Page History

None

None

None

None

codingScheme.representsVersion

No comments

None

None

None

None

codingScheme.codingScheme

Hard coded in java file as "UMLS_SemNet"

None

None

None

None

codingScheme.formalName

Hard coded in java file as "UMLS Semantic Network"

None

None

None

None

codingScheme.defaultLanguage

Hard coded in java file as "en"

None

None

None

None

codingScheme.approxNumConcepts

Hard coded in java file as

None

None

None

None

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

None

codingScheme.copyright

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

license.txt

None

None

None

codingScheme.registeredName

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

license.txt

None

None

None

codingScheme.concepts.dc

Hard coded in java file as "concepts"

license.txt

None

None

None

codingScheme.relations.dc

Hard coded in java file as "relations"

license.txt

None

None

None

codingScheme.mappings.dc

Hard coded in java file as "mappings"

license.txt

None

None

None

codingScheme.localNameList

No comments

license.txt

None

None

None

codingScheme.localNameList.

Hard coded in java file as "UMLS_SemNet"

license.txt

None

None

None

codingScheme.localNameList

No comments

license.txt

None

None

None

codingScheme.localNameList.

No comments

license.txt

None

None

None

codingScheme.source

No comments

license.txt

None

None

None

codingScheme.source.content

No comments

license.txt

None

None

None

codingScheme.localNameList

No comments

license.txt

None

None

None

codingScheme.localNameList.

No comments

license.txt

None

None

None

codingScheme.localNameList

No comments

license.txt

None

None

None

codingScheme.localNameList.

No comments

license.txt

None

None

None

codingScheme.localNameList

No comments

license.txt

None

None

None

codingScheme.localNameList.

No comments

license.txt

None

None

None

codingScheme.localNameList

No comments

license.txt

None

None

None

codingScheme.localNameList.

No comments

license.txt

None

None

None

mappings.supportedFormat

No comments

license.txt

None

None

None

mappings.supportedFormat.localId

Hard coded in java file as "text/plain"

license.txt

None

None

None

mappings.supportedFormat.urn

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

license.txt

None

None

None

mappings.supportedAssociation

No comments

SRDEF

RL

None

None

mappings.supportedAssociation.localId

No comments

SRDEF

RL

None

None

mappings.supportedContext

No comments

SRDEF

RL

None

None

mappings.supportedSource

No comments

SRDEF

RL

None

None

mappings.supportedSource.localId

Hard coded in java file as "NLM"

SRDEF

RL

None

None

mappings.supportedSource.urn

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

SRDEF

RL

None

None

mappings.supportedHierarchy

No comments

SRDEF

RL

None

None

mappings.supportedHierarchy.localId

Hard coded in java file as "is_a"

SRDEF

RL

None

None

mappings.supportedHierarchy.isForwardNavigable

Hard coded as "true"

SRDEF

RL

None

None

mappings.supportedHierarchy.rootCode

Hard coded as "@"

SRDEF

RL

None

None

mappings.supportedHierarchy.associationList

Hard coded in java file as "hasSubtype"

SRDEF

RL

None

None

mappings.supportedAssociationQualifier

v No comments

SRFLD

COL

None

None

mappings.supportedProperty

No comments

SRFLD

COL

None

None

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

None

mappings.supportedProperty.urn

Hard coded in java file as ""

SRFLD

COL

None

None

mappings.supportedLanguage

No comments

SRFLD

COL

None

None

mappings.supportedLanguage.localId

Hard coded in java file as "en"

SRFLD

COL

None

None

mappings.supportedLanguage.urn

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

SRFLD

COL

None

None

mappings.supportedCodingScheme

No comments

SRFLD

COL

None

None

mappings.supportedCodingScheme.localId

Hard coded in java file as "UMLS_SemNet"

SRFLD

COL

None

None

mappings.supportedCodingScheme.urn

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

SRFLD

COL

None

None

mappings.supportedRepresentationalForm

No comments

SRFLD

COL

None

None

mappings.supportedConceptStatus

No comments

SRFLD

COL

None

None

mappings.supportedPropertyLink

No comments

SRFLD

COL

None

None

mappings.supportedPropertyQualifier

No comments

SRFLD

COL

None

None

mappings.supportedDataType

No comments

SRDEF

UI

None

None

concept.id(inherited from Entity)

No comments

SRDEF

STY/RL

None

None

concept.enitityDescription(inheritance path Entity->versionableAndDescribable)

