This is a review of Reference and Application Ontologies.
This article describes what reference ontologies and application ontologies are, and how they can be used together. It is a well-written introduction to the subject. What follows are my suggestions for improvement.
In the first paragraph, it says both that application ontologies are for “domain specific use” and also used for modelling “cross-domain experiments”. While not necessarily at odds with each other, these two sentences may confuse readers.
In the last Background section, there is: “Finally reference ontologies do not necessarily contain sufficient combinations of classes (e.g. intersections or unions) to represent experimental data. For example information about a cell line includes a cell type and tissue from which it derives, and information about the individual from which tissue was obtained.” It is unclear why this exemplifies the sentence preceding it (the “Finally…” sentence). An additional sentence here explaining the link between them would be useful.
There is the phrase “(e.g. need an example)” in the second paragraph for the “Motivation…” section. I think the example is not there yet.
In the examples of application ontologies, the NIFSTD section would benefit from further structuring, as it is a little confusing as-is. I would suggest making a bulleted list containing paragraphs 2 and 3, and begin the first paragraph with “The NeuroInformatics Framework – NIF, formerly known as BIRN, is ….”