[PRE REVIEW]: PopMedNet: A scalable and extensible open-source informatics platform designed to facilitate the implementation and operation of distributed health data networks

[whedon]

Submitting author: @ddeehere (Daniel Dee) Repository: https://github.com/PopMedNet-Team/popmednet Version: 2021.4 Editor: @danielskatz Reviewers: @jhancock4d, @lrasmus Managing EiC: Kevin M. Moerman

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Author instructions

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

@ddeehere if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

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

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

@whedon commands

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

@whedon generate pdf

[whedon]

Wordcount for paper.md is 740

[whedon]

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

OK DOIs

- 10.13063/2327-9214.1213 is OK
- 10.1097/MLR.0b013e3181d9919f is OK
- 10.17294/2330-0698.1149 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[Kevin-Mattheus-Moerman]

@whedon check repository

[whedon]

Wordcount for paper.md is 740

[Kevin-Mattheus-Moerman]

@openjournals/dev can you see why the repo check does not include LOC metrics?

[Kevin-Mattheus-Moerman]

@ddeehere I have assigned the query-scope label just now. This is to flag this submission for scope review by our editorial board. This scope review should take about 2 weeks.

Although the software seems very useful to me, in this particular case it is unclear to me if this work represents "research software". JOSS only considers software which has a clear scientific research application. If you feel this work matches our definition of research software perhaps add comments here to help convince us, and rewrite a section of the paper to clearly highlight the research applications of this work. After reading such a section it should become clear how/why one would use the software in research and why it is important enough to cite it in research publications using this software.

If at any time you'd like t update the paper you can call the following in a comment: @whedon generate pdf

[ddeehere]

Thank you for your feedback.

PopMedNet is designed to support collaborative public health research where there is a need to balance the protection of private information with the need to share such information between many medical institutions. It does this by implementing a distributed querying system with a strong but fine grain governance system that is only converted to SQL when the query arrives at the local data source.

You may see some examples of the researches being done using this tool at: pcori.org and sentinelinitiative.org

While the tool is originally designed for public health research, this same idea may be applicable to any other field where there is a need to both protect and share information. (I have seen potential for this in library science and paleontology.)

I realize that this tool may be somewhat different from other JOSS submissions in that it is not a mathematical package or an algorithm, but I hope that it can still be accepted as a useful tool.

[kthyng]

@whedon check repository

[whedon]

Wordcount for paper.md is 740

[kthyng]

Mystery solved! The repo zip is 118MB, so that is why check repo isn't working. Here are the cloc statistics:

(myenv) kthyng@adams Downloads % cloc ~/Downloads/popmednet-master.zip 
    9433 text files.
    9154 unique files.                                          
    1546 files ignored.

github.com/AlDanial/cloc v 1.90  T=30.89 s (255.5 files/s, 53883.0 lines/s)
------------------------------------------------------------------------------------
Language                          files          blank        comment           code
------------------------------------------------------------------------------------
XML                                 904           7318          29508         489479
C#                                 3699          55119          35332         292561
SQL                                  33            265             42         219418
JavaScript                         1439          40104          61469         167764
CSV                                   9              0              0          65457
TypeScript                          253           9287           3605          56568
MSBuild script                      124           4724            278          33160
JSON                                626             69              0          32170
Razor                               573           1830           1823          29523
CSS                                 157           1497            886          11484
XSLT                                 11            468            648           3753
SVG                                   5              0              0           2502
LESS                                 16            500            128           2308
Visual Studio Solution                7              7              7           1092
XSD                                   7             63             48            636
WiX source                            3             31             25            445
PowerShell                            6             51             27            235
ASP                                   1             44              0            194
F#                                    3             26              0            133
SAS                                   5             63             87            105
DOS Batch                             7             27             10             90
Markdown                              2             33              0             73
TeX                                   1              3              0             37
XAML                                  1              0              0             31
F# Script                             1              7              3             26
ASP.NET                               2              0              0              2
------------------------------------------------------------------------------------
SUM:                               7895         121536         133926        1409246
------------------------------------------------------------------------------------

[ddeehere]

@Kevin-Mattheus-Moerman I am following up to see if there is anything else I need to do other than wait. I responded to your comments 6 days ago. Not sure if that's sufficient justification or not. Please let me know. Thank you.

[danielskatz]

@ddeehere - We've just finished the scope discussion, and this has been approved to be reviewed. I'll remove the scope query label and start working on finding an editor to start the review

[danielskatz]

👋 @csoneson - do you think you can edit this submission? It's a little different than most submissions...

[danielskatz]

@whedon invite @csoneson as editor

[whedon]

@csoneson has been invited to edit this submission.

[ddeehere]

👋 @csoneson - do you think you can edit this submission? It's a little different than most submissions...

Yes, we can edit the submission. Can you provide some guidance on where we differ from others so that we know where we are deficient? Thank you.

