1. 1 EVS and caDSR The Semantic Backbone Sherri de Coronado, EVS, CBIIT Aug 2009

2. Topics Enterprise Vocabulary Services (EVS) - Background Terminology Services: LexEVS 5.0 EVS Use Cases: caDSR and FDA Access to EVS terminologies through LexEVS, Browsers, Grid Services Links to more information 2

3. EVS and LexEVS provide the Semantic Bedrock for caBIG and others The NCI Enterprise Vocabulary Services Project provides the terminological foundation upon which sharing and re-use of data, services and applications, and other resources depend. Many users, many collaborators: The caBIG community, NCI and certain other NIH institutes, and organizations such as FDA and CDISC. NCI Metathesaurus 1 st published in 1999. NCI Thesaurus in production since 2000, and is the main terminology upon used by the NCI metadata and data models infrastructure. BiomedGT ontology is the newest addition, in development. EVS project publishes freely available tools for terminology and ontology development and for serving terminology and ontology data. 3

4. EVS: NCI Metathesaurus NLM’s UMLS Metathesaurus extended with additional required vocabularies, with proprietary removed Workhorse, good for synonymy, definitions Contains mappings among over 50 vocabularies Used as online dictionary and thesaurus, for mapping and document indexing Released about 4x per year, major releases with UMLS updates twice a year Browsers: Now Available: http://ncim.nci.nih.govhttp://ncim.nci.nih.gov In Bioportal: http://bioportal.nci.nih.gov (new version of LexEVS with better Meta support in the fall)http://bioportal.nci.nih.gov In deprecation, but still operational: http://ncimeta.nci.nih.gov http://ncimeta.nci.nih.gov 4

5. NCI Thesaurus Reference Terminology for NCI, caBIG, Partners Underpins caCORE, caGRID semantics Broad coverage of the cancer research and clinical domain including prevention and treatment trials Neoplastic and other Diseases, Findings and Abnormalities,Anatomy, Tissues, Subcellular Structures, Agents, Drugs, Chemicals, Genes and Gene Products, Biological Processes, Animal Models, Research Techniques, etc. Published monthly, open content license DL Based, for consistency and completeness Concept History published Accessible through browser, LexEVS API, Grid Analytic Service, and download Browsers New: http://ncit.nci.nih.govhttp://ncit.nci.nih.gov Also a source in NCI Bioportal: http://bioportal.nci.nih.gov/ncbo/faces/index.xhtml http://bioportal.nci.nih.gov/ncbo/faces/index.xhtml 5

6. NCI Bioportal: Browser access to terminologies loaded in LexEVS 6 http://bioportal.nci.nih.gov

7. LexEVS 5.0 What is LexEVS? LexEVS is a collection of APIs that provide users with the ability to access controlled terminologies supplied by the NCI Enterprise Vocabulary Services (EVS) Project. The controlled terminologies hosted by the NCI EVS Project are published via the Open-Source LexEVS Terminology Server. 7

8. caDSR:11179 Based Metadata Repository 8

9. DE Binding to EVS Terminology 9 https://cdebrowser.nci.nih.gov/ CDEBrowser/

10. Binding Data, Metadata to Terminology caCORE SDK UML Modeling Tool (provided by user) Information model that will define data classes, attributes and relationships Semantic Connector Annotate UML model with ontology concepts: bridges the world of databases to that of structured semantics. UML Loader (run by NCI staff) Loads model into the caDSR metadata registry Model and associated semantics are available at runtime Code Generator Model and a code template are inputs into generator Creates the ‘caCORE-like’ n-tier software system with Java and Web Services APIs 10

11. Selected Use Cases for EVS EVS Used Directly for Drug / Clinical Integration Agents, Clinical Trials and Adverse Events CTEP and DCP clinical trials PDQ Cancer Clinical Trials Registry & NCI Drug Dictionary Federal Medication Terminologies (FMT) or FedMed FDA Structured Product Labeling and other terminology subsets caBIG infrastructure and application use cases Infrastructure providing semantic interoperability caTIES – use NCIt content/hierarchy to extract and code information from pathology reports caMOD – Cancer Models database, API access for annotation caNanoLab – content added to NCIt FDA/NCI/CDISC/BRIDG – harmonization/ development - standards 11

12. Milligram Concept in NCIt 12

13. “Milligram” is part of FDA SPL Subset 13

14. FDA Structured Product Label 14 2.2. Describing the strength of an active ingredient powder for oral suspension Text:: MiracleDrug for Oral Suspension is a white powder. When constituted as directed, MiracleDrug for Oral Suspension contains 20 mg of gooddrug per 5 mL. http://www.fda.gov/cder/regulatory/ersr/FDA_SPL_dataelementsexamples.pdf XML: <translation code="C28253" CodeSystem="2.16.840.1.113883.3.26.1.1" displayName="MILLIGRAM" value="20" /> <translation code="C28254" codeSystem="2.16.840.1.113883.3.26.1.1" displayName="MILLILITER" value="5" /> goodingredient sodium goodingredient NCIT Concept Code and OID

