LexEVS 6.5.1 Value Set Architecture

Better logging to help determine if there were any failures for resolving the 760+ value sets.

• We can write a value set loader that ignores these.
• We can ignore targetToSource=false

• In browser, value set path, group by standards authority/ sourced terminology, click on collapse.
• In order to create the top nodes, need to find that annotation.
• Kim queries against these for Value Set metadata

• There are several users.  We should keep this for 6.x
• Re evaluate if needed after 6.x

Provide concurrent value set loading capability

Provide programmatic access to value set definition XML files

We need efficient way to retrieve this day (Kim)

• Return time should be in seconds

yes

Search value sets by code or name that matches with any member (concept) of a value set using a user-specified (exactMatch, startsWith, or contains) algorithm.

(Browser) Source specific information - need to call LexEVS API for each vs

Iterator without having to further query

Kim mentioned this when you click the value set button.  Needs further definition and investigation. Kim's notes:

Provide source specific value set resolution data through an iterator.

    Formats:

    (Case 1) Value sets with a non-NCIt default coding scheme (e.g., NDF-RT).

        Code

        Preferred Name

        Coding Scheme Name,

        Namespace

    (Case 2) Value sets with a NCIt default coding scheme and has no non-NCI supportedSource,

               NCIt Concept Code

               NCIt Preferred Term

               NCIt Synonyms

               NCIt Definition

    (Case 3) Value sets with a NCIt default coding scheme and has at least one non-NCI supportedSource (e.g., FDA),

               NCIt Concept Code

               Source Name (e.g., FDA Name)

               NCIt Preferred Term

               NCIt Synonyms

               Source Definition (e.g., FDA Definition)

               NCIt Definition

               (Note: If there are multiple supportedSource, then use the first supportedSource.)

Build source (i.e., standards authority) view and terminology view of value set hierarchy efficiently from the NCIt Source, the NDFRT source and value set definitions as they exist the database.

We need to understand the values and procedures needed to support this better

First, a terminology Termonilogy_Value_set.owl is constructed for supporting the

creation of value set hierarchies.

Each concept in the Termonilogy_Value_set terminology is assigned a unique TVS code, for example, TVS_FDA (see below).

The hierarchical relationship among concepts in the Termonilogy_Value_set is uniquely defined by

the subClassOf relationship. One can view this hierarchical structure as a

graph with each node representing a bin which holds value sets.

Value sets are placed into these bins in accordance with

the value of the source tag as appearing in its corresponding value set definition xml file.

For example, the value set, FDA CDRH GUDID Terminology, will be placed into the bin with an id or tag called TVS_CDRH_GUID_Component

because in the XML file, there is a source tag with value TVS_CDRH_GUID_Component:

    <source>TVS_CDRH_GUID_Component</source>

Note that a value set can be placed into multiple bins.

(A) A sample class in the terminology Termonilogy_Value_set.owl:

  <owl:Class rdf:ID="TVS_CDRH_GUDID">

    <rdfs:subClassOf>

      <owl:Class rdf:ID="TVS_FDA"/>

    </rdfs:subClassOf>

    <Source rdf:datatype="http://www.w3.org/2001/XMLSchema#string"

    >FDA_CDRH_GUDID</Source>

    <Display rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean"

    >false</Display>

    <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"

    >FDA CDRH GUDID Terminology</rdfs:label>

    <Description rdf:datatype="http://www.w3.org/2001/XMLSchema#string"

    >A set of terminology created to support the efforts of the FDA CDRH Global Unique Device Identification Database project.</Description>

    <Preferred_Name rdf:datatype="http://www.w3.org/2001/XMLSchema#string"

    >FDA CDRH GUDID Terminology</Preferred_Name>

  </owl:Class>

(B) A sample Value set definition XML file, FDA CDRH GUDID Terminology:

<?xml version="1.0" encoding="UTF-8"?>

<valueSetDefinition xmlns="http://LexGrid.org/schema/2010/01/LexGrid/valueSets" isActive="true"

     status="1" valueSetDefinitionURI="http://evs.nci.nih.gov/valueset/C106039"

     valueSetDefinitionName="FDA CDRH GUDID Terminology"

     defaultCodingScheme="NCI_Thesaurus"

     conceptDomain="Intellectual Product">

     <ns1:owner xmlns:ns1="http://LexGrid.org/schema/2010/01/LexGrid/commonTypes">NCI</ns1:owner>

     <ns2:entityDescription xmlns:ns2="http://LexGrid.org/schema/2010/01/LexGrid/commonTypes">

         A set of terminology created to support the efforts of the FDA CDRH Global Unique Device Identification

         Database project.</ns2:entityDescription>

     <mappings>

         <ns3:supportedCodingScheme xmlns:ns3="http://LexGrid.org/schema/2010/01/LexGrid/naming"

              localId="NCI_Thesaurus"

              uri="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"

              isImported="true">NCI_Thesaurus

         </ns3:supportedCodingScheme>

         <ns4:supportedConceptDomain xmlns:ns4="http://LexGrid.org/schema/2010/01/LexGrid/naming" localId="Intellectual Product">Intellectual Product

         </ns4:supportedConceptDomain>

         <ns5:supportedNamespace xmlns:ns5="http://LexGrid.org/schema/2010/01/LexGrid/naming" localId="NCI_Thesaurus" uri="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#" equivalentCodingScheme="NCI_Thesaurus">NCI_Thesaurus

         </ns5:supportedNamespace>

         <ns6:supportedSource xmlns:ns6="http://LexGrid.org/schema/2010/01/LexGrid/naming" localId="CDRH">

             CDRH

         </ns6:supportedSource>

         <ns7:supportedSource xmlns:ns7="http://LexGrid.org/schema/2010/01/LexGrid/naming" localId="FDA">

             FDA

         </ns7:supportedSource>

     </mappings>

     <source>TVS_CDRH_GUID_Component</source>

     <properties/>

     <definitionEntry ruleOrder="0" operator="OR">

         <entityReference entityCode="C106039" entityCodeNamespace="NCI_Thesaurus" referenceAssociation="Concept_In_Subset" transitiveClosure="true" leafOnly="true" targetToSource="true"/>

     </definitionEntry>

</valueSetDefinition>

There are two views of value set hierarchies in the NCI term browser.

(See https://nciterms.nci.nih.gov/ncitbrowser/ajax?action=create_src_vs_tree&nav_type=valuesets&mode=0)

(1) Value sets grouped by Standards Authority.

(2) Value sets by Source Terminology.

At term browser initialization, value set metadata containing the data in all value set definition XML files are

retrieved from the database through the LexEVSAPI and used for constructing the above two value set hierarchies.

The first hierarchy (Value sets grouped by Standards Authority) is constructed by the value of the source, such as TVS_CDRH_GUID_Component above.

The second hierarchy is constructed using the same method with an additional step that bins are partitioned in according to

the value of the value of defaultCodingScheme as shown in the value set definition XML files.

This informs our value set meta data resolution performance requirement, but is not currently a requirement on it's own.