[REVIEW]: stanscofi and benchscofi: a new standard for drug repurposing by collaborative filtering

[editorialbot]

Submitting author: @clreda (Clémence Réda)
Repository: https://github.com/RECeSS-EU-Project/stanscofi/
Branch with paper.md (empty if default branch):
Version: v.2.0.0, v.2.0.0
Editor: @Nikoleta-v3
Reviewers: @jaybee84, @abhishektiwari
Archive: 10.5281/zenodo.10561760

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/8c32602b0c4b97e70c7a3bca5f3eebc0"><img src="https://joss.theoj.org/papers/8c32602b0c4b97e70c7a3bca5f3eebc0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8c32602b0c4b97e70c7a3bca5f3eebc0/status.svg)](https://joss.theoj.org/papers/8c32602b0c4b97e70c7a3bca5f3eebc0)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@jaybee84 & @abhishektiwari, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @Nikoleta-v3 know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @abhishektiwari

📝 Checklist for @jaybee84

[editorialbot]

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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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (722.9 files/s, 142478.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          13            281           1120           1526
TeX                              1             38              0            343
Jupyter Notebook                 1              0           3115            338
Markdown                         3             87              0            235
YAML                             5             19             15            193
JSON                             3              0              0            158
reStructuredText                10             45             41             75
DOS Batch                        1              8              1             26
make                             1              4              7              9
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            39            482           4299           2906
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1752

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1089/genedge.5.1.39 is OK
- 10.1016/j.apsb.2022.02.002 is OK
- 10.1038/s41598-019-54849-w is OK
- 10.1186/s13321-020-00450-7 is OK
- 10.1016/j.eswa.2017.05.004 is OK
- 10.1093/bib/bbab581 is OK
- 10.1186/s12859-019-2983-2 is OK
- 10.1109/icdm.2010.127 is OK
- 10.1186/s12859-020-03898-4 is OK
- 10.1109/TCBB.2022.3212051 is OK
- 10.1109/TCBB.2023.3254163 is OK
- 10.1016/j.patter.2023.100804 is OK
- 10.1007/3-540-44886-1_25 is OK
- 10.1093/bioinformatics/bty013 is OK
- 10.1093/cid/ciab350 is OK
- 10.5281/zenodo.8038847 is OK
- 10.5281/zenodo.8241505 is OK
- 10.5281/zenodo.7982964 is OK
- 10.5281/zenodo.7982969 is OK
- 10.1038/msb.2011.26 is OK
- 10.1093/bioinformatics/bty013 is OK
- 10.1093/bioinformatics/btw770 is OK
- 10.3389/fphar.2021.784171 is OK
- 10.1093/bioinformatics/btz965 is OK
- 10.1016/j.asoc.2021.107135 is OK
- 10.1093/bioinformatics/btz331 is OK
- 10.1093/bioinformatics/btw228 is OK
- 10.1145/3308558.3313562 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[Nikoleta-v3]

Hey @jaybee84, @abhishektiwari this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements ✅ As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #5973 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any 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 (@Nikoleta-v3) if you have any questions/concerns. 😄 🙋🏻

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[abhishektiwari]

Review checklist for @abhishektiwari

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/RECeSS-EU-Project/stanscofi/?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@clreda) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[jaybee84]

Review checklist for @jaybee84

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/RECeSS-EU-Project/stanscofi/?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@clreda) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[Nikoleta-v3]

Hey @abhishektiwari and @jaybee84 👋🏻, any updates on your reviews? 😄

[abhishektiwari]

I will share initial feedback early next week.

[Nikoleta-v3]

Thank you 🙏🏻 and thank you again for your time!

[jaybee84]

@Nikoleta-v3 Thanks for the reminder. I will also complete it within the next week.

[abhishektiwari]

@clreda Initial comment on structure of Paper itself.

— Just for consistency purposes, the Summary should come before Statement of need.
— When I read current Summary it does not describe the high-level functionality and purpose of the software for a diverse, non-specialist audience. See example paper here.

[abhishektiwari]

@clreda I spent a few hours trying to install the package but neither pip nor conda instructions work (details added on the GitHub issue here). I use Mac M2 laptop and tried running these with Rosetta mode but no luck. Is there a Dockerfile one can use to test these packages?

