[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.3608243

Status

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

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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:

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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?

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:

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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

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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!

brainstorm · 2020-01-10T07:30:12Z

@whedon check references from branch joss-paper

whedon · 2020-01-10T07:30:15Z

Attempting to check references... from custom branch joss-paper

whedon · 2020-01-10T07:30:36Z

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

MISSING DOIs

- https://doi.org/10.1089/cmb.2005.12.554 may be missing for title: Word sense disambiguation in the biomedical domain: an overview
- https://doi.org/10.1016/j.jbi.2013.09.009 may be missing for title: Determining the difficulty of Word Sense Disambiguation
- https://doi.org/10.3115/1572364.1572374 may be missing for title: Disambiguation of Biomedical Abbreviations
- https://doi.org/10.1016/j.jbi.2010.08.009 may be missing for title: Disambiguation in the biomedical domain: the role of ambiguity type
- https://doi.org/10.18653/v1/p19-1569 may be missing for title: Language Modelling Makes Sense: Propagating Representations through WordNet for Full-Coverage Word Sense Disambiguation
- https://doi.org/10.18653/v1/p18-1230 may be missing for title: Incorporating Glosses into Neural Word Sense Disambiguation
- https://doi.org/10.1197/jamia.m1533 may be missing for title: A multi-aspect comparison study of supervised word sense disambiguation

INVALID DOIs

- None

brainstorm · 2020-01-10T07:32:11Z

@whedon generate pdf

whedon · 2020-01-10T07:32:52Z

👉 Check article proof 📄 👈

brainstorm · 2020-01-10T07:37:08Z

Looks good to my too, @johnbachman, next step is for you to deposit it on Zenodo and we'll archive it in JOSS, let me know if you run into any problems with that. Pretty close to publication now ;)

johnbachman · 2020-01-13T16:24:44Z

Great, will do, thanks to all!

johnbachman · 2020-01-14T18:24:07Z

(Edited with correct info)

Hi @brainstorm, the release for the paper is up at Zenodo here: https://zenodo.org/record/3608243

The version is 0.5.3, DOI is 10.5281/zenodo.3608243

Also, a question--should we add in DOIs for the 7 listed as "missing"?

brainstorm · 2020-01-14T19:27:27Z

@whedon generate pdf

whedon · 2020-01-14T19:28:28Z

👉 Check article proof 📄 👈

johnbachman · 2020-01-14T19:28:47Z

@brainstorm Sorry, updated the comment above with correct DOI information

brainstorm · 2020-01-14T19:30:59Z

@whedon set https://zenodo.org/record/3608243 as archive

whedon · 2020-01-14T19:31:02Z

https://zenodo.org/record/3608243 doesn't look like an archive DOI.

brainstorm · 2020-01-14T19:31:35Z

@whedon set 10.5281/zenodo.3608243 as archive

whedon · 2020-01-14T19:31:39Z

OK. 10.5281/zenodo.3608243 is the archive.

brainstorm · 2020-01-14T19:33:04Z

No worries John, gotcha. @danielskatz LGTM, can you find any irregularity pre-publishing it for good?

danielskatz · 2020-01-15T11:16:39Z

👋 @openjournals/joss-eics - I think this may be ready for you

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

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[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

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

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whedon commented Sep 5, 2019 •

edited

johnbachman commented Jan 14, 2020 •

edited