diff --git a/1.TestQueries/GraphIsLoaded.rq b/1.TestQueries/GraphIsLoaded.rq new file mode 100644 index 0000000..1894fe3 --- /dev/null +++ b/1.TestQueries/GraphIsLoaded.rq @@ -0,0 +1,4 @@ +# Count all triples in the PlantMetWiki named graph +SELECT (COUNT(*) AS ?nTriples) +FROM +WHERE { ?s ?p ?o . } \ No newline at end of file diff --git a/1.TestQueries/ListEntities.rq b/1.TestQueries/ListEntities.rq new file mode 100644 index 0000000..52a7924 --- /dev/null +++ b/1.TestQueries/ListEntities.rq @@ -0,0 +1,6 @@ +PREFIX wp: +# Quick peek at some entity types +SELECT DISTINCT ?type +FROM +WHERE { ?s a ?type . } +LIMIT 50 \ No newline at end of file diff --git a/2.PMNQueries/MetabolitesInSpeciesPotato.rq b/2.PMNQueries/MetabolitesInSpeciesPotato.rq new file mode 100644 index 0000000..85e80c8 --- /dev/null +++ b/2.PMNQueries/MetabolitesInSpeciesPotato.rq @@ -0,0 +1,14 @@ +PREFIX gpml: +PREFIX dcterms: +PREFIX dc: +PREFIX rdf: +prefix wp: + +select distinct ?metabolite (str(?titleLit) as ?title) +FROM +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 new file mode 100644 index 0000000..d2fbc26 --- /dev/null +++ b/2.PMNQueries/ProteinsforTaxonomyIDs.rq @@ -0,0 +1,15 @@ +PREFIX gpml: +PREFIX dcterms: +PREFIX dc: +PREFIX rdf: +prefix wp: +prefix ncbi: + +select distinct ?protein (str(?titleLit) as ?title) +FROM +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 new file mode 100644 index 0000000..0e7d970 --- /dev/null +++ b/3.BGCCrosslinksQueries/AllBGCLinks.rq @@ -0,0 +1,9 @@ +PREFIX ro: + +SELECT ?bgc ?gene +FROM +WHERE { + ?bgc ro:0000051 ?gene . +} +ORDER BY ?bgc ?gene +LIMIT 200 \ No newline at end of file diff --git a/3.BGCCrosslinksQueries/LinksfromMetadata.rq b/3.BGCCrosslinksQueries/LinksfromMetadata.rq new file mode 100644 index 0000000..fa6351c --- /dev/null +++ b/3.BGCCrosslinksQueries/LinksfromMetadata.rq @@ -0,0 +1,12 @@ +PREFIX ro: +PREFIX dcterms: + +# dcterms:source "MIBIG" / "plantiSMASH" on the cluster nodes +SELECT ?bgc ?gene +FROM +WHERE { + ?bgc ro:0000051 ?gene ; + dcterms:source "plantiSMASH" . # can change to MIBIG +} +ORDER BY ?bgc ?gene +LIMIT 200 \ No newline at end of file diff --git a/3.BGCCrosslinksQueries/MIBiGLinks.rq b/3.BGCCrosslinksQueries/MIBiGLinks.rq new file mode 100644 index 0000000..6eaa47c --- /dev/null +++ b/3.BGCCrosslinksQueries/MIBiGLinks.rq @@ -0,0 +1,10 @@ +PREFIX ro: + +SELECT ?bgc ?gene +FROM +WHERE { + ?bgc ro:0000051 ?gene . + FILTER(STRSTARTS(STR(?bgc), "https://bioregistry.io/mibig:")) +} +ORDER BY ?bgc ?gene +LIMIT 200 \ No newline at end of file diff --git a/3.BGCCrosslinksQueries/PathwayExample.rq b/3.BGCCrosslinksQueries/PathwayExample.rq new file mode 100644 index 0000000..ece6c76 --- /dev/null +++ b/3.BGCCrosslinksQueries/PathwayExample.rq @@ -0,0 +1,17 @@ +PREFIX ro: +PREFIX wp: +PREFIX dc: +PREFIX dcterms: + +# Retrieve thalianol pathway +SELECT DISTINCT ?pw (STR(?titleLit) AS ?title) +FROM +WHERE { + ro:0000051 ?gene . + + ?interaction wp:participants ?gene ; + dcterms:isPartOf ?pw . + + ?pw dc:title ?titleLit . +} +ORDER BY ?title \ No newline at end of file diff --git a/3.BGCCrosslinksQueries/plantiSMASHLinks.rq b/3.BGCCrosslinksQueries/plantiSMASHLinks.rq new file mode 100644 index 0000000..1f2c35e --- /dev/null +++ b/3.BGCCrosslinksQueries/plantiSMASHLinks.rq @@ -0,0 +1,10 @@ +PREFIX ro: + +SELECT ?bgc ?gene +FROM +WHERE { + ?bgc ro:0000051 ?gene . + FILTER(STRSTARTS(STR(?bgc), "https://plantismash.bioinformatics.nl/precalc/v2/")) +} +ORDER BY ?bgc ?gene +LIMIT 200 \ No newline at end of file diff --git a/4.FederatedQueries/WikidataInChiKeys.rq b/4.FederatedQueries/WikidataInChiKeys.rq new file mode 100644 index 0000000..2a639b4 --- /dev/null +++ b/4.FederatedQueries/WikidataInChiKeys.rq @@ -0,0 +1,8 @@ +SELECT DISTINCT ?metabolite ?inchikey +FROM +WHERE { + ?metabolite ?p ?o . + FILTER(STRSTARTS(STR(?metabolite), "https://identifiers.org/inchikey/")) + BIND(STRAFTER(STR(?metabolite), "https://identifiers.org/inchikey/") AS ?inchikey) +} +LIMIT 50 \ No newline at end of file diff --git a/4.FederatedQueries/WikidataLookupByInChIKeys.rq b/4.FederatedQueries/WikidataLookupByInChIKeys.rq new file mode 100644 index 0000000..8797598 --- /dev/null +++ b/4.FederatedQueries/WikidataLookupByInChIKeys.rq @@ -0,0 +1,14 @@ +PREFIX wdt: +PREFIX rdfs: + +# Given the size of Wikidata, this query takes long to execute (~1 min) +SELECT ?wd ?label +FROM +WHERE { + SERVICE { + VALUES ?inchikey { "RYYVLZVUVIJVGH-UHFFFAOYSA-N" } # caffeine + ?wd wdt:P235 ?inchikey . + OPTIONAL { ?wd rdfs:label ?label . FILTER(LANG(?label)="en") } + } +} +LIMIT 10 \ No newline at end of file diff --git a/4.FederatedQueries/WikidataTest.rq b/4.FederatedQueries/WikidataTest.rq new file mode 100644 index 0000000..d7c9663 --- /dev/null +++ b/4.FederatedQueries/WikidataTest.rq @@ -0,0 +1,9 @@ +PREFIX wdt: +SELECT ?wd +FROM +WHERE { + SERVICE { + ?wd wdt:P31 . + } +} +LIMIT 5 \ No newline at end of file diff --git a/A. Metadata/datacounts/averageDatanodes.rq b/A. Metadata/datacounts/averageDatanodes.rq deleted file mode 100644 index 88f62b2..0000000 --- a/A. Metadata/datacounts/averageDatanodes.rq +++ /dev/null @@ -1,10 +0,0 @@ -SELECT (AVG(?no) AS ?avg) - (MIN(?no) AS ?min) - (MAX(?no) AS ?max) -WHERE { - SELECT ?Pathway (COUNT(?DataNodes) AS ?no) - WHERE { - ?DataNodes a wp:DataNode ; - dcterms:isPartOf ?Pathway. - ?Pathway a wp:Pathway.} -} diff --git a/A. Metadata/datacounts/averageGeneProducts.rq b/A. Metadata/datacounts/averageGeneProducts.rq deleted file mode 100644 index 4b04573..0000000 --- a/A. Metadata/datacounts/averageGeneProducts.rq +++ /dev/null @@ -1,10 +0,0 @@ -SELECT (AVG(?no) AS ?avg) - (MIN(?no) AS ?min) - (MAX(?no) AS ?max) -WHERE { - SELECT ?Pathway (COUNT(?DataNodes) AS ?no) - WHERE { - ?DataNodes a wp:GeneProduct ; - dcterms:isPartOf ?Pathway. - ?Pathway a wp:Pathway.} -} diff --git a/A. Metadata/datacounts/averageInteractions.rq b/A. Metadata/datacounts/averageInteractions.rq deleted file mode 100644 index 11e4d75..0000000 --- a/A. Metadata/datacounts/averageInteractions.rq +++ /dev/null @@ -1,10 +0,0 @@ -SELECT (AVG(?no) AS ?avg) - (MIN(?no) AS ?min) - (MAX(?no) AS ?max) -WHERE { - SELECT ?Pathway (COUNT(?DataNodes) AS ?no) - WHERE { - ?DataNodes a wp:Interaction ; - dcterms:isPartOf ?Pathway. - ?Pathway a wp:Pathway.} -} diff --git a/A. Metadata/datacounts/averageMetabolites.rq b/A. Metadata/datacounts/averageMetabolites.rq deleted file mode 100644 index 5936678..0000000 --- a/A. Metadata/datacounts/averageMetabolites.rq +++ /dev/null @@ -1,10 +0,0 @@ -SELECT (AVG(?no) AS ?avg) - (MIN(?no) AS ?min) - (MAX(?no) AS ?max) -WHERE { - SELECT ?Pathway (COUNT(?DataNodes) AS ?no) - WHERE { - ?DataNodes a wp:Metabolite ; - dcterms:isPartOf ?Pathway. - ?Pathway a wp:Pathway.} -} diff --git a/A. Metadata/datacounts/averageProteins.rq b/A. Metadata/datacounts/averageProteins.rq deleted file mode 100644 index 7dd1832..0000000 --- a/A. Metadata/datacounts/averageProteins.rq +++ /dev/null @@ -1,10 +0,0 @@ -SELECT (AVG(?no) AS ?avg) - (MIN(?no) AS ?min) - (MAX(?no) AS ?max) -WHERE { - SELECT ?Pathway (COUNT(?DataNodes) AS ?no) - WHERE { - ?DataNodes a wp:Protein ; - dcterms:isPartOf ?Pathway. - ?Pathway a wp:Pathway.