[PRE REVIEW]: FAIRmaterials: Ontology Tools with Data FAIRification in Development

[editorialbot]

Submitting author: @Alexhb02 (Alexander Harding Bradley)
Repository: https://github.com/cwru-sdle/FAIRmaterials
Branch with paper.md (empty if default branch): main
Version: 0.4.2.2
Editor: @atrisovic
Reviewers: @berquist, @emanueledelsozzo
Managing EiC: Daniel S. Katz

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/b38d892fdc407c82379ea4f164110674/status.svg)](https://joss.theoj.org/papers/b38d892fdc407c82379ea4f164110674)

Author instructions

Thanks for submitting your paper to JOSS @Alexhb02. Currently, there isn't a JOSS editor assigned to your paper.

@Alexhb02 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (722.0 files/s, 236739.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             1            338              5           1755
SVG                              2              0            299           1483
R                                4            169            298            797
Python                           8            205            282            636
Markdown                         4            139              0            367
CSV                             10              0              0            145
TeX                              1              8              0             93
TOML                             1              5              0             76
Rmd                              3            487           3528             33
-------------------------------------------------------------------------------
SUM:                            34           1351           4412           5385
-------------------------------------------------------------------------------

Commit count by author:

     8	Jonathan Gordon
     1	Jonathan-E-Gordon

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 2575

✅ The paper includes a Statement of need section

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/sdata.2016.18 is OK
- 10.1145/2757001.2757003 is OK

MISSING DOIs

- 10.1007/978-3-319-17966-7_21 may be a valid DOI for title: WebVOWL: Web-based Visualization of Ontologies
- No DOI given, and none found for title: Graphviz Python Package
- No DOI given, and none found for title: RDFLib: Python Library for working with RDF
- 10.32614/cran.package.diagrammer may be a valid DOI for title: DiagrammeR: Graph/Network Visualization
- 10.32614/cran.package.rdflib may be a valid DOI for title: rdflib: Tools to Manipulate and Query Semantic Dat...
- No DOI given, and none found for title: PyPI: The Python Package Index
- No DOI given, and none found for title: CRAN: The Comprehensive R Archive Network

INVALID DOIs

- None

[editorialbot]

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

[editorialbot]

⚠️ An error happened when generating the pdf. Author (Roger H. French) is missing affiliation.

[danielskatz]

👋 @Alexhb02 - note that your paper does not compile. Please follow the example paper and note that you can click on the error above to find out more about it. In addition, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf after making changes to the .md file or when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

[Jonathan-E-Gordon]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/sdata.2016.18 is OK
- 10.32614/CRAN.package.DiagrammeR is OK
- 10.1145/2757001.2757003 is OK
- 10.32614/CRAN.package.rdflib is OK

MISSING DOIs

- 10.1007/978-3-319-17966-7_21 may be a valid DOI for title: WebVOWL: Web-based Visualization of Ontologies
- No DOI given, and none found for title: Graphviz Python Package
- No DOI given, and none found for title: RDFLib: Python Library for working with RDF
- No DOI given, and none found for title: PyPI: The Python Package Index
- No DOI given, and none found for title: CRAN: The Comprehensive R Archive Network

INVALID DOIs

- None

[Jonathan-E-Gordon]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[danielskatz]

@Alexhb02 & @Jonathan-E-Gordon - JOSS papers are expected to be 250-1000 words in length. This paper is currently over 2500, as shown by the @editorialbot check repository command. If JOSS accepts this for review, you will have to reduce it. Additionally, the remaining suggested DOI appears correct, so at some point, you will need to add it to the entry in the .bib file.

But before we get to that point, I'm going to ask the editors to discuss if it meets the substantial scholarly effort criterion for review by JOSS, due to the relatively small number of lines of code. You should hear back in couple of weeks or so.

As part of this review, editors will look at the repo's commit history. It appears very brief, making me suspect that development happened before the repository was created. Can you say anything about the work that isn't visible here? How many contributors have their been? How much work was involved (in person-months perhaps), and over what period?

[danielskatz]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Jonathan-E-Gordon]

@danielskatz The software was published on CRAN and PyPI in 2021. Due to lab policy, we developed the software in a private Bitbucket repository, which has accumulated over 400 commits since 2021. In January 2024, we initiated a redesign of the software, resulting in 110 commits from 9 authors, representing approximately 7 person-months of work. We can send the whole commit history if that is helpful. This software will also be cited in a Scientific Data paper currently under review, titled “Materials Data Science Ontology (MDS-Onto): Unifying Domain Knowledge in Materials and Applied Data Science” and we believe this software will be very valuable for those generating ontologies, addressing a need in various academic domains.

[danielskatz]

1200 is probably fine.

[Jonathan-E-Gordon]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (728.7 files/s, 233600.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             1            338              5           1619
SVG                              2              0            299           1483
R                                4            169            298            797
Python                           8            205            282            636
Markdown                         4            113              0            278
CSV                             10              0              0            145
TeX                              1              8              0             96
TOML                             1              5              0             76
Rmd                              3            487           3528             33
-------------------------------------------------------------------------------
SUM:                            34           1325           4412           5163
-------------------------------------------------------------------------------

Commit count by author:

    10	Jonathan Gordon
     1	Jonathan-E-Gordon

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1502

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

[Jonathan-E-Gordon]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (726.0 files/s, 232325.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             1            338              5           1607
SVG                              2              0            299           1483
R                                4            169            298            797
Python                           8            205            282            636
Markdown                         4            112              0            271
CSV                             10              0              0            145
TeX                              1              8              0             96
TOML                             1              5              0             76
Rmd                              3            487           3528             33
-------------------------------------------------------------------------------
SUM:                            34           1324           4412           5144
-------------------------------------------------------------------------------

Commit count by author:

    11	Jonathan Gordon
     1	Jonathan-E-Gordon

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1391

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

[atrisovic]

Hi @danielskatz I am about to complete one of my reviews, so I can review this one. Thank you!

[atrisovic]

@editorialbot add me as editor

[editorialbot]

Assigned! @atrisovic is now the editor

[danielskatz]

👋 @atrisovic - I don't see any progress on getting this started in last month. What's going on?

[atrisovic]

Hi All,
Apologies for the delay. I was on holiday and then had a few busy weeks.
@Jonathan-E-Gordon and @Alexhb02 please let me know if you have any suggestions for potential reviewers.

[atrisovic]

Hi @berquist,
I am reaching out to invite you to review a manuscript titled "FAIRmaterials: Ontology Tools with Data FAIRification in Development," currently under consideration at the Journal of Open Source Software (JOSS).
Your insights and feedback on this work would be valuable and much appreciated. To help with the review, we have a reviewers' checklist with useful guidelines.
Thank you in advance for considering this invitation.
Ana Trisovic, JOSS Topic Editor

[berquist]

Hi @berquist, I am reaching out to invite you to review a manuscript titled "FAIRmaterials: Ontology Tools with Data FAIRification in Development," currently under consideration at the Journal of Open Source Software (JOSS). Your insights and feedback on this work would be valuable and much appreciated. To help with the review, we have a reviewers' checklist with useful guidelines. Thank you in advance for considering this invitation. Ana Trisovic, JOSS Topic Editor

Yes, I would be happy to review this. Any additional reviewers should be stronger than me in R, though 😅

[atrisovic]

Wonderful, thank you!

[atrisovic]

@editorialbot add @berquist as reviewer

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@berquist added to the reviewers list!

[atrisovic]

@editorialbot add @emanueledelsozzo as reviewer

[editorialbot]

@emanueledelsozzo added to the reviewers list!

[atrisovic]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7287.

[emanueledelsozzo]

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