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Overview

This section is an addendum to the LexEVS 5.0 Design and Architecture Guide. It provides detail on how different formats are loaded into the LexEVS v5.0 model.

The Unified Medical Language System (UMLS) and Rich Release Format (RRF) Files

The UMLS' large medical thesaurus is available as a set of text based, "|" separated files which can be made subset into individual terminologies depending on the user's needs. NCI's MetaThesaurus is also RRF formatted. We map individual terminologies, the entire NCI MetaThesaurus and the UMLS terminology SEMNET into LexGrid Using specific loaders and mappings for each.

  • Supported Coding Scheme Attributes: These aren't mapped as categories to a model element. That is, a supported association has an attributeTag column with a corresponding name, but it's context is implied in the name of the supported attribute. For instance, supported associations will have an attributeTag of "association" but that tag corresponds to no element in the model element SupportedAssociation. Instead the context is implied in the name of the element SupportedAssociation.
  • Preferred Presentation Selection: Preferred Presentation is determined first by sorting the presentations to include first those in the default language of the Terminology. Following that and given there is more than one presentation in the default language the "most preferred" is determined in the following manner:
    Using the "isPref" column, the "TS" and "STT" columns in the MRCONSO RRF file, or a combination of these columns. The MRRANK file overrides these columns.
  • Preferred Definition Selection: Definitions in UMLs are not ranked, the first definition found for a concept in the source file MRDEF.RRF is set to preferred.
  • Special SNOMED adjustments for concept presentation language: Snomed handles it's language default settings differently than other UMLS terminologies, we hard code it's default language as "en" as a result.
    Presentation language is determined by combining the values of SUI, LUI and CUI from MRCONSO and selecting the ATV value from MRSAT where SAB always equals SNOMEDCT and the ATN value is either LANGUAGECODE or SUBSETLANGUAGECODE.
  • Association Qualifiers for medDRA and others: MedDRA employs SMQ's or Standardized Medical Queries as a method of classifying portions of this terminology. These are expressed in MRSAT.RRF when the AUI in the METAUI column is replaced by a RUI code. In LexBIG is RUI is identified in the MRREL.RRF source as relationships are loaded and the associated ATN and ATV values from the MRSAT.RRF row are populated as association qualifier name and value.
  • Hierarchies expressed in source contexts: Hierarchies in the UMLS are expressed in the MRREL.RRF file as source, target pairs. However source hierarchies may also be expressed in the MRHEIR.RRF file. These context based hierarchies are realized in LexBIG by accessing the MRHEIR source where the HCD column value is populate. When this is the case, as in MESH, the path of AUI's to root from the code in the HCD column is processed as a hierarchy. LexBIG's behavior is as follows:
    • Entries in MRHIER that define multiple contexts (HCD field) per CUI will trigger additional tracking within the LexBIG environment.
    • Each link is tracked via the corresponding contextual chain(Path To Root field). To do this, we add association qualifiers that tag the association between each participating concept. The qualifier name is 'HCD' and the value will be the HCD field value from the MRHIER file.
    • An individual association between two concepts can participate in multiple context chains by assigning additional association qualifiers. A complete flow across the entire chain of links (essentially reconstructing PTR field) can be derived by recursive evaluation of surrounding links that have the same context qualifications. Since each concept can carry multiple text presentations, property qualifiers will be used to track the individual terms used in each context.
    • As with associations, multiple qualifiers can be assigned to each text property. Once again, the qualifier name will be 'HCD' and the value will be the HCD field value from the MRHIER file.
    • In order to query context-specific relationships, we can first use the API to filter the relationships a concept participates in, then query neighboring nodes to determine the complete context path, and finally map back to specific terms through the registered HCD qualifiers .

OBO Mapping

The OBO each remark in the document header will be combined and put into the coding scheme entityDescription.

For example:

remark: autogenerated-by:     DAG-Edit version 1.320
remark: saved-by:             mariacos
remark: date:                 Fri Jun 27 09:41:28 EDT 2003
remark: version: $Revision: 1.1 $

Protege OWL

DatatypeProperty Representation

Owl

<owl:DatatypeProperty rdf:ID="currency">
          <rdfs:domain rdf:resource="#Money"/>
          <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
     </owl:DatatypeProperty>

In LexGrid, a DatatypeProperty is combination of a conceptProperty and Assocation.

Concept Property

<lgCon:concept id="Money">
      <lgCommon:entityDescription>Money</lgCommon:entityDescription>
      ....
     <lgCon:conceptProperty propertyId="P0003" propertyName="currency">
        <lgCommon:text>xsd:string</lgCommon:text>
      </lgCon:conceptProperty>
    </lgCon:concept>

Association

<lgRel:association id="hasDomain" forwardName="hasDomain"
isReflexive="false" isSymmetric="false"
isTransitive="true" reverseName="kindIsDomainOf">
      <lgRel:sourceConcept sourceEntityType="association"
sourceId="currency">
        <lgRel:targetConcept targetEntityType="concept"
targetId="Money"/>
      </lgRel:sourceConcept>

 <lgRel:association id="currency">
      <associationProperty propertyId="P0007"
propertyName="isDatatypeProperty">
        <lgCommon:text>true</lgCommon:text>
      </associationProperty>
      <associationProperty propertyId="P0008"
propertyName="isObjectProperty">
        <lgCommon:text>false</lgCommon:text>
      </associationProperty>
    </lgRel:association>

 <lgRel:association id="datatype" forwardName="datatype">
      <lgRel:sourceConcept sourceEntityType="association"
sourceId="currency">
        <lgRel:targetDataValue dataId="D0001">
          <lgRel:dataValue>string</lgRel:dataValue>
        </lgRel:targetDataValue>

Equivalent Class Representation

Owl

<owl:Class rdf:ID="Father">
    <owl:equivalentClass>
      <owl:Class>
        <owl:intersectionOf rdf:parseType="Collection">
          <owl:Class rdf:about="#Person"/>
          <owl:Restriction>
            <owl:onProperty>
              <owl:FunctionalProperty rdf:about="#hasSex"/>
            </owl:onProperty>
            <owl:hasValue rdf:resource="#MaleSex"/>
          </owl:Restriction>
          <owl:Restriction>
            <owl:someValuesFrom rdf:resource="#Person"/>
            <owl:onProperty>
              <owl:ObjectProperty rdf:about="#hasChild"/>
            </owl:onProperty>
          </owl:Restriction>
        </owl:intersectionOf>
      </owl:Class>
    </owl:equivalentClass>
  </owl:Class>

In LexGrid, the equivalentClass is represented as an Association.

Association

<lgRel:association id="equivalentClass"
forwardName="equivalentClass" isReflexive="true" isSymmetric="true"
isTransitive="true" reverseName="equivalentClass">
  <lgRel:sourceConcept sourceEntityType="concept" sourceId="Father">
        <lgRel:targetConcept targetEntityType="concept" 	targetId="A38"/>
      </lgRel:sourceConcept>

Restriction Representation

Owl

<owl:Class rdf:ID="Large-Format">
          <rdfs:subClassOf rdf:resource="#Camera"/>
          <rdfs:subClassOf>
               <owl:Restriction>
                     <owl:onProperty rdf:resource="#body"/>
                     <owl:allValuesFrom rdf:resource="#BodyWithNonAdjustableShutterSpeed"/>
               </owl:Restriction>
          </rdfs:subClassOf>
     </owl:Class>

In LexGrid, a restriction is a combination of association and qualifier.

Association

<lgRel:association codingSchemeId="p1" id="body"
forwardName="body" isFunctional="false"
isReverseFunctional="false"
isSymmetric="false" isTransitive="false">
      <lgRel:sourceConcept sourceCodingScheme="p1"
sourceEntityType="concept" sourceId="Large-Format">
        <lgRel:targetConcept targetEntityType="concept"
targetId="BodyWithNonAdjustableShutterSpeed">
          <lgRel:associationQualification
associationQualifier="owl:allValuesFrom"/>
        </lgRel:targetConcept>
      </lgRel:sourceConcept>
      <associationProperty propertyId="P0021"
propertyName="isDatatypeProperty">
        <lgCommon:text>false</lgCommon:text>
      </associationProperty>
      <associationProperty propertyId="P0022"
propertyName="isObjectProperty">
        <lgCommon:text>true</lgCommon:text>
      </associationProperty>
    </lgRel:association>

Additional Examples

Owl
<owl:Class rdf:ID="Father">
    <owl:equivalentClass>
      <owl:Class>
        <owl:intersectionOf rdf:parseType="Collection">
          <owl:Class rdf:about="#Person"/>
          <owl:Restriction>
            <owl:onProperty>
              <owl:FunctionalProperty rdf:about="#hasSex"/>
            </owl:onProperty>
            <owl:hasValue rdf:resource="#MaleSex"/>
          </owl:Restriction>
          <owl:Restriction>
            <owl:someValuesFrom rdf:resource="#Person"/>
            <owl:onProperty>
              <owl:ObjectProperty rdf:about="#hasChild"/>
            </owl:onProperty>
          </owl:Restriction>
        </owl:intersectionOf>
      </owl:Class>
    </owl:equivalentClass>
  </owl:Class>
LexGrid
<lgRel:association id="equivalentClass"
forwardName="equivalentClass" isReflexive="true"
isSymmetric="true"
isTransitive="true" reverseName="equivalentClass">
  <lgRel:sourceConcept sourceEntityType="concept"
sourceId="Father">
        <lgRel:targetConcept targetEntityType="concept"
targetId="A38"/>
      </lgRel:sourceConcept>


 <lgRel:association codingSchemeId="" id="hasSex"
forwardName="hasSex" isFunctional="true"
isReverseFunctional="false"
isSymmetric="false" isTransitive="false">
    <lgRel:sourceConcept sourceEntityType="concept"
sourceId="A38">
        <lgRel:targetConcept targetEntityType="concept"
targetId="MaleSex">
          <lgRel:associationQualification
associationQualifier="owl:hasValue"/>
        </lgRel:targetConcept>

<lgRel:association codingSchemeId="rdfs" id="subClassOf"
forwardName="subClassOf" isFunctional="false"
isReflexive="true"
isSymmetric="false" isTransitive="true"
reverseName="hasSubClass">
   <lgRel:sourceConcept sourceEntityType="concept"
sourceId="A38">
        <lgRel:targetConcept targetEntityType="concept"
targetId="Person"/>
      </lgRel:sourceConcept>

 <lgRel:association codingSchemeId="" id="hasChild"
forwardName="hasChild" isFunctional="false"
isReverseFunctional="false" isSymmetric="false"
isTransitive="false">
   <lgRel:sourceConcept sourceEntityType="concept"
sourceId="A38">
        <lgRel:targetConcept targetEntityType="concept"
targetId="Person">
          <lgRel:associationQualification
associationQualifier="owl:someValuesFrom"/>
        </lgRel:targetConcept>

<lgCon:concept id="A38" isAnonymous="true">
      <lgCommon:entityDescription>Person and
(hasSex has MaleSex)
and (hasChild some Person)</lgCommon:entityDescription>
      <lgCon:presentation propertyId="P0002"
propertyName="textualPresentation" isPreferred="true">
        <lgCommon:text>Person and (hasSex has MaleSex) and
(hasChild
some Person)</lgCommon:text>
      </lgCon:presentation>
      <lgCon:conceptProperty propertyId="P0001"
propertyName="type">
        <lgCommon:text>owl:intersectionOf</lgCommon:text>
      </lgCon:conceptProperty>
    </lgCon:concept>

Property Restriction Representation

Anonymous LexGrid concepts are created for property restrictions (UnionOf, hasValue).

Example 1

Owl
<owl:Class>
        <owl:unionOf rdf:parseType="Collection">
          <owl:Class rdf:about="#Hot"/>
          <owl:Class rdf:ID="Medium"/>
          <owl:Class rdf:about="#Mild"/>
        </owl:unionOf>
      </owl:Class>
LexGrid
<lgCon:concept id="A17" isAnonymous="true">
      <lgCommon:entityDescription>Hot or Medium or
Mild</lgCommon:entityDescription>
      <lgCon:presentation propertyId="P0001"
propertyName="textualPresentation" isPreferred="true">
        <lgCommon:text>Hot or Medium or Mild</lgCommon:text>
      </lgCon:presentation>
      <lgCon:conceptProperty propertyId="P0002"
propertyName="isUnion">
        <lgCommon:text>true</lgCommon:text>
      </lgCon:conceptProperty>
      <lgCon:conceptProperty propertyId="P0003"
propertyName="isIntersection">
        <lgCommon:text>false</lgCommon:text>
      </lgCon:conceptProperty>
      <lgCon:conceptProperty propertyId="P0004"
propertyName="isEnumeration">
        <lgCommon:text>false</lgCommon:text>
      </lgCon:conceptProperty>
    </lgCon:concept>

Example 2

Owl
<owl:Restriction>
                <owl:onProperty rdf:resource="#hasTopping"/>
                <owl:allValuesFrom>
                    <owl:Class>
                        <owl:unionOf rdf:parseType="Collection">
                            <owl:Class rdf:about="#MozzarellaTopping"/>
                            <owl:Class rdf:about="#PeperoniSausageTopping"/>
                            <owl:Class rdf:about="#JalapenoPepperTopping"/>
                            <owl:Class rdf:about="#TomatoTopping"/>
                            <owl:Class rdf:about="#HotGreenPepperTopping"/>
                        </owl:unionOf>
                    </owl:Class>
                </owl:allValuesFrom>
            </owl:Restriction>
LexGrid
<lgRel:association id="hasTopping" forwardName="hasTopping"
isFunctional="false" isNavigable="true" isReverseFunctional="true"
isSymmetric="false" isTransitive="false">

    <lgRel:sourceEntity sourceCodingScheme="pizza"
sourceEntityType="concept" sourceId="AmericanHot">
        <lgRel:targetEntity targetCodingScheme="pizza"
targetEntityType="concept" targetId="A16">
          <lgRel:associationQualification
associationQualifier="owl:allValuesFrom"/>
        </lgRel:targetEntity>
      </lgRel:sourceEntity>
  </lgRel:association>


        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="#hasTopping"/>
                <owl:allValuesFrom>
                    <owl:Class>
                        <owl:unionOf rdf:parseType="Collection">
                            <owl:Class
rdf:about="#MozzarellaTopping"/>
                            <owl:Class
rdf:about="#PeperoniSausageTopping"/>
                            <owl:Class
rdf:about="#JalapenoPepperTopping"/>
                            <owl:Class rdf:about="#TomatoTopping"/>
                            <owl:Class
rdf:about="#HotGreenPepperTopping"/>
                        </owl:unionOf>
                    </owl:Class>
                </owl:allValuesFrom>
            </owl:Restriction>
        </rdfs:subClassOf>


<lgCon:concept id="A16" isActive="true" isAnonymous="true">
      <lgCommon:entityDescription>MozzarellaTopping or
PeperoniSausageTopping or JalapenoPepperTopping or TomatoTopping or
HotGreenPepperTopping</lgCommon:entityDescription>
      <lgCon:presentation propertyId="P0002"
propertyName="textualPresentation" isPreferred="true">
        <lgCommon:text>MozzarellaTopping or PeperoniSausageTopping
or JalapenoPepperTopping or TomatoTopping or
HotGreenPepperTopping</lgCommon:text>
      </lgCon:presentation>
      <lgCon:conceptProperty propertyId="P0001" propertyName="type">
        <lgCommon:text>owl:unionOf</lgCommon:text>
      </lgCon:conceptProperty>
    </lgCon:concept>

NCI OWL

Top-level containers for relations are created, which separate the association types based on the notion of 'associations' and 'roles' as defined by NCI:

  • Associations are "non-inheritable, non-defining relations between concepts"
  • Roles are "inheritable relationships"

A LexGrid concept is created for every anonymous class present in the OWL ontology.

