Schubert et al. claimed in previous work that mutations in STX1B are associated with epilepsy. We present here a formalization of that claim, stating that all things of class “STX1B mutation” that are in the context of a thing of class “human” frequently have a relation of type “co-occurs with” to a thing of class “epilepsy” in the same context.
1. IntroductionSchubert et al. [2 ] state that “Our results thus implicate STX1B and the presynaptic release machinery in fever-associated epilepsy syndromes.”. We present here a formalization of the main scientific claim from this quote by using a semantic template called the super-pattern [1 ].
2. FormalizationOur formalization looks as follows:
In the context class we use the class “human” (Q5) from Wikidata. In the subject class, we use a new minted class “STX1B mutation” that is a subclass of “mutation” (Q42918) from Wikidata and is related to the class “STX1B” (Q18048867) from Wikidata. In the object class we use the class “epilepsy” (Q41571) from Wikidata.
3. RDF codeThis is our formalization as a nanopublication in TriG format:
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@prefix sub: <http://purl.org/np/RAeRSya2qIYymsBxiqOZP_oaQpHXUVXiydKvPCFM-7DDQ#> .
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@prefix dct: <http://purl.org/dc/terms/> .
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@prefix npx: <http://purl.org/nanopub/x/> .
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@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix orcid: <https://orcid.org/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix sp: <https://w3id.org/linkflows/superpattern/terms/> .
sub:Head {
this: np:hasAssertion sub:assertion ;
np:hasProvenance sub:provenance ;
np:hasPublicationInfo sub:pubinfo ;
a np:Nanopublication .
}
sub:assertion {
sub:spi a sp:SuperPatternInstance ;
rdfs:label "Mutations in STX1B are associated with epilepsy" ;
sp:hasContextClass <http://www.wikidata.org/entity/Q5> ;
sp:hasSubjectClass <http://purl.org/np/RAPVWYH0x-xyDa9PfBcGUFly3m1FNEO43KG9s0uH-y6yo#STX1B-mutation> ;
sp:hasQualifier sp:frequentlyQualifier ;
sp:hasRelation sp:cooccursWith ;
sp:hasObjectClass <http://www.wikidata.org/entity/Q41571> .
}
sub:provenance {
sub:activity a sp:FormalizationActivity ;
prov:used <http://doi.org/10.1038/ng.3130> , sub:quote ;
prov:wasAssociatedWith orcid:0000-0001-6501-0806 , orcid:0000-0002-6532-5880 , orcid:0000-0002-7979-9921 .
sub:assertion prov:wasGeneratedBy sub:activity .
sub:quote prov:value "Our results thus implicate STX1B and the presynaptic release machinery in fever-associated epilepsy
syndromes" ;
prov:wasQuotedFrom <http://doi.org/10.1038/ng.3130> .
}
sub:pubinfo {
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npx:hasPublicKey
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npx:hasSignature
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nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RAB_oy10D3XUP-zYlqGz7Uj58AsUXhEKeGqmRFg5LSgDM> ;
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nt:wasCreatedFromTemplate <http://purl.org/np/RAv68imZrEjfcp2rnEg1hzoBqEVc0cQMtp9_1Za0BxNM4> .
}
The following nanopublications introduce the newly minted classes in TriG format.
This is the class definition of “STX1B mutation”:
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@prefix dct: <http://purl.org/dc/terms/> .
@prefix nt: <https://w3id.org/np/o/ntemplate/> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix orcid: <https://orcid.org/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
sub:Head {
this: np:hasAssertion sub:assertion ;
np:hasProvenance sub:provenance ;
np:hasPublicationInfo sub:pubinfo ;
a np:Nanopublication .
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sub:assertion {
sub:STX1B-mutation a <http://www.w3.org/2002/07/owl#Class> ;
rdfs:label "STX1B mutation" ;
rdfs:subClassOf <http://www.wikidata.org/entity/Q42918> ;
skos:definition "mutation in STX1B" ;
skos:relatedMatch <http://www.wikidata.org/entity/Q18048867> .
}
sub:provenance {
sub:assertion prov:wasAttributedTo orcid:0000-0001-6501-0806 .
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sub:pubinfo {
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npx:hasPublicKey
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npx:hasSignatureTarget this: .
this: dct:created "2021-06-21T14:08:44.937+02:00"^^xsd:dateTime ;
dct:creator orcid:0000-0001-6501-0806 ;
npx:introduces sub:STX1B-mutation ;
nt:wasCreatedFromProvenanceTemplate <http://purl.org/np/RANwQa4ICWS5SOjw7gp99nBpXBasapwtZF1fIM3H2gYTM> ;
nt:wasCreatedFromPubinfoTemplate <http://purl.org/np/RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM> ;
nt:wasCreatedFromTemplate <http://purl.org/np/RAdpgRpigXtt8iPV9uOPf3wIT3qzOI8Sg2Q72CNV8g-Yo> .
}