} -} diff --git a/A. Metadata/datacounts/countDataNodes.rq b/A. Metadata/datacounts/countDataNodes.rq deleted file mode 100644 index 39776f5..0000000 --- a/A. Metadata/datacounts/countDataNodes.rq +++ /dev/null @@ -1,4 +0,0 @@ -SELECT DISTINCT count(?DataNodes) as ?DataNodeCount -WHERE { - ?DataNodes a wp:DataNode . -} diff --git a/A. Metadata/datacounts/countGeneProducts.rq b/A. Metadata/datacounts/countGeneProducts.rq deleted file mode 100644 index d801061..0000000 --- a/A. Metadata/datacounts/countGeneProducts.rq +++ /dev/null @@ -1,4 +0,0 @@ -SELECT DISTINCT count(?geneProduct) as ?GeneProductCount -WHERE { - ?geneProduct a wp:GeneProduct . -} diff --git a/A. Metadata/datacounts/countInteractions.rq b/A. Metadata/datacounts/countInteractions.rq deleted file mode 100644 index 6986d60..0000000 --- a/A. Metadata/datacounts/countInteractions.rq +++ /dev/null @@ -1,4 +0,0 @@ -SELECT DISTINCT count(?Interaction) as ?InteractionCount -WHERE { - ?Interaction a wp:Interaction . -} diff --git a/A. Metadata/datacounts/countMetabolites.rq b/A. Metadata/datacounts/countMetabolites.rq deleted file mode 100644 index fe74f13..0000000 --- a/A. Metadata/datacounts/countMetabolites.rq +++ /dev/null @@ -1,4 +0,0 @@ -SELECT DISTINCT count(?Metabolite) as ?MetaboliteCount -WHERE { - ?Metabolite a wp:Metabolite . -} diff --git a/A. Metadata/datacounts/countPathways.rq b/A. Metadata/datacounts/countPathways.rq deleted file mode 100644 index 28d1bf3..0000000 --- a/A. Metadata/datacounts/countPathways.rq +++ /dev/null @@ -1,4 +0,0 @@ -SELECT DISTINCT count(?Pathway) as ?PathwayCount -WHERE { - ?Pathway a wp:Pathway, skos:Collection . -} diff --git a/A. Metadata/datacounts/countProteins.rq b/A. Metadata/datacounts/countProteins.rq deleted file mode 100644 index 758277f..0000000 --- a/A. Metadata/datacounts/countProteins.rq +++ /dev/null @@ -1,4 +0,0 @@ -SELECT DISTINCT count(?protein) as ?ProteinCount -WHERE { - ?protein a wp:Protein . -} diff --git a/A. Metadata/datacounts/countSignalingPathways.rq b/A. Metadata/datacounts/countSignalingPathways.rq deleted file mode 100644 index b81151d..0000000 --- a/A. Metadata/datacounts/countSignalingPathways.rq +++ /dev/null @@ -1,8 +0,0 @@ -SELECT count(distinct ?pathway) as ?pathwaycount -WHERE { - ?tag1 a owl:Class ; - rdfs:label ?label . - ?tag rdfs:subClassOf* ?tag1. - ?pathway a wp:Pathway; wp:ontologyTag ?tag. -FILTER regex(str(?label), "signaling pathway") -} diff --git a/A. Metadata/datacounts/linkoutCounts.rq b/A. Metadata/datacounts/linkoutCounts.rq deleted file mode 100644 index dc0efcf..0000000 --- a/A. Metadata/datacounts/linkoutCounts.rq +++ /dev/null @@ -1,12 +0,0 @@ -SELECT ?pred (COUNT(DISTINCT ?entity) AS ?count) WHERE { - VALUES ?pred { - # metabolites - wp:bdbChEBI wp:bdbChemspider wp:bdbHmdb wp:bdbPubChem - # gene products - wp:bdbEnsembl wp:bdbEntrezGene wp:bdbHgncSymbol - # interactions - wp:bdbRhea wp:bdbUniprot - } - ?entity ?pred [] -} GROUP BY ?pred - ORDER BY DESC(?count) diff --git a/A. Metadata/datasources/WPforChemSpider.rq b/A. Metadata/datasources/WPforChemSpider.rq deleted file mode 100644 index c96ceac..0000000 --- a/A. Metadata/datasources/WPforChemSpider.rq +++ /dev/null @@ -1,11 +0,0 @@ -#List of WikiPathways for ChemSpider identifiers - -select distinct ?pathwayRes (str(?wpid) as ?pathway) (str(?title) as ?pathwayTitle) (fn:substring(?csId,36) as ?chemspider) where { - ?gene a wp:Metabolite ; - dcterms:identifier ?id ; - dcterms:isPartOf ?pathwayRes ; - wp:bdbChemspider ?csId . - ?pathwayRes a wp:Pathway ; - dcterms:identifier ?wpid ; - dc:title ?title . -} diff --git a/A. Metadata/datasources/WPforEnsembl.rq b/A. Metadata/datasources/WPforEnsembl.rq deleted file mode 100644 index 721f26d..0000000 --- a/A. Metadata/datasources/WPforEnsembl.rq +++ /dev/null @@ -1,11 +0,0 @@ -#List of WikiPathways for Ensembl identifiers - -select distinct ?pathwayRes (str(?wpid) as ?pathway) (str(?title) as ?pathwayTitle) (fn:substring(?ensId,32) as ?ensembl) where { - ?gene a wp:GeneProduct ; - dcterms:identifier ?id ; - dcterms:isPartOf ?pathwayRes ; - wp:bdbEnsembl ?ensId . - ?pathwayRes a wp:Pathway ; - dcterms:identifier ?wpid ; - dc:title ?title . -} diff --git a/A. Metadata/datasources/WPforHGNC.rq b/A. Metadata/datasources/WPforHGNC.rq deleted file mode 100644 index 6d2b66f..0000000 --- a/A. Metadata/datasources/WPforHGNC.rq +++ /dev/null @@ -1,11 +0,0 @@ -#List of WikiPathways for HGNC symbols - -select distinct ?pathwayRes (str(?wpid) as ?pathway) (str(?title) as ?pathwayTitle) (fn:substring(?hgncId,37) as ?HGNC) where { - ?gene a wp:GeneProduct ; - dcterms:identifier ?id ; - dcterms:isPartOf ?pathwayRes ; - wp:bdbHgncSymbol ?hgncId . - ?pathwayRes a wp:Pathway ; - dcterms:identifier ?wpid ; - dc:title ?title . -} diff --git a/A. Metadata/datasources/WPforHMDB.rq b/A. Metadata/datasources/WPforHMDB.rq deleted file mode 100644 index 800bf8f..0000000 --- a/A. Metadata/datasources/WPforHMDB.rq +++ /dev/null @@ -1,11 +0,0 @@ -#ist of WikiPathways for HMDB identifiers - -select distinct ?pathwayRes (str(?wpid) as ?pathway) (str(?title) as ?pathwayTitle) (fn:substring(?hmdbId,29) as ?hmdb) where { - ?gene a wp:Metabolite ; - dcterms:identifier ?id ; - dcterms:isPartOf ?pathwayRes ; - wp:bdbHmdb ?hmdbId . - ?pathwayRes a wp:Pathway ; - dcterms:identifier ?wpid ; - dc:title ?title . -} diff --git a/A. Metadata/datasources/WPforNCBI.rq b/A. Metadata/datasources/WPforNCBI.rq deleted file mode 100644 index 66a49f2..0000000 --- a/A. Metadata/datasources/WPforNCBI.rq +++ /dev/null @@ -1,11 +0,0 @@ -#List of WikiPathways for NCBI Gene identifiers - -select distinct ?pathwayRes (str(?wpid) as ?pathway) (str(?title) as ?pathwayTitle) (fn:substring(?ncbiGeneId,33) as ?NCBIGene) where { - ?gene a wp:GeneProduct ; - dcterms:identifier ?id ; - dcterms:isPartOf ?pathwayRes ; - wp:bdbEntrezGene ?ncbiGeneId . - ?pathwayRes a wp:Pathway ; - dcterms:identifier ?wpid ; - dc:title ?title . -} diff --git a/A. Metadata/datasources/WPforPubChemCID.rq b/A. Metadata/datasources/WPforPubChemCID.rq deleted file mode 100644 index f4055fc..0000000 --- a/A. Metadata/datasources/WPforPubChemCID.rq +++ /dev/null @@ -1,11 +0,0 @@ -#List of WikiPathways for PubChem CID identifiers - -select distinct ?pathwayRes (str(?wpid) as ?pathway) (str(?title) as ?pathwayTitle) (fn:substring(?cid,46) as ?PubChem) where { - ?gene a wp:Metabolite ; - dcterms:identifier ?id ; - dcterms:isPartOf ?pathwayRes ; - wp:bdbPubChem ?cid . - ?pathwayRes a wp:Pathway ; - dcterms:identifier ?wpid ; - dc:title ?title . -} \ No newline at end of file diff --git a/A. Metadata/linksets.rq b/A. Metadata/linksets.rq deleted file mode 100644 index 6d5d7a0..0000000 --- a/A. Metadata/linksets.rq +++ /dev/null @@ -1,9 +0,0 @@ -SELECT DISTINCT ?dataset (str(?titleLit) as ?title) ?date ?license -WHERE { - ?dataset a void:Linkset ; - dcterms:title ?titleLit . - OPTIONAL { - ?dataset dcterms:license ?license ; - pav:createdOn ?date . - } -} diff --git a/A. Metadata/linksets.ttl b/A. Metadata/linksets.ttl deleted file mode 100644 index 1a32f29..0000000 --- a/A. Metadata/linksets.ttl +++ /dev/null @@ -1,22 +0,0 @@ -@prefix ex: . -@prefix rdf: . -@prefix rdfs: . -@prefix schema: . -@prefix sh: . - -ex:metadata a sh:SPARQLExecutable, - sh:SPARQLSelectExecutable ; - rdfs:comment "Lists all linksets defined in this database with their titles, licenses, and creation dates."