basecode.properties

# set to true to enable specific ontologies
load.diseaseOntology=false
load.fmaOntology=false
load.chebiOntology=false
load.cellTypeOntology=false
load.mouseDevelOntology=false
load.mammalPhenotypeOntology=false
load.humanPhenotypeOntology=false
load.obiOntology=false
load.seqOntology=false
load.medicOntology=false
load.nifstdOntology=false
load.experimentalFactorOntology=false
load.uberonOntology=false

# where possible, use URLs from http://www.obofoundry.org/
url.chebiOntology=http://purl.obolibrary.org/obo/chebi.owl
url.diseaseOntology=http://purl.obolibrary.org/obo/doid.owl
url.cellTypeOntology=http://purl.obolibrary.org/obo/cl.owl
url.mouseDevelOntology=http://purl.obolibrary.org/obo/emapa.owl
url.mammalPhenotypeOntology=http://purl.obolibrary.org/obo/mp.owl
url.humanPhenotypeOntology=http://purl.obolibrary.org/obo/hp.owl
url.seqOntology=http://purl.obolibrary.org/obo/so.owl
url.unitsOntology=http://purl.obolibrary.org/obo/uo.owl
# according to http://www.obofoundry.org/ontology/clo.html this "should" point to https://raw.githubusercontent.com/CLO-ontology/CLO/master/src/ontology/clo_merged.owl
url.cellLineOntology=http://purl.obolibrary.org/obo/clo.owl
# Uberon version without extensions: I think this is the right file from purl
url.uberonOntology=http://purl.obolibrary.org/obo/uberon.owl

# as recommended at https://www.ebi.ac.uk/efo/ (this has changed several times)
url.efOntology=https://www.ebi.ac.uk/efo/efo.owl
url.obiOntology=http://purl.obolibrary.org/obo/obi.owl

# no longer actively used.
url.fmaOntology=http://purl.obolibrary.org/obo/fma.owl

ontology.index.dir=
ontology.cache.dir=
ncbo.api.key=

rserve.start.command=
rlibpath=