[REVIEW]: Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature #1708

whedon · 2019-09-05T02:36:08Z

Submitting author: @johnbachman (John Bachman)
Repository: https://github.com/indralab/adeft
Version: 0.5.3
Editor: @brainstorm
Reviewer: @GullyAPCBurns, @gbader
Archive: 10.5281/zenodo.3610528

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/a7edba4e988abfc85b01b034d373a729/status.svg)](https://joss.theoj.org/papers/a7edba4e988abfc85b01b034d373a729)

Reviewers and authors:

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Reviewer instructions & questions

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

Make sure you're logged in to your GitHub account
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 @brainstorm know.

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

Review checklist for @GullyAPCBurns

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

I confirm that I read and will adhere to the JOSS 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 (@johnbachman) 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 @gbader

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

I confirm that I read and will adhere to the JOSS 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 (@johnbachman) 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?

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

whedon · 2019-09-05T02:36:11Z

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

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

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

whedon · 2019-09-05T02:36:12Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-09-05T02:36:56Z

👉 Check article proof 📄 👈

brainstorm · 2019-09-16T00:54:01Z

@GullyAPCBurns @gbader, please go ahead and review away ;)

https://joss.readthedocs.io/en/latest/review_checklist.html

brainstorm · 2019-09-21T00:31:21Z

@GullyAPCBurns @gbader, if you have doubts about how to proceed, please ask!

gbader · 2019-09-26T17:55:06Z

Hello. I completed the review. The paper and software look good. My graduate student @JohnGiorgi helped review the software. We were able to get it to work and it successfully disambiguated “ER” (endoplasmic reticulum) in some test text.

brainstorm · 2019-09-27T02:44:33Z

Great, thanks @gbader!

I've noticed that you left out "State of the field" in your review, @johnbachman, could you please address that in the manuscript?

@GullyAPCBurns, let us know if you have any difficulties with the review process, I'm here to assist!

johnbachman · 2019-09-27T13:44:49Z

@brainstorm Will do!

johnbachman · 2019-10-11T17:39:41Z

@whedon generate pdf

whedon · 2019-10-11T17:39:43Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-10-11T17:40:08Z

👉 Check article proof 📄 👈

johnbachman · 2019-10-11T17:41:40Z

@brainstorm @gbader We added a new paragraph to the manuscript briefly describing where Adeft fits in the context of word sense disambiguation more generally.

brainstorm · 2019-10-20T06:37:45Z

Thanks @johnbachman! @GullyAPCBurns, please let me know if you have any doubts about the review process?

danielskatz · 2019-11-02T14:03:17Z

👋 @GullyAPCBurns, @gbader - How are your reviews coming?

gbader · 2019-11-02T17:52:43Z

The new paragraph looks great. In my view, this paper should be accepted.

Sorry for the delay. I like the idea of this journal, but one issue with running peer review on github is that the emails all come from github, which I happen to have filtered due to the large number of automated emails I get from github.

brainstorm · 2019-11-27T23:39:46Z

Thanks @gbader for your input, we are still waiting for @GullyAPCBurns... shall we regard him as missing reviewer at this point as he's not replying?

labarba · 2019-12-21T16:07:57Z

@brainstorm — this submission has been silent for a while. It looks like you have an MIA reviewer. I suppose you did try to reach them by other means? (email, Twitter) It may be time to take some executive decision here on finding a replacement reviewer.

johnbachman · 2019-12-24T19:56:31Z

I contacted @GullyAPCBurns by email on Dec 13th, he said he would be able to review.

GullyBurns · 2020-01-08T23:47:36Z

Sincere apologies for having been unresponsive. I will recommit to completing this review as quickly as possible in the next two weeks.

whedon · 2020-01-08T23:51:56Z

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

GullyAPCBurns · 2020-01-09T18:07:39Z

@danielskatz, I can't seem to check any of the boxes on the above form. Am I missing something very obvious?

danielskatz · 2020-01-09T18:19:59Z

Please see the first comment - did you accept the invite as mentioned in step 2 there?

GullyAPCBurns · 2020-01-09T18:22:15Z

Got it. Confirmed and yet more apologies for the delay.

