Paszek et al. claimed in previous work that glycocalyx bulk mechanically drives integrin clustering in cancer cells engaged with the extracellular matrix. We present here a formalization of that claim, stating that all things of class “glycocalyx bulk” that are in the context of a thing of class “ecm bound cancer cell” generally have a relation of type “increases” to a thing of class “integrin clustering” in the same context.
1. IntroductionPaszek et al. [2 ] state that “Expression of large tumour-associated glycoproteins in non-transformed mammary cells promoted focal adhesion assembly and facilitated integrin-dependent growth factor signalling to support cell growth and survival.”. 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 a new minted class “ecm bound cancer cell” that is a subclass of “cancer cell” (Q4118072) from Wikidata and is related to the class “extracellular matrix” (Q193825) from Wikidata. In the subject class, we use a new minted class “glycocalyx bulk” that is related to the class “glycocalyx” (Q898356) from Wikidata. In the object class we minted a new class “integrin clustering” that is a subclass of “integrin binding” (Q14633861) from Wikidata and is related to the class “focal adhesion” (Q904514) from Wikidata.
3. RDF codeThis is our formalization as a nanopublication in TriG format:
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sp:hasRelation <https://w3id.org/linkflows/superpattern/terms/increases> ;
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The following nanopublications introduce the newly minted classes in TriG format.
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This is the class definition of “glycocalyx bulk”:
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This is the class definition of “integrin clustering”:
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