If no equivalent class for a concept, it is considered primitive and is indicated by creating a concept property set to 'true.'

NCI OWL Embedded XML

Property text with embedded XML fragments are identified by by the following identifiers:

  • qual-name
  • qual-value
  • qual

If the extracted tag is one of XML Text identifiers:

  • Value
  • term-name
  • def-definition
  • go-term

The text of the property is set to the tag value.

If the extracted tag is one of XML Source Name identifiers:

  • term-source
  • def-source

A property source is created and the tag value identifies the source.

If the property is a presentation and the extracted tag is XML Representational Form:

term-group

The representational form of the presentation property is set to the tag value.

If the extracted tag is one of DB XRef Prefix:

dbxref.*

A property qualifier is created. The property qualifier id is set to the tag, the value is set to the tag value.

HL7 RIM

Building a Single Coding Scheme

To build a single coding scheme from the HL7 MS Access database, implementation is similar to how the NCI MetaThesaurus is stored in LexGrid.

For example, here is how entries MTHU021347 and MTHU033458 in ICPC2ICD10ENG (NCI MethThesaurus C1394796) are structured in LexGrid:

  • Coding Scheme: NCI MetaThesaurus - urn:oid:2.16.840.1.113883.3.26.1.2
  • Concept Code: C1394796
  • Entity Description: decompensation; heart, senile
  • Status: Active
  • Is Active: true
  • Is Anonymous: false
  • Presentation: decompensation; heart, senile
  • Property Name: textualPresentation
  • Property Id: T-1
  • Language: ENG
  • Is Preferred: true
  • Representational Form: PT
  • Source: ICPC2ICD10ENG , Role: null, SubRef: null
  • Property Qualifier Id: source-code , Property Qualifier Content: MTHU021347
  • Presentation: heart; decompensation, senile
  • Property Name: textualPresentation
  • Property Id: T-2
  • Language: ENG
  • Is Preferred: false
  • Representational Form: PT
  • Source: ICPC2ICD10ENG , Role:''' null, SubRef: null
  • Property Qualifier Id: source-code , Property Qualifier Content: MTHU033458
  • ConceptProperty: Mental or Behavioral Dysfunction
  • Property Name: Semantic_Type
  • Property Id: SemType-1

In HL7, code systems, concepts, and designations are in the following tables:

VCS_concept_code_xref

Internal concept identifier

Code system

OID

Concept code

Case difference Status

10011

2.16.840.1.113883.5.55

M

0

A

10011

2.16.840.1.113883.5.55

R

0

A

10013

2.16.840.1.113883.5.55

RQ

0

A

10014

2.16.840.1.113883.5.55

NP

0

A

10015

2.16.840.1.113883.5.55

NR

0

A

10016

2.16.840.1.113883.5.55

RE

0

A

10017

2.16.840.1.113883.5.55

X

0

A

10019

2.16.840.1.113883.5.57

R

0

A

10020

2.16.840.1.113883.5.57

D

0

A

10021

2.16.840.1.113883.5.57

I

0

A

10022

2.16.840.1.113883.5.57

K

0

A

10023

2.16.840.1.113883.5.57

V

0

A

10025

2.16.840.1.113883.5.57

ESA

0

A

10026

2.16.840.1.113883.5.57

ESD

0

A

10027

2.16.840.1.113883.5.57

ESC

0

A

10028

2.16.840.1.113883.5.57

ESAC

0

A

VCS_concept_designation

Internal Id

Designation

seq - for case differences

language

preferredForLanguage

10011

Mandatory

0

en

-1

10011

Required - V2.x

0

en

0

Query of HL7 internal id, concept code and designation

codeSystemName

Code system OID

Internal concept identifier

Concept code

Designation

HL7ConformanceInclusion

2.16.840.1.113883.5.55

10011

R

Required - V2.x

HL7ConformanceInclusion

2.16.840.1.113883.5.55

10011

M

Mandatory

HL7ConformanceInclusion

2.16.840.1.113883.5.55

10011

M

Required - V2.x

HL7ConformanceInclusion

2.16.840.1.113883.5.55

10011

R

Mandatory

Representing HL7 in LexGrid

To represent HL7 in LexGrid:

  • A single coding scheme will be created in LexGrid.
  • Each VCS_concept_code_xref.internalId will be represented as a LexGrid Concept Code.
  • The LexGrid Concept Code will be generated by the concatination of VCS_concept_code_xref.internalId and VCS_concept_code_xref.conceptCode2 (separated by a colon ':' ).
  • Not only the duplicates that exist within coding schemes will be dealt with using the id/mnemonic concatenation but also those duplicates that exist between coding schemes.
  • A LexGrid Concept Code Presentation Property will be created for each HL7 designation (VCS_concept_designation).
  • The Presentation Property will include Presentation (HL7 Designation), Source (HL7 codeSystemName) and a Property Qualifier of source-code (HL7 Concept Code).

For example, the following structure represents both HL7 10011 entries in code system 2.16.840.1.113883.5.55:

  • Coding Scheme: HL7 - urn:oid:2.16.840.1.113883.3.26.1.2
  • Concept Code: 10011:M
  • Entity Description: >The message element must appear every time the message is communicated and its value must not be null. This condition is subject to the rules of multiplicity and conditionality. If a non-null default value is defined for the element, a null value may be communicated.
  • Status: Active
  • Is Active: true
  • Is Anonymous: false
  • Presentation: Mandatory
    • Property Name: textualPresentation
    • Property Id: T-1
    • Language: ENG
    • Is Preferred: true
    • Representational Form: PT
    • Source: HL7ConformanceInclusion , Role: null, SubRef: null
    • Property Qualifier Id: source-code , Property Qualifier Content: M
  • Presentation: Required - V2.x
    • Property Name: textualPresentation
    • Property Id: T-2
    • Language: ENG
    • Is Preferred: false
    • Representational Form: PT
    • Source: HL7ConformanceInclusion Role: null, SubRef: null
    • Property Qualifier Id: source-code , Property Qualifier Content: M
  • Coding Scheme: HL7 - urn:oid:2.16.840.1.113883.3.26.1.2
  • Concept Code: 10011:R
  • Entity Description: >The message element must appear every time the message is communicated and its value must not be null. This condition is subject to the rules of multiplicity and conditionality. If a non-null default value is defined for the element, a null value may be communicated.
  • Status: Active
  • Is Active: true
  • Is Anonymous: false
  • Presentation: Mandatory
    • Property Name: textualPresentation
    • Property Id: T-1
    • Language: ENG
    • Is Preferred: true
    • Representational Form: PT
    • Source: HL7ConformanceInclusion , Role: null, SubRef: null
    • Property Qualifier Id: source-code , Property Qualifier Content: R
  • Presentation: Required - V2.x
    • Property Name: textualPresentation
    • Property Id: T-2
    • Language: ENG
    • Is Preferred: false
    • Representational Form: PT
    • Source: HL7ConformanceInclusion, Role: null, SubRef: null
    • Property Qualifier Id: source-code , Property Qualifier Content: R

Loading the HL7 RIM as a Monolithic Coding Scheme

To load the HL7 Rim as a monolithic coding scheme:

  1. Load coding scheme data as HL7 Rim Metadata from the Model table (rather than the coding scheme data for each HL7 coding scheme).
    1. Mapping of these values will be incomplete:
      1. Mapping proposal:

        LexGrid

        HL7 RIM

        <codingSchemeName>

        <modelID>

        <formalName>

        <name>

        <registeredName>

        http://www.hl7.org/Library/data-model/RIM *

        <defaultLanguage>

        en*

        <representsVersion>

        <versionNumber>

        <isNative>

        0*

        <approximateNumberofConcepts>

        Result of count on concept bearing table?

        <firstRelease>

        MISSING

        <modifiedInRelease>

        MISSING

        <deprecated>

        MISSING

        <entityDescription>

        <description>

        <copyright>

        MISSING

    2. No URN exists and we may need to consider creating one (see entry for registeredName).
  2. Locate and load all mappings (such as supportedAssociations and supportedProperties).
    1. Create a supportedHiearchy with a root node of @ on hasSubtype?
  3. Iterate through the code system table rows and get each coding scheme.
    1. Create and persist an "@" node in the database
    2. Prepare an artificial "top node" for each coding scheme. (Metadata persisted here as concept properties?) This will result in 250 top nodes.
      1. The artificial top nodes will need to have a concept code created for them.
      2. Attach to "@" the artificial top nodes as a hasSubtype.
      3. Locate the actual top nodes of each coding scheme by querying the relations table to see if they exist as a target code, if not, they are top nodes so attach them to the artificial top node via hasSubtype.
    3. Translate the RRF source property loads to the EMF world.
      1. Load the concepts ensuring that the coding scheme name is loaded as a "source" property
      2. Load the relations ensuring that the source and target coding scheme data is loaded with the coding scheme name.
  4. Concurrent to this process create an updated "HL7 RIM to LexGrid for NCI" mapping from the current Excel mapping document.

LexGrid Text

The text files that can be imported must use the following formats. Items surrounded by <> are required. Items further surrounded by [] are optional. \t represents a tab - the default delimiter - however other delimiters may be used.

Lines beginning with # are comments.

Format A

<codingSchemeName>\t<codingSchemeId>\t<defaultLanguage>\t<formal
Name>[\t<version>][\t<source>][\t<description>][\t<copyright>]
<name1>[\t <description>]
\t <name2>[\t <description>]
\t\t <name3>[\t <description>]
\t\t <name4>[\t <description>]
  • The leading tabs represent hierarchical "hasSubtype" relationship nesting:
    (name1 hasSubtype name2 and name2 hasSubtype name3)
  • Concept Codes will be automatically generated.
  • If a name is used more than once - it will be assigned the same code.
  • If a description is used more than once (for a given name) only the first description will be stored.

Format B

In this format, concept codes can be provided. This is the same as "Format A" with the inclusion of concept codes as part of the input.

<code>\t<name>[\t<description>]

If the same code occurs twice, the names must match. Description rules same as "Format A."

Example of Format A

#lines starting with "#" are comments

#blank lines are ok

#the first "real" line of the file must be of the following format:
#<codingSchemeName>\t<codingSchemeId>\t<defaultLanguage>\t<formalName>[\t<version>][\t<source>][\t<description>][\t<copyright>]

colors	1.2.3	en	colors coding scheme	 1.0	Someone's Head	a simple example coding scheme using colors	This isn't worth copyrighting

#The rest of the file (for format A) should look like this:

Color	        Holder of colors
Red
Green	        The color Green
Light Green	foobar
Dark Green	The color dark green
Blue
Red
Green	        The color Green

Example of Format B

#lines starting with "#" are comments

#blank lines are ok

#the first "real" line of the file must be of the following format:
#<codingSchemeName>\t<codingSchemeId>\t<defaultLanguage>\t<formalName>[\t<version>][\t<source>][\t<description>][\t<copyright>]

colors2	1.2.4	en	colors coding scheme	1.1	Someone's Head	a simple example coding scheme using colors	This isn't worth copyrighting

#The rest of the file (for format B) should look like this:

1	Color	             Holder of colors
4	Red
6	Green	             The color Green
7	Light Green
8	Dark Green
5	Blue
8	Dark Green	     The color dark green
6	Green	             A different color of green

LexEVS Loader Mappings

The following sections give detailed mappings from source formats to LexEVS.