No comments

SRDEF

STY/RL

None

None

concept.conceptProperty

No comments

SRDEF

NH

None

None

concept.conceptProperty.text.content

No comments

SRDEF

NH

None

None

concept.conceptProperty.format

Hard coded in java file as "text/plain"

SRDEF

NH

None

None

concept.conceptProperty.propertyName

Hard coded in java file as "NH"

SRDEF

NH

None

None

concept.conceptProperty.propertyId

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

SRDEF

NH

None

None

concept.presentation

No comments

SRDEF

NH

None

None

concept.presentation.propertyName (inherited from Property)

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

SRDEF

NH

None

None

concept.presentation.propertyId

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

SRDEF

STY/RL, ABR

None

None

concept.presentation.text.content

No comments

SRDEF

STY/RL, ABR

None

None

concept.presentation.format

Hard coded in java file as "text/plain"

SRDEF

STY/RL, ABR

None

None

concept.presentation.isPreferred

Hard coded in java file as true.

SRDEF

STY/RL, ABR

None

None

concept.definition.propertyName (inherited from Property)

Hard coded in java file as "DEF"

SRDEF

STY/RL, ABR

None

None

concept.definition.propertyId

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

SRDEF

DEF

None

None

concept.definition.text.content

No comments

SRDEF

DEF

None

None

concept.definition.format

Hard coded in java file as "text/plain"

SRDEF

DEF

None

None

concept.definition.isPreferred

Hard coded in java file as true.

SRDEF

DEF

None

None

concept.comment

No comments

SRDEF

EX

None

None

concept.comment.propertyName (inherited from Property)

Hard coded in java file as "EX"

SRDEF

EX

None

None

concept.comment.text.content

No comments

SRDEF

EX

None

None

concept.comment.format

Hard coded in java file as "text/plain"

SRDEF

EX

None

None

concept.comment.propertyId

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

SRDEF

EX

None

None

concept.instruction

No comments

SRDEF

EX

None

None

concept.instruction.propertyName (inherited from Property)

Hard coded in java file as "UN"

SRDEF

UN

None

None

concept.instruction.text.content

No comments

SRDEF

UN

None

None

concept.instruction.format

Hard coded in java file as "text/plain"

SRDEF

UN

None

None

concept.instruction.propertyId

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

SRSTR

RL

  None  

None

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  

None

association.isTransitive

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

SRSTR

RL

  None  

None

association.forwardName

Reversed when value of RL is "isa"

SRSTR

STY/RL

  None  

None

associationInstance.sourceId

Reversed when value of RL is "isa"

SRSTR

STY/RL

  None  

None

associationTarget.targetId

  No comments

SRDEF

RIN

  None  

None

association.reverseName

  No comments

SRDEF

DEF

  None  

None

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

When SRDEF value RT is "RL"

SRSTRE1

UI/STY(first argument)

  None  

None

associationInstance.sourceId

Reversed when value of RL is "isa"

SRSTRE1

UI/STY(2nd argument)

  None  

None

associationTarget.targetId

Reversed when value of RL is "isa"

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

  None

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

  None

codingScheme.copyright

No comments

MRSAB.RRF

SCC

None

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

  None

x

codingScheme.codingScheme

Hard coded in java file as "NCI MetaThesaurus"

  MRDOC.RRF  

EXPL

  None

x

codingScheme.formalName

Hard coded in java file as "NCI MetaThesaurus"

  MRDOC.RRF  

EXPL

  None

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

mappings.supportedFormat

Hard coded as constant in java file as "Format"

  MRDOC.RRF  

EXPL  

Detailed explanation

mappings.supportedFormat.localId

Hard coded as one of several constants in a java file

  MRDOC.RRF  

EXPL  

Detailed explanation

mappings.supportedAssociation

Hard coded as constant in java file as "Association"

MRREL.RRF

REL, RELA

Relationship, Relationship attribute

  NA

mappings.supportedAssociation.localId

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"

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.

  MRRANK.RRF  

RANK  

Termgroup ranking

  NA

concept.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

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

x

concept.conceptProperty.propertyQualifier.content

No comments

MRCONSO.RRF

CODE

None

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.

Document Header

format-version

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

Not mapped.

Document Header

saved-by

Ignored but included if contained in the remark entity.

Document Header

auto-generated-by

Ignored but included if contained in the remark entity.

Document Header

subsetdef

Not mapped.