@en ; - sh:prefixes _:sparql_examples_prefixes ; - sh:select """SELECT DISTINCT ?dataset (str(?titleLit) as ?title) ?date ?license -WHERE { - ?dataset a void:Linkset ; - dcterms:title ?titleLit . - OPTIONAL { - ?dataset dcterms:license ?license ; - pav:createdOn ?date . - } -} -""" ; - schema:target ; - schema:keywords "linkset", "metadata" . diff --git a/A. Metadata/metadata.rq b/A. Metadata/metadata.rq deleted file mode 100644 index 9c55307..0000000 --- a/A. Metadata/metadata.rq +++ /dev/null @@ -1,7 +0,0 @@ -SELECT DISTINCT ?dataset (str(?titleLit) as ?title) ?date ?license -WHERE { - ?dataset a void:Dataset ; - dcterms:title ?titleLit ; - dcterms:license ?license ; - pav:createdOn ?date . -} \ No newline at end of file diff --git a/A. Metadata/metadata.ttl b/A. Metadata/metadata.ttl deleted file mode 100644 index 295ffec..0000000 --- a/A. Metadata/metadata.ttl +++ /dev/null @@ -1,19 +0,0 @@ -@prefix ex: . -@prefix rdf: . -@prefix rdfs: . -@prefix schema: . -@prefix sh: . - -ex:metadata a sh:SPARQLExecutable, - sh:SPARQLSelectExecutable ; - rdfs:comment "Returns the title of the dataset, creation date, and license."@en ; - sh:prefixes _:sparql_examples_prefixes ; - sh:select """SELECT DISTINCT ?dataset (str(?titleLit) as ?title) ?date ?license -WHERE { - ?dataset a void:Dataset ; - dcterms:title ?titleLit ; - dcterms:license ?license ; - pav:createdOn ?date . -}""" ; - schema:target ; - schema:keywords "license", "metadata" . diff --git a/A. Metadata/prefixes.rq b/A. Metadata/prefixes.rq deleted file mode 100644 index e652d55..0000000 --- a/A. Metadata/prefixes.rq +++ /dev/null @@ -1,9 +0,0 @@ -PREFIX sh: -PREFIX xsd: - -SELECT ?prefix ?namespace WHERE { - [] sh:declare [ - sh:prefix ?prefix ; - sh:namespace ?namespace - ] . -} \ No newline at end of file diff --git a/A. Metadata/prefixes.ttl b/A. Metadata/prefixes.ttl deleted file mode 100644 index 2770b13..0000000 --- a/A. Metadata/prefixes.ttl +++ /dev/null @@ -1,21 +0,0 @@ -@prefix ex: . -@prefix rdf: . -@prefix rdfs: . -@prefix schema: . -@prefix sh: . - -ex:metadata a sh:SPARQLExecutable, - sh:SPARQLSelectExecutable ; - rdfs:comment "Lists prefixes used in this database."@en ; - sh:prefixes _:sparql_examples_prefixes ; - sh:select """PREFIX sh: -PREFIX xsd: - -SELECT ?prefix ?namespace WHERE { - [] sh:declare [ - sh:prefix ?prefix ; - sh:namespace ?namespace - ] . -}""" ; - schema:target ; - schema:keywords "prefix", "namespace" . diff --git a/A. Metadata/species/PWsforSpecies.rq b/A. Metadata/species/PWsforSpecies.rq deleted file mode 100644 index 113ef8f..0000000 --- a/A. Metadata/species/PWsforSpecies.rq +++ /dev/null @@ -1,8 +0,0 @@ -SELECT DISTINCT ?wpIdentifier ?pathway ?page -WHERE { - ?pathway dc:title ?title . - ?pathway foaf:page ?page . - ?pathway dc:identifier ?wpIdentifier . - ?pathway wp:organismName "Mus musculus" . #Replace "Mus musculus" with other species: "Homo sapiens", "Rattus norvegicus", "Danio rerio" - } -ORDER BY ?wpIdentifier diff --git a/A. Metadata/species/countDataNodePerSpecies.rq b/A. Metadata/species/countDataNodePerSpecies.rq deleted file mode 100644 index 97aea3f..0000000 --- a/A. Metadata/species/countDataNodePerSpecies.rq +++ /dev/null @@ -1,7 +0,0 @@ -select (count(distinct ?datanode) as ?count) (str(?label) as ?species) where { - ?datanode a wp:DataNode ; - dcterms:isPartOf ?pw . - ?pw dc:title ?title ; - wp:organism ?organism ; - wp:organismName ?label . -} GROUP BY ?label ORDER BY DESC(?count) diff --git a/A. Metadata/species/countGeneProductsPerSpecies.rq b/A. Metadata/species/countGeneProductsPerSpecies.rq deleted file mode 100644 index 33fe557..0000000 --- a/A. Metadata/species/countGeneProductsPerSpecies.rq +++ /dev/null @@ -1,7 +0,0 @@ -select (count(distinct ?gene) as ?count) (str(?label) as ?species) where { - ?gene a wp:GeneProduct ; - dcterms:isPartOf ?pw . - ?pw dc:title ?title ; - wp:organism ?organism ; - wp:organismName ?label . -} GROUP BY ?label ORDER BY DESC(?count) diff --git a/A. Metadata/species/countMetabolitesPerSpecies.rq b/A. Metadata/species/countMetabolitesPerSpecies.rq deleted file mode 100644 index 3897da6..0000000 --- a/A. Metadata/species/countMetabolitesPerSpecies.rq +++ /dev/null @@ -1,7 +0,0 @@ -select (str(?label) as ?species) (count(distinct ?metabolite) as ?count) where { - ?metabolite a wp:Metabolite ; - dcterms:isPartOf ?pw . - ?pw dc:title ?title ; - wp:organism ?organism ; - wp:organismName ?label . -} GROUP BY ?label ORDER BY DESC(?count) diff --git a/A. Metadata/species/countPathwaysPerSpecies.rq b/A. Metadata/species/countPathwaysPerSpecies.rq deleted file mode 100644 index 7300184..0000000 --- a/A. Metadata/species/countPathwaysPerSpecies.rq +++ /dev/null @@ -1,7 +0,0 @@ -SELECT DISTINCT (str(?label) as ?name) ?organism (count(?pw) as ?pathwayCount) -WHERE { - ?pw dc:title ?title ; - wp:organism ?organism ; - wp:organismName ?label . -} -ORDER BY DESC(?pathwayCount) diff --git a/A. Metadata/species/countProteinsPerSpecies.rq b/A. Metadata/species/countProteinsPerSpecies.rq deleted file mode 100644 index 11b912a..0000000 --- a/A. Metadata/species/countProteinsPerSpecies.rq +++ /dev/null @@ -1,7 +0,0 @@ -select (count(distinct ?protein) as ?count) (str(?label) as ?species) where { - ?protein a wp:Protein ; - dcterms:isPartOf ?pw . - ?pw dc:title ?title ; - wp:organism ?organism ; - wp:organismName ?label . -} GROUP BY ?label ORDER BY DESC(?count) diff --git a/B. Communities/AOP/allPathways.rq b/B. Communities/AOP/allPathways.rq deleted file mode 100644 index e9d9a35..0000000 --- a/B. Communities/AOP/allPathways.rq +++ /dev/null @@ -1,10 +0,0 @@ -PREFIX wp: -PREFIX dc: -PREFIX cur: - -SELECT DISTINCT ?pathway (str(?title) as ?PathwayTitle) -WHERE { - ?pathway wp:ontologyTag cur:AOP ; - a wp:Pathway ; - dc:title ?title . -} \ No newline at end of file diff --git a/B. Communities/AOP/allPathways.ttl b/B. Communities/AOP/allPathways.ttl deleted file mode 100644 index 3f7ac59..0000000 --- a/B. Communities/AOP/allPathways.ttl +++ /dev/null @@ -1,22 +0,0 @@ -@prefix ex: . -@prefix rdf: . -@prefix rdfs: . -@prefix schema: . -@prefix sh: . - -ex:metadata a sh:SPARQLExecutable, - sh:SPARQLSelectExecutable ; - rdfs:comment "List all pathways in the AOP community portal and their title."@en ; - sh:prefixes _:sparql_examples_prefixes ; - sh:select """PREFIX wp: -PREFIX dc: -PREFIX cur: - -SELECT DISTINCT ?pathway (str(?title) as ?PathwayTitle) -WHERE { - ?pathway wp:ontologyTag cur:AOP ; - a wp:Pathway ; - dc:title ?title . -}""" ; - schema:target ; - schema:keywords "prefix", "namespace" . diff --git a/B. Communities/AOP/allProteins.rq b/B. Communities/AOP/allProteins.rq deleted file mode 100644 index 2cc9987..0000000 --- a/B. Communities/AOP/allProteins.rq +++ /dev/null @@ -1,8 +0,0 @@ -SELECT DISTINCT ?pathway (str(?label) as ?Protein) -WHERE { -?pathway wp:ontologyTag cur:AOP ; - a wp:Pathway . -?protein a wp:Protein ; - rdfs:label ?label ; - dcterms:isPartOf ?pathway . -} diff --git a/B. Communities/CIRM Stem Cell Pathways/allPathways.rq b/B. Communities/CIRM Stem Cell Pathways/allPathways.rq deleted file mode 100644 index 8f9752c..0000000 --- a/B. Communities/CIRM Stem Cell Pathways/allPathways.rq +++ /dev/null @@ -1,5 +0,0 @@ -SELECT DISTINCT ?pathway (str(?title) as ?PathwayTitle) -WHERE { -?pathway wp:ontologyTag cur:CIRM_Related ; -a wp:Pathway ; -dc:title ?title .