GullyAPCBurns · 2020-01-10T07:25:33Z

I was able to review the paper and software. The code looks great and the documentation is exemplary. I ran the available Jupyter notebooks and was able to disambiguate 'Gut Cancer (GC)' effectively.

Again, I apologize for not having done this immediately. I'd recommend that you proceed with publication 'as is'.

brainstorm · 2020-01-10T07:30:08Z

Great, thanks @GullyAPCBurns!

kyleniemeyer · 2020-01-16T17:01:27Z

@whedon check references

whedon · 2020-01-16T17:01:46Z

Reference check summary:

OK DOIs

- 10.1093/bioinformatics/btl534 is OK
- 10.1093/bioinformatics/btq129 is OK
- 10.15252/msb.20177651 is OK
- 10.1145/1459352.1459355 is OK
- 10.1089/cmb.2005.12.554 is OK
- 10.1016/j.jbi.2013.09.009 is OK
- 10.3115/1572364.1572374 is OK
- 10.1016/j.jbi.2010.08.009 is OK
- 10.18653/v1/p19-1569 is OK
- 10.1197/jamia.m1533 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.18653/v1/p18-1230 is INVALID because of 'https://doi.org/' prefix

kyleniemeyer · 2020-01-16T17:03:09Z

@johnbachman your earlier requests to check the references didn't work because the PDF needed to be rebuilt first—thanks for adding those!

Can you remove https://doi.org/ from that one DOI causing an error? That should be the last edit needed.

johnbachman · 2020-01-16T18:13:12Z

Will do. After that's done, I will tag and release the latest version and update the Zenodo link.

johnbachman · 2020-01-16T18:13:20Z

@whedon generate pdf

whedon · 2020-01-16T18:13:53Z

👉 Check article proof 📄 👈

johnbachman · 2020-01-16T18:15:22Z

@whedon check references

whedon · 2020-01-16T18:15:40Z

Reference check summary:

OK DOIs

- 10.1093/bioinformatics/btl534 is OK
- 10.1093/bioinformatics/btq129 is OK
- 10.15252/msb.20177651 is OK
- 10.1145/1459352.1459355 is OK
- 10.1089/cmb.2005.12.554 is OK
- 10.1016/j.jbi.2013.09.009 is OK
- 10.3115/1572364.1572374 is OK
- 10.1016/j.jbi.2010.08.009 is OK
- 10.18653/v1/p19-1569 is OK
- 10.18653/v1/p18-1230 is OK
- 10.1197/jamia.m1533 is OK

MISSING DOIs

- None

INVALID DOIs

- None

johnbachman · 2020-01-16T18:25:31Z

@whedon set 10.5281/zenodo.3610528 as archive

whedon · 2020-01-16T18:25:34Z

I'm sorry @johnbachman, I'm afraid I can't do that. That's something only editors are allowed to do.

johnbachman · 2020-01-16T18:26:27Z

@brainstorm @kyleniemeyer The updated Zenodo archive (for Adeft version 0.5.5) is 10.5281/zenodo.3610528. Once that is updated we should be good to go.

kyleniemeyer · 2020-01-16T18:45:06Z

@whedon set 10.5281/zenodo.3610528 as archive

whedon · 2020-01-16T18:45:11Z

OK. 10.5281/zenodo.3610528 is the archive.

kyleniemeyer · 2020-01-16T18:45:22Z

@whedon accept

whedon · 2020-01-16T18:45:27Z

Attempting dry run of processing paper acceptance...

whedon · 2020-01-16T18:45:46Z

Reference check summary:

OK DOIs

- 10.1093/bioinformatics/btl534 is OK
- 10.1093/bioinformatics/btq129 is OK
- 10.15252/msb.20177651 is OK
- 10.1145/1459352.1459355 is OK
- 10.1089/cmb.2005.12.554 is OK
- 10.1016/j.jbi.2013.09.009 is OK
- 10.3115/1572364.1572374 is OK
- 10.1016/j.jbi.2010.08.009 is OK
- 10.18653/v1/p19-1569 is OK
- 10.18653/v1/p18-1230 is OK
- 10.1197/jamia.m1533 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2020-01-16T18:46:01Z

Check final proof 👉 openjournals/joss-papers#1231

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1231, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kyleniemeyer · 2020-01-16T18:51:23Z

@whedon accept deposit=true

whedon · 2020-01-16T18:51:29Z

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

whedon · 2020-01-16T18:52:15Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2020-01-16T18:52:15Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01708 joss-papers#1232
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01708
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

kyleniemeyer · 2020-01-16T18:57:22Z

Congrats @johnbachman on your article's publication in JOSS!