Document Header

import

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

Document Header

typeref

Deprecated.

Document Header

synonymtypedef

Not mapped.

Document Header

idspace

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

Document Header

default-relationship-id-prefix

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.

codingScheme.defaultLanguage

Hardcoded "en"

codingScheme.isNative

Hardcoded "true"

Stanza

id

CodedEntry.conceptCode

Stanza

name

CodedEntry.entityDescription

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="61462832af3a9d49-d5df4298-47574c82-af848d5d-f6f461826f483907baae45b2"><ac:plain-text-body><![CDATA[

CodedEntry.presentation['textualPresentation'].text

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="05a1c47a9efee223-ad30e469-4da94817-b85e9baf-37143eea3bd25514cb5c8235"><ac:plain-text-body><![CDATA[

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

]]></ac:plain-text-body></ac:structured-macro>

Stanza

alt_id

CodedEntry.property.property="alt_id"

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="0d0609dd84f65258-3390250f-4fe447aa-a7728e30-32f2ec211904e9435418bfc8"><ac:plain-text-body><![CDATA[

CodedEntry.property['alt_id'].propertyId

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="c12e3e9a5beb80a4-69a1db8b-4e7e4755-bc0b8e1f-f54b930f8785c915098d8d89"><ac:plain-text-body><![CDATA[

CodedEntry.property['alt_id'].text

]]></ac:plain-text-body></ac:structured-macro>

Stanza

is_anonymous

CodedEntry.isAnonymous = true

Stanza

is_obsolete

CodedEntry.isActive = false

Stanza

def

CodedEntry.definition

CodedEntry.definition.isPreferred = true

Stanza

def.dbxref

See dbxref

Stanza

comment

CodedEntry.comment.text

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="2aaf87b18ded538b-9586b5dc-45bc4d46-92768a3c-cc05503d52ad0bc39b11d199"><ac:plain-text-body><![CDATA[

Stanza

subset

property[subset tag]

See subsetdef

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="9c599bf64bdb162c-2c1c35a7-40404d87-b34f8ec0-04738cd7c87d5054af233d05"><ac:plain-text-body><![CDATA[

Stanza

syonym

presentation['textualPresentation'].text

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="4a9d38151f2e6eef-12d2ce87-473d4019-b4d99ff2-726f7f7892e2c07c3e62f230"><ac:plain-text-body><![CDATA[

Stanza

synonym.scope

presentation['textualPresentation'].degreeOfFidelity

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="6f88c132e9355c1b-0412f94c-4cd840c5-a1508c5d-14ecc405747fc6f4c0011f8c"><ac:plain-text-body><![CDATA[

Stanza

synonym.type

presentation['textualPresentation'].representationalForm

]]></ac:plain-text-body></ac:structured-macro>

Stanza

synonym.dbxref

(see dbxref)

Stanza

exact_synonym

See synonym

Stanza

narrow_synonym

See synonym

Stanza

broad_synonym

See synonym

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="924ddd637f708024-4408b4a8-41e84d51-9cf2b21d-eb06d281e2b69d2d2b65c8b3"><ac:plain-text-body><![CDATA[

Stanza

xref

associations.['mapsTo']

]]></ac:plain-text-body></ac:structured-macro>

Stanza

xref_analog

See synonym

Stanza

xref_unk

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="4ea2919cb8055544-0d825e13-45224ee0-aca5aaef-359600c897235e822e644853"><ac:plain-text-body><![CDATA[

Stanza

is_a

associations.['hasSubtype']

Reverse of the source and target.

]]></ac:plain-text-body></ac:structured-macro>

Stanza

is_a.namespace

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 section

Stanza

intersection_of

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

Stanza

union_of

Same as OWL

Stanza

disjoint_from

Same as OWL

Stanza

relationship

associations.

Stanza

relationship.not_necessary

associations..associationQualifier

Stanza

relationship.inverse_necessary

associations..associationQualifier

Stanza

relationship.namespace

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

Stanza

relationship.derived

associations..associationQualifier

Stanza

relationship.cardinality

associations..associationQualifier

Stanza

relationship.maxCardinality

associations..associationQualifier

Stanza

relationship.minCardinality

associations..associationQualifier

Stanza

is_obsolete

codedEntry.isActive = false

codedEntry.conceptStatus="is_obsolete"

Stanza

replaced_by

Stanza

consider

Not Mapped

Stanza

use_term

(deprecated)

dbxref

dbxref name

CodedEntry..source

supportedSource

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

Not mapped.

dbxref

trailing modifiers

Not mapped.

