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+- list_species() - List available species.
+
+ PREFIX gn: <http://genenetwork.org/id/>
+ PREFIX gnc: <http://genenetwork.org/category/>
+ PREFIX owl: <http://www.w3.org/2002/07/owl#>
+ PREFIX gnt: <http://genenetwork.org/term/>
+ PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+ PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+ PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
+
+ SELECT DISTINCT * WHERE {
+ ?s rdf:type gnc:species .
+ ?s ?p ?o .
+ }
+
+
+- list_groups("drosophila") - List available groups of datasets
+
+ PREFIX gn: <http://genenetwork.org/id/>
+ PREFIX gnc: <http://genenetwork.org/category/>
+ PREFIX owl: <http://www.w3.org/2002/07/owl#>
+ PREFIX gnt: <http://genenetwork.org/term/>
+ PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+ PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+ PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
+
+ SELECT ?inbredSet WHERE {
+ ?species rdf:type gnc:species .
+ ?species skos:altLabel "drosophila" .
+ ?inbredSet rdf:type gnc:inbredSet .
+ ?inbredSet gnt:belongsToSpecies ?species .
+ }
+
+
+- list_datasets("BXD") - List available datasets for a given group (here, "BXD").
+
+ PREFIX v: <http://www.w3.org/2006/vcard/ns#>
+ PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+ PREFIX gdmt: <http://vocab.fairdatacollective.org/gdmt/>
+ PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+ PREFIX geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>
+ PREFIX gnt: <http://genenetwork.org/term/>
+ PREFIX gn: <http://genenetwork.org/id/>
+ PREFIX gnc: <http://genenetwork.org/category/>
+ PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+ PREFIX owl: <http://www.w3.org/2002/07/owl#>
+ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+ PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
+ PREFIX dct: <http://purl.org/dc/terms/>
+ PREFIX gdmt: <http://vocab.fairdatacollective.org/gdmt/>
+
+ SELECT DISTINCT ?datasetName WHERE {
+ ?dataset rdf:type/rdfs:subClassOf gnc:dataset .
+ ?dataset rdfs:label ?datasetName .
+ ?dataset gnt:belongsToInbredSet ?inbredSet .
+ ?inbredSet skos:altLabel "BXD" .
+ }
+
+- info_dataset("CB_M_1004_P") - Get meta information about a data set.
+
+ PREFIX v: <http://www.w3.org/2006/vcard/ns#>
+ PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+ PREFIX gdmt: <http://vocab.fairdatacollective.org/gdmt/>
+ PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+ PREFIX geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>
+ PREFIX gnt: <http://genenetwork.org/term/>
+ PREFIX gn: <http://genenetwork.org/id/>
+ PREFIX gnc: <http://genenetwork.org/category/>
+ PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+ PREFIX owl: <http://www.w3.org/2002/07/owl#>
+ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+ PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
+ PREFIX dct: <http://purl.org/dc/terms/>
+
+ SELECT DISTINCT * WHERE {
+ ?s rdfs:label "CB_M_1004_P" .
+ ?s ?p ?o .
+ }
+
+
+- info_datasets("B6D2F2") - Get meta information about all data sets for a group.
+
+ PREFIX v: <http://www.w3.org/2006/vcard/ns#>
+ PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+ PREFIX gdmt: <http://vocab.fairdatacollective.org/gdmt/>
+ PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+ PREFIX geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>
+ PREFIX gnt: <http://genenetwork.org/term/>
+ PREFIX gn: <http://genenetwork.org/id/>
+ PREFIX gnc: <http://genenetwork.org/category/>
+ PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+ PREFIX owl: <http://www.w3.org/2002/07/owl#>
+ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+ PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
+ PREFIX dct: <http://purl.org/dc/terms/>
+
+ SELECT DISTINCT * WHERE {
+ ?s rdf:type/rdfs:subClassOf gnc:dataset .
+ ?s gnt:belongsToInbredSet ?inbredSet .
+ ?inbredSet skos:altLabel "B6D2F2" .
+ ?s ?p ?o .
+ }
+
+- info_pheno("BXD", "10038") - Get summary information for a phenotype
+
+ PREFIX dct: <http://purl.org/dc/terms/>
+ PREFIX gn: <http://genenetwork.org/id/>
+ PREFIX owl: <http://www.w3.org/2002/07/owl#>
+ PREFIX gnc: <http://genenetwork.org/category/>
+ PREFIX gnt: <http://genenetwork.org/terms/>
+ PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+ PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+ PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+ PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
+ PREFIX fabio: <http://purl.org/spar/fabio/>
+
+ SELECT DISTINCT * WHERE {
+ ?s rdf:type gnc:phenotype .
+ ?inbredSet skos:altLabel "BXD" .
+ ?s gnt:belongsToInbredSet ?inbredSet.
+ ?s gnt:traitName "10001" .
+ ?s ?p ?o .
+ OPTIONAL {
+ ?pub fabio:hasPubMedId ?pmid .
+ ?s dct:isReferencedBy ?pmid .
+ ?pub ?pubTerms ?pubResult .
+ }
+ }
+
+> - get_pheno("BXD", "10646") - Get phenotype values for a classical trait.
+
+> - get_geno("BXD") - Get genotypes for a group.
+
+> - run_gemma("BXDPublish", "10015") - Perform a genome scan with gemma
+> - run_rqtl("BXDPublish", "10015") - Perform a genome scan with R/qtl
+> - run_correlation("HC_M2_0606_P", "BXDPublish", "1427571_at") - Finds traits that are correlated with a given trait.