Editors should edit references-edit.omn - then use the Makefile to generate references.owl
All documentation should be in markdown (md) format. In particular, "ontology markdown" (OMD), an extension of markdown.
With OMD, ontology classes are written as their labels encloses in single backticks. These are then converted to markdown URL syntax yielding:
[LABEL](http://purl.obolibrary.org/obo/ID)
The editors references file is in Manchester syntax (OMN) and can be edited in Protege, or edited directly in a text editor - there is an emacs mode in this directory.