1. Vocabulary Knowledge Center Adoption Stories of the NCI Semantic Infrastructure (and VKC Update) Robert Freimuth, PhD October 20, 2009

2. Agenda Introduction NCRI ONIX OpenPHI CTSA Ontology Mapper CSHARE VKC Activities and Projects Discussion

3. Vocabulary Knowledge Center Support for vocabulary authoring and management tools Wiki site Documentation and training Community Outreach Discussion forums Bug reports, feature requests Source code repository Supported software LexGrid, LexBIG, LexEVS LexWiki NCI Protégé Coordinated support for NCI CBIIT tools E.g., caCORE, caDSR

4. Agenda Introduction NCRI ONIX OpenPHI CTSA Ontology Mapper CSHARE VKC Activities and Projects Discussion

5. NCRI UK National Cancer Research Institute Partnership of more than 20 public and private organizations Goal: Promote data sharing Data standards Forming alliances Developing an IT infrastructure Figure showing that NCRI connects to NHS, EMBL- EBI, NCIN, and caBIG. It also shows that NCRI hopes to encourage data sharing by cultural changes and by developing the ONIX informatics platform Modified from A. Hogg, NCRI Willingness to share Ability to share Cultural Change through Community Alliances Help to build a Cancer Informatics Platform via ONIX

6. NCRI ONIX Oncology Information Exchange Released July 2009 Adding connected resources Figure showing how ONIX connects to caBIG resources (data, vocabulary services), EBI resources (Elixir, data services), NCRI research capability programme (data sources), CancerGrid, and others (imaging and pathology, MRU, British library) Modified from A. Hogg, NCRI Built using caBIG technology caCORE, Introduce, caGrid, LexEVS

7. ONIX and Vocabularies ONIX uses the LexEVS 5.0 terminology server NCI-Thesaurus Gene Ontology ONIX QuickSearch Federated queries across databases Find and add synonyms, spelling variants, preferred terms to queries Working toward creation of a federated vocabulary service Encourage publication of content Exploring authoring tools (e.g., LexWiki)

8. Agenda Introduction NCRI ONIX OpenPHI CTSA Ontology Mapper CSHARE VKC Activities and Projects Discussion

9. OpenPHI Open Personalized Health Informatics Private bioinformatics startup Mission Build a system to enhance every family's health Reduce barriers to health databases, publications, and knowledge Focuses on the integration of existing tools Open Access, Open Source, Open Data Products HealthAlbum: Personal health record HealthMining: Data mining of biomedical repositories HealthLibrarian: Semantic search engine

10. OpenPHI HealthLibrarian Public data sets loaded into a single data warehouse Parsing and tagging performed by NIH/NLM Lexicon tools Indexing by Apache Lucene Data sources Medline FDA NIH grants BioMed Central Clinical Trials Drugs Care Providers etc Figure showing how multiple data sources form the digital repository, and are mapped to terms from the NCI-Thesaurus Modified from J. Lacal, OpenPHI

11. OpenPHI HealthLibrarian LexEVS used to serve NCI-T Uses synonyms and term normalization Cloud computing Amazon EC2 LAMP (Linux, Apache, MySQL, PHP & Python) Version 3 in development Present information from multiple viewpoints Figure showing how the HealthLibrarian provides different views: 1) community view (public health db, air quality, substance releases), 2) anatomical view (system, organ, tissue), 3) biological view (gene, protein), 4) chemical view (drug, compound). All views connect to a disease. Modified from J. Lacal, OpenPHI

12. Agenda Introduction NCRI ONIX OpenPHI CTSA Ontology Mapper CSHARE VKC Activities and Projects Discussion

13. i2b2 Informatics for Integrating Biology and the Bedside NIH-funded National Center for Biomedical Computing Building a "scalable computational framework to address the bottleneck limiting the translation of genomic findings and hypotheses in model systems or organisms relevant to human health" New computational paradigms and methodologies Focus on three polygenic diseases (airway disease, hypertension, type 2 diabetes mellitus) and one monogenic model characterized by polygenic modifiers (Huntington’s Disease) Cells compose the hive Interoperable services with web interfaces Minimal computable semantics Deep semantics are defined by each cell and interpreted by the user

14. i2b2 Database Concept table design Data is loaded into a static data model Each "name" is a hierarchical string of concepts Figure showing the concept table design. There are 5 physical tables in the design; 4 each connect to a common central table. Modified from R. Wynden, Ontology Mapper

15. Ontology Mapper The Ontology Mapper Cell is a general purpose instance mapper Translates messy local data into one or more standard formats (ontologies) Translates local semantics to standard semantics (e.g., NCI-T) Local instances of LexEVS E.g., from a given cell in the hive to ISO 11179 data model caGrid cell exposes i2b2 resources on caGrid Maps are created in a Protégé Prompt plug-in and can be shared over HL7 CTS II both as open source or as commercially sold assets Can be loaded into caDSR Ontology Mapper shifts resources from IT (application building) to handling user requests for data access via dynamically constructed views of data (Data Repository Analysts) Mapped on demand

