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Menu LexEVS 6.0 CTS2 to Include
Menu LexEVS 6.0 CTS2 to Include

Introduction

LexEVS CTS2 Code System Authoring API provides capability to author Code System and its contents.

Here are the authoring functions that can be performed on Associations in a Code System:

Create

This function provides capability to create:

  • New Association
  • Add Qualifiers to the Association
  • Determine Source and Target Code Systems for the Association
  • New Coding Scheme consisting of mappings of one system's concepts to another.
  • New Mapping for an existing mapping scheme
  • New Association for an existing coding scheme.

Status Change

This function provides capability to update Status attributes:

  • Association Status

Interface

Code Block
org.lexevs.cts2.LexEvsCTS2 cts2 = org.lexevs.cts2.LexEvsCTS2Impl.defaultInstance();
org.lexevs.cts2.author.AssociationAuthoringOperation associationAuthoring = 
cts2.getAuthoringOperation().getAssociationAuthoringOperation();

Revision Information

Authoring requires information helping to determine whether the edited coding scheme element is new or revises an existing association. This requires not only a containing revision, but also a entry state object for each versionable element of the Association being created. A single object of each is passed into the association creating method providing mandatory information about this revision which in most use cases here is a new association.

org.LexGrid.versions.Revision

Revision object has following attributes:

  • java.lang.String changeAgent - (Optional) The source that participated in this particular change.
  • java.lang.String changeInstruction - (Optional) A human or machine readable set of instructions on how to apply this change.
  • java.lang.String revisionId - (Mandatory) The unique identifier of this revision.
  • java.lang.Long editOrder - (Optional) The relative order that this revision is to be applied if in a systemRelease.
  • java.util.Date revisionDate - (Optional) The end date for which this version is operative (considered commited).
  • java.lang.String description - (Optional) The description of the resource/change.
  • java.lang.String systemReleaseURI - (Optional) The official URI of this release

org.LexGrid.versions.EntryState

  • java.lang.String containingRevision - (Mandatory)The revision that contains this particular entry state change
    private java.lang.Long relativeOrder - (Optional)The relative order that this state change should be applied within the context of the containing revision
  • private org.LexGrid.versions.types.ChangeType changeType - (Context determined. NEW for new association)The type of change that occurred between this state and the previous.
  • private java.lang.String prevRevision - (Optional)The unique identifier of the state of this entry was at prior to this change.

Association Authoring Functions

Create Association Operations

createAssociation(boolean createMappingScheme, Revision revision, EntryState entryState, AbsoluteCodingSchemeVersionReference mappingScheme, AbsoluteCodingSchemeVersionReference sourceCodeSystemIdentifier, AbsoluteCodingSchemeVersionReference targetCodeSystemIdentifier, String sourceConceptCodeIdentifier, String targetConceptCodeIdentifier, String relationsContainerName, String associationType, AssociationQualification[] associationQualifiers)

Description:

Creates new Association

Input:

  • boolean createMappingScheme - create a mapping coding scheme if one does not exist
  • org.LexGrid.versions.Revision revision - create a mapping coding scheme if one does not exist
  • org.LexGrid.versions.EntryState entryState - revision data container granular to the versionable class.
  • Aorg.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference mappingScheme - existing mapping scheme, required if adding mapped association
  • org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference sourceCodeSystemIdentifier - minimum code system identification
  • org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference targetCodeSystemIdentifier - minimum code system identification
  • java.lang.String sourceConceptCodeIdentifier - source concept code
  • java.lang.String targetConceptCodeIdentifier - target concept code
  • java.lang.String relationsContainerName - relations container identifier
  • java.lang.String associationType - association type identifier
  • org.LexGrid.relations.AssociationQualification[] associationQualifiers - qualifications to add to this association

Output:

org.LexGrid.relations.AssociationSource - Created Association Structure

Exception:

org.LexGrid.LexBIG.Exceptions.LBException

Sample Call:

  • Step 1: Create Revision Elements:
    Code Block
    Revision revision = new Revision(); - initalize Revision object
revision.setChangeAgent("Mayo Foundation"); - Set the change agent if desired
Text changeInstructions = new Text(); - initialize Text Object
changeInstructions.setContent("To be applied at next source release"); - Define change instructions if desired.
revision.setChangeInstructions(changeInstructions); - Set change instructions
revision.setEditOrder(new Long(1)); - Set edit order
EntityDescription entityDescription = new EntityDescription(); - Initialize EntityDescription Object
entityDescription.setContent("TestCTS2AssociationRevision"); - Set content for this object
revision.setEntityDescription(entityDescription); - Set revision entityDescription

