master/ldif/examples/life-science/mappings/ALL-to-Wiki.r2r.ttl
Commiter: Andrea Matteini
Author: Andrea Matteini
Revision: 67000aced3
File Size: 25.3 KB
(September 29, 2011 10:32 UTC) 8 months ago
updated documentation
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@prefix r2r: <http://www4.wiwiss.fu-berlin.de/bizer/r2r/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix mp: <http://www.example.org/smw-lde/smwTransformations/> .
#####################################################################################################
# KEGG GENES mappings
#####################################################################################################
###
# Gene
###
mp:Gene
a r2r:ClassMapping;
r2r:prefixDefinitions """smwcat: <http://mywiki/resource/category/> .
smwprop: <http://mywiki/resource/property/> .
pathway: <http://wiking.vulcan.com/neurobase/kegg_pathway/resource/vocab/> .
genes: <http://wiking.vulcan.com/neurobase/kegg_genes/resource/vocab/> .
xsd: <http://www.w3.org/2001/XMLSchema#> .""";
r2r:sourcePattern "?SUBJ a genes:gene";
r2r:targetPattern "?SUBJ a smwcat:Gene";
.
# Properties of Gene
mp:GeneID
a r2r:PropertyMapping;
r2r:mappingRef mp:Gene;
r2r:sourcePattern "?SUBJ genes:GeneId ?x";
r2r:targetPattern "?SUBJ smwprop:KeggGeneId ?'x'^^xsd:string";
.
mp:GeneDefinition
a r2r:PropertyMapping;
r2r:mappingRef mp:Gene;
r2r:sourcePattern "?SUBJ genes:definition ?x";
r2r:targetPattern "?SUBJ smwprop:Description ?'x'^^xsd:string";
.
mp:GeneName
a r2r:PropertyMapping;
r2r:mappingRef mp:Gene;
r2r:sourcePattern "?SUBJ genes:name ?x";
r2r:targetPattern "?SUBJ smwprop:Label ?'x'^^xsd:string";
.
mp:hasPathway
a r2r:PropertyMapping;
r2r:mappingRef mp:Gene;
r2r:sourcePattern "?SUBJ genes:hasPathway ?x";
r2r:targetPattern "?SUBJ smwprop:IsInvolvedIn ?x . ?x smwprop:Involves ?SUBJ";
.
mp:hasDisease
a r2r:PropertyMapping;
r2r:mappingRef mp:Gene;
r2r:sourcePattern "?SUBJ genes:hasDisease ?x";
r2r:targetPattern "?SUBJ smwprop:Causes ?x . ?x smwprop:IsCausedBy ?SUBJ";
.
# external Links
mp:GeneLinkUniProt
a r2r:PropertyMapping;
r2r:mappingRef mp:Gene;
r2r:sourcePattern "?SUBJ genes:externalLink ?x";
r2r:transformation "?id = regexToList('UniProt:(.+)', ?x)";
r2r:targetPattern
"?SUBJ smwprop:UniprotId ?'id'^^xsd:string";
.
mp:GeneLinkMGI
a r2r:PropertyMapping;
r2r:mappingRef mp:Gene;
r2r:sourcePattern "?SUBJ genes:externalLink ?x";
r2r:transformation "?id = regexToList('MGI:(.+)', ?x)";
r2r:targetPattern
"?SUBJ smwprop:MgiMarkerAccessionId ?'id'^^xsd:string";
.
mp:GeneLinkEnsembl
a r2r:PropertyMapping;
r2r:mappingRef mp:Gene;
r2r:sourcePattern "?SUBJ genes:externalLink ?x";
r2r:transformation "?id = regexToList('Ensembl:(.+)', ?x)";
r2r:targetPattern
"?SUBJ smwprop:EnsemblId ?'id'^^xsd:string";
.
mp:GeneLinkHGNC
a r2r:PropertyMapping;
r2r:mappingRef mp:Gene;
r2r:sourcePattern "?SUBJ genes:externalLink ?x";
r2r:transformation "?id = regexToList('HGNC:(.+)', ?x)";
r2r:targetPattern
"?SUBJ smwprop:HGNCId ?'id'^^xsd:string";
.