Many thanks to @GullyAPCBurns and @gbader for reviewing, and @brainstorm for editing.

whedon · 2020-01-16T18:57:27Z

🎉🎉🎉 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.01708/status.svg)](https://doi.org/10.21105/joss.01708)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01708">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01708/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01708/status.svg
   :target: https://doi.org/10.21105/joss.01708

This is how it will look in your documentation:

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johnbachman · 2020-01-16T19:27:09Z

Thanks all!! @brainstorm @kyleniemeyer @gbader @GullyAPCBurns

whedon added the review label Sep 5, 2019

whedon assigned brainstorm Sep 5, 2019

whedon mentioned this issue Sep 5, 2019

[PRE REVIEW]: Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature #1526

Closed

whedon assigned gbader Sep 6, 2019

whedon assigned GullyAPCBurns Jan 10, 2020

whedon added the accepted label Jan 16, 2020

kyleniemeyer closed this as completed Jan 16, 2020

whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020

editorialbot mentioned this issue Dec 9, 2023

[PRE REVIEW]: Augmenty: A Python Library for Structured Text Augmentation #6134

Closed

editorialbot mentioned this issue Jan 22, 2024

[PRE REVIEW]: BibDedupe: An Open-Source Python Library for Bibliographic Record Deduplication #6258

Closed

[REVIEW]: Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature #1708

[REVIEW]: Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature #1708

Comments

whedon commented Sep 5, 2019 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @GullyAPCBurns

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @gbader

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Sep 5, 2019

whedon commented Sep 5, 2019

whedon commented Sep 5, 2019

brainstorm commented Sep 16, 2019

brainstorm commented Sep 21, 2019

gbader commented Sep 26, 2019

brainstorm commented Sep 27, 2019

johnbachman commented Sep 27, 2019

johnbachman commented Oct 11, 2019

whedon commented Oct 11, 2019

whedon commented Oct 11, 2019

johnbachman commented Oct 11, 2019

brainstorm commented Oct 20, 2019

danielskatz commented Nov 2, 2019

gbader commented Nov 2, 2019

brainstorm commented Nov 27, 2019

labarba commented Dec 21, 2019

johnbachman commented Dec 24, 2019

GullyBurns commented Jan 8, 2020

whedon commented Jan 8, 2020

GullyAPCBurns commented Jan 9, 2020

danielskatz commented Jan 9, 2020

GullyAPCBurns commented Jan 9, 2020

GullyAPCBurns commented Jan 10, 2020

brainstorm commented Jan 10, 2020

kyleniemeyer commented Jan 16, 2020

whedon commented Jan 16, 2020

kyleniemeyer commented Jan 16, 2020

johnbachman commented Jan 16, 2020

johnbachman commented Jan 16, 2020

whedon commented Jan 16, 2020

johnbachman commented Jan 16, 2020

whedon commented Jan 16, 2020

johnbachman commented Jan 16, 2020

whedon commented Jan 16, 2020

johnbachman commented Jan 16, 2020 • edited Loading

kyleniemeyer commented Jan 16, 2020

whedon commented Jan 16, 2020

kyleniemeyer commented Jan 16, 2020

whedon commented Jan 16, 2020

whedon commented Jan 16, 2020

whedon commented Jan 16, 2020

kyleniemeyer commented Jan 16, 2020

whedon commented Jan 16, 2020

whedon commented Jan 16, 2020

whedon commented Jan 16, 2020

kyleniemeyer commented Jan 16, 2020

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johnbachman commented Jan 16, 2020

whedon commented Sep 5, 2019 •

edited

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johnbachman commented Jan 16, 2020 •

edited

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