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Feedback Paper Submission#37

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ndaelman-hu wants to merge 49 commits into
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paper-submission
Draft

Feedback Paper Submission#37
ndaelman-hu wants to merge 49 commits into
mainfrom
paper-submission

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@ndaelman-hu

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This is just a tool for getting feedback. It does NOT get merged into main.

- Extension of author list, courtesy of @ndaelman-hu

Changes to be committed:
	new file:   paper/draft.tex
	new file:   paper/parse-patrol.png
	new file:   paper/ref.bib
-- TODO: add spepcifics on the solutions we provide + results observed

Changes to be committed:
	modified:   draft.tex
-- TODO: update statement on future work

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	modified:   draft.tex
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	modified:   draft.tex
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	modified:   draft.tex
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	modified:   draft.tex
-- Add svg file for editing with InkScape

Changes to be committed:
	modified:   parse-patrol.png
	new file:   parse-patrol.svg
-- AI generate overview of Git PR authorship

Changes to be committed:
	modified:   draft.tex
	new file:   git-contriubtions.tex
- Save edits InkScape

Changes to be committed:
	modified:   draft.tex
	modified:   parse-patrol.svg
@ndaelman-hu
ndaelman-hu marked this pull request as draft November 14, 2025 10:32
@QuantumChemist

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The author contributions are missing atm. It is one of the manuscript requriements.

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The author contributions are missing atm. It is one of the manuscript requriements.

They should be at the bottom of draft.text.

 \section*{Author Contributions}

\textbf{N.D.}: Conceptualization, Software, Original Code Draft, Visualization, Writing - Editing,
\textbf{C.E.}: Conceptualization, Software, Visualization, Video Editing, Writing - Original Manuscript Text Draft, Figure, Editing
\textbf{R.M.}: Implementation asynchronous servers, Extension Testing Infrastructure - Conceptualization Revision 
\textbf{S.K.}: Rollout Parser Support 

@QuantumChemist

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The author contributions are missing atm. It is one of the manuscript requriements.

They should be at the bottom of draft.text.

 \section*{Author Contributions}

\textbf{N.D.}: Conceptualization, Software, Original Code Draft, Visualization, Writing - Editing,
\textbf{C.E.}: Conceptualization, Software, Visualization, Video Editing, Writing - Original Manuscript Text Draft, Figure, Editing
\textbf{R.M.}: Implementation asynchronous servers, Extension Testing Infrastructure - Conceptualization Revision 
\textbf{S.K.}: Rollout Parser Support 

yeah, it was the overleaf version where it was missing. Just saw that 1 min ago. Sorry 🙈

@QuantumChemist

QuantumChemist commented Nov 14, 2025

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I really like the new version of the manuscript. It has much more soul than the very technical version, that I had drafted 🤣

There are just two one issue left for now:
1. We should reference the figure somewhere (Edit, I found it 🙈 . Sorry, was overreading it)

  1. I find the expression "Parse-Patrol combines the best of both worlds" a bit hyped (too bad that HypeLessLi doesn't work on overleaf). But I didn't change it for now because maybe you disagree?

@ndaelman-hu

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I really like the new version of the manuscript. It has much more soul than the very technical version, that I had drafted 🤣

There are just two one issue left for now: 1. We should reference the figure somewhere (Edit, I found it 🙈 . Sorry, was overreading it)

1. I find the expression "Parse-Patrol combines the best of both worlds" a bit hyped (too bad that [HypeLessLi](https://github.com/SimonNir/HypeLessLi) doesn't work on overleaf). But I didn't change it for now because maybe you disagree?

How about: "Parse-Patrol combines various community parsers into a single cohesive interface for AI and human developer alike."

- Add empty citation markers

Changes to be committed:
	modified:   draft.tex
@ndaelman-hu

ndaelman-hu commented Nov 14, 2025

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  • Anyone willing to help with filling the citation markers?
  • MCP should refer to the original paper, can we double-check that it is so?
  • I have a citation in mind for the community. Leave that up to me.
  • The registry and pypi could be urls.