mp:GeneLinkHPRD
a r2r:PropertyMapping;
r2r:mappingRef mp:Gene;
r2r:sourcePattern "?SUBJ genes:externalLink ?x";
r2r:transformation "?id = regexToList('HPRD:(.+)', ?x)";
r2r:targetPattern
"?SUBJ smwprop:HPRDId ?'id'^^xsd:string";
.
mp:GeneLinkNCBIGI
a r2r:PropertyMapping;
r2r:mappingRef mp:Gene;
r2r:sourcePattern "?SUBJ genes:externalLink ?x";
r2r:transformation "?id = regexToList('NCBI-GI:(.+)', ?x)";
r2r:targetPattern
"?SUBJ smwprop:NCBIGIId ?'id'^^xsd:string";
.
mp:GeneLinkNCBIGeneID
a r2r:PropertyMapping;
r2r:mappingRef mp:Gene;
r2r:sourcePattern "?SUBJ genes:externalLink ?x";
r2r:transformation "?id = regexToList('NCBI-GeneID:(.+)', ?x)";
r2r:targetPattern
"?SUBJ smwprop:NCBIGeneId ?'id'^^xsd:string";
.
mp:GeneLinkOMIM
a r2r:PropertyMapping;
r2r:mappingRef mp:Gene;
r2r:sourcePattern "?SUBJ genes:externalLink ?x";
r2r:transformation "?id = regexToList('OMIM:(.+)', ?x)";
r2r:targetPattern
"?SUBJ smwprop:OMIMId ?'id'^^xsd:string";
.
mp:GeneLinkIMGT
a r2r:PropertyMapping;
r2r:mappingRef mp:Gene;
r2r:sourcePattern "?SUBJ genes:externalLink ?x";
r2r:transformation "?id = regexToList('IMGT:(.+)', ?x)";
r2r:targetPattern
"?SUBJ smwprop:IMGTId ?'id'^^xsd:string";
.
###
# Disease
###
mp:Disease
a r2r:ClassMapping;
r2r:prefixDefinitions """smwcat: <http://mywiki/resource/category/> .
smwprop: <http://mywiki/resource/property/> .
pathway: <http://wiking.vulcan.com/neurobase/kegg_pathway/resource/vocab/> .
genes: <http://wiking.vulcan.com/neurobase/kegg_genes/resource/vocab/> .
xsd: <http://www.w3.org/2001/XMLSchema#> .""";
r2r:sourcePattern "?SUBJ a genes:disease";
r2r:targetPattern "?SUBJ a smwcat:Disease";
.
# Properties of Disease
mp:DiseaseID
a r2r:PropertyMapping;
r2r:mappingRef mp:Disease;
r2r:sourcePattern "?SUBJ genes:id ?x";
r2r:targetPattern "?SUBJ smwprop:KeggDiseaseId ?'x'^^xsd:string";
.
mp:DiseaseLabel
a r2r:PropertyMapping;
r2r:mappingRef mp:Disease;
r2r:sourcePattern "?SUBJ rdfs:label ?x";
r2r:targetPattern "?SUBJ smwprop:Label ?'x'^^xsd:string";
.
###
# Pathway
###
mp:Pathway
a r2r:ClassMapping;
r2r:prefixDefinitions """smwcat: <http://mywiki/resource/category/> .
smwprop: <http://mywiki/resource/property/> .
pathway: <http://wiking.vulcan.com/neurobase/kegg_pathway/resource/vocab/> .
genes: <http://wiking.vulcan.com/neurobase/kegg_genes/resource/vocab/> .
xsd: <http://www.w3.org/2001/XMLSchema#> .""";
r2r:sourcePattern "?SUBJ a genes:pathway";
r2r:targetPattern "?SUBJ a smwcat:Pathway";
.
