January 19, 2011 Sherri de Coronado, Semantic Services Center for Bioinformatics and Information Technology

Interoperability Interoperability: The ability of a system...to use the parts or equipment of another system Source: Merriam-Webster web site Interoperability: The ability of two or more systems or components to exchange information and to use the information that has been exchanged. Source: IEEE Standard Computer Dictionary, 1990 Semantic interoperability Syntactic interoperability

Extending Interoperability Beyond the Enterprise cancer Biomedical Informatics Grid (caBIG) -Shared infrastructure, applications and data -Enable cancer research community to focus on innovation and move research from bench to bedside and back -Shared vocabulary, data elements, data models facilitate information exchange -Interoperable applications developed to common standard -Making research data available for mining and integration Several new ARRA initiatives leveraging this infrastructure to extend interoperability principles to the broader healthcare community

Semantic Infrastructure Futures

Still Required: Terminology Services for NCI & Collaborators Terminology Editing Software (NCI Protégé – Protégé 3.4 with extensions) Terminology Content (NCI Thesaurus), published monthly Terminology Content (NCI Metathesaurus) Terminology Content (other standard terminologies like LOINC) Terminology Server (LexEVS and OWL/ RRF/ LexGrid/ OBO loaders, and now Value Set, Pick List and Mapping support/ export) accessible via APIs Browsers for NCI Thesaurus, NCI Metathesaurus and other terminologies served via LexEVS, now being modified for value set query, resolution and export, and mapping query/ review

High Value Use Cases

NCI Thesaurus (NCIt)

What ‘s in NCIt ?

Semantic Diversity plants fungus virus bacterium eukaryote archaeon animal vertebrates amphibian bird fish reptile mammal human embryonic structure anatomical abnormality anatomical structure medical device laboratory tests bodyparts &organs congenital abnormality language clinical drug tissue sign or symptoms nucleic acid findings regulation or law gene geographic area research activity cell s Mental process molecular sequence disease or syndrome neoplastic process experimental model of disease genetic function therapeutic or preventative procedure educational activity natural phenomenon event behavior family group health care activity activity organization laboratory procedure quantitative concept element,ion,isotope

Terminology Subsets

FDA-NCI Memorandum of Understanding

NCI-FDA Terminology Collaboration

FDA Structured Product Labels

SPL in NCIt

CDISC Terminology

NCIthesaurus Search Box Version information Choices, choices...

Term search Search on term - mg - 5 results

Code Search 6 sources Search on Code - 1 result

Concept details from Browser Definition(s) Semantic Type

Concept Relationships & Associations Subset Associations: How concepts are "bundled" Subset Associations: How concepts are "bundled"

NCI Metathesaurus

NCI Metathesaurus 3,600,000 terms 76 Sources 1,400,000 concepts

NCImetathesaurus 11 Sources Choose your source

NCITerm Browser Sources

EVS Products & Services Are Open NCI Thesaurus is Open Content NCI Metathesaurus is Mostly Open Source ( See Each Source’s License) NCI EVS Servers Are Freely Accessible - On the Web: Via API: All Software Developed by NCI EVS is Public Open Source and Free for the Asking:

Methods of Content Retrieval

NCIt ftp site You can download the entire NCIt in various formats

Shared Content Standards

Consolidated Content Services SNOMED CT ® FedMed UCUM

NCIt Editing Priorities for 2011 Terminology associated with standardized case report forms of all kinds Safety reporting (drug, device, food) EHR related terminology for the caCIS project, which is an ambulatory oncology EHR extension. Terminology in support of the NCPDP SCRIPT standard for e-prescribing Structured product labeling Nanotechnology (Nanoparticle characterization etc) Imaging (Probably device related expansion of SDTM) caHUB (Cancer Human Biobank project)

NCIt Management Goals for 2011 Publish better terminology provenance information -Example: What was done to a terminology when it was loaded into LexEVS for a particular purpose Terminology Metadata: Continued progress on ongoing terminology metadata collaboration with NCBO and NCRI, with goals of -adopting a core of metadata about terminology, and (for NCI) implementing on caBIG Vocab Knowledge Center - creating better ways of disseminating info that helps people choose what terminologies to use

LexEVS Terminology Server Hosts multiple coding schemes/ terminologies including NCIt Uses LexGrid Model (now extended to comply with the draft CTS2 spec) OWL, RRF and other loaders to convert and load terminologies LexGrid 6.0 just released, adds value set, pick list and mapping capabilities Documentation, see: LexEVS on caBIG Vocabulary Knowledge Center WikiLexEVS

