[REVIEW]: A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it.

whedon commented 6 years ago

Submitting author: @bryan-brancotte (Bryan Brancotte) Repository: https://github.com/IFB-ElixirFr/edam-browser Version: v1.0.0 Editor: @pjotrp Reviewer: @alexgarciac Archive: 10.5281/zenodo.1314288

Status

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Markdown: [![status](http://joss.theoj.org/papers/0f6e424f64f3eca9989e929826bd3fad/status.svg)](http://joss.theoj.org/papers/0f6e424f64f3eca9989e929826bd3fad)

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) 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

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

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Review checklist for @alexgarciac

Conflict of interest

[x] 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

[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] Version: Does the release version given match the GitHub release (v1.0.0)?
[x] Authorship: Has the submitting author (@bryan-brancotte) 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?
[ ] 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

bryan-brancotte commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

bryan-brancotte commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

bryan-brancotte commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

hmenager commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

hmenager commented 6 years ago

Hello @pjotrp and @alexgarciac, we have now finished revising the paper, based on the suggestions you made @alexgarciac. Thank you so much for all your comments, I hope the new version of the manuscript adresses all of them. Please let us know if there are still some outstanding issues with the submission.

pjotrp commented 6 years ago

@alexgarciac are you happy to release this submission into the public domain?

pjotrp commented 6 years ago

ping @alexgarciac

alexgarciac commented 6 years ago

Hi, I have read the latest version and it looks ready to go. @pjotrp answering your question: yes, ready to go into the public domain.

alexgarciac commented 6 years ago

all check boxes (the pertinent ones) on the issue tracker have been checked.

pjotrp commented 6 years ago

Thank you @alexgarciac! :+1: Thank you @bryan-brancotte for your great contribution, there should be more linked data contributions like these.

The review process is now complete. To finalize your submission and accept your paper in JOSS, we need two things. First, can you confirm that all references in your bibliography have a DOI (if one exists).

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Create a GitHub release of the current version of your software repository
Deposit that release with Zenodo, figshare, or a similar DOI issuer.
Post a comment here with the DOI for the release.

bryan-brancotte commented 6 years ago

Thanks @alexgarciac @pjotrp for making this contribution being published ! Here is the DOI https://doi.org/10.5281/zenodo.1314288

pjotrp commented 6 years ago

@whedon set 10.5281/zenodo.1314288 as archive

whedon commented 6 years ago

OK. 10.5281/zenodo.1314288 is the archive.

pjotrp commented 6 years ago

@arfon we are ready to accept this paper. @bryan-brancotte note that arfon is still on holiday, so it may take a little while.

bryan-brancotte commented 6 years ago

no problem, thanks

arfon commented 6 years ago

@alexgarciac - many thanks for your review here and to @pjotrp for editing this submission ✨

@bryan-brancotte - your paper is now accepted into JOSS and your DOI is: https://doi.org/10.21105/joss.00698 ⚡️:rocket: :boom:

whedon commented 6 years ago

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

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

Markdown:
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HTML:
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  <img src="http://joss.theoj.org/papers/10.21105/joss.00698/status.svg" alt="DOI badge" >
</a>

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