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

[whedon]

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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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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The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @pjotrp know.

Review checklist for @alexgarciac

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?
• Version: Does the release version given match the GitHub release (v1.0.0)?
• 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

• 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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @alexgarciac it looks like you're currently assigned as the reviewer for 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:

2. 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

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #698 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 16 0 16 0 0 260 0 --:--:-- --:--:-- --:--:-- 262
Could not find bibliography file: paper_resources/paper.bib
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

[pjotrp]

Dear @bryan-brancotte, sorry for the delay. Mostly because someone stopped communicating - hard to deal with that. But we'll move on now. To expedite the work can you add the bibliography and compile the PDF until it works? Also please go through above check list and ascertain the reviewer can check the boxes. Much faster if you make sure we can tick them than wait for a back and forth. Meanwile @alexgarciac can you go through the JOSS tips for review at http://joss.theoj.org/about#reviewer_guidelines. Thanks!

[hmenager]

Hi @pjotrp, thanks a lot for handling this. Regarding the bibliography, the compilation error seems weird, because the bib file is actually there as far as I can tell (https://github.com/IFB-ElixirFr/edam-browser/blob/master/paper_resources/paper.bib). On the previous round @arfon actually provided the pdf manually. Is there something we should correct in the markdown or the bibtex to avoid the compilation errors? Thanks again!

[arfon]

@hmenager - the issue here is that there are two papers so @whedon doesn't know what to do:

1. tmp/698/paper.md
2. tmp/698/paper_resources/long_paper.md

I've compiled this locally and uploaded here: 10.21105.joss.00698.pdf

[pjotrp]

The second paper should be renamed?

[arfon]

The second paper should be renamed?

Yes. The regex goes looking for anything with paper.md in the title. Honestly it doesn't really matter, you just can't ask Whedon to auto-compile the paper here.

[pjotrp]

@hmenager do you mind confirming we should be able to check all relevant boxes?

[hmenager]

@pjotrp I will check that carefully with @bryan-brancotte, and get back to you real soon. From quickly checking the list above, I think we miss a release and the contribution guidelines. We'll ping you as soon as these are done.

[pjotrp]

Excellent.

[bryan-brancotte]

Hi @pjotrp, we renamed the long_paper.md and reviewed all the boxes: they should be good to check.

[bryan-brancotte]

Note that CI is pending on validation from https://github.com/IFB-ElixirFr/edam-browser/issues/15

[pjotrp]

@alexgarciac please start the review by ticking the boxes at the top of this page.

[alexgarciac]

@pjotrp I have ticked the boxes but, a naive question: where do I hit submit?

[alexgarciac]

@pjotrp also, there are typos and issues wrt the language, how do I send these to the authors?

[pjotrp]

@alexgarciac you can report on the projects issue tracker (when relevant) and here. This issue tracker we use to do the actual public review. There is no submit button :). Just respond here.

[alexgarciac]

Hi, I have checked the appropriate boxes. the ones not checked have comments in the issue tracker of the edam prj.

[alexgarciac]

Other review comments (also made over the EDAM issue tracker). the symbol "->" indicates each issue reported in the EDAM issue tracker.

-> Please add DOIs to the references where applicable. For instance,
https://doi.org/10.1186/s12859-015-0456-9 for https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0456-9 in your bib file this is with no DOI, see below.

@Article{hoehndorf2015aber,
title={Aber-OWL: a framework for ontology-based data access in biology},
author={Hoehndorf, Robert and Slater, Luke and Schofield, Paul N and Gkoutos, Georgios V},
journal={BMC bioinformatics},
volume={16},
number={1},
pages={26},
year={2015},
publisher={BioMed Central}
}

Same is true for other references.

-> There are issues with the language. Please have this paper proof read by a native speaker. there are parts in the manuscript that requiere some attention. For instance

To facilitate these suggestions, the EDAM Browser lets users access a form letting them propose changes at any point of their exploration.

You could say something like: In order to make it easy for the community to submit comments to the ontology editors, we have implemented a form that facilitates this communication.

the section "easy of community..." should be just "Facilitating community feedback" The five lines in this section need some work -less is more here.

At:
Labelling, indexing and describing a Bioinformatics resource, whether it is a software, a database, or a service is of a great help when it comes to promoting it to various user communities. As an example, the ELIXIR bio.tools (Ison et al. 2015) registry contains more than ten thousands software and service entries. In this context, the use of controlled vocabularies to describe the resources is of a paramount importance. In bio.tools, this need is addressed by the EDAM Ontology (Ison et al. 2013), which proposes a controlled vocabulary hierarchically organized around four axes which describe types of data, formats, operations and topics.

