general_ontofox.txt

[URI of the OWL(RDF/XML) output file]
http://purl.obolibrary.org/obo/ro_example/imports/general_import.owl

[Source ontology]
BFO

[Low level source term URIs] 
http://purl.obolibrary.org/obo/BFO_0000001
includeAllChildren


[Top level source term URIs and target direct superclass URIs]
http://purl.obolibrary.org/obo/BFO_0000001

[Source term retrieval setting]
includeAllIntermediates

[Source annotation URIs]
includeAllAxiomsRecursively

###########################################


[Source ontology]
OBI

[Low level source term URIs] 
http://purl.obolibrary.org/obo/OBI_0000070 # Assay
# insulin concentration measurement assay
# insulin concentration measurement data item

http://purl.obolibrary.org/obo/IAO_0000136 # is about
http://purl.obolibrary.org/obo/OBI_0000295 # is specified input of
http://purl.obolibrary.org/obo/OBI_0000312 # is specified output of

[Top level source term URIs and target direct superclass URIs]
http://purl.obolibrary.org/obo/BFO_0000001

[Source term retrieval setting]
includeAllIntermediates

[Source annotation URIs]
includeAllAxiomsRecursively


###########################################

[Source ontology]
PATO

[Low level source term URIs]
http://purl.obolibrary.org/obo/PATO_0001334 # diameter

[Top level source term URIs and target direct superclass URIs]
http://purl.obolibrary.org/obo/PATO_0000001

[Source term retrieval setting]
includeAllIntermediates

[Source annotation URIs]
includeAllAxioms


###########################################

[Source ontology]
CHEBI

[Low level source term URIs]
http://purl.obolibrary.org/obo/CHEBI_145810 #insulin

[Top level source term URIs and target direct superclass URIs]
http://purl.obolibrary.org/obo/CHEBI_24431

[Source term retrieval setting]
includeAllIntermediates

[Source annotation URIs]
includeAllAxioms
#includeAllAxiomsRecursively #### SUPER SLOW WITH THIS IN PROTEGE?

###########################################

[Source ontology]
UBERON

[Low level source term URIs]
http://purl.obolibrary.org/obo/UBERON_0001981 # blood vessel
http://purl.obolibrary.org/obo/UBERON_0000178 # blood

[Top level source term URIs and target direct superclass URIs]
http://purl.obolibrary.org/obo/UBERON_0001062 # anatomical entity

[Source term retrieval setting]
includeAllIntermediates

[Source annotation URIs]
includeAllAxioms

###########################################

[Source ontology]
OBA

[Low level source term URIs]
http://purl.obolibrary.org/obo/OBA_0000183 # blood vessel diameter

[Top level source term URIs and target direct superclass URIs]
http://purl.obolibrary.org/obo/PATO_0000001 # Quality

[Source term retrieval setting]
includeAllIntermediates

[Source annotation URIs]
includeAllAxioms

###########################################

[Source ontology]
GO

[Low level source term URIs]
http://purl.obolibrary.org/obo/GO_0038023 # signaling receptor activity
#http://purl.obolibrary.org/obo/GO_0004872 # Receptor activity
http://purl.obolibrary.org/obo/GO_0016301 # Kinase activity
http://purl.obolibrary.org/obo/GO_0042310 # Vasoconstriction

[Top level source term URIs and target direct superclass URIs]
http://purl.obolibrary.org/obo/GO_0003674 # molecular function
http://purl.obolibrary.org/obo/GO_0008150 # biological process

[Source term retrieval setting]
includeAllIntermediates

[Source annotation URIs]
includeAllAxioms

###########################################

[Source ontology]
MONDO

[Low level source term URIs]
http://purl.obolibrary.org/obo/MONDO_0005266 # diabetic retinopathy

[Top level source term URIs and target direct superclass URIs]
owl:Thing

[Source term retrieval setting]
includeAllIntermediates

[Source annotation URIs]
includeAllAxioms

###########################################

[Source ontology]
HP

[Low level source term URIs]
http://purl.obolibrary.org/obo/HP_0005308 # Pulmonary artery vasoconstriction

[Top level source term URIs and target direct superclass URIs]
owl:Thing

[Source term retrieval setting]
includeAllIntermediates

[Source annotation URIs]
#includeAllAxiomsRecursively ###### THIS CREATES A PROBLEM - JAVA STACK ERROR
includeAllAxioms

###########################################

[Source ontology]
RO

[Low level source term URIs]
http://purl.obolibrary.org/obo/RO_0001025 #located in
http://purl.obolibrary.org/obo/RO_0002211 #regulates
http://purl.obolibrary.org/obo/RO_0002200 #has phenotype
http://purl.obolibrary.org/obo/BFO_0000050 #part of
http://purl.obolibrary.org/obo/RO_0002233 #has input
http://purl.obolibrary.org/obo/RO_0002411 #causally upstream of
# http://purl.obolibrary.org/obo/RO_0000052 #inheres in
http://purl.obolibrary.org/obo/RO_0000080 #quality of

[Top level source term URIs and target direct superclass URIs]


[Source term retrieval setting]
includeAllIntermediates

[Source annotation URIs]
includeAllAxioms