getOntologyMappings


        The ontology class URI for which mappings to EFO are required.
    

searchuri


        SPARQL endpoint to query data from. Default value is the live Atlas SPARQL endpoint but this can be overidden.     
    

endpoint


    Get mappings for a given class URI from an ontology other than EFO using the NCBO BioPortal. Function is useful for querying the Atlas RDF using your own ontology. 
    For instance, if you are using ICD-10 or SnoMed this function will enable you to extract any mappings to EFO, used to annotate the Atlas data, thereby enabling querying 
    by your ontology of interest. The returned EFO class should then be used to query Atlas using the other query functions.


Query the Gene Expression Atlas RDF data at the European Bioinformatics Institute using genes, experimental factors (such as disease, cell type, compound treatments), pathways and proteins. Also contains a function to perform an enrichment of your gene list across Experimental Factor Ontology (EFO) using the Atlas background set.

James Malone

AtlasRDF

Gene Expression Atlas query and gene set enrichment package.

getOntologyMappings function

The ontology class URI for which mappings to EFO are required.

SPARQL endpoint to query data from. Default value is the live Atlas SPARQL endpoint but this can be overidden.

Get mappings for a given class URI from an ontology other than EFO using the NCBO BioPortal. Function is useful for querying the Atlas RDF using your own ontology. 
    For instance, if you are using ICD-10 or SnoMed this function will enable you to extract any mappings to EFO, used to annotate the Atlas data, thereby enabling querying 
    by your ontology of interest. The returned EFO class should then be used to query Atlas using the other query functions.

getOntologyMappings: Get mappings for a given ontology class URI to EFO using the NCBO BioPortal

Description

Usage

Arguments

Value

References

Examples