Add SPARQL instructions by Bonz

1 files changed, 139 insertions, 0 deletions

diff --git a/api/sparql-endpoint.md b/api/sparql-endpoint.md
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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.