[PRE REVIEW]: Kalamari: A Representative Set of Genomes of Public Health Concern

[editorialbot]

Submitting author: @lskatz (Lee Katz)
Repository: https://github.com/lskatz/Kalamari
Branch with paper.md (empty if default branch): paper
Version: v5.7.0
Editor: Pending
Reviewers: Pending
Managing EiC: Kevin M. Moerman

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[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "%" (NAME) [#<BibTeX::Bibliography data=[3]>, "@", #<BibTeX::Entry >, {:title=>["Entrez Direct: E-utilities on the UNIX Command Line"], :booktitle=>["Entrez Programming Utilities Help"], :author=>["Kans, J."], :year=>["2013"], :month=>["4"], :day=>["23"], :edition=>["Updated 2024 May 9"], :publisher=>["National Center for Biotechnology Information"], :address=>["Bethesda, MD, USA"], :url=>["https://www.ncbi.nlm.nih.gov/books/NBK179288/"]}]

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (1502.8 files/s, 161741.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Perl                             9            254             99           1140
Markdown                         5            121              0            359
YAML                             5             17             13            309
Bourne Shell                     6             68             37            207
TeX                              1             12              1            177
Python                           1             22              3             67
-------------------------------------------------------------------------------
SUM:                            27            494            153           2259
-------------------------------------------------------------------------------

Commit count by author:

   169	Lee Katz - Aspen
    41	Lee Katz
     2	Scott Nguyen
     1	Curtis Kapsak
     1	SVN-PhD

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1403

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[editorialbot]

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

[editorialbot]

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[lskatz]

License info:

🟡 License found: Other (Check here for OSI approval)

As a response, I went ahead and updated to MIT license on the master branch to help avoid any issues with the creative commons license.

[lskatz]

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[lskatz]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1056/NEJMsr1813907 is OK
- 10.1128/AEM.02577-16 is OK
- 10.1093/nar/gkr1178 is OK
- 10.1186/1471-2105-10-421 is OK
- 10.1186/gb-2014-15-3-r46 is OK
- 10.1186/s13059-019-1891-0 is OK
- 10.1038/s41467-019-11306-6 is OK
- 10.1099/mgen.0.000976 is OK
- 10.1099/mgen.0.000206 is OK
- 10.3389/fmicb.2023.1225207 is OK
- 10.1186/s13059-016-0997-x is OK
- 10.1186/s13059-018-1554-6 is OK
- 10.1093/nar/gkv1189 is OK
- 10.1093/nar/gkab776 is OK

MISSING DOIs

- No DOI given, and none found for title: Entrez Direct: E-utilities on the UNIX Command Lin...

INVALID DOIs

- None

[lskatz]

The Entrez Direct does not unfortunately have a DOI but I do believe I have cited it to the best of my ability. They have a "cite this page" link which resolves to this popup:

[lskatz]

Hi, I think the following potential reviewers would be great.

• @jenniferlu717
• @k-florek
• @oschwengers
• @pmenzel
• @Ebedthan

[Kevin-Mattheus-Moerman]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

@lskatz Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. For the moment I've triggered a scope review by the editorial board. This is to check if this work is in scope (given the relatively narrow functionality centered around providing access to a database) and, given the small size, if the work conforms to our substantial scholarly effort criteria. This scope review should take about two weeks to complete.

[Kevin-Mattheus-Moerman]

@lskatz Unfortunately the editorial board has determined that due to its relatively small size and narrow functionality around providing database access, this work is not in scope for JOSS. We will now proceed to reject this submission.

Note that this rejected does not mean this work is not useful or not well done, it merely means that it is not in scope for JOSS.

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.