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

[editorialbot]

Submitting author: !--author-handle-->@clreda<!--end-author-handle-- (Clémence Réda) Repository: https://github.com/RECeSS-EU-Project/stanscofi/ Branch with paper.md (empty if default branch): Version: v2.0.0 Editor: !--editor-->@Nikoleta-v3<!--end-editor-- Reviewers: @jaybee84, @abhishektiwari Managing EiC: Kevin M. Moerman

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Thanks for submitting your paper to JOSS @clreda. Currently, there isn't a JOSS editor assigned to your paper.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (607.1 files/s, 119620.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          13            281           1120           1526
TeX                              1             38              0            341
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           2904
-------------------------------------------------------------------------------

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
- 10.1186/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
- 10.1038/msb.2011.26 is OK
- 10.1093/bioinformatics/bty013 is OK
- 10.1093/bioinformatics/btw770 is OK
- 10.3389/fphar.2021.784171 is OK
- 10.1016/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

- 10.1109/icdm.2010.127 may be a valid DOI for title: Factorization machines
- 10.1093/bioinformatics/btz965 may be a valid DOI for title: Neural inductive matrix completion with graph convolutional networks for miRNA-disease association prediction

INVALID DOIs

- 110.5281/zenodo.7982969 is INVALID

[editorialbot]

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

[clreda]

@editorialbot check references

[clreda]

Potential reviewers: singhkakan darinddv struckma jaybee84

[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

[clreda]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@clreda thanks for this submission. Can you clarify what this JOSS submission involves in therms of code reviewed.

Am I correct in saying that it involves the joint software contained in the following 2 repositories: https://github.com/RECeSS-EU-Project/stanscofi https://github.com/RECeSS-EU-Project/benchscofi

The former is listed here as the core repository for the paper etc and the stanscofi aspects. The software report :point_up: above reflects the content for this repository.

The latter is for benchscofi and running cloc locally provided.

github.com/AlDanial/cloc v 1.90  T=0.06 s (790.7 files/s, 158768.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          35            647            800           3026
Jupyter Notebook                 4              0           3405            794
Markdown                         2            114              0            263
JSON                             2              0              0            113
YAML                             2              6              9             57
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            46            767           4214           4256
-------------------------------------------------------------------------------

[Kevin-Mattheus-Moerman]

@editorialbot invite @jmschrei as editor

[editorialbot]

Invitation to edit this submission sent!

[clreda]

@Kevin-Mattheus-Moerman Thanks for managing the reviewing process!

Yes, the submission involves both stanscofi and benchscofi repositories. The joint code allows to benchmark several drug repurposing approaches on several datasets, whereas automating as much as possible the model training and validation procedures. The reason why the code is split into two repositories is to increase modularity and usability of the code, as stanscofi and benchscofi serve different purposes. stanscofi is targeted at the automation of the drug repurposing pipeline for model training and testing, whereas benchscofi only aims at providing implementations of the state-of-the-art, and relies on the stanscofi module.

Please let me know if the paragraph above answers your concerns.

[jmschrei]

@Kevin-Mattheus-Moerman unfortunately, I need a break from managing submissions as I'm going on the faculty job market this cycle. I should be more free in a month.

[Kevin-Mattheus-Moerman]

@lpantano do you think you could help edit this one?

[Kevin-Mattheus-Moerman]

@editorialbot invite @lpantano as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@lpantano :wave:

[lpantano]

Hi, sorry, I am in a family leave in Spain due to an emergency. Better for other to take it since I don't know how my next month looks like.

[Kevin-Mattheus-Moerman]

@editorialbot invite @Nikoleta-v3 as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@Nikoleta-v3 this may be somewhat outside of your core area but since you also work on data science I thought you may be able to help.

[Nikoleta-v3]

Sure!

[Nikoleta-v3]

@editorialbot assign me as editor

[editorialbot]

Assigned! @Nikoleta-v3 is now the editor

[Nikoleta-v3]

Potential reviewers: singhkakan darinddv struckma jaybee84

Thank you for the suggestions! I will start inviting potential reviewers tomorrow.

[Nikoleta-v3]

👋🏻 @singhkakan @darinddv @struckma @jaybee84 would any of you be willing to review this submission for JOSS?

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

The submission I'd like you to review is titled: "A new standard for drug repurposing by collaborative filtering: stanscofi and benchscofi". You can find more information at the top of this Github issue 🆙

Please let me know if you're available 😄 Thank you!

[jaybee84]

@Nikoleta-v3 I would be happy to review this. Thanks for inviting me.

[Nikoleta-v3]

Thank you! 🙏🏻

[Nikoleta-v3]

@editorialbot add @jaybee84 as reviewer

[editorialbot]

@jaybee84 added to the reviewers list!

[abhishektiwari]

@Nikoleta-v3 I am familiar with CADD and Cheminformatics domains and open to review to this submission.

[Nikoleta-v3]

Amazing 🙌🏻 thank you!

[Nikoleta-v3]

@editorialbot add @abhishektiwari as reviewer

[editorialbot]

@abhishektiwari added to the reviewers list!

[Nikoleta-v3]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5973.