LexEVS Terminology Server: Ver 5.1 Includes the following components: - Java API - Java interface based on LexGrid 5.0 Object Model - REST/HTTP Interface - Offers an HTTP based query mechanism. Results are returned in either XML or HTML formats - SOAP/Web Services Interface - Provides a programming language neutral Service-Oriented Architecture (SOA) - Distributed LexBIG (DLB) API - A Java interface that relies on a LexEVS Proxy and *Distributed LexEVS Adapter to provide remote clients access to the native LexEVS API - LexEVS 5.0 Grid Service - An interface which uses the caGRID infrastructure to provide access to the native LexEVS API via he caGRID Services

LexEVS 6.0 / CTS2 – What is CTS2? Common Terminology Services - Release 2 specifies a set of service interfaces to standardize necessary functional operations of a terminology service. -Administration -Search/ Query -Mapping Support -Authoring/ Maintenance Focused on extending existing Health Level 7 (HL7) Common Terminology Services (CTS) specification based on consensus requirements from the user community (including LexEVS users). Developed as an HL7 Service Functional Model (SFM); accepted as an HL7 draft standard for trial use (DSTU) and is currently an Object Management Group (OMG) RFP. OMG vote expected in June 2011

What’s new in LexEVS 6.0 LexEVS 6.0 will add comprehensive support for CTS 2 functionalities that are either partially supported or unsupported in LexEVS 5.1. Provide expanded support for value sets Develop the ability to provide local extensions to code sets Provide expanded mapping ability among code sets Develop other capabilities called for in the CTS 2 specification

LexEVS 6.0 Updates (highlights) Association/Mapping Functionality Association Administrative Functionality Association Search / Query Functionality Association Author / Curation Functionality Search / Query Functionality Value Set Search / Query Concept Domain Search / Query Local Extension Search / Query Authoring / Curation Functionality Code System Authoring / Curation Value Set Authoring / Curation Concept Domain and Usage Context Authoring / Curation

Mapping capabilities in LexEVS are supported by associations, stored in a coding scheme format like other vocabularies A map relates a single specific coded concept within a specified code system (source) to a corresponding single specific coded concept (target) within the same or another code system. Mapping coding scheme does not contain concept details; it relies on participating source and target schemes to provide that information LexEVS 6.0: Mapping Implementation

If the map relates to code systems available in LexEVS, then the map contains resolvable concepts. Associations Properties Associations Properties Associations Properties SNOWMED CT: Disseminated carcinomatosis ICD9: 199 Disseminated malignant neoplasm NCI Thesaurus: C27469 Disseminated Carcinoma NCIT to ICD9 Mapping Scheme ICD9 to SNOWMEDCT Mapping Scheme Other mappings as defined by users and communities and loaded as mapping schemes concept mappings resolvable due to internal links to live terminologies Relationship links to other NCIT concepts Relationship links to other ICD9 concepts Relationship links to other SNOWMED CT concepts Mapping Implementation (Continued)

Early Mapping Implementation in Browser

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Example: NCIt to ICD9CM Mapping Early Implementation

Example: NCIt to ICD9CM Mapping Early Implementation

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LexEVS 6.0: Value Set Services What Is A Value Set Definition? A Value Set represents a uniquely identifiable set of concept codes grouped for a specific purpose. The Value Set Definition is the mechanism for describing the contents of a Value Set. The contents are concept codes defined in referencing Code System. Value Set can contain concept codes from one or more Code Systems.

LexEVS 6.0: Value Set Services Value Set Representation / Resolution Content of Value Sets –Code system – all concept codes in referencing code system –Value Set Definition – all concept codes defined in referencing Value Set Def –Code system/concept code – individual code –Code system/concept code + relationship + additional rules (leaf only, targetToSource,...) –Code System/Property Name or Value match – all concept codes in the referencing code system that matches property name or property value. –Combination of any of the above with or/and/difference operators Resolution –A value set definition has to be made against a specific version of a code system. ( But it doesn’t have to be resolved against the same version.) –Philosophy: Even a simple list (a, b, c, d) needs to be resolved as, at some future date, “c” might be retired. –Resolution does not create a static artifact.

Value Set Viewer: Design Stage Search, Browse, Resolve, View, Export

Another Critical Need: Value Set Editor Started: tool to create and edit value set definitions Steps (current design) -Enter metadata -Define components (code, name, property, relationship, enumeration of codes, or entire vocabulary) with a presentation property (e.g. preferred name), coding scheme, matching criteria, etc., using and/or -Preview value set using “Resolve” Example, one could create the FDA subsets as value sets, using the association “concept in subset”, or in theory, create an anatomy subset that includes the is-a and part-of relationships.

Other LexEVS work slated for this year Better REST/ SOAP APIs -Enable through these for example, Getting relationship information Get a version of a value set, Get a change set of the differences between two versions OWL 2 support for loaders and exports Probably patch release in spring, and 6.1 release towards end of year.

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