# Properties of Pathway
mp:PathwayID
a r2r:PropertyMapping;
r2r:mappingRef mp:Pathway;
r2r:sourcePattern "?SUBJ genes:id ?x";
r2r:targetPattern "?SUBJ smwprop:KeggPathwayId ?'x'^^xsd:string";
.
mp:PathwayLabel
a r2r:PropertyMapping;
r2r:mappingRef mp:Pathway;
r2r:sourcePattern "?SUBJ rdfs:label ?x";
r2r:targetPattern "?SUBJ smwprop:Label ?'x'^^xsd:string";
.
#####################################################################################################
# ABA mappings
#####################################################################################################
###
# Gene
###
mp:GeneABA
a r2r:ClassMapping;
r2r:prefixDefinitions """smwcat: <http://mywiki/resource/category/> .
smwprop: <http://mywiki/resource/property/> .
aba: <http://brain-map.org/gene/0.1#> .
uniprot: <http://purl.uniprot.org/core/> .
skos: <http://www.w3.org/2004/02/skos/core#> .
rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
xsd: <http://www.w3.org/2001/XMLSchema#>""";
r2r:sourcePattern "?SUBJ a aba:gene";
r2r:targetPattern "?SUBJ a smwcat:Gene";
.
# Properties of Gene
mp:GeneidABA
a r2r:PropertyMapping;
r2r:mappingRef mp:GeneABA;
r2r:transformation "?newX = [2 < strlen(?x) ? ?x : list()]" ; # only values of len > 2 are mapped (because of empty strings)
r2r:sourcePattern "?SUBJ aba:geneid ?x";
r2r:targetPattern "?SUBJ smwprop:AbaGeneId ?'newX'^^xsd:string"; ###MER: actually we must translate from unsignedInt to string here
.
mp:EntrezgeneidABA
a r2r:PropertyMapping;
r2r:mappingRef mp:GeneABA;
r2r:transformation "?newX = [strlen(?x) > 2 ? ?x : list()]" ; # only values of len > 2 are mapped (because of empty strings)
r2r:sourcePattern "?SUBJ aba:entrezgeneid ?x";
r2r:targetPattern "?SUBJ smwprop:EntrezGeneId ?'newX'^^xsd:int"; ###MER: actually we must translate from int to string here
.
mp:GenenameABA
a r2r:PropertyMapping;
r2r:mappingRef mp:GeneABA;
r2r:sourcePattern "?SUBJ aba:genename ?x";
r2r:targetPattern "?SUBJ smwprop:Label ?'x'^^xsd:string";
.
mp:GenesymbolABA
a r2r:PropertyMapping;
r2r:mappingRef mp:GeneABA;
r2r:sourcePattern "?SUBJ aba:genesymbol ?x";
r2r:targetPattern "?SUBJ smwprop:GeneSymbol ?'x'^^xsd:string";
.
mp:MgimarkeraccessionidABA
a r2r:PropertyMapping;
r2r:mappingRef mp:GeneABA;
r2r:transformation "?newX = [strlen(?x) > 2 ? ?x : list()]" ; # only values of len > 2 are mapped (because of empty strings)
r2r:sourcePattern "?SUBJ aba:mgimarkeraccessionid ?x";
r2r:targetPattern "?SUBJ smwprop:MgiMarkerAccessionId ?'newX'^^xsd:string";
.
###
# GeneAlias
###
mp:GenealiasABA
a r2r:PropertyMapping;
r2r:mappingRef mp:GeneABA;
r2r:sourcePattern "?SUBJ aba:gene-aliases ?x . ?x aba:aliassymbol ?s";
r2r:targetPattern "?SUBJ smwprop:AlternativeLabel ?'s'^^xsd:string";
.
