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[REVIEW]: Pubmed Parser: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset XML Dataset #1979

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whedon opened this issue Dec 21, 2019 · 63 comments
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@whedon whedon commented Dec 21, 2019

Submitting author: @titipata (Titipat Achakulvisut)
Repository: https://github.com/titipata/pubmed_parser
Version: v0.2.3
Editor: @majensen
Reviewer: @timClicks, @tleonardi
Archive: 10.5281/zenodo.3660006

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/207c45f0d1fc3b190cbeff2b2c27d128"><img src="https://joss.theoj.org/papers/207c45f0d1fc3b190cbeff2b2c27d128/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/207c45f0d1fc3b190cbeff2b2c27d128/status.svg)](https://joss.theoj.org/papers/207c45f0d1fc3b190cbeff2b2c27d128)

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

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

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Please try and complete your review in the next two weeks

Review checklist for @timClicks

Conflict of interest

  • 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

General checks

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

Functionality

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

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

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

Conflict of interest

  • 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

General checks

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

Functionality

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

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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • 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?
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@whedon whedon commented Dec 21, 2019

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

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf
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@whedon whedon commented Dec 21, 2019

Attempting to check references...
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@whedon whedon commented Dec 21, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Dec 21, 2019


OK DOIs

- 10.1186/s12859-019-2958-3 is OK
- 10.7287/peerj.preprints.27479v2 is OK
- 10.18653/v1/w18-2307 is OK
- 10.3233/shti190172 is OK
- 10.1371/journal.pone.0198030 is OK
- 10.1109/hpcc/smartcity/dss.2019.00217 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Dec 21, 2019

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@majensen majensen commented Jan 7, 2020

Happy New Year @timClicks, @tleonardi - just a gentle reminder to please begin your review of #1979.
Thanks

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@titipata titipata commented Jan 22, 2020

Hi all,

Just a quick update here.

  • For the repository, I updated it according to @tleonardi comments. I added documentation guidelines for the repository and in README. I also created a test folder (integrated with TravisCI) and sphinx documentation on the repository which I will be updating in this coming week. We hope to make the documentation better!

  • For the writing, we fixed the documents according to the reviews. These include some writing and references. Let me know if it can be further improved!

  • For the authorship, we discussed and changed the authorship to just me, Daniel Acuna (mentor, provide ideas, contribute to source code), and Konrad Kording (mentor/advisor and provide funding). I think that will be suitable.

  • We add the statement of need in the first paragraph of the README. We have a wide range of audiences so we stated as a tool for NLP researchers. I'm not sure how it should be done properly.

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@majensen majensen commented Jan 23, 2020

@timClicks, how is it going with your review?

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@tleonardi tleonardi commented Jan 27, 2020

@whedon generate pdf

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@whedon whedon commented Jan 27, 2020

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@tleonardi tleonardi commented Jan 27, 2020

Hi @titipata,
I'm happy with all the changes you've made, great job writing and automating the tests!
I only have a few concerns left, mostly regarding the README and documentation.

I think it would be important, at the beginning of the README, to describe what kind of information is contained in the XML files and what can be obtained with pubmed_parser.
You could also add an index with links to the various sections of the README (Installation, Documentation, Examples, Citation, etc...).
Regarding the documentation, I think many functions lack a high level explanation of what they do: what do the input XMLs contain? What's contained in the results returned?
Lastly, I've just opened an issue indicating some missing bits in the API docs.
All the rest is looking good!

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@titipata titipata commented Jan 27, 2020

@tleonardi Thank you so much for the details comments! I'll update the API documentation according to your comment by the end of this week. I will also edit the README so that it contains information about the XML files. I'll tag you once it's done.

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@majensen majensen commented Jan 29, 2020

@timClicks are you still able to review this work (#1979)? Thanks for any update.

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@timClicks timClicks commented Jan 29, 2020

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@timClicks timClicks commented Jan 29, 2020

@titipata Thank you for taking the time to publish this package as open source software. I've reviewed it and the paper, and have nothing further to add above @tleonardi's comments.

@majensen I have reviewed the submission and recommend accepting it for publication.

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@majensen majensen commented Jan 29, 2020

@timClicks very much appreciated. I will start my due diligence -- @titipata you may see some minor PRs come your way. Hope to accomplish over next couple of days.

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@titipata titipata commented Jan 29, 2020

Thank you so much @tleonardi @timClicks @majensen for all your efforts and great reviews! We really appreciate it! Looking forward to the PRs.

