Joss-reviews: [REVIEW]: matchms - processing and similarity evaluation of mass spectrometry data

[whedon]

Submitting author: @florian-huber (Florian Huber)
Repository: https://github.com/matchms/matchms
Version: 0.4.0
Editor: @arfon
Reviewer: @bittremieux, @kaibioinfo
Archive: 10.5281/zenodo.4001991

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Reviewers and authors:

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Reviewer instructions & questions

@bittremieux & @kaibioinfo, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

✨ Please try and complete your review in the next six weeks ✨

Review checklist for @bittremieux

Conflict of interest

• [X] 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

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

General checks

• [X] Repository: Is the source code for this software available at the repository url?
• [X] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [X] Contribution and authorship: Has the submitting author (@florian-huber) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [X] Installation: Does installation proceed as outlined in the documentation?
• [X] Functionality: Have the functional claims of the software been confirmed?
• [X] 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

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

• [X] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [X] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [X] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [X] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [X] 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?

Review checklist for @kaibioinfo

Conflict of interest

• [x] 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

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

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@florian-huber) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @bittremieux, @kaibioinfo it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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[whedon]

Reference check summary:

OK DOIs

- 10.1038/nbt.3597 is OK
- 10.1073/pnas.1203689109 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1021/acs.jproteome.8b00717 is OK
- 10.1093/nar/gkz1019 is OK
- 10.1002/jms.1777 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1038/s41592-019-0686-2 is INVALID because of 'https://doi.org/' prefix
- 10.1021/jasms.8b04453 is INVALID

[arfon]

@bittremieux, @kaibioinfo - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Any questions/concerns please let me know.

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[kaibioinfo]

I added three issues:

One rather major:
Current scope of the software is not clear from the paper (https://github.com/matchms/matchms/issues/95#issue-651066231)

And two minors:
Cosine similarity misses weighting and removal of precursor
https://github.com/matchms/matchms/issues/96#issue-651068504

Regular expression for molecular formulas is ambiguous
https://github.com/matchms/matchms/issues/94#issue-651063454

[bittremieux]

I would recommend a few more citations to relevant (Python) packages that cover similar functionality, such as OpenMS/pyOpenMS and spectrum_utils (disclaimer: this is my own package). MSnbase is a highly relevant R package as well. Given the high overlap between matchms and spectrum_utils a more detailed comparison in terms of spectrum processing functionality and computational efficiency might be warranted, although as spectrum_utils developer I leave the final decision about this to @arfon.

Minor comments for the manuscript:

• Abstract: "full quantitative analysis" -> I suggest to rephrase this to avoid confusion with quantitative metabolomics experiments, i.e. where the abundance of the metabolites is measured.
• The correct reference for Numba is: https://doi.org/10.1145/2833157.2833162

I agree with the issues raised by @kaibioinfo, especially on scope. This is not necessarily a major problem, but should be clarified better. Additionally, I have created two more small issues:

• matchms/matchms#100: Install matchms using pip.
• matchms/matchms#101: Documentation improvements.

[arfon]

Thanks @bittremieux, @kaibioinfo for your feedback/reviews. @florian-huber - please let us know here when you've managed to incorporate feedback from the reviews.

[florian-huber]

Thanks @arfon and in particular @bittremieux and @kaibioinfo for reviewing.
The raised comments were very valuable and helped us improve the package.

We generally agree with the feedback we received, and think that we could address most issues.
The main exception is making matchms a pip installable package (https://github.com/matchms/matchms/issues/100), which is complicated because matchms relies on rdkit, a conda package. Still, we hope to address this in the future, maybe releasing a lightweight matchms version for pip.

Other than that, we incorporated https://github.com/matchms/matchms/issues/94, https://github.com/matchms/matchms/issues/101 and the minor comments by @bittremieux above. I believe we addressed the main points of https://github.com/matchms/matchms/issues/96 by fixing and extending the cosine score functions. In addition, we currently work on providing more filter functions do address the remaining points (PR https://github.com/matchms/matchms/pull/119). Since most of the still missing functionality could -though cumbersome- be achieve using present filters, this might be less urgent with respect to the JOSS manuscript.

