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Diffstat (limited to 'api')
| -rw-r--r-- | api/sparql-endpoint.md | 139 |
1 files changed, 139 insertions, 0 deletions
diff --git a/api/sparql-endpoint.md b/api/sparql-endpoint.md new file mode 100644 index 0000000..fd3df3b --- /dev/null +++ b/api/sparql-endpoint.md @@ -0,0 +1,139 @@ +- 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. |