#####################################################################################################
# UNIPROT mappings
#####################################################################################################
# Uniprot:Gene => aba:Gene
mp:GeneUNIPROT
a r2r:ClassMapping;
r2r:prefixDefinitions """smwcat: <http://mywiki/resource/category/> .
smwprop: <http://mywiki/resource/property/> .
uniprot: <http://purl.uniprot.org/core/> .
skos: <http://www.w3.org/2004/02/skos/core#> .
rdfs: <http://www.w3.org/2000/01/rdf-schema#> .""";
r2r:sourcePattern "?SUBJ a uniprot:Gene";
r2r:targetPattern "?SUBJ a smwcat:Gene";
.
mp:GeneNameUNIPROT
a r2r:PropertyMapping;
r2r:mappingRef mp:GeneUNIPROT;
r2r:sourcePattern "?SUBJ skos:prefLabel ?o";
r2r:targetPattern "?SUBJ smwprop:GeneSymbol ?'o'^^xsd:string";
.
# Uniprot:Protein (encodedBy uniprot:Gene) -> rdfs:seeAlso | database = GeneID: http://purl.uniprot.org/geneid/XXXXX => Gene -> entrezgeneid = XXXXX
mp:EntrezGeneIdUNIPROT
a r2r:PropertyMapping;
r2r:mappingRef mp:GeneUNIPROT;
r2r:sourcePattern "?protein uniprot:encodedBy ?SUBJ . ?protein rdfs:seeAlso ?dbentry . ?dbentry uniprot:database 'GeneID'";
r2r:transformation "?id = regexToList('http://purl.uniprot.org/geneid/(.+)', ?dbentry)";
r2r:targetPattern "?SUBJ smwprop:EntrezGeneId ?'id'^^xsd:int";
.
# Uniprot:Protein (encodedBy uniprot:Gene) -> rdfs:seeAlso | database = MGI : http://purl.uniprot.org/mgi/XXXXX => Gene: mgimarkeraccessionid = MGI:XXXXX
mp:MGIMarkerAccessionIdUNIPROT
a r2r:PropertyMapping;
r2r:mappingRef mp:GeneUNIPROT;
r2r:sourcePattern "?protein uniprot:encodedBy ?SUBJ . ?protein rdfs:seeAlso ?dbentry . ?dbentry uniprot:database 'MGI'";
r2r:transformation "?id = regexToList('http://purl.uniprot.org/mgi/(.+)', ?dbentry)";
r2r:targetPattern "?SUBJ smwprop:MgiMarkerAccessionId ?'id'^^xsd:string";
.
mp:UniprotIdUNIPROT
a r2r:PropertyMapping;
r2r:mappingRef mp:GeneUNIPROT;
r2r:sourcePattern "?protein uniprot:encodedBy ?SUBJ" ;
r2r:transformation "?id = regexToList('http://purl.uniprot.org/uniprot/(.+)', ?protein)";
r2r:targetPattern "?SUBJ smwprop:UniprotId ?'id'^^xsd:string";
.
# Uniprot:Protein (encodedBy uniprot:Gene) -> rdfs:seeAlso | database = KEGG: http://purl.uniprot.org/kegg/XXXXX => Gene -> smwprop:KeggGeneId = XXXXX
mp:KeggGeneIdUNIPROT
a r2r:PropertyMapping;
r2r:mappingRef mp:GeneUNIPROT;
r2r:sourcePattern "?protein uniprot:encodedBy ?SUBJ . ?protein rdfs:seeAlso ?dbentry . ?dbentry uniprot:database 'KEGG'";
r2r:transformation "?id = regexToList('http://purl.uniprot.org/kegg/(.+)', ?dbentry)";
r2r:targetPattern "?SUBJ smwprop:KeggGeneId ?'id'^^xsd:string";
.
#####################################################################################################
# PHARMGKB mappings
#####################################################################################################
###
# Pathway
###
mp:PathwayPHARMGKB
a r2r:ClassMapping;
r2r:prefixDefinitions """smwcat: <http://mywiki/resource/category/> .
smwprop: <http://mywiki/resource/property/> .
pharmgkb: <http://chem2bio2rdf.org/pharmgkb/resource/> .
xsd: <http://www.w3.org/2001/XMLSchema#> .""";
r2r:sourcePattern "?SUBJ a pharmgkb:PharmGKB_Pathways";
r2r:targetPattern "?SUBJ a smwcat:Pathway";
.
