1. Download Blazegraph here.
2. Download RDF data here ; file called wikipathways-2021xx10-rdf-wp.zip .
3. Start Blazgraph (make sure to remove old data, ending with .ttl and .jnl in folder where Blazegraph is downloaded):

Windows (through git bash, note that a adjusted properties file is needed to allow for large file formats.)

cd C:\Users\NAME_USER\FOLDER_WITH_BLAZEGRAPH\Blazegraph
java -jar blazegraph.jar propertyFile (RWStore.properties)

Linux (from the command line)

cd ~/FOLDER_WITH_BLAZEGRAPH/Blazegraph
java -jar blazegraph.jar

To write shorter SPARQL queries, prefixes can be used. In the WikiPathways SPARQL endpoint, several prefixes are loaded by default; in Blazegraph these need to be loaded before each query, and are listed here.

Queries:

1. Metabolic Conversions

   SELECT DISTINCT ?interaction ?sourceDb ?targetDb ?mimtype ?pathway (str(?titleLit) as ?title) ?sourceCHEBI ?targetDbCHEBI ?sourceHMDB ?targetDbHMDB ?InteractionID  WHERE {  
   ?pathway a wp:Pathway ;
                wp:organismName "Homo sapiens"^^xsd:string ; 
         dc:title ?titleLit . 	
   FILTER (EXISTS {?pathway wp:ontologyTag cur:AnalysisCollection}  .
   FILTER EXISTS {?pathway wp:ontologyTag cur:Reactome_Approved}) .    
   FILTER (EXISTS {?pathway wp:ontologyTag cur:LIPID_MAPS}) .
   ?interaction dcterms:isPartOf ?pathway ;			
            a wp:DirectedInteraction ;
    wp:source ?source ;
    wp:target ?target .  
   OPTIONAL{?interaction a ?mimtype}. 
   VALUES ?mimtype {wp:ComplexBinding wp:Conversion wp:Inhibition wp:Catalysis wp:Stimulation wp:TranscriptionTranslation wp:DirectedInteraction} .  
   ?source a wp:Metabolite . 
   ?source wp:bdbWikidata ?sourceDb . 
   OPTIONAL{?source wp:bdbChEBI ?sourceCHEBI}.
   OPTIONAL{?source wp:bdbHmdb ?sourceHMDB}.
   ?target a wp:Metabolite . 
   ?target wp:bdbWikidata ?targetDb . 
   OPTIONAL{?target wp:bdbChEBI ?targetDbCHEBI}. 
   OPTIONAL{?target wp:bdbHmdb ?targetDbHMDB}. 
   OPTIONAL{?interaction wp:bdbRhea ?InteractionID} .
   }
   ORDER BY DESC(?InteractionID)
   

2. Pathway Metadata

   SELECT DISTINCT ?interaction ?sourceDb ?targetDb ?PWOnt ?DiseaseOnt ?curationstatus ?InteractionRef ?PWref ?sourceLit ?targetLit WHERE {
   ?pathway a wp:Pathway ; 
                 wp:organismName "Homo sapiens"^^xsd:string ; 
                 dc:title ?titleLit . 
   ?interaction dcterms:isPartOf ?pathway ; 
        a wp:DirectedInteraction ; 
        wp:source ?source ;
        wp:target ?target . 
   ?source a wp:Metabolite . 
   ?source wp:bdbWikidata ?sourceDb . 
   ?target a wp:Metabolite . 
   ?target wp:bdbWikidata ?targetDb . 
   OPTIONAL{?pathway wp:pathwayOntologyTag ?PWOnt} . 
   OPTIONAL{?pathway wp:diseaseOntologyTag ?DiseaseOnt} . 
   OPTIONAL{?pathway wp:ontologyTag ?curationstatus} . 
   OPTIONAL{?interaction dcterms:bibliographicCitation ?InteractionRef} . 
   OPTIONAL{?pathway dcterms:references ?PWref} . 
   OPTIONAL{?source dcterms:bibliographicCitation ?sourceLit} . 
   OPTIONAL{?target dcterms:bibliographicCitation ?targetLit} . 
   }
   

3. SELECT DISTINCT ?interaction ?sourceDb ?targetDb ?proteinDBWPs ?proteinName WHERE {  
   ?pathway a wp:Pathway ; 
           wp:ontologyTag cur:AnalysisCollection ;
           wp:organismName "Homo sapiens"^^xsd:string ; 
           dc:title ?titleLit . 
   ?interaction dcterms:isPartOf ?pathway ;				
           a wp:DirectedInteraction .  
   wp:source ?source . 
   wp:target ?target .   
   ?source a wp:Metabolite . 
   ?source wp:bdbWikidata ?sourceDb . 
   ?target a wp:Metabolite . 
   ?target wp:bdbWikidata ?targetDb . 
   ?interactions2 dcterms:isPartOf ?pathway;
                      a wp:Catalysis; 
                     wp:source ?sources2;
                    wp:target ?interaction . 
   OPTIONAL{?sources2 wp:bdbEnsembl ?proteinDBWPs}.
   OPTIONAL{?sources2 rdfs:label ?proteinName} .