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titleContents of this Page
Table of Contents
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Overview

LexBIG software architecture and implementation is designed to facilitate flexibility and future expansion. The following diagrams are intended to aid the understanding of LexBIG service integration in context of the larger caBIG® universe and specific deployment scenarios:

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Info
titleNote

It is not required that the database be located on the same system as the program runtime.

LexBIG Runtime Direct Programmatic Access diagramImage Modified

This diagram depicts access through caCORE Enterprise Vocabulary Services (EVS) to a LexBIG vocabulary engine.

LexBIG Runtime Consolidated Host - EVS Access diagramImage Modified

The primary goal is to provide a compatible experience for existing EVS browsers and client applications.

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This would be done to facilitate alternate communications with the LexBIG server (e.g. through web services as described belowin the text that follows).

The LexBIG API is designed with web and grid-level enablment in mind. This diagram depicts deployments that wrap the current API to allow the runtime to be accessed through web or grid services.

LexBIG Runtime Consolidated Host - Web Service Access diagram described in the text.Image Modified

What is LexGrid?

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The following graphic shows coding schems.
This graphic shows the codingScheme class and the properties described in the text.Image Modified

Concepts

Each concept represents a unique entity within the code system, which can be further described by properties and related to other concepts through relations.

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A binary relation from a set of entities to a set of entities and/or data. The entityType for the class concept must be "association".

This graphic shows the conceptAndinstances class with the properties described in the text.Image Modified

entities

codingScheme

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A binary relation from a set of entities to a set of entities and/or data. The entityType for the class concept must be "association."

This graphic shows the entities class with the properties described in the text.Image Modified

entity

entity

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The following graphic displays an entity.

This graphic shows the entity class and the properties are described in the text.Image Modified

Relations

Relations are used to define and qualify associations between concepts.

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The following figure shows an association.

This graphic shows the association class and the properties are described in the textImage Modified

associationInstance

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The following figure shows associationinstance.

This graphic shows the associationInstance class with the properties described in the text.Image Modified

Naming

These elements are primarily used to define metadata for a coding scheme, mapping locally used names to global references.

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The following figure shows naming.

This graphic shows the naming class with the properties described in the text.Image Modified

LexBIG Model

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The following figure shows the LexBIG core elements.

This graphic shows the core extension and the components within core are described in the text that follows.Image Modified

Components of interest include:

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The following figure shows the interfaceelements.

This graphic shows the InterfaceElements extension and the components within InterfaceElements are described in the text that follows.Image Modified

Components of interest include:

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The following figure shows the NCIHistory.

This graphic shows the NCIHistory extension and the components within NCIHistory are described in the text that follows.Image Modified

Components of interest include:

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  • Service Metadata: Coding Schema Metadata and Licensing
  • Query Service: Lexical Set Operations, Graph Operations, History
  • Service Manager: Loaders and Indexers
  • Extensions: Plug-ins

This graphic shows the LexBIG service components described in the text.Image Modified

The LexBIG Service is designed to run standalone or as part of a larger network of services. It is comprised of four primary subsystems: Service Management, Service Metadata, Query Operations, and Extensions. The Service Manager provides administration control for loading a vocabulary and activating a service. The Service Metadata provides external clients with information about the vocabulary content (e.g. NCI Thesaurus) and appropriate licensing information. The Query Operations provide numerous functions for querying and traversing vocabulary content. Finally, the Extensions component provides a mechanism to extend the specific service functions, such as Loaders, or re-wrap specific query operations into convenience methods.

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The following figure shows how the caGrid Hosting Environment comprises the LexBIG Service. The LexBIG Service comprises Service Metadata, Query Service, Service Manager, and Extensions. Service Metadata has a link outside the Hosting environment to a Service Discovery.

This graphic shows the caGRID hosting environment as described in the text.Image Modified

The LexBIG architecture provides the underpinnings LexBIG services to be made accessible through the caGRID environment in the future, where LexBIG services might optionally be deployed in a caGRID Globus container. caGrid provides a Globus service for service registration and discovery. LexBIG services deployed to the grid would be registered in the NCICB registry and be searchable through the NCICB index service.

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The following figure shows the components of the Service Manager: Indexers, Loaders, Loader Administration, and Service Administration. The Loaders are extendable to LexGrid XML, OWL, RRF, OBO, and Other.

