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Demonstration queries

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krobasky edited this page Sep 26, 2017 · 24 revisions

This resource can be mined for interesting knowledge. Below are some examples, click on a question to run it in YASGUI:

Find disease associations

What diseases are associated with Lymphedema?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX lymphedema: <http://purl.obolibrary.org/obo/NCIT_C3207>
PREFIX DiseaseHasAssociatedDisease: <http://purl.obolibrary.org/obo/NCIT_R126>
SELECT DISTINCT ?disease ?disease_label 
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?disease DiseaseHasAssociatedDisease: lymphedema: .
?disease rdfs:label ?disease_label .
}

Find diseases related to a particular anatomic site

What disease have the reproductive system as the primary anatomic site?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX repro: <http://purl.obolibrary.org/obo/NCIT_C12841>
PREFIX HasPrimaryAnatomicSite: <http://purl.obolibrary.org/obo/NCIT_R101>
SELECT DISTINCT ?disease ?disease_label
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?disease HasPrimaryAnatomicSite: repro: .
?disease rdfs:label ?disease_label .
}

What diseases have the primary anatomic site of the lung?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX lung: <http://purl.obolibrary.org/obo/NCIT_C12468>
PREFIX HasPrimaryAnatomicSite: <http://purl.obolibrary.org/obo/NCIT_R101>
SELECT DISTINCT ?disease ?disease_label
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?disease HasPrimaryAnatomicSite: lung: .
?disease rdfs:label ?disease_label .
}

Find procedures that target a particular anatomical site

What are procedures target the colon?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX colon: <http://purl.obolibrary.org/obo/NCIT_C12382>
PREFIX ProcedureHasTarget: <http://purl.obolibrary.org/obo/NCIT_R163>
SELECT DISTINCT ?procedure ?procedure_label
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?disease ProcedureHasTarget: colon: .
?disease rdfs:label ?procedure_label .
}

What are procedures target the lung?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX lung: <http://purl.obolibrary.org/obo/NCIT_C12468>
PREFIX ProcedureHasTarget: <http://purl.obolibrary.org/obo/NCIT_R163>
SELECT DISTINCT ?procedure ?procedure_label
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?disease ProcedureHasTarget: lung: .
?disease rdfs:label ?procedure_label .
}

Find regimens containing specific components

What regimens include Declopramide?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX Declopramide: <http://purl.obolibrary.org/obo/NCIT_C1772>
PREFIX ChemotherapyRegimenHasComponent: <http://purl.obolibrary.org/obo/NCIT_R123>
SELECT DISTINCT ?regimen ?regimen_label
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?regimen ChemotherapyRegimenHasComponent: Declopramide: .
?regimen rdfs:label ?regimen_label .
}

What regimens include cisplatin?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX Cisplatin: <http://purl.obolibrary.org/obo/NCIT_C376>
PREFIX ChemotherapyRegimenHasComponent: <http://purl.obolibrary.org/obo/NCIT_R123>
SELECT DISTINCT ?regimen ?regimen_label
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?regimen ChemotherapyRegimenHasComponent: Cisplatin: .
?regimen rdfs:label ?regimen_label .
}

What regimens include Doxorubicin?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX Doxorubicin: <http://purl.obolibrary.org/obo/NCIT_C456>
PREFIX ChemotherapyRegimenHasComponent: <http://purl.obolibrary.org/obo/NCIT_R123>
SELECT DISTINCT ?regimen ?regimen_label
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?regimen ChemotherapyRegimenHasComponent: Doxorubicin: .
?regimen rdfs:label ?regimen_label .
}

What regimens include Leucovorin Calcium?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX LeucovorinCalcium: <http://purl.obolibrary.org/obo/NCIT_C607>
PREFIX ChemotherapyRegimenHasComponent: <http://purl.obolibrary.org/obo/NCIT_R123>
SELECT DISTINCT ?regimen ?regimen_label
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?regimen ChemotherapyRegimenHasComponent: LeucovorinCalcium: .
?regimen rdfs:label ?regimen_label .
}

What regimens include Dexamethasone?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX Dexamethasone: <http://purl.obolibrary.org/obo/NCIT_C422>
PREFIX ChemotherapyRegimenHasComponent: <http://purl.obolibrary.org/obo/NCIT_R123>
SELECT DISTINCT ?regimen ?regimen_label
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?regimen ChemotherapyRegimenHasComponent: Dexamethasone: .
?regimen rdfs:label ?regimen_label .
}

Find regimens specific to a particular disease

What regimens are accepted for use with Breast Carcinoma?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX BreastCancer: <http://purl.obolibrary.org/obo/NCIT_C4872>
PREFIX RegimenHasAcceptedUseForDisease: <http://purl.obolibrary.org/obo/NCIT_R172>
SELECT DISTINCT ?regimen ?regimen_label
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?regimen RegimenHasAcceptedUseForDisease: BreastCancer: .
?regimen rdfs:label ?regimen_label .
}

