krobasky
commented
7 years ago I wrote a few queries, but they don't return anything -- is that OK, or am I doing it wrong?
For example, here's the first query: http://yasgui.org/short/rJrg9w_qb
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX DiseaseClass: <http://purl.obolibrary.org/obo/NCIT_C2991>
PREFIX RegimenHasAcceptedUseForDisease: <http://purl.obolibrary.org/obo/NCIT_R172>
PREFIX ChemicalOrDrugAffectsGeneProduct: <http://purl.obolibrary.org/obo/NCIT_R146>
PREFIX ChemicalOrDrugIsMetabolizedByEnzyme: <http://purl.obolibrary.org/obo/NCIT_R122>
PREFIX GeneProductIsEncodedByGene: <http://purl.obolibrary.org/obo/NCIT_R54>
SELECT DISTINCT ?disease_labels ?gene_labels
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?diseases rdfs:subClassOf* DiseaseClass: .
?diseases rdfs:label ?disease_labels .
?therapies RegimenHasAcceptedUseForDisease: ?diseases .
?proteins ChemicalOrDrugIsMetabolizedByEnzyme: ?therapies .
?genes GeneProductIsEncodedByGene: ?proteins .
?genes rdfs:label ?gene_labels .
}
mbrush
balhoff
decorons
For coming up with queries, it may help to use the cmap here that shows all paths through the data. Below are a few examples of queries we can see should be supported, along with the path the query would take through top-level types in NCIt. Queries get more complex as you go down the list.
What genes are targeted by drugs used to treat cancer x? Query path:
Disease or Disorder -> Chemotherapy Regimen or Agent Combination -> Drug, Food, Chemical or Biomedical Material -> GeneWhat pathways are targeted by drugs used to treat cancer x? Query path:
Disease or Disorder -> Gene -> Biochemical PathwayWhat signaling pathways are affected in cancer x? Query path:
Disease or Disorder -> Molecular Abnormality -> Gene -> Biochemical PathwayWhat drugs target the highest number of pathways? Query path:
Drug, Food, Chemical or Biomedical Material -> Gene -> COUNT(Biochemical Pathway)What other drugs target genes in the same signaling pathway as drug X? Query path:
Drug, Food, Chemical or Biomedical Material -> Gene Product -> Gene -> Biochemical Pathway -> Gene -> Gene Product -> Drug, Food, Chemical or Biomedical MaterialA possible drug re-purposing query (based on WD example here) Find cancers that may be treated by drugs used to treat non-cancers (based on fact that the one or more of the genes known to be targeted by the drug are associated with the cancer) Query path:
Disease or Disorder -> Drug, Food, Chemical or Biomedical Material -> Gene Product -> Gene -> Drug, Food, Chemical or Biomedical Material -> Disease or DisorderA drug re-purposing query extension: Can go further and constrain results to include only matches based on shared genes annotated to apoptosis or cell proliferation GO terms. Query path:
Disease or Disorder -> Drug, Food, Chemical or Biomedical Material -> Gene Product -> Gene (filter by GO annotation) -> Drug, Food, Chemical or Biomedical Material -> Disease or Disorder