} diff --git a/B. Communities/CIRM Stem Cell Pathways/allProteins.rq b/B. Communities/CIRM Stem Cell Pathways/allProteins.rq deleted file mode 100644 index 367a6c7..0000000 --- a/B. Communities/CIRM Stem Cell Pathways/allProteins.rq +++ /dev/null @@ -1,8 +0,0 @@ -SELECT DISTINCT ?pathway (str(?label) as ?Protein) -WHERE { -?pathway wp:ontologyTag cur:CIRM_Related ; - a wp:Pathway . -?protein a wp:Protein ; - rdfs:label ?label ; - dcterms:isPartOf ?pathway . -} diff --git a/B. Communities/COVID19/allPathways.rq b/B. Communities/COVID19/allPathways.rq deleted file mode 100644 index 5088812..0000000 --- a/B. Communities/COVID19/allPathways.rq +++ /dev/null @@ -1,5 +0,0 @@ -SELECT DISTINCT ?pathway (str(?title) as ?PathwayTitle) -WHERE { -?pathway wp:ontologyTag cur:COVID19 ; -a wp:Pathway ; -dc:title ?title .} diff --git a/B. Communities/COVID19/allProteins.rq b/B. Communities/COVID19/allProteins.rq deleted file mode 100644 index e576ae1..0000000 --- a/B. Communities/COVID19/allProteins.rq +++ /dev/null @@ -1,8 +0,0 @@ -SELECT DISTINCT ?pathway (str(?label) as ?Protein) -WHERE { -?pathway wp:ontologyTag cur:COVID19 ; - a wp:Pathway . -?protein a wp:Protein ; - rdfs:label ?label ; - dcterms:isPartOf ?pathway . -} diff --git a/B. Communities/Inborn Errors of Metabolism/allMetabolicPWs.rq b/B. Communities/Inborn Errors of Metabolism/allMetabolicPWs.rq deleted file mode 100644 index ea5dd27..0000000 --- a/B. Communities/Inborn Errors of Metabolism/allMetabolicPWs.rq +++ /dev/null @@ -1,8 +0,0 @@ -SELECT distinct ?pathway ?label ?tag -WHERE { - ?tag1 a owl:Class ; - rdfs:label ?label . - ?tag rdfs:subClassOf* ?tag1. - ?pathway a wp:Pathway; wp:ontologyTag ?tag. -FILTER regex(str(?label), "metabolic pathway") -} diff --git a/B. Communities/Inborn Errors of Metabolism/allPathways.rq b/B. Communities/Inborn Errors of Metabolism/allPathways.rq deleted file mode 100644 index 0dc3ac8..0000000 --- a/B. Communities/Inborn Errors of Metabolism/allPathways.rq +++ /dev/null @@ -1,5 +0,0 @@ -SELECT DISTINCT ?pathway (str(?title) as ?PathwayTitle) -WHERE { -?pathway wp:ontologyTag cur:IEM ; -a wp:Pathway ; -dc:title ?title .} diff --git a/B. Communities/Inborn Errors of Metabolism/allProteins.rq b/B. Communities/Inborn Errors of Metabolism/allProteins.rq deleted file mode 100644 index f5f0bb2..0000000 --- a/B. Communities/Inborn Errors of Metabolism/allProteins.rq +++ /dev/null @@ -1,8 +0,0 @@ -SELECT DISTINCT ?pathway (str(?label) as ?Protein) -WHERE { -?pathway wp:ontologyTag cur:IEM ; - a wp:Pathway . -?protein a wp:Protein ; - rdfs:label ?label ; - dcterms:isPartOf ?pathway . -} diff --git a/B. Communities/Inborn Errors of Metabolism/countMetabolicPWs.rq b/B. Communities/Inborn Errors of Metabolism/countMetabolicPWs.rq deleted file mode 100644 index 03f8ffe..0000000 --- a/B. Communities/Inborn Errors of Metabolism/countMetabolicPWs.rq +++ /dev/null @@ -1,8 +0,0 @@ -SELECT count(distinct ?pathway) as ?pathwaycount -WHERE { - ?tag1 a owl:Class ; - rdfs:label ?label . - ?tag rdfs:subClassOf* ?tag1. - ?pathway a wp:Pathway; wp:ontologyTag ?tag. -FILTER regex(str(?label), "metabolic pathway") -} diff --git a/B. Communities/Inborn Errors of Metabolism/countProteinsMetabolitesRheaDiseases.rq b/B. Communities/Inborn Errors of Metabolism/countProteinsMetabolitesRheaDiseases.rq deleted file mode 100644 index e2b25f1..0000000 --- a/B. Communities/Inborn Errors of Metabolism/countProteinsMetabolitesRheaDiseases.rq +++ /dev/null @@ -1,47 +0,0 @@ -#Prefixes required which might not be available in the SPARQL endpoint by default -PREFIX wp: -PREFIX rdfs: -PREFIX dcterms: - -#Variable selection -SELECT DISTINCT (str(?title) as ?pathwayName) ?PWID -(count(distinct ?geneProduct) AS ?ProteinsInPWs) (count(distinct ?metaboliteNode) AS ?MetabolitesInPWs) -(count(distinct ?interactionID) AS ?RheaInPWs) (count(distinct ?interactionMissing) AS ?NoRheaInPWs) -(count(distinct ?omim) as ?diseaseIDs) - -WHERE { - - ?pathway wp:ontologyTag cur:IEM . - ?pathway dcterms:identifier ?PWID. #Obtain the ID - ?pathway wp:isAbout ?gpmlRDF_ID . #find the corresponding GPML link - ?pathway dc:title ?title . #Obtain the title - - { - ?geneProduct dcterms:isPartOf ?pathway . #Only those part of PW - ?geneProduct a wp:Protein . #Filter for Protein DataNodes - } - UNION - { - ?metaboliteNode a wp:Metabolite . #Filter for Metabolite DataNodes - ?metaboliteNode dcterms:isPartOf ?pathway . #Only those part of PW - } - UNION - { - OPTIONAL{?interaction wp:bdbRhea ?interactionID . #Find interactions with a Rhea ID - ?interaction dcterms:isPartOf ?pathway .} #Only those part of PW - } - UNION - { - OPTIONAL{?interactionMissing dcterms:isPartOf ?pathway . #Find additional interactions - ?interactionMissing rdf:type wp:Conversion . #That are of type 'metabolic conversion' - FILTER NOT EXISTS {?interactionMissing wp:bdbRhea ?interactionID . } #Without a Rhea ID - } - } - UNION { - ?diseaseNode dcterms:isPartOf ?gpmlRDF_ID . #Only check for matching pathways - ?diseaseNode rdf:type gpml:Label . #Only include textLabels - ?diseaseNode gpml:href ?omim . #That have an href attribute - FILTER regex(?omim, "omim.org", "i") #Only keep hrefs if they contain 'omim.org' - } - -} ORDER BY ASC(?pathway) diff --git a/B. Communities/Lipids/LIPIDMAPS_Federated.rq b/B. Communities/Lipids/LIPIDMAPS_Federated.rq deleted file mode 100644 index d993ac5..0000000 --- a/B. Communities/Lipids/LIPIDMAPS_Federated.rq +++ /dev/null @@ -1,17 +0,0 @@ -#Pathways describing the biology of oxygenated hydrocarbons (LMFA12) -PREFIX chebi: - -SELECT ?lipid ?name ?formula ?lmid (GROUP_CONCAT(?wpid_;separator=", ") AS ?pathway) -WHERE { - SERVICE { - VALUES ?category { } - ?lipidmaps rdfs:label ?name ; - rdfs:subClassOf* ?category ; - chebi:formula ?formula . - } - BIND (IRI(CONCAT("https://identifiers.org/lipidmaps/", - SUBSTR(STR(?lipidmaps), 31))) AS ?lmid) - ?lipid wp:bdbLipidMaps ?lmid ; - dcterms:isPartOf ?pathway . - ?pathway a wp:Pathway ; dcterms:identifier ?wpid_ . -} diff --git a/B. Communities/Lipids/LipidClassesTotal.rq b/B. Communities/Lipids/LipidClassesTotal.rq deleted file mode 100644 index e195239..0000000 --- a/B. Communities/Lipids/LipidClassesTotal.rq +++ /dev/null @@ -1,11 +0,0 @@ -SELECT count(DISTINCT ?lipidID) as ?IndividualLipidsPerClass -WHERE { ?metabolite a wp:Metabolite ; - dcterms:identifier ?id ; - dcterms:isPartOf ?pathwayRes ; - wp:bdbLipidMaps ?lipidID . #Metabolite DataNodes need to have a LIPID MAPS ID, for this query to count correctly (some lipids might be missed due to missing Xrefs) - ?pathwayRes a wp:Pathway ; - wp:organismName "Homo sapiens"; #Filter for a species (ommit when querying all pathways available for all species) - dcterms:identifier ?wpid ; - dc:title ?title . - FILTER regex(str(?lipidID), "FA" ). #Filter for a LIPID MAPS ID subclass: 'FA' Fatty Acids ; 'GL' Glycerolipid ; 'GP' Glycerophospholipid ; 'SP' Sphingolipids ; 'ST' Sterol lipids ; 'PR' Prenol Lipids ; 'SL' Saccharolipids ; 'PK' Polyketides -} diff --git a/B. Communities/Lipids/LipidsClassesCountPerPathway.rq b/B. Communities/Lipids/LipidsClassesCountPerPathway.rq deleted file mode 100644 index 63601ac..0000000 --- a/B. Communities/Lipids/LipidsClassesCountPerPathway.rq +++ /dev/null @@ -1,13 +0,0 @@ -SELECT DISTINCT ?pathwayRes (str(?wpid) AS ?pathway) (str(?title) AS ?pathwayTitle) (count(DISTINCT ?lipidID) AS ?Class_LipidsInPWs) -WHERE { ?metabolite a wp:Metabolite ; - dcterms:identifier ?id ; - dcterms:isPartOf ?pathwayRes ; - wp:bdbLipidMaps ?lipidID . #Metabolite DataNodes need to have a LIPID MAPS ID, for this query to count correctly (some lipids might be missed due to missing Xrefs) - ?pathwayRes a wp:Pathway ; - wp:organismName "Homo sapiens" ; #Filter for a species (ommit when querying all pathways available for all species) - dcterms:identifier ?wpid ; - dc:title ?title . - FILTER regex(str(?lipidID), "FA" ). #Filter for a LIPID MAPS ID subclass: 'FA' Fatty Acids ; 'GL' Glycerolipid ; 'GP' Glycerophospholipid ; 'SP' Sphingolipids ; 'ST' Sterol lipids ; 'PR' Prenol Lipids ; 'SL' Saccharolipids ; 'PK' Polyketides -} - -ORDER BY DESC(?Class_LipidsInPWs) diff --git a/B. Communities/Lipids/LipidsCountPerPathway.rq b/B. Communities/Lipids/LipidsCountPerPathway.rq deleted file mode 100644 index 75f5406..0000000 --- a/B. Communities/Lipids/LipidsCountPerPathway.rq +++ /dev/null @@ -1,14 +0,0 @@ -prefix lipidmaps: #IRI can be used to create URLs from identifiers in line 7 -select distinct ?pathwayRes (str(?wpid) as ?pathway) (str(?title) as ?pathwayTitle) (count(distinct ?lipidID) AS ?LipidsInPWs) -where { - ?metabolite a wp:Metabolite ; #Define what are metabolites - dcterms:identifier ?id ; #Find the identifier of a certain metabolite - dcterms:isPartOf ?pathwayRes ; #Define metabolites are part of a pathway - wp:bdbLipidMaps ?lipidID . #Find the LIPID MAPS identifier for a certain metabolite - ?pathwayRes a wp:Pathway ; #Define what is a pathway - wp:organismName "Homo sapiens" ; #Filter pathways on species Human - dcterms:identifier ?wpid ; #Obtain identifier of pathway - dc:title ?title . #Obtain title of pathway -} - -ORDER BY DESC(?LipidsInPWs) diff --git a/B. Communities/Lipids/allPathways.rq b/B. Communities/Lipids/allPathways.rq deleted file mode 100644 index 8db0ced..0000000 --- a/B. Communities/Lipids/allPathways.rq +++ /dev/null @@ -1,5 +0,0 @@ -SELECT DISTINCT ?pathway (str(?title) as ?PathwayTitle) -WHERE { -?pathway wp:ontologyTag cur:Lipids ; -a wp:Pathway ; -dc:title ?title .} diff --git a/B. Communities/Lipids/allProteins.rq b/B. Communities/Lipids/allProteins.rq deleted file mode 100644 index 0d68bbd..0000000 --- a/B. Communities/Lipids/allProteins.rq +++ /dev/null @@ -1,8 +0,0 @@ -SELECT DISTINCT ?pathway (str(?label) as ?Protein) -WHERE { -?pathway wp:ontologyTag cur:Lipids ; - a wp:Pathway . -?protein a wp:Protein ; - rdfs:label ?label ; - dcterms:isPartOf ?pathway . -} diff --git a/B. Communities/RareDiseases/allPathways.rq b/B. Communities/RareDiseases/allPathways.rq deleted file mode 100644 index d00228f..0000000 --- a/B. Communities/RareDiseases/allPathways.rq +++ /dev/null @@ -1,5 +0,0 @@ -SELECT DISTINCT ?pathway (str(?title) as ?PathwayTitle) -WHERE { -?pathway wp:ontologyTag cur:RareDiseases ; -a wp:Pathway ; -dc:title ?title .} diff --git a/B. Communities/RareDiseases/allProteins.rq b/B. Communities/RareDiseases/allProteins.rq deleted file mode 100644 index 7d15f83..0000000 --- a/B. Communities/RareDiseases/allProteins.rq +++ /dev/null @@ -1,8 +0,0 @@ -SELECT DISTINCT ?pathway (str(?label) as ?Protein) -WHERE { -?pathway wp:ontologyTag cur:RareDiseases ; - a wp:Pathway . -?protein a wp:Protein ; - rdfs:label ?label ; - dcterms:isPartOf ?pathway . -} diff --git a/B. Communities/Reactome/getPathways.rq b/B. Communities/Reactome/getPathways.rq deleted file mode 100644 index be5611b..0000000 --- a/B. Communities/Reactome/getPathways.rq +++ /dev/null @@ -1,5 +0,0 @@ -SELECT DISTINCT ?pathway (str(?titleLit) as ?title) -WHERE { - ?pathway wp:ontologyTag cur:Reactome_Approved ; - dc:title ?titleLit . -} diff --git a/B. Communities/Reactome/refsReactomeAndWP.rq b/B. Communities/Reactome/refsReactomeAndWP.rq deleted file mode 100644 index 6e2f146..0000000 --- a/B. Communities/Reactome/refsReactomeAndWP.rq +++ /dev/null @@ -1,6 +0,0 @@ -SELECT (COUNT(DISTINCT ?pubmed) AS ?count) -WHERE { - ?pubmed a wp:PublicationReference . - { ?pubmed dcterms:isPartOf/wp:ontologyTag cur:AnalysisCollection } - { ?pubmed dcterms:isPartOf/wp:ontologyTag cur:Reactome_Approved } -} diff --git a/B. Communities/Reactome/refsReactomeNotWP.rq b/B. Communities/Reactome/refsReactomeNotWP.rq deleted file mode 100644 index 9ea9796..0000000 --- a/B. Communities/Reactome/refsReactomeNotWP.rq +++ /dev/null @@ -1,6 +0,0 @@ -SELECT (COUNT(DISTINCT ?pubmed) AS ?count) -WHERE { - ?pubmed a wp:PublicationReference . - MINUS { ?pubmed dcterms:isPartOf/wp:ontologyTag cur:AnalysisCollection } - { ?pubmed dcterms:isPartOf/wp:ontologyTag cur:Reactome_Approved } -} diff --git a/B. Communities/Reactome/refsWPNotReactome.rq b/B. Communities/Reactome/refsWPNotReactome.rq deleted file mode 100644 index 380e272..0000000 --- a/B. Communities/Reactome/refsWPNotReactome.rq +++ /dev/null @@ -1,6 +0,0 @@ -SELECT (COUNT(DISTINCT ?pubmed) AS ?count) -WHERE { - ?pubmed a wp:PublicationReference . - { ?pubmed dcterms:isPartOf/wp:ontologyTag cur:AnalysisCollection } - MINUS { ?pubmed dcterms:isPartOf/wp:ontologyTag cur:Reactome_Approved } -} diff --git a/B. Communities/WormBase/allPathways.rq b/B. Communities/WormBase/allPathways.rq deleted file mode 100644 index 36082c6..0000000 --- a/B. Communities/WormBase/allPathways.rq +++ /dev/null @@ -1,5 +0,0 @@ -SELECT DISTINCT ?pathway (str(?title) as ?PathwayTitle) -WHERE { -?pathway wp:ontologyTag cur:WormBase_Approved ; -a wp:Pathway ; -dc:title ?title .} diff --git a/B. Communities/WormBase/allProteins.rq b/B. Communities/WormBase/allProteins.rq deleted file mode 100644 index 0239f7a..0000000 --- a/B. Communities/WormBase/allProteins.rq +++ /dev/null @@ -1,8 +0,0 @@ -SELECT DISTINCT ?pathway (str(?label) as ?Protein) -WHERE { -?pathway wp:ontologyTag cur:WormBase_Approved ; - a wp:Pathway . -?protein a wp:Protein ; - rdfs:label ?label ; - dcterms:isPartOf ?pathway . -} diff --git a/C. Collaborations/AOP-Wiki/MetaboliteInAOP-Wiki.rq b/C. Collaborations/AOP-Wiki/MetaboliteInAOP-Wiki.rq deleted file mode 100644 index 8fe9714..0000000 --- a/C. Collaborations/AOP-Wiki/MetaboliteInAOP-Wiki.rq +++ /dev/null @@ -1,13 +0,0 @@ -PREFIX aopo: -PREFIX cheminf: - -SELECT DISTINCT (str(?title) as ?pathwayName) ?chemical ?ChEBI ?ChemicalName ?mappedid ?LinkedStressor - -WHERE { - ?pathway a wp:Pathway ; wp:organismName "Homo sapiens"; dcterms:identifier ?WPID ; dc:title ?title . - ?chemical a wp:Metabolite; dcterms:isPartOf ?pathway; wp:bdbChEBI ?mappedid . - SERVICE { - ?mappedid a cheminf:000407; cheminf:000407 ?ChEBI . - ?cheLook a cheminf:000000; dc:title ?ChemicalName ; dcterms:isPartOf ?LinkedStressor ; skos:exactMatch ?mappedid . - }} -limit 1 diff --git a/C. Collaborations/MetaNetX/reactionID_mapping.rq b/C. Collaborations/MetaNetX/reactionID_mapping.rq deleted file mode 100644 index a356ffa..0000000 --- a/C. Collaborations/MetaNetX/reactionID_mapping.rq +++ /dev/null @@ -1,43 +0,0 @@ -#Prefixes required which might not be available in the SPARQL endpoint by default -PREFIX wp: -PREFIX rdfs: -PREFIX dcterms: -#Prefixes for the MetaNetX RDF: -PREFIX mnx: -PREFIX owl: -PREFIX rdf: -PREFIX rdfs: -PREFIX rhea: - -#Variable selection -SELECT DISTINCT (str(?title) as ?pathwayName) ?PWID ?interactionID ?reac - -WHERE { -#Pathway Model IDs of interest -VALUES ?PWID {"WP5275"} - - ?pathway a wp:Pathway . #Define what a pathway is - ?pathway dcterms:identifier ?PWID. #Obtain the ID - ?pathway dc:title ?title . #Obtain the title - - ?interaction wp:bdbRhea ?interactionID . #Find interactions with a Rhea ID - ?interaction dcterms:isPartOf ?pathway . #Only those part of PW - - ##The IRI for Rhea-IDs from WikiPathways starts with https://identifiers.org/rhea/, where the one from MetaNetX starts with "http://rdf.rhea-db.org/ , so we need to rewrite the IRI - BIND( # Bind the created IRI into a new variable (called ?newIRI) - IRI( # Convert the string back to an IRI - CONCAT( # Concatenate item 1 and 2 together as one string - "http://rdf.rhea-db.org/", # First item to concat (more items can be added with a comma - #Second item to concat: - SUBSTR( # Obtain a substring - STR(?interactionID), # Convert the Rhea IRI from WikiPathways to a string, - 30) # removing the first 29 charachters - )) AS ?newIRI # Name for the new variable - ) - SERVICE { - SELECT DISTINCT ?reac - WHERE{ - ?reac mnx:reacXref rhea:17658 .