Review Comment:
The paper presents an analysis of some selected ontologies: some of them not born for the specific food domain (e.g., SSN/SOSA, OWL-TIme ontology), others with different objectives with respect to the needs of the food domain (e.g., PROV-O), and some more targeting the domain of analysis (e.g., OBO foundry ontologies). These ontologies are analysed with the goal of identifying elements that can be relevant for harmonising food processes modelling and in general processes modelling within OBO foundry ontologies. The authors conclude the analysis with a discussion, specifically related to food recipes, seen as food processes; a prototype with the FoodOn ontology is presented.
The paper has been classified as a survey paper that, according to the rules and guidelines of Semantic Web Journal are papers that should have the potential to become well-known, highest quality introductory and overview texts, and should be suitable as introductory text, targeting researchers, PhD students to get started on the covered topic.
From my perspective, the paper in its current form definitely lacks these elements and my overall judgement is reject.
I explain below the reasons for this evaluation by providing a first overall feedback on the paper and then detailed comments on specific sentences of the paper, that further justify my overall judgement.
In general the paper is in scope of the special issue and presents an interesting topic. However, a number of issues are highlighted in the following.
The paper seems a draft: number of sections highlighted in yellow, different occurrences of “figure X”, as a placeholder for including a figure reference, links to some web sites that seem once again placeholders for a successive inclusion in the bibliography. Many figures are included in the paper but they are never referenced in the text and so never explained.
There are sometimes bibliographic elements in red ([1]). There is the indication of some sections that are not part of the paper (e.g., “OWL reasoning in a process ontology”). The bibliography includes repeated numbering, probably due to some issues on exporting in PDF from a Microsoft Word document.
In addition, I have concerns regarding:
1) the survey analysis;
2) the overall narrative of the paper
3) some semantic modelling proposed in the paper
1) In particular, I believe the analysis, which should be the core of the paper, is not sufficiently clear and this limits the possibility for this paper to be “suitable as introductory text, targeting researchers, PhD students to get started on the covered topic.”, as required by the journal guidelines.
Section 2 starts the assessment of the state of the art but there is no a clear description of the methodology followed for the assessment. This is a crucial point: from my perspective, a survey paper should clearly explain the method that has been chosen for analysing specific works, with a dedicated section that for instance explains the different approaches to process modelling and the criteria of the analysis. The paper then should follow those criteria in the description of the state of the art, and in the comparative analysis. In addition, the paper is entitled “Food process ontology requirements” but these requirements, that probably are important to introduce the different criteria of the analysis, are briefly introduced as last section of the paper. This is quite weird.
In the conclusions, the authors summarise the work presented as “a gap analysis”, but to be honest I do not see a truly gap analysis, I just see some general descriptions of processes with some references to the OBO ontologies, and some ontologies such as OWL-Time that is definitely important but, I wouldn’t have categorised it as the core for the food process modelling. Once again, the lack of a methodology for the assessment prevents readers to fully understand the reasoning followed by the authors.
In addition, I believe that some important ontologies are missing in the analysis. For instance Dolce-Ultra light, that, at some point, is mentioned as only a prefix of a few classes aligned with SOSA/SSN, provides interesting elements for modelling plan, workflow etc. but this is not considered in the paper.
In the ontology world related to food, this work published at ISWC - https://link.springer.com/chapter/10.1007%2F978-3-319-46547-0_18 appears just searching in google. This is not part of the bibliography. It seems including some classes for modelling characteristics that are cited in the conclusions of the paper as future work.
Agrovoc is another important thesaurus of the sector that is missing in the paper. Is there a reason?
Also, ontology design patterns, related to process/activity, are never considered in the paper but I believe they can be useful in specific cases of the discussion.
Finally, the discussion section, that I supposed it was related to the state of the art analysis, is instead a proposal of a model for the specific domain of the food recipes. In this section, a prototype in FoodOn is presented. FoodOn is never referenced in the paper but there is a publication of this work available https://doi.org/10.1038/s41538-018-0032-6 . It is a work of some of the authors and surprisingly is not part of the bibliography of this work.
2) The narrative of the paper should be also revised for me. The description is not organic and linear. The paper is full of paragraphs that suddenly introduce things that are never referenced in the bibliography, and for which, in some cases, it is difficult to understand why introducing them. For instance, in section 3.6 the authors suddenly speak of food ontologies after a long discussion on PROV-O and sensor-based ontologies like SSN/SOSA; again, the scope of the discussion on publishing book, in the form used to present it, is unclear. This further confirms that, from my point of view, the overall approach to the survey should be revised.
In addition, there are sentences that are never motivated. For instance: “other ontologies or model framework were considered but not given in-depth review”. That’s might be ok, but why? Only for FTTO - Food Ontology for Traceability Purpose - the authors motivate the exclusion from the analysis because the ontology does not take the same approach as the one used in OBO. BTW: I am not sure this is a valid reason to exclude it in a survey paper regarding food processes, if you considered PROV-O for instance in the analysis. In addition, mixing ontologies and notations such as BPMN sound strange, unless very well motivated reasons in a methodology for the analysis are introduced.
