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https://gforge.nci.nih.gov/docman/view.php/491/23714/lexevsapi60_notes.html https://ncisvn.nci.nih.gov/svn/docs/trunk/lexevs/LexEVSProjectDocuments/v6.0/ReleaseDocumentationandFiles/LexEVS_600_RELEASE_NOTES.doc
https://cbiit-download.nci.nih.gov/evs/LexEVS/v6.0/Release/LexEVS_600_RELEASE_NOTES.doc
on LexEVS Release Notes Download List to Include change link to wiki
Craig Stancl
Deepak Sharma
Kevin Peterson
Scott Bauer
Sridhar Dwarkanath
Zonghui Lian
Division of Biomedical Statistics and Informatics
Department of Health Science Research
Mayo Foundation
Rochester, MN

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Developers:
Craig Stancl; Deepak Sharma; Kevin Peterson; Scott Bauer; Sridhar Dwarkanath; Zonghui Lian;
Division of Biomedical Statistics and Informatics,
Department of Health Science Research
Mayo Foundation, Rochester, MN

Panel
titleTable of Contents
Table of Contents
minLevel2

Table of Contents
Introduction
CTS2 Implementation
OWL/RDF Export
Integer Primary Keys
Mapping Extension
Supplement Extension
Value Sets (gForge # 26650)
Versioning (gForge # 26651)
XML Loaders
XML Exporter
GForge Items
LexGrid model changes

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Introduction

This document contains major functionalities that are included in LexEVS 6.0.0 Release.

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CTS2 Implementation

  • Initial Interfaces
    • The initial set of Interface and API has been created. Input parameters and output values are still evolving, but interfaces are in place reflect the functionality of CTS2.

CTS2 Administration Development (see: org.lexevs.cts2.admin.AdminOperation)

  • Import Code System
    • (see: org.lexevs.cts2.admin.load.CodeSystemLoadOperation )
    • Loads a 'NEW' Revision of a Coding Scheme into the System. If Revision info is not supplied by the user (such as Revision Id), it will be generated. Utilizes existing LexEVS loader functionality.
  • Change Code System Status
    • (see: org.lexevs.cts2.author.CodeSystemAuthoringOperation )
  • Import Value Set Version
    • (see: org.lexevs.cts2.admin.load.ValueSetLoadOperation)
  • Export Code System Content
    • (see: org.lexevs.cts2.admin.load.CodeSystemLoadOperation )
  • Register for Notification
    • (see: org.lexevs.cts2.admin.NotificationAdminOperation )
    • Allows the user to register for notification of a System State Change. There are various events that occur in the system, and a user may choose to listen for one or more of them.
  • Update Notification Registration
    • (see: org.lexevs.cts2.admin.NotificationAdminOperation )
    • Allows the user to alter an existing Notification Registration.
  • Update Notification Registration Status
    • (see: org.lexevs.cts2.admin.NotificationAdminOperation )
    • Allows the user to 'SUSPEND', 'REINSTATE', or 'REMOVE' a notification from the system.

CTS2 Authoring Development (see: org.lexevs.cts2.author.AuthoringOperation )

    • Association Authoring Operations (see: org.lexevs.cts2.author.AssociationAuthoringOperation )
      • Create association in an established coding scheme using the Revision model.
      • Create association in an established mapping dedicated coding scheme using the Revision model.
      • Create association mapping. Create mappings between coding schemes and persist as new coding scheme with default metadata settings. Persist using the Revision model.
      • Create association mapping. Create mappings between coding schemes and persist as a coding scheme with user defined metadata values. Persist using the Revision model.
      • Create association mapping: Create mappings between coding schemes with persisted concept values pulled from target schemes current in a LexEVS service instance. Persist using the Revision model.
      • Create association type. Create a new AssociationPredicate value and persist is using the Revision model.
    • ValueSet Authoring
      • (see: org.lexevs.cts2.author.ValueSetAuthoringOperation)

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OWL/RDF Export

  • OWL/RDF Export functionality has been added, allowing the export of loaded LexEVS content into OWL format.
    • (see: org.LexGrid.LexBIG.Extensions.Export.OWL_Exporter)

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    • GForge #30058: AssociationData is not exported. Thus, the owl/rdf exporter cannot handle the owl:hasValue, owl:maxCardinality, owl:minCardinality, owl:cardinality constraints.

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Integer Primary Keys

  • Primary keys are now configurable – either a GUID or a Sequential Integer scheme can be used. Sequential Integers offer better performance, while GUIDs enable portability between databases.