This graphic shows the Service Management subsystem as described in the text.Image Modified

This subsystem provides administrative access to functions related to management and publication of LexBIG vocabularies. These functions are generally considered to be reserved for LexBIG administrators, with detailed instructions on how to secure and carry out related tasks described by the LexBIG Administrator's Guide.

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The following graphic shows that the Metadata Service comprises Coding Scheme Metadata, Licensing, and Discover and Index Service.

This graphic shows the Metadata Service component as described in the text.Image Modified

This subsystem provides information about accessible vocabularies, related licensing/copyright information, and registration/discovery of LexBIG services.

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The following figure shows the Query Subsystem which comprises Lexical Set Operations, Graph Operations, and History. Graph Operations sends data to LexBIG API and LexBIG Data Model (Loaders and Indexers) and LexGRID Vocabulary Model and Repository.

This graphic shows the Query Subsystem component as described in the text.Image Modified

This subsystem provides the functionality required to fulfill caCORE/EVS and other vocabulary requests. The Query Service is comprised of Lexical Operations, Graph Operations, Metadata, and History Operations.

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Client accesses LexEVS Grid Node Container via SOAP/HTTP. The LexEVS Grid Node accesses EVSAPI and then LexBIG via RMI. LexBIG accesses Database Servers containing vocabulary data. The database servers and loaded vocabulary configuration is a sample only.

This graphic shows the Grid Service as described in the text.Image Modified

LexEVS Grid Service and EVSAPI need not be deployed to physically separate servers, but it is recommended that if they are co-located on the same server, they should be deployed to separate JBoss containers.

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  • caGRID Service Context
    • Resource Creator, Resource Home, and Resource Locator.
    • Service Context which performs Service Context Grid Calls.
  • Resource Instances
    • Each of the three Resource Instances comprise Operations and Resource Properties.
    • Each Resource Instance forwards data to LexBIG.

This graphic shows the GridService architecture as described in the text.Image Modified

LexEVS Grid Service Class Diagram

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The sequence diagram for the operation "getSupportedCodingSchemes" is described belowin the text that follows:

LexEVS Grid Service Sequence DiagramImage Modified

General Call Sequence Example

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The client calls caGrid, 'getSupportedCodingSchemes()', caGrid Services calls Distributed LexBIG, 'getSupportedCodingSchemes()', LexBIG returns result of call to caGrid Service, and the results are returned to the client with all the appropriate caGrid security mechanisms.

This graphic shows a sample call sequence as described in the text.Image Modified

Assumptions

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  • The client invokes a caGrid Service.
  • caGrid Node Hosting Service uses Distributed LexBIG to implement a call.
  • Distributed LexBIG returns the requested information to caGrid Service.
  • caGrid Service returns a response to the client.

This graphic shows the call sequence as described in the text.Image Modified

API Examples

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Searching for concepts in NCI Thesaurus containing the string "Gene"

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SearchingForConcepts Snippet
SearchingForConcepts Snippet

Service Contexts and State

Along with the Main Service (as described above), the Server will also host the following Service Contexts. These Service Contexts are not meant to be called directly as Grid Services. The main function of these Service Contexts is to provide additional functionality to the Main Service. The following figure shows how the Service Context comprises a CodedNodeSet that have properties, such as ResolvedConceptReferenceList, Destroy, SetTermination Time, and other tasks.

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In the figure below, two LexEVS Grid Service Calls are highlighted, 'getCodingSchemeConcepts' and 'getNodeGraph'. These two Grid Service Calls have been selected because they return to the user a "Reference" to a Service Context. For 'getCodingSchemeConcepts', the return type is CodedNodeSetReference (which references the CodedNodeSet Service Context). For 'getNodeGraph', the return type is CodedNodeGraphReference (which references the CodedNodeGraph Service Context).

This graphic shows a Service Context Reference as described in the text.Image Modified

Resources

LexEVS Grid Services use the WS-Resource Framework (WSRF) to allow for stateful calls to the server. When a client requests a Service Context, the client is not only issued a Reference to the Service Context that was requested, but to a unique stateful Resource on the server as well. This Resource is used in the LexEVS Grid Services as a way of statefully holding objects for further use by the client.

