NIH | National Cancer Institute | NCI Wiki  

Versions Compared

Old Version 20

changes.mady.by.user Bauer, Scott (NIH/NCI) [C]

Saved on

compared with

New Version 21

changes.mady.by.user Bauer, Scott (NIH/NCI) [C]

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

Table of Contents

Introduction

The Asserted Value Set services are integrated parts of the LexEVS API. It provides several functions:

...

Most coding scheme representations and entity reference sets are resolved by the unique URL of the coding scheme.  Some allow a definition of a concept or text match.  All methods offer a resolution service to some set of values.  These mechanisms are largely read functions requiring a listing of known values or an exact match of a unique identifier.  Only one method offers what could be classified as a search. 

 

SourceAssertedValueSetService Class Diagram

 

LexEVS Asserted Value Set Definition Services API

LexEVS Value Set Definition Services provides three major functions:

...

Each of these functions are described in following sections.

 

List Functions

  • List all value sets as coding schemes
  • List all value set entities in the asserted source system

...

Description:

Lists all coding schemes – no entities resolved

Input:

none

Output:

List<CodingScheme>

Exception:

LBException

Implementation Details:

Implementation:
Call this method on the associated LexEVS Asserted Value Set service instance to list a full set of coding schemes minus their entities
Sample Call:

  • Step 1: Instantiate SourceAssertedValueSetService if it is not done yet:

    Code Block
    org.lexgrid.valuesets.SourceAssertedValueSetServiceImpl  assVSServ = new SourceAssertedValueSetServiceImpl(new AssertedValueSetParameters.Builder().build());

  • Step 2: List all the coding scheme representations of the value sets

    Code Block
    List<CodingScheme> schemes = assVSService.getMinimalSourceAssertedValueSetSchemes();

     

     

Coding Scheme Read Functions

  • Get value sets by concept reference - Input an object that matches namespace and unique code of a value set member to return a list of containing schemes
  • Get value sets by entity code - input is entity code only, no namespace is defined to read the value set that contains this as a value set member
  • Get a single value set for its unique URI - The input should be an unique identifier for a coding scheme representation of a value set in the system
  • Get a value set or value sets defined by a unique entity - The input is a unique entity code that identifies the top node of a given value set
  • Get scheme references for a coding scheme representation - Pulls from a coding scheme those schemes from which the entities of the coding scheme representation of the value set is derived.

...

Description:

Gets minimal representations of coding schemes based on what was used to resolve a value set

Input:

CodingScheme cs: CodingScheme object with full metadata populated, entity representation not necessary

Output:

AbsoluteCodingSchemeVersionReferenceList:  Might be more than one coding scheme that defines this value set

Exception:

none

Implementation Details:

Implementation:
Call this method on the associated LexEVS Asserted Value Set service instance to determine what coding schemes define the value set. 
Sample Call:

  • Step 1: Instantiate SourceAssertedValueSetService if it is not done yet:

    Code Block
    org.lexgrid.valuesets.SourceAssertedValueSetServiceImpl  assVSServ = new SourceAssertedValueSetServiceImpl(new AssertedValueSetParameters.Builder().build());

  • Step 2: Get a coding scheme using one of the Asserted Value Set Service methods: 

    Code Block
    CodingScheme cs = assVSServ.getSourceAssertedValueSetForValueSetURI(new URI("http://evs.nci.nih.gov/valueset/CDISC/C12434")) ;

  • Step  3: List all the coding schemes defined by the top node designated by the unique identifier

    Code Block
    AbsoluteCodingSchemeVersionReferenceList list = assVSServ.getListOfCodingSchemeVersionsUsedInResolution(cs);

     

     

Concept Reference Read Functions

  • Get references for unique URI identifier - Unique identifier returns all value set members of that coding scheme representation of a value set.
  • Get a list of string unique identifiers of references that are a top node - All top nodes of a system are returned based on the identification of the node that has a reference to the top of the hierarchy

...

Description:

Gets String references to all top node leaves under a root node

Input:

String rootCode: String representation of the unique identifier of the Asserted Value Set root entity

Output:

List<String>:  String references to entity top node designations of the Asserted Value Sets

Exception:

none

Implementation Details:

Implementation:
Call this method on the associated LexEVS Asserted Value Set service instance to get all top node string identifier references
Sample Call:

  • Step 1: Instantiate SourceAssertedValueSetService if it is not done yet:

    Code Block
    org.lexgrid.valuesets.SourceAssertedValueSetServiceImpl  assVSServ = new SourceAssertedValueSetServiceImpl(new AssertedValueSetParameters.Builder().build());

  • Step 2: Get a list of all the top nodes in the Asserted Value Set system:

    Code Block
    List<String> list = assVSServ.getSourceAssertedValueSetTopNodesForRootCode("C54443");

     

     

Search Function

  • Get value set coding scheme reference based on a text match for a member entity - Can be used with a text match algorithm determining match type.

...

Description:

Gets minimal coding scheme references of value sets for a text match

Input:

String matchText: Text to match on for contains, exact, other algorithms as allowed.

MatchAlgorithm matchType: Type of matching for any given match type in this enum.

Output:

List<AbsoluteCodingSchemeVersionReference>:  String references to entity top node designations of the Asserted Value Sets

Exception:

none

Implementation Details:

Implementation:
Call this method on the associated LexEVS Asserted Value Set service instance to get any coding scheme references that have a member entity with text matching the text and algorithm
Sample Call:

  • Step 1: Instantiate SourceAssertedValueSetService if it is not done yet:

    Code Block
    org.lexgrid.valuesets.SourceAssertedValueSetServiceImpl  assVSServ = new SourceAssertedValueSetServiceImpl(new AssertedValueSetParameters.Builder().build());

  • Step 2: Get a list of all the top nodes in the Asserted Value Set system:

    Code Block
    List<AbsoluteCodingSchemeVersionReference> list = assVSServ.getSourceAssertedValueSetsforTextSearch("blood", MatchAlgorithm.PRESENTATION_EXACT);

     

     

 

System Testing

The System test case for the LexEVS Value Set Definition service is performed using the JUnit test suite:

...

This test suite will be run as part of regular LexEVS test suite AllTestsNormalConfigs.

Installation / Packaging

Value Set Definition Services are integrated parts of core LexEVS API and are packaged and installed with other LexEVS services.

...