[PRE REVIEW]: A new standard for drug repurposing by collaborative filtering: stanscofi and benchscofi #5870

editorialbot · 2023-09-25T08:44:31Z

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

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)

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The text was updated successfully, but these errors were encountered:

editorialbot · 2023-09-25T08:44:33Z

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editorialbot · 2023-09-25T08:44:35Z

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 · 2023-09-25T08:44:37Z

Wordcount for paper.md is 1752

editorialbot · 2023-09-25T08:45:07Z

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 · 2023-09-25T08:46:06Z

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

clreda · 2023-09-25T09:52:51Z

@editorialbot check references

clreda · 2023-09-25T09:53:23Z

Potential reviewers:
singhkakan
darinddv
struckma
jaybee84

editorialbot · 2023-09-25T09:53:38Z

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 · 2023-09-25T09:55:58Z

@editorialbot generate pdf

editorialbot · 2023-09-25T09:57:28Z

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

Kevin-Mattheus-Moerman · 2023-09-26T11:32:30Z

@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 ☝️ 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 · 2023-09-26T11:36:20Z

@editorialbot invite @jmschrei as editor

editorialbot · 2023-09-26T11:36:22Z

Invitation to edit this submission sent!

clreda · 2023-09-26T14:34:43Z

@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 · 2023-09-26T19:29:19Z

@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 · 2023-10-04T21:18:58Z

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

Kevin-Mattheus-Moerman · 2023-10-04T21:19:08Z

@editorialbot invite @lpantano as editor

editorialbot · 2023-10-04T21:19:11Z

Invitation to edit this submission sent!

Kevin-Mattheus-Moerman · 2023-10-13T08:09:20Z

@lpantano 👋

lpantano · 2023-10-13T16:07:01Z

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 · 2023-10-16T09:43:27Z

@editorialbot invite @Nikoleta-v3 as editor

editorialbot · 2023-10-16T09:43:29Z

Invitation to edit this submission sent!

Kevin-Mattheus-Moerman · 2023-10-16T09:44:22Z

@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 · 2023-10-17T17:43:27Z

Sure!

Nikoleta-v3 · 2023-10-17T17:43:47Z

@editorialbot assign me as editor

editorialbot · 2023-10-17T17:43:51Z

Assigned! @Nikoleta-v3 is now the editor

Nikoleta-v3 · 2023-10-17T17:45:24Z

Potential reviewers: singhkakan darinddv struckma jaybee84

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

Nikoleta-v3 · 2023-10-18T08:08:21Z

👋🏻 @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 · 2023-10-18T16:47:13Z

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

Nikoleta-v3 · 2023-10-19T07:50:04Z

Thank you! 🙏🏻

Nikoleta-v3 · 2023-10-19T07:51:08Z

@editorialbot add @jaybee84 as reviewer

editorialbot · 2023-10-19T07:51:10Z

@jaybee84 added to the reviewers list!

abhishektiwari · 2023-10-21T21:01:23Z

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

Nikoleta-v3 · 2023-10-23T09:10:25Z

Amazing 🙌🏻 thank you!

Nikoleta-v3 · 2023-10-23T09:10:44Z

@editorialbot add @abhishektiwari as reviewer

editorialbot · 2023-10-23T09:10:46Z

@abhishektiwari added to the reviewers list!

Nikoleta-v3 · 2023-10-23T09:14:38Z

@editorialbot start review

editorialbot · 2023-10-23T09:14:41Z

OK, I've started the review over in #5973.

editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Sep 25, 2023

editorialbot added Python TeX labels Sep 25, 2023

Kevin-Mattheus-Moerman added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Oct 4, 2023

editorialbot assigned Nikoleta-v3 Oct 17, 2023

editorialbot assigned jaybee84 Oct 19, 2023

editorialbot assigned abhishektiwari Oct 23, 2023

editorialbot closed this as completed Oct 23, 2023

[PRE REVIEW]: A new standard for drug repurposing by collaborative filtering: stanscofi and benchscofi #5870

[PRE REVIEW]: A new standard for drug repurposing by collaborative filtering: stanscofi and benchscofi #5870

Comments

editorialbot commented Sep 25, 2023 • edited

Status

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clreda commented Sep 25, 2023 • edited

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Nikoleta-v3 commented Oct 17, 2023 • edited

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editorialbot commented Sep 25, 2023 •

edited

clreda commented Sep 25, 2023 •

edited

Nikoleta-v3 commented Oct 17, 2023 •

edited