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@majensen majensen commented Feb 1, 2020

@whedon generate pdf

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@whedon whedon commented Feb 1, 2020

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@majensen majensen commented Feb 1, 2020

@whedon check references

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@whedon whedon commented Feb 1, 2020

Reference check summary:

OK DOIs

- 10.1186/s12859-019-2958-3 is OK
- 10.7287/peerj.preprints.27479v2 is OK
- 10.18653/v1/w18-2307 is OK
- 10.3233/shti190172 is OK
- 10.1371/journal.pone.0198030 is OK
- 10.1109/hpcc/smartcity/dss.2019.00217 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@majensen majensen commented Feb 1, 2020

Hi @titipata - I've created a PR for you to consider: titipata/pubmed_parser#84

Also, in the code example in the text, would you consider changing
data/medline16n0902.xml.gz
to
data/pubmed20n0014.xml.gz
since the latter file is actually present in the data directory of the repo? Then a user can simply run the sample code after cloning and installing.

thanks

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@majensen majensen commented Feb 1, 2020

Hi @tleonardi - I notice one box is left unchecked on your review (Functionality documentation). Do you still have issues here? Thanks for having a look.

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@tleonardi tleonardi commented Feb 3, 2020

Hi @majensen,
I just hadn't checked the last changes that @titipata introduced after my last comments. I have checked now and the API docs look good! I haven't seen changes in the README, but my suggestions where mostly minor details. No need to hold the publication because of this.
Overall, pubmed_parser is a solid software that's going to be of great help to the scientific community (as shown by the number of publications that already use it). I am happy to recommend it for publication in JOSS.
Congrats @titipata, great job!

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@whedon whedon commented Feb 7, 2020

OK. 10.5281/zenodo.3648715 is the archive.

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@majensen majensen commented Feb 7, 2020

@whedon set 0.2.2 as version

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@whedon whedon commented Feb 7, 2020

OK. 0.2.2 is the version.

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@majensen majensen commented Feb 7, 2020

@openjournals/joss-eics, the reviewers and I recommend this work for publication; please review. Thanks!

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@kthyng kthyng commented Feb 7, 2020

@whedon generate pdf

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@whedon whedon commented Feb 7, 2020

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@kthyng kthyng commented Feb 7, 2020

@titipata Your paper looked good but your references had typos. I fixed them in a PR. See if you want to merge the changes: #86

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@titipata titipata commented Feb 8, 2020

@kthyng Thank you so much for the fix. I merged the PR!

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@titipata titipata commented Feb 8, 2020

@majensen @kthyng Do I need to create a new archive release and DOI for the repository?

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@majensen majensen commented Feb 8, 2020

@titipata I believe you can update the archive with a new version and keep the DOI- just report back the new version here. Thanks!

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@titipata titipata commented Feb 8, 2020

@majensen I somehow updated to v0.2.3 instead and the associated DOI should be 10.5281/zenodo.3660006 instead. Sorry for the confusion but this should be the final version!

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@kthyng kthyng commented Feb 8, 2020

@whedon add 10.5281/zenodo.3660006 as archive

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@whedon whedon commented Feb 8, 2020

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands
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@kthyng kthyng commented Feb 8, 2020

@whedon set 10.5281/zenodo.3660006 as archive

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@whedon whedon commented Feb 8, 2020

OK. 10.5281/zenodo.3660006 is the archive.

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@kthyng kthyng commented Feb 8, 2020

@whedon set v0.2.3 as version

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@whedon whedon commented Feb 8, 2020

OK. v0.2.3 is the version.

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@kthyng kthyng commented Feb 8, 2020

@whedon accept

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@whedon whedon commented Feb 8, 2020

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Feb 8, 2020

Reference check summary:

OK DOIs

- 10.1186/s12859-019-2958-3 is OK
- 10.7287/peerj.preprints.27479v2 is OK
- 10.18653/v1/w18-2307 is OK
- 10.3233/shti190172 is OK
- 10.1371/journal.pone.0198030 is OK
- 10.1109/hpcc/smartcity/dss.2019.00217 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Feb 8, 2020

Check final proof 👉 openjournals/joss-papers#1282

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1282, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@kthyng kthyng commented Feb 8, 2020

@whedon accept deposit=true

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@whedon whedon commented Feb 8, 2020

Doing it live! Attempting automated processing of paper acceptance...
@whedon whedon added the accepted label Feb 8, 2020
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@whedon whedon commented Feb 8, 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Feb 8, 2020

🚨🚨🚨 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 👉 openjournals/joss-papers#1283
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01979
  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...

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@kthyng kthyng commented Feb 8, 2020

Congratulations to @titipata on your new publication! Thanks to @majensen for editing, and to @timClicks and @tleonardi for your time and expertise reviewing.

@kthyng kthyng closed this Feb 8, 2020
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@whedon whedon commented Feb 8, 2020

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01979/status.svg)](https://doi.org/10.21105/joss.01979)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01979">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01979/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01979/status.svg
   :target: https://doi.org/10.21105/joss.01979

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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@titipata titipata commented Feb 9, 2020

Thanks @kthyng! And thank you so much @majensen, @tleonardi, @tleonardi for editing our submission.

tag @daniel-acuna @koerding here!

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