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="ad2a3a6d5107fba3-b3a5cf24-44544811-9967bfee-913c43c7793a507760c0e5d1"><ac:plain-text-body><![CDATA[

typeDef Stanza

domain

associations.['has_domain']

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="f5a54a909c7620f2-a8d8f1e3-49754059-813bbba4-aaafb59b23bcfe05096c322a"><ac:plain-text-body><![CDATA[

typeDef Stanza

range

associations.['has_range']

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="9cac0c7cf47a60f2-b27c87cf-4dcb4308-a123bc0a-60d35436f13e0946f66cb24d"><ac:plain-text-body><![CDATA[

typeDef Stanza

is_cyclic

property['is_cyclic']

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="ea3ea27db93198d7-5e6d2bf4-4a594905-b5a4a0ba-963cb343cca814ae78937a73"><ac:plain-text-body><![CDATA[

typeDef Stanza

is_reflexive

property['is_reflexive']

]]></ac:plain-text-body></ac:structured-macro>

association.isReflexive

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="bf30d56b3e0ed47d-31f8145e-4e714bd8-8a068703-13be9bb390cfa0468f2fc685"><ac:plain-text-body><![CDATA[

typeDef Stanza

is_symmetric

property['is_symmetric']

]]></ac:plain-text-body></ac:structured-macro>

association.isSymmetric

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="45e114c9e797746c-d61ddad6-457a4803-9fb0847b-4c6cfb5f2af3b8845c681af5"><ac:plain-text-body><![CDATA[

typeDef Stanza

is_transitive

property['is_transitive']

]]></ac:plain-text-body></ac:structured-macro>

association.isTransitive

typeDef Stanza

inverse_of

association.inverse

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

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="7e35e98f276706dd-bf8b7b47-4e2a4ef2-82ed8541-f40ac60d1c288a5a69f47277"><ac:plain-text-body><![CDATA[

instance stanza

instance_of

association['has_instance']

]]></ac:plain-text-body></ac:structured-macro>

instance stanza

CodedEntry.property.property=""

data type properties go in Coded Entry property section

Model

<modelID>

<codingSchemeName>

<name>

<formalName>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="352698928af29c65-05f078b9-421241d2-997e9f69-aa2c59e1090238949f9ac953"><ac:plain-text-body><![CDATA[

<registeredName>

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

http://www.hl7.org/Library/data-model/RIM] *[1]

]]></ac:plain-text-body></ac:structured-macro>

<defaultLanguage>

en*

<versionNumber>

<representsVersion>

<isNative>

0*

<approximateNumberofConcepts>

Result of count on concept bearing table?

<firstRelease>

MISSING

<modifiedRelease>

MISSING

<deprecated>

MISSING

<description>

<entityDescription>

<copyright>

MISSING

VCS_code_system

codeSystemId

codingScheme.registeredName

Moved to metadata file.

codeSystemType

commonTypes::Properties

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

codeSystemName

concept.conceptCode

Moved to metadata file.

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="12b6d7d5c25dd1ea-63c6ba46-470a4e2a-b5e8847c-3c1862b84d96b5243ae0dbc3"><ac:plain-text-body><![CDATA[

codeSystemName

concept.presentation['textualPresentation'].text

]]></ac:plain-text-body></ac:structured-macro>

fullName

codingScheme.formalName

description

codingScheme.entityDescription

Moved to metadata file.

releaseId

codingScheme.representsVersion

Moved to metadata file.

copyrightNotice

codingScheme.copyright

Moved to metadata file.

literal('en')

codingScheme.defaultLanguage

Moved to metadata file.

VCS_concept_code_xref

internalId

Concept Code

concept.conceptCode

RIM db column conceptCode2

Case Difference

commonTypes::Properties

Basically a proprty 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

Status

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

RIM db column conceptStatus

concept.conceptStatus

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

VCS_concept_designation

internalId

foreign key

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="85fdfcf474fb1ebe-daf2d660-42ac4b94-990397bd-abfd314afb10f03a4ccf7a90"><ac:plain-text-body><![CDATA[

designation

concept.presentation['textualPresentation'].text

]]></ac:plain-text-body></ac:structured-macro>

designationSeq

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="60c1176147d49151-5af3eb9d-4b944b47-a15a9410-b028ee9c36c58a0910ef14a4"><ac:plain-text-body><![CDATA[

language

concept.presentation['textualPresentation'].language

Can be omitted if language = default language

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="1fbafda3d1adb6df-96ca8b34-42844c1a-9afaa5ca-ae1d9e1c8c0157498d0e0ff6"><ac:plain-text-body><![CDATA[

preferredForLanguage

concept.presentation['textualPresentation'].isPreferred

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="24683a3e6f19eafd-7a4e17c0-42cc4096-873b81b2-5f2669a769375447d4b8684c"><ac:plain-text-body><![CDATA[