} - } - -} ORDER BY ASC(?pathway) diff --git a/C. Collaborations/MolMeDB/ONEpubchem_MANYpathways.rq b/C. Collaborations/MolMeDB/ONEpubchem_MANYpathways.rq deleted file mode 100644 index 13f6ae9..0000000 --- a/C. Collaborations/MolMeDB/ONEpubchem_MANYpathways.rq +++ /dev/null @@ -1,17 +0,0 @@ -SELECT DISTINCT ?pathwayRes (str(?wpid) as ?pathway) (str(?title) as ?pathwayTitle) ((substr(str(?COMPOUND),46)) as ?PubChem) WHERE -{ - SERVICE { - skos:exactMatch ?COMPOUND. - filter (strstarts(str(?COMPOUND), 'http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID')) - } - - ?gene a wp:Metabolite ; - dcterms:identifier ?id ; - dcterms:isPartOf ?pathwayRes ; - wp:bdbPubChem ?COMPOUND . - - ?pathwayRes a wp:Pathway ; - wp:organismName "Homo sapiens"; - dcterms:identifier ?wpid ; - dc:title ?title . -} diff --git a/C. Collaborations/MolMeDB/SUBSETpathways_ONEpubchem.rq b/C. Collaborations/MolMeDB/SUBSETpathways_ONEpubchem.rq deleted file mode 100644 index 9f6e1fd..0000000 --- a/C. Collaborations/MolMeDB/SUBSETpathways_ONEpubchem.rq +++ /dev/null @@ -1,19 +0,0 @@ -SELECT DISTINCT ?pathwayRes (str(?wpid) as ?pathway) (str(?title) as ?pathwayTitle) ((substr(str(?COMPOUND),46)) as ?PubChem) WHERE { - SERVICE { - SERVICE { - VALUES ?wpid {"WP4224" "WP4225" "WP4571"} - - ?gene a wp:Metabolite ; - dcterms:identifier ?id ; - dcterms:isPartOf ?pathwayRes ; - wp:bdbPubChem ?COMPOUND . - - ?pathwayRes a wp:Pathway ; - wp:organismName "Homo sapiens" ; - dcterms:identifier ?wpid ; - dc:title ?title . - } - - skos:exactMatch ?COMPOUND. - } -} diff --git a/C. Collaborations/neXtProt/ProteinCellularLocation.rq b/C. Collaborations/neXtProt/ProteinCellularLocation.rq deleted file mode 100644 index 85ec675..0000000 --- a/C. Collaborations/neXtProt/ProteinCellularLocation.rq +++ /dev/null @@ -1,24 +0,0 @@ -PREFIX : -select distinct ?pathwayname ?entry str(?gen) (group_concat(distinct str(?loclab); SEPARATOR = ",") as ?locations) where { - {?geneProduct a wp:Protein} - union - {?geneProduct a wp:GeneProduct} - ?geneProduct rdfs:label ?gen . - filter(!regex(?gen,"[ a-z-]")). - ?geneProduct dcterms:isPartOf ?pathway . - ?pathway a wp:Pathway . - ?pathway wp:organism ?organism . - filter(contains(str(?organism),"9606")) - ?pathway dc:title ?pathwayname . - filter(regex(?pathwayname,"Rett")). - service { - ?entry a :Entry ; - :gene / :name ?gen ; - :isoform ?iso. - ?iso :cellularComponent ?locannot . - ?locannot :term ?locterm . - ?locterm rdfs:label ?loclab . - ?locannot :evidence ?locev . - ?locev :quality :GOLD . - }} -order by ?pathwayname diff --git a/C. Collaborations/neXtProt/ProteinMitochondria.rq b/C. Collaborations/neXtProt/ProteinMitochondria.rq deleted file mode 100644 index 2bf6379..0000000 --- a/C. Collaborations/neXtProt/ProteinMitochondria.rq +++ /dev/null @@ -1,24 +0,0 @@ -PREFIX : -PREFIX cv: - -select distinct ?pathwayname (group_concat(distinct ?gen , ',') as ?genes) where { - {?geneProduct a wp:Protein} - union - {?geneProduct a wp:GeneProduct} - ?geneProduct rdfs:label ?gen . - filter(!regex(?gen,"[ a-z-]")). - ?geneProduct dcterms:isPartOf ?pathway . - ?pathway a wp:Pathway . - ?pathway wp:organism ?organism . - filter(contains(str(?organism),"9606")) - ?pathway dc:title ?pathwayname . - filter(regex(?pathwayname,"Rett")). - service { - ?entry a :Entry . - ?entry :gene / :name ?gen . - ?entry :isoform / :cellularComponent ?loc . - values ?mitoloc {cv:SL-0173 cv:GO_0005739 } # SL and GO values for mitochondrion - ?loc :term / :childOf ?mitoloc. # mitochondrion - ?loc :evidence / :quality :GOLD . - }} -order by ?pathwayname diff --git a/C. Collaborations/smallMolecules_Rhea_IDSM/molecularSimularity_Reactions.rq b/C. Collaborations/smallMolecules_Rhea_IDSM/molecularSimularity_Reactions.rq deleted file mode 100644 index c2e632a..0000000 --- a/C. Collaborations/smallMolecules_Rhea_IDSM/molecularSimularity_Reactions.rq +++ /dev/null @@ -1,45 +0,0 @@ -PREFIX owl: -PREFIX ebi: -PREFIX sachem: -PREFIX idsm: -PREFIX dcterms: -PREFIX wp: -PREFIX sso: -PREFIX rh: -PREFIX rdfs: -PREFIX xsd: - -SELECT distinct ?chebioSrc ?similarSrc ?chebioTgt ?similarTgt ?reaction WHERE { - ?interaction dcterms:isPartOf ?pathway ; a wp:Conversion ; - wp:source ?source ; - wp:target ?target . - ?source wp:bdbChEBI ?chebiSrc . - ?target wp:bdbChEBI ?chebiTgt . - ?pathway dcterms:identifier "WP4225". - BIND(iri(concat("http://purl.obolibrary.org/obo/CHEBI_", substr(str(?chebiSrc),37))) AS ?chebioSrc) - BIND(iri(concat("http://purl.obolibrary.org/obo/CHEBI_", substr(str(?chebiTgt),37))) AS ?chebioTgt) - - -#IDSM -SERVICE { - - ?chebioSrc ^sso:is-attribute-of / sso:has-value ?molfileSrc . - ?chebioTgt ^sso:is-attribute-of / sso:has-value ?molfileTgt . - [ sachem:compound ?similarSrc; sachem:score ?scoreSrc ] - sachem:similaritySearch [ - sachem:query ?molfileSrc ; -# sachem:cutoff "0.98"^^xsd:double - ]. - [ sachem:compound ?similarTgt; sachem:score ?scoreTgt ] - sachem:similaritySearch [ - sachem:query ?molfileTgt ; -# sachem:cutoff "0.98"^^xsd:double - ]. - } - -# SERVICE { -# ?reaction rh:side / rh:contains / rh:compound / rh:chebi ?similarSrc , ?similarTgt . -# ?reaction rdfs:subClassOf rh:Reaction . -# } - - } diff --git a/D. General/GenesofPathway.rq b/D. General/GenesofPathway.rq deleted file mode 100644 index f040b00..0000000 --- a/D. General/GenesofPathway.rq +++ /dev/null @@ -1,8 +0,0 @@ -select distinct ?pathway (str(?label) as ?geneProduct) where { - ?geneProduct a wp:GeneProduct . - ?geneProduct rdfs:label ?label . - ?geneProduct dcterms:isPartOf ?pathwayRev . - ?pathwayRev a wp:Pathway . - ?pathwayRev dc:identifier ?pathway . - ?pathwayRev dcterms:identifier "WP1560" . #Replace "WP1560" with WP ID of interest -} diff --git a/D. General/InteractionsofPathway.rq b/D. General/InteractionsofPathway.rq deleted file mode 100644 index cf65977..0000000 --- a/D. General/InteractionsofPathway.rq +++ /dev/null @@ -1,11 +0,0 @@ -SELECT DISTINCT ?pathway ?interaction ?participants ?DataNodeLabel -WHERE { - - ?pathway a wp:Pathway ; - dc:identifier . - ?interaction dcterms:isPartOf ?pathway ; - a wp:Interaction ; - wp:participants ?participants . - ?participants a wp:DataNode ; - rdfs:label ?DataNodeLabel . -} diff --git a/D. General/MetabolitesofPathway.rq b/D. General/MetabolitesofPathway.rq deleted file mode 100644 index f4f2497..0000000 --- a/D. General/MetabolitesofPathway.rq +++ /dev/null @@ -1,7 +0,0 @@ -select distinct ?pathway (str(?label) as ?Metabolite) where { - ?Metabolite