wikipathways · elenadelpup · Dec 3, 2025 · Dec 3, 2025 · Dec 5, 2025 · Dec 5, 2025
diff --git a/1.TestQueries/GraphIsLoaded.rq b/1.TestQueries/GraphIsLoaded.rq
@@ -0,0 +1,4 @@
+# Count all triples in the PlantMetWiki named graph
+SELECT (COUNT(*) AS ?nTriples)
+FROM <http://plantmetwiki.bioinformatics.nl/>
+WHERE { ?s ?p ?o . }
diff --git a/1.TestQueries/ListEntities.rq b/1.TestQueries/ListEntities.rq
@@ -0,0 +1,6 @@
+PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
+# Quick peek at some entity types
+SELECT DISTINCT ?type
+FROM <http://plantmetwiki.bioinformatics.nl/>
+WHERE { ?s a ?type . }
+LIMIT 50
diff --git a/2.PMNQueries/MetabolitesInSpeciesPotato.rq b/2.PMNQueries/MetabolitesInSpeciesPotato.rq
@@ -0,0 +1,14 @@
+PREFIX gpml:    <http://vocabularies.wikipathways.org/gpml#>
+PREFIX dcterms: <http://purl.org/dc/terms/>
+PREFIX dc:      <http://purl.org/dc/elements/1.1/>
+PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
+prefix wp:      <http://vocabularies.wikipathways.org/wp#>
+
+select distinct ?metabolite (str(?titleLit) as ?title)
+FROM <http://plantmetwiki.bioinformatics.nl/>
+where {
+  ?metabolite a wp:Metabolite ;
+    dcterms:isPartOf ?pw .
+  ?pw dc:title ?titleLit ;
+    wp:organismName "Solanum tuberosum" .
+}
diff --git a/2.PMNQueries/ProteinsforTaxonomyIDs.rq b/2.PMNQueries/ProteinsforTaxonomyIDs.rq
@@ -0,0 +1,15 @@
+PREFIX gpml:    <http://vocabularies.wikipathways.org/gpml#>
+PREFIX dcterms: <http://purl.org/dc/terms/>
+PREFIX dc:      <http://purl.org/dc/elements/1.1/>
+PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
+prefix wp:      <http://vocabularies.wikipathways.org/wp#>
+prefix ncbi:    <http://purl.obolibrary.org/obo/NCBITaxon_>
+
+select distinct ?protein (str(?titleLit) as ?title)
+FROM <http://plantmetwiki.bioinformatics.nl/>
+where {
+  ?protein a wp:Protein ;
+    dcterms:isPartOf ?pw .
+  ?pw dc:title ?titleLit ;
+    wp:organism ncbi:4113 .
+  }
diff --git a/3.BGCCrosslinksQueries/AllBGCLinks.rq b/3.BGCCrosslinksQueries/AllBGCLinks.rq
@@ -0,0 +1,9 @@
+PREFIX ro: <http://purl.obolibrary.org/obo/RO_>
+
+SELECT ?bgc ?gene
+FROM <http://plantmetwiki.bioinformatics.nl/>
+WHERE {
+  ?bgc ro:0000051 ?gene .
+}
+ORDER BY ?bgc ?gene
+LIMIT 200
diff --git a/3.BGCCrosslinksQueries/LinksfromMetadata.rq b/3.BGCCrosslinksQueries/LinksfromMetadata.rq
@@ -0,0 +1,12 @@
+PREFIX ro: <http://purl.obolibrary.org/obo/RO_>
+PREFIX dcterms: <http://purl.org/dc/terms/>
+
+# dcterms:source "MIBIG" / "plantiSMASH" on the cluster nodes
+SELECT ?bgc ?gene
+FROM <http://plantmetwiki.bioinformatics.nl/>
+WHERE {
+  ?bgc ro:0000051 ?gene ;
+       dcterms:source "plantiSMASH" . # can change to MIBIG
+}
+ORDER BY ?bgc ?gene
+LIMIT 200
diff --git a/3.BGCCrosslinksQueries/MIBiGLinks.rq b/3.BGCCrosslinksQueries/MIBiGLinks.rq
@@ -0,0 +1,10 @@
+PREFIX ro: <http://purl.obolibrary.org/obo/RO_>
+
+SELECT ?bgc ?gene
+FROM <http://plantmetwiki.bioinformatics.nl/>
+WHERE {
+  ?bgc ro:0000051 ?gene .
+  FILTER(STRSTARTS(STR(?bgc), "https://bioregistry.io/mibig:"))
+}
+ORDER BY ?bgc ?gene
+LIMIT 200
diff --git a/3.BGCCrosslinksQueries/PathwayExample.rq b/3.BGCCrosslinksQueries/PathwayExample.rq
@@ -0,0 +1,17 @@
+PREFIX ro: <http://purl.obolibrary.org/obo/RO_>
+PREFIX wp:  <http://vocabularies.wikipathways.org/wp#>
+PREFIX dc:  <http://purl.org/dc/elements/1.1/>
+PREFIX dcterms: <http://purl.org/dc/terms/>
+
+# Retrieve thalianol pathway 
+SELECT DISTINCT ?pw (STR(?titleLit) AS ?title)
+FROM <http://plantmetwiki.bioinformatics.nl/>
+WHERE {
+  <https://bioregistry.io/mibig:BGC0000670> ro:0000051 ?gene .
+
+  ?interaction wp:participants ?gene ;
+              dcterms:isPartOf ?pw .
+
+  ?pw dc:title ?titleLit .