OWL Mapping - 4.2.1

OWL Mapping - Protégé (4.2.1)

OWL Element
OWL: RDF Schema Features

LexGrid

Comments

owl:ontology

codingScheme

No comments

xml:lang

codingScheme.defaultLanguage

Default is 'en'

dc:title

codingScheme.formalName

No comments

rdfs:label

codingScheme.localName

No comments

URI

codingScheme.registeredName

No comments

owl:versionInfo

codingScheme.representsVersion

Default is 'UNASSIGNED'

dc:rights

codingScheme.copyright

No comments

owl:Class (Thing, Nothing)

concept

No comments

rdf:ID

concept.conceptCode

No comments

rdf:ID

concept.isActive

Hard coded as "Active"

rdf:ID

concept.isAnonymous

No comments

rsfs:label

concept.entityDescription

No comments

rdf:comment

concept.comment

No comments

rdfs:subClassOf

association

No comments

rdfs:subClassOf

association.id = "subClassOf"

No comments

rdfs:subClassOf

association.forwardName = "subClassOf"

No comments

rdfs:subClassOf

association.isFunctional = "false"

No comments

rdfs:subClassOf

association.isNavigable = "true"

No comments

rdfs:subClassOf

association.isReflexive="true"

No comments

rdfs:subClassOf

association.isSymmetric="false"

No comments

rdfs:subClassOf

association.isTransitive="true"

No comments

rdf:Property (ObjectProperty)

association

An association between two classes (hasDomain, hasRange)

rdf:Property (ObjectProperty)

association
concept.conceptProperty

An association between one class (domain) and one asscoication (hasDomain and hasDataProperty). The conceptProperty defines the range.

rdfs:subPropertyOf

association

No comments

rdfs:subPropertyOf

association.id = "subPropertyOf"

No comments

rdfs:subPropertyOf

association.forwardName = "subPropertyOf"

No comments

rdfs:subPropertyOf

association.isFunctional = "false"

No comments

rdfs:subPropertyOf

association.isNavigable = "true"

No comments

rdfs:subPropertyOf

association.isReflexive="true"

No comments

rdfs:subPropertyOf

association.isSymmetric="false"

No comments

rdfs:subPropertyOf

association.isTransitive="true"

No comments

rdfs:domain

association

No comments

rdfs:domain

association.id = "hasDomain"

No comments

rdfs:domain

association.forwardName = "hasDomain"

No comments

rdfs:domain

association.isNavigable = "true"

No comments

rdfs:domain

association.isReflexive="false"

No comments

rdfs:domain

association.isSymmetric="false"

No comments

rdfs:domain

association.isTransitive="true"

No comments

rdfs:range

association

No comments

rdfs:range

association.id = "hasRange"

No comments

rdfs:range

association.forwardName = "hasRange"

No comments

rdfs:range

association.isNavigable = "true"

No comments

rdfs:range

association.isReflexive="false"

No comments

rdfs:range

association.isSymmetric="false"

No comments

rdfs:range

association.isTransitive="false"

No comments

Individual

association

A 'hasInstance' association is created. (ie. sourceId = Country, targetId = America)

Individual

association.id = "hasInstance"

No comments


OWL Element
OWL (In)Equality

LexGrid

Comments

owl:equivalentClass

association

No comments

owl:equivalentClass

association.id = "equivalentClass"

No comments

owl:equivalentClass

association.forwardName = "equivalentClass"

No comments

owl:equivalentClass

association.isFunctional = "false"

No comments

owl:equivalentClass

association.isNavigable = "true"

No comments

owl:equivalentClass

association.isReflexive="true"

No comments

owl:equivalentClass

association.isSymmetric="true"

No comments

owl:equivalentClass

association.isTransitive="true"

No comments

owl:equivalentClass

association.reverseName="equivalentClass"

No comments

owl:equivalentProperty

association

No comments

owl:equivalentProperty

association.id = "equivalentProperty"

No comments

owl:equivalentProperty

association.forwardName = "equivalentProperty"

No comments

owl:equivalentProperty

association.isFunctional = "false"

No comments

owl:equivalentProperty

association.isNavigable = "true"

No comments

owl:equivalentProperty

association.isReflexive="true"

No comments

owl:equivalentProperty

association.isSymmetric="true"

No comments

owl:equivalentProperty

association.isTransitive="true"

No comments

owl:equivalentProperty

association.reverseName="equivalentProperty"

No comments

owl:sameAs

association

No comments

owl:sameAs

association.id = "sameAs"

No comments

owl:sameAs

association.forwardName = "sameAs"

No comments

owl:sameAs

association.isFunctional = "false"

No comments

owl:sameAs

association.isNavigable = "true"

No comments

owl:sameAs

association.isReflexive="true"

No comments

owl:sameAs

association.isSymmetric="true"

No comments

owl:sameAs

association.isTransitive="true"

No comments

owl:sameAs

association.reverseName="sameAs"

No comments

differentFrom

association

No comments

differentFrom

association.id = "differentFrom"

No comments

differentFrom

association.forwardName = "differentFrom"

No comments

differentFrom

association.isFunctional = "false"

No comments

differentFrom

association.isNavigable = "true"

No comments

differentFrom

association.isReflexive="true"

No comments

differentFrom

association.isSymmetric="true"

No comments

differentFrom

association.isTransitive="true"

No comments

differentFrom

association.reverseName= "differentFrom"

No comments

owl:AllDifferent

association

No comments

owl:AllDifferent

association.id = "AllDifferent"

No comments

owl:AllDifferent

association.forwardName = "AllDifferent"

No comments

owl:AllDifferent

association.isFunctional = "false"

No comments

owl:AllDifferent

association.isNavigable = "true"

No comments

owl:AllDifferent

association.isReflexive="true"

No comments

owl:AllDifferent

association.isSymmetric="true"

No comments

owl:AllDifferent

association.isTransitive="true"

No comments

owl:AllDifferent

association.reverseName= "AllDifferent"

No comments


OWL Element
OWL: Property Characteristics

LexGrid

Comments

owl:inverseOf

association

No comments

owl:inverseOf

association.id = "inverseOf"

No comments

owl:inverseOf

association.forwardName = "inverseOf"

No comments

owl:inverseOf

association.isFunctional = "false"

No comments

owl:inverseOf

association.isNavigable = "true"

No comments

owl:inverseOf

association.isReflexive="true"

No comments

owl:inverseOf

association.isSymmetric="true"

No comments

owl:inverseOf

association.isTransitive="true"

No comments

owl:inverseOf

association.reverseName="inverseOf"

No comments

owl:TransitiveProperty

association.isTransitive

association property 'isTransitive'

owl:SymmetricProperty

association.isSymmetric

association property 'isSymmetric'

owl:InverseFunctionalProperty

association.isReverseFunctional

association property 'isReverseFunctional'

owl:FunctionalProperty

association.isFunctional

association property 'isFunctional'


OWL Element
OWL: Property Restrictions

LexGrid

Comments

owl:Restriction

concept

Create an anonymous concept for the restriction

owl:Restriction

concept.id

System generated

owl:Restriction

concept.isActive = true

No comments

owl:Restriction

concept.isAnonymous = true

Hardcoded "True"

owl:onProperty

association.id

No comments

owl: allValuesFrom

concept.entityDescription

String of allValuesFrom values

owl: allValuesFrom

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

owl: allValuesFrom

concept.presentation.propertyName

Hardcoded "textualPresentation"

owl: allValuesFrom

concept.presentation.isPreferred = true

Hardcoded "true"

owl: allValuesFrom

concept.presentation.text

String of allValuesFrom values

owl: allValuesFrom

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl: allValuesFrom

concept.conceptProperty.propertyName = type

Hardcoded "type"

owl: allValuesFrom

concept.conceptProperty.text = "owl:unionOf"

No comments

owl: someValuesFrom

concept.entityDescription

String of someValuesFrom values

owl: someValuesFrom

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

owl: someValuesFrom

concept.presentation.propertyName

Hardcoded "textualPresentation"

owl: someValuesFrom

concept.presentation.isPreferred = true

Hardcoded "true"

owl: someValuesFrom

concept.presentation.text

String of someValuesFrom values

owl: someValuesFrom

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl: someValuesFrom

concept.conceptProperty.propertyName = type

Hardcoded "type"

owl: someValuesFrom

concept.conceptProperty.text = "owl:intersectionOf"

No comments

owl:intersectionOf

concept.entityDescription

String of intersectionOf values (ie. Pizza and not VegetarianPizza)

owl:intersectionOf

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

owl:intersectionOf

concept.presentation.propertyName

Hardcoded "textualPresentation"

owl:intersectionOf

concept.presentation.isPreferred = true

Hardcoded "true"

owl:intersectionOf

concept.presentation.text

String of intersectionOf values (ie. Pizza and not VegetarianPizza)

owl:intersectionOf

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl:intersectionOf

concept.conceptProperty.propertyName = type

Hardcoded "type"

owl:intersectionOf

concept.conceptProperty.text = "owl:intersectionOf"

No comments

UnionOf

concept.conceptProperty.text = "owl:unionOf"

concept.conceptProperty.text = "owl:unionOf"

owl:complementOf

association

association.id = "subClassOf"

owl:oneOf

concept.entityDescription

String of oneOf values

owl:oneOf

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

owl:oneOf

concept.presentation.propertyName

Hardcoded "textualPresentation"

owl:oneOf

concept.presentation.isPreferred = true

Hardcoded "true"

owl:oneOf

concept.presentation.text

String of oneOf values

owl:oneOf

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl:oneOf

concept.conceptProperty.propertyName = type

Hardcoded "type"

owl:oneOf

concept.conceptProperty.text = "owl:intersectionOf"

No comments

owl:hasValue

associationQualification.nameAndValueList.content

No comments

owl:minCardinality

concept.entityDescription

String of minCardinality Values (ie. (hasTopping min 3) and Pizza)

owl:minCardinality

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

owl:minCardinality

concept.presentation.propertyName

Hardcoded "textualPresentation"

owl:minCardinality

concept.presentation.isPreferred = true

Hardcoded "true"

owl:minCardinality

concept.presentation.text

String of minCardinality Value (ie. (hasTopping min 3) and Pizza)

owl:minCardinality

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl:minCardinality

concept.conceptProperty.propertyName = type

Hardcoded "type"

owl:minCardinality

concept.conceptProperty.text = "owl:intersectionOf"

No comments

owl:maxCardinality

concept.entityDescription

String of maxCardinality Values (ie. (hasTopping max 2) and Pizza)

owl:maxCardinality

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

owl:maxCardinality

concept.presentation.propertyName

Hardcoded "textualPresentation"

owl:maxCardinality

concept.presentation.isPreferred = true

Hardcoded "true"

owl:maxCardinality

concept.presentation.text

String of maxCardinality Values (ie. (hasTopping max 2) and Pizza)

owl:maxCardinality

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl:maxCardinality

concept.conceptProperty.propertyName = type

Hardcoded "type"

owl:maxCardinality

concept.conceptProperty.text = "owl:intersectionOf"

String of cardinality Values

owl:cardinality

concept.entityDescription

No comments

owl:cardinality

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

owl:cardinality

concept.presentation.propertyName

Hardcoded "textualPresentation"

owl:cardinality

concept.presentation.isPreferred = true

Hardcoded "true"

owl:cardinality

concept.presentation.text

String of cardinality Values

owl:cardinality

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl:cardinality

concept.conceptProperty.propertyName = type

Hardcoded "type"

owl:cardinality

concept.conceptProperty.text = "owl:intersectionOf"

No comments

owl:disjointWith

association

association.id = "disjointWith"


OWL Element
OWL: Annotation Property

LexGrid

Comments

rdfs:label

Presentation

No Comments

rdfs:label

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

rdfs:label

concept.presentation.propertyName = "textualPresentation"

Hardcoded "textualPresentation"

rdfs:label

concept.presentation.isPreferred = true

Hardcoded "true"

rdfs:label

concept.presentation.text

Value of rdfs:label

rdfs:comment

Comment

No comments

rdfs:comment

concept.comment.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

rdfs:comment

concept.comment.propertyName = "comment"

Hardcoded "comment"

rdfs:comment

concept.presentation.text

Value of rdfs:comment

rdfs:seeAlso

conceptProperty

No comments

rdfs:isDefinedBy

conceptProperty

No comments


OWL Element
OWL: Versioning

LexGrid

Comments

owl:versionInfo

codingScheme.representsVersion

No comments

priorVersion

None

Not mapped

backwardCompatibleWith

None

Not mapped

owl:incompatibleWith

association

No comments

owl:incompatibleWith

association.id = "incompatibleWith"

No comments

owl:incompatibleWith

association.forwardName = "incompatibleWith"

No comments

owl:incompatibleWith

association.isFunctional = "false"

No comments

owl:incompatibleWith

association.isNavigable = "true"

No comments

owl:incompatibleWith

association.isReflexive="true"

No comments

owl:incompatibleWith

association.isSymmetric="true"

No comments

owl:incompatibleWith

association.isTransitive="true"

No comments

owl:incompatibleWith

association.reverseName="incompatibleWith"

No comments

DeprecatedClass

Concept attribute setIsActive = false

Not mapped

DeprecatedProperty

None

Not mapped

OWL Mapping - 5.0

WL Mapping - Protégé (5.0)

OWL Element
OWL: RDF Schema Features

LexEVS

Comments

owl:ontology

codingScheme

No comments

xml:lang

codingScheme.defaultLanguage

Default is 'en'

dc:title

codingScheme.formalName

No comments

rdfs:label

codingScheme.localName

No comments

URI

codingScheme.registeredName

No comments

owl:versionInfo

codingScheme.representsVersion

Default is 'UNASSIGNED'

dc:rights

codingScheme.copyright

No comments

owl:Class (Thing, Nothing)

concept

No comments

rdf:ID

concept.conceptCode

No comments

rdf:ID

concept.isActive

Hard coded as "Active"

rdf:ID

concept.isAnonymous

No comments

rdf:ID

concept.isDefined

No comments

rsfs:label

concept.entityDescription

No comments

rdf:comment

concept.comment

No comments

rdfs:subClassOf

association

No comments

rdfs:subClassOf

association.id = "subClassOf"

No comments

rdfs:subClassOf

association.forwardName = "subClassOf"

No comments

rdfs:subClassOf

association.isFunctional = "false"

No comments

rdfs:subClassOf

association.isNavigable = "true"

No comments

rdfs:subClassOf

association.isReflexive="true"

No comments

rdfs:subClassOf

association.isSymmetric="false"

No comments

rdfs:subClassOf

association.isTransitive="true"

No comments

rdf:Property (ObjectProperty)

association

An association between two classes (domain, range)

rdf:Property (ObjectProperty)

association
concept.conceptProperty

An association between one class (domain) and one association (domain and hasDataProperty). The conceptProperty defines the range.

rdfs:subPropertyOf

association

No comments

rdfs:subPropertyOf

association.id = "subPropertyOf"

No comments

rdfs:subPropertyOf

association.forwardName = "subPropertyOf"