16. Agenda Introduction NCRI ONIX OpenPHI CTSA Ontology Mapper CSHARE VKC Activities and Projects Discussion

17. CDISC Clinical Data Interchange Standards Consortium Global, open, multidisciplinary, non-profit organization Established standards to support the acquisition, exchange, submission and archive of clinical research data and metadata Mission: To develop and support global, platform-independent data standards that enable information system interoperability to improve medical research and related areas of healthcare. >230 Members Need to harmonize data elements across organizations Genzyme, GSK, Eli Lilly, Mayo Clinic, MD Anderson

18. CSHARE CDISC Shared Health and Research Electronic Library Based on LexWiki Collaborative terminology authoring platform based on Semantic MediaWiki Enables harmonization of data elements Different sources Different terminologies Features Categorize, browse, and search data elements Group related data elements Propose harmonized data elements More to come! Metadata registries: Thursday Oct 22, 11:15-12:15 (G. Jiang) Live demonstration by the Vocabulary Knowledge Center (TBD)

19. Agenda Introduction NCRI ONIX OpenPHI CTSA Ontology Mapper CSHARE VKC Activities and Projects Discussion

20. Upcoming Presentations International Semantic Web Conference A RDF-base Normalized Model for Biomedical Lexical Grid (C.Tao, et al) LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies (C.Tao, et al) AMIA Annual Symposium caBIG ® Vocabulary Knowledge Center (R. Freimuth, et al) Comparing and Evaluating Terminology Services APIs: RxNav, UMLSKS, and LexBIG (J. Pathak, et al) Measuring Semantic Richness of Biomedical Ontologies Using OWL Constructs (G.Jiang, et al) An Approach for Representing Ontologies Modeled in LexGrid in OWL (C.Tao, et al) The Enterprise Data Trust at Mayo Clinic: A semantically integrated warehouse of biomedical data (C.Chute, et al)

21. Tool Releases NCI Protégé 1.4 Release scheduled for October 2009 Last major release of the NCIEditTab Protégé plug-in Enhancements Refactoring for maintenance and performance Added ability to use negation ("NOT") in queries Added Lucene Match, Property Present, and Property Absent search types Significantly extended flexibility of lexical queries Export to spreadsheet includes super classes

22. Tool Releases LexEVS 5.1 Release scheduled for December 2009 Enhancements Support for content in RRF (e.g., NCI Meta-Thesauraus) Value domain support (pick lists) Query performance and behavior enhancements Improved loader framework (modularity) BDA (Build and Deployment Automation) support for deployment to remote servers

23. LexEVS 5.0 Boot Camp November 17-19, 2009 NCI CBIIT Training Facility (Rockville, MD) Target audience Intermediate to advanced LexEVS users Users migrating from EVS 3.x or LexEVS 4.x Goals Understand new components of the LexGrid model Utilize the API in local, distributed, and grid environments Install and configure LexEVS 5.0 (all 3 environments) Learn about the extensions, loaders, and convenience methods Learn how to use the GUI See the VKC wiki for more information

24. LexAjax Develop an Ajax interface for LexEVS Project goals Develop an Ajax based service based on the LexEVS API and LexGrid data model that can support a variety of web based auto completion, dropdown forms, etc. Develop a basic set of graphics widgets. Integrate the graphics widget into LexWiki to provide a set of tools that can be used with Semantic Forms and other wiki based terminology access tools. Benefits include Further integration of semantic infrastructure Enhanced capability to serve terminology content to web applications Release scheduled for December 2009

25. Special Projects Terminology Index Expanding the list of terminologies Soliciting use cases and experiences Standards Organizations Coordinating with VCDE effort Terminology focus (e.g., HL7 CTS2) NCI Semantic Infrastructure Requirements Support for the Concept of Operations

26. Agenda Introduction NCRI ONIX OpenPHI CTSA Ontology Mapper CSHARE VKC Activities and Projects Discussion

27. Feedback and Requests We want your feedback to guide our future activities! Do you want the VKC to provide specific products or resources? Tell us! Figure showing the location of the "feedback" link on the Vocabulary Knowledge Center web page (in the navigational bar under "vocabkc contents")

28. Contact the Vocabulary Knowledge Center Visit our web site online https://cabig- kc.nci.nih.gov/Vocab/KC Post a question to the discussion forums https://cabig- kc.nci.nih.gov/Vocab/forums Send us an e-mail vocabkc@mayo.edu Figure: Screen shot of the Vocabulary Knowledge Center home page (for visual interest only) Materials are available at the registration table