[PRE REVIEW]: PAVER: Pathway Analysis Visualization with Embedding Representations

[editorialbot]

Submitting author: @willgryan (William G Ryan V)
Repository: https://github.com/willgryan/PAVER/
Branch with paper.md (empty if default branch):
Version: 0.0.0.9000
Editor: Pending
Reviewers: Pending
Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/a54a1a176f653bf025e42617911abdfe"><img src="https://joss.theoj.org/papers/a54a1a176f653bf025e42617911abdfe/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/a54a1a176f653bf025e42617911abdfe/status.svg)](https://joss.theoj.org/papers/a54a1a176f653bf025e42617911abdfe)

Author instructions

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

@willgryan if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

Hello human, 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:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (1357.9 files/s, 152592.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               22            427            367           1182
Markdown                         4            171              0            668
TeX                              1             19              0            517
YAML                             2              1              4             74
Rmd                              2             46             68             33
JSON                             1              0              0             19
-------------------------------------------------------------------------------
SUM:                            32            664            439           2493
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1126/science.1170411 is OK
- 10.1007/978-1-0716-2257-5_25 is OK
- 10.1101/2023.08.28.555113 is OK
- 10.1097/ACM.0b013e3181f41e8c is OK
- 10.1111/imcb.12404 is OK
- 10.3389/fgene.2020.610798 is OK
- 10.3389/fphys.2015.00383 is OK
- 10.3389/fbinf.2021.638255 is OK
- 10.1371/journal.pcbi.1010348 is OK
- 10.1186/gb-2011-12-8-125 is OK
- 10.1038/s41467-019-11461-w is OK
- 10.1038/sdata.2016.18 is OK
- 10.1093/bib/bbac003 is OK
- 10.48550/arXiv.1301.3781 is OK
- 10.5281/zenodo.8156248 is OK
- 10.1038/75556 is OK
- 10.1371/journal.pcbi.1010348 is OK
- 10.46570/utjms.vol11-2023-822 is OK
- 10.46570/utjms.vol12-2024-823 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 776

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

A framework for generating interactive reports for cancer genome analysis
Submitting author: @aokad
Handling editor: @pjotrp (Retired)
Reviewers: @chfi
Similarity score: 0.8209

TDAstats: R pipeline for computing persistent homology in topological data analysis
Submitting author: @rrrlw
Handling editor: @leeper (Retired)
Reviewers: @corybrunson
Similarity score: 0.8117

graphsim: An R package for simulating gene expression data from graph structures of biological pathways
Submitting author: @TomKellyGenetics
Handling editor: @majensen (Active)
Reviewers: @rcannood, @corybrunson
Similarity score: 0.8102

wolfexplorer: a tool for visualization and exploration of complex multi-year multi-specimen datasets
Submitting author: @zkuralt
Handling editor: @trallard (Retired)
Reviewers: @amoeba
Similarity score: 0.8081

geneXplainR: An R interface for the geneXplain platform
Submitting author: @pstegma
Handling editor: @mgymrek (Retired)
Reviewers: @selbouhaddani
Similarity score: 0.8057

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[Kevin-Mattheus-Moerman]

@willgryan thanks for this submission. As AEiC I am here to help with initial steps for your submission. I have just triggered a scope review as I need some help from the editorial board to determine if this work is in scope. This scope review will check if this work is in scope in terms of the functionality offered, as well as if it conforms to our substantial scholarly effort criteria. The scope review should take about 2 weeks to complete.

[Kevin-Mattheus-Moerman]

@willgryan the editorial board has concluded the scope review for this work. Unfortunately it is was found not to be in scope due to its relatively small size and limited functionality.

We will now proceed to reject this submission from JOSS.

We do hope you will consider JOSS for any future (re)submissions that are of a more substantial nature.

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.

[willgryan]

@Kevin-Mattheus-Moerman much thanks to the editorial board for their time and thoughtful consideration! I will be sure to keep "limited functionality" in mind for future submissions 🙂

[Kevin-Mattheus-Moerman]

@willgryan yes, and just to elaborate on the "functionality", typically JOSS publishes software with a strong scientific research application, i.e. software which has/can have an impact on scientific findings. A minor utility tool for instance typically doesn't, is likely not cited, and therefore is out of scope for JOSS. Although we have published some predominantly visualisation related software packages, we usually look for analysis applications too. So for future submissions, make sure they are more substantial in terms of code functionality offered, and ensure they include analysis+visualisation both of which are important to scientific research.

[willgryan]

@Kevin-Mattheus-Moerman thanks for explaining! I might have unintentionally misled the editorial board by including "visualization" in the software name PAVER.

I believe PAVER's main contribution is its analysis functionality. Summarization of pathways identified in omics experiments into groups and identifying the most-representative term (MRT) of each group remains an open scientific problem for bioinformatics. Different methods & tools have been published on this topic over the years to address this, e.g., 1, 2, 3.

Along those lines, PAVER implements a novel algorithm for summarizing pathways and identifying a group's MRT using the concept of average embeddings. The visualization functionality is meant to help end users interpret the results of their analysis with PAVER.

As a bioinformatics researcher, I don't see PAVER as a minor utility tool. It directly addresses a strong scientific problem for our field using a novel approach. IMHO, it has already made a significant impact of scientific findings as well, cited 3 times so far for the purpose of analyzing and interpreting the results of omics pathway analyses. I would hope the editorial board could reconsider our submission in light of this information 🙂