Food Process Ontology Requirements

Tracking #: 3096-4310

Damion Dooley
Magalie Weber
Liliana Ibanescu
Matthew Lange
Lauren Chan
Larisa Soldatova1
Chen Yang
Robert Warren
Cogan Shimizu
Hande Kucuk McGinty
William Hsiao

Responsible editor: 
Guest Editors Global Food System 2021

Submission type: 
Full Paper
People often value the sensual, celebratory, and health aspects of food, but behind this experience exists many other value-laden agricultural production, distribution, manufacturing, and physiological processes that support or undermine a healthy population and a sustainable future. The complexity of such processes is evident in both every-day food preparation of recipes and in industrial food manufacturing, packaging and storage, each of which depends critically on human or machine agents, chemical or organismal ingredient references, and the explicit instructions and implicit procedures held in formulations or recipes. An integrated ontology landscape does not yet exist to cover all the entities at work in this farm to fork journey. It seems necessary to construct such a vision by reusing expert-curated fit-to-purpose ontology subdomains and their relationship, material, and more abstract organization and role entities. The challenge is to make this merger be, by analogy, one language, rather than nouns and verbs from a dozen or more dialects which cannot be used directly in statements about some aspect of the farm to fork journey without expensive translation or substantial dialect education in order to understand a particular text or domain of knowledge. This work focuses on the ontology components - object and data properties and annotations - needed to model food processes or more general process modelling within the context of the Open Biological and Biomedical Ontology Foundry and congruent ontologies. Ideally these components can be brought together in a general process ontology that can be specialized not only for the food domain but for carrying out other protocols as well. Many operations involved in food identification, preparation, transportation and storage - shaking, boiling, mixing, freezing, labeling, shipping - are actually common to activities from manufacturing and laboratory work to local or home food preparation.
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Solicited Reviews:
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Review #1
Anonymous submitted on 24/May/2022
Minor Revision
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’s recipe related model‬ ‪as it has a number of process related‬ ‪elements. ‬“ —> I would rather say “and finally we discuss about’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).

Review #2
By Marco Brandizi submitted on 10/Jul/2022
Minor Revision
Review Comment:

In addition to what I wrote in my first review (reported below), the paper is now more readable and complete.

I only have one minor issue, see below.

I am really sorry for my very late answer, which depended on lost email messages on my side.

- Page 5, begin of 1.2:
[We target OBO because we favour OBO’s strategy ... and more emphasis on defining classes of entity at either end of an object property...]

Sorry, maybe it's me, but I can't follow the English in "defining classes of entity". Do you mean "entity classes", or "classes about entities"?

=== General comments from first review ===

The manuscript presents the main issues that occurs in modelling food processing with ontology engineering, with a discussion that focuses on recipe modelling.

Furthermore, the authors offer a survey of the state of the art regarding the topic, showing approaches and solutions adopted by existing ontologies for tackling the problem of food processing and the general problem of modelling planned and unplanned processes with computational ontologies. The text is very interesting and comprehensive, hence it is certainly worth a publication.