No comments

rdfs:subPropertyOf

association.isFunctional = "false"

No comments

rdfs:subPropertyOf

association.isNavigable = "true"

No comments

rdfs:subPropertyOf

association.isReflexive="true"

No comments

rdfs:subPropertyOf

association.isSymmetric="false"

No comments

rdfs:subPropertyOf

association.isTransitive="true"

No comments

rdfs:domain

association

No comments

rdfs:domain

association.id = "domain"

No comments

rdfs:domain

association.forwardName = "domain"

No comments

rdfs:domain

association.isNavigable = "true"

No comments

rdfs:domain

association.isReflexive="false"

No comments

rdfs:domain

association.isSymmetric="false"

No comments

rdfs:domain

association.isTransitive="true"

No comments

rdfs:range

association

No comments

rdfs:range

association.id = "range"

No comments

rdfs:range

association.forwardName = "range"

No comments

rdfs:range

association.isNavigable = "true"

No comments

rdfs:range

association.isReflexive="false"

No comments

rdfs:range

association.isSymmetric="false"

No comments

rdfs:range

association.isTransitive="false"

No comments

Individual

association

An 'instance' association is created. (ie. sourceId = Country, targetId = America)

Individual

association.id = "instance"

No comments


OWL Element
OWL (In)Equality

LexEVS

Comments

owl:equivalentClass

association

No comments

owl:equivalentClass

association.id = "equivalentClass"

No comments

owl:equivalentClass

association.forwardName = "equivalentClass"

No comments

owl:equivalentClass

association.isFunctional = "false"

No comments

owl:equivalentClass

association.isNavigable = "true"

No comments

owl:equivalentClass

association.isReflexive="true"

No comments

owl:equivalentClass

association.isSymmetric="true"

No comments

owl:equivalentClass

association.isTransitive="true"

No comments

owl:equivalentClass

association.reverseName="equivalentClass"

No comments

owl:equivalentProperty

association

No comments

owl:equivalentProperty

association.id = "equivalentProperty"

No comments

owl:equivalentProperty

association.forwardName = "equivalentProperty"

No comments

owl:equivalentProperty

association.isFunctional = "false"

No comments

owl:equivalentProperty

association.isNavigable = "true"

No comments

owl:equivalentProperty

association.isReflexive="true"

No comments

owl:equivalentProperty

association.isSymmetric="true"

No comments

owl:equivalentProperty

association.isTransitive="true"

No comments

owl:equivalentProperty

association.reverseName="equivalentProperty"

No comments

owl:sameAs

association

No comments

owl:sameAs

association.id = "sameAs"

No comments

owl:sameAs

association.forwardName = "sameAs"

No comments

owl:sameAs

association.isFunctional = "false"

No comments

owl:sameAs

association.isNavigable = "true"

No comments

owl:sameAs

association.isReflexive="true"

No comments

owl:sameAs

association.isSymmetric="true"

No comments

owl:sameAs

association.isTransitive="true"

No comments

owl:sameAs

association.reverseName="sameAs"

No comments

differentFrom

association

No comments

differentFrom

association.id = "differentFrom"

No comments

differentFrom

association.forwardName = "differentFrom"

No comments

differentFrom

association.isFunctional = "false"

No comments

differentFrom

association.isNavigable = "true"

No comments

differentFrom

association.isReflexive="true"

No comments

differentFrom

association.isSymmetric="true"

No comments

differentFrom

association.isTransitive="true"

No comments

differentFrom

association.reverseName= "differentFrom"

No comments

owl:AllDifferent

association

No comments

owl:AllDifferent

association.id = "AllDifferent"

No comments

owl:AllDifferent

association.forwardName = "AllDifferent"

No comments

owl:AllDifferent

association.isFunctional = "false"

No comments

owl:AllDifferent

association.isNavigable = "true"

No comments

owl:AllDifferent

association.isReflexive="true"

No comments

owl:AllDifferent

association.isSymmetric="true"

No comments

owl:AllDifferent

association.isTransitive="true"

No comments

owl:AllDifferent

association.reverseName= "AllDifferent"

No comments


OWL Element
OWL: Property Characteristics

LexEVS

Comments

owl:inverseOf

association

No comments

owl:inverseOf

association.id = "inverseOf"

No comments

owl:inverseOf

association.forwardName = "inverseOf"

No comments

owl:inverseOf

association.isFunctional = "false"

No comments

owl:inverseOf

association.isNavigable = "true"

No comments

owl:inverseOf

association.isReflexive="true"

No comments

owl:inverseOf

association.isSymmetric="true"

No comments

owl:inverseOf

association.isTransitive="true"

No comments

owl:inverseOf

association.reverseName="inverseOf"

No comments

owl:TransitiveProperty

association.isTransitive

association property 'isTransitive'

owl:SymmetricProperty

association.isSymmetric

association property 'isSymmetric'

owl:InverseFunctionalProperty

association.isReverseFunctional

association property 'isReverseFunctional'

owl:FunctionalProperty

association.isFunctional

association property 'isFunctional'


OWL Element
OWL: Property Restrictions

LexEVS

Comments

owl:Restriction

concept

Create an anonymous concept for the restriction

owl:Restriction

concept.id

System generated

owl:Restriction

concept.isActive = true

No comments

owl:Restriction

concept.isAnonymous = true

Hardcoded "True"

owl:onProperty

association.id

No comments

owl: allValuesFrom

concept.entityDescription

String of allValuesFrom values

owl: allValuesFrom

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

owl: allValuesFrom

concept.presentation.propertyName

Hardcoded "textualPresentation"

owl: allValuesFrom

concept.presentation.isPreferred = true

Hardcoded "true"

owl: allValuesFrom

concept.presentation.text

String of allValuesFrom values

owl: allValuesFrom

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl: allValuesFrom

concept.conceptProperty.propertyName = type

Hardcoded "type"

owl: allValuesFrom

concept.conceptProperty.text = "owl:unionOf"

owl: someValuesFrom

concept.entityDescription

String of someValuesFrom values

owl: someValuesFrom

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

owl: someValuesFrom

concept.presentation.propertyName

Hardcoded "textualPresentation"

owl: someValuesFrom

concept.presentation.isPreferred = true

Hardcoded "true"

owl: someValuesFrom

concept.presentation.text

String of someValuesFrom values

owl: someValuesFrom

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl: someValuesFrom

concept.conceptProperty.propertyName = type

Hardcoded "type"

owl: someValuesFrom

concept.conceptProperty.text = "owl:intersectionOf"

No comments

owl:intersectionOf

concept.entityDescription

String of intersectionOf values (ie. Pizza and not VegetarianPizza)

owl:intersectionOf

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

owl:intersectionOf

concept.presentation.propertyName

Hardcoded "textualPresentation"

owl:intersectionOf

concept.presentation.isPreferred = true

Hardcoded "true"

owl:intersectionOf

concept.presentation.text

String of intersectionOf values (ie. Pizza and not VegetarianPizza)

owl:intersectionOf

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl:intersectionOf

concept.conceptProperty.propertyName = type

Hardcoded "type"

owl:intersectionOf

concept.conceptProperty.text = "owl:intersectionOf"

No comments

UnionOf

concept.conceptProperty.text = "owl:unionOf"

No comments

owl:complementOf

association

association.id = "subClassOf"

owl:oneOf

concept.entityDescription

String of oneOf values

owl:oneOf

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

owl:oneOf

concept.presentation.propertyName

Hardcoded "textualPresentation"

owl:oneOf

concept.presentation.isPreferred = true

Hardcoded "true"

owl:oneOf

concept.presentation.text

String of oneOf values

owl:oneOf

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl:oneOf

concept.conceptProperty.propertyName = type

Hardcoded "type"

owl:oneOf

concept.conceptProperty.text = "owl:intersectionOf"

No comments

owl:hasValue

associationQualification.nameAndValueList.content

No comments

owl:minCardinality

concept.entityDescription

String of minCardinality Values (ie. (hasTopping min 3) and Pizza)

owl:minCardinality

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

owl:minCardinality

concept.presentation.propertyName

Hardcoded "textualPresentation"

owl:minCardinality

concept.presentation.isPreferred = true

Hardcoded "true"

owl:minCardinality

concept.presentation.text

String of minCardinality Value (ie. (hasTopping min 3) and Pizza)

owl:minCardinality

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl:minCardinality

concept.conceptProperty.propertyName = type

Hardcoded "type"

owl:minCardinality

concept.conceptProperty.text = "owl:intersectionOf"

No comments

owl:maxCardinality

concept.entityDescription

String of maxCardinality Values (ie. (hasTopping max 2) and Pizza)

owl:maxCardinality

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

owl:maxCardinality

concept.presentation.propertyName

Hardcoded "textualPresentation"

owl:maxCardinality

concept.presentation.isPreferred = true

Hardcoded "true"

owl:maxCardinality

concept.presentation.text

String of maxCardinality Values (ie. (hasTopping max 2) and Pizza)

owl:maxCardinality

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl:maxCardinality

concept.conceptProperty.propertyName = type

Hardcoded "type"

owl:maxCardinality

concept.conceptProperty.text = "owl:intersectionOf"

No comments

owl:maxCardinality

String of cardinality Values

No comments

owl:cardinality

concept.entityDescription

No comments

owl:cardinality

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

owl:cardinality

concept.presentation.propertyName

Hardcoded "textualPresentation"

owl:cardinality

concept.presentation.isPreferred = true

Hardcoded "true"

owl:cardinality

concept.presentation.text

String of cardinality Values

owl:cardinality

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl:cardinality

concept.conceptProperty.propertyName = type

Hardcoded "type"

owl:cardinality

concept.conceptProperty.text = "owl:intersectionOf"

No comments

owl:disjointWith

association

association.id = "disjointWith"


OWL Element
OWL: Annotation Property

LexEVS

Comments

rdfs:label

Presentation

No comments

rdfs:label

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

rdfs:label

concept.presentation.propertyName = "textualPresentation"

Hardcoded "textualPresentation"

rdfs:label

concept.presentation.isPreferred = true

Hardcoded "true"

rdfs:label

concept.presentation.text

Value of rdfs:label

rdfs:comment

Comment

No comments

rdfs:label

concept.comment.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

rdfs:label

concept.comment.propertyName = "comment"

Hardcoded "comment"

rdfs:label

concept.presentation.text

Value of rdfs:comment

rdfs:seeAlso

conceptProperty

No comments

rdfs:isDefinedBy

conceptProperty

No comments


OWL Element
OWL: Versioning

LexEVS

Comments

owl:versionInfo

codingScheme.representsVersion

No comments

priorVersion

None

Not mapped

backwardCompatibleWith

None

Not Mapped

owl:incompatibleWith

association

No comments

owl:incompatibleWith

association.id = "incompatibleWith"

No comments

owl:incompatibleWith

association.forwardName = "incompatibleWith"

No comments

owl:incompatibleWith

association.isFunctional = "false"

No comments

owl:incompatibleWith

association.isNavigable = "true"

No comments

owl:incompatibleWith

association.isReflexive="true"

No comments

owl:incompatibleWith

association.isSymmetric="true"

No comments

owl:incompatibleWith

association.isTransitive="true"

No comments

owl:incompatibleWith

association.reverseName="incompatibleWith"

No comments

DeprecatedClass

Concept attribute setIsActive = false

Not mapped

DeprecatedProperty

None

Not mapped

OWL Mapping - NCI OWL

OWL Element
OWL: RDF Schema Features

LexGrid

Comments

owl:ontology

codingScheme

Hardcoded "NCI_Thesaurus"

xml:lang

codingScheme.defaultLanguage

Hardcoded "en"

dc:title

codingScheme.formalName

Hardcoded "NCI Thesaurus"

rdfs:label

codingScheme.localName

Hardcoded "NCI_Thesaurus"

rdfs:label

None

Hardcoded "40010"

rdfs:label

None

Hardcoded "urn:oid:2.16.840.1.113883.3.26.1.1"

URI

codingScheme.registeredName

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

owl:versionInfo

codingScheme.representsVersion

No comments

dc:rights

codingScheme.copyright

Read from hardcoded "Terms.txt" file.

rdfs:comment

codingScheme.entityDescription

No comments

rdfs:comment

codingScheme.isNative

Hardcoded "true"

owl:Class (Thing, Nothing)

concept

No comments

code

concept.id

code

concept.isActive

Hard coded as "true" unless class "owl:DeprecatedClass", then 'false'

code

concept.isAnonymous

No comments

rsfs:label

concept.entityDescription

No comments

rdf:comment

concept.comment

No comments

rdf:comment

conceptProperty

Indicate whether the concept is primative (has no equavalent classes)

rdf:comment

concept.conceptProperty.propertyName

Hard coded as "primitive"

rdf:comment

concept.conceptProperty.text

"true"

rdf:comment

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

rdf:comment

presentation

Provide default presentation to match concept entity description if not provided as property

rdf:comment

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

rdf:comment

concept.presentation.propertyName

Hardcoded "NCI_Preferred_Term"

rdfs:label

concept.presentation.text

concept.entityDescription

rdf:comment

conceptProperty

Property with designated concept name label (per NCI requirements and used in codeToName/nameToCode lookup).

rdf:comment

concept.conceptProperty.propertyName

Hard coded as "CONCEPT_NAME"

rdfs:label

concept.conceptProperty.text

concept.entityDescription

rdfs:label

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

rdfs:label

relation

Top-level container for associations (non-inheritable, non-defining relationships between concepts.

rdfs:label

relations.dc

Hard coded as "associations"

rdfs:label

relations.isNative

Hard coded as "true"

rdfs:label

relations.entityDescription

Hard coded as "Non-inheritable non-defining relations."

rdfs:label

relation

Top-level container for roles (inheritable relationships)

rdfs:label

relations.dc

Hard coded as "roles"

rdfs:label

relations.isNative

Hard coded as "true"

rdfs:label

relations.entityDescription

Hard coded as "Inheritable/defining relations."

rdfs:subClassOf

association

Association for subtype hierarchy.

rdfs:subClassOf

association.id = "hasSubtype"

No comments

rdfs:subClassOf

association.forwardName = "hasSubtype"

