A Systematic Survey of Temporal Requirements of Bio-Health Ontologies

Tracking #: 2050-3263

Jared Leo
Nicolas Matentzoglu
Uli Sattler
Bijan Parsia

Responsible editor: 
Pascal Hitzler

Submission type: 
Full Paper
The Description Logic SROIQ(D), as the logical core of the W3C standard Web Ontology Language (OWL 2), is a widely used formalism for ontologies in the life sciences. Bio-health applications including healthcare and life science domains commonly have a need to represent temporal information such as medication frequency or stage-based development. Different classes of temporal phenomena may generate different sorts of requirements on SROIQ(D) or extensions of SROIQ(D). In this paper, we deliver the first precise investigation into identifying exactly what kinds of temporal requirements are most important for bio-health ontologies. We conduct an empirical investigation of the OBO Foundry using a bespoke methodological approach by searching each of its ontologies for specific temporal features and go on to calculate the importance of these features using a sophisticated set of measures. By doing so, we derive a formal set of Temporal Requirements that act as a set of guidelines which a language or logical extension to OWL 2 would need to satisfy in order to meet the temporal requirements of bio-health ontologies.
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Solicited Reviews:
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Review #1
Anonymous submitted on 07/Jan/2019
Review Comment:

I believe the authors have done a good job of addressing the comments of the previous reviews, and overall the additions make the manuscript more clear, in particular the addition of several example of temporal attributes. A couple of minor comments:

- on page 10, in the axiom listing I think 'p1' should be 'P1' (e.g. – P2 ⊑ ∃partOf.p1)
- 'Pareto' is inconsistently capitalized.

Review #2
Anonymous submitted on 07/Jan/2019
Minor Revision
Review Comment:

The reviewers largely responded satisfactorily to my concerns in the previous review.

% Minor Suggestions:
I would like paragraph 1 of section 3 to be a bit more verbose. For me, it was difficult to keep straight the relationships between the terms.
Make smartmatching a definition.
inconsistent sigfigs in results section

% Errata
Missing bold S in first axioms of first example.
back tick used instead of apostrophe next to the \exists
Fig 1. caption, X=class name should be removed
(continuants (c) extra forward paren
t+2 not in math mode section 3.2
capitalization not consistent with P1, etc. maybe? Same with o1, following. unless it's supposed to be instance vs class distinction?
in \exists immediateTransformationOf there is a weird kerning issue.
capital Pareto 4.3.1

Review #3
Anonymous submitted on 27/Jan/2019
Review Comment:

This manuscript was submitted as 'full paper' and should be reviewed along the usual dimensions for research contributions which include (1) originality, (2) significance of the results, and (3) quality of writing.

The authors have submitted a significantly improved paper. They have addressed the issues pointed out in my review (and also the other reviews). I recommend to accept the new version.