a wp:Metabolite ; - rdfs:label ?label ; - dcterms:isPartOf ?pathway . - ?pathway a wp:Pathway ; - dcterms:identifier "WP1560" . #Replace "WP1560" with WP ID of interest -} diff --git a/D. General/OntologyofPathway.rq b/D. General/OntologyofPathway.rq deleted file mode 100644 index f4a715f..0000000 --- a/D. General/OntologyofPathway.rq +++ /dev/null @@ -1,9 +0,0 @@ -SELECT (?o as ?pwOntologyTerm) (str(?titleLit) as ?title) ?pathway -WHERE { - ?pathwayRDF wp:ontologyTag ?o ; - dc:identifier ?pathway ; - dc:title ?titleLit ; - dcterms:identifier "WP1560" . #Replace "WP1560" with WP ID of interest - - FILTER (! regex(str(?pathway), "group")) -} diff --git a/E. Literature/allPathwayswithPubMed.rq b/E. Literature/allPathwayswithPubMed.rq deleted file mode 100644 index 1716dee..0000000 --- a/E. Literature/allPathwayswithPubMed.rq +++ /dev/null @@ -1,6 +0,0 @@ -SELECT DISTINCT ?pathway ?pubmed -WHERE - {?pubmed a wp:PublicationReference . - ?pubmed dcterms:isPartOf ?pathway } -ORDER BY ?pathway -LIMIT 50 diff --git a/E. Literature/allReferencesForInteraction.rq b/E. Literature/allReferencesForInteraction.rq deleted file mode 100644 index b44b619..0000000 --- a/E. Literature/allReferencesForInteraction.rq +++ /dev/null @@ -1,10 +0,0 @@ -SELECT DISTINCT ?pathway ?interaction ?pubmed ?partnerref WHERE { - ?pathway a wp:Pathway ; - dc:identifier . - ?interaction dcterms:isPartOf ?pathway ; - a wp:Interaction ; - wp:participants ?partner; - dcterms:references ?pubmed . - OPTIONAL{?partner dc:identifier ?partnerID ; - dcterms:references ?partnerref .} -} LIMIT 100 diff --git a/E. Literature/countRefsPerPW.rq b/E. Literature/countRefsPerPW.rq deleted file mode 100644 index 95a6891..0000000 --- a/E. Literature/countRefsPerPW.rq +++ /dev/null @@ -1,5 +0,0 @@ -SELECT DISTINCT ?pathway COUNT(?pubmed) AS ?numberOfReferences -WHERE - {?pubmed a wp:PublicationReference . - ?pubmed dcterms:isPartOf ?pathway } -ORDER BY DESC(?numberOfReferences) diff --git a/E. Literature/referencesForInteraction.rq b/E. Literature/referencesForInteraction.rq deleted file mode 100644 index 64ab62c..0000000 --- a/E. Literature/referencesForInteraction.rq +++ /dev/null @@ -1,12 +0,0 @@ -SELECT DISTINCT ?pathway ?interaction ?pubmed -WHERE { - - ?pathway a wp:Pathway ; - dc:identifier . #filter for one pathway - ?interaction dcterms:isPartOf ?pathway ; - a wp:Interaction ; - dcterms:references ?pubmed ; - wp:participants ?participants . - ?participants a wp:DataNode ; - rdfs:label ?DataNodeLabel . -} diff --git a/E. Literature/referencesForSpecificInteraction.rq b/E. Literature/referencesForSpecificInteraction.rq deleted file mode 100644 index 3d3aaff..0000000 --- a/E. Literature/referencesForSpecificInteraction.rq +++ /dev/null @@ -1,8 +0,0 @@ -SELECT DISTINCT ?pathway ?interaction ?pubmed WHERE { - ?pathway a wp:Pathway . - ?pathway dc:identifier . #filter for pathway - ?interaction dcterms:isPartOf ?pathway . - ?interaction a wp:Interaction . - ?interaction wp:participants . #filter for interaction - ?interaction dcterms:references ?pubmed . -} LIMIT 100 diff --git a/F. Datadump/CyTargetLinkerLinksetInput.rq b/F. Datadump/CyTargetLinkerLinksetInput.rq deleted file mode 100644 index cf0ae34..0000000 --- a/F. Datadump/CyTargetLinkerLinksetInput.rq +++ /dev/null @@ -1,10 +0,0 @@ -select distinct (str(?title) as ?PathwayName) (str(?wpid) as ?PathwayID) (fn:substring(?genename,37) as ?GeneName) (fn:substring(?ncbiGeneId,34) as ?GeneID) where { - ?gene a wp:DataNode ; - dcterms:identifier ?id ; - dcterms:isPartOf ?pathwayRes ; - wp:bdbEntrezGene ?ncbiGeneId ; - wp:bdbHgncSymbol ?genename . - ?pathwayRes a wp:Pathway ; - dcterms:identifier ?wpid ; - dc:title ?title . -} diff --git a/F. Datadump/dumpOntologyAndPW.rq b/F. Datadump/dumpOntologyAndPW.rq deleted file mode 100644 index 410959a..0000000 --- a/F. Datadump/dumpOntologyAndPW.rq +++ /dev/null @@ -1,10 +0,0 @@ -SELECT DISTINCT ?depicts (str(?titleLit) as ?title) (str(?speciesLabelLit) as ?speciesLabel) ?identifier ?ontology -WHERE { - ?pathway foaf:page ?depicts . - ?pathway dc:title ?titleLit . - ?pathway wp:organism ?species . - ?pathway wp:organismName ?speciesLabelLit . - ?pathway dc:identifier ?identifier . - - OPTIONAL {?pathway wp:ontologyTag ?ontology .} -} diff --git a/F. Datadump/dumpPWsofSpecies.rq b/F. Datadump/dumpPWsofSpecies.rq deleted file mode 100644 index 01020a6..0000000 --- a/F. Datadump/dumpPWsofSpecies.rq +++ /dev/null @@ -1,8 +0,0 @@ -SELECT DISTINCT ?wpIdentifier ?pathway ?title ?page -WHERE { - ?pathway dc:title ?title ; - foaf:page ?page ; - dc:identifier ?wpIdentifier ; - wp:organismName "Mus musculus" . - } -ORDER BY ?wpIdentifier diff --git a/G. Curation/MetabolitesDoubleMappingWikidata.rq b/G. Curation/MetabolitesDoubleMappingWikidata.rq deleted file mode 100644 index e266d47..0000000 --- a/G. Curation/MetabolitesDoubleMappingWikidata.rq +++ /dev/null @@ -1,10 +0,0 @@ -# Finding double mappings to Wikidata for metabolites: - -PREFIX wdt: - -SELECT DISTINCT ?metaboliteID (GROUP_CONCAT(DISTINCT ?wikidata;separator=", ") AS ?results) WHERE { - ?metaboliteID a wp:Metabolite . - ?metaboliteID wp:bdbWikidata ?wikidata . - ?metaboliteID wp:bdbWikidata ?wikidata2 . - FILTER(?wikidata != ?wikidata2) -} GROUP BY ?metaboliteID diff --git a/G. Curation/MetabolitesNotClassified.rq b/G. Curation/MetabolitesNotClassified.rq deleted file mode 100644 index ef60820..0000000 --- a/G. Curation/MetabolitesNotClassified.rq +++ /dev/null @@ -1,12 +0,0 @@ -#Metabolites not classified as such - -prefix wp: -prefix rdfs: -prefix dcterms: - -select (str(?datasourceLit) as ?datasource) (count(?identifier) as ?count) -where { - ?mb dc:source ?datasourceLit ; - dcterms:identifier ?identifier . - FILTER NOT EXISTS { ?mb a wp:Metabolite } -} order by desc(?count) diff --git a/G. Curation/MetabolitesWithoutLinkWikidata.rq b/G. Curation/MetabolitesWithoutLinkWikidata.rq deleted file mode 100644 index 0ad8ae6..0000000 --- a/G. Curation/MetabolitesWithoutLinkWikidata.rq +++ /dev/null @@ -1,9 +0,0 @@ -#Metabolites without a link to Wikidata - -PREFIX wdt: - -SELECT DISTINCT ?metabolite WHERE { - ?metabolite a wp:Metabolite . - OPTIONAL { ?metabolite wp:bdbWikidata ?wikidata . } - FILTER (!BOUND(?wikidata)) -} diff --git a/G. Curation/PWsWithoutDatanodes.rq b/G. Curation/PWsWithoutDatanodes.rq deleted file mode 100644 index 7e1f0d9..0000000 --- a/G. Curation/PWsWithoutDatanodes.rq +++ /dev/null @@ -1,13 +0,0 @@ -#Pathways without (annotated) datanodes - -prefix wp: -prefix rdfs: -prefix dcterms: -prefix xsd: - -SELECT DISTINCT ?pathway -WHERE{ -?pathway a wp:Pathway, skos:Collection . -FILTER NOT EXISTS {?node dcterms:isPartOf ?pathway. -?node a wp:DataNode} -} diff --git a/G. Curation/PWsWithoutRef.rq b/G. Curation/PWsWithoutRef.rq deleted file mode 100644 index 2073eb7..0000000 --- a/G. Curation/PWsWithoutRef.rq +++ /dev/null @@ -1,7 +0,0 @@ -#Pathways without literature references - -SELECT (STR(?speciesLabelLit) AS ?species) (STR(?titleLit) AS ?title) ?pathway WHERE { - ?pathway a wp:Pathway ; dc:title ?titleLit ; wp:organismName ?speciesLabelLit . - MINUS { ?pubmed a wp:PublicationReference . - ?pubmed dcterms:isPartOf ?pathway } -} ORDER BY ASC(?species) ASC(?title) diff --git a/G. Curation/countPWsMetabolitesOccurSorted.rq b/G. Curation/countPWsMetabolitesOccurSorted.rq deleted file mode 100644 