Refer to the following sources for more information:

  • How caGrid uses the WS-Resource Framework (WSRF)

    Code Block
    Link provided for historical purposes http://www.cagrid.org/wiki/Metadata:WSRF
  • How Resources are implemented in the LexEVS Grid Service

    Code Block
    Link provided for historical purposes http://gforge.nci.nih.gov/docman/view.php/491/13736/LexEVSGrid.ppt

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  1. The client requests a Service Context, such as CodedNodeSet.
  2. The Grid Node receives the call and forwards the call to EVSAPI.
  3. EVSAPI calls getCodingSchemeConcept on the local LexBIG installation.
  4. The Grid Node creates a resource for the CodedNodeSetImpl object for future use.
  5. The client is returned the Service Context Client for the CodedNodeSet.

This graphic describes the service context sequence as described in the text.Image Modified

Service Context and Resource Assignment

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To construct a CodedNodeSet, the user calls getCodingSchemeConcepts as described above. When the user creates a CodedNodeSet through the API call getCodingSchemeConcepts, the server creates and stores the CodedNodeSet server-side as a Resource. This Resource is associated with the client and will be accessible only by the client that created it.

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To construct a CodedNodeGraph, the user calls getNodeGraph as described above. When the user creates a CodedNodeGraph through the API call getNodeGraph, the server creates and stores the CodedNodeGraph server-side as a Resource. This Resource is associated with the client and will be accessible only by the client that created it.

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To construct a LexBIGServiceConvenienceMethods, the user calls getGenericExtensions as described above. When the user creates a LexBIGServiceConvenienceMethods through the API call getGenericExtensions, the server creates and stores the LexBIGServiceConvenienceMethods server-side as a Resource. This Resource is associated with the client and will be accessible only by the client that created it.

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To construct a LexBIGServiceMetadata, the user calls getServiceMetadata as described above. When the user creates a LexBIGServiceMetadata through the API call getServiceMetadata , the server creates and stores the LexBIGServiceMetadata server-side as a Resource. This Resource is associated with the client and will be accessible only by the client that created it.

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To construct a HistoryService, the user calls getHistoryService as described above. When the user creates a HistoryService through the API call getHistoryService, the server creates and stores the HistoryService server-side as a Resource. This Resource is associated with the client and will be accessible only by the client that created it.

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To construct a Sort, the user calls getSortAlgorithm as described above. When the user creates a Sort through the API call getSortAlgorithm, the server creates and stores the Sort server-side as a Resource. This Resource is associated with the client and will be accessible only by the client that created it.

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To construct a Filter, the user calls getFilter as described above. When the user creates a Filter through the API call getFilter, the server creates and stores the Sort server-side as a Resource. This Resource is associated with the client and will be accessible only by the client that created it.

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If the URL is well-formed, proper connection is tested. If the connection attempt fails, a ConnectException is thrown containing the reason for the failure.

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LexGridServiceConnection Snippet
LexGridServiceConnection Snippet

This example shows a typical connection to the LexEVS Grid Service, with the two potential Exceptions being caught and handled as necessary.

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A client establishes access to a secured vocabulary via the following Grid Service Calls:

  1. Step 1:Connect to the LexBIG caGrid Service

    Code Block
    
    LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(url);
    
  2. Step 3:Build an org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification to hold the Coding Scheme name.

    Code Block
    
    CodingSchemeIdentification codingScheme = new CodingSchemeIdentification();
    codingScheme.setName("codingScheme");
    
  3. Step 4:Build an gov.nih.nci.evs.security.SecurityToken containing the security information for the desired Coding Scheme.

    Code Block
    
    SecurityToken token = new SecurityToken();
    token.setAccessToken("securityToken");
    
  4. Step 5:Invoke the LexBIG caGrid service as follows: This will return a reference to a new "LexBIGServiceGrid" instance that is associated with the security properties that were passed in.

    Code Block
    
    LexBIGServiceGrid lbsg = lbs.setSecurityToken(codingScheme, token);
    

    It is important to note that the Grid Service "setSecurityToken" returns an org.LexGrid.LexBIG.cagrid.LexEVSGridService.stubs.types
    .LexEVSGridServiceReference.LexEVSGridServiceReference
    object. This reference must be used to access the secured vocabularies.

Implementation

Each call to "setSecurityToken" sets up a secured connection to Distributed LexBIG with the access privileges included in the SecurityToken parameter. The LexEVSGridServiceReference that is returned to the client contains a unique key identifier to the secure connection that has been created on the server. All subsequent calls the client makes through this LexEVSGridServiceReference will be made securely. If additional SecurityTokens are passed in through the "setSecurityToken" Grid Service, the additional security will be added and maintained.

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