Review Comment:
Overall Comments and Summary
This paper details the modifications made to the existing ontologies RiceDO and TreatO, and RiceMan, a semantic-based framework, which were all three introduced in a 2019 paper by the same authors (Jearanaiwongkul et al., 2019).
In the current manuscript, the authors outline the steps they undertook to revise the RiceDO based on several existing resources: Rice Knowledge Bank Thai version (Thai-RKB), Rice Knowledge Bank (RKB) by IRRI, and the Rice Ontology (RO) (aka Crop Ontology Rice Trait Ontology). They describe revisions to the TreatO ontology, based on the information from IRRI’s RKB’s fact sheets and other plant disease management resources. These changes came about after they had consulted two (unnamed) ontology engineers and a number of issues had been identified.
They also detail the changes made to the RiceMan application, the system architecture and user interface, and how the Observation Data are constructed and composed from multiple observations. The remainder of the paper details an evaluation they undertook of the ontologies and the RiceMan system.
While the manuscript has a number of issues, it does represent a valuable and significant contribution to the field. The approach of integrating the two ontologies for diagnosis and treatment recommendations in a smart phone application is unique, to my knowledge. Also, the added functionality of extrapolating over time and geographical locations will be useful for their users.
Overall, the manuscript is excessively long. The Background section could be condensed and made more concise, and sections 2.2 and 2.3 could be combined. I also suggest eliminating the introductory paragraphs in each section for example:
(P2, L5): “We take a look into the literature of modeled knowledge
base in agriculture area.”
(P5, L20): “This section designs and develops ontologies for rice disease identification and control recommendation to be used by RiceMan system.”
(P13, L32): “We discuss the design and execution of our evaluation in this section.”
There are a large number of grammatical issues and problems with the wording of the sentences throughout the manuscript. There are numerous issues with mixing up past and present tenses, and missing or misused articles. I suggest the authors should enlist the help of an English-speaking editor to address these issues.
In the Background section, the authors review a number of existing ontologies and semantic web technologies. In Section 2.1, the authors present a number of ontologies and vocabularies and there are a number of inaccuracies. AGROVOC (not ‘Agrovoc’) should not be referred to as an ontology- it is a controlled vocabulary. The Crop Ontology Rice Trait Ontology should not be referred to as the “RO” as that acronym refers to the Relation Ontology (http://www.obofoundry.org/ontology/ro.html). The correct prefix for the Crop Ontology Rice Trait Ontology is CO_320 and it is inaccurate to say that it is modeled in OWL, as it is not. Some of the ontologies are not properly referenced, such as the Plant Ontology (Cooper et al., 2013; Cooper et al., 2018; Walls et al., 2019) and the Crop Ontology Rice Trait Ontology (Arnaud et al., 2013; Cooper et al., 2018), as it is incorrect to cite Agroportal as the reference for the CO Rice Ontology. In addition, the authors should also include the Rice Diagnostic tool ‘Rice Doctor”, developed by IRRI (http://www.knowledgebank.irri.org/decision-tools/rice-doctor).
It's confusing that some of the resources are discussed in the past tense, such as the Plant Ontology, PlantVillage and Plantwise Knowledge Bank, while others are discussed in the present tense, such as AGROVOC. Some of the sentences have a mixture of present and past tenses.
Table 1 contains inaccurate information about the domains of the PO and the CO Rice Trait Ontology and would be more useful if it was a comparison of the other existing applications and web technologies detailed in Section 2.2 and 2.3.
In Section 3, the authors detail the design and revisions to the RiceDO and TreatO ontologies, based on the Competency Questions and the evaluation of the ontologies by two unnamed ‘ontology engineers’. Later, in Section 5.2, the revised ontologies were evaluated by “five evaluators who were ontology engineers and ontology experts” Since there is no information as to who did the evaluations and what their credentials were, it is difficult to put much stock into these evaluations. One of the most important principles of ontology design is to reuse relevant parts of existing ontologies. In the RiceDO, the rice diseases are imported from the PDO, but the ‘PlantPart’ and ‘GrowthStageGroup’ branch of the ontology does not import the relevant classes from the Plant Ontology. None of the classes in the RiceDO have textual definitions or unique identifiers (besides the classes from PDO). I suggest the authors should consult the list of principles of good ontology design (http://www.obofoundry.org/principles/fp-000-summary.html) by the OBO Foundry (Smith et al., 2007).
In Section 4 System Requirements, and Figure 3 Use Case Diagram shows the primary users as being farmers, agronomists and scholars. The inclusion of knowledge engineers as “users” of the system does not make sense and could be removed. (P9, L34)
Figure 6 and its description seems out of place. I suggest moving it up to Section 4, where the RiceMan Application development is discussed.
Figure 8 needs to be cleaned up to improve readability and labeled with numbers similar to Figure 6.
Section 5, the details of the evaluation of the RiceMan and the ontologies is much too long and detailed. This could be summarized in a few paragraphs and the extensive details and tables could be presented in a supplementary file.
Finally, the opening statement of the Conclusion is inaccurate, as the RiceMan application was introduced in the 2019 paper by the same authors. Also, the authors suggest that “Though RiceDO and TreatO are built for RiceMan, they can be extensively applied and reused for other development of expert
systems for agriculture domain.” This is not true as these ontologies are presented, but may be possible with some revisions to bring them into compliance with accepted standards.
Literature cited
Cooper L, Meier A, Laporte M-A, Elser JL, Mungall C, Sinn BT, Cavaliere D, Carbon S, Dunn NA, Smith B, et al (2018) The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. Nucleic Acids Research 46: D1168–D1180
Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW, Smith B, Preece J, Athreya B, Mungall CJ, Rensing S, et al (2013) The Plant Ontology as a tool for comparative plant anatomy and genomic analyses. Plant and Cell Physiology 54: e1–e1
Jearanaiwongkul W, Anutariya C, Andres F (2019) A Semantic-Based Framework for Rice Plant Disease Management. New Gener Comput 37: 499–523
Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, et al (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotech 25: 1251–1255
Walls RL, Cooper L, Elser J, Gandolfo MA, Mungall CJ, Smith B, Stevenson DW, Jaiswal P (2019) The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. Front Plant Sci. doi: 10.3389/fpls.2019.00631
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