[PRE REVIEW]: scribl: A system for the semantic capture of relationships in biological literature

[editorialbot]

Submitting author: !--author-handle-->@alexlancaster<!--end-author-handle-- (Alexander Lancaster) Repository: https://github.com/amberbiology/scribl Branch with paper.md (empty if default branch): manuscript Version: v0.8.0-a1 Editor: !--editor-->@atrisovic<!--end-editor-- Reviewers: @benlansdell, @mhucka Managing EiC: Kevin M. Moerman

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

@alexlancaster 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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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1001.1 files/s, 120276.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          11            228            138           1556
Markdown                         2             94              0            328
CSV                              5              0              0            282
YAML                             6             20             55            273
TeX                              1              9              0            140
JSON                             1              0              0             64
TOML                             1             10              1             46
-------------------------------------------------------------------------------
SUM:                            27            361            194           2689
-------------------------------------------------------------------------------

Commit count by author:

    33  Alex Lancaster
     6  dependabot[bot]
     1  Gordon Webster

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1098

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU Affero General Public License v3.0 (Check here for OSI approval)

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

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

OK DOIs

- 10.1007/3-540-45848-4_59 is OK
- 10.1016/j.febslet.2005.02.005 is OK
- 10.1145/3183713.3190657 is OK
- 10.1093/nar/gkab1028 is OK
- 10.15252/msb.20199110 is OK
- 10.1186/gb-2008-9-s2-s8 is OK
- 10.1186/s13742-015-0077-2 is OK
- 10.1093/bioinformatics/btm401 is OK

MISSING DOIs

- No DOI given, and none found for title: The Kappa Language and Kappa Tools
- No DOI given, and none found for title: Exploring network structure, dynamics, and functio...

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@editorialbot invite @atrisovic as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@alexlancaster (if you haven't already, I didn't see them) please add clear contributing guidelines to your project. We recommend having a CONTRIBUTING.md file, and to link to it from your README. This site contains some examples: https://contributing.md/example/

[alexlancaster]

@alexlancaster (if you haven't already, I didn't see them) please add clear contributing guidelines to your project. We recommend having a CONTRIBUTING.md file, and to link to it from your README. This site contains some examples: https://contributing.md/example/

Hi Kevin, yes, thanks for pointing that out. I'll go ahead and add the contributors guide shortly.

[alexlancaster]

@Kevin-Mattheus-Moerman : CONTRIBUTING.md added in https://github.com/amberbiology/scribl/commit/ab67760411e998ac6c405a16543dd7d8d6f8a6a9

[atrisovic]

@editorialbot assign me as editor

[editorialbot]

Assigned! @atrisovic is now the editor

[atrisovic]

Hi @alexlancaster I will edit your submission and do my best to facilitate the review process. If you have any suggestions for potential reviewers, please let me know here in this thread (without tagging them with an @).

[alexlancaster]

Hi @alexlancaster I will edit your submission and do my best to facilitate the review process. If you have any suggestions for potential reviewers, please let me know here in this thread (without tagging them with an @).

Hi @atrisovic - thanks! I took a quick look at the database of reviewers. There are a lot that seem great. I'll take a longer look too, but a couple of names to start might be: Ben Lansdell and Michael Hucka.

[alexlancaster]

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

MISSING DOIs

- No DOI given, and none found for title: The Kappa Language and Kappa Tools

There is no DOI for this software, the official documentation: https://kappalanguage.org/documentation recommends citing using the following, which we did:

P. Boutillier, J. Feret, J. Krivine, and W. Fontana. The Kappa Language and Tools (version of <insert date on cover>), kappalanguage.org.

- No DOI given, and none found for title: Exploring network structure, dynamics, and functio...

It looks like this is part of a DOE conference series, and the official URL: https://www.osti.gov/biblio/960616 provides BibTeX reference, but does not provide a DOI.

[atrisovic]

Hi @benlansdell, I am writing to invite you to review a paper titled "scribl: A system for the semantic capture of relationships in biological literature", which is currently in the review process 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! Ana Trisovic, JOSS Topic Editor

[benlansdell]

Hi @atrisovic, looks like an interesting project. I can likely help out. What is the expected turn around time? I have some other commitments this week that are soaking up my extra time, so won't be able to look at this for another week.

[atrisovic]

I think that should be fine, we are looking to complete the reviews within a month or two.

[benlansdell]

I think that should be fine, we are looking to complete the reviews within a month or two.

Got it, sounds good. Then, yes, I'm happy to be a reviewer.

[atrisovic]

@editorialbot add @benlansdell as reviewer

[editorialbot]

@benlansdell added to the reviewers list!

[alexlancaster]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[atrisovic]

@editorialbot add @mhucka as reviewer

[editorialbot]

@mhucka added to the reviewers list!

[atrisovic]

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[atrisovic]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6645.