# Properties of Pathway
mp:PathwayIDPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:PathwayPHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:PharmGKB_Accession_Id ?x";
r2r:targetPattern "?SUBJ smwprop:PharmGKBId ?'x'^^xsd:string";
.
mp:PathwayLabelPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:PathwayPHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:Name ?x";
r2r:targetPattern "?SUBJ smwprop:Label ?'x'^^xsd:string";
.
mp:PathwayHasDiseasePHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:PathwayPHARMGKB;
r2r:sourcePattern """?rel rdf:type pharmgkb:PharmGKB_Relationships .
?rel pharmgkb:Related_Pathways ?SUBJ .
?rel pharmgkb:c2b2r_Related_Diseases ?x""";
r2r:targetPattern "?SUBJ smwprop:IsDisruptedBy ?x";
.
mp:PathwayHasDrugPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:PathwayPHARMGKB;
r2r:sourcePattern """?rel rdf:type pharmgkb:PharmGKB_Relationships .
?rel pharmgkb:Related_Pathways ?SUBJ .
?rel pharmgkb:Related_Drugs ?x""";
r2r:targetPattern "?SUBJ smwprop:IsTargetedBy ?x";
.
mp:PathwayHasGenePHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:PathwayPHARMGKB;
r2r:sourcePattern """?rel rdf:type pharmgkb:PharmGKB_Relationships .
?rel pharmgkb:Related_Pathways ?SUBJ .
?rel pharmgkb:Related_Genes ?x""";
r2r:targetPattern "?SUBJ smwprop:Involves ?x";
.
###
# Disease
###
mp:DiseasePHARMGKB
a r2r:ClassMapping;
r2r:prefixDefinitions """smwcat: <http://mywiki/resource/category/> .
smwprop: <http://mywiki/resource/property/> .
pharmgkb: <http://chem2bio2rdf.org/pharmgkb/resource/> .
xsd: <http://www.w3.org/2001/XMLSchema#> .""";
r2r:sourcePattern "?SUBJ a pharmgkb:PharmGKB_Diseases";
r2r:targetPattern "?SUBJ a smwcat:Disease";
.
# Properties of Disease
mp:DiseaseIDPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:DiseasePHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:PharmGKB_Accession_Id ?x";
r2r:targetPattern "?SUBJ smwprop:PharmGKBId ?'x'^^xsd:string";
.
mp:DiseaseMeSHIDPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:DiseasePHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:MeSH_Id ?x";
r2r:targetPattern "?SUBJ smwprop:MeSHId ?'x'^^xsd:string";
.
mp:DiseaseLabelPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:DiseasePHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:Name ?x";
r2r:targetPattern "?SUBJ smwprop:Label ?'x'^^xsd:string";
.
# FIXME doesn't work
mp:DiseaseAlternativeLabelPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:DiseasePHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:Alternate_Names ?x";
r2r:transformation """?labels = itRegexToList('"(.+?)"', ?x)""";
r2r:targetPattern "?SUBJ smwprop:AlternativeLabel ?'labels'^^xsd:string";
.
mp:DiseaseHasPathwayPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:DiseasePHARMGKB;
r2r:sourcePattern """?rel rdf:type pharmgkb:PharmGKB_Relationships .
?rel pharmgkb:c2b2r_Related_Diseases ?SUBJ .
?rel pharmgkb:Related_Pathways ?x""";
r2r:targetPattern "?SUBJ smwprop:Disrupts ?x";
.
mp:DiseaseHasDrugPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:DiseasePHARMGKB;
r2r:sourcePattern """?rel rdf:type pharmgkb:PharmGKB_Relationships .
?rel pharmgkb:c2b2r_Related_Diseases ?SUBJ .
?rel pharmgkb:Related_Drugs ?x""";
r2r:targetPattern "?SUBJ smwprop:IsTreatedBy ?x";
.
mp:DiseaseHasGenePHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:DiseasePHARMGKB;
r2r:sourcePattern """?rel rdf:type pharmgkb:PharmGKB_Relationships .
