NIH | National Cancer Institute | NCI Wiki  

WIKI MAINTENANCE NOTICE

Please be advised that NCI Wiki will be undergoing maintenance Monday, July 22nd between 1700 ET and 1800 ET and will be unavailable during this period.
Please ensure all work is saved before said time.

If you have any questions or concerns, please contact the CBIIT Atlassian Management Team.

Error rendering macro 'rw-search'

null

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 17 Next »

Introduction

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

Getting Source Asserted Value Sets as CodingScheme or Coding Scheme reference objects

Getting the entities of Source Asserted Value Sets as ResolvedConceptReference objects as Lists or Iterators

Getting a list of all unique identifiers of value set top nodes from this source terminology

Getting a list of all schemes used to resolve a given set of values from a resolved value set coding scheme

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 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:

  • List function
  • Read function
  • Search function

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

List All Value Sets As Fully Populated Coding Schemes

listAllSourceAssertedValueSets()

Description:

Lists all coding schemes each with its own entity set fully 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 along with all of their entities
Sample Call:

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

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

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

    List<CodingScheme> schemes = assVSService.listAllSourceAssertedValueSets();

     

     

 

List all Coding Schemes without entities

getMinimalSourceAssertedValueSetSchemes()

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:

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

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

    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.

Get Value Sets by Concept Reference

getSourceAssertedValueSetsForConceptReference(ConceptReference ref)

Description:

Lists all coding schemes containing a particular concept reference

Input:

ConceptReference ref - Configurable to contain both the unique identifier and the namespace of the target coding scheme (both are tied to the asserting source in this case)

Output:

List<CodingScheme>

Exception:

none

Implementation Details:

Implementation:
Call this method on the associated LexEVS Asserted Value Set service instance to get a coding scheme representation of a vale set containing this concept reference
Sample Call:

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

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

  • Step 2: Construct the ConceptReference object:

    ConceptReference ref = new ConceptReference();
ref.setConceptCode("C1234");
ref.setCodeNamespace("ncit");

  • Step 3: List all the coding scheme representations of the value sets

    List<CodingScheme> schemes = assVSServ.getSourceAssertedValueSetsForConceptReference(ref);

 

Get Value Sets For Entity Code

getSourceAssertedValueSetForValueSetURI

Description:

Lists all coding schemes that have a top node defined by a unique entity code

Input:

String matchCode: unique identifier of the top node entity

Output:

List<CodingScheme>:  Might be more than one value set defined by this top node.

Exception:

LBException

Implementation Details:

Implementation:
Call this method on the associated LexEVS Asserted Value Set service instance to get one or more coding scheme representations of value sets that have a top node defined by this identifier
Sample Call:

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

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

  • Step 2: List all the coding schemes defined by the top node designated by the unique identifier

    List<CodingScheme> schemes = assVSServ.getSourceAssertedValueSetforTopNodeEntityCode("C12434");

     

     

 

Get a single value set for its unique URL

getSourceAssertedValueSetForValueSetURI

Description:

Gets a coding scheme representation of a value set based on its unique URI designation

Input:

URI uri: unique identifier of the top node entity wrapped in a URI object

Output:

CodingScheme:  Might be more than one value set defined by this top node.

Exception:

LBException

Implementation Details:

Implementation:
Call this method on the associated LexEVS Asserted Value Set service instance to get a single coding scheme representation of a value set using it's unique identifier wrapped in a URI object.
Sample Call:

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

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

  • Step 2: Instantiate a URI object using a string representation of the URI designation

    URI uri = new URI("http://evs.nci.nih.gov/valueset/CDISC/C12434");

  • Step 2: List all the coding schemes defined by the top node designated by the unique identifier

    CodingScheme scheme = assVSServ.getSourceAssertedValueSetForValueSetURI(uri);

     

     

 

Get Coding Scheme References for Any Source Schemes Used to Resolve a Coding Scheme Representation of a Value Set

getListOfCodingSchemeVersionsUsedInResolution

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:

    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: 

    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

    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

Get Resolved Concept References for the Coding Scheme Unique Identifier

getSourceAssertedValueSetIteratorForURI
getSourceAssertedValueSetEntitiesForURI

Description:

Gets Resolved Concept Reference representations of entity values in a value set based on the unique identifier of the coding scheme representation

Input:

String uri: String representation of the coding scheme unique identifier

Output:

ResolvedConceptReferenceList or ResolvedConceptReferencesIterator:  Entities listed or iterated over that are members of the value set defined by the unique URI designation

Exception:

none

Implementation Details:

Implementation:
Call this method on the associated LexEVS Asserted Value Set service instance to get entities from a unique value set
Sample Call:

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

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

  • Step 2: Get an iterator over the entity members of the value set

    ResolvedConceptReferencesIterator iterator = assVSServ.getSourceAssertedValueSetIteratorForURI("http://evs.nci.nih.gov/valueset/CDISC/C119014");

  • or get a list

    ResolvedConceptReferenceList list = assVSServ.getSourceAssertedValueSetEntitiesForURI("http://evs.nci.nih.gov/valueset/CDISC/C119014");

     

     

 

Get Top Node References

 getSourceAssertedValueSetTopNodesForRootCode

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:

    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: 

    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.

 

Get a Value Set from Text Match

getSourceAssertedValueSetsforTextSearch

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:

    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: 

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

     

     

 

 

  • No labels