LexEVS 6.0 UML Mappings

MRSAB.RRF

SVER

Release date or version number of a source

NA

codingScheme.representsVersion

No comments

MRSAB.RRF

SSN

Source short name

NA

codingScheme.codingSchemeName

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

NA

codingScheme.codingSchemeURI

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"

x

codingScheme.codingSchemeName

Hard coded in java file as "NCI MetaThesaurus"

x

codingScheme.formalName

Hard coded in java file as "NCI MetaThesaurus"

x

codingScheme.defaultLanguage

Hard coded in java file as "ENG"

MRCONSO.RRF

x

codingScheme.approxNumConcepts

Count of CODE value in MRCONSO.RRF

x

codingScheme.entityDescription

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

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/."

NA

codingScheme.localNameList

Hard coded as constant in java file as "localName"

MRSAB.RRF

SON

Source Official Name

NA

codingScheme.localNameList.

No comments

NA

codingScheme.localNameList

Hard coded as constant in java file as "localName"

NA

codingScheme.localNameList.

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

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

x

codingScheme.localNameList

Hard coded as constant in java file as "localName"

x

codingScheme.localNameList.

Hard coded in java file as "NCI Thesaurus"

x

codingScheme.localNameList

Hard coded as constant in java file as "localName"

x

codingScheme.localNameList.

Hard coded in java file as "NCI_Thesaurus"

x

codingScheme.localNameList

Hard coded as constant in java file as "localName"

x

codingScheme.localNameList.

Hard coded in java file as "10001"

x

codingScheme.localNameList

Hard coded as constant in java file as "source"

x

codingScheme.localNameList.

Hard coded in java file as "RRF Files"

NA

mappings.supportedFormat

Hard coded as constant in java file as "Format"

NA

mappings.supportedFormat.localId

Hard coded as one of several constants in a java file

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

NA

mappings.supportedContext

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

NA

mappings.supportedSource

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

NA

No comments

NA

mappings.supportedHierarchy

Hard coded as constant in java file as "Hierarchy"

NA

mappings.supportedAssociationQualifier

Hard coded as constant in java file as "AssociationQualifier"

NA

mappings.supportedProperty

Hard coded as constant in java file as "Property"

NA

mappings.supportedLanguage

Hard coded as constant in java file as "Language"

NA

mappings.supportedCodingScheme

Hard coded as constant in java file as "CodingScheme"

NA

mappings.supportedRepresentationalForm

Hard coded as constant in java file as "RepresentationalForm"

NA

mappings.supportedConceptStatus

Hard coded as constant in java file as "ConceptStatus"

NA

mappings.supportedPropertyLink

Hard coded as constant in java file as "PropertyLink"

NA

mappings.supportedPropertyQualifier

Hard coded as constant in java file as "PropertyQualifier"

NA

mappings.supportedDataType

Hard coded as constant in java file as "DataType"

MRCONSO.RRF

CODE

Unique Identifier or code for string in source

NA

Entity.entityCode

No comments

MRCONSO.RRF

CUI

Unique identifier for Entity

x

Entity.entityCode

No comments

NA

Entity.isActive

Hardcoded in parameter as true.

NA

Entity.status

Hard coded as constant in java file as "Active"

NA

Entity.isAnonymous

Hardcoded in parameter as false.

MRCONSO.RRF

STR

String

NA

Entity.entityDescription

No comments

NA

No comments

No comments

NA

Entity.Property.Format

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

NA

Entity.Property.propertyName

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

NA

Entity.Property.usageContext

No comments

NA

Entity.Property.propertyId

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

NA

Entity.presentation.propertyId

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

NA

Entity.comment.propertyId

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

NA

Entity.definition.propertyId

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

NA

Entity.instruction.propertyId

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

MRCONSO.RRF

CUI

Unique identifier for Entity

NA

Entity.Property.text.content.

