This is a review of What is an upper level ontology?

In this article, Robert nicely covers the different aspects that upper level ontologies need to consider to prescribe a coherent view of the world for its adopters.

Here are some specific comments that need to be addressed:

1. Instead of using electron as an example, i would use something more concrete – like a  car.

2. Explain the notation for ” )1,2)”

3. Elaborate on abstract entities – why are these important, and give some examples.

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 ….”

Upper Level Ontologies

References to ontologies which use the upper level ontologies cited BFO, DOLCE etc would be useful, as would some examples of ontologies that use these, and the differences between them. A reference to a review article would suffice.

This is not a comprehensive list of upper level ontologies, SUMO and BioTOP could be added, or some statement that there are others.

Some critique of available upper level ontologies would  help the user – there are several, why are they different, what is their philosophical perspective?

Upper level ontologies are not necessarily stable, specifically BFO has changed a lot during the development of OBI. Some discussion of the consequences and process of this would be useful.

There are unsolved problems with upper level ontologies, representation of numbers, temporal representation, etc . A list of these problems would help readers understand that this a discursive field, with no single truth, rather current prevailing opinion

What are the overheads of using an upper level ontology vs. the benefits. GO was built initially without this, does it matter, should GO be refactored to fit BFO?

This may not be the most relevant place, but relations also provide some of the structure needed to integrate ontologies, so some reference to the relations ontology and RO2 would be useful.

Acknowledgements

This paper is an open access work distributed under the terms of the Creative Commons Attribution License 3.0 (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided that the original author and source are attributed.

The paper and its publication environment form part of the work of the Ontogenesis Network, supported by EPSRC grant EP/E021352/1.