Peer Review History
Original SubmissionNovember 9, 2023 |
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PONE-D-23-37198Arctos: Community-driven innovations for managing biodiversity and cultural collectionsPLOS ONE Dear Dr. Cicero, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Arrange the manuscript so that also Material & Methods as well as Results are included;Avoid repetition between Abstract and Introduction trying to cut text when it does not add particular value to the rich info already provided;Provide some example outcomes of files / data eventually as supplementary material;Offer more details on financial sustainability of Arctos and how it compares / integrates with already existing platforms. Please submit your revised manuscript by Feb 26 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
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Kind regards, Carlo Meloro Academic Editor PLOS ONE Journal Requirements: 1. When submitting your revision, we need you to address these additional requirements. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 2. Thank you for stating the following in the Acknowledgments Section of your manuscript: We thank all members of the Arctos Working Group for their unflagging efforts to improve Arctos and keep it an active, functioning, and engaged community and platform. We also thank the generations of undergraduate and graduate students, post-baccalaureates, collection managers, curators, and technicians who perform daily collection tasks using Arctos at member institutions. The following individuals and collaborators have contributed invaluable expertise, perspectives, and support that have helped to enrich and expand Arctos as both a data platform and community: Stan Blum, John Deck, Jonathan Dunnum, Joyce Gross, Steffi Ickert-Bond, Gordon Jarrell, Craig Moritz, Kyndall B.P. Hildebrandt, Barbara Stein, Lam Voong, Cam Webb, John Wieczorek; Global Biotic Interactions (GloBI; Jorrit Poelen), Global Genome Biodiversity Network (GGBN; Katharine Barker), Integrated Digitized Biocollections (iDigBio; Gil Nelson, Deborah Paul, Erica Krimmel), and the Texas Advanced Computing Center (TACC; Chris Jordan). We thank the National Science Foundation for funding specific to the development and sustainability of Arctos (DBI-9630909, DBI-9876837, DEB-9981915, DBI-2034593, DBI-2034568, DBI-2034577), as well as the Robert & Patricia Switzer Foundation for awarding Arctos a Leadership Grant in 2023; additional grants from various sources have funded collection-specific initiatives that resulted in Arctos improvements. Finally, we thank Community Initiatives, especially Brandy Shah and Rose Cohen Westbrooke, for their guidance and expertise in our transition to fiscal sponsorship. We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: The author(s) received no specific funding for this work. Please include your amended statements within your cover letter; we will change the online submission form on your behalf. Additional Editor Comments: This is a well written paper that present the benefits of Arctos. I like the paper structure although I must say that I dislike repetition that in the current status of the article are present quite a lot. This occurs especially in between the Abstract and the Introduction so I recommend to change one or the other. Another thing that should be better implemented is the structure into Methods and Results / Discussion section. A good example you can try to follow is this: The ROCEEH Out of Africa Database (ROAD): A large-scale research database serves as an indispensable tool for human evolutionary studies https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0289513 I do not think that you need some extra analyses or statistics to be added to the paper, you just need to organise them a little bit in a more effective way. For instance, based on your map it seems that your database deals with collections worldwide although you got mainly 4 countries that contribute to it. It would be good to clarify the geographic scale of this impressive database that at the moment is quite rich in details [which is at the same time scary and exciting for the first time users]. It would be good to have examples of search tools and effective way to extract data using .csv format or .txt because the amount of info included in Arctos is quite a lot and arranged as text with multiple outcomes (let’s say a sort of guidelines to optimise specimen/collection searches). Last but not least, it will be important to clarify the staff time effort and financial scheme a bit more in details to show how sustainable and replicable this system is. Below I provide some detailed comments that I hope you will be able to address: The use of the word biological should be broaden in the context of including also geology and mineralogy...perhaps with "natural" or eventually add the world "geological" to biological. This appears already in the abstract and is repeated in the Introduction The first part of the Intro 66-77 is too similar to the abstract or the other way round. Try to change on or the other to avoid repetition. I suggest to change the abstract and make it a bit more efficient in summarising the strengths of Arctos Line 88: what FAIR stands for? Move its definition in parenthesis straight after the term FAIR and not in line 89 Line 92-97: this sounds like a repetition of what you introduced before, make it shorter as a single sentence just before introducing ARCTOS Line 97-1-4: again this is the same as in the Abstract, so please change one or the other Line 128: what do you mean for "archives"? do you mean written archive records or more specific to some of the museum object records? Line 131: nice but it would be good to see some good examples from the literature...any example ref. showing the productive scientific dialogue Arctos introduced? Line 181: this is a bit repetitive now and it would be good if you could add some numbers to these data. How many collector managers? how many researchers? educators? and so on...but more specifically what is their role / responsibility? Line 188: nice, does this mean that Arctos will be ideally also open to other part of the world or is specifically dealing with US federal government only? Line 204-212: all good here but I wonder how the community comes together? Through the web? do you do regular zoom meeting? who is in charge of organising them? I assume there is still some dedicated personnel that check Arctos functionality / web security and so on...this should be specified a bit. There must be IT personnel dedicated to Arctos...how many and how much does that cost? It would be good to know for anyone interested in joining or developing something similar. Also, what are the responsibility of anyone that decides to join? You answer this a bit in the next section but it is not clear how many members each panel has and where are they based. Is Arctos management part of their "job role"? In UK for instance the NHM collection managements are pretty much busy and the