?rel pharmgkb:c2b2r_Related_Diseases ?SUBJ .
?rel pharmgkb:Related_Genes ?x""";
r2r:targetPattern "?SUBJ smwprop:IsCausedBy ?x";
.
###
# Drug
###
mp:DrugPHARMGKB
a r2r:ClassMapping;
r2r:prefixDefinitions """smwcat: <http://mywiki/resource/category/> .
smwprop: <http://mywiki/resource/property/> .
pharmgkb: <http://chem2bio2rdf.org/pharmgkb/resource/> .
xsd: <http://www.w3.org/2001/XMLSchema#> .""";
r2r:sourcePattern "?SUBJ a pharmgkb:pharmGKB_Drugs";
r2r:targetPattern "?SUBJ a smwcat:Drug";
.
# Properties of Drug
mp:DrugIDPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:DrugPHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:PharmGKB_Accession_Id ?x";
r2r:targetPattern "?SUBJ smwprop:PharmGKBId ?'x'^^xsd:string";
.
# Properties of Drug
mp:DrugDrugbankIDPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:DrugPHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:DrugBank_Id ?x";
r2r:transformation "?id = regexToList('http://chem2bio2rdf.org/drugbank/resource/drugbank_drug/(.+?)', ?x)";
r2r:targetPattern "?SUBJ smwprop:DrugBankId ?'id'^^xsd:string";
.
mp:DrugLabelPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:DrugPHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:Name ?x";
r2r:targetPattern "?SUBJ smwprop:Label ?'x'^^xsd:string";
.
# FIXME doesn't work
mp:DrugAlternativeLabelPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:DrugPHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:Alternate_Names ?x";
r2r:transformation """?labels = itRegexToList('"(.+?)"', ?x)""";
r2r:targetPattern "?SUBJ smwprop:AlternativeLabel ?'labels'^^xsd:string";
.
mp:DrugHasPathwayPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:DrugPHARMGKB;
r2r:sourcePattern """?rel rdf:type pharmgkb:PharmGKB_Relationships .
?rel pharmgkb:Related_Drugs ?SUBJ .
?rel pharmgkb:Related_Pathways ?x""";
r2r:targetPattern "?SUBJ smwprop:Targets ?x";
.
mp:DrugHasDiseasePHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:DrugPHARMGKB;
r2r:sourcePattern """?rel rdf:type pharmgkb:PharmGKB_Relationships .
?rel pharmgkb:Related_Drugs ?SUBJ .
?rel pharmgkb:c2b2r_Related_Diseases ?x""";
r2r:targetPattern "?SUBJ smwprop:Treats ?x";
.
mp:DrugHasGenePHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:DrugPHARMGKB;
r2r:sourcePattern """?rel rdf:type pharmgkb:PharmGKB_Relationships .
?rel pharmgkb:Related_Drugs ?SUBJ .
?rel pharmgkb:Related_Genes ?x""";
r2r:targetPattern "?SUBJ smwprop:Targets ?x";
.
# skipped: SMILES, Type
###
# Gene
###
mp:GenePHARMGKB
a r2r:ClassMapping;
r2r:prefixDefinitions """smwcat: <http://mywiki/resource/category/> .
smwprop: <http://mywiki/resource/property/> .
pharmgkb: <http://chem2bio2rdf.org/pharmgkb/resource/> .
xsd: <http://www.w3.org/2001/XMLSchema#> .""";
r2r:sourcePattern "?SUBJ a pharmgkb:PharmGKB_Genes";
r2r:targetPattern "?SUBJ a smwcat:Gene";
.
