wikipathways / wikipathways/WikiPathwaysCurator

Curation Query for Conversions

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#14 4 comments 0 reactions 1 assignee View on GitHub

@RyAMiller is already working on this.

Since May 21, 2020.

enhancement
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Java
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Description

While doing some work pertaining to WikiPathway sementics, I used the query

      SELECT (substr(str(?o),41) as ?IntType) (COUNT(?o) as ?IntCount)
      WHERE {
        ?entity a ?o . 
        ?entity a wp:Interaction . 
        ?entity dcterms:isPartOf <http://identifiers.org/wikipathways/WP1423_r106690> .
        ?entity dcterms:isPartOf ?pathway .
        ?pathway    a wp:Pathway ;
            wp:ontologyTag <http://vocabularies.wikipathways.org/wp#Curation:AnalysisCollection> ;
            wp:organismName        "Homo sapiens"^^xsd:string .
      } ORDER BY DESC(?IntCount)`

for the pathway. WP1423. It is a pathway about Sphingolipid Metabolism. A majority of the interactions look to be conversions of metabolites from one form to another facilitated by enzyme catalysis. All of conversion events are only classified as DirectedInteractions and do not have the type "conversion."

All catalysis events that convert a metabolite from one form to another would be conversions, correct? It seems like this might help to identify interactions that should by type 'conversion' but not.

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