index 5fccacf..0000000 --- a/G. Curation/countPWsMetabolitesOccurSorted.rq +++ /dev/null @@ -1,12 +0,0 @@ -#Sorting the metabolites by the number of pathways they occur in - -PREFIX wdt: - -SELECT ?metabolite (count(DISTINCT ?pathwayRes) as ?pathways) WHERE { - ?metabolite a wp:Metabolite ; - dcterms:identifier ?id ; - dcterms:isPartOf ?pathwayRes . - ?pathwayRes a wp:Pathway . - OPTIONAL { ?metabolite wp:bdbWikidata ?wikidata . } - FILTER (!BOUND(?wikidata)) -} GROUP BY ?metabolite ORDER BY DESC(?pathways) diff --git a/G. Curation/countPWsWithoutRef.rq b/G. Curation/countPWsWithoutRef.rq deleted file mode 100644 index b726bb7..0000000 --- a/G. Curation/countPWsWithoutRef.rq +++ /dev/null @@ -1,5 +0,0 @@ -SELECT count(DISTINCT ?pathway) WHERE { - ?pathway a wp:Pathway ; dc:title ?titleLit ; wp:organismName ?speciesLabelLit . - MINUS { ?pubmed a wp:PublicationReference . - ?pubmed dcterms:isPartOf ?pathway } -} diff --git a/H. Chemistry/IDSM_similaritySearch.rq b/H. Chemistry/IDSM_similaritySearch.rq deleted file mode 100644 index b26ab26..0000000 --- a/H. Chemistry/IDSM_similaritySearch.rq +++ /dev/null @@ -1,36 +0,0 @@ -PREFIX owl: -PREFIX ebi: -PREFIX sachem: -PREFIX idsm: -PREFIX dcterms: -PREFIX wp: -PREFIX sso: -PREFIX rh: -PREFIX rdfs: -PREFIX xsd: -SELECT distinct ((substr(str(?chebioSrc),32)) as ?SourceOrigin) ((substr(str(?similarSrc),32)) as ?SourceSimilar) ((substr(str(?chebioTgt),32)) as ?TargetOrigin) ((substr(str(?similarTgt),32)) as ?TargetSimilar) #?reaction -WHERE { - ?interaction dcterms:isPartOf ?pathway ; a wp:Conversion ; - wp:source ?source ; - wp:target ?target . - ?source wp:bdbChEBI ?chebiSrc . - ?target wp:bdbChEBI ?chebiTgt . - ?pathway dcterms:identifier "WP4225". - BIND(iri(concat("http://purl.obolibrary.org/obo/CHEBI_", substr(str(?chebiSrc),37))) AS ?chebioSrc) - BIND(iri(concat("http://purl.obolibrary.org/obo/CHEBI_", substr(str(?chebiTgt),37))) AS ?chebioTgt) -#IDSM -SERVICE { - ?chebioSrc ^sso:is-attribute-of / sso:has-value ?molfileSrc . - ?chebioTgt ^sso:is-attribute-of / sso:has-value ?molfileTgt . - [ sachem:compound ?similarSrc; sachem:score ?scoreSrc ] - sachem:similaritySearch [ - sachem:query ?molfileSrc ; - sachem:cutoff 98e-2 - ]. - [ sachem:compound ?similarTgt; sachem:score ?scoreTgt ] - sachem:similaritySearch [ - sachem:query ?molfileTgt ; - sachem:cutoff 98e-2 - ] . - } - } diff --git a/H. Chemistry/smiles.rq b/H. Chemistry/smiles.rq deleted file mode 100644 index 7566849..0000000 --- a/H. Chemistry/smiles.rq +++ /dev/null @@ -1,5 +0,0 @@ -PREFIX cheminf: - -SELECT ?mol ?smilesDepict WHERE { - ?mol wp:bdbWikidata/cheminf:CHEMINF_000018 ?smilesDepict . -} LIMIT 25 diff --git a/I. DirectedSmallMoleculesNetwork (DSMN)/controlling duplicate mappings from Wikidata.rq b/I. DirectedSmallMoleculesNetwork (DSMN)/controlling duplicate mappings from Wikidata.rq deleted file mode 100644 index 0bc6003..0000000 --- a/I. DirectedSmallMoleculesNetwork (DSMN)/controlling duplicate mappings from Wikidata.rq +++ /dev/null @@ -1,28 +0,0 @@ -### Part 1: ### -#Required prefixes for querying WikiPathways content in Blazegraph -PREFIX gpml: -PREFIX wp: -PREFIX wprdf: -PREFIX biopax: -PREFIX cas: -PREFIX dc: -PREFIX dcterms: -PREFIX foaf: -PREFIX ncbigene: -PREFIX pubmed: -PREFIX rdf: -PREFIX rdfs: -PREFIX skos: -PREFIX xsd: -PREFIX cur: - -### Part 2: ### -#Control for double mappings to Wikidata IDs. -SELECT DISTINCT ?metaboliteID -(GROUP_CONCAT(DISTINCT ?wikidata;separator=", ") AS ?results) -WHERE { - ?metaboliteID a wp:Metabolite . - ?metaboliteID wp:bdbWikidata ?wikidata . - ?metaboliteID wp:bdbWikidata ?wikidata2 . -FILTER(?wikidata != ?wikidata2) -} GROUP BY ?metaboliteID diff --git a/I. DirectedSmallMoleculesNetwork (DSMN)/extracting directed metabolic reactions.rq b/I. DirectedSmallMoleculesNetwork (DSMN)/extracting directed metabolic reactions.rq deleted file mode 100644 index 53d0931..0000000 --- a/I. DirectedSmallMoleculesNetwork (DSMN)/extracting directed metabolic reactions.rq +++ /dev/null @@ -1,40 +0,0 @@ -### Part 1: ### -SELECT DISTINCT ?interaction ?sourceDb ?targetDb ?mimtype -?pathway (str(?titleLit) as ?title) -?sourceCHEBI ?targetDbCHEBI ?sourceHMDB ?targetDbHMDB ?InteractionID -WHERE { - -### Part 2: ### -?pathway a wp:Pathway ; - wp:organismName "Homo sapiens" ; - dc:title ?titleLit . - -### Part 3A: ### -FILTER (EXISTS {?pathway wp:ontologyTag cur:AnalysisCollection}) . -### Part 3B: ### -#FILTER (EXISTS {?pathway wp:ontologyTag cur:Reactome_Approved}) . -### Part 3C: ### -#FILTER (EXISTS {?pathway wp:ontologyTag cur:Lipids}) . - -### Part 4: ### -?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} . - -### Part 5: ### -?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}. - -### Part 6: ### -OPTIONAL{?interaction wp:bdbRhea ?InteractionID} . -} ORDER BY DESC(?InteractionID) diff --git a/I. DirectedSmallMoleculesNetwork (DSMN)/extracting ontologies and references for metabolic reactions.rq b/I. DirectedSmallMoleculesNetwork (DSMN)/extracting ontologies and references for metabolic reactions.rq deleted file mode 100644 index 7a91a0e..0000000 --- a/I. DirectedSmallMoleculesNetwork (DSMN)/extracting ontologies and references for metabolic reactions.rq +++ /dev/null @@ -1,29 +0,0 @@ -### Part 1: ### -SELECT DISTINCT ?interaction ?sourceDb ?targetDb ?PWOnt ?DiseaseOnt -?curationstatus ?InteractionRef ?PWref ?sourceLit ?targetLit -WHERE { -?pathway a wp:Pathway ; - wp:organismName "Homo sapiens"; - 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 . - -### Part 2: ### -#OPTIONAL{?pathway wp:pathwayOntologyTag ?PWOnt} . -#OPTIONAL{?pathway wp:diseaseOntologyTag ?DiseaseOnt} . - -### Part 3: ### -#OPTIONAL{?pathway wp:ontologyTag ?curationstatus} . - -### Part 4: ### -OPTIONAL{?interaction dcterms:bibliographicCitation ?InteractionRef} . -OPTIONAL{?pathway dcterms:references ?PWref} . -OPTIONAL{?source dcterms:bibliographicCitation ?sourceLit} . -OPTIONAL{?target dcterms:bibliographicCitation ?targetLit} . -} diff --git a/I. DirectedSmallMoleculesNetwork (DSMN)/extracting protein titles and identifiers for metabolic reactions.rq b/I. DirectedSmallMoleculesNetwork (DSMN)/extracting protein titles and identifiers for metabolic reactions.rq deleted file mode 100644 index 0ec618e..0000000 --- a/I. DirectedSmallMoleculesNetwork (DSMN)/extracting protein titles and identifiers for metabolic reactions.rq +++ /dev/null @@ -1,24 +0,0 @@ -### Part 1: ### -SELECT DISTINCT ?interaction ?sourceDb ?targetDb ?proteinDBWPs ?proteinName -WHERE { -?pathway a wp:Pathway ; -wp:ontologyTag cur:AnalysisCollection ; -wp:organismName "Homo sapiens"; -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 . - -### Part 2: ### -?interactions2 dcterms:isPartOf ?pathway; - a wp:Catalysis; - wp:source ?sources2; - wp:target ?interaction . -OPTIONAL{?sources2 wp:bdbEnsembl ?proteinDBWPs}. -OPTIONAL{?sources2 rdfs:label ?proteinName} . -} diff --git a/README.md b/README.md index fa4c7c2..8e7f04e 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,7 @@ -# SPARQLQueries +# SPARQLQueries Examples -Queries for the [WikiPathways Snorql UI](http://sparql.wikipathways.org/) automated loading +Queries for the [PlantMetWiki SNORQL UI (SPARQL Explorer)](https://plantmetwiki.bioinformatics.nl/) automated loading + +## License + +[ GNU GENERAL PUBLIC LICENSE](LICENSE) \ No newline at end of file