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

In AtlasRDF: Gene Expression Atlas query and gene set enrichment package.

Description

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.

Usage

    getOntologyMappings(searchuri, endpoint = "http://www.ebi.ac.uk/rdf/services/atlas/sparql")

Arguments

searchuri	The ontology class URI for which mappings to EFO are required.
endpoint	SPARQL endpoint to query data from. Default value is the live Atlas SPARQL endpoint but this can be overidden.

Value

List of EFO URI(s) to which the class maps

Author(s)

James Malone, Simon Jupp

References

NCBO BioPortal - http://bioportal.bioontology.org/

Examples

###find mappings in EFO from  <http://purl.bioontology.org/ontology/SNOMEDCT/87163000>  (leukemia in snomed)
#getOntologyMappings("<http://purl.bioontology.org/ontology/SNOMEDCT/87163000>")
  

Example output

Loading required package: hash
hash-3.0.1 provided by Decision Patterns

Loading required package: SPARQL
Loading required package: XML
Loading required package: RCurl
Loading required package: bitops

AtlasRDF documentation built on Nov. 17, 2017, 9:33 a.m.