No comments

rdfs:subClassOf

association.reverseName = "isA"

No comments

rdfs:subClassOf

association.isNavigable = "true"

Hard coded as "true"

rdfs:subClassOf

association.isReflexive="true"

Hard coded as "true"

rdfs:subClassOf

association.isSymmetric="false"

Hard coded as "false"

rdfs:subClassOf

association.isTransitive="true"

Hard coded as "true"

hasElement

association

Association used to register component classes as elements of anonymous node representations.

hasElement

association.id = "hasElement"

No comments

hasElement

association.forwardName = "hasElement"

No comments

hasElement

association.isNavigable = "true"

Hard coded as "true"

hasElement

association.isSymmetric="false"

Hard coded as "false"

hasElement

association.isTransitive="true"

Hard coded as "true"

rdfs:domain

association

Association for role_has_domain relations

rdfs:domain

association.id = "Role_Has_Domain"

No comments

rdfs:domain

association.forwardName = "roleHasDomain"

No comments

rdfs:domain

association.reverseName = "kindIsDomainOf"

No comments

rdfs:domain

association.isNavigable = "true"

Hard coded as "true"

rdfs:domain

association.isReflexive="false"

Hard coded as "false"

rdfs:domain

association.isSymmetric="false"

Hard coded as "false"

rdfs:domain

association.isTransitive="true"

Hard coded as "true"

rdfs:range

association

Association for range relations

rdfs:range

association.id = "Role_Has_Range"

No comments

rdfs:range

association.forwardName = "roleHasRange"

No comments

rdfs:range

association.reverseName = "kindIsRangeOf"

No comments

rdfs:range

association.isNavigable = "true"

Hard coded as "true"

rdfs:range

association.isReflexive="false"

Hard coded as "false"

rdfs:range

association.isSymmetric="false"

Hard coded as "false"

rdfs:range

association.isTransitive="false"

Hard coded as "false"

rdf:Property (ObjectProperty)

association

An association between two classes (hasDomain, hasRange)

rdfs:subPropertyOf

None

Not mapped


OWL Element
OWL (In)Equality

LexGrid

Comments

owl:equivalentClass

association

Association for equivalent class.

owl:equivalentClass

association.id = "equivalentClass"

No comments

owl:equivalentClass

association.forwardName = "equivalentClass"

No comments

owl:equivalentClass

association.reverseName = "equivalentClass"

No comments

owl:equivalentClass

association.isNavigable = "true"

Hard coded as "true"

owl:equivalentClass

association.isReflexive="true"

Hard coded as "true"

owl:equivalentClass

association.isSymmetric="true"

Hard coded as "true"

owl:equivalentClass

association.isTransitive="true"

Hard coded as "true"


OWL Element
OWL: Property Characteristics

LexGrid

Comments

owl:inverseOf

association

No comments

owl:inverseOf

association.id = "inverseOf"

No comments

owl:inverseOf

association.forwardName = "inverseOf"

No comments

owl:inverseOf

association.isFunctional = "false"

No comments

owl:inverseOf

association.isNavigable = "true"

No comments

owl:inverseOf

association.isReflexive="true"

No comments

owl:inverseOf

association.isSymmetric="true"

No comments

owl:inverseOf

association.isTransitive="true"

No comments

owl:inverseOf

association.reverseName="inverseOf"

No comments

owl:TransitiveProperty

association.isTransitive

association property 'isTransitive'

owl:SymmetricProperty

association.isSymmetric

association property 'isSymmetric'

owl:InverseFunctionalProperty

association.isReverseFunctional

association property 'isReverseFunctional'

owl:FunctionalProperty

association.isFunctional

association property 'isFunctional'


OWL Element
OWL: Property Restrictions

LexGrid

Comments

owl:Restriction

concept

Anonymous concept created.

owl:Restriction

concept.entityDescription = "RestrictionOn: " + association name

Concatination of "Restriction On: " and assocation name

owl:Restriction

concept.isAnonymous = true

No comments

owl: allValuesFrom

associationQualification.association.Qualifier = "AllValuesFrom"

No comments

owl: someValuesFrom

associationQualification.association.Qualifier = "someValuesFrom"

No comments

owl:intersectionOf

concept.entityDescription

Concatination of "Restriction On: " and assocation name

owl:intersectionOf

concept.isAnonymous = true

No comments

owl:intersectionOf

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

owl:intersectionOf

concept.presentation.propertyName

Hardcoded "textualPresentation"

owl:intersectionOf

concept.presentation.isPreferred = true

Hardcoded "true"

owl:intersectionOf

concept.presentation.text

Set to concept.entityDescription

owl:intersectionOf

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl:intersectionOf

concept.conceptProperty.propertyName = type

Hardcoded "type"

owl:intersectionOf

concept.conceptProperty.text = "owl:intersectionOf"

No comments

owl:unionOf

concept.entityDescription

Concatination of "Restriction On: " and assocation name

owl:intersectionOf

concept.isAnonymous = true

No comments

owl:intersectionOf

concept.presentation.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

owl:intersectionOf

concept.presentation.propertyName

Hardcoded "textualPresentation"

owl:intersectionOf

concept.presentation.isPreferred = true

Hardcoded "true"

owl:intersectionOf

concept.presentation.text

Set to concept.entityDescription

owl:intersectionOf

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl:intersectionOf

concept.conceptProperty.propertyName = type

Hardcoded "type"

owl:intersectionOf

concept.conceptProperty.text = "owl:unionOf"

No comments

owl:oneOf

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

owl:oneOf

concept.conceptProperty.propertyName = "owl:oneOf"

Hardcoded "owl:oneOf"

owl:oneOf

concept.conceptProperty.text

String of oneOf values


OWL: Annotation Property

LexGrid

Comments

rdfs:comment

Comment

No comments

rdfs:comment

concept.comment.propertyId

Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value.

rdfs:comment

concept.comment.propertyName = "comment"

Hardcoded "comment"

rdfs:comment

concept.presentation.text

Value of rdfs:comment

rdfs:comment

 

No comments

rdfs:seeAlso

conceptProperty

No comments

rdfs:isDefinedBy

conceptProperty

No comments


OWL Element
OWL: Versioning

LexGrid

Comments

owl:versionInfo

codingScheme.representsVersion

No comments

priorVersion

None

Not mapped

backwardCompatibleWith

None

Not mapped

DeprecatedClass

None

Not mapped

DeprecatedProperty

None

Not mapped

Legacy Complex Prop Mapping

Legacy Complex Properties Mapping

Tag

Presentation

Source

Representational Form

Qualifier

Model Element

Value Column Name

Model Element

go-term

x

NA

NA

NA

None

propertyValue

None

go-id

NA

NA

NA

x

propertyQualifierId

val1

PropertyQualifier attribute content?

go-source

NA

NA

NA

x

propertyQualifierId

val1

PropertyQualifier attribute content?

source-date

NA

NA

NA

x

propertyQualifierId

val1

PropertyQualifier attribute content?

term-name

x

NA

NA

NA

None

propertyValue

None

term-group

NA

NA

x

NA

None

representationalForm

property attribute

term-source

NA

x

NA

NA

None

attributeValue

source

def-source

NA

x

NA

NA

None

attributeValue

source

def-definition

x

NA

NA

NA

None

propertyValue

definition

Definition_Review_Date

NA

NA

NA

x

propertyQualifierId

val1

PropertyQualifier attribute content?

Definition_Reviewer_Name

NA

NA

NA

x

propertyQualifierId

val1

PropertyQualifier attribute content?

UMLS SemNet Mapping

Coding Scheme RRF File Name

Coding Scheme RRF Column Name

Coding Scheme RRF Definition

Coding Scheme NCI Meta Only

Coding Scheme LexGrid Model Element

Coding Scheme Comments

None

None

None

NA

codingScheme.representsVersion

No comments

None

None

None

NA

codingScheme.codingScheme

Hard coded in java file as "UMLS_SemNet"

None

None

None

NA

codingScheme.formalName

Hard coded in java file as "UMLS Semantic Network"

None

None

None

NA

codingScheme.defaultLanguage

Hard coded in java file as "en"

None

None

None

NA

codingScheme.approxNumConcepts

Hard coded in java file as

None

None

None

NA

codingScheme.entityDescription

Hard coded in java file as "The UMLS Semantic Network is one of three UMLS Knowledge Sources developed as part of the Unified Medical Language System project. The network provides a consistent categorization of all concepts represented in the UMLS Metathesaurus."

license.txt

None

None

NA

codingScheme.copyright

Read from license.txt file or hard coded reference in java file

license.txt

None

None

NA

codingScheme.registeredName

Hard coded in java file as "urn:lsid:nlm.nih.gov:semnet"

license.txt

None

None

NA

codingScheme.concepts.dc

Hard coded in java file as "concepts"

license.txt

None

None

NA

codingScheme.relations.dc

Hard coded in java file as "relations"

license.txt

None

None

NA

codingScheme.mappings.dc

Hard coded in java file as "mappings"

license.txt

None

None

NA

None

No comments

license.txt

None

None

NA

codingScheme.localNameList

No comments

license.txt

None

None

NA

codingScheme.localNameList.

Hard coded in java file as "UMLS_SemNet"

license.txt

None

None

NA

codingScheme.localNameList

No comments

license.txt

None

None

NA

codingScheme.localNameList.

No comments

license.txt

None

None

NA

codingScheme.source

No comments

license.txt

None

None

NA

codingScheme.source.content

No comments

license.txt

None

None

NA

codingScheme.localNameList

No comments

license.txt

None

None

NA

codingScheme.localNameList.

No comments

license.txt

None

None

NA

codingScheme.localNameList

No comments

license.txt

None

None

NA

codingScheme.localNameList.

No comments

license.txt

None

None

NA

codingScheme.localNameList

No comments

license.txt

None

None

NA

codingScheme.localNameList.

No comments

license.txt

None

None

NA

codingScheme.localNameList

No comments

license.txt

None

None

NA

codingScheme.localNameList.

No comments

license.txt

None

None

NA

mappings.supportedFormat

No comments

license.txt

None

None

NA

mappings.supportedFormat.localId

Hard coded in java file as "text/plain"

license.txt

None

None

NA

mappings.supportedFormat.urn

Hard coded in java file as "urn:oid:2.16.840.1.113883.6.10:text_plain"

license.txt

None

None

NA

mappings.supportedAssociation

No comments

SRDEF

RL

None

NA

mappings.supportedAssociation.localId

No comments

SRDEF

RL

None

NA

mappings.supportedContext

No comments

SRDEF

RL

None

NA

mappings.supportedSource

No comments

SRDEF

RL

None

NA

mappings.supportedSource.localId

Hard coded in java file as "NLM"

SRDEF

RL

None

NA

mappings.supportedSource.urn

Hard coded in java file as "urn:lsid:nlm.nih.gov"

SRDEF

RL

None

NA

mappings.supportedHierarchy

No comments

SRDEF

RL

None

NA

mappings.supportedHierarchy.localId

Hard coded in java file as "is_a"

SRDEF

RL

None

NA

mappings.supportedHierarchy.isForwardNavigable

Hard coded as "true"

SRDEF

RL

None

NA

mappings.supportedHierarchy.rootCode

Hard coded as "@"

SRDEF

RL

None

NA

mappings.supportedHierarchy.associationList

Hard coded in java file as "hasSubtype"

SRDEF

RL

None

NA

mappings.supportedAssociationQualifier

No comments

SRFLD

COL

None

NA

mappings.supportedProperty

No comments

SRFLD

COL

None

NA

mappings.supportedProperty.localId

If SRDEF appears in the FIL column then this is treated a potential supported property and is entered in supported properties as such.

SRFLD

COL

None

NA

mappings.supportedProperty.urn

Hard coded in java file as ""

SRFLD

COL

None

NA

mappings.supportedLanguage

No comments

SRFLD

COL

None

NA

mappings.supportedLanguage.localId

Hard coded in java file as "en"

SRFLD

COL

None

NA

mappings.supportedLanguage.urn

Hard coded in java file as "urn:oid:2.16.840.1.113883.6.84:en"

SRFLD

COL

None

NA

mappings.supportedCodingScheme

No comments

SRFLD

COL

None

NA

mappings.supportedCodingScheme.localId

Hard coded in java file as "UMLS_SemNet"

SRFLD

COL

None

NA

mappings.supportedCodingScheme.urn

Hard coded in java file as "urn:lsid:nlm.nih.gov:semnet"

SRFLD

COL

None

NA

mappings.supportedRepresentationalForm

No comments

SRFLD

COL

None

NA

mappings.supportedConceptStatus

No comments

SRFLD

COL

None

NA

mappings.supportedPropertyLink

No comments

SRFLD

COL

None

NA

mappings.supportedPropertyQualifier

No comments

SRFLD

COL

None

NA

mappings.supportedDataType

No comments


Concepts RRF File Name

Concepts RRF Column Name

Concepts RRF Definition

Concepts NCI Meta Only

Concepts LexGrid Model Element

Concepts Comments

SRDEF

UI

None

NA

concept.id(inherited from Entity)

No comments

SRDEF

STY/RL

None

NA

concept.enitityDescription(inheritance path Entity->versionableAndDescribable)

No comments

SRDEF

STY/RL

None

NA

concept.conceptProperty

No comments

SRDEF

NH

None

NA

concept.conceptProperty.text.content

No comments

SRDEF

NH

None

NA

concept.conceptProperty.format

Hard coded in java file as "text/plain"

SRDEF

NH

None

NA

concept.conceptProperty.propertyName

Hard coded in java file as "NH"

SRDEF

NH

None

NA

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

SRDEF

NH

None

NA

concept.presentation

No comments

SRDEF

NH

None

NA

concept.presentation.propertyName (inherited from Property)

Hard coded in java file as "STY/RL" or "ABR"

SRDEF

NH

None

NA

concept.presentation.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

SRDEF

STY/RL, ABR

None

NA

concept.presentation.text.content

No comments

SRDEF

STY/RL, ABR

None

NA

concept.presentation.format

hard coded in java file as "text/plain"

SRDEF

STY/RL, ABR

None

NA

concept.presentation.isPreferred

hard coded in java file as true.