15. Subsets 15

16. Access to FDA Terminology Subsets 16

17. Code Snippet for API Query: To get a set of concepts public void getConceptsThatHaveTarget() throws Exception { //all associations will have this code as a target String haveTargetConceptCode = "C54452” //restrict to only this type of association String association = "subClassOf”; //build a CodedNodeSet for restricting the graph below CodedNodeSet cns = lexevsService.getCodingSchemeConcepts("NCI Thesaurus", null);cns.restrictToCodes(Constructors.createConceptReferenceList(haveTargetConceptCode) ); //build a CodedNodeGraph and restrict to only associations with a given target CodedNodeGraph cng = lexevsService.getNodeGraph("NCI Thesaurus", null, null); cng.restrictToTargetCodes(cns); //restrict the graph to a given association name cng.restrictToAssociations(Constructors.createNameAndValueList(association), null); //resolve and print results ResolvedConceptReference[] rcr = 17

18. Using LexEVS API and GRID Node: Well documented Query shown also works on Grid (Grid Analytic Service) LexEVS: General information and links to everything! https://cabig- kc.nci.nih.gov/Vocab/KC/index.php/LexEVS_Version_5.0 <https://cabig- kc.nci.nih.gov/Vocab/KC/index.php/LexEVS_Version_5.0 Javadocs: http://lexevsapi.nci.nih.gov/lexevsapi50/docs/ https://gforge.nci.nih.gov/docman/view.php/491/17174/LexEVS _50_JavaDocs.zip Code examples: http://gforge.nci.nih.gov/docman/view.php/491/17544/LexEVS_ 50_Example_Code.zip https://cabig- kc.nci.nih.gov/Vocab/KC/index.php/LexEVS_Version_5.0https://cabig- kc.nci.nih.gov/Vocab/KC/index.php/LexEVS_Version_5.0 http://lexevsapi.nci.nih.gov/lexevsapi50/docs/ https://gforge.nci.nih.gov/docman/view.php/491/17174/LexEVS _50_JavaDocs.zip http://gforge.nci.nih.gov/docman/view.php/491/17544/LexEVS_ 50_Example_Code.zip 18

19. Using LexEVS and GRID service, cont’d Analytical Grid Service: https://cabig- kc.nci.nih.gov/Vocab/KC/index.php/LexEVS_5.0_Programmer% 27s_Guide#LexEVS_Analytical_Grid_Service_API Data Grid Service: https://cabig- kc.nci.nih.gov/Vocab/KC/index.php/LexEVS_5.0_Programmer% 27s_Guide#LexEVS_Data_Grid_Service_API https://cabig- kc.nci.nih.gov/Vocab/KC/index.php/LexEVS_5.0_Programmer% 27s_Guide#LexEVS_Analytical_Grid_Service_API https://cabig- kc.nci.nih.gov/Vocab/KC/index.php/LexEVS_5.0_Programmer% 27s_Guide#LexEVS_Data_Grid_Service_API 19

20. New NCIt Browser 20

21. Tabbed for Easy Viewing 21

22. Relationships Tab 22

23. Synonym Source and Term Type 23

24. Summary: Take Home Messages NCIt and other terminologies in EVS are the semantic Bedrock of the caBIG infrastructure, enabling application and data integration, and in the future, federated query and reasoning against data on the GRID. You can access and use EVS terminologies in multiple ways: through caDSR, browsing, download, via APIs (java or distributed java, caGRID analytic or data services, QBE, CQL) in your own applications. Everything in EVS is open. Software is available. Terminology (with a few exceptions) is open with very minimal requirements for use. (e.g. if you take NCIt and do something to it, call it something else.) Lots of documentation and support through Vocabulary Knowledge Center. 24

25. Acknowledgements: EVS Team CBIIT Staff Frank Hartel hartel@exchange.nih.govhartel@exchange.nih.gov Margaret Haber mhaber@mail.nih.govmhaber@mail.nih.gov Gilberto Fragoso fragosog@mail.nih.govfragosog@mail.nih.gov Larry Wright lwright@mail.nih.govlwright@mail.nih.gov Sherri de Coronado decorons@mail.nih.govdecorons@mail.nih.gov Editing/Production/QA – Lockheed-Martin NCI Thesaurus and BiomedGT Editors NCI Metathesaurus Editors NCI Metathesaurus Production/QA Technical Support – SAIC and Lockheed-Martin (Tracy Safran, Rob Wynne, John Park) Vocabulary Knowledge Center – Mayo Clinic Software Development/ Maintenance – Mayo Clinic, Northrup- Grumman, Dionne-Associates, Stanford, Clark&Parsia LLC Testing – Ekagra, Lockheed-Martin 25