Dear Dr Cox,

Thank you very much for submitting your manuscript "Ten Simple Rules for making a vocabulary FAIR" for consideration at PLOS Computational Biology.

As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. In light of the reviews (below this email), we would like to invite the resubmission of a significantly-revised version that takes into account the reviewers' comments.

We cannot make any decision about publication until we have seen the revised manuscript and your response to the reviewers' comments. Your revised manuscript is also likely to be sent to reviewers for further evaluation.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to the review comments and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

Important additional instructions are given below your reviewer comments.

Please prepare and submit your revised manuscript within 60 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email. Please note that revised manuscripts received after the 60-day due date may require evaluation and peer review similar to newly submitted manuscripts.

Thank you again for your submission. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Scott Markel, Ph.D.

Ten Simple Rules Editor

PLOS Computational Biology

Scott Markel

Ten Simple Rules Editor

PLOS Computational Biology

***********************

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: Two Documents attached:

1. pdf of manuscript with comments using Acrobat

2. pdf of document with comments and suggestions (CoxEtAl10RulesVocabularySMR.pdf)

Reviewer #2: The authors present here a succinct and comprehensive set of advise for both encoding vocabularies in Semantic Web standards and for making vocabularies fit well into the FAIR principles for Data Management. Having been responsible for publishing a number of controlled vocabularies, I find their steps here to a well laid out Best Practice. As such this is a timely paper and the authors are to be congratulated for their input and presentation. I have only one very minor comment, which is that on lines 42, 94 and 95 the render the phrase "linked data" and "linked-data", which I would more normally expect to see as "Linked Data".

Once again - thank you for the opportunity to review this well written paper.

Reviewer #3: This paper proposes a set of 10 rules to provide FAIR vocabularies. The work is interesting and worth being published as FAIR data and related initiatives are gaining momentum. In this sense, the first recommendation for improving the paper would be to align the proposed rules to the previous works as "Best Practices for Implementing FAIR Vocabularies and Ontologies on the Web" (http://ebooks.iospress.nl/volumearticle/56005 and arxiv version https://arxiv.org/abs/2003.13084) and the FAIRsFAIR D2.2 FAIR Semantics: First recommendations (https://zenodo.org/record/3707985). Authors may also be interested in the special issue https://www.mitpressjournals.org/doi/full/10.1162/dint_e_00023

Other important comments to enhance the current paper are:

Line 171: What do you mean by "Resource Description Framework (RDF) vocabularies"? the references mix the RDF and RDFS recommendations with Dublin Core. RDF is the data model for the web, RDFS is the language for vocabularies and OWL is a language for ontologies. Finally Dublin Core is a controlled vocabulary that happens to be implemented in RDFS and in OWL (depending elements or terms.) Please clarify these concepts. It would be advisable also to clarify in general than OWL is the ontology language and SKOS is an OWL ontology to represent thesaurus, not a particular language itself as in general lines from 175 to 187 might be a bit misleading, in particular lines 185-187 as the constructs that are "missed" in OWL are actually built in SKOS based on OWL and the reasoning features are defined in OWL.

Regarding the table for steps for SKOS and OWL conversion I would suggest to keep it just for SKOS as there are several points in the OWL column. In general I feel that that column could lead to conceptual errors to the readers, overall not experts in knowledge representation, as it seems to oversimplify a great amount of work about ontological engineering. While the steps for converting to a SKOS are clear and could be automated, for building an ontology there are a number of consideration that should be made and given the type of publication it would be more suitable to keep it to SKOS rather than entering in an ontological engineering work. The points about the table are:

-- "Identify terms": "or as an instance of an owl:Class if it is the most specific concept in the vocabulary " --> not always, one may want to have all as classes and create individual for the last level. It depends on the use.

-- "Encode term labels and synonyms" --> In general, it is a bad practice to use the owl:equivalentClass construct to define synonyms, they could be added as several labels to a given class or with other annotations but not creating N classes in the same ontology unless there is a good reason for that.

-- "Define the hierarchy of terms" --> transforming broader/narrower relationships to rdfs:subClassOf would lead to semantic errors and reasoning issues. See that in a thesaurus we can have PC - narrower - mouse. If we make mouse subclass of PC is a semantic inconsistency as individuals of mouse will be classified as individuals of PC. In this cases a transformation is not that simple and if one wants to transform a thesaurus into an ontology there should be some modelling decisions to be taken.

-- minor: rdfs:comment is used in steps 3 and 5 for different purposes, the original type of annotation would be lost.

-- "Add per-item metadata": for the case of ontologies the LOV, MOD https://github.com/sifrproject/MOD-Ontology and Widoco guidelines could be included but as said, I would suggest keeping the table for SKOS.

