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Paper deep reading

Skill Robertmorrisluminousenergy177/paper-deep-reading-skill/paper-deep-reading

Convert research paper PDFs into structured Obsidian notes with automated translations, figure analysis, and concept explanations for deep study.

Install
npx -y skills add Robertmorrisluminousenergy177/paper-deep-reading-skill --skill paper-deep-reading

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

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  • 27 days oldThe repository was created 27 days ago. New is not bad, but a brand new repository carrying a familiar-sounding name is the shape a typosquat arrives in, and there has been no time for anyone else to find a problem with it.
  • 0 stars0 stars. Stars are a popularity signal and not a quality one, but at this level it is likely that nobody has read this closely except its author, and you would be relying on your own review.

What its author says it does

Copied from the file, not written here

Create beginner-friendly deep-reading notes for journal and research paper PDFs. Use when Codex needs to learn a paper, translate it paragraph by paragraph, build an Obsidian knowledge-base note, extract and place figures, write detailed figure notes, explain concepts for beginners, maintain a question log, or export the note to PDF. Also use for Chinese requests such as 学习文献, 精读论文, 逐段翻译, 图注解释, 问题荟萃, and Obsidian 笔记.

SKILL.md

4.0 KB, 735 tokens by cl100k_base, as published. Nobody here has run it

Paper Deep Reading

Purpose

Turn a journal paper into a polished learning artifact: one main Obsidian Markdown note with paragraph-level translation, placed figures, detailed figure notes, beginner explanations, glossary support, a question log, and optional PDF export.

Use the PDF skill or an equivalent render-and-inspect workflow whenever the source is a PDF. For two-column journal articles, rendered pages are the source of truth for reading order and figure placement.

Default Workflow

  1. Inspect the source PDF: title, authors, sections, page count, figures, captions, tables, references to supplements, and any copyright-sensitive constraints.
  2. Create a vault-style output folder with assets/figures/, exports/, and one main Markdown note unless the user asks for multiple notes.
  3. Translate and explain paragraph by paragraph. Number natural paragraphs as P01, P02, etc.; correct OCR or extraction order against page renders.
  4. Insert each figure near the paragraph that first uses it. Store images under assets/figures/ with stable descriptive names.
  5. For every main figure, write a figure note that explains what type of figure it is, what each panel does, what claim it supports, why it matters, and why the authors included it.
  6. Add beginner support at first use of key concepts, methods, axes, formulas, materials, and mechanisms. Mark claim boundaries: measured, calculated, inferred, or proposed.
  7. Maintain a question log for knowledge questions. Merge repeated questions into the closest existing entry instead of duplicating long explanations.
  8. Verify Markdown links, figure paths, section coverage, and whether the output is readable in Obsidian.
  9. Export to PDF only when requested. Render the note, inspect representative pages visually, and place final PDFs in exports/.

Required References

Read only the reference files needed for the user's request:

  • references/reading-workflow.md: full paper-to-note workflow and quality gates.
  • references/figure-note-guide.md: how to crop, place, and explain figures.
  • references/beginner-explanation-guide.md: how to explain a difficult field to a novice without oversimplifying.
  • references/obsidian-note-style.md: note structure, callouts, links, and CSS expectations.
  • references/question-log-guide.md: how to maintain the learning question log and merge repeated concepts.

Bundled Resources

  • assets/note-template.md: starting structure for the main paper note.
  • assets/question-log-template.md: structure for the separate question log.
  • assets/figure-note-template.md: reusable figure-note block.
  • assets/obsidian-css-snippet.css: optional Obsidian CSS for readable callouts and figures.
  • scripts/validate_note_structure.py: lightweight validation for headings, images, callouts, and repeated question IDs.
  • scripts/export_obsidian_note_pdf.js: Markdown/Obsidian image rendering to PDF through Playwright.
  • scripts/extract_pdf_assets.py: optional PyMuPDF helper to render pages and extract embedded images.

Output Standards

  • Prefer one substantial Markdown note over many small files.
  • Keep images close to the text that explains them.
  • Write figure notes specific to the paper, not generic captions.
  • Explain graph axes before interpreting trends.
  • Avoid unsupported claims. Say when a point is an inference from the paper.
  • Do not publicly include copyrighted full-text translations in example repositories unless the source license permits it.
  • Before finishing, report the note path, figure count, question-log status, and any export path.

Gives 0 of the 12 instructions most note taking skills give in 735 tokens

Counted across 686 of the 876 authors here whose files we hold, read 2026-08-07

  • include a visual element on every slidein 44 of 686, across 13 files
  • use wikilinks for internal vault linksin 36 of 686, across 12 files
  • commit to a single visual motif across every slidein 34 of 686, across 9 files
  • use subagents to visually inspect rendered slidesin 31 of 686, across 7 files
  • read pptxgenjs guide before creating presentations from scratchin 30 of 686, across 6 files
  • keep 0.5 inch minimum marginsin 30 of 686, across 7 files
  • re-verify affected slides after every fixin 27 of 686, across 5 files
  • run content QA checks before declaring successin 26 of 686, across 3 files
  • Use Markdown links for external URLs onlyin 26 of 686, across 11 files
  • pick a bold topic specific color palettein 24 of 686, across 2 files
  • read editing guide before editing existing presentationsin 23 of 686, across 1 file
  • use one dominant color across all slidesin 23 of 686, across 1 file

Said here and by no other author read

  • inspect source PDF structure and contents
  • create vault folder and main markdown note
  • translate and explain paragraph by paragraph
  • insert each figure near first mentioning paragraph
  • write detailed notes for every main figure
  • add beginner explanations for key concepts

Grouped from the skills themselves: near-identical wordings counted once, and counted by distinct author, so one author publishing three of these counts once. Length counted with cl100k_base; the agent that loads this file may tokenize it differently.

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