The ANthropological Notation Ontology (ANNO): A core ontology for annotating human bones and deriving phenotypes

The paper presents an ANthropological Notation Ontology (ANNO) for annotating human bones and deriving phenotypes, which consists of two components, including ANNOdc and ANNOds. The authors introduce the design idea of these two components in detail and integrate ANNO into AnthroWorks3D, which could be helpful for generating and analyzing 3D models of human skeletal remains. Finally, the authors discuss the potential applications of ANNO and give future directions for improving this ontology.
Although authors have modified the manuscript in this revised version, several parts of this version should be improved.

Major issues:
1.The authors should mark the revised places in red or other colors and provide a corresponding document, which contains the detailed responses for the review comments.
2.I am very concerned about the limitations of the automatic ontology matching methods (e.g., AML, LogMap), when they are employed for this task. Please briefly explain the reason why do not employ the automatic ontology matching methods.
3.I am very curious about the entailed results of designed ontology. In other words, whether there exist any inconsistencies of ANNO by employing reasoning algorithms (e.g., HermiT, Pellet). Please provide the analysis of entailed results in detail.

The current manuscript is a further revised version of the previous major revised one. The content of the current manuscript looks nice. I do not have any other issues about the it.

Originality and Significance:
The manuscript introduces the Anthropological Notation Ontology (ANNO), a novel framework that addresses a significant gap in the standardized documentation and analysis of human skeletal remains. The integration of ANNO with AnthroWorks3D is particularly innovative, offering a practical application for the ontology in a digital environment.
Quality of the Manuscript:
The paper is well-structured, with a clear presentation of the problem, the development of ANNO, its integration with existing tools, and the implications for the field of anthropology. The use of the onto-axiomatic method for the development of ANNO is a robust approach that adds to the credibility of the ontology.
Clarity and Readability:
The manuscript is generally well-written and easy to follow. The figures and tables are clear and support the text effectively. However, some sections, particularly those detailing the technical aspects of ANNO's development, could benefit from further simplification to make the content accessible to a broader audience.
Methodology:
The authors have meticulously described the methodology for developing ANNO, including the use of the General Formal Ontology (GFO) as a top-level ontology. The clear explanation of the conceptualization and axiomatization phases is commendable.
Results and Discussion:
The results section effectively demonstrates the utility of ANNO in annotating human bones and deriving phenotypes. The discussion is insightful, particularly in highlighting the potential applications of ANNO in various fields and the importance of continued development and refinement.
References:
The references are comprehensive and up-to-date, providing a solid foundation for the work presented. However, the authors may want to consider including additional literature that discusses the challenges and benefits of ontology integration in other domains.
Figures and Tables:
The visual aids are well-designed and informative. However, the figure depicting the integration of ANNO with AnthroWorks3D could be expanded to include a more detailed explanation or a flowchart illustrating the process.
Technical Soundness:
The technical aspects of the paper are sound, with a clear explanation of the ontological structure and its components. The use of OWL 2 for the ontology's implementation is appropriate and aligns with current standards in ontology development.
Potential Issues:
While the paper is strong in many areas, it would benefit from a more detailed discussion on the limitations of ANNO and potential challenges in its application. Addressing these points will provide a more balanced view of the ontology's capabilities.
Recommendation:

The manuscript is recommended for publication with minor revisions. The authors should consider the points raised in this review to enhance the clarity and impact of their work.
Overall Evaluation:
The paper presents a contribution to the field of anthropology and ontology development. ANNO's potential to transform the way human skeletal data is recorded and analyzed is evident. With some minor revisions, this paper will be a valuable resource for researchers and practitioners in the field.