Other comments are:

In rule 8 LOV should be added as registry as it is widely used by many communities and Ontobee.

Line 32 and 61: the term glossary seems to be used as synonym for controlled vocabularies and could be a bit inaccurate. I'd suggest using and referring to the ontology spectrum by McGuinness http://www.ksl.stanford.edu/people/dlm/papers/ontologies-come-of-age-mit-press-(with-citation).htm

Line 61 to 65: I don't see why those example "may not be initially recognised as vocabularies" if word-lists are vocabularies list of terms which are unit of measure are too.

Minor comments:

Line 73 to 76: the list of digital documents is too narrow, it might include relational databases, XML files, etc.

Line 81: ".." remove one "."

**********

Have all data underlying the figures and results presented in the manuscript been provided?

Large-scale datasets should be made available via a public repository as described in the PLOS Computational Biology data availability policy, and numerical data that underlies graphs or summary statistics should be provided in spreadsheet form as supporting information.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: None

**********

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: Yes: Stephen M Richard

Reviewer #2: No

Reviewer #3: No

Figure Files:

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org.

Data Requirements:

Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example in PLOS Biology see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

Reproducibility:

To enhance the reproducibility of your results, PLOS recommends that you deposit laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions, please see http://journals.plos.org/compbiol/s/submission-guidelines#loc-materials-and-methods

Attachments

Attachment

Submitted filename: CoxEtAl10RulesVocabularySMR.pdf

Attachment

Submitted filename: PCOMPBIOL-D-20-02105_reviewerCoxEtAlVocabulariesOnTheWeb.pdf

Dear Dr Cox,

Thank you very much for submitting your manuscript "Ten Simple Rules for making a vocabulary FAIR" for consideration at PLOS Computational Biology. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. The reviewers appreciated the attention to an important topic. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations.

Please prepare and submit your revised manuscript within 30 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to all review comments, and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

Important additional instructions are given below your reviewer comments.

Thank you again for your submission to our journal. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Scott Markel, Ph.D.

Ten Simple Rules Editor

PLOS Computational Biology

Scott Markel

Ten Simple Rules Editor

PLOS Computational Biology

***********************

A link appears below if there are any accompanying review attachments. If you believe any reviews to be missing, please contact ploscompbiol@plos.org immediately:

[LINK]

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: The revised version is excellent. Thanks for putting this together!

Reviewer #2: This revision looks excellent - I recommend for publishing

Reviewer #3: Thank you very much for your detailed comments and the effort improving the paper.

There are substantial changes in the manuscript addressing the reviewer's comments. I think the paper has improved and actually it a good starting point for converting legacy terminologies to FAIR vocabularies.

I only have some small comments:

Line 73: is there an "and" or "or" missing before "(b)"?

Lines 226 to 229: It is common to use # for small vocabularies or ontologies, it would be better to have that mentioned. I understand it is different if you are transforming a huge KOS.

Table skos and owl, point "Define the hierarchy of terms" in the owl column: "A narrower concept or subclass" --> I would avoid mentioning here "narrower", maybe "A more specific concept or subclass... ". Also, I would add a clarification stating that in owl the subclass is oriented to subsets of elements which is not exactly the same as "narrower/broader" for SKOS.

Table skos and owl, point "Define the whole vocabulary" about the sentence: "Every member term should have a rdfs:isDefinedBy relationship to the ontology" --> Could this be optional for when the element URI is defined in the same namespace as the ontology URI?

Regarding the options to transform vocabularies to SKOS or OWL, I find very useful OpenRefine. Not sure how easy to use is for non-experts in RDF or semantic technologies.

**********

Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #2: Yes

**********

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: Yes: Stephen M Richard

Reviewer #2: No

Reviewer #3: No

**********

Have all data underlying the figures and results presented in the manuscript been provided?

Large-scale datasets should be made available via a public repository as described in the PLOS Computational Biology data availability policy, and numerical data that underlies graphs or summary statistics should be provided in spreadsheet form as supporting information.

Reviewer #1: Yes

Reviewer #3: Yes

Figure Files:

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org.

Data Requirements:

Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example in PLOS Biology see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

Reproducibility:

To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

References:

Review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript.

If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Dear Dr Cox,

We are pleased to inform you that your manuscript 'Ten Simple Rules for making a vocabulary FAIR' has been provisionally accepted for publication in PLOS Computational Biology.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Computational Biology. 

Best regards,

Scott Markel, Ph.D.

Ten Simple Rules Editor

PLOS Computational Biology

Scott Markel

Ten Simple Rules Editor

PLOS Computational Biology

***********************************************************