getCvterms {celsius}R Documentation

Retrieve ontology term (aka CV term) data structures (lists) by query phrase

Description

Useful for searching ontologies by ontology term name

Usage

  lungTerms = getCvterms(celsiusObject, q="lung", db="MA");

Arguments

celsiusObject Provide a celsius server object with appropriate URLs
q Query phrase. Meta-character "*" may be used as a wildcard
db DBspace of CV to be queried, e.g. "GO" for Gene Ontology, "MA" for Mouse Adult Anatomy Ontology

Value

Returns a vector of lists. Each list corresponds to an ontology term, with attributes: * accession - ontology term accession, e.g. "MA:0000415" * name - ontology term name, e.g. "lung" * db - db of ontology term, e.g. "MA" * ontology - name of ontology, e.g. "Mouse_anatomy_by_time_xproduct"

Author(s)

Allen Day

Examples

#make a celsius instance
celsius = new( "celsiusServer",
  celsiusUrl="http://celsius.genomics.ctrl.ucla.edu" );

#get annotation term information
lungTerms = getCvterms( celsius, q = "lung", db = "MA" );
ovuTerms = getCvterms( celsius, q = "ovu*" );

[Package celsius version 1.0.7 Index]