Creates new Association

• 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

org.LexGrid.relations.AssociationSource - Created Association Structure

org.LexGrid.LexBIG.Exceptions.LBException

• 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);

Updates Association Status

• 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

boolean - flag for successful update

org.LexGrid.LexBIG.Exceptions.LBException

• 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);