Can you share what OS is supported by stanscofi?

Update: Added GitHub issue with instructions to run stanscofi as a Docker container. Please feel free to include them for users and/or contributors.

[clreda]

Dear @abhishektiwari, thanks a lot for accepting to review this manuscript!

I have tried to address the issue in the installation, please let me know how it goes. Thank you very much for the instructions to run on Docker, I will add them to the repository and documentation! EDIT: in commit ff312993

As for the comments on the manuscript itself, (I will address those concerns this week) edit: please refer to the newest version of the paper.

[clreda]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[abhishektiwari]

Thanks, @clreda I have now worked my way through the stanscofi and was able to validate package functionality.

I am now having issue with benchscofi due it's restrictive tensorflow requirements.

Created ticket here: RECeSS-EU-Project/benchscofi#1

[clreda]

I have replied to your issue. I believe the best course of action is to provide for users the alternative installation guide, which relies on pip dependency conflict solver, and keep the current one to ensure smooth automated tests. Please feel free to mention other possibilities which might improve user functionality

[Nikoleta-v3]

Hello @abhishektiwari @jaybee84👋🏻, any updates regarding your reviews?

@clreda, I can see that RECeSS-EU-Project/stanscofi#2 is now closed. In the future, could you indicate the commit hash (or even better, the pull request) that resolved the issue? It will make reviewers' life a bit easier 😄

[abhishektiwari]

@Nikoleta-v3 I will revisit paper again, and expect final feedback by end of week.

[abhishektiwari]

@clreda Looked at revised paper structure, still not sold on current summary. I generally think software paper summary as an elevator pitch - problem statement, solution, key value proposition, any additional detail for target audience. Revised version mentions the problem statement but not the solution.

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1089/genedge.5.1.39 is OK
- 10.1016/j.apsb.2022.02.002 is OK
- 10.1038/s41598-019-54849-w is OK
- 10.1186/s13321-020-00450-7 is OK
- 10.1016/j.eswa.2017.05.004 is OK
- 10.1093/bib/bbab581 is OK
- 10.1186/s12859-019-2983-2 is OK
- 10.1109/icdm.2010.127 is OK
- 10.1186/s12859-020-03898-4 is OK
- 10.1109/TCBB.2022.3212051 is OK
- 10.1109/TCBB.2023.3254163 is OK
- 10.1016/j.patter.2023.100804 is OK
- 10.1007/3-540-44886-1_25 is OK
- 10.1093/bioinformatics/bty013 is OK
- 10.1093/cid/ciab350 is OK
- 10.5281/zenodo.8038847 is OK
- 10.5281/zenodo.8241505 is OK
- 10.5281/zenodo.7982964 is OK
- 10.5281/zenodo.7982969 is OK
- 10.1038/msb.2011.26 is OK
- 10.1093/bioinformatics/bty013 is OK
- 10.1093/bioinformatics/btw770 is OK
- 10.3389/fphar.2021.784171 is OK
- 10.1093/bioinformatics/btz965 is OK
- 10.1016/j.asoc.2021.107135 is OK
- 10.1093/bioinformatics/btz331 is OK
- 10.1093/bioinformatics/btw228 is OK
- 10.1145/3308558.3313562 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

ID ref-luo2018computational already defined

[clreda]

Dear @Nikoleta-v3 I have just fixed the reference issue mentioned above (commit d7bdc43). The process should end up successfully now.

[Nikoleta-v3]