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  1. DB_PRIMARY_KEY_STRATEGY indicates which strategy will be used
  2. for the primary key of the database tables.
  3. WARNING - This cannot be change after the initial
  4. schema installation.
    #
  5. Allowable values include:
    #
    #"GUID"
    • Primary Keys are implemented as random GUIDs.
      #"SEQUENTIAL_INTEGER"
    • Primary Keys will be sequentially incremented
    • as Integer values.
      DB_PRIMARY_KEY_STRATEGY=GUID Anchor_Toc280791210_STRATEGY=GUID_Toc280791210

      Mapping Extension

      (see: org.LexGrid.LexBIG.Extensions.Generic.MappingExtension)

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    • Faster retrieval of Mapping ontology relationships as compared to standard CodedNodeGraph methods
    • Expanded Sorting capabilities to include:
      • Source Code
      • Target Code
      • Source Entity Description
      • Target Entity Description
      • Relationship Name
      • A Named Qualifier
    • Ability to count the number of codes that participate in a mapping ontology without having to traverse
    • Determine whether or not an Ontology can be considered a 'Mapping' Ontology.
      • A 'Mapping' Ontology is defined in this case as having at least ALL Relations containers marked as 'isMapping=true'

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Supplement Extension

(see: org.LexGrid.LexBIG.Extensions.Generic.SupplementExtension)

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    • Determine whether or not a giving Coding Scheme is acting as a Coding Scheme Supplement.
    • Resolve the Parent Coding Scheme of a given Coding Scheme Supplement.

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Value Sets (gForge # 26650)

  • Administrative functions :
    • Ability to load Value Set and Pick List Definitions in to LexGrid repository
    • Ability to remove Value Set and Pick List Definitions from LexGrid repository.
    • Ability to export Value Set and Pick List Definition in LexGrid XML format.
  • Query functions :
    • Ability to list all the Value Set and Pick List Definitions loaded in the system.
    • Ability to dynamically resolve Value Set and Pick List Definition with/without user supplied restrictions.
    • Ability to check if a concept code is part of given Value Set.
    • Ability to check if one Value Set is sub set of other Value Set.
    • Ability to apply restrictions like term, coding scheme version, etc and resolve Value Set and Pick List Definition.
    • Ability to list all the coding schemes referenced by a Value Set Definition.
    • Ability to list all Value Set Definition URIs that references a Coding Scheme. Etc.
  • Authoring functions :
    • Ability to load/update/remove Value Set Definition, DefinitionEntry and Properties using Versioning API.
  • Scripts :
    • LoadValueSetDefinition(.bat and .sh) –Loads Value Set Definition in LexGrid XML file into repository.
    • LoadPickListDefinition(.bat and .sh) – Loads Pick List Definition in LexGrid XML file into repository.
  • GUI :
    • New GUI (LB_VSD_GUI in gui folder of LexEVS API install directory) is developed to test all the functionalities that are available for Value Set Definitions. This tool should mainly be used for testing purpose and not in production. Here are few major functions available through this GUI tool:
      • Create new Value Set Definition
      • Update existing Value Set Definition
      • Remove existing Value Set Definition
      • Load Value Set and Pick List Definition from LexGrid XML file
      • List all Value Set and Pick List Definitions present in the system
      • Add/update/remove DefinitionEntries (rule sets)
      • Add/update/remove properties
      • Resolve Value Set and Pick List Definition using specific set of coding scheme and version that are loaded in the system
      • Ability to validate if the changes made returns desired result before saving changes to the database
      • Export Value Set and Pick List Definitions in LexGrid XML format
      • Following query functions are also available:
        • Filter by Coding Scheme Reference
        • Filter by Concept Domain
        • Check if concept code is valid entry in Value Set Resolution
        • Filter by a term
        • Check if one Value Set is subset of other
        • Filter by Value Set Definition Name
  • JUnit :
    • Junit to test all the Value Set functionalities are included in lbTest java package.
      • Org.LexGrid.valuedomain.test.VDAllTests.java – Loads test data, runs both Value Set and Pick list functionality tests, and removes loaded test data.

Note: Usage Context and Concept Domain is not included in this release, but will be in next release.

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Versioning (gForge # 26651)

Versioning is a new functionality that has been added to LexEVS API in this release. Versioning API is divided into two parts, loader and query API. For this release, loader API is included; query API will be included in next release.

