[PRE REVIEW]: An Introduction to `prismAId`: Open-Source and Open Science AI for Advancing Information Extraction in Systematic Reviews #7569

editorialbot · 2024-12-04T15:27:15Z

Submitting author: @ricboer0 (Riccardo Boero)
Repository: https://github.com/open-and-sustainable/prismaid
Branch with paper.md (empty if default branch): joss-submission
Version: v0.6.4
Editor: @crvernon
Reviewers: @philip928lin, @jhculb
Managing EiC: Chris Vernon

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b304d9af36e75fd2b10ebcdb55add064"><img src="https://joss.theoj.org/papers/b304d9af36e75fd2b10ebcdb55add064/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b304d9af36e75fd2b10ebcdb55add064/status.svg)](https://joss.theoj.org/papers/b304d9af36e75fd2b10ebcdb55add064)

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The text was updated successfully, but these errors were encountered:

editorialbot · 2024-12-04T15:27:18Z

Hello human, 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:

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editorialbot · 2024-12-04T15:27:48Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (2254.5 files/s, 206600.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Go                              64            694            950           4075
Markdown                        12            358              0           1231
YAML                             6             72             31            423
TeX                              1             14              0            220
JavaScript                       1             47             25            208
TOML                             5             29             19            188
CSS                              1              9              1             42
R                                1              9             78             34
Julia                            2             10              7             33
Python                           1              6              3             24
JSON                             1              0              0             19
C                                1              4              2             15
C/C++ Header                     1              3              2              4
-------------------------------------------------------------------------------
SUM:                            97           1255           1118           6516
-------------------------------------------------------------------------------

Commit count by author:

   696	Riccardo Boero
    12	GitHub Action

editorialbot · 2024-12-04T15:27:52Z

Paper file info:

📄 Wordcount for paper.md is 3583

✅ The paper includes a Statement of need section

editorialbot · 2024-12-04T15:27:57Z

License info:

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

editorialbot · 2024-12-04T15:28:00Z

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

✅ OK DOIs

- 10.1186/s13643-021-01626-4 is OK
- 10.1002/jrsm.1553 is OK
- 10.1002/jcv2.12234 is OK
- 10.1038/s42256-020-00287-7 is OK
- 10.1007/s00607-023-01181-x is OK
- 10.1136/bmjopen-2023-072254 is OK
- 10.1038/s43588-023-00527-x is OK
- 10.48550/arXiv.2308.00951 is OK
- 10.1080/02763869.2019.1588072 is OK
- 10.5281/zenodo.11210796 is OK
- 10.3390/cli12080116 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: LLM In-Context Recall is Prompt Dependent
- No DOI given, and none found for title: Question Decomposition Improves the Faithfulness o...
- No DOI given, and none found for title: prismAId - Open Science AI Tools for Systematic, P...
- No DOI given, and none found for title: prismAId - Documentaiton website

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-12-04T15:28:58Z

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

editorialbot · 2024-12-04T15:29:43Z

Five most similar historical JOSS papers:

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Handling editor: @chartgerink (Retired)
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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.

ricboer0 · 2024-12-04T15:35:05Z

@editorialbot commands

editorialbot · 2024-12-04T15:35:09Z

Hello @ricboer0, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

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@editorialbot generate pdf

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@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

crvernon · 2024-12-04T15:41:07Z

👋 @ricboer0 - while I am getting you a topic editor assigned, please reduce the word count of your paper to around 1000 words. Thanks.

ricboer0 · 2024-12-04T15:43:06Z

@crvernon awesome, I'll work on that. Thanks.

ricboer0 · 2024-12-05T14:34:41Z

@editorialbot check repository

editorialbot · 2024-12-05T14:35:10Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (2281.5 files/s, 207220.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Go                              64            694            950           4075
Markdown                        12            336              0           1210
YAML                             6             72             31            423
JavaScript                       1             47             25            208
TOML                             5             29             19            188
TeX                              1             11              0            187
CSS                              1              9              1             42
R                                1              9             78             34
Julia                            2             10              7             33
Python                           1              6              3             24
JSON                             1              0              0             19
C                                1              4              2             15
C/C++ Header                     1              3              2              4
-------------------------------------------------------------------------------
SUM:                            97           1230           1118           6462
-------------------------------------------------------------------------------

Commit count by author:

   697	Riccardo Boero
    12	GitHub Action

editorialbot · 2024-12-05T14:35:15Z

Paper file info:

📄 Wordcount for paper.md is 2259

✅ The paper includes a Statement of need section

editorialbot · 2024-12-05T14:35:19Z

License info:

