Requirement
Requirement to select a substance or a modification of that substance .... use case: during authoring to prompt the user with all the active ingredient options. Clinician chooses a drug and wants to refine the selection using modification-of substances.
Background
Although The modification-of attribute is a transitive property in OWL, and used during subsumption, the NNF rules state that X relationships are redundant and must not be part of the output.
Options:
OWL. Transitive properties have a similar characteristic to an is-a relationships but without stating a subtype relationship.
In SNOMED CT an OWL property chains are used to help organise the hierarchy, allowing products with modified substance to be subsumed into concept groupers defined using the base substance. However in this case the base substance should not be inherited into the product with the modified substance. The base (not modified) version of the substance is found as redundant and removed during NNF calculation. See OWL Guide: 2.5. Generating Necessary Normal Form Relationships from the OWL Refsets
Example property chain: "|Has active ingredient|o |Is modification of|" is a sub-property of "|Has active ingredient|".
Example hierarchy:
Parent
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Child
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Because
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And Property Chain:
SubObjectPropertyOf(
ObjectPropertyChain(
:127489000 |Has active ingredient (attribute)|
:738774007 |Is modification of (attribute)|
)
:127489000 |Has active ingredient (attribute)|
)
.. which results in OWL seeing the non modified ingredient as a property of the concept for the purpose of subsumption.
Finally
TransitiveObjectProperty(:738774007 |Is modification of (attribute)|)
This could be used by the ECL engines.
Solution Options:
- ECL SolutionECL: << 372687004 |Amoxicillin (substance)|
OR ( << 105590001 |Substance (substance)| : << 738774007 |Is modification of (attribute)| = << 372687004 |Amoxicillin (substance)| )
OR ( << 105590001 |Substance (substance)| : << 738774007 |Is modification of (attribute)| = ( << 105590001 |Substance (substance)| : << 738774007 |Is modification of (attribute)| = << 372687004 |Amoxicillin (substance)| ) )
OR ( << 105590001 |Substance (substance)| : << 738774007 |Is modification of (attribute)| = ( << 105590001 |Substance (substance)| : << 738774007 |Is modification of (attribute)| = ( << 105590001 |Substance (substance)| : << 738774007 |Is modification of (attribute)| = << 372687004 |Amoxicillin (substance)| ) ) )
)- Pros: Already works, if you know the maximum number of transitive hops
- Cons: It's not pretty. It may work for modification-of but may not work for longer transitive chains like part-of (body structures)
- NNF changeChange Solution: Keep the modification-of relationships using a new characteristic type to support querying.
- Pros: Do not need to increase number of concepts or complexity of ECL engines.
- Cons: Big change in the spec? Could be misinterpreted. Seems risky.
- ECL Engine and language changeLanguage Change Solution: Build a transitive closure for each transitive property, in the same way that we do for the is-a relationship. We would also need special ECL syntax for this.
- Pros: No content change. No classification change.
- Cons: Slightly more work in ECL engines.
- Example: Kai Kewley pseudo-code needed
- Pseudo-code: Kai Kewley
- In an ECL engine, when building the ECL index:
- Identify which properties are transitive:
Set<String> transitiveProperties = owlOntology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY).stream()
.map(axiom -> axiom.getProperty().getNamedProperty().getIRI().getShortForm())
.collect(Collectors.toSet());
- Build up a set of transitive property ancestors:
- Concept:
Map<String, Set<String>> transitiveTypeAncestorMap;
addRelationship(source, destination, type) {
if (transitiveProperties.contains(type)) {
transitiveTypeAncestorMap.get(type).add(destination);
}
}
- Include transitive property ancestors in ECL index:
- conceptId: 351000220100 |Minocycline hydrochloride dihydrate (substance)|
- 738774007_ancestors = (52886009 |Minocycline hydrochloride (substance)|, 372653009 |Minocycline (substance)|)
- 738774007_parents = ()
733930001_ancestors = ()
- ...
- ECL Language could allow something like:
- << [+738774007 |Is modification of|] meaning use modification of transitive hierarchy in addition to is-a hierarchy.
- or << [+*] meaning use all available transitive hierarchies
- Examples:
- < |Product| : << |Has active ingredient| = << [+738774007 |Is modification of|] |Amoxicillin|
- < |Product| : << |Has active ingredient| = << [+*] |Amoxicillin|
- Content Change SolutionContent change: Create a grouper substance to include that substance and all single and multi-hop the modification substances.
- Pros: Would work without other changes. This technique has precedent in the body structure hierarchy.
- Cons: Approx. three times the number of substance concepts. May be hard for implementers who want a clean list. Because of the high number (around 2K) of substances with a modification relationship these groups would need to be generated.
- Current content in numbers:
- 2,297 Substances have the modification-of attribute
- 89 Substance groupers exist with naming: "Substance-X and/or substance-X derivative"
- 37 Product groupers exist with naming: "Product containing substance-X and/or substance-X derivative"