These are some OBO Foundry ontologies that can be used with the Nexus-PORTAL-DOORS ontologies.
As of 2017-07-31, they are available at the OBO Foundry web site:
http://www.obofoundry.org/

foundational ontology:
Basic Formal Ontology
http://www.obofoundry.org/ontology/bfo.html
Relations Ontology
http://www.obofoundry.org/ontology/ro.html

spacial relationships:
Biological Spatial Ontology
http://www.obofoundry.org/ontology/bspo.html

mathematics:
Ontology of Biological and Clinical Statistics
http://www.obofoundry.org/ontology/obcs.html
The Statistical Methods Ontology
http://www.obofoundry.org/ontology/stato.html

science methodology:
Ontology for Biomedical Investigations
http://www.obofoundry.org/ontology/obi.html
Evidence ontology
http://www.obofoundry.org/ontology/eco.html

development:
Human Developmental Stages
http://www.obofoundry.org/ontology/hsapdv.html

behavior:
Neuro Behavior Ontology
http://www.obofoundry.org/ontology/nbo.html

diseases:
Human Disease Ontology
http://www.obofoundry.org/ontology/doid.html
Symptom Ontology
http://www.obofoundry.org/ontology/symp.html

software/data management:
Information Artifact Ontology
http://www.obofoundry.org/ontology/iao.html
The Data Use Ontology
http://www.obofoundry.org/ontology/duo.html