3) Finally, there are some figures that probably propose some modelling. In one of them I have some doubts, from a semantic perspective, about the application of OWL-Time properties. In particular, in OWL Time ontology time:hasBeginning and time:hasEnd have as domain time:TermporalEntity which is the union of time:Instant or time:Interval.
In Figure 10, these properties are linked to a process. So the authors are saying that a process is a time:TemporalEntity (union of time:Instant, time:TimeInterval) and I do not think is correct. Same applies for temporalDuration. From my perspective a process has some temporal entity not is a temporal entity in the sense defined in OWL time ontology. In fact you say afterwards a process can have a temporal duration. With this respect, referring to a foundational ontology such as DOLCE-ultra light can be beneficial here to clarify these concepts.
Some other detailed comments:
Introduction section: “but in this paper we focus on the more general language required for modelling.” —> what do you mean precisely? It should be better explained.
Fig. 1 is never referenced in the text. It seems referring to the discussion of the process objectives; it is not clear if it is something derived from state of the art or an elaboration of the authors.
Fig. 2 never referenced in the paper
CyVerse and Galaxy are not included in the bibliography
Why Petri nets are mentioned in a section that is the state of the art on Ontology-based processing models? For me it is confusing.
Blockchain suddenly appear in the paper with no reference
“Examples are detailed in model applications below” —> better say “in Figure 4” rather than “below”
“It must be completed before proceeding to the next step. In this respect, a control-oriented process of “steps” forces autonomous processes into a linear sequence.” —> it seems to me that this sentence is a very simplified version of process models. This linear sequence does not take into account other more complex processes where parallelism is also possible. I did not see such a discussion in section 2.1.3 if the objective here is to describe process models.
PROCO is not referenced
OBO main references should be in the bibliography
SSSOM should be in the bibliography
All the ontologies mentioned in section 3.1 should be in the bibliography
“It may seem confusing to explore an ontology entity and see another ontology’s terms used in one or a few of its axioms” —> why confusing?
Which is (Figure X)?? Figure 11?
Fig.12 never referenced in the text.
“Exact 2 approaches this with an intermediate level of process model containing input and output relations and materials, and contains over 90 “experimental actions” one finds in a laboratory context, and a general “has proposition” object relation that connects an action to various contextual objects such as expressing a condition for an action to proceed, a duration, or a “protocol method” to follow.” —> this sentence is difficult to read. I would suggest it to re-write it.
In some parts, the discussion about PROV-O sounds to me not really appropriate. For instance: “although it awkwardly refrains from providing features that support a general process model mandate.” —> ontologies are created to meet specific requirements in domain modelling. Don't you think that probably the objectives of the model were not exactly what you have in mind in this document?
In addition, “PROV-O introduces its own time data properties rather than reusing OWL-Time” —> said like that, it sounds like a precise modelling choice of PROV-O. Actually, there is a historical reason for this and it should probably be mentioned (for long time OWL-Time was a W3C note only, and its adoption in ontologies like PROV-O has been compromised by the uncertain status of the OWL-Time specifications. Now OWL-Time is standardised but this happened after the publication as Web standard of PROV-O).
“OBI in contrast has a planned process execute a plan specification or protocol.” —> do you mean “OBI in contrast has a planned process that executes a plan specification or protocol.” If so, I would suggest you to re-write it in this way.
“modelling th process of observations” —> the*
Fig. 17 never referenced in the text.
“see 5.3. Events versus records in https://doi.org/10.1016/j.websem.2018.06.003) “ —> I would say “the interested readers can refer to [X] for a discussion on events versus records modelling for the observations” and [X] should be in the bibliography.
“assay ‘has output’ some ‘measurement datum’ and ‘is about’ some entity” —> Well, here you put not only the about what, but also the output, In SSN/SOSA the output is the result linked to the observation, that in turn is linked to FeatureOfInterest.
“The different domain sub-ontologies that specialize the PO2 core model will be developed in different projects (for example, dairy, meat, and bakery food production) to represent the characteristics of foods during their manufacturing process.” —> before you said that the PO2 ontology has two layers: core and domain. Is the domain layer available? According to this sentence it seems no. This should be clarified.
In Figure 19 it would have been beneficial including prefixes to understand which classes are from OBO network of ontologies and specifically PO2 and which ones from SOSA/SSN.
Fig. 20 seems a quite important figure that compares the analysed ontologies, and it is never explained in the text.
I really do not get the point, with respect to the overall discussion, on the impact on SPARQL queries for having general properties In some context general properties can be effective and used and I do not see such a complex SPARQL query.
“We turn to applying an ontology-friendly modeling paradigm to recipes which are generally a set of …” —> what is an ontology-friendly modelling paradigm? What do you mean?
“Its fundamental meaning is the putting together of components in appropriate relationships or structures, according to a formula (https://en.wikipedia.org/wiki/Formulation)” —> reference in the text to wikipedia on a generic term? I would avoid this.
“Figure X illustrates ..” —> are you referring to Fig. 26?
ENVO —> what’s that? The Environment Ontology? Explain the acronym and put a reference in the bibliography
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