corrections.ttl

# post-factum corrections to the underlying ontologies

@prefix bao:   <http://www.bioassayontology.org/bao#> .
@prefix bat:   <http://www.bioassayontology.org/bat#> .
@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl:   <http://www.w3.org/2002/07/owl#> .
@prefix obo:   <http://purl.obolibrary.org/obo/> .

# the 'bat:preferredParent' indicates that when two 'owl:equivalentClass' terms could be placed analogously
# in a hierarchy, the preferred one is used as the branch master; this occurs frequently when the BAO borrows
# terms from other ontologies (such as GO), which can get a bit messy

# biological process
obo:GO_0008150 a bat:preferredParent .
obo:GO_0008150 bat:finalLabel "biological process" .

# cellular component
obo:GO_0005575 a bat:preferredParent .
obo:GO_0005575 bat:finalLabel "cellular component" .

# molecular function
obo:GO_0003674 a bat:preferredParent .
obo:GO_0003674 bat:finalLabel "molecular function" .

# disease
obo:DOID_4 a bat:preferredParent .

# cell line cell
obo:CLO_0000001 a bat:preferredParent .
obo:CLO_0000001 owl:equivalentClass bao:BAO_0002931 .

# use the original UO units
bao:BAO_0000077 a bat:eliminated .
obo:UO_0000000 a bat:preferredParent .

# subclass breaking: the 'notSubClass' directive overrides a subclass that has been specified in one of the
# source ontologies, i.e. makes it as if it were not so, regardless of the order in which the ontologies were
# processed

# molecular function: subclassed from a weird singleton, for no apparent reason
# (but: it's rather difficult to disentangle because the BAO is rewriting a lot of it)
#obo:GO_0003674 rdfs:subClassOf bao:BAO_0003114 .
#obo:GO_0003674 bat:notSubClass bao:BAO_0003117 .
#bao:BAO_0003075 bat:notSubClass bao:BAO_0003117 .
#bao:BAO_0003117 bat:notSubClass bao:BAO_0003114 .