sparql_queries_NTDs_RDF_examples.txt

# What genes are associated to Leishmaniasis and Chagas Disease (include external identifiers for Ensembl)?
PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX mesh: <https://bioregistry.io/mesh:>

SELECT DISTINCT ?gene ?genename ?ensemblid
WHERE {
  ?gene a biolink:Gene;
  		  biolink:gene_associated_with_condition mesh:D007896,
                                               mesh:D014355;
   
  rdfs:label ?genename;
  biolink:xref ?ensemblid;
  FILTER(regex(STR(?ensemblid), "ensembl", "i")).
}

# List 20 SNVs of genes associated to African Trypanosomiasis, including their phenotypes and chromosome locations
PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX mesh: <https://bioregistry.io/mesh:>

SELECT DISTINCT ?gene ?genename ?SNV ?SNVpehnotype ?SNVallele ?chr
WHERE {
  ?gene a biolink:Gene;
  		  biolink:gene_associated_with_condition mesh:D014355;
  rdfs:label ?genename.
  
  ?SNV a biolink:Snv;
  	     biolink:is_sequence_variant_of ?gene;
  biolink:has_phenotype ?SNVpehnotype;
  biolink:has_attribute ?SNVallele;
  biolink:has_sequence_location ?chr.
}
LIMIT 20

# List 10 drug-SNVs associations, including their alleles and phenotypes
PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX mesh: <https://bioregistry.io/mesh:>

SELECT DISTINCT ?drug ?drugname ?SNV ?SNVallele ?SNVpehnotype
WHERE {
  ?drug a biolink:Drug;
  rdfs:label ?drugname.
  
  ?SNV a biolink:Snv;
  	     biolink:associated_with ?drug;
  biolink:has_attribute ?SNVallele;
  biolink:has_phenotype ?SNVpehnotype.
}
LIMIT 10

# What drugs are used to treat Chagas disease and African Trypanosomiasis (include external identifiers for PubChem)?
PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX mesh: <https://bioregistry.io/mesh:>

SELECT DISTINCT ?drug ?drugname ?pubchem_id
WHERE {
    ?drug a biolink:Drug;
  		  biolink:treats mesh:D014353,
                       mesh:D014355;
  rdfs:label ?drugname;
  biolink:xref ?pubchem_id;
  FILTER(regex(STR(?pubchem_id), "pubchem", "i")).
}

# What drugs are used to treat at least two out of the three NTDs (include external identifiers for CHEMBL)?
PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX mesh: <https://bioregistry.io/mesh:>

SELECT DISTINCT ?drug ?drugname ?chembl_id
WHERE {
  {
    ?drug a biolink:Drug;
  		  biolink:treats mesh:D014355,
  					           mesh:D014353;
  rdfs:label ?drugname;
  biolink:xref ?chembl_id;
  FILTER(regex(STR(?chembl_id), "chembl", "i")).
  }UNION{
  	?drug a biolink:Drug;
  		  biolink:treats mesh:D014353,
  					           mesh:D007896;
  rdfs:label ?drugname;
  biolink:xref ?chembl_id;
  FILTER(regex(STR(?chembl_id), "chembl", "i")).
  }UNION{
  	?drug a biolink:Drug;
  		  biolink:treats mesh:D014355,
  					           mesh:D007896;
  rdfs:label ?drugname;
  biolink:xref ?chembl_id;
  FILTER(regex(STR(?chembl_id), "chembl", "i")).
  }
}

# What drug against Chagas disease has the highest number of protein targets?
PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX mesh: <https://bioregistry.io/mesh:>

SELECT ?drug ?drugname (COUNT(DISTINCT ?protein) AS ?n_proteintargets)
WHERE {
  ?drug a biolink:Drug;
  		  biolink:treats mesh:D014355;
  		  biolink:physically_interacts_with ?protein;
   
  rdfs:label ?drugname .
}
GROUP BY ?drug
ORDER BY DESC(?n_proteintargets)
LIMIT 1

# What are the top 20 biological processes with the highest number of genes associated to Leishmaniasis?
PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX mesh: <https://bioregistry.io/mesh:>

SELECT ?bio_process ?bio_processname (COUNT(DISTINCT ?gene) AS ?count)
WHERE {    
  ?gene a biolink:Gene;
  		  biolink:gene_associated_with_condition mesh:D007896;
      	biolink:acts_upstream_of ?bio_process.
  
  ?bio_process a biolink:BiologicalProcess;
   
  rdfs:label ?bio_processname .
}
GROUP BY ?bio_process
ORDER BY DESC(?count)
LIMIT 20

# What are the top 20 molecular functions  with the highest number of genes associated to Chagas Disease?
PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX mesh: <https://bioregistry.io/mesh:>

SELECT ?mol_funct ?mol_functname (COUNT(DISTINCT ?gene) AS ?count)
WHERE {    
  ?gene a biolink:Gene;
  		  biolink:gene_associated_with_condition mesh:D014355;
      	biolink:participates_in ?mol_funct.
  
  ?mol_funct a biolink:MolecularActivity;
   
  rdfs:label ?mol_functname .
}
GROUP BY ?mol_funct
ORDER BY DESC(?count)
LIMIT 20

# What are the top 10 cellular components with the highest number of genes associated to African Trypanosomiasis?
PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX mesh: <https://bioregistry.io/mesh:>

SELECT ?cell_comp ?cell_compname (COUNT(DISTINCT ?gene) AS ?count)
WHERE {    
  ?gene a biolink:Gene;
  		  biolink:gene_associated_with_condition mesh:D014353;
      	biolink:active_in ?cell_comp.
  
  ?cell_comp a biolink:CellularComponent;
   
  rdfs:label ?cell_compname .
}
GROUP BY ?cell_comp
ORDER BY DESC(?count)
LIMIT 10

# What are the top 30 pathways associated to the highest number of genes involved in Leishmaniasis (include the data source of the pathways)?
PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX mesh: <https://bioregistry.io/mesh:>

SELECT ?path ?path_name ?datasource (COUNT(DISTINCT ?gene) AS ?count)
WHERE {    
  ?gene a biolink:Gene;
  		  biolink:gene_associated_with_condition mesh:D007896;
      	biolink:participates_in ?path.
  
  ?path a biolink:Pathway;
   
  rdfs:label ?path_name;
  biolink:provided_by ?datasource.
}
GROUP BY ?path
ORDER BY DESC(?count)
LIMIT 30

# What are the top 20 pathways associated to the highest number of genes involved in the three NTDs (include the data source of the pathways)?
PREFIX biolink: <https://w3id.org/biolink/vocab/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX mesh: <https://bioregistry.io/mesh:>

SELECT ?path ?path_name ?datasource (COUNT(DISTINCT ?gene) AS ?count)
WHERE {    
  ?gene a biolink:Gene;
  		  biolink:gene_associated_with_condition mesh:D014353,
                                               mesh:D014355,
                                               mesh:D007896;
      	biolink:participates_in ?path.
  
  ?path a biolink:Pathway;
  rdfs:label ?path_name ;
  biolink:provided_by ?datasource.
}
GROUP BY ?path
ORDER BY DESC(?count)
LIMIT 20