Finally, the major point raised by @kaibioinfo in https://github.com/matchms/matchms/issues/95 (overlapping with recommendation by @bittremieux to make the scope clearer) was addressed in two ways.
We extended the importing options of matchms, now including mzML, mzXML, msp, and metabolomics-USI. In addition, we now refer to more related packages and state more clearly the limitations of matchms (see https://github.com/matchms/matchms/issues/95 for more detailed description).

Manuscript and code update:

• the mentioned changes were made into a new matchms release (version 0.5.0).
• the edited paper and bibliography was added to the master branch.
• we added one additional author (Efraín Manuel Villanueva Castilla, who contributed code to this latest release).

Please let us know if that is sufficiently addressing the feedback, or further changes need to be made.
Many thanks!

[kaibioinfo]

I'm happy with the revision.

[florian-huber]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[bittremieux]

It looks good for me as well, I just have a few really minor comments:

• Missing reference for mzML on page 1: 10.1074/mcp.R110.000133
• I would recommend consistent and correct spelling of some terms throughout the manuscript and figures, for example: Inchi/InchiKey -> InChI/InChIKey, Smiles -> SMILES, _m/z_ should be italicized, NumPy, SciPy

[florian-huber]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[florian-huber]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[florian-huber]

Thanks for the comments @bittremieux.
We changed the spelling as you suggested (in text and figures).

[bittremieux]

Excellent. I don't think the mzML paper is actually cited yet in the manuscript where it is first mentioned though.

[florian-huber]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[florian-huber]

Thanks a lot for checking this! I corrected the reference entry, it should now be inserted where mzML is first mentioned.

[florian-huber]

@arfon Let me know if there is anything we should do to proceed. Thanks!

[arfon]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[arfon]

@bittremieux & @kaibioinfo - if you have a moment to revisit the checklists above to mark off the last few items (which I believe have now been addressed) that would be much appreciated.

[arfon]

@florian-huber - I've made a couple of minor edits in https://github.com/matchms/matchms/pull/137.

After merging https://github.com/matchms/matchms/pull/137, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

[florian-huber]

Great, thanks @arfon
I merged the minor edits and made a new release (0.5.2) which is now on Zenodo.
The DOI is 10.5281/zenodo.4001991

(https://doi.org/10.5281/zenodo.4001991)

[bittremieux]

Checklist completed.

[arfon]

@whedon set 10.5281/zenodo.4001991 as archive

[whedon]

OK. 10.5281/zenodo.4001991 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1038/nbt.3597 is OK
- 10.1145/2833157.2833162 is OK
- 10.1073/pnas.1203689109 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1021/acs.jproteome.8b00717 is OK
- 10.1093/nar/gkz1019 is OK
- 10.1002/jms.1777 is OK
- 10.1002/pmic.201300246 is OK
- 10.1038/nmeth.3959 is OK
- 10.1021/acs.analchem.9b04884 is OK
- 10.1093/bioinformatics/bty046 is OK
- 10.1101/2020.05.09.086066 is OK
- 10.1074/mcp.R110.000133 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1021/jasms.8b04453 is INVALID

[whedon]

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1680

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1680, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[arfon]

>
> INVALID DOIs
> 
> - 10.1021/jasms.8b04453 is INVALID

Not sure what's going on with that DOI, (perhaps the publisher never registered it) but it's definitely correct for this: https://pubs.acs.org/doi/pdf/10.1021/jasms.8b04453

@florian-huber - this is ready to accept and publish. The EiC on rotation will handle this in the next couple of days.

[florian-huber]

Thanks a lot @arfon!

And short feedback: as first-time submitter to JOSS I really liked the clear and transparent process, as well as the constructive feedback. Really nice!

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1685
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02411
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? Notify your editorial technical team...

[arfon]

@bittremieux, @kaibioinfo - many thanks for your reviews here ✨

@florian-huber - your paper is now accepted into JOSS :zap::rocket::boom:

[whedon]

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

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