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[REVIEW]: Atramhasis: A webbased SKOS editor #5040
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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks. For a list of things I can do to help you, just type:
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@gaurav & @SvenLieber - Thanks for agreeing to review this submission. As you can see above, you each should use the command As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines. The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention We aim for reviews to be completed within about 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time. Please feel free to ping me (@danielskatz) if you have any questions/concerns. |
Review checklist for @gauravConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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Hi everybody, Thank you so much for an opportunity to review this manuscript! I got stuck pretty early on in the review process because the Atramhasis repository doesn't have installation instructions. I tried following the installation instructions at your readthedocs.io page page, but running
Could you please copy the basic instructions for starting Atramhasis into the repository's README file? I'll keep trying to get Atramhasis to run, but if you have any insights into why running that command resulted in a version conflict, please let me know! Here are my comments on the GitHub repository so far:
Here are my comments on the manuscript so far:
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Thank you for agreeing to review our software! For installation, I would recommend creating a demo environment via https://atramhasis.readthedocs.io/en/latest/demo.html. This should work with python 3.8, 3.9 and 3.10. We'll check into that version conflict. Looks like you're running Python 3.9? |
Update paper with correct citation of SKOS, URIs, correct spelling of JSON-LD and reference to JSON-LD 1.1 and better reference to figure 2. |
Review checklist for @SvenLieberConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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@gaurav I've expanded the list of authors of the paper with the people who were involved in development in a significant way, although some of them have left our organisation and were not involved in this paper. |
Software paper reviewHi everyone, thanks for inviting me as a reviewer, the software package seems very interesting! First of all, I would like to congratulate the authors and all contributors for this software. The tool seems to be actively maintained on GitHub by using different features such as issues and milestones. Additionally, the tool seems to be successfully used in production. I gladly tick the "Substantial Scholarly Effort" box after also have checked the cited peer-reviewed paper from 2017 with contributions of the current authors. That original paper nicely outlines different issues such as efficient algorithms for searching the possibly infinite depth tree structure of thesauri or the different semantics for The software paper has a clear description of the high-level functionality with given examples. Thus, I would consider it properly described also for non-specialists. The statement of need highlights that the tool is useful for users without knowledge of SKOS or RDF, it provides a UI abstracting these specifications for two different types of users: users consulting a thesauri and the editors of thesauri. Working in the cultural heritage field myself, I acknowledge that more user-friendly tools are needed. The rest of the section lists several features with some descriptions about why there are useful, e.g. drop-down lists and widgets for end-users or convenient REST services for developers. The sentence about the Linked Data Fragments server could be more descriptive, why was this chosen and what need is fulfilled with it? This would help readers who are not familiar with LDF better understand the decision decision of including it for example compared to a regular SPARQL endpoint. I mentioned the distinction between users and editors made in the paper, which I find a very interesting point. Here, the paper could outline better who the audiences actually are, currently I find descriptions such as " ..that allows users to create, maintain and consult", "A concept being something a researcher wants to describe", or "editors do not write RDF statements". I think a more clear description of the different types of users and their needs would be beneficial, also with respect to my following point. There is no dedicated state of the field section. Yet, for SKOS editors there are several existing Open Source solutions with different trade-offs, such as SkoHub, Skosmos or even the more general Protégé, WebProtégé, or VocBench. Overall, the paper is well written. The references are fine for a paper of this length (besides the fact of the missing state of the field which may require additional references or footnotes to point to other SKOS editors). I'm happy to answer any questions and help the authors improve their submission. |
Functionality ReviewAfter running the demo and playing around with the tool a bit, here my review in addition to related opened issues (see above). Overall I found the tool intuitive to use and did not encounter any issues. I browsed existing concept schemes and edited existing concepts via the admin interface. Based on these example scenarios, I would consider that the tool has a state-of-the-art web interface. For example, when opening the admin menu on the right the main window greys out which makes clear that the focus is now on the menu. Content of a concept scheme in the menu on the right is also loaded on-demand which makes sense for large concept schemes and which I consider also a common functionality. In the following I will only focus on a few minor things.
One rather odd thing is, that I was not able to create new concept scheme via the UI. However, this was also not claimed in the software paper and the documentation clearly says that concept schemes have to be created via different interfaces. Hence the following paragraph is just some feedback and my thoughts regarding this. I was wondering, is the addition of the feature "create concept scheme from the UI" foreseen in the future? The creation of new concept schemes seems like a very basic functionality to me, especially when starting to use the tool. I will provide a different comment for the review of the documentation early next week. |
I would like to thank both reviewers for their valuable feedback. I've already made some changes and opened some tickets for further changes. I'll try to address all comments over the next few days and weeks. If i do miss some, please let me know. |
@koenedaele - are you still working on this? Are there specific changes the reviewers should look at, at this point? Or should we wait until you have done more? |
@danielskatz I'm still working on this. I've linked a ticket in the Atramhasis repo that contains the requested changes so I can track them. Some of them were quite simple, some of the requests on more information require more work. I will ask for a new review once I have a version that I'm reasonably happy with. My main worry is that answering all requests for extra information pushes the paper beyond the normal size limits for joss. But I'm first writing those parts and we can see if parts need to be cut again. |
👋 @openjournals/csism-eics, this paper is ready to be accepted and published. Check final proof 👉📄 Download article If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4051, then you can now move forward with accepting the submission by compiling again with the command |
Also, the DOI above (10.1007/978-3-030-00668-6_15) appears to be a correct one for the reference - if you agree, please add it to the entry in your bib file, and let me know, then I'll regenerate the proof |
@editorialbot check references |
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@danielskatz I've update the reference and the Zenodo title |
@editorialbot recommend-accept @koenedaele - again this will generate the proof that I'll next proofread, since I didn't with the previous version |
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👋 @openjournals/csism-eics, this paper is ready to be accepted and published. Check final proof 👉📄 Download article If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4052, then you can now move forward with accepting the submission by compiling again with the command |
@koenedaele - I've made some suggestions for small changes in OnroerendErfgoed/atramhasis#804 - please merge this or let me know what you disagree with, then we can continue the process of acceptance and publication. |
@danielskatz Thank you! I've merged the changes. |
@editorialbot recommend-accept hopefully final proof... |
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👋 @openjournals/csism-eics, this paper is ready to be accepted and published. Check final proof 👉📄 Download article If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4053, then you can now move forward with accepting the submission by compiling again with the command |
@editorialbot accept |
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Congratulations to @koenedaele (Koen Van Daele) and co-authors!! And thanks to @gaurav and @SvenLieber for reviewing! |
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@danielskatz @gaurav @SvenLieber Thanks for your time and effort. This has been the best experience I've ever had in submitting a paper due to the tooling you're using and the very open and friendly review process. I've volunteerd to review as well. |
@editorialbot reaccept |
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🌈 Paper updated! New PDF and metadata files 👉 openjournals/joss-papers#4494 |
Submitting author: @koenedaele (Koen Van Daele)
Repository: https://github.com/OnroerendErfgoed/atramhasis
Branch with paper.md (empty if default branch): joss_paper
Version: 1.3.2
Editor: @danielskatz
Reviewers: @gaurav, @SvenLieber
Archive: 10.5281/zenodo.7733994
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