@QuantumChemist

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I really like the new version of the manuscript. It has much more soul than the very technical version, that I had drafted 🤣
There are just two one issue left for now: 1. We should reference the figure somewhere (Edit, I found it 🙈 . Sorry, was overreading it)

1. I find the expression "Parse-Patrol combines the best of both worlds" a bit hyped (too bad that [HypeLessLi](https://github.com/SimonNir/HypeLessLi) doesn't work on overleaf). But I didn't change it for now because maybe you disagree?

How about: "Parse-Patrol combines various community parsers into a single cohesive interface for AI and human developer alike."

this sounds good to me!

@QuantumChemist QuantumChemist left a comment

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My idea how to cite the MCP server "original work"

Comment thread paper/ref.bib
Comment thread paper/draft.tex Outdated
Sideboard and others added 4 commits November 14, 2025 15:22
- Elaborate on the community issues and impact
-- TODO: add paragraph on AI in the intro
- Swap "dependency" for the more Pythonic "module"

Changes to be committed:
	modified:   draft.tex
Added references for Python Package Index and MCP Servers Registry.
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btw I would be in favour of merging this into main in the end to have our contribution to the manuscript as part of the repo 😄

QuantumChemist and others added 3 commits November 14, 2025 16:28
Updated references to MCP Registry and PyPi with hyperlinks.
…-submission

- Correct typos

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	modified:   draft.tex
ndaelman-hu and others added 18 commits November 14, 2025 17:27
Changes to be committed:
	modified:   draft.tex
- Use figure terminology
- Broaden title to include scientific parsers in general

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	modified:   draft.tex
- Unify the figure text box between both branches

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	modified:   draft.tex
	modified:   parse-patrol.png
-- fold bulletpoints back into text
-- remove redundant phrases
- Extend coverage of agentic pitfalls

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	modified:   draft.tex
- Merge paragraph on database and parser communities
- Revise phrasing
- Add manual polishing

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	modified:   draft.tex
- Extend caption along the entire page width
- Change type setting caption
- Trim paragraph

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	modified:   draft.tex
avoid naming specific software, package, db support and focus on the concept instead.
- Remove unused references

Changes to be committed:
	modified:   draft.tex
	modified:   ref.bib
Clarified language regarding LLMs and MCP, improving readability and precision in the explanation of parser infrastructure and its integration with AI tools.

@RubelMozumder RubelMozumder left a comment

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It looks really great.

Comment thread paper/draft.tex Outdated
Comment thread paper/draft.tex Outdated
Comment thread paper/draft.tex Outdated
Comment thread paper/draft.tex Outdated
-- clarify phrasing on I/O dependency, how a lack of docs is handled, why we introduce MCP servers as modules too
-- add reference to MCP intro
-- explain where the Git link points to and which version was originally submitted

Changes to be committed:
	modified:   draft.tex
	modified:   ref.bib
Changes to be committed:
	modified:   draft.tex
  - Shorten text to meet length requirements by removing redundant phrasing
  - Replace "outsources" with "sidesteps" and "input/output" with "source/target"
  - Add "however" transition and clarify component registration flow
  - Refine dual-mode explanation: introduce tool schemas and explain interface evolution
  - Standardize terminology: "predefined prompts", capitalize mode names, remove "hosts"

Changes to be committed:
	modified:   draft.tex
- Correct caption: capitalization, phrasing Upper branch, boldness sections
- Correct phrasing figure: "Parser Output conform User-Defined Schemas"

Changes to be committed:
	modified:   draft.tex
	modified:   parse-patrol.png
	modified:   parse-patrol.svg
@ndaelman-hu

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Okay, the commit marked at this timestamp is the submitted version. Unless prompted by FAIRmat, this version does NOT get modified further.

ndaelman-hu added a commit that referenced this pull request Nov 18, 2025
Updated the README to include a link for the Model Context Protocol, a suggested in #37 .
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5 participants