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[REVIEW]: Jabberwocky: an ontology-aware toolkit for manipulating text #2168

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whedon opened this issue Mar 19, 2020 · 13 comments
Open

[REVIEW]: Jabberwocky: an ontology-aware toolkit for manipulating text #2168

whedon opened this issue Mar 19, 2020 · 13 comments
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@whedon whedon commented Mar 19, 2020 •
edited by wdduncan

Submitting author: @sap218 (Samantha Pendleton)
Repository: https://github.com/sap218/jabberwocky
Version: v0.5.0.1
Editor: @majensen
Reviewer: @wdduncan, @balhoff
Archive: Pending

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/10502055165be490feaa389d51fe99d6"><img src="https://joss.theoj.org/papers/10502055165be490feaa389d51fe99d6/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/10502055165be490feaa389d51fe99d6/status.svg)](https://joss.theoj.org/papers/10502055165be490feaa389d51fe99d6)

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

@wdduncan & @balhoff, 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 @wdduncan

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 (@sap218) 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 @balhoff

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 (@sap218) 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?
@whedon whedon added the review label Mar 19, 2020
@whedon whedon mentioned this issue Mar 19, 2020
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@whedon whedon commented Mar 19, 2020

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @wdduncan, @balhoff 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:

watching

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

notifications

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 Mar 19, 2020

👉 Check article proof 📄 👈

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@whedon whedon commented Mar 19, 2020 

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1093/database/bau033 may be missing for title: tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles
- https://doi.org/10.3115/v1/p14-5010 may be missing for title: The Stanford CoreNLP natural language processing toolkit
- https://doi.org/10.1093/nar/gkr972 may be missing for title: Disease Ontology: a backbone for disease semantic integration
- https://doi.org/10.1016/j.ajhg.2008.09.017 may be missing for title: The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease
- https://doi.org/10.1093/bib/bbv011 may be missing for title: The role of ontologies in biological and biomedical research: a functional perspective

INVALID DOIs

- None
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@majensen majensen commented Mar 19, 2020

Quick thing if you can @sap218 - can you add the URLs that whedon-the-bot found above to your refs?
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@sap218 sap218 commented Mar 19, 2020

Currently I have (as an example for tagtog):

@ARTICLE{Cejuela2014-lv,
  title    = "tagtog: interactive and text-mining-assisted annotation of gene
              mentions in {PLOS} full-text articles",
  author = ..........,
  url      = {https://doi.org/10.1093/database/bau033}
}

and it prints as "Retrieved from: https://doi.org/10.1093/database/bau033"

is "url" the correct bibtex key?

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@arfon arfon commented Mar 19, 2020

@sap218 - please change them to keys like this:

doi  = "10.1093/database/bau033"

i.e. change the url to doi and strip off the https://doi.org/ preamble.
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@majensen majensen commented Mar 21, 2020

Thanks @arfon
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@sap218 sap218 commented Mar 21, 2020

Thanks @arfon - @majensen I believe I have fixed the DOI issue now
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@arfon arfon commented Mar 21, 2020

@whedon check references
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@whedon whedon commented Mar 21, 2020 

Reference check summary:

OK DOIs

- 10.1093/database/bau033 is OK
- 10.3115/v1/p14-5010 is OK
- 10.1093/nar/gkr972 is OK
- 10.1016/j.ajhg.2008.09.017 is OK
- 10.1093/bib/bbv011 is OK

MISSING DOIs

- None

INVALID DOIs

- None
@wdduncan wdduncan mentioned this issue Mar 29, 2020
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@wdduncan wdduncan commented Mar 30, 2020

I finished the checklist.

Comments:

  1. I could not install the repo as per the instructions. When running the install script, I received error:
ERROR: TEST FAILED: /Users/wdduncan/.local/lib/python3.7/site-packages/ does NOT support .pth files 
error: bad install directory or PYTHONPATH

This could be b/c I am using OS X, or perhaps b/c I installed using venv.

2.. The examples reference a file named /ontology/pocketmonsters.owl. But this file is not in the repo.

The github documentation would benefit from having examples of expected output and descriptions of what the output means.

The paper refers to the jabberwocky-tests as a way to see the software at work. But that directory contains no instructions.

How long is the software supposed paper to be?
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@majensen majensen commented Mar 30, 2020

@sap218 please have a look at above issues of @wdduncan
@wdduncan - paper can be long or short, as long as it covers the requirements in the "Software paper" section of the review
thanks!
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@danielskatz danielskatz commented Mar 30, 2020

Well, actually, a goal of JOSS is that papers should be reasonably short. In https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain, we say, "the paper should be between 250-1000 words" though some papers are somewhat longer.
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