SRDEF

STY/RL, ABR

None

NA

concept.definition.propertyName (inherited from Property)

Hard coded in java file as "DEF"

SRDEF

STY/RL, ABR

None

NA

concept.definition.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

SRDEF

DEF

None

NA

concept.definition.text.content

No comments

SRDEF

DEF

None

NA

concept.definition.format

Hard coded in java file as "text/plain"

SRDEF

DEF

None

NA

concept.definition.isPreferred

Hard coded in java file as true.

SRDEF

DEF

None

NA

concept.comment

No comments

SRDEF

EX

None

NA

concept.comment.propertyName (inherited from Property)

Hard coded in java file as "EX"

SRDEF

EX

None

NA

concept.comment.text.content

No comments

SRDEF

EX

None

NA

concept.comment.format

hard coded in java file as "text/plain"

SRDEF

EX

None

NA

concept.comment.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

SRDEF

EX

None

NA

concept.instruction

No comments

SRDEF

EX

None

NA

concept.instruction.propertyName (inherited from Property)

Hard coded in java file as "UN"

SRDEF

UN

None

NA

concept.instruction.text.content

No comments

SRDEF

UN

None

NA

concept.instruction.format

hard coded in java file as "text/plain"

SRDEF

UN

None

NA

concept.instruction.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.


Relations RRF File Name

Relations RRF Column Name

Relations RRF Definition

Relations NCI Meta Only

Relations LexGrid Model Element

Relations Comments

SRSTR

RL

None

NA

association.id (inherited from Entity)

In the case of RL value is "isa" the id is hard coded to hasSubtype. The direction of the association is also reversed

SRSTR

RL

None

NA

association.isTransitive

hard coded to true if the value of RL is "isa"

SRSTR

RL

None

NA

association.forwardName

Reversed when value of RL is "isa"

SRSTR

STY/RL

None

NA

associationInstance.sourceId

Reversed when value of RL is "isa"

SRSTR

STY/RL

None

NA

associationTarget.targetId

No comments

SRDEF

RIN

None

NA

association.reverseName

No comments

SRDEF

DEF

None

NA

association.entityDescription.content (inheritance path for entityDescription is Entity->versionableAndDescribable)

When SRDEF value RT is "RL"

SRSTRE1

UI/STY(first argument)

None

NA

associationInstance.sourceId

Reversed when value of RL is "isa"

SRSTRE1

UI/STY(2nd argument)

None

NA

associationTarget.targetId

Reversed when value of RL is "isa"

UMLS Mapping

Coding Scheme
File Name

Coding Scheme
RRF Column Name

Coding Scheme
RRF Definition

Coding Scheme
NCI Meta Only

Coding Scheme
LexGrid Model Element

Coding Scheme
Comments

MRSAB.RRF

SVER

Release date or version number of a source

NA

codingScheme.representsVersion

No comments

MRSAB.RRF

SSN

Source short name

NA

codingScheme.codingScheme

No comments

MRSAB.RRF

SON

Source Official Name

NA

codingScheme.formalName

No comments

MRSAB.RRF

LAT

Language of Term(s)

NA

codingScheme.defaultLanguage

No comments

MRSAB.RRF

TRF

Term frequency for a source

NA

codingScheme.approxNumConcepts

No comments

MRSAB.RRF

SCIT

Source citation

NA

codingScheme.entityDescription

Inherits entityDescription from versionableAndDescribable

MRSAB.RRF

SCC

Content contact info for a source

NA

codingScheme.copyright

No comments

MRSAB.RRF

SCC

Content contact info for a source

NA

codingScheme.registeredName

Pulled from iso mapping configuration file using method getISOString(RSAB from MRSAB.RRF)

MRDOC.RRF

EXPL

Detailed explanation

x

codingScheme.representsVersion

Where Dockey = "RELEASE" and value = "umls.release.name"

MRDOC.RRF

EXPL

Detailed explanation

x

codingScheme.codingScheme

Hard coded in java file as "NCI MetaThesaurus"

MRDOC.RRF

EXPL

Detailed explanation

x

codingScheme.formalName

Hard coded in java file as "NCI MetaThesaurus"

MRDOC.RRF

EXPL

Detailed explanation

x

codingScheme.defaultLanguage

Hard coded in java file as "ENG"

MRCONSO.RRF

None

None

x

codingScheme.approxNumConcepts

Count of CODE value in MRCONSO.RRF

MRCONSO.RRF

None

None

x

codingScheme.entityDescription

Hard coded in java file as "NCI MetaThesaurus loaded from RRF files."

MRCONSO.RRF

None

None

x

codingScheme.copyright

Hard coded in java file as "Some material in the NCI Metathesaurus is from copyrighted sources of the respective copyright claimants. All sources appearing in the NCI Metathesaurus are licensed or authorized for NCI use. Users of the NCI Metathesaurus are responsible for compliance with the terms of these licenses and with any copyright restrictions and are referred to NCI Center of Bioinformatics for license terms and to the copyright notices appearing in the original sources, all of which are obtainable online by reference at http://ncimeta.nci.nih.gov/."

MRCONSO.RRF

None

None

NA

codingScheme.localNameList

Hard coded as constant in java file as "localName"

MRSAB.RRF

SON

Source Official Name

NA

codingScheme.localNameList.

No comments

MRSAB.RRF

SON

Source Official Name

NA

codingScheme.localNameList

Hard coded as constant in java file as "localName"

MRSAB.RRF

SON

Source Official Name

NA

codingScheme.localNameList.

Pulled from iso mapping configuration file using method getISOString(RSAB from MRSAB.RRF)

MRSAB.RRF

SON

Source Official Name

NA

codingScheme.source

Hard coded as constant in java file as "source"

MRDOC.RRF

EXPL

Detailed explanation

NA

codingScheme.source.content

String concatenation of "UMLS-" and value of EXPL

MRDOC.RRF

EXPL

Detailed explanation

x

codingScheme.localNameList

Hard coded as constant in java file as "localName"

MRDOC.RRF

EXPL

Detailed explanation

x

codingScheme.localNameList.

Hard coded in java file as "NCI Thesaurus"

MRDOC.RRF

EXPL

Detailed explanation

x

codingScheme.localNameList

Hard coded as constant in java file as "localName"

MRDOC.RRF

EXPL

Detailed explanation

x

codingScheme.localNameList.

Hard coded in java file as "NCI_Thesaurus"

MRDOC.RRF

EXPL

Detailed explanation

x

codingScheme.localNameList

Hard coded as constant in java file as "localName"

MRDOC.RRF

EXPL

Detailed explanation

x

codingScheme.localNameList.

Hard coded in java file as "10001"

MRDOC.RRF

EXPL

Detailed explanation

x

codingScheme.localNameList

Hard coded as constant in java file as "source"

MRDOC.RRF

EXPL

Detailed explanation

x

codingScheme.localNameList.

Hard coded in java file as "RRF Files"

MRDOC.RRF

EXPL

Detailed explanation

NA

mappings.supportedFormat

Hard coded as constant in java file as "Format"

MRDOC.RRF

EXPL

Detailed explanation

NA

mappings.supportedFormat.localId

Hard coded as one of several constants in a java file

MRDOC.RRF

EXPL

Detailed explanation

NA

mappings.supportedAssociation

Hard coded as constant in java file as "Association"

MRREL.RRF

REL, RELA

Relationship, Relationship attribute

NA

mappings.supportedAssociation.localId

No comments

MRREL.RRF

REL, RELA

Relationship, Relationship attribute

NA

mappings.supportedContext

Hard coded as constant in java file as "Context" May not be used in individual RRF load

MRREL.RRF

REL, RELA

Relationship, Relationship attribute

NA

mappings.supportedSource

Hard coded as constant in java file as "Source" May not be used in individual RRF load

MRREL.RRF

REL, RELA

Relationship, Relationship attribute

NA

mappings.supportedHierarchy

Hard coded as constant in java file as "Hierarchy"

MRREL.RRF

REL, RELA

Relationship, Relationship attribute

NA

mappings.supportedAssociationQualifier

Hard coded as constant in java file as "AssociationQualifier"

MRREL.RRF

REL, RELA

Relationship, Relationship attribute

NA

mappings.supportedProperty

Hard coded as constant in java file as "Property"

MRREL.RRF

REL, RELA

Relationship, Relationship attribute

NA

mappings.supportedLanguage

Hard coded as constant in java file as "Language"

MRREL.RRF

REL, RELA

Relationship, Relationship attribute

NA

mappings.supportedCodingScheme

Hard coded as constant in java file as "CodingScheme"

MRREL.RRF

REL, RELA

Relationship, Relationship attribute

NA

mappings.supportedRepresentationalForm

Hard coded as constant in java file as "RepresentationalForm"

MRREL.RRF

REL, RELA

Relationship, Relationship attribute

NA

mappings.supportedConceptStatus

Hard coded as constant in java file as "ConceptStatus"

MRREL.RRF

REL, RELA

Relationship, Relationship attribute

NA

mappings.supportedPropertyLink

Hard coded as constant in java file as "PropertyLink"

MRREL.RRF

REL, RELA

Relationship, Relationship attribute

NA

mappings.supportedPropertyQualifier

Hard coded as constant in java file as "PropertyQualifier"

MRREL.RRF

REL, RELA

Relationship, Relationship attribute

NA

mappings.supportedDataType

Hard coded as constant in java file as "DataType"


Concepts
RRF File Name

Concepts
RRF Column Name

Concepts
RRF Definition

Concepts
NCI Meta Only

Concepts
LexGrid Model Element

Concepts
Comments

MRCONSO.RRF

CODE

Unique Identifier or code for string in source

NA

concept.conceptCode

No comments

MRCONSO.RRF

CUI

Unique identifier for concept

x

concept.conceptCode

No comments

MRCONSO.RRF

CUI

Unique identifier for concept

NA

concept.isActive

Hardcoded in parameter as true.

MRCONSO.RRF

CUI

Unique identifier for concept

NA

concept.conceptStatus

Hard coded as constant in java file as "Active"

MRCONSO.RRF

CUI

Unique identifier for concept

NA

concept.isAnonymous

Hardcoded in parameter as false.

MRCONSO.RRF

STR

String

NA

concept.entityDescription

No comments

MRCONSO.RRF

STR

String

NA

concept.conceptProperty.Format

Hard coded as constant in java file as "text/plain" or null

MRCONSO.RRF

STR

String

NA

concept.conceptProperty.propertyName

May be hard coded as constant in java file as one of several properties.

MRCONSO.RRF

STR

String

NA

concept.conceptProperty.usageContext

No comments

MRCONSO.RRF

STR

String

NA

concept.conceptProperty.propertyId

Generated value for property using "P" concatenated with a steadily incremented numerical value.

MRCONSO.RRF

STR

String

NA

concept.presentation.propertyId

Generated value for property textual presentation using "T" concatenated with a steadily incremented numerical value.

MRCONSO.RRF

STR

String

NA

concept.comment.propertyId

Generated value for property comment using "C" concatenated with a steadily incremented numerical value.

MRCONSO.RRF

STR

String

NA

concept.definition.propertyId

Generated value for property definition using "D" concatenated with a steadily incremented numerical value.

MRCONSO.RRF

STR

String

NA

concept.instruction.propertyId

Generated value for property instruction using "I" concatenated with a steadily incremented numerical value.

MRCONSO.RRF

CUI

Unique identifier for concept

NA

concept.conceptProperty.text.content.

No comments

MRCONSO.RRF

CUI

Unique identifier for concept

NA

concept.conceptProperty.propertyId

Generated value for property using "CUI" concatenated with a steadily incremented numerical value.

MRCONSO.RRF

CUI

Unique identifier for concept

NA

concept.conceptProperty.propertyName

Hard coded as constant in java file as "UMLS_CUI"

MRCONSO.RRF

CUI

Unique identifier for concept

NA

concept.conceptProperty.propertyType

Hard coded as constant in java file as "property"

MRCONSO.RRF

CUI

Unique identifier for concept

NA

concept.conceptProperty.format

Left as null

MRSTY.RRF

STY

Semantic type

NA

concept.conceptProperty.text.content

No comments

MRSTY.RRF

STY

Semantic type

NA

concept.conceptProperty.propertyId

Generated value for property using "SemType" concatenated with a steadily incremented numerical value.

MRSTY.RRF

STY

Semantic type

NA

concept.conceptProperty.propertyName

Hard coded as constant in java file as "Semantic_Type"

MRSTY.RRF

STY

Semantic type

NA

concept.conceptProperty.propertyType

Hard coded as constant in java file as "property"

MRSTY.RRF

STY

Semantic type

NA

concept.conceptProperty.format

Hard coded as constant in java file as "text/plain"

MRCONSO.RRF

LAT

Language of Term(s)

NA

concept.conceptProperty.language

Logic of code simply selects the first definition in the source as the preferred source

MRCONSO.RRF

TS

Term status

NA

concept.presentation.isPreferred

One or a combination of these RRF values determines whether a presentation is preferred: LAT, TS, STT, ISPREF, RANK.

MRCONSO.RRF

STT

String type

NA

concept.presentation.isPreferred

One or a combination of these RRF values determines whether a presentation is preferred: LAT, TS, STT, ISPREF, RANK.

MRCONSO.RRF

ISPREF

Indicates whether AUI is preferred

NA

concept.presentation.isPreferred

One or a combination of these RRF values determines whether a presentation is preferred: LAT, TS, STT, ISPREF, RANK.

MRRANK.RRF

RANK

Termgroup ranking

NA

concept.presentation.isPreferred

One or a combination of these RRF values determines whether a presentation is preferred: LAT, TS, STT, ISPREF, RANK.