No comments

NA

Entity.Property.propertyId

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

NA

Entity.Property.propertyName

hard coded as constant in java file as "UMLS_CUI"

NA

Entity.Property.propertyType

hard coded as constant in java file as "property"

NA

Entity.Property.format

left as null

MRSTY.RRF

STY

Semantic type

NA

Entity.Property.text.content

NA

Entity.Property.propertyId

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

NA

Entity.Property.propertyName

hard coded as constant in java file as "Semantic_Type"

NA

Entity.Property.propertyType

hard coded as constant in java file as "property"

NA

Entity.Property.value.dataType

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

MRCONSO.RRF

LAT

Language of Term(s)

NA

Entity.Property.language

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

MRCONSO.RRF

TS

Term status

NA

Entity.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

Entity.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

Entity.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

Entity.presentation.isPreferred

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

NA

Entity.presentation.isPreferred

The first presentation for each language is automatically marked as isPreferred="true" after using comparator to sort list of presentations using comparator to evaluate each presentation based on a combination of values from LAT, TS, STT, ISPREF, RANK.

MRDEF.RRF

DEF

Definition

NA

Entity.definition.text.content

No comments

NA

Entity.definition.isPreferred

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

NA

No comments

MRSAT.RRF

ATN

Attribute name

NA

Entity.Property.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

Entity.Property.value

No comments

MRSAT.RRF

ATN

Attribute name

NA

Entity.Property.propertyQualifier.propertyQualifierName

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

MRSAT.RRF

ATV

Attribute value

NA

Entity.Property.propertyQualifier.value

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

MRSAT.RRF

ATUI

Unique identifier for attribute

NA

Entity.Property.propertyId

No comments

MRSAT.RRF

METAUI

Metathesaurus asserted unique identifier

NA

Entity.Property.PropertyQualifier.propertyQualifierName

set to "METAUI"

MRSAT.RRF

METAUI

Metathesaurus asserted unique identifier

NA

Entity.Property.PropertyQualifier.value

METAUI column value

MRSAT.RRF

STYPE

The name of the column in MRCONSO.RRF or MRREL.RRF that contains the identifier to which the attribute is attached

NA

Entity.Property.PropertyQualifier.propertyQualifierName

set to "STYPE"

MRSAT.RRF

STYPE

The name of the column in MRCONSO.RRF or MRREL.RRF that contains the identifier to which the attribute is attached

NA

Entity.Property.PropertyQualifier.value

STYPE column value

MRSAT.RRF

SUPPRESS

Suppressible flag

NA

Entity.Property.PropertyQualifier.propertyQualifierName

set to "SUPPRESS"

MRSAT.RRF

SUPPRESS

Suppressible flag

NA

Entity.Property.PropertyQualifier.value

STYPE column value if not null

MRCONSO.RRF

SAB

x

Entity.Property.source.content

No comments

x

Entity.Property.propertyQualifier.propertyQualifierName

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

MRCONSO.RRF

CODE

x

Entity.Property.propertyQualifier.value

No comments

x

Entity.Property.propertyQualifier.propertyQualifierName

hard coded as constant in java file as "AUI"

MRCONSO.RRF

AUI

x

Entity.Property.propertyQualifier.value

No comments

NA

Entity.presentation.representationalForm

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

MRCONSO.RRF

TTY

Term type in source

NA

Entity.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.

NA

Entity.Property.propertyQualifier.propertyQualifierId

hard coded as "HCD"

MRHIER.RRF

HCD

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

NA

Entity.Property.propertyQualifier.content

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

MRREL.RRF

CUI1

Unique identifier for first concept

NA

No comments

MRREL.RRF

AUI1

Unique identifier for first atom

NA

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

No comments

MRREL.RRF

AUI2

Unique identifier for second atom

NA

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

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

AssociationPredicate.associationName

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

AssociationPredicate.associationName

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. Currentely only MedDRA uses these.

MRSAT.RRF

ATN

NA

AssociatedConcept.nameAndValueList.name

No comments

MRSAT.RRF

ATV

NA

AssociationQualification.nameAndValueList.content

No comments

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

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

AssociationEntity.forwardName

unqualified REL or RELA value (inverse_isa remains the same)

MRDOC.RRF

EXPL

Detailed explanation

NA

AssociationEntity.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".

NA

association.isNavigable

hard coded as Boolean with value true.

MRREL.RRF

SAB, REL, RELA

Source abbreviation

NA

AssociationEntity.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.

NA

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

Hard coded to: "UMLS-defined relationships"

NA

relations.containerName

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

MRREL.RRF

REL, RELA

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.

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.

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.

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

Hard coded to "en"

codingScheme.defaultLanguage

No comments

MRSAT.RRF

ATV

None

concept.presentation.language

Unique to snomed.