Test for errors in `rdf:type` annotations

[jmillanacosta]

See the following query, where an ENSG is annotated as both Pathway and DataNode but not Gene

PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

SELECT DISTINCT ?gene ?geneAll WHERE {
  ?gene a wp:Pathway, wp:DataNode .
  FILTER CONTAINS(STR(?gene), "ENSG")
  optional{?geneAll a wp:Pathway, wp:DataNode ; a wp:Gene . }
}

SPARQL results (1 results in 0.06 seconds)

gene	geneAll
https://identifiers.org/ensembl/ENSG00000100030	-

What other tests need to be written?

[egonw]

Use this query:

PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
PREFIX gpml: <http://vocabularies.wikipathways.org/gpml#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

SELECT DISTINCT ?pathway ?gene WHERE {
  ?gene gpml:xrefId ?id ; gpml:type "Pathway" .
  ?pathway gpml:hasDataNode ?gene .
  FILTER CONTAINS(STR(?id), "ENSG")
}