VCS_concept_description

internalId

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

foreign key

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="42eb4a94ccb6d174-ca8cf5a0-4e08476c-b296bc9a-9f7b2199eac2acaa0c02c851"><ac:plain-text-body><![CDATA[

description

concept.presentation['textualPresentation'].text

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="b54f0b4e35a001de-ccc5c65c-4e9246eb-a288b9b7-da0d396f6e8e2e39293436a2"><ac:plain-text-body><![CDATA[

language

concept.presentation['textualPresentation'].language

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="cabde7193aa51264-469333f2-4cb14d88-8604b21e-ec54594f0c3ee2b33269b6b0"><ac:plain-text-body><![CDATA[

literal('true')

concept.presentation['textualPresentation'].isPreferred

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="9dcc203cdfa6b5d6-642dd32f-42914e53-9395b763-589e87096a52f22cc7d17e91"><ac:plain-text-body><![CDATA[

uniqueId()

concept.presentation['textualPresentation'].propertyId

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="ceda66bd7e43d178-d7868bf4-439a4992-af44be17-bc180476d47c030c409321cd"><ac:plain-text-body><![CDATA[

literal('definition')

concept.presentation['textualPresentation'].property

]]></ac:plain-text-body></ac:structured-macro>

VCS_concept_property

internalId

foreign key

propertyCode

concept.property.property

propertySeq

Currently not used by HL7

propartyValue

concept.property.text

language

concept.property.language

VCS_concept_relationship

relationCode

association.association

sourceInternalId

associationInstance.sourceConcept

targetInternalId

associationTarget.targetConcept

Model

modelID

systemRelease.releaseId

name

service.service

versionNumber

service.version

lastModifiedDate

systemRelease.releaseDate

developingOrganization

systemRelease.releaseAgency

committeeID

description

systemRelease.entityDescription

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

systemRelease.releaseURN

literal('true')

systemRelease.isLatest

Also have to set the prior release isLatest to false

preceding-sibling/releaseOrder + 1

systemRelease.releaseOrder

Model

modelID

commonTypes::Properties

(Special mapping for NCI)

name

codingScheme.localName

versionNumber

codingScheme.representsVersion

lastModifiedDate

commonTypes::Properties

developingOrganization

commonTypes::Properties

committeeID

description

codingScheme.entityDescription

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

codingScheme.registeredName

literal('true')

commonTypes::Properties

Also have to set the prior release isLatest to false

preceding-sibling/releaseOrder + 1

commonTypes::Properties

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="412138698213d4a9-0fc68c26-4e144690-bd17988d-9fa8f71a66aab85254ba8bbe"><ac:plain-text-body><![CDATA[

RIM_vocabulary_domain

vocDomain

codingscheme["VocabularyDomain"].concept.conceptCode

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

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="de193a54b15921e6-1649422c-45b142ec-a1198732-1dde5b21c011be6e4ed899bb"><ac:plain-text-body><![CDATA[

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

preferredPresentation

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="3f6fa0e0b5939546-8c6d701a-4be5430f-9dfcad93-27550a61b4047d5ac171bb7e"><ac:plain-text-body><![CDATA[

description

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

preferredDefinition for code

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="30e4e6d5c94d160e-e50b693b-455743c1-b1599975-cf97c0157c6de73f88674f61"><ac:plain-text-body><![CDATA[

restrictsDomain

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

Should this be hasSubtype or something else?