NHM data portal (https://data.nhm.ac.uk/) is possibly curated by extra additional / time / staff / volunteers. How much time is that and what is the working force involved for Arctos? In Fig. 2 would be good to figure out who are the 4 countries involved and if there is aim and scope to expand this geographically The colour of the frequency bar is ok but seems trivial to understand. If this is just a nice visualisation perhaps use colour gradients across blue or always the same colour (the first orange bar looks quite odd) In Fig. 3 it will be good to know how many people per committed are present Line 283: is there any example of digital records that are easy to find. Let's say I want to find in Arctos all the 3D models of vertebrate skull. Is it possible to find it? Perhaps some screenshot example on how to find this kind of record or on where it is registered would be good to show. Also I wonder if there is a double check system on the records that might be biased or inaccurate or might not correspond to original recording (e.g. sometimes collections change acronym or catalogue numbers that used to be written in paper). Any record of catalogues / or change in specimens code or way to correct / update an old record? Line 491: I like this example but the figure associated to it is quite conceptual...it will be good to have maybe as a supplementary file the whole record in pdf associated to these specimens via the database. Same stands for maps / records ....some examples that can help the users to do an effective search. I tried some functionality myself and realised that the amount of info is massive so you need to be quite focused when searching a particular item. Line 590 onwards: I think you need to be more specific here. Who are the partners interested in financing Arctos and how sustainable over the long term this is going to be? In short readers will be interested to understand if your proposed Arctos database system can be joined inn or re-created for other museums by paying attention to financial constraints and time that museum staff need to work on this. How much average time a museum curator must dedicate to ensure Arctos will survive over long term? How many "permanent" dedicated workers are needed to take care of Arctos? and most importantly: what sort of cyber security is applied and how much does that cost? [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. 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 Reviewer #2: No ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: N/A ********** 3. 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 Reviewer #2: No ********** 4. 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 Reviewer #2: Yes ********** 5. 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: Thank you very much for allowing me to review your manuscript Arctos: Community-driven innovations for managing biodiversity and cultural collections. It can be challenging to describe database systems effectively, and this paper achieves this, although there are a few suggestions for improvement. Major comments ------------------ The abstract establishes the objective of this paper to highlight the unique aspects of Arctos. However, no reference is made to other leading collection management systems (Specify; KE EMu). A comparison with these systems is required to ground-truth this claim of uniqueness. For example, the paper claims a key unique feature of Arctos is its ability to connect with external repositories, but is similar functionality not provided by Specify and KE EMu? A comparison of the Arctos model with other collection management systems would be helpful as part of establishing the difference between the systems. Existing comparisons exist [1], but the paper should discuss how the Arctos model can best support the information requirements of collections. The section “A sustainable future for Arctos” needs clarification. The authors assert that this model was implemented in 2022, in which case some results should be included. Have non-profit organisations been found to provide fiscal support and establish a long-term future for Arctos? Have the resource constraints mentioned been solved? If it is the case that non-profit organisations have been providing support but cannot be named for contractual reasons, this should be made explicit. Data licensing and privacy information would also be useful, particularly with Arctos’ capability to share data entities across collections. If this sharing is cross-institutional, does the use of the system require institutions to permit the reuse of their data? Does the system allow data embargoes? The paper describes Artos’ ability to “store and share biographical information about agents across collections,” which has user privacy implications that should be addressed. Minor comments ------------------- The paper describes the database model, but a schematic diagram would aid understanding of this model. A few additional citations are needed: “Lucee-based web interface” (page 7) “Apache 2” (page 7) The paper describes the user community well, but it would be interesting to mention the development community. As this project is open-source, are there community or other technical contributions? References ------------ [1] https://www.idigbio.org/wiki/images/4/4a/Brenskelle-iDB2.pdf Reviewer #2: I suggest you substitute "natural" for "biological" throughout the paper, since geological material (rocks, minerals, fossils, but also cores, seismic records, etc) are also abundantly present in collections and they are neither biological nor cultural. The paper would also benefit from a very brief "Conclusion" paragraph, just after "A sustainable future for Arctos", where you would summarize and wrap up the advantages of Arctos. ********** 6. 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Revision 1 |
Arctos: Community-driven innovations for managing natural and cultural collections PONE-D-23-37198R1 Dear Dr. Cicero, 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. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Carlo Meloro Academic Editor PLOS ONE Additional Editor Comments (optional): You did a good job in addressing all the main concerns of the paper. 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 Reviewer #2: All comments have been addressed ********** 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 Reviewer #2: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: N/A ********** 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 Reviewer #2: Yes ********** 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 Reviewer #2: Yes ********** 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 changes do address my comments sufficiently. I get the point that a comparison with other similar systems is beyond the scope of this paper, but perhaps could be something for a future paper. Reviewer #2: (No Response) ********** 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 Reviewer #2: No ********** |
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