MRCONSO.RRF

RANK

Termgroup ranking 

NA

concept.presentation.isPreferred

No comments

MRDEF.RRF

DEF

Definition

NA

concept.definition.text.content

No comments

MRDEF.RRF

DEF

Definition

NA

concept.definition.isPreferred

Logic of code simply selects the first definition in the source as the preferred source

MRSAT.RRF

ATN

Attribute name

NA

concept.conceptProperty.propertyType

Translated to a LexGrid property type. For values AN, CX, HN this property is typed as a "COMMENT" in LexGrid. For value EV this property is typed "PRESENTATION" This only occurs when the STYPE points to the CODE, SCUI or SDUI columns in MRREL.RRF or MRCONSO.RRF. If the STYPE points to SAUI then the values are loaded as property qualifiers.

MRSAT.RRF

ATV

Attribute value

NA

concept.conceptProperty.propertyValue

No comments

MRSAT.RRF

ATN

Attribute name

NA

concept.conceptProperty.propertyQualifier.propertyQualifierId

If the STYPE points to SAUI then the value is loaded as a property qualifier attribute

MRSAT.RRF

ATV

Attribute value

NA

concept.conceptProperty.propertyQualifier.content

If the STYPE points to SAUI then the value is loaded as a property qualifier attribute

MRCONSO.RRF

SAB

None

x

concept.conceptProperty.source.content

No comments

MRCONSO.RRF

SAB

None

x

concept.conceptProperty.propertyQualifier.propertyQualifierId

Hard coded as constant in java file as "source-code"

MRCONSO.RRF

CODE

None

x

concept.conceptProperty.propertyQualifier.content

No comments

MRCONSO.RRF

CODE

None

x

concept.conceptProperty.propertyQualifier.propertyQualifierId

hard coded as constant in java file as "AUI"

MRCONSO.RRF

AUI

None

x

concept.conceptProperty.propertyQualifier.content

No comments

MRCONSO.RRF

AUI

None

NA

concept.presentation.representationalForm

When ATN value is EV this presentation will be given a representationalForm of "Abbrev."

MRCONSO.RRF

TTY

Term type in source

NA

concept.presentation.representationForm

When TTY value is FN then representationalForm is represented as "Full Form" Otherwise the representationalForm is the same as the TTY source (i.e. if TTY is PT then representationalForm is PT.) PT is one of the preferred presentations.

MRCONSO.RRF

TTY

Term type in source 

NA

concept.conceptProperty.propertyQualifier.propertyQualifierId

Hard coded as "HCD"

MRHIER.RRF

HCD

Source asserted hierarchical number or code for this atom in this context

NA

concept.conceptProperty.propertyQualifier.content

This propertyQualifier is present when the HCD is populated in the the MRHIER file. The corresponding code and property for concept or code is qualified as a code or concept with a context derived heirarchy.


Relations
RRF File Name

RRF Column Name

RRF Definition

NCI Meta Only

LexGrid Model Element

Comments

MRREL.RRF

CUI1

Unique identifier for first concept

NA

None

No comments

MRREL.RRF

AUI1

Unique identifier for first atom

NA

None

No comments

MRCONSO.RRF

CODE

Unique Identifier or code for string in source

NA

ConceptReference.conceptCode (Model element is a ResolvedConceptReference with the value sourceOf attached to the appropriate AssociationList containing this particular REL or RELA association name.)

Mapping to the CODE depends upon the CUI or a combination of CUI and AUI values. If the CODE value is "NOCODE" then LexBIG concatenates "NOCODE" with a "-" and the CUI value. Target or source code value requires use of the DIR flag which indicates the directionality of the relationship in REL or RELA. CUI1 can be used as a pointer to the source CODE value if DIR equals Y, else CUI1 is the targetCode. Similarly, if an AUI exists AUI1 can be an indicator for CODE value to be either or source or target depending on the DIR flag.

MRREL.RRF

CUI2

Unique identifier for second concept

NA

None

No comments

MRREL.RRF

AUI2

Unique identifier for second atom

NA

None

No comments

MRCONSO.RRF

CODE

Unique Identifier or code for string in source

NA

ConceptReference.conceptCode (Model element is a ResolvedConceptReference with the value targetOf attached to the appropriate AssociationList containing this particular REL or RELA association name.)

Mapping to the CODE depends upon the CUI or a combination of CUI and AUI values. If the CODE value is "NOCODE" then LexBIG concatenates "NOCODE" with a "-" and the CUI value. Target or source code value requires use of the DIR flag which indicates the directionality of the relationship in REL or RELA. CUI2 can be used as a pointer to the source CODE value if DIR equals Y, else CUI1 is the targetCode. Similarly, if an AUI exists AUI2 can be an indicator for CODE value to be either or source or target depending on the DIR flag.

MRREL.RRF

DIR

Source asserted directionality flag

NA

None

The UMLS directional flag. Y indicates that this is the direction of the RELA relationship in its source; N indicates that it is not; otherwise indicates that it is not important or has not yet been determined. (If blank RELA, we interpret as 'N', based on empirical review of meta files).

MRREL.RRF

RELA

Relationship attribute

NA

association.id (id inherited from Entity)

Source defined associations. If RELA value is "inverse_isa" then it is changed to "hasSubtype." All others mapped as defined in source.

MRREL.RRF

REL

Relationship

NA

association.id (id inherited from Entity)

UMLS defined associations

MRSAT.RRF

METAUI

Metathesaurus asserted unique identifier

NA

Presence of RUI in MRSAT.RRF METAUI column indicates the association defined in MRREL has an association qualifier. Currently only MedDRA uses these.

No comments

MRSAT.RRF

ATN

None

NA

AssociatedConcept.nameAndValueList.name

No comments

MRSAT.RRF

ATV

None

NA

AssociationQualification.nameAndValueList.content

No comments

MRSAT.RRF

ATV

None

NA

AssociatedConcept.nameAndValueList.name

qualifier name is hard coded to "HCD" This association qualifier is attached to an association when the HCD field in MRHIER.RRF is populated. Associations are identified by evaluating a structured series of AUI's that describe the path to root (PTR field in MRHIER) Once these associations are identified they have and association qualifier attached to them with the value of the HCD loaded as the qualifier.

MRHIER.RRF

HCD

None

NA

AssociationQualification.nameAndValueList.content

No comments

MRSAB.RRF

SSN

Source short name

NA

association.codingSchemeId (Inherited from Entity)

No comments

MRREL.RR

REL or RELA

Relationship or Relationship attribute

NA

association.forwardName

unqualified REL or RELA value (inverse_isa remains the same)

MRDOC.RRF

EXPL

Detailed explanation

NA

association.reverseName

Where DOCKEY in MRDOC equals REL or RELA and value is the association name and TYPE is REL or RELA name prepended to "_inverse".

MRDOC.RRF

EXPL

Detailed explanation

NA

association.inverse

Hard coded as a blank string.

MRDOC.RRF

EXPL

Detailed explanation

NA

association.isAntiReflexive

Hard coded to null

MRDOC.RRF

EXPL

Detailed explanation

NA

association.isAntiSymmetric

Hard coded to null

MRDOC.RRF

EXPL

Detailed explanation

NA

association.isAntiTransitive

Hard coded to null

MRDOC.RRF

EXPL

Detailed explanation

NA

association.isAntiTransitive

Hard coded to null

MRDOC.RRF

EXPL

Detailed explanation

NA

association.isNavigable

Hard coded as Boolean with value true.

MRDOC.RRF

EXPL

Detailed explanation

NA

association.isReflexive

Hard coded to null

MRDOC.RRF

EXPL

Detailed explanation

NA

association.isReverseFunctional

Hard coded to null.

MRDOC.RRF

EXPL

Detailed explanation

NA

association.isSymmetric

Hard coded to null

MRREL.RRF

SAB, REL, RELA

Source abbreviation

NA

association.isTransitive

True when the name of the association can be mapped to a source defined in the SAB attribute of MRREL.RRF. Not the SAB value itself, but extrapolated from it using SAB to REL, RELA relationship.

MRREL.RRF

SAB, REL, RELA

Source abbreviation

NA

association.isTranslationAssociation

Hard coded to null.

MRREL.RRF

SAB, REL, RELA

Source abbreviation

NA

association.targetCodingScheme

Hard coded to null.

MRREL.RRF

SAB, REL, RELA

Source abbreviation

NA

association.entityDescription.content (inheritance path for entityDescription is Entity->versionableAndDescribable)

Hard coded to: "UMLS-defined relationships"

MRREL.RRF

SAB, REL, RELA

Source abbreviation

NA

relations.dc

If REL, this is hard coded as "UMLS-Relations" if RELA then it is hard coded to "Relations"

MRREL.RRF

REL, RELA

Source abbreviation

x

propertyLink.link

This is a link established when the MRREL.RRF file contains a relationship where the CUI is related to itself. Under these conditions the relationship is mapped as a property link with the MRREL defined relationship mapped as the link value.

MRREL.RRF

REL, RELA 

Source abbreviation

x

propertyLink.sourceProperty

Generated as a propertyId for concept, ex: "T-10" This is retrieved based on the AUI value in MRCONSO.RRF from the entityPropertyMultiAttrib table where the AUI equals the attributeValue column.

MRREL.RRF

REL, RELA

Source abbreviation

x

propertyLink.targetProperty

Generated as a propertyId for concept, ex: "T-10" This is retrieved based on the AUI value in MRCONSO.RRF from the entityPropertyMultiAttrib table where the AUI equals the attributeValue column.

SNOMED UMLS Mapping

RRF File Name

RRF Column Name

RRF Definition

LexGrid Model Element

Comments

RSAB.RRF

SVER

Release date or version number of a source

codingScheme.representsVersion

No comments

RSAB.RRF

SSN

Source short name

codingScheme.codingScheme?

No comments

RSAB.RRF

SON

Source Official Name

codingScheme.formalName

No comments

RSAB.RRF

SON

Hard coded to "en"

codingScheme.defaultLanguage

No comments

MRSAT.RRF

ATV

None

concept.presentation.language

Unique to snomed.

OBO Mapping

OBO Class

OBO Entity

LexGrid Model Element

Notes

Document Header

format-version

None

Not mapped

Document Header

data-version

CodingScheme.representsVersion

Creates a codingSchemeVersion and SystemRelease record. If not specified, then hard coded "UNASSIGNED"

Document Header

version

CodingScheme.representsVersion

Deprecated - use data-version if present.

Document Header

date

None

Not mapped

Document Header

saved-by

None

Ignored but included if contained in the remark entity.

Document Header

auto-generated-by

None

Ignored but included if contained in the remark entity.

Document Header

subsetdef

None

Not mapped

Document Header

import

None

Deprecated - Imports are used to assemble a larger document from smaller.

Document Header

typeref

None

Deprecated

Document Header

synonymtypedef

None

Not mapped

Document Header

idspace

None

Not mapped.The idspace is a triple - localName, URN and description.

Document Header

default-relationship-id-prefix

None

Not mapped

Document Header

id-mapping

CodingScheme.supportedAssociation

This is more generalized than the LexGrid model, as it supports mapping between any id's. Note that its primary purpose, however, is to handle supportedAssociation.

Document Header

remark

CodingScheme.entityDescription

Will combine multiple remark entities into the entityDescription.

Document Header

default-namespace

codingScheme.codingScheme

Will use default-namespace if provided; otherwise will use filename without the extension.

Document Header

default-namespace

codingScheme.formalName

Will use default-namespace if provided; otherwise will use filename without the extension.

Document Header

default-namespace

codingScheme.registeredName

Combination of "urn:lsid:bioontology.org:" and if provided, the value in "default-namespace"; but if not will use filename without the extension.

Document Header

default-namespace

codingScheme.defaultLanguage

Hardcoded "en"

Document Header

default-namespace

codingScheme.isNative

Hardcoded "true"

Stanza

id

CodedEntry.conceptCode

No comments

Stanza

name

CodedEntry.entityDescription

No comments

Stanza

name

CodedEntry.presentation['textualPresentation'].text

No comments

Stanza

name

CodedEntry.presentation['textualPresentation'].isPreferred = true

No comments

Stanza

alt_id

None

No comments

Stanza

alt_id 

CodedEntry.property['alt_id'].propertyId

No comments

Stanza

alt_id

CodedEntry.property['alt_id'].text

No comments

Stanza

is_anonymous

CodedEntry.isAnonymous = true

No comments

Stanza

is_obsolete

CodedEntry.isActive = false

No comments

Stanza

def

CodedEntry.definition

No comments

 

 

CodedEntry.definition.isPreferred = true

No comments

Stanza

def.dbxref

NA

See dbxref

Stanza

comment

CodedEntry.comment.text

No comments

Stanza

subset

property[subset tag]

See subsetdef

Stanza

syonym

presentation['textualPresentation'].text

No comments

Stanza

synonym.scope

presentation['textualPresentation'].degreeOfFidelity

No comments

Stanza

synonym.type

presentation['textualPresentation'].representationalForm

No comment

Stanza

synonym.dbxref

NA

See dbxre

Stanza

exact_synonym

NA

See synonym

Stanza

narrow_synonym

NA

See synonym

Stanza

broad_synonym

NA

See synonym

Stanza

xref

associations.['mapsTo']

No comment

Stanza

xref_analog

NA

See synonym

Stanza

xref_unk

None

No comments

Stanza

is_a

associations.['hasSubtype']

Reverse of the source and target.

Stanza

is_a.namespace

None

If present, the supplied namespace becomes the owning "codingScheme".

Stanza

is_a.derived

associations.hasSubtype.associationQualifier

If present, need to include derived in the supportedAssociationQualifiers sectio.

Stanza

intersection_of

None

Processed the same way that OWL intersection operator is processed. This includes creation of anonymous sets.

Stanza

union_of

None

Same as OWL

Stanza

disjoint_from

None

Same as OWL

Stanza

relationship

associations.

No comments

Stanza

relationship.not_necessary

associations..associationQualifier

No comments

Stanza

relationship.inverse_necessary

associations..associationQualifier

No comments

Stanza

relationship.namespace

None

If present, the supplied namespace becomes the owning "codingScheme".

