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

editorialbot commented 10 months ago

Submitting author: !--author-handle-->@clreda@Nikoleta-v3<!--end-editor-- Reviewers: @jaybee84, @abhishektiwari Archive: 10.5281/zenodo.10561760

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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 commented 7 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 7 months ago

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 commented 7 months ago

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

ID ref-luo2018computational already defined

clreda commented 7 months ago

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

Nikoleta-v3 commented 7 months ago

Thank you; that was fast 😄

Nikoleta-v3 commented 7 months ago

@editorialbot recommend-accept

editorialbot commented 7 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 7 months ago

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 commented 7 months ago

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4938, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 7 months ago

@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:

[x] 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.
[x] 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:

[x] 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 commented 7 months ago

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

editorialbot commented 7 months ago

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

clreda commented 7 months ago

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 commented 7 months ago

@editorialbot generate pdf

Kevin-Mattheus-Moerman commented 7 months ago

@editorialbot set 10.5281/zenodo.10561760 as archive

editorialbot commented 7 months ago

Done! archive is now 10.5281/zenodo.10561760

editorialbot commented 7 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 7 months ago

@editorialbot accept

editorialbot commented 7 months ago

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

editorialbot commented 7 months ago

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.

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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" ```

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editorialbot commented 7 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 7 months ago

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

Here's what you must now do:

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

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 6 months ago

Congralations on this publication @clreda !

Thanks for editing @Nikoleta-v3

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

editorialbot commented 6 months ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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clreda commented 6 months ago

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!

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