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    • Loader validates each of the versionable object before loading it. Below are the criteria for a valid versionable object.
    • EntryState must be present.
    • If the change type is NEW
    • The object being loaded should not exist in lexEVS system. (Exception : The <Versionable Object> being added already exist.)
    • prevRevision of entryState should be null. (Exception : Changes of type NEW are not allowed to have previous revisions.)
    • If the change type is other than NEW
    • The object being revised should be present in the lexEVS system. (Exception : The codingScheme being revised doesn't exist.)
    • The object must have prevRevision, except when the versionable object is revised first time after the "initial load". (Initial load : CodingScheme/ValueSet/PickList loaded with out a user defined revision)
    • The prevRevision should match the newest revision id of the given versionable object that is already loaded in the lexEVS system. (Exception : Revision source is not in sync with the database revisions. Previous revision id does not match with the latest revision id of the <Versionable object>. Please update the authoring instance with all the revisions and regenerate the source. )
  • JUnit :
    • VersionableEventAuthoringTest in lbTest package.

...

    • )
  • JUnit :
    • VersionableEventAuthoringTest in lbTest package.

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XML Loaders

  • Streaming XML (gForge # 26652): Ability to stream vocabulary contents in LexGrid XML format into LexGrid repository.
  • Ability to load contents at following entry points:
    • Coding Scheme
    • Value Set Definition
    • Pick List Definition
    • Revision
  • JUnit :
    • Junit to test above functionalities are included in lbTest java package.

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...

XML Exporter

  • Content can be exported to a LexGrid XML file by use of the LexGrid XML Exporter.
  • The LexGrid XML Exporter can be accessed from a command line or from the LexGrid GUI.
  • As of Prototype 3, the following content export scenarios are supported from the command line, GUI or both:
    • Entire code system (both)
    • Concepts only (GUI)
    • Associations only (GUI)
    • Specific Association (GUI)
  • Accessing function within the GUI:
    • Entire code system:
      • At the menu: Commands -> Enable Admin Options
      • Select code system
      • At the menu: Export Terminology -> Export as LexGrid XML
    • Concepts only:
      • Select code system
      • Click 'Get Code Set' button
      • Select the CodedNodeSet (CS) from the list
      • Click the 'LgExport' button
    • Associations only:
      • Select code system
      • Click 'Get Code Graph' button
      • Select the CodedNodeGraph (CG) from the list. Note: restrict the set of associations by name:
  • Click the 'Add' button in the Restrictions frame
  • Then, in the 'Configure LexBIG' window:
  • Select 'Restrict to Associations' in the 'Restriction Type' drop down
  • Select the association name in the 'Associations' selection box
  • Click the OK button
  • Click the 'LgExport' button

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  • Command line
    • Does not currently support the same level of function as the GUI. Only entire code systems can be exported via the command line. Additional filtering options will be available from the command line at a later date (Alpha 1).
    • When calling the XML Exporter from the command line always specify the force option '-f'. Otherwise the export will fail saying the output file already exists. This is a bug and will fixed during Alpha1 development.
  • Scaling issues. Exporting of concepts should take place via streaming the content to the file and so should not be constrained by memory. At this time, however, associations are loaded into memory and so memory may be a factor in exporting code systems with many associations. This will be addressed during Alpha 1 development.

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GForge Items

21720 – Load MRMAP data

  • MRMAP data is now loaded as a Mapping Coding Scheme

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  • This issue has been resolved in LexEVS 6.0 Prototype 3 and later releases. Tested and verified.
  • JUnit Test case is created and successfully executed with implementation class "org.LexGrid.LexBIG.Impl.bugs.GForge22296" in project lbTest.

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LexGrid model changes

Package ValueSets:

  • Renamed element ValueDomainDefinition to ValueSetDefinition and container ValueDomains to ValueSets. GForge # 27021.
  • Added attribute 'conceptDomain' of type 'conceptDomain' to class 'valueSetDefinition' to support CTS 2 SFM.
  • Added class 'propertyReference' and 'propertyMatchValue' to support CTS 2 SFM.
    • propetyReference contains : 'codingScheme'(Required), 'propertyName', 'propertyMatchValue'
    • propertyMatchValue extends from 'text' and contains attribute 'matchAlgorithm'
  • Made 'definitionEntry' versionable to support CTS 2 SFM.
  • Made class 'valueSetDefinition' and 'pickListDefinition' as entry point. This change allows to load and export Value Set Definition and Pick List Definition individually.

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