Please be more concise, remove unnecessary adjectives such as "paramount". Focus on what this onto is for and how your software is addressing some issue wrt the development process. In this case, you are i) facilitating the navigation and ii) making is easy for the community to communicate issues to the ontology developers via a simple form.

• Ok. the abstract should simply present what you did. Please reorganize as problem statement, proposed solution and availability. then there should be the "A short summary describing the high-level functionality of the software". this is somewhat in your sections "availability", "info display", "performance and flexibility" and "easy....". So, the paper is disorganized. You only need to state the problem you are solving, describe the overall solution, present an example that illustrates how your solution is addressing or solving the problem that you have stated (here you present the functionality of the software, what does the software do so that it solves the problem). Just this simple.

In order to present the functionality of the software consider building a user story that brings together the problem from the perspective of the user; your software is in your own words "This browser is tailored to the needs of EDAM users that might not be ontology experts" so just build the user story from this perspective. there is also another perspective; that somewhat solved by the communication channel you are bridging between the community and the ontology developers via a form. This should also be part of the user story. Then simply state how your software is solving these stories. Use this part in order to present most, if not all, the functionalities of your software.

-> Please look at

Its interface is not designed to be a generic ontology navigation and edition platform, a goal already achieved by many other systems (AberOWL(Hoehndorf et al. 2015), BioPortal(Whetzel et al. 2011), OLS - Ontology Lookup Service(Jupp et al. 2015), Ontobee(Xiang et al. 2011), WebProtégé(Tudorache et al. 2013)).

I presume the "its" refers to the EDAM interface. Just use the form "the edam interface....." Please be mindful here because BioPortal is not an ontology editor, it is an ontology publication platform. You could edit the ontology by hand if you want to. By the same token, Ontobee is not an ontology editor. Just organize this part of your paper making sure that you are distinguishing a publication platform/ontology repository vs an ontology editor.

Also, WebProtégé(Tudorache et al. 2013)), why do u have )) ?

One more, leave a space between the name of the software and the parenthesis indicating the reference -please check this everywhere in the manuscript.

-> Please in the manuscript, as well as in the readme for the git make sure that u clearly address the following issues:

1- This one requires attention more in the manuscript than in the readme. As you state that your form is meant to support the evolution of the ontology then there is a community component. are comments going to be visible for everyone to see and keep commenting on? is this commenting feature just a form by means of which issues go straight into a git issue tracker? Below some more specifics on this point.

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

2- This one is specific for the manuscript and also requieres that you update your bib file.

References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

3- this one is more related to the manuscript because IMHO your software development is easy to follow. However, a visit to the documentation in the actual code and overall project would not harm. In the manuscript you need to better describe the functionality of the software. the software is very simple, this is good, but it is poorly described in the paper. You may want to relate the description of the functionality to specific use cases.

Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).

4- Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution. I could not find the list of dependencies.

[pjotrp]

Thans @alexgarciac for your very thorough review. @bryan-brancotte I think it is a good idea to look at all suggestions and see if you can improve the paper. The goal is to present your work in the best way so people start using it! I don't think it is a lot of work, so it is close to being accepted with minor revisions only.

Of the missing check boxes, I think only the one on community guidelines to be really important. See if we can check that box. Also DOIs and installation instructions would be a good idea.

[pjotrp]

ping @bryan-brancotte

[bryan-brancotte]

Hi @pjotrp
Thank to @alexgarciac for all those comments. I had a quite dense week and going to be offline for two weeks so I will not be able to take into account the suggestions in the mean time. As soon as I am back online be assured that it will be on the top of my todo list.
Best regards

[pjotrp]

OK, no problem. As long as we know about it we don't worry.

[bryan-brancotte]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[bryan-brancotte]

@whedon generate pdf

[whedon]

--> Check article proof 📄 <--

[bryan-brancotte]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[bryan-brancotte]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[hmenager]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[hmenager]

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]

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

[pjotrp]

ping @alexgarciac

[alexgarciac]

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]

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

[pjotrp]

Thank you @alexgarciac! 👍 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).

Second, we need you to deposit a copy of your software repository (including any revisions made during the JOSS review process) with a data-archiving service. To do so:

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

[bryan-brancotte]

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

[pjotrp]

@whedon set 10.5281/zenodo.1314288 as archive

[whedon]

OK. 10.5281/zenodo.1314288 is the archive.

[pjotrp]

@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]

no problem, thanks

[arfon]

@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]

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

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