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="6c4ebf556a38e997-d693a1ea-47894e0b-af4581cb-9bb4569b026014c6e92bd111"><ac:plain-text-body><![CDATA[

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

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="2b154b7bfc53152b-65991ba5-439b4d31-8e8cafd4-2e1512a061534858d430f2ce"><ac:plain-text-body><![CDATA[

VOC_code_reference

usedToBuildValueSet

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

]]></ac:plain-text-body></ac:structured-macro>

referencesConceptCode

...valueDomainEntry/conceptCode

1) id is synthesized
2) Only stored if isHeadCode == false or includeReferencedCode == true

referencesInternalId

Internal id's aren't exposed in lexGrid

relationship

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

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

includeReferencedCode

...valueDomainEntry/isSelectable

Not in current implementation

leafOnly

Not used in HL7 Model

directChildrenOnly

Not used in HL7 Model

isHeadCode

Only used when referenced in VOC_value_set_constructor.

referencesCodeSystem

.../valueDomainEntry.codingScheme

Shortcut in HL7 model. Must = VOC_value_set.basedOnCodeSystem

arbitraryUniqueValue()

.../valueDomainEntry.id

VOC_registered_code_system

codeSystemId

VOC_registered_code_system isn't currently transferred to Lexgrid

sponsor

publisher

versionReportingMethod

licensingInformation

This field should really be transfer to copyright?

inUMLS

systemSpecificLocatorInfo

uri

isExternal

VOC_value_set

valueSetId

valueDomain.registeredName

valueSetName

valueDomain.valueDomain

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

basedOnCodeSystem

valueDomain.defaultCodingScheme

Optional in HL7, required in LexGrid.

description

valueDomain.entityDescription

definingExpression

Not used.

allCodes

if 'true': valueDomain.conceptCode = "@", valueDomain.includeChildren='true'

isTaxonomicSet

No mapping available

valueSetAuthority

Included in valueSetID

valueSetNumber

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="7a64a675afd8f8b8-d7f175f7-4d9e430c-adcf8125-6d954af12559952246161b96"><ac:plain-text-body><![CDATA[

VOC_value_set_constructor

usedToBuildValueSet

new valueDomainEntry(parent = valueDomain[valueSetId=current()/.],id=unique())

]]></ac:plain-text-body></ac:structured-macro>

includesOrExcludesSet

valueDomainEntry.includesValueDomain

includeHeadCode

valueDomainEntry.isSelectable

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="d25b9de9d36637ed-3c866d22-48e74fdb-ab188bf8-d48e21ea7b5dd069d737f7cf"><ac:plain-text-body><![CDATA[

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

Assumes that there always is a head code.

]]></ac:plain-text-body></ac:structured-macro>

VOC_vocabulary_domain_value_set

representsVocDomain

(selector)

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="3f6b6d7357338493-155232f8-4a7a4688-a4c3a7fe-dccc34a495486660805743c4"><ac:plain-text-body><![CDATA[

definedByValueSet

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

have to get 'representsVocDomain' into supportedProperty header

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="292087a2ddec2224-d67c8bea-473c41d2-ab0d9733-2c01952401c75d1c78519f10"><ac:plain-text-body><![CDATA[

appliesInContext

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

Have to get all the contexts in the VocabularyDomain supportedContext header

]]></ac:plain-text-body></ac:structured-macro>

VCS_release_version

releaseId

codingSchemeVersion.version

This is not the way that things are done at the moment. At the moment, VCS_release_versions are loaded into systemRelease. Entered if one or more concept/relationship change.

valueDomainVersion.version

Set iff one or more value sets change

literal("false")

codingSchemeVersion.isComplete

All versions are delta's in this model

releaseAgency

releaseDate

codingSchemeVersion.versionDate

valueDomainVersion.versionDate

description

codingSchemeVersion.entityDescription

valueDomainVersion.entityDescription

editorID

There is no place for these currently.

forWhomID

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

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

Source Definition

Comments

Column

1

2

3

4

5

6

7

8

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="b98949e843ccd4bd-4a9cc981-43a9417a-ac37818b-a5d8dc4f5053a9fbd9a75d65"><ac:plain-text-body><![CDATA[

Line

1

<codingSchemeName>

<codingSchemeId>

<defaultLanguage>

<formalName>

[<version>]

[<source>]

[<description>]

[<copyright>]

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

]]></ac:plain-text-body></ac:structured-macro>

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="1735ad9b820ab301-1137c616-49b24e28-9bfca2f4-47db91fc24253056b0849ef0"><ac:plain-text-body><![CDATA[

2

[<code>]

<name>

[<description>]

Beginning of concepts in coding scheme.

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="b3ad2eb7b5d82ed6-967e9940-4ae24f5d-a2b0a1b8-1cb530fc8ce7ff5cab88ab4c"><ac:plain-text-body><![CDATA[

3

[<code>]

<name>

[<description>]

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