# Properties of Gene
mp:GeneIDPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:GenePHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:PharmGKB_Accession_Id ?x";
r2r:targetPattern "?SUBJ smwprop:PharmGKBId ?'x'^^xsd:string";
.
mp:GeneLabelPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:GenePHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:Name ?x";
r2r:targetPattern "?SUBJ smwprop:Label ?'x'^^xsd:string";
.
mp:GeneEntrezGeneIDPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:GenePHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:Entrez_Id ?x";
r2r:transformation "?id = regexToList('http://bio2rdf.org/geneid:(.+?)', ?x)";
r2r:targetPattern "?SUBJ smwprop:EntrezGeneId ?'id'^^xsd:int";
.
mp:GeneSymbolPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:GenePHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:Symbol ?x";
r2r:transformation "?id = regexToList('http://chem2bio2rdf.org/uniprot/resource/gene/(.+?)', ?x)";
r2r:targetPattern "?SUBJ smwprop:GeneSymbol ?'id'^^xsd:string";
.
# TBD
mp:GeneAlternativeSymbolsPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:GenePHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:Alternate_Symbols ?x";
r2r:transformation """?labels = itRegexToList('"(.+?)"', ?x)""";
r2r:targetPattern "?SUBJ smwprop:AlternativeLabel ?'labels'^^xsd:string";
.
# FIXME doesn't work
mp:GeneAlternativeLabelPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:GenePHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:Alternate_Names ?x";
r2r:transformation """?labels = itRegexToList('"(.+?)"', ?x)""";
r2r:targetPattern "?SUBJ smwprop:AlternativeLabel ?'labels'^^xsd:string";
.
mp:GeneUniProtIDPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:GenePHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:UniProt_Id ?x";
r2r:transformation "?id = regexToList('http://chem2bio2rdf.org/uniprot/resource/uniprot/(.+?)', ?x)";
r2r:targetPattern "?SUBJ smwprop:UniprotId ?'id'^^xsd:string";
.
mp:GeneEnsemblIDPHARMGKB
a r2r:PropertyMapping;
r2r:mappingRef mp:GenePHARMGKB;
r2r:sourcePattern "?SUBJ pharmgkb:Ensembl_Id ?x";
r2r:targetPattern "?SUBJ smwprop:EnsemblId ?'x'^^xsd:string";
.
#####################################################################################################
# KEGGPATH mappings
#####################################################################################################
###
# Pathway
###
mp:PathwayKEGGPATH
a r2r:ClassMapping;
r2r:prefixDefinitions """smwcat: <http://mywiki/resource/category/> .
smwprop: <http://mywiki/resource/property/> .
pathway: <http://wiking.vulcan.com/neurobase/kegg_pathway/resource/vocab/> .
xsd: <http://www.w3.org/2001/XMLSchema#> .""";
r2r:sourcePattern "?SUBJ a pathway:pathway";
r2r:targetPattern "?SUBJ a smwcat:Pathway";
.
# Properties of Pathway
mp:PathwayIDKEGGPATH
a r2r:PropertyMapping;
r2r:mappingRef mp:PathwayKEGGPATH;
r2r:sourcePattern "?SUBJ pathway:id ?x";
r2r:targetPattern "?SUBJ smwprop:KeggPathwayId ?x";
.
mp:PathwayLabelKEGGPATH
a r2r:PropertyMapping;
r2r:mappingRef mp:PathwayKEGGPATH;
r2r:sourcePattern "?SUBJ rdfs:label ?x";
r2r:targetPattern "?SUBJ smwprop:Label ?x";
.
mp:PathwayDescriptionKEGGPATH
a r2r:PropertyMapping;
r2r:mappingRef mp:PathwayKEGGPATH;
r2r:sourcePattern "?SUBJ pathway:description ?x";
r2r:targetPattern "?SUBJ smwprop:Description ?'x'^^xsd:string";
.
mp:PathwayHasDiseaseKEGGPATH
a r2r:PropertyMapping;
r2r:mappingRef mp:PathwayKEGGPATH;
r2r:sourcePattern "?SUBJ pathway:hasDisease ?x";
r2r:targetPattern "?SUBJ smwprop:IsDisruptedBy ?x . ?x smwprop:Disrupts ?SUBJ";
.
