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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.
lmdb
> - get_geno("BXD") - Get genotypes for a group.
lmdb
> - 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.
NA
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