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align SPOR substance definitions with IDMP substances #513

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tw-osthus opened this issue Oct 27, 2023 · 0 comments
Open

align SPOR substance definitions with IDMP substances #513

tw-osthus opened this issue Oct 27, 2023 · 0 comments
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@tw-osthus
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tw-osthus commented Oct 27, 2023

SPOR substances defines substances as a controlled vocabulary term (with term names and term identifiers) and adds
molecular formula
molecular weight
substance type -> SPOR RMS substance type
InchiKey
comment
external code XEVMPD
external code UNII
to the term.

The substance types is an extension to the IDMP substance classes and the other properties exist as properties for IDMP substances.

for example Aluminium is

	<owl:NamedIndividual rdf:about="https://spor.ema.europa.eu/v2/SubstanceDefinition/100000092806">
		<rdf:type rdf:resource="&idmp-spor;SPORControlledVocabularyTerm"/>
		<rdfs:label>SPOR substance 100000092806 - Aluminium</rdfs:label>
		<idmp-spor:hasSPORTermName>
			<idmp-spor:SPORTermName>
				<cmns-txt:hasTextValue>Aluminium</cmns-txt:hasTextValue>
				<mvf:hasLanguage rdf:resource="&lcc-639-1;English"/>
			</idmp-spor:SPORTermName>
		</idmp-spor:hasSPORTermName>
		<cmns-id:isIdentifiedBy>
			<idmp-spor:SPORTermIdentifier>
				<cmns-txt:hasTextValue>100000092806</cmns-txt:hasTextValue>
			</idmp-spor:SPORTermIdentifier>
		</cmns-id:isIdentifiedBy>
		<cmns-cls:isClassifiedBy rdf:resource="https://spor.ema.europa.eu/v1/lists/100000075826/terms/100000075845"/>
	</owl:NamedIndividual>

Aluminium as IDMP substance is

	<owl:NamedIndividual rdf:about="&idmp-amp;Aluminium">
		<rdf:type rdf:resource="&idmp-sub;ChemicalSubstance"/>
		<rdfs:label>Aluminium</rdfs:label>
		<idmp-sub:hasDefiningMolecularFormula>Al</idmp-sub:hasDefiningMolecularFormula>
		<idmp-sub:hasDefiningStructure>
			<idmp-sub:MolecularStructure>
				<idmp-sub:hasInChIKeyValue>XAGFODPZIPBFFR-UHFFFAOYSA-N</idmp-sub:hasInChIKeyValue>
				<idmp-sub:hasSMILESValue>[Al]</idmp-sub:hasSMILESValue>
			</idmp-sub:MolecularStructure>
		</idmp-sub:hasDefiningStructure>
	</owl:NamedIndividual>

How do we align IDMP substances with SPOR substances?

Both are instances so we cannot use subclassing!

Candidates are

  • <SPOR substance>cmns-dsg:denotes <IDMP substance>
  • <SPOR substance> cmns-cls:classifies <IDMP substance>
  • <SPOR substance> owl:sameAs <IDMP substance>
  • <SPOR substance> rdf:type idmp-spor:SPORControlledVocabularyTerm, idmp-sub:Substance

The last option seems to be the easiest and in alignment with SPOR intention but is invasive to SPOR.

denotes would fit for the controlled vocabulary aspect
classifies would fit in so far that SPOR substances specify (define) of substance aspects, but is very weak
same as may be too strong

@tw-osthus tw-osthus self-assigned this Oct 27, 2023
@mereolog mereolog added this to the Release 1.0.0 milestone Nov 27, 2023
@mereolog mereolog removed this from the Release 1.0.0 milestone Jan 4, 2024
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