EntryState entryState = new EntryState(); - Initialize EntryStateObject
entryState.setChangeType(ChangeType.NEW); - This is a new association -- set ChangeType to "NEW"
entryState.setContainingRevision("FirstRevision_12_09_2010"); - Define the revision identifier 
entryState.setRelativeOrder(new Long(1)); - Set relative order
  • Step 2: Define a source scheme:
    Code Block
    AbsoluteCodingSchemeVersionReference sourceCodeSystemIdentifier = new AbsoluteCodingSchemeVersionReference();
sourceCodeSystemIdentifier.setCodingSchemeURN("http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#");
sourceCodeSystemIdentifier.setCodingSchemeVersion(10.10a);
  • Step 3: Define a target scheme:
    Code Block
    AbsoluteCodingSchemeVersionReference targetCodeSystemIdentifier = new AbsoluteCodingSchemeVersionReference();
targetCodeSystemIdentifier.setCodingSchemeURN("urn:oid:2.16.840.1.113883.6.2");
targetCodeSystemIdentifier.setCodingSchemeVersion(200909);
  • Step 4: Name the unique identifier of the source concept:
    Code Block
    String sourceConceptCodeIdentifier = "C27469";
  • Step 5: Name the unique identifier of the target concept:
    Code Block
    String targetConceptCodeIdentifier = "199";
  • Step 6: Identify or name a new relations container
    Code Block
    String relationsContainerName = "relations";
  • Step 7: Name the association
    Code Block
    String associationType = "SY";
  • Step 8: call create method to create the association:
    AssociationSource association = associationAuthoringOp.createAssociation(false, revision, entryState,

    null, sourceCodeSystemIdentifier, targetCodeSystemIdentifier,
    sourceConceptCodeIdentifier, targetConceptCodeIdentifier,
    relationsContainerName, associationType, null);

Update Association Operations

updateAssociationStatus(Revision revision, EntryState entryState, AbsoluteCodingSchemeVersionReference scheme, String relationsContainer, String associationName, String sourceCode, String sourceNamespace, String targetCode, String targetNamespace, String instanceId, String status, boolean isActive)

Description:

Updates Association Status

Input:

  • org.LexGrid.versions.Revision revision - create a mapping coding scheme if one does not exist
  • org.LexGrid.versions.EntryState entryState - revision data container granular to the versionable class.
  • org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference scheme - Scheme targeted for update.
  • java.lang.String relationsContainerName - relations container identifier
  • java.lang.String associationName - association identifier
  • java.lang.String sourcCode - source concept code
  • java.lang.String sourceNamespace - code system identification
  • java.lang.String targetCode - target concept code
  • java.lang.String targetNamespace - minimum code system identification
  • java.lang.String instanceId - instance identifier for the association
  • java.lang.String status - Status designation can be user defined
  • boolean isActive - flag for Active status

Output:

boolean - flag for successful update

Exception:

org.LexGrid.LexBIG.Exceptions.LBException

Sample Call:

  • Step 1: Create Revision Elements:
    Code Block
    Revision revision = new Revision(); - initalize Revision object
revision.setChangeAgent("Mayo Foundation"); - Set the change agent if desired
Text changeInstructions = new Text(); - initialize Text Object
changeInstructions.setContent("To be applied at next source release"); - Define change instructions if desired.
revision.setChangeInstructions(changeInstructions); - Set change instructions
revision.setEditOrder(new Long(1)); - Set edit order
EntityDescription entityDescription = new EntityDescription(); - Initialize EntityDescription Object
entityDescription.setContent("TestCTS2AssociationRevision"); - Set content for this object
revision.setEntityDescription(entityDescription); - Set revision entityDescription

EntryState entryState = new EntryState(); - Initialize EntryStateObject
entryState.setChangeType(ChangeType.MODIFY); - Association is being revised.  Set ChangeType to "MODIFY"
entryState.setContainingRevision("FirstRevision_12_09_2010"); - Define the revision identifier 
entryState.setRelativeOrder(new Long(1)); - Set relative order
  • Step 2: Define the scheme for the association update:
    Code Block
    AbsoluteCodingSchemeVersionReference scheme = new AbsoluteCodingSchemeVersionReference();
scheme.setCodingSchemeURN("http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#");
scheme.setCodingSchemeVersion(10.10a);
  • Step 3: Name the unique identifier of the source concept:
    Code Block
    String sourceCode = "C27469";
  • Step 4: Define the namespace of the source concept supported for this coding scheme
    Code Block
    String sourceNamespace = "NCI Thesaurus"
  • Step 5: Name the unique identifier of the target concept:
    Code Block
    String targetCode = "C27469";
  • Step 6: Identify or name a new relations container
    Code Block
    String relationsContainerName = "relations";
  • Step 7: Define the association
    Code Block
    String associationName = "Disease_Has_Abnormal_Cell";
  • Step 8: Identify the instance of this association to be updated.
    Code Block
    String instanceID = "instance001";
  • Step 9: Define the new status
    Code Block
    String status = "PENDING_RETIREMENT";
  • Step 10: Set isActive flag if necessary
    Code Block
    boolean isActive = false;
  • Step 11: call create method to create the association:
    AssociationSource association = associationAuthoringOp.updateAssociationStatus(revision, entryState,

    scheme, relationsContainerName, associationName, sourceCode,
    namespace, targetCode, namespace, instanceId, status,
    isActive);
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