Stanza

relationship.derived

associations..associationQualifier

No comments

Stanza

relationship.cardinality

associations..associationQualifier

No comments

Stanza

relationship.maxCardinality

associations..associationQualifier

No comments

Stanza

relationship.minCardinality

associations..associationQualifier

No comments

Stanza

is_obsolete

codedEntry.isActive = false

No comments

Stanza

replaced_by

None

No comment

Stanza

consider

None

Not mapped

Stanza

use_term

None

Deprecated

dbxref

dbxref name

CodedEntry..source

No comments

dbxref

supportedSource

None

dbxref name format is inconsistent. In most cases, it can be the localName of supportedSource, but special processing may be necessary in the case of URL's, etc

dbxref

dbxref description

None

Not mapped

dbxref

trailing modifiers

None

Not mapped

typeDef Stanza

domain

associations.['has_domain']

No comments

typeDef Stanza

range

associations.['has_range']

No comments

typeDef Stanza

is_cyclic

property['is_cyclic']

No comment

typeDef Stanza

is_reflexive

property['is_reflexive']

No comments

 

 

association.isReflexive

No comments

typeDef Stanza

is_symmetric

property['is_symmetric']

No comments

 

 

association.isSymmetric

No comments

typeDef Stanza

is_transitive

property['is_transitive']

No comments

 

 

association.isTransitive

No comments.

typeDef Stanza

inverse_of

association.inverse

No comments

instance stanza

id

Same rules as general stanza

Same rules as general stanza

instance stanza

name

same rules as general stanza

Same rules as general stanza

instance stanza

instance_of

association['has_instance']

No comments

instance stanza

data type properties go in Coded Entry property section

None

No comments

HL7 RIM Mapping

HL7 Table

HL7 Column

LexGrid Model Element

Notes

Intentionally Not Mapped Outstanding Issues

Model

<modelID>

<codingSchemeName>

No notes

None

None

Model

<name>

<formalName>

No notes

None

None

Model

<name>

<registeredName>

http://www.hl7.org/Library/data-model/RIM

None

None

Model

<name>

<defaultLanguage>

en*

None

None

Model

<versionNumber>

<representsVersion>

No notes

None

None

Model

<versionNumber>

<isNative>

0*

None

None

Model

<versionNumber>

<approximateNumberofConcepts>

Result of count on concept bearing table?

None

None

Model

<versionNumber>

<firstRelease>

MISSING

None

None

Model

<versionNumber>

<modifiedRelease>

MISSING

None

None

Model

<versionNumber>

<deprecated>

MISSING

None

None

Model

<description>

<entityDescription>

No notes

None

None

Model

<description>

<copyright>

MISSING

None

None

VCS_code_system

codeSystemId

codingScheme.registeredName

Moved to metadata file.

None

None

VCS_code_system 

codeSystemType

commonTypes::Properties

This is an HL7 specific code system property to distinguish internal vs external code systems. Moved to metadata file.

None

None

VCS_code_system

codeSystemName

concept.conceptCode

Moved to metadata file.

None

None

VCS_code_system

codeSystemName

concept.presentation['textualPresentation'].text

No Notes

None

None

VCS_code_system

fullName

codingScheme.formalName

No notes

None

None

VCS_code_system

description

codingScheme.entityDescription

Moved to metadata file.

None

None

VCS_code_system

releaseId

codingScheme.representsVersion

Moved to metadata file.

None

None

VCS_code_system

copyrightNotice

codingScheme.copyright

Moved to metadata file.

None

None

VCS_code_system

literal('en')

codingScheme.defaultLanguage

Moved to metadata file.

None

None

VCS_concept_code_xref

internalId

None

No notes

None

None

VCS_code_system

Concept Code

concept.conceptCode

No notes

RIM db column conceptCode2

None

VCS_code_system

Case Difference

commonTypes::Properties

Basically a property to outline whether there are case differences in the Concept Code or not (mainly used, but not restricted tor units of measure)

RIM db column codeInstance

None

VCS_code_system

Status

concept.isActive=(conceptStatus=='A'?)

No notes

RIM db column conceptStatus

None

VCS_code_system

Status

concept.conceptStatus

Not used by HL7. A = isActive, R = retired

None

None

VCS_concept_designation

internalId

None

foreign key

None

VCS_concept_designation 

designation

concept.presentation'textualPresentation'].text

No notes

None

None

 

designationSeq

None

No notes

None

None

VCS_concept_designation

language

concept.presentation['textualPresentation'].language

Can be omitted if language = default language

None

None

VCS_concept_designation

preferredForLanguage

concept.presentation['textualPresentation'].isPreferred

No notes

 

None

VCS_concept_description

internalId

with(codeSystem[deref(internalId)].concept[deref(internalId)]).definition

foreign key

None

VCS_concept_description

description

concept.presentation['textualPresentation'].text

No notes

None

None

VCS_concept_description

language

concept.presentation['textualPresentation'].language

No notes

None

None

VCS_concept_description

literal('true')

concept.presentation['textualPresentation'].isPreferred

No notes

None

None

VCS_concept_description

uniqueId()

concept.presentation['textualPresentation'].propertyId

No notes

None

None

VCS_concept_description

literal('definition')

concept.presentation['textualPresentation'].property

No notes

None

None

VCS_concept_property

internalId

None

No notes

foreign key

None

VCS_concept_property 

propertyCode

concept.property.property

No notes

None

None

VCS_concept_property

propertySeq

None

Currently not used by HL7

None

None

VCS_concept_property

propartyValue

concept.property.text

No notes

None

None

VCS_concept_property

language

concept.property.language

No notes

None

None

VCS_concept_relationship

relationCode

association.association

No notes

None

None

VCS_concept_relationship 

sourceInternalId

associationInstance.sourceConcept

No notes

None

None

VCS_concept_relationship

targetInternalId

associationTarget.targetConcept

No notes

None

None

Model

modelID

systemRelease.releaseId

No notes

None

None

Model

name

service.service

No notes

None

None

Model

versionNumber

service.version

No notes

None

None

Model

lastModifiedDate

systemRelease.releaseDate

No notes

None

None

Model

developingOrganization

systemRelease.releaseAgency

No notes

None

None

Model

committeeID

None

No notes

None

None

Model

description

systemRelease.entityDescription

No notes

None

None

Model

concat('urn:oid:2.16.840.1.113883:',
systemRelease.releaseId)

systemRelease.releaseURN

No notes

None

None

Model

literal('true')

systemRelease.isLatest

Also have to set the prior release isLatest to false

None

None

Model

preceding-sibling/releaseOrder + 1

systemRelease.releaseOrder

No notes

None

None

Model

modelID

commonTypes::Properties

No notes

None

None

(Special mapping for NCI)

name

codingScheme.localName

No notes

None

None

(Special mapping for NCI)

versionNumber

codingScheme.representsVersion

No notes

None

None

(Special mapping for NCI)

lastModifiedDate

commonTypes::Properties

No notes

None

None

(Special mapping for NCI)

developingOrganization

commonTypes::Properties

No notes

None

None

(Special mapping for NCI)

committeeID

None

No notes

None

None

(Special mapping for NCI)

description

codingScheme.entityDescription

No notes

None

None

(Special mapping for NCI)

concat('urn:oid:2.16.840.1.113883:',
systemRelease.releaseId)

codingScheme.registeredName

No notes

None

None

(Special mapping for NCI)

literal('true')

commonTypes::Properties

Also have to set the prior release isLatest to false

None

None

(Special mapping for NCI)

preceding-sibling/releaseOrder + 1

commonTypes::Properties

No notes

None

None

RIM_vocabulary_domain

vocDomain

codingscheme["VocabularyDomain"].concept.conceptCode

Vocabulary Domains are carried in a code system of vocabulary domains.

None

None

RIM_vocabulary_domain

None

codingscheme["VocabularyDomain"].concept.presentation
["textualPresentation"].text

preferredPresentation

None

None

RIM_vocabulary_domain

description

codingscheme["VocabularyDomain"].concept.definition.text

preferredDefinition for code

None

None

RIM_vocabulary_domain

restrictsDomain

codingscheme["VocabularyDomain"].association
["hasSubtype"].sourceConcept

Should this be hasSubtype or something else?

None

None

RIM_vocabulary_domain

None

codingscheme["VocabularyDomain"].association["hasSubtype"].
targetconcept = vocDomain

No notes

None

None

VOC_code_reference

usedToBuildValueSet

with(valueDomain[registeredName=current()/.]

No notes

None

None

VOC_code_reference 

referencesConceptCode

None

#id is synthesized

  1. Only stored if isHeadCode

None

None

VOC_code_reference

referencesInternalId

None

Internal id's aren't exposed in lexGrid

None

None

VOC_code_reference

relationship

...valueDomainEntry/includeChildren = (relationship == 'hasSubtype')

Won't deal w/ non-hasSubtype relationships, but HL7 doesn't have any.

None

VOC_code_reference

includeReferencedCode

...valueDomainEntry/isSelectable

Not in current implementation

None

None

VOC_code_reference

leafOnly

None

Not used in HL7 Model

None

None

VOC_code_reference

directChildrenOnly

None

Not used in HL7 Model

None

None

VOC_code_reference

isHeadCode

 

Only used when referenced in VOC_value_set_constructor.

None

VOC_code_reference

referencesCodeSystem

.../valueDomainEntry.codingScheme

Shortcut in HL7 model. Must = VOC_value_set.basedOnCodeSystem

None

None

VOC_code_reference

arbitraryUniqueValue()

.../valueDomainEntry.id

No notes

None

None

VOC_registered_code_system

codeSystemId

VOC_registered_code_system isn't currently transferred to Lexgrid

No notes

None

None

VOC_registered_code_system

sponsor

None

No notes

None

None

VOC_registered_code_system

publisher

None

No notes

 

VOC_registered_code_system

versionReportingMethod

None

No notes

None

None

VOC_registered_code_system

licensingInformation

None

This field should really be transfer to copyright?

None

None

VOC_registered_code_system

inUMLS

None

No notes

None

None

VOC_registered_code_system

systemSpecificLocatorInfo

None

No notes

None

None

VOC_registered_code_system

uri

None

No notes

None

None

VOC_registered_code_system

isExternal

None

No notes

None

None

VOC_value_set

valueSetId

valueDomain.registeredName

No notes

None

None

VOC_value_set

valueSetName

valueDomain.valueDomain

Name is the key in LexGrid, and is optional in HL7 - will need to be addressed.

None

None

VOC_value_set

basedOnCodeSystem

valueDomain.defaultCodingScheme

Optional in HL7, required in LexGrid.

None

None

VOC_value_set

description

valueDomain.entityDescription

No notes

None

None

VOC_value_set

definingExpression

None

Not used.

None

None

VOC_value_set

allCodes

None

No notes

None

None

VOC_value_set

isTaxonomicSet

None

No mapping available

None

None

VOC_value_set

valueSetAuthority

None

Included in valueSetID

None

None

VOC_value_set

valueSetNumber

None

No notes

None

None

VOC_value_set_constructor

usedToBuildValueSet

None

No notes

None

None

VOC_value_set_constructor

includesOrExcludesSet

valueDomainEntry.includesValueDomain

No notes

None

None

VOC_value_set_constructor

includeHeadCode

valueDomainEntry.isSelectable

No notes

None

None

VOC_value_set_constructor

 

valueDomainEntry.conceptCode = VOC_code_reference
[usedToBuildValueSet=current().usedToBuildValueSet and
isHeadCode=true].referencesConceptCode

Assumes that there always is a head code.

None

None

VOC_vocabulary_domain_value_set

representsVocDomain

(selector)

None

None

None

VOC_vocabulary_domain_value_set 

definedByValueSet

codingscheme['VocabularyDomain'].concept[representsVocDomain]
.property['definedByValueSet'].text

have to get 'representsVocDomain' into supportedProperty header

None

None

VOC_vocabulary_domain_value_set

appliesInContext

codingscheme['VocabularyDomain'].concept[representsVocDomain]
.property['definedByValueSet'].usageContext

Have to get all the contexts in the VocabularyDomain supportedContext header

None

None

VCS_release_version

releaseId

codingSchemeVersion.version

No notes

None

None

VCS_release_version 

valueDomainVersion.version

Set if one or more value sets change

No notes

None

None

VCS_release_version

literal("false")

codingSchemeVersion.isComplete

All versions are delta's in this model

None

None

VCS_release_version

releaseAgency

None

No notes

None

None

VCS_release_version

releaseDate

codingSchemeVersion.versionDate

No notes

None

None

VCS_release_version

valueDomainVersion.versionDate

None

No notes

None

None

VCS_release_version

description

codingSchemeVersion.entityDescription

No notes

None

None

VCS_release_version

valueDomainVersion.entityDescription

None

No notes

None

None

VCS_release_version

editorID

None

There is no place for these currently.

None

None

VCS_release_versio

forWhomID

None

No notes

None

None

VCS_release_version

concat('urn:oid:2.16.840.1.113883:',systemRelease.releaseId)

None

This corresponds to the containing system release when the sytem release occurs. It is empty until then.

None

None

LexGrid Text Mapping

Line

Source Definition Column 1

Source Definition Column 2

Source Definition Column 3

Source Definition Column 4

Source Definition Column 5

Source Definition Column 6

Source Definition Column 7

Source Definition Column 8

Comments

1

<codingSchemeName>

<codingSchemeId>

<defaultLanguage>

<formalName>

[<version>]

[<source>]

[<description>]

[<copyright>]

This must be the first line. It contains the coding scheme metadata.

2

[<code>]

<name>

[<description>]

None

None

None

None

None

Beginning of concepts in coding scheme.

3

[<code>]

<name>

[<description>]

None

None

None

None

None

Represent hierarchical 'hasSubtype' relationship nesting (name hasSubtype name)


Text Element Coding Scheme

LexGrid

Comments

codingSchemeName

codingScheme.codingSchemeName

No comments

codingSchemeId

codingScheme.codingSchemeId

No comments

defaultLanguage

codingScheme.defaultLanguage

No comments

formalName

codingScheme.formalName

No comments

version

codingScheme.representsVersion

Optional

source

codingScheme.source

Optional

description

codingScheme.entityDescription

Optional

copyright

codingScheme.copyright

Optional


Text Element Concepts

LexGrid

Comments

code

concept.conceptCode

Optional

name

concept.conceptName

No comments

description

concept.entityDescription

No comments


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