[danielskatz]

👋 @ddeehere - I think you missed that fact that the invitation to edit was to @csoneson. JOSS reviews include a number of roles, including

• an Assistant Editor-in-Chief (AEiC), currently me
• an editor, to be found by the AEiC, not currently filled
• at least two reviewers, to be found by the editor, not currently filled
• the author, you

There isn't any action for you at this point

[csoneson]

@danielskatz - sorry, I'm afraid this is really quite a bit out of my comfort zone/experience on the implementation side 😬 If it's possible to find someone with experience in web applications or database querying, I think that would be a better fit in this case.

[danielskatz]

@whedon assign me as editor

I'll take it :)

[whedon]

OK, the editor is @danielskatz

[danielskatz]

@ddeehere - I'll be the editor. The next step is to find at least 2 reviewers. If you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

[ddeehere]

@ddeehere - I'll be the editor. The next step is to find at least 2 reviewers. If you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

@danielskatz - Are external reviewers ok or do I have to pick from the list you provided? I am thinking martinmodrak may be appropriate since he's list C# as a technology he knows and/or borishejblum as he is involved in epidemiology and public health.

[danielskatz]

external are fine - the list is just one resource if useful (of course, please keep in mind the JOSS conflict of interest guidelines)

[danielskatz]

@ddeehere - any further suggestions?

[danielskatz]

👋 @martinmodrak & @borishejblum - would one or both of you be willing to review this JOSS submission?

[ddeehere]

@danielskatz:

@ddeehere - any further suggestions?

For external reviewers, would a developer who works for the same company (but not directly involved in the PopMedNet development) be acceptable? How about a subcontractor for Harvard Pilgrim Health Care Institute (who's the primary mover of PopMedNet) be acceptable? I am thinking in terms of whether that will violate conflict of interest guidelines. Neither of them are actively involved in PopMedNet.

[danielskatz]

someone from the same company would not make sense, but someone who is a user would

[borishejblum]

👋 @martinmodrak & @borishejblum - would one or both of you be willing to review this JOSS submission?

Unfortunately no, this is too far out of my area of expertise. You might want to ask @scossin or @vianneyJouhet

[martinmodrak]

Unfortunately, this is both at the very edge of my knowledge (I did some WinForms a long time ago, but have never used ASP.NET, I also now only bare minimum on security) and quite a large project - I won't be able to set aside time to review it responsibly at the moment.

[danielskatz]

👋 @scossin & @vianneyJouhet - would one or both of you be willing to review this JOSS submission?

JOSS is a free, open-source, community driven and developer-friendly online journal (no publisher is seeking to raise revenue from the volunteer labor of researchers!).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged.

JOSS reviews involve downloading and installing the software, and inspecting the repository and submitted paper for key elements. See https://joss.readthedocs.io/en/latest/review_criteria.html

Editors and reviewers post comments on the Review issue, and authors respond to the comments and improve their submission until acceptance (or withdrawal, if they feel unable to satisfy the review).

[danielskatz]

👋 @ddeehere - I probably need some more suggestions from you.

[danielskatz]

👋 @scossin & @vianneyJouhet - just checking with you both again re https://github.com/openjournals/joss-reviews/issues/3851#issuecomment-963542710

[ddeehere]

@danielskatz - I am checking with a few contacts to see if any could review without violating conflict of interest rule.

👋 @ddeehere - I probably need some more suggestions from you.

[danielskatz]

@whedon generate pdf

[whedon]

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

[danielskatz]

I've been reaching out to a lot of people about being potential reviewers, and one has accepted - thanks @jsaw5

[danielskatz]

I'll add you in the system now, but we won't start the review until we find at least one more reviewer

[danielskatz]

@whedon assign @jsaw5 as reviewer

[whedon]

OK, @jsaw5 is now a reviewer

[danielskatz]

Unfortunately, @jsaw5 is not going to be able to review this, so I'm removing her

[danielskatz]

@whedon remove @jsaw5 as reviewer

[whedon]

OK, @jsaw5 is no longer a reviewer

[ddeehere]

@danielskatz I have reached out and waiting to hear from potential reviewers from outside JOSS volunteers.

[danielskatz]

Thanks - I'm continuing to do this as well

[danielskatz]

@ddeehere - I've had no luck finding reviewers. Unfortunately, if we cannot find reviewers, we cannot proceed. I hope you will have more luck than I have.

[ddeehere]

@ddeehere - I've had no luck finding reviewers. Unfortunately, if we cannot find reviewers, we cannot proceed. I hope you will have more luck than I have.

@danielskatz I found someone who's keeping it open to try to review before January. He did recommend another person, which I will reach out to see if he's available.

[ddeehere]

@danielskatz I got someone who's willing to review it. He's asking if there are examples of other reviews he can look at to give him some guidance on what he has to do. Can you point me to some reviews of other submissions? Thanks and Happy Holidays!

[danielskatz]

@ddeehere - every published paper from JOSS (https://joss.theoj.org/papers/published) has a link on the right side for Paper review. In addition, https://joss.readthedocs.io/en/latest/reviewer_guidelines.html provides general guidelines.