep 6, 2010 (next release Nov 19, 2010): (online version) emantic_Infrastructure_2.0_Roadmap_Sept_6_2010.pdf (pdf version) emantic_Infrastructure_2.0_Roadmap_Sept_6_2010.pdf SI 2.0 Roadmap community input form: _Infrastructure_Community_Input_Form.xlsx 25