Review Comment:
The document has greatly improved in both presentation and form.
It no longer looks like a draft and many references (to figures, missing sections and bibliography) in the text have been corrected, as also reported by the authors in their letter.
In general, it seems that the authors provide more justification of the reasoning and narrative. This helps possible readers.
The section entitled "Scope of process ontology survey", which responds to my earlier comment on the introduction of a methodology for the survey, although not a true methodology in my opinion, clarifies aspects that were previously not at all clear.
In this sense I am not fully convinced this paper can be classified as a survey. I mean, surely there is an analysis of the state of the art but this is in function of what is required in OBO community with then a proposal to fill in the gap. It is probably a normal paper with an extensive “related work” section! But this is my personal opinion.
In general, I think the paper targets principally the OBO community although a few state-of-the-art W3C OWL ontologies are also discussed. This reduces the possible audience in my opinion; however, the paper is in scope of the special issue of the journal, as also highlighted in my previous review.
I noticed that the semantic issues I reported in my previous review about the use of the OWL-Time ontology have been fixed.
There are still some minor changes that I suggest the authors to address before the final publication.
I report them below.
“A main objective of this gap analysis work
is to provide recommendations for a generic
process modelling framework…”—> I would rather say: “A main objective of the gap analysis work we propose in this paper is to provide recommendations for a generic process modelling framework…”
“We aim primarily to review current OWL ontologies that have object properties and classes needed for an OBO process model “—> I would rather say “We aim primarily to review state of the art OWL ontologies that…..”. “Current” sounds strange to me in this sentence.
This sentence is difficult to read “We focus on comparing entities involved in
temporal, part-hood, input and output, and participant / actor, and process dependencies which are required to model food processing and more general lab or manufacturing protocols sufficiently. “. I would revise it in the following way: “We focus on comparing both entities involved in temporal, part-hood, input/output and participant /actor, and process dependencies which are required to sufficiently model food processing and more general lab or manufacturing protocols”.
“These entities can then be added-to” —> “These entities can then be added to”
“and finally touch on Schema.org’s recipe related model as it has a number of process related elements. “ —> I would rather say “and finally we discuss about Schema.org’s recipe model as it has a number of process related elements”.
This sentence is not very clear to me “They use what appear to be provisional recipe model term identifiers that are ideally replaced by our recommended term’s identifiers as they are finalized.” What does it mean “as they are finalised”? Please better specify it.
“However, SKOS provides a looser logical framework than what we seek
to utilize in OWL (there is no way to express compound term axioms for example)[20], so it was not reviewed ” —> I guess that here you mean that controlled vocabularies modelled through the use of SKOS have not been considered in your gap analysis. If so, I would write it in this way.
“We were unable to source and review the FTTO ontology directly” —> why? Please provide a motivation.
The order of figure 10 and 11 must be re-considered: before figure 10 and after figure 11. Pay also attention to the text: if current figure 10 comes after, rename the caption in figure 11.
“An observation: As a noun, an observation (or “result” in SOSA, rather than SOSA’s “Observation” activity) is a data structure output of an invasive or non-invasive observation process effectively at an instant or duration of time” (page 13) —> I would not introduce such a level of detail of SOSA in this point of the paper. SOSA is explained at page 21 so this part can be understood only by people who really know very well the different semantic shadows of that model. I would simply avoid the sentence between brackets “( or “result” in SOSA, rather than SOSA’s “Observation” activity)”.
In essence I would rephrase it as follows: “As a noun, an observation is intended as an output data structure, not an activity, from an invasive or non-invasive observation process in an instant or duration of time.”
“with some provisios” —> should be “provisions”.
“This assumes a sensor only outputs Observations - if a sensor also outputs other types of things, then the object must also be filtered.” —> could you please write an example of “other types of things”? Because a sensor typically senses something it observes from my point of view.
“Observation: A data item which is the output of an observation process, and which has measures as components.” —> why do not you call it ObservationOuput? This would avoid confusion with the discussion about SOSA/SSN’s entities that identifies an Observation as an activity (BTW: this is related to the above discussion about SOSA).
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