NagO- an ontology on UK dependent territories, their link to the Nagoya Protocol policy framework and terminology from related domains

The goal of this article is the development of an ontology NagO. NagO is a domain ontology focused on terms regarding the United Kingdom and its external territories and their link to the Nagoya Protocol policy framework, processes and people involved.

The abstract clearly and concisely presents the purpose of the article. The main idea for developing the Nagoya Ontology (NagO) is to semantically model the complex policy framework around the Nagoya Protocol and to unveil the legal relationships between sovereign states and their external territories, illustrating the United Kingdom as a study case.
I don’t have any comments here.

The introduction very clearly presents the reasons why the authors have decided to develop the Nagoya Ontology. Obtaining heterogeneous information about the sovereignty of different external territories of countries and not free access to reliable information on the status of these territories under the Nagoya Protocol gives the authors reason to emphasize the need to develop Nagoya Ontology.
I don’t have any suggestions here.

Quality and relevance of the described ontology.

I think the ontology is qualitative and relevant.
1. The information in NagO is carefully selected and it follows the Basic Formal Ontologyconcept and the guidelines under the OBO Foundry. For the sovereignty branch of NagO, the Island Rights Initiative provides the majority of information by displaying the constitutional links and governmental relationships of every external territory of the United Kingdom. The approach to collecting and presenting the information contained in NagO is described systematically.
2.The ontologies, which provide terminology for NagO, include ENVO[16], IAO[17], BFO[8] and RO[18], and they were automatically imported using the ontology development kit [19]. The Dublin Core Metadata Initiative terms [20] and NCBITaxon [21] have been added with a manual import in Protegé.
3.Specifically looking at the term definitions gave the authors an insight of how these terms are related to each other. The basis for this step was reading about administrational and political processes and unveiling the distinct people involved, the roles they have and what input is needed for certain processes. The ABS Clearing House offers information on country profiles and documents in relation to the Nagoya protocol.
4.Where public data information was not found, personal inquiries were made to the government departments. The OBO Foundry delivers definitions and relations for the biodiversity and territory branches of NagO (ENVO, SDGIO, GO, NCBITaxon and GEO, GAZ respectively).
5.In Figure 1, the authors represent an overview of the NagO domain scope intersections with an associated topic and possible connections to existing ontologies. In the “Key Futures” Section they present and describe the connection of NagO with other existing ontologies in different domains connected with the Nagoya Protocol and the identify niches where semantic development is needed.
6.The authors define some semantic patterns in the ontology. An example can be seen in Figure 3 - geographic territories are related to people and processes. There are three more semantic patterns defined in the ontology: Territory instances and the execution of a certain government type (e.g. self-governance); UK external territories and their connection to the United Kingdom; Ministerial departments and their connection to the head of state. All these semantic patterns can be used in other domains.
7.With the example for use of the ontology, the authors demonstrate that NagO can be used to query constitutional links of geographic regions. They also claim that it can be used to find role capacities of the people involved and relevant processes and instances of the Nagoya Protocol.
8.In the last section of the article, different opportunities are discussed to extend NagO in different domains.
9.NagO is free and openly accessible in English on “https://github.com/hseifert/NagO”.

Illustration, clarity and readability of the describing paper, which shall convey to the reader the key aspects of the described ontology.

I think the paper is well written and all ideas are adequately presented with figures and tables. The developed ontology is properly described and the content of the article is clear and readable. All Figures and tables are explicit and comprehensible.
All files – ReadMe, nago.owl, nago-full.owl and the others are freely available at https://github.com/hseifert/nago/tree/develop

Review comments:

1.My major comment is about the “Background” section. In this section, the authors again present the reason to create the NagO ontology and its connection with other domains. I think it will be interesting to the readers if there are some similar ontologies about other protocols (conventions) to be referred here.
2.The methodology for creating the ontology and gathering knowledge is well described. Various domains related to the Nagoya protocol are presented. These domains are included in the NagO-related ontology. There is a need to describe the connection to these related ontologies. Which classes are really re-used and how do the different ontological commitments relate to each other?
3.“Both figures 2 and 3 include shortcut relations used for this illustration” – I didn’t see the shortcut relation in Figure 3.
4.I think the authors can extend the usage scenario, for example with finding role capacities of people involved. This will more fully present the potential of the NagO ontology.

The Nagoya protocol on Access and Benefit Sharing defines the legal processes constraining both the collection and reuse of data in Biodiversity studies. To find information regarding the existing studies and the administrative processes to collect and reuse the data requires to retrieve information from various heterogeneous databases and documents. It becomes particularly complex if you consider studies in regions of the world for which sovereignty is unclear as in the case of the United Kingdom and their external territories.
The authors are presenting in this paper a proof-of-principle ontology designed to improve the current situation by supporting the implementation of the FAIR principles. The NagO ontology is a cross domain ontology which aggregates ontologies for biodiversity, geography together with additional terms describing organizational and legal aspects of the Nagoya protocol and the different stakeholders involved. The ontology follows the OBO Foundry principles making it interoperable with the biodiversity relevant ontologies and some geographical ontologies. These various ontologies are aligned under the Basic Formal Ontology which provide a consistent semantic and logical framework.

