PONE-D-22-27603OntoTrek: 3D visualization of application ontology class hierarchiesPLOS ONE

Dear Dr. Hsiao,

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PLOS ONE

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Comments to the Author

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Reviewer #1: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

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Reviewer #1: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

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Reviewer #1: Yes

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5. Review Comments to the Author

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Reviewer #1: The authors describe a 3-D visualization system for browsing the content of an ontology. One of the main motivations seems to be to be able to visualize which content from external terminologies is imported into the ontology and under which branches of the ontology it is found. In testing the interface is challenging to use. For any ontology with more than a tiny number of classes, it is hard to see the different nodes, and the UI zooms in and out confusingly. A positive aspect is that ontology content from different sources is colored differently, so that the source can be observed at a glance.

I think there are three main aspects the authors could clarify or develop further that would help to make this system more usable:

1. Performance is a serious problem when browsing real world ontologies in the system.

2. The majority of usages of external content in OBO ontologies is via composition, rather than inheritance. For example an HPO phenotype is related to the affected anatomical structure. For this reason it would be valuable to traverse these kinds of links rather than just subClassOf.

3. The main issue that I think should either receive more development, or be addressed more clearly in the paper, is what purpose does the third dimension serve? It seems like many of their ideas (e.g., clearly denoting external content, showing the branching pattern from superclass to subclass) could be supported by a (possibly more scalable) two dimensional system. If one dimension denotes more-general-to-more-specific, and the second dimension separates peer terms from each other, what does change in the third dimension indicate?

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Reviewer #1: No

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OntoTrek: 3D visualization of application ontology class hierarchies

PONE-D-22-27603R1

Dear Dr. Hsiao,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Abel C.H. Chen

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

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4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The figure images are somewhat low resolution; the live application is a bit sharper. If possible, I suggest updating them.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

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