- list_species() - List available species.
PREFIX gn:
PREFIX gnc:
PREFIX owl:
PREFIX gnt:
PREFIX skos:
PREFIX rdf:
PREFIX rdfs:
PREFIX taxon:
SELECT DISTINCT * WHERE {
?s rdf:type gnc:species .
?s ?p ?o .
}
- list_groups("drosophila") - List available groups of datasets
PREFIX gn:
PREFIX gnc:
PREFIX owl:
PREFIX gnt:
PREFIX skos:
PREFIX rdf:
PREFIX rdfs:
PREFIX taxon:
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:
PREFIX foaf:
PREFIX gdmt:
PREFIX skos:
PREFIX geoSeries:
PREFIX gnt:
PREFIX gn:
PREFIX gnc:
PREFIX rdf:
PREFIX owl:
PREFIX rdfs:
PREFIX taxon:
PREFIX dct:
PREFIX 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:
PREFIX foaf:
PREFIX gdmt:
PREFIX skos:
PREFIX geoSeries:
PREFIX gnt:
PREFIX gn:
PREFIX gnc:
PREFIX rdf:
PREFIX owl:
PREFIX rdfs:
PREFIX taxon:
PREFIX dct:
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:
PREFIX foaf:
PREFIX gdmt:
PREFIX skos:
PREFIX geoSeries:
PREFIX gnt:
PREFIX gn:
PREFIX gnc:
PREFIX rdf:
PREFIX owl:
PREFIX rdfs:
PREFIX taxon:
PREFIX dct:
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:
PREFIX gn:
PREFIX owl:
PREFIX gnc:
PREFIX gnt:
PREFIX skos:
PREFIX rdf:
PREFIX rdfs:
PREFIX xsd:
PREFIX pubmed:
PREFIX 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.