Business' relevance

Whereas CQ1 starts with an active moiety, and identifies all substances having that have a common active moiety, CQ2 aims to identify starts with a substance and identifies the active moiety for a the substance. A substance is defined as a matter of defined composition that has discrete existence, whose origin may be biological, mineral or chemical.

Diagram for model pattern

DrawiobordertruediagramNameCQ1asimpleViewerfalsewidthlinksautotbstyletoplboxtruediagramWidth366revision1Figure 1: Simplified version showing the linking of a substance to an active moiety. The property "has active moiety" uses a shortcut for the pattern shown in Figure 2.A moiety is an entity within a substance that has a complete and continuous molecular structure. The strength of a pharmaceutical product is often based on what is referred to as the active moiety of the molecule, responsible for the physiological or pharmacological action of the drug substance. Linking a substance and it's active moiety not only gives immediate clarity on how the substance potentially exerts it's pharmacological activity, but also (due to the way the ontology is modeled) gives an overview of how active moieties can be differently defined under different contexts.

Diagram for Query Pattern

Figure 2: Linking a substance to an active moiety. This patterns allows traversing the model to find all substances that participate in some substance constituency whose active moiety role is played by some moiety (which in the regulatory context is another substance).

Test Data

GSRS

SPARQL Query

prefix idmp-sub:    <Diagram 1: Query pattern diagram for SPARQL Query

Test Data

Amlodipine example: https://spec.pistoiaalliance.orggithub.com/edmcouncil/idmp/ontologyblob/ISOmaster/ISO11238-Substances/>
prefix rdf:         <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix rdfs:        <http://www.w3.org/2000/01/rdf-schema#>
prefix skos:        <http://www.w3.org/2004/02/skos/core#>
prefix cmns-pts:    <https://www.omg.org/spec/Commons/PartiesAndSituations/>
prefix cmns-dsg:    <https://www.omg.org/spec/Commons/Designators/>
prefix cmns-cstdsg: <https://www.omg.org/spec/Commons/ContextualDesignators/>
prefix gsrs-sub:    <https://gsrs.ncats.nih.gov/api/v1/substances/>SELECT DISTINCT ?ActiveMoiety ?ActiveMoityName ?ActiveMoietyRoleContext
FROM <https://spec.pistoiaalliance.org/idmp/ontology>
FROM <https://data.pistoiaalliance.org/idmp/gsrs>
WHERE {
    # use the FDA UNII code to refer to the substance
    BIND(gsrs-sub:B786J7A343 AS ?Substance )
 
    # ensure the entity is indeed a substance
    ?Substance a/rdfs:subClassOf* idmp-sub:Substance .
    # find the active moieties
    ?ActiveMoiety cmns-pts:playsRole ?Role .
    ?Role cmns-pts:isRealizedIn ?Substance ;
          a/rdfs:subClassOf* idmp-sub:ActiveMoietyRole ;
          .
       
    OPTIONAL {?Role cmns-cstdsg:isApplicableIn ?ActiveMoietyRoleContext }
    OPTIONAL {?ActiveMoiety skos:prefLabel ?ActiveMoityName }
}

...

EXT/Examples/AmlodipineExample.rdf

Terlipressin Example: https://github.com/edmcouncil/idmp/blob/master/EXT/Examples/TerlipressinExample.rdf

SPARQL Query

https://github.com/edmcouncil/idmp/blob/master/etc/CQ/Example/uc1_cq2.sparql

Expected Query Result for Amlodipine Example Data

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Expected Query Result for Terlipressin Example Data

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