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:
a.The motivation for this work should be emphasized in the Introduction section. I still do not understand the functions or meaning of ANNO.
b.I am very concerned about the limitations of the automatic ontology matching methods (e.g., AML, LogMap), when they are employed for this task.
c.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).
d.How many use cases could be present by combining this ontology with AnthroWorks3D, and which core concepts of ANNO are utilized? I suggest that authors could complement the above statistical information.

Minor issues:
1.The format of references needs to be further standardized such as [69], [70], [74].

Strengths.
1.The proposed ontology is important for annotating human bones and deriving phenotypes.
2.The core design of ANthropological Notation Ontology is presented in detailed.
3.The provided resource and webpage can be assessed.

Weaknesses.
1.The core skills of the work are not outstanding enough.
2.Lack of detailed statistical explanations and analysis.

The Anthropological Notation Ontology (ANNO) is a valuable tool for the systematic and standardized classification of recovered bones into the skeletal system. It enables detailed descriptions of skeletal pieces and defines functions that aid in deriving different phenotypes of humans, which is particularly useful in forensic and historical anthropology.

ANNO comprises two main components: ANNOdc, a domain-core ontology that offers essential anatomical categories, and ANNOds, a domain-specific ontology designed for annotating structures of the human skeleton. This ontological framework is seamlessly integrated into AnthroWorks3D, a sophisticated photogrammetry pipeline and application tailored for the creation and analysis of 3D models of human skeletal remains.

The integration follows a three-ontology approach, with the General Formal Ontology serving as the top-level ontology, ANNOdc as the task ontology, and ANNOds as the domain ontology. This structure allows AnthroWorks3D to implement access solely to the entities of the task ontology, while dynamically importing the entities of the corresponding domain ontology.

However, a few clarifications and potential improvements could enhance the manuscript:

1.It would be helpful to include a brief introduction to ontologies and their importance in anthropology, especially for readers who may not be familiar with the concept.
2.The manuscript could benefit from a more detailed explanation of how ANNOdc and ANNOds differ and complement each other within the framework.
3.Providing specific examples of how ANNO supports the analysis of skeletal remains, perhaps through case studies or hypothetical scenarios, would make the manuscript more engaging and illustrative.
4.The intended readers for this paper are rather exclusive and significantly limited.

Overall, this manuscript presents a valuable contribution to the field of anthropology, particularly in forensic and historical contexts. With some minor clarifications and additions, it could serve as a good reference for future research in this area.

The manuscript has been revised significantly according to the reviewers' comments. And each of my comments has been addressed in this revised version.

By organizing the structure of the manuscript and clearly describing the related work, the methodology and the developed ontology, the revised version is much better than the previous version. Besides, the language has also been improved significantly.

I have no further questions, so I agree to accept this paper.