caBIG™ Terminology Services Path to Grid Enablement Thomas Johnson 1, Scott Bauer 1, Kevin Peterson 1, Christopher Chute 1, Johnita Beasley 2, Frank Hartel 2 1 Mayo Clinic, 2 NCICB Acknowledgements We wish to thank all members of the NCICB EVS and Mayo LexGrid teams, who continue to contribute to the architecture, development and deployment of LexEVS services. We wish to thank those who continue to provide mentorship for caDSR registration, caGrid™ and related tooling, and the Silver Level review process including Robert Freimuth, Tahsin Kurc, Scott Oster, Joshua Phillips, Nicole Thomas, John White, and Claire Wolfe. CurrentPrototype Query API – LexBIG (Partial) Sample Applications Query API – LexBIG (Full) Deployment Future Query API – EVS (Partial) Query functions are provided as an analytic service. Methods were selected from the EVS API to address basic query needs, providing access to concepts in the NCI Thesaurus and NCI MetaThesaurus vocabularies. As with the model, patterning behavior after the older EVS 3.2 API resulted in problematic characteristics, such as the use of separate and functionally dissimilar methods for querying concepts in the NCI MetaThesaurus and other vocabularies. Model – EVS 3.2 Registration Deployment Distributed LexBIG API caCORE 4.0 LexWrapper LexBIG Convenience Methods 3.2 EVS API Java SOAP REST Java MySQL LexBIG DB Lucene Index FIles caCORE3.2DTSRPCDTS Metaphrase M e t a t h e s a u r u s I n d i v i d u a l T e r m i n o l o g i e s 3.2EVS Model SOAP 3.2 EVS API REST Java The Legacy Infrastructure Model – LexBIG (Partial) In parallel with the EVS API 4.1 release, a prototype caGrid™ service was developed based on the formal information model used by the LexBIG terminology infrastructure. The LexBIG model is informed by HL7 CTS and ISO standards, and capable of defining all caBIG™ terminologies in terms of a common representation. As a result, this model is considered to be the foundation of future EVS releases. For the prototype, a limited section or vertical ‘slice’ of the model was selected to support common query functions (pictured above). Deployment and Registration As with the current EVS grid service, LexBIG-based grid functions are provided as an analytic service. Implemented methods were selected as a representative sample of the LexBIG query API, allowing basic retrieval of concepts, properties, and associations. Grid services are implemented in a stateful manner; this allows programs written against the grid service to mirror programs against the LexBIG Java API. The partial LexBIG model was approved and registered to the caDSR. This was carried out as proof of concept for review and registration of the full model in the next release. Prototyped services are currently deployed to a sandbox caGrid environment within the Mayo Clinic, but are not externally accessible. Model – LexBIG (Full) As part of the EVS API 4.2 release, a caGrid™ service will be developed based on a fully expanded version of the LexBIG model (pictured above). Once approved and registered to the caDSR, the fully enhanced model will undergo Silver Level review and serve as a basis for future generations of EVS services. In the 4.2 release this model, also referred to as the ‘LexEVS’ model, will coexist with the legacy EVS model. In the EVS API 5.0 release this model will serve as the primary representation for EVS data as the legacy model is retired. Sample caGrid Service call getSupportedCodingSchemes() Terminology services became available in caGrid™ 1.0 with the release of EVS API 4.0, and will continue in caGrid™ 1.1 with the release of EVS API 4.1. These initial services are based on the legacy EVS model (release 4.1 is based on model version 3.2, pictured above). This model was inferred by classes, parameters, and return values in the older EVS 3.2 API. As a result, it also inherited problematic characteristics such as the definition of unrelated but semantically similar classes for representing MetaThesaurus concepts and concepts in other vocabularies. LexBIG Installation caGrid Node hosting Service Client Client Invokes caGrid Service caGrid Service uses Distributed LexBIG to implement call Distributed LexBIG returns requested information to caGrid Service returns response to client Services are deployed to an NCICB-hosted server serving as a node on the caGrid™ and fulfilled through the EVS caCORE infrastructure. This infrastructure is currently being transitioned from a legacy architecture to one based on the caBIG™-sponsored LexBIG project. Whereas the legacy infrastructure imposed unique processing of MetaThesaurus content, the LexBIG infrastructure provides a common API for query of all sources. getMetaSourcesgetMetaSources() Returns all Metathesaurus Sources contained in the EVS. getServiceSecurityMetadatagetServiceSecurityMetadata() Returns the service's security metadata. getVocabularyNamesgetVocabularyNames() Returns all the vocabularies present in the Description Logic in caCORE 3.1 EVS service. searchDescLogicConceptsearchDescLogicConcept(EVSDescLogicConceptSearchParams eVSDescLogicConceptSearchParams) Searches a valid Vocabulary such as NCI Thesaurus and returns Description Logic concepts that meet the search criteria.EVSDescLogicConceptSearchParams searchMetaThesaurussearchMetaThesaurus(EVSMetaThesaurusSearchParams eVSMetaThesaurusSearchParams) Searches NCI meta thesaurus and returns Meta Thesaurus information that meet the search criteria.EVSMetaThesaurusSearchParams searchSourceByCodesearchSourceByCode(EVSSourceSearchParams eVSSourceSearchParams) Searches the Meta Thesaurus based on Source code.EVSSourceSearchParams caGrid™ Node Hosting Service Client Program In addition to the model being approved and registered to caDSR, services are currently registered for availability on the caGrid Portal. The portal provides a visual display of services running on the caGrid infrastructure as well as institutions that are participating in the caBIG program. 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 Sample applications have been developed against the prototype LexBIG service as proof of concept, including command-line driven programs and a modified version of the LexBIG Graphical User Interface. Because the stateful nature of the LexBIG API has been preserved, existing applications were quickly migrated to the grid with little change to core logic. In the EVS API 4.2 release, the prototype service will be enhanced to provide full functionality of the LexBIG query API and submitted for Silver Level review. In the 4.2 release this service, also referred to as the ‘LexEVS’ service, will be externally published and will coexist with the legacy EVS service. In the EVS 5.0 release, the LexEVS service will provide the primary interface to EVS functions as the legacy service is retired. As part of EVS API 4.2 release activities, the LexEVS service will be deployed to NCICB production servers and externally accessible on the caGrid™. Internally, this service will rely on the distributed LexBIG API to invoke operations on a separate server where a complete LexBIG instance has been installed and populated with vocabulary content. Database storage for serviced vocabularies may reside in yet another tier. In addition to NCICB, it is anticipated that other installations of LexEVS services will be deployed and registered to the caGrid™. These installations will contribute to a federated system of terminologies, allowing extended discovery and use in grid-based applications. 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