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

ricboer0 · 2024-12-05T14:41:13Z

@editorialbot check repository

editorialbot · 2024-12-05T14:41:44Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (2279.0 files/s, 206846.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Go                              64            694            950           4075
Markdown                        12            333              0           1207
YAML                             6             72             31            423
JavaScript                       1             47             25            208
TOML                             5             29             19            188
TeX                              1             11              0            187
CSS                              1              9              1             42
R                                1              9             78             34
Julia                            2             10              7             33
Python                           1              6              3             24
JSON                             1              0              0             19
C                                1              4              2             15
C/C++ Header                     1              3              2              4
-------------------------------------------------------------------------------
SUM:                            97           1227           1118           6459
-------------------------------------------------------------------------------

Commit count by author:

   698	Riccardo Boero
    12	GitHub Action

editorialbot · 2024-12-05T14:41:51Z

Paper file info:

📄 Wordcount for paper.md is 1971

✅ The paper includes a Statement of need section

editorialbot · 2024-12-05T14:41:55Z

License info:

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

ricboer0 · 2024-12-05T14:43:11Z

@editorialbot generate pdf

editorialbot · 2024-12-05T14:45:05Z

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

editorialbot · 2024-12-05T14:45:54Z

Five most similar historical JOSS papers:

PyExperimenter: Easily distribute experiments and track results
Submitting author: @tornede
Handling editor: @timtroendle (Retired)
Reviewers: @ArsamAryandoust, @schnorr
Similarity score: 0.6766

LISC: A Python Package for Scientific Literature Collection and Analysis
Submitting author: @TomDonoghue
Handling editor: @danielskatz (Active)
Reviewers: @timClicks, @linuxscout
Similarity score: 0.6745

Mantik: A Workflow Platform for the Development of Artificial Intelligence on High-Performance Computing Infrastructures
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AstronomicAL: an interactive dashboard for visualisation, integration and classification of data with Active Learning
Submitting author: @grant-m-s
Handling editor: @crvernon (Active)
Reviewers: @crhea93, @rmorgan10
Similarity score: 0.6693

⚠️ 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.

crvernon · 2024-12-05T15:12:30Z

Also, @ricboer0 - could you remove the formatting around prisimAId in your title in the paper. This causes issues in JOSS formatting. Thanks!

crvernon · 2024-12-05T15:13:10Z

@editorialbot assign me as editor

I think I'll just take this on myself.

editorialbot · 2024-12-05T15:13:15Z

Assigned! @crvernon is now the editor

ricboer0 · 2024-12-05T15:18:36Z

@editorialbot check repository

ricboer0 · 2024-12-05T15:18:42Z

@editorialbot generate pdf

editorialbot · 2024-12-05T15:19:04Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (2178.3 files/s, 197548.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Go                              64            694            950           4075
Markdown                        12            330              0           1205
YAML                             6             72             31            423
JavaScript                       1             47             25            208
TOML                             5             29             19            188
TeX                              1             11              0            185
CSS                              1              9              1             42
R                                1              9             78             34
Julia                            2             10              7             33
Python                           1              6              3             24
JSON                             1              0              0             19
C                                1              4              2             15
C/C++ Header                     1              3              2              4
-------------------------------------------------------------------------------
SUM:                            97           1224           1118           6455
-------------------------------------------------------------------------------

Commit count by author:

   699	Riccardo Boero
    12	GitHub Action

editorialbot · 2024-12-05T15:19:08Z

Paper file info:

📄 Wordcount for paper.md is 1824

✅ The paper includes a Statement of need section

editorialbot · 2024-12-05T15:19:12Z

License info:

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

editorialbot · 2024-12-05T15:20:37Z

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

editorialbot · 2024-12-05T15:21:24Z

Five most similar historical JOSS papers:

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Submitting author: @tornede
Handling editor: @timtroendle (Retired)
Reviewers: @ArsamAryandoust, @schnorr
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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.

ricboer0 · 2024-12-05T15:31:03Z

Thanks @crvernon for the support so far.
A couple of questions.
A) I managed to cut half of the original submission, now at 1,800 words. Is it good enough? Going down now is more difficult.
B) is there a way to reference the github repository from the markdown? I put it as an entry in references but i see a nice link on the left side of the article proof. Otherwise I'll just mention the repository in text with no link.

crvernon · 2024-12-05T15:46:55Z

@ricboer0 - Let's leave the paper at its current length for now. The repo will be referenced in the final draft automatically once compiled, so no need to add an additional reference in text. Thanks!

ricboer0 · 2024-12-05T15:51:38Z

@editorialbot generate pdf

editorialbot · 2024-12-05T15:53:27Z

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

editorialbot · 2024-12-05T15:54:16Z

Five most similar historical JOSS papers:

