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MAYO CLINIC DIVISION OF BIOMEDICAL INFORMATICS
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<big><big>LexGrid Source Mapping Guide</big>LexGrid Vocabulary Services for caBIG® (LexBIG)
Version 1.0
Last Modified: April 13, 2009</big>2009
Authors: Scott Bauer, Craig Stancl</center>
Related Documents
LexGrid_Loader_Mapping.xls
Unified Medical Language System
The Unified Medical Language System (UMLS) and Rich Release Format (RRF)
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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.
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*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.
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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:
| Code Block |
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<owl:DatatypeProperty rdf:ID="currency">
<rdfs:domain rdf:resource="#Money"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
</owl:DatatypeProperty> |
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<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:
| Code Block |
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<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> |
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| Code Block |
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<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:
| Code Block |
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<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> |
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<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).
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<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:
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If no equivalent class for a concept, it is considered primitive and is indicated by creating a concept property set to 'true.'
Embedded XML
Property text with embedded XML fragments are identified by by the following identifiers:
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A property qualifier is created. The property qualifier id is set to the tag, the value is set to the tag value.
HL7 RIM
To build a single coding scheme from the HL7 MS Access database, implementation is similar to how the NCI MetaThesaurus is stored in LexGrid.
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3. Iterate through the code system table rows and get each coding scheme.
a. Create and persist an "@" node in the database
b. Prepare an artificial "top node" for each coding scheme. (Metadata persisted here as concept properties?) This will result in 250 top nodes.
i. The artificial top nodes will need to have a concept code created for them.
ii. Attach to "@" the artificial top nodes as a hasSubtype.
iii. 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.
c. Translate the RRF source property loads to the EMF world.
i. Load the concepts ensuring that the coding scheme name is loaded as a "source" property
ii. 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.
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