mp:PathwayHasDrugKEGGPATH
a r2r:PropertyMapping;
r2r:mappingRef mp:PathwayKEGGPATH;
r2r:sourcePattern "?SUBJ pathway:hasDrug ?x";
r2r:targetPattern "?x smwprop:IsTargetedBy ?SUBJ . ?x smwprop:Targets ?SUBJ";
.
mp:PathwayHasGeneKEGGPATH
a r2r:PropertyMapping;
r2r:mappingRef mp:PathwayKEGGPATH;
r2r:sourcePattern "?SUBJ pathway:hasGene ?x";
r2r:targetPattern "?SUBJ smwprop:Involves ?x . ?x smwprop:IsInvolvedIn ?SUBJ";
.
###
# Disease
###
mp:DiseaseKEGGPATH
a r2r:ClassMapping;
r2r:prefixDefinitions """smwcat: <http://mywiki/resource/category/> .
smwprop: <http://mywiki/resource/property/> .
pathway: <http://wiking.vulcan.com/neurobase/kegg_pathway/resource/vocab/> .
xsd: <http://www.w3.org/2001/XMLSchema#> .""";
r2r:sourcePattern "?SUBJ a pathway:disease";
r2r:targetPattern "?SUBJ a smwcat:Disease";
.
# Properties of Disease
mp:DiseaseIDKEGGPATH
a r2r:PropertyMapping;
r2r:mappingRef mp:DiseaseKEGGPATH;
r2r:sourcePattern "?SUBJ pathway:id ?x";
r2r:targetPattern "?SUBJ smwprop:KeggDiseaseId ?'x'^^xsd:string";
.
mp:DiseaseLabelKEGGPATH
a r2r:PropertyMappingKEGGPATH;
r2r:mappingRef mp:Disease;
r2r:sourcePattern "?SUBJ rdfs:label ?x";
r2r:targetPattern "?SUBJ smwprop:Label ?'x'^^xsd:string";
.
###
# Drug
###
mp:DrugKEGGPATH
a r2r:ClassMapping;
r2r:prefixDefinitions """smwcat: <http://mywiki/resource/category/> .
smwprop: <http://mywiki/resource/property/> .
pathway: <http://wiking.vulcan.com/neurobase/kegg_pathway/resource/vocab/> .
xsd: <http://www.w3.org/2001/XMLSchema#> .""";
r2r:sourcePattern "?SUBJ a pathway:drug";
r2r:targetPattern "?SUBJ a smwcat:Drug";
.
# Properties of Drug
mp:DrugIDKEGGPATH
a r2r:PropertyMapping;
r2r:mappingRef mp:DrugKEGGPATH;
r2r:sourcePattern "?SUBJ pathway:id ?x";
r2r:targetPattern "?SUBJ smwprop:KeggDrugId ?'x'^^xsd:string";
.
mp:DrugLabelKEGGPATH
a r2r:PropertyMapping;
r2r:mappingRef mp:DrugKEGGPATH;
r2r:sourcePattern "?SUBJ rdfs:label ?x";
r2r:targetPattern "?SUBJ smwprop:Label ?'x'^^xsd:string";
.
###
# Gene
###
mp:GeneKEGGPATH
a r2r:ClassMapping;
r2r:prefixDefinitions """smwcat: <http://mywiki/resource/category/> .
smwprop: <http://mywiki/resource/property/> .
pathway: <http://wiking.vulcan.com/neurobase/kegg_pathway/resource/vocab/> .
xsd: <http://www.w3.org/2001/XMLSchema#> .""";
r2r:sourcePattern "?SUBJ a pathway:gene";
r2r:targetPattern "?SUBJ a smwcat:Gene";
.
# Properties of Gene
mp:GeneIDKEGGPATH
a r2r:PropertyMapping;
r2r:mappingRef mp:GeneKEGGPATH;
r2r:sourcePattern "?SUBJ pathway:id ?x";
r2r:targetPattern "?SUBJ smwprop:KeggGeneId ?'x'^^xsd:string";
.
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