Thank you; that was fast 😄

[Nikoleta-v3]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1089/genedge.5.1.39 is OK
- 10.1016/j.apsb.2022.02.002 is OK
- 10.1038/s41598-019-54849-w is OK
- 10.1186/s13321-020-00450-7 is OK
- 10.1016/j.eswa.2017.05.004 is OK
- 10.1093/bib/bbab581 is OK
- 10.1186/s12859-019-2983-2 is OK
- 10.1109/icdm.2010.127 is OK
- 10.1186/s12859-020-03898-4 is OK
- 10.1109/TCBB.2022.3212051 is OK
- 10.1109/TCBB.2023.3254163 is OK
- 10.1016/j.patter.2023.100804 is OK
- 10.1007/3-540-44886-1_25 is OK
- 10.1093/bioinformatics/bty013 is OK
- 10.1093/cid/ciab350 is OK
- 10.5281/zenodo.8038847 is OK
- 10.5281/zenodo.8241505 is OK
- 10.5281/zenodo.7982964 is OK
- 10.5281/zenodo.7982969 is OK
- 10.1038/msb.2011.26 is OK
- 10.1093/bioinformatics/btw770 is OK
- 10.3389/fphar.2021.784171 is OK
- 10.1093/bioinformatics/btz965 is OK
- 10.1016/j.asoc.2021.107135 is OK
- 10.1093/bioinformatics/btz331 is OK
- 10.1093/bioinformatics/btw228 is OK
- 10.1145/3308558.3313562 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/bcm-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#4938, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@clreda as AEiC I will now help to process this work for acceptance in JOSS. Since this concerns two packages, i.e. stanscofi and benchscofi, we need to re-do/change a couple of things here first.

Please can you complete the following:

• Please create a release for the reviewed software for both stanscofi and benchscofi. Next report back here with the version tags used for these releases, for both software packages. I am guessing this will be v.2.0.0 and v.2.0.0 ? I will proceed with this just now, but let me know if this needs to be amended. The version tag we'll assign here will be a a collection of the two separated by a comma, e.g. v.2.0.0, v.2.0.0.
• Please create a single merged archive containing both the content for stanscofi and benchscofi, and report back here with the DOI. Next ensure its title matches the paper title, and that you assign the MIT license. For the version tag use the merged one, i.e. v.2.0.0, v.2.0.0.

In addition:

• I'd like to suggest a renaming of the title, it is more common to have the software project name(s) first, e.g.: stanscofi and benchscofi: A new standard for drug repurposing by collaborative filtering. This is only a recommendation, but let me know if you are in agreement. If so, please amend the paper and ensure the archive title matches.

[Kevin-Mattheus-Moerman]

@editorialbot set v.2.0.0, v.2.0.0 as version

[editorialbot]

Done! version is now v.2.0.0, v.2.0.0

[clreda]

Dear @Kevin-Mattheus-Moerman, thanks for your help.

Release version for stanscofi: v2.0.0
Release version for benchscofi: v2.0.0
Joint archive DOI: Version v2.0.0,v2.0.0 10.5281/zenodo.10561760

I agree with your suggestion, and I have changed the title accordingly (commit c1e0260) in both the paper and the Zenodo archive.

Please let me know if there is anything else needed.

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[Kevin-Mattheus-Moerman]

@editorialbot set 10.5281/zenodo.10561760 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10561760

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Réda
  given-names: Clémence
  orcid: "https://orcid.org/0000-0003-3238-0258"
- family-names: Vie
  given-names: Jill-Jênn
  orcid: "https://orcid.org/0000-0002-9304-2220"
- family-names: Wolkenhauer
  given-names: Olaf
  orcid: "https://orcid.org/0000-0001-6105-2937"
doi: 10.5281/zenodo.10561760
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Réda
    given-names: Clémence
    orcid: "https://orcid.org/0000-0003-3238-0258"
  - family-names: Vie
    given-names: Jill-Jênn
    orcid: "https://orcid.org/0000-0002-9304-2220"
  - family-names: Wolkenhauer
    given-names: Olaf
    orcid: "https://orcid.org/0000-0001-6105-2937"
  date-published: 2024-01-25
  doi: 10.21105/joss.05973
  issn: 2475-9066
  issue: 93
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5973
  title: "stanscofi and benchscofi: a new standard for drug repurposing
    by collaborative filtering"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05973"
  volume: 9
title: "stanscofi and benchscofi: a new standard for drug repurposing by
  collaborative filtering"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05973 joss-papers#4953
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05973
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[Kevin-Mattheus-Moerman]

Congralations on this publication @clreda !

Thanks for editing @Nikoleta-v3

And a special thank you to the reviewers: @jaybee84, @abhishektiwari

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05973/status.svg
   :target: https://doi.org/10.21105/joss.05973

This is how it will look in your documentation:

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[clreda]

Thank you very much for coordinating the publication @Kevin-Mattheus-Moerman and a lot of thanks to @Nikoleta-v3, @jaybee84 and @abhishektiwari for their help in considerably improving the use of the softwares!