Robertmorrisluminousenergy177 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
- Inspect the source PDF: title, authors, sections, page count, figures, captions, tables, references to supplements, and any copyright-sensitive constraints.
- Create a vault-style output folder with
assets/figures/,exports/, and one main Markdown note unless the user asks for multiple notes. - Translate and explain paragraph by paragraph. Number natural paragraphs as
P01,P02, etc.; correct OCR or extraction order against page renders. - Insert each figure near the paragraph that first uses it. Store images under
assets/figures/with stable descriptive names. - 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.
- Add beginner support at first use of key concepts, methods, axes, formulas, materials, and mechanisms. Mark claim boundaries: measured, calculated, inferred, or proposed.
- Maintain a question log for knowledge questions. Merge repeated questions into the closest existing entry instead of duplicating long explanations.
- Verify Markdown links, figure paths, section coverage, and whether the output is readable in Obsidian.
- 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.