+}
+ORDER BY ?title
diff --git a/3.BGCCrosslinksQueries/plantiSMASHLinks.rq b/3.BGCCrosslinksQueries/plantiSMASHLinks.rq
@@ -0,0 +1,10 @@
+PREFIX ro: <http://purl.obolibrary.org/obo/RO_>
+
+SELECT ?bgc ?gene
+FROM <http://plantmetwiki.bioinformatics.nl/>
+WHERE {
+  ?bgc ro:0000051 ?gene .
+  FILTER(STRSTARTS(STR(?bgc), "https://plantismash.bioinformatics.nl/precalc/v2/"))
+}
+ORDER BY ?bgc ?gene
+LIMIT 200
diff --git a/4.FederatedQueries/WikidataInChiKeys.rq b/4.FederatedQueries/WikidataInChiKeys.rq
@@ -0,0 +1,8 @@
+SELECT DISTINCT ?metabolite ?inchikey
+FROM <http://plantmetwiki.bioinformatics.nl/>
+WHERE {
+  ?metabolite ?p ?o .
+  FILTER(STRSTARTS(STR(?metabolite), "https://identifiers.org/inchikey/"))
+  BIND(STRAFTER(STR(?metabolite), "https://identifiers.org/inchikey/") AS ?inchikey)
+}
+LIMIT 50
diff --git a/4.FederatedQueries/WikidataLookupByInChIKeys.rq b/4.FederatedQueries/WikidataLookupByInChIKeys.rq
@@ -0,0 +1,14 @@
+PREFIX wdt:  <http://www.wikidata.org/prop/direct/>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+# Given the size of Wikidata, this query takes long to execute (~1 min)
+SELECT ?wd ?label
+FROM <http://plantmetwiki.bioinformatics.nl/>
+WHERE {
+  SERVICE <https://query.wikidata.org/sparql> {
+    VALUES ?inchikey { "RYYVLZVUVIJVGH-UHFFFAOYSA-N" }  # caffeine
+    ?wd wdt:P235 ?inchikey .
+    OPTIONAL { ?wd rdfs:label ?label . FILTER(LANG(?label)="en") }
+  }
+}
+LIMIT 10
diff --git a/4.FederatedQueries/WikidataTest.rq b/4.FederatedQueries/WikidataTest.rq
@@ -0,0 +1,9 @@
+PREFIX wdt: <http://www.wikidata.org/prop/direct/>
+SELECT ?wd
+FROM <http://plantmetwiki.bioinformatics.nl/>
+WHERE {
+  SERVICE <https://query.wikidata.org/sparql> {
+    ?wd wdt:P31 <http://www.wikidata.org/entity/Q11173> .
+  }
+}
+LIMIT 5
diff --git a/A. Metadata/datacounts/averageDatanodes.rq b/A. Metadata/datacounts/averageDatanodes.rq
diff --git a/A. Metadata/datacounts/averageGeneProducts.rq b/A. Metadata/datacounts/averageGeneProducts.rq
diff --git a/A. Metadata/datacounts/averageInteractions.rq b/A. Metadata/datacounts/averageInteractions.rq
diff --git a/A. Metadata/datacounts/averageMetabolites.rq b/A. Metadata/datacounts/averageMetabolites.rq
diff --git a/A. Metadata/datacounts/averageProteins.rq b/A. Metadata/datacounts/averageProteins.rq
diff --git a/A. Metadata/datacounts/countDataNodes.rq b/A. Metadata/datacounts/countDataNodes.rq
diff --git a/A. Metadata/datacounts/countGeneProducts.rq b/A. Metadata/datacounts/countGeneProducts.rq
diff --git a/A. Metadata/datacounts/countInteractions.rq b/A. Metadata/datacounts/countInteractions.rq
diff --git a/A. Metadata/datacounts/countMetabolites.rq b/A. Metadata/datacounts/countMetabolites.rq
diff --git a/A. Metadata/datacounts/countPathways.rq b/A. Metadata/datacounts/countPathways.rq
diff --git a/A. Metadata/datacounts/countProteins.rq b/A. Metadata/datacounts/countProteins.rq
diff --git a/A. Metadata/datacounts/countSignalingPathways.rq b/A. Metadata/datacounts/countSignalingPathways.rq
diff --git a/A. Metadata/datacounts/linkoutCounts.rq b/A. Metadata/datacounts/linkoutCounts.rq
diff --git a/A. Metadata/datasources/WPforChemSpider.rq b/A. Metadata/datasources/WPforChemSpider.rq
diff --git a/A. Metadata/datasources/WPforEnsembl.rq b/A. Metadata/datasources/WPforEnsembl.rq
diff --git a/A. Metadata/datasources/WPforHGNC.rq b/A. Metadata/datasources/WPforHGNC.rq
diff --git a/A. Metadata/datasources/WPforHMDB.rq b/A. Metadata/datasources/WPforHMDB.rq
diff --git a/A. Metadata/datasources/WPforNCBI.rq b/A. Metadata/datasources/WPforNCBI.rq
diff --git a/A. Metadata/datasources/WPforPubChemCID.rq b/A. Metadata/datasources/WPforPubChemCID.rq
diff --git a/A. Metadata/linksets.rq b/A. Metadata/linksets.rq
diff --git a/A. Metadata/linksets.ttl b/A. Metadata/linksets.ttl
diff --git a/A. Metadata/metadata.rq b/A. Metadata/metadata.rq
diff --git a/A. Metadata/metadata.ttl b/A. Metadata/metadata.ttl