LexEVS Overview Mayo Clinic Rochester, Minnesota June 2009

What is LexGrid? The LexGrid package represents a comprehensive set of software and services to load, publish, and access vocabulary or ontological resources. Built on common information model representing multiple vocabularies Utilize common repositories, software components, APIs, and tools Ground in standards (e.g. HL7 CTS, ISO 11179)

What is LexGrid? The LexGrid package represents a comprehensive set of software and services to load, publish, and access vocabulary or ontological resources. Built on common information model representing multiple vocabularies Utilize common repositories, software components, APIs, and tools Ground in standards (e.g. HL7 CTS, ISO 11179) Source OMG LQS … OWL Standards ISO XML HL7 CTS OtherOBO Content Represent LexGrid Model Data Index Export Import OWL XML OBO Text Protégé RRF XML Tools Access SERVICESSERVICES Java API Lex* CTS2 CTS Embed.NET Web Clients Grid Clients Documentation Examples Open

What is LexBIG? A specific API to serve vocabularies based on the LexGrid model, developed for the Cancer Biomedical Informatics Grid (caBIG®) community. Coordinated infrastructure for Cancer Research Clinical Trials, Integrative Cancer Research, Tissue Banking and Pathology Tools, In vivo Imaging Vocabulary, Common Data Elements, Architecture Open source implementation. Underpins current NCI Enterprise Vocabulary Services (EVS). Represents the next generation EVS API. Additional contributions and tuning to meet the needs of the NCBO community, based on development of NCBO BioPortal services.

What is LexEVS? Adopted as project name to describe merging of LexGrid model and LexBIG API as the mainstream EVS interfaces. Collection of programmable interfaces 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. Introduced as Distributed API and grid-level services in EVS version 4.x, and completing transition to caCORE SDK-generated interfaces (RESTFul API, SOAP services, etc) in EVS 5.0.

What is LexEVS 5.0? LexEVS 5.0 is the first release to completely shift from the EVS Model and EVS API to LexEVS API and LexGrid Model. The 2008/01 model is updated to the 2009/01 LexGrid Model New Data Services are now provided for the Grid and web service interfaces XSL transformations are provided for legacy LexGrid data. Unified OWL loader (Migration from the NCI OWL loader and a generic OWL loader to a single loader) Updated to work with caCORE SDK 4.1 LexEVS 5.0 introduces LexGrid-based Query-By-Example (QBE) services

LexEVS Conceptual Overview LexEVS consists of LexGrid Model & Storage, LexEVS Java API, LexEVS Distributed Service and LexEVS caGrid Service. LexEVS caGrid Service LexEVS Distributed Service LexEVS Java API LexGrid Model & Storage Browsers and Applications

LexEVS API Now we will discuss LexEVS API. LexEVS Java API LexGrid Model & Storage

LexEVS API – Characteristics API coverage Administrative FunctionsAdministrative Functions Query Code Systems and Available MetadataQuery Code Systems and Available Metadata Query Concepts, Concept Properties, and QualificationsQuery Concepts, Concept Properties, and Qualifications Query Concept Relationships and QualificationsQuery Concept Relationships and Qualifications API characteristics Conscious separation of service and data classesConscious separation of service and data classes Deferred query resolutionDeferred query resolution Payload optimizationPayload optimization Support iterationSupport iteration Defined extension points (loaders, exporters, sort algorithms, filters, convenience methods)Defined extension points (loaders, exporters, sort algorithms, filters, convenience methods)

LexEVS API - Distributed Now we will discuss LexEVS Distributed API. LexEVS Distributed Service LexEVS Java API LexGrid Model & Storage

LexEVS API - Distributed Same API functions; requires change to service declaration only Does not expose administration options Database Server Distributed LexEVS Server RMI LexEVS on Local System LexEVS Install Database Server LexEVS Install JDBC Direct Distributed LexBIG API Proxy Client System LexEVS Client Proxy

LexEVS API – caGrid Service Now we will discuss LexEVS caGrid Service LexEVS caGrid Service LexEVS Distributed Service LexEVS Java API LexGrid Model & Storage

The caGrid Service consists of client system, caGrid Host Server, Distributed LexEVS Server and Database Server. Database Server Distributed LexEVS Server RMI LexEVS on Local System LexEVS Install Database Server LexEVS Install JDBC Direct Distributed Database Server LexBIG API Proxy Client System caGrid Host Server Client System Distributed LexEVS Server RMI LexEVS Install Grid JDBC TCP LexEVS Proxy LexEVS Client Proxy LexEVS API – caGrid Service

caGrid Services use same API functions and only require change to service declaration only. ClientcaGrid ServiceDistributed LexBIG Calls caGrid ‘getSupportedCodingSchemes()’ Calls Distributed LexBIG ‘getSupportedCodingSchemes() Returns result of call to caGrid Service Results are returned to client with all appropriate caGrid security mechanisms

LexEVS caCORE SDK APIs Now we will discuss LexEVS caCORE SDK APIs. caCORE SDK APIs LexGrid Model & Storage

Query-by-example (QBE) system Based on LexGrid model Java Language Binding Web Services (SOAP) Web Services (REST HTTP / XML) caCORE EVS Server Web Services XML / HTML Java QBE LexBIG Install DAO Cache Service Layer Database Server JDBC LexEVS caCORE SDK APIs Hibernate

caCORE SDK APIs – QBE Example SDK-Generated Query by Example User Interface is demonstrated by the domain class browser. SDK-Generated Query by Example User Interface:

caCORE SDK APIs – Rest Example SDK Generated REST request output in HTML (XML is also available). Example Restful Request (HTML)… Example Restful Output (HTML shown, XML also available)…

Browsers and Applications Now we will discuss browsers and applications that utilize LexEVS. LexBIG/EVS caGrid Service LexBIG/EVS Distributed Service LexBIG/EVS Java API LexGrid Model & Storage Browsers and Applications

The LexEVS GUI Provides graphical interface to exercise API functionality. LexBIG GUI Provides graphical interface to exercise API functionality.

caBIG LexEVS Adopters LexEVS is used in various projects within the caBIG community. For example: Meta Data Registry and UK Cancer Grid (cgMDR) cgMDR is a collaborative development effort with involving the NCI CBIIT MDR Team and the team from the UK Cancer Grid to build plugins that will facilitate meta data reuse and development amongst the caBIG community. Cancer Models Database (caMOD) caMOD provides information about animal models for human cancer to the public research community. Cancer Data Standards Registry and Repository (caDSR) The caDSR is a database and a set of APIs and tools used to create, edit, control, deploy and find common data elements (CDEs) for metadata consumers and for UML model development.

LexEVS Resources LexEVS Project caBIG® Vocabulary Knowledge Center Wiki Comprehensive resource for LexEVS caBIG® Vocabulary Knowledge Center Forums Provides ability to ask LexEVS questions and find answers LexEVS 5.0 Migration Guide Documentation to assist adopters to migrate to LexEVS 5.0