The paper is well written and provides a clear overview of the context and the problems the ontology aims to address as well as a seemingly exhaustive list of the relevant data sources. The general design process of the ontology is clearly described with few exceptions that I list as minor comments below. This ontology is definitely relevant for the domain. However, I have several major concerns regarding the article, the ontology and the related data.

First, although the context is clear, the work is not supported by concrete use-cases from the domain which would illustrate the purpose and usage of the ontology. In section 5, usage scenarios seems to be more prospective scenarios than real tested ones. This definitely undermines the presentation of the work. I would suggest the authors to revise the paper to add concrete examples of use which would ground the work in practice and provide more clarity on practical challenges and added value for non-expert readers. These examples should provide both the related competency questions used for the design and the associated SPARQL queries to support the testing and exploration for new users. These queries could be shared on the github together with the ontology. Based on my understanding of the ontology and the context, I would suggest the authors to enhance the content of the ABS Clearing House (accessible through an API) to provide the missing link between the external territories and their sovereign country. This could be done by leveraging the Nagoya Look Up service mentioned in the article and developed by the authors.

My second major concern is related to the ontology itself. A lot of effort has been put to import biodiversity related ontologies such as ENVO or even the NCBITaxon while the main addition of the ontology focuses on the legal and organizational aspects of the information as shown by the example patterns used to illustrate the ontology. The paper does not actually show the connection between this organizational aspect of the ontology and the biodiversity, geographical aspects. This raises the question of the relevance to import these ontologies. Furthermore, as the author acknowledge in the paper, the ontology is actually really narrow while its scope is quite large. I would suggest the authors to extend it to at least other European countries such as France or the Netherlands which also have external territories and to consider at least one conflicted area. This would definitely enhance the usefulness of the ontology and also extend the ontology for governmental and sovereignty concepts.

My second major concerns about the ontology is related to the shortcuts used to build this first version of the ontology. First these shortcuts are not clearly explained in the paper. To understand the explanations, one needs to be an expert on the BFO and RO ontologies. I would suggest to clarify the text. In addition, one of these shortcuts implies that signatory roles are actual subclasses of “Homo Sapiens”. First this is semantically and logically wrong and second I am wondering about the need to describe persons based on their species. Why not using existing terms to describe persons? This issue actually would have an impact on the usage in applications.

My final set of major concerns is related to the data. The author are sharing the ontology on github. However, it is hard to understand which ontology file to use. The readme provides little documentation on the various files (e.g nago-base.owl, nago-full.owl, nago.owl). A first analysis of the ontology using Protégé revealed that none of these file includes both the additional NagO classes and their associated instances. After some digging I found the “complete” ontology in the src folder named nago-edit.owl. This is really cumbersome for interested users. It seems this particular github structure is tightly linked with the use of the ontology starter kit. I would recommend the authors to revise their README file to provide more information about its content. In addition, the ontology has little descriptive metadata (missing authors, contributor, description of the scope, …) and the link http://obofoundry.org/ontology/nago is broken.

Although this work is of high interest to support the enforcement of the Nagoya protocol and the implementation of the FAIR principles within this context, as presented here the ontology is clearly incomplete and would benefit from additional work.

Minor concerns
- Section 2 – Background
o Page 2 – column 2 line 31: “NagO aims to connect the vocabulary of different topics”. Should be “vocabularies” as many are existing and considered
o Page 3 – column 1 line 3-7: “The challenge is transforming (…) the observed data discrepancies”: this sentence is unclear, please rewrite
- Section 3 – Approach
o Page 3 – column 1 line 13 – “NagO was created (…)”: it follows the OBO principle and leverage the logical framework of the Basic Formal Ontology as Top level ontology. You should also mention that the ontology has 5 branches here.
o Page 3 – column 1 line 23-24 – “A general overview was developed and then extended with document terminology as well as Nagoya protocol processes and involved instance”: A general overview of what? What do you mean by document terminology?
o Page 3 – column 1 line 33 – “Very few of the necessary vocabulary (…)”: replace vocabulary by terms
o Page 3 – column 2 line 1-3 – “The consensus between all researched (…) as an overlap of definitions”: this sentence is not clear. Could you please rewrite?
o Page 3 – column 2 line 24-25 – “In order to put these terms into perspective they were looked at in a broader context”: Are referring to the people, document and process? This sentence is not clear to me. Please clarify.
o Page 3 – column 2 line 44-48 – “However, the ABS Clearing House itself provides openly accessible information on the role of genetic material (…) protocol text.”: What do you mean by “the role of genetic material”?
- Section 4 – Key features
o Page 4 – column 1 line 3 – “ There are five branches which NagO consolidates: (…)”: As the authors used already the term of branches for the describing the different part of the ontology, I would suggest finding a new term. This is confusing to the reader.
o Page 5 – column 1 line 30 – column 2 line 4 – “In summary, NagO combines (…) for business stakeholders”: this sentence does not make sense. Please rewrite.
o Figure 3 – shortcut relation is missing.
o Page 6 – column 2 line 11 – “(…) have been chosen very consciously”: replace by cautiously?
o Page 6 – column 2 line 12-15 – “For example, while (…) as these axioms”: this sentence is unclear. Please reformulate.
o Page 6 – column 2 line 16 – “Rather than creating BFO roles for terms”: what do you mean?
o Page 7 – table 1 – The table is not mentioned in the article. It can be removed.
- Section 5 – Usage scenarios
- Section 9 – Annex: the list of concept seems to be incomplete.