Find a regimen specific to a disease, and that has a particular component

What regimens are accepted for use with Breast Carcinoma and contain doxorubicin?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX Disease_Has_Associated_Anatomic_Site: <http://purl.obolibrary.org/obo/NCIT_R100>
PREFIX BreastCarcinoma: <http://purl.obolibrary.org/obo/NCIT_C4872>
PREFIX Doxorubicin: <http://purl.obolibrary.org/obo/NCIT_C456>
PREFIX RegimenHasAcceptedUseForDisease: <http://purl.obolibrary.org/obo/NCIT_R172>
PREFIX ChemotherapyRegimenHasComponent: <http://purl.obolibrary.org/obo/NCIT_R123>
SELECT DISTINCT ?regimen ?label 
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE { 
  ?regimen RegimenHasAcceptedUseForDisease: BreastCarcinoma: .
  ?regimen ChemotherapyRegimenHasComponent: Doxorubicin: .
  ?regimen rdfs:label ?label .
}

Genetic-based queries

What are the oncogenes?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX oncogene: <http://purl.obolibrary.org/obo/NCIT_C19540>
SELECT DISTINCT ?oncogene ?oncogene_label
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?oncogene rdfs:subClassOf* oncogene: .
?oncogene rdfs:label ?oncogene_label .
}

What are the gene fusions?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX FusionGene: <http://purl.obolibrary.org/obo/NCIT_C28510>
SELECT DISTINCT ?fusion ?fusion_label
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?fusion rdfs:subClassOf* FusionGene: .
?fusion rdfs:label ?fusion_label .
}

What are the genetic abnormalities in ETV6?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ETV6: <http://purl.obolibrary.org/obo/NCIT_C18312>
PREFIX MolecularAbnormalityInvolvesGene: <http://purl.obolibrary.org/obo/NCIT_R177>
SELECT DISTINCT ?abnormality ?abnormality_label
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?abnormality MolecularAbnormalityInvolvesGene: ETV6: .
?abnormality rdfs:label ?abnormality_label .
}

What genes are involved in non-small cell lung cancer pathways?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX NSCLCPathway: <http://purl.obolibrary.org/obo/NCIT_C91445>
PREFIX GeneIsElementInPathway: <http://purl.obolibrary.org/obo/NCIT_R130>
SELECT DISTINCT ?gene ?gene_label
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?gene GeneIsElementInPathway: NSCLCPathway: .
?gene rdfs:label ?gene_label .
}

What diseases map to the HBB gene?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX HBBGene: <http://purl.obolibrary.org/obo/NCIT_C84951>
PREFIX DiseaseMappedToGene: <http://purl.obolibrary.org/obo/NCIT_R176>
SELECT DISTINCT ?disease ?disease_label
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph-redundant.ttl>
WHERE {
?disease DiseaseMappedToGene: HBBGene: .
?disease rdfs:label ?disease_label .
}

What are the disease/biomarker mappings?

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX Gene_Product_Is_Biomarker_Of:  <http://purl.obolibrary.org/obo/NCIT_R47>
PREFIX Gene_Is_Biomarker_Of:  <http://purl.obolibrary.org/obo/NCIT_R39>

SELECT DISTINCT ?diseaseLabel ?pLabel ?geneOrProductLabel
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph.ttl>
WHERE {
VALUES ?property {
   Gene_Product_Is_Biomarker_Of:
   Gene_Is_Biomarker_Of:
  }
?geneOrProduct ?property ?disease .
?disease rdfs:label ?diseaseLabel .
?property rdfs:label ?pLabel .
?geneOrProduct rdfs:label ?geneOrProductLabel .
}
ORDERBY ?diseaseLabel

What are the mappings between disease and chemo regimen drug targets (genes)?

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>
PREFIX ChemotherapyRegimenHasComponent: <http://purl.obolibrary.org/obo/NCIT_R123>
SELECT DISTINCT ?disease_label ?gene_label 
FROM <http://purl.obolibrary.org/obo/ncit.owl>
FROM <http://purl.obolibrary.org/obo/ncit/ncit-property-graph.ttl>
WHERE { 
  ?disease rdfs:subClassOf* DiseaseClass: .
  ?disease rdfs:label ?disease_label .
  ?therapy RegimenHasAcceptedUseForDisease: ?disease .
  ?therapy ChemotherapyRegimenHasComponent: ?chemical .
  ?chemical ChemicalOrDrugIsMetabolizedByEnzyme: ?protein .
  ?protein GeneProductIsEncodedByGene: ?gene .
  ?gene rdfs:label ?gene_label . 
}
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