[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
Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b38d892fdc407c82379ea4f164110674"><img src="https://joss.theoj.org/papers/b38d892fdc407c82379ea4f164110674/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b38d892fdc407c82379ea4f164110674/status.svg)](https://joss.theoj.org/papers/b38d892fdc407c82379ea4f164110674)

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) by leaving comments 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

@berquist & @emanueledelsozzo, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @atrisovic know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @emanueledelsozzo

📝 Checklist for @berquist

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

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

✅ OK DOIs

- 10.1038/sdata.2016.18 is OK
- 10.1007/978-3-319-17966-7_21 is OK
- 10.32614/CRAN.package.DiagrammeR is OK
- 10.1145/2757001.2757003 is OK
- 10.32614/CRAN.package.rdflib is OK

🟡 SKIP DOIs

- 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

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=7.97 s (444.2 files/s, 183560.1 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                         3271         177729         266453         817403
C                                11           4228          17439         104274
CSV                              43              0              0          37450
C/C++ Header                     28           1277           2142           7605
SVG                              13              0            310           5286
CSS                              34            631            591           3623
Cython                           11            484            435           2223
HTML                              4            356              8           1711
JavaScript                        7            187            131           1440
Fortran 90                       53            116             86            892
R                                 4            169            298            797
Markdown                          9            150              0            404
Fortran 77                       21             26             50            382
reStructuredText                  4             91              1            294
TeX                               6             53             93            253
C++                               1             13             14            143
PowerShell                        1             49             90            108
Meson                             3             21              9            102
XML                               2              0              1             79
YAML                              1              0              0             48
Fish Shell                        1             13             14             42
INI                               3              5              0             34
Rmd                               3            487           3528             33
C Shell                           1             10              5             12
Bourne Again Shell                1              1              3             10
zsh                               1              1              6              7
Lua                               1              0              1              2
JSON                              1              0              0              1
--------------------------------------------------------------------------------
SUM:                           3539         186097         291708         984658
--------------------------------------------------------------------------------

Commit count by author:

    12	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)

[editorialbot]

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

[emanueledelsozzo]

Review checklist for @emanueledelsozzo

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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 https://github.com/cwru-sdle/FAIRmaterials?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@Alexhb02) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• 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?

[berquist]

Review checklist for @berquist

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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 https://github.com/cwru-sdle/FAIRmaterials?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@Alexhb02) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • According to Git history, only one author (Jonathan E. Gordon) has contributed to the software.
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• 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?

[berquist]

Software report:

This is misleading because a Python virtualenv was added to version control; it will need to be rerun once cwru-sdle/FAIRmaterials#1 is merged.