PyExperimenter: Easily distribute experiments and track results
Submitting author: @tornede
Handling editor: @timtroendle (Retired)
Reviewers: @ArsamAryandoust, @schnorr
Similarity score: 0.6817

PhysioLabXR: A Python Platform for Real-Time, Multi-modal, Brain–Computer Interfaces and Extended Reality Experiments
Submitting author: @ApocalyVec
Handling editor: @mstimberg (Active)
Reviewers: @lucask07, @nastaran62
Similarity score: 0.6802

pygetpapers: a Python library for automated retrieval of scientific literature
Submitting author: @ayush4921
Handling editor: @chartgerink (Retired)
Reviewers: @khinsen, @VeroniqueLegrand, @kjappelbaum
Similarity score: 0.6787

LISC: A Python Package for Scientific Literature Collection and Analysis
Submitting author: @TomDonoghue
Handling editor: @danielskatz (Active)
Reviewers: @timClicks, @linuxscout
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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.

ricboer0 · 2024-12-05T15:58:08Z

@editorialbot generate pdf

editorialbot · 2024-12-05T16:00:08Z

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

editorialbot · 2024-12-05T16:00:58Z

Five most similar historical JOSS papers:

PyExperimenter: Easily distribute experiments and track results
Submitting author: @tornede
Handling editor: @timtroendle (Retired)
Reviewers: @ArsamAryandoust, @schnorr
Similarity score: 0.6817

PhysioLabXR: A Python Platform for Real-Time, Multi-modal, Brain–Computer Interfaces and Extended Reality Experiments
Submitting author: @ApocalyVec
Handling editor: @mstimberg (Active)
Reviewers: @lucask07, @nastaran62
Similarity score: 0.6782

pygetpapers: a Python library for automated retrieval of scientific literature
Submitting author: @ayush4921
Handling editor: @chartgerink (Retired)
Reviewers: @khinsen, @VeroniqueLegrand, @kjappelbaum
Similarity score: 0.6751

LISC: A Python Package for Scientific Literature Collection and Analysis
Submitting author: @TomDonoghue
Handling editor: @danielskatz (Active)
Reviewers: @timClicks, @linuxscout
Similarity score: 0.6704

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Handling editor: @emdupre (Active)
Reviewers: @richford, @tachukao
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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.

crvernon · 2024-12-05T21:08:21Z

👋 @philip928lin - Would you be willing to review this submission to JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

philip928lin · 2024-12-05T21:10:30Z

👋 @philip928lin - Would you be willing to review this submission to JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

@crvernon Yes, I am willing to review this submission. Thanks for the invitation.

crvernon · 2024-12-05T21:15:08Z

@editorialbot add @philip928lin as reviewer

editorialbot · 2024-12-05T21:15:11Z

@philip928lin added to the reviewers list!

crvernon · 2024-12-24T14:41:21Z

👋 @jhculb - Would you be willing to review this submission to JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

jhculb · 2024-12-24T15:24:14Z

Hi, I think I should have some time to do so, yes :)

👋 @jhculb - Would you be willing to review this submission to JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

crvernon · 2024-12-24T15:37:26Z

@editorialbot add @jhculb as reviewer

editorialbot · 2024-12-24T15:37:28Z

@jhculb added to the reviewers list!

crvernon · 2024-12-24T15:38:24Z

@editorialbot start review

👋 - Alright @ricboer0, @philip928lin and @jhculb - I am going to close this Pre-Review and kick off the full review which you should receive a notification for. Thanks!

editorialbot · 2024-12-24T15:38:28Z

OK, I've started the review over in #7616.

editorialbot added pre-review Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels Dec 4, 2024

editorialbot added Go TeX R labels Dec 4, 2024

editorialbot assigned crvernon Dec 5, 2024

editorialbot assigned philip928lin Dec 5, 2024

editorialbot assigned jhculb Dec 24, 2024

editorialbot closed this as completed Dec 24, 2024

[PRE REVIEW]: An Introduction to prismAId: Open-Source and Open Science AI for Advancing Information Extraction in Systematic Reviews #7569

[PRE REVIEW]: An Introduction to prismAId: Open-Source and Open Science AI for Advancing Information Extraction in Systematic Reviews #7569

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[PRE REVIEW]: An Introduction to `prismAId`: Open-Source and Open Science AI for Advancing Information Extraction in Systematic Reviews #7569

[PRE REVIEW]: An Introduction to `prismAId`: Open-Source and Open Science AI for Advancing Information Extraction in Systematic Reviews #7569

editorialbot commented Dec 4, 2024 •

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