lexevs overview mayo clinic rochester, minnesota june 2009
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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 11179
XML
HL7 CTS
Other
OBO
Content
Represent
LexGridModel
Data
Index
Export
ImportOWL
XML
OBO
Text
Protégé
RRF
XML
Tools
Access
SERVICES
JavaAPI
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
LexGridModel & Storage
Browsers and Applications
LexEVS API
•Now we will discuss LexEVS API.
LexEVS Java API
LexGridModel & 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, Defined extension points (loaders, exporters, sort algorithms, filters, convenience methods)convenience methods)
LexEVS API - Distributed
•Now we will discuss LexEVS Distributed API.
LexEVS Distributed Service
LexEVS Java API
LexGridModel & 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
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
LexGridModel & 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
JDBC
Direct
Distributed
Database Server
LexBIG API Proxy
Client System
caGrid Host ServerClient System Distributed LexEVS Server
RMI
LexEVS Install
Grid
JDBCTCP
LexEVS Proxy
LexEVS Client Proxy
LexEVS Client Proxy
LexEVS API – caGrid Service
LexEVS API – caGrid Service
•caGrid Services use same API functions and only require change to service declaration only.
Client caGrid Service Distributed LexBIGCalls caGrid ‘getSupportedCodingSchemes()’
Calls Distributed LexBIG‘getSupportedCodingSchemes()
Returns result of call to caGrid Service
Results are returned to clientwith all appropriate caGrid security mechanisms
LexEVS caCORE SDK APIs
•Now we will discuss LexEVS caCORE SDK APIs.
caCORE SDK APIs
LexGridModel & 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 ServicesWeb Services
XML / HTMLXML / HTML
Java QBEJava QBE
LexBIG Install
DAO
Cache
Service L
ayer
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
LexGridModel & Storage
Browsers and Applications
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.
https://gforge.nci.nih.gov/projects/cgmdr/• Cancer Models Database (caMOD)
caMOD provides information about animal models for human cancer to the public research community.
https://cabig.nci.nih.gov/tools/caMOD• 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.
http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/cadsr
LexEVS Resources
• LexEVS Project
http://gforge.nci.nih.gov/projects/lexevs/
• caBIG® Vocabulary Knowledge Center Wiki
Comprehensive resource for LexEVShttps://cabig-kc.nci.nih.gov/Vocab/KC/index.php/Main_Page
• caBIG® Vocabulary Knowledge Center Forums
Provides ability to ask LexEVS questions and find answershttps://cabig-kc.nci.nih.gov/Vocab/forums/
• LexEVS 5.0 Migration Guide
Documentation to assist adopters to migrate to LexEVS 5.0https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/LexEVS_5.0_Migration_Guide
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