nature-reader

# Full-Paper Markdown Reader Use this skill to turn a research paper into a complete Markdown reading artifact. The default output should read like a bilingual paper companion, not a summary dump: - keep the extractable prose, paragraph structure, and section flow - show original text and Chinese translation together at block level - extract figures and tables as assets and place them at the first substantive mention or interpretation point - keep captions attached to figures/tables with English caption text and Chinese caption translation - preserve stable page and block anchors for traceability - write a complete `paper.md` by default, plus `source_map.json`, `translation_notes.md`, and `assets/` This skill is for papers, preprints, and conference proceedings across disciplines. It is not limited to Nature-family journals. ## When to use Use this skill when the user wants any of the following: - translate an entire paper into a complete Markdown document - make a paper easier to read without losing the original wording - generate a full-paper reading file with original/translation alignment - keep figures or tables visually close to the claims they support - preserve exact source locations for every substantive block - build a source-grounded markdown artifact rather than a slide deck or short summary If the user only wants a summary, use a summarization skill instead. If the user only wants citation search, use a citation skill instead. ## Non-negotiable defaults When the user asks for paper translation, reading, `nature-reader`, `中英文对照`, `原文对照`, `全文翻译`, or `翻译解读`, produce a paragraph-level bilingual reader by default. Do not replace the reader with: - a Chinese-only summary - a paper review without original/translation alignment - figure captions without figure/table crops - a list of key points detached from source locations - only the abstract, introduction, or selected highlights If constraints prevent full processing, still create a draft reader and clearly label missing pages, missing figures/tables, untranslated blocks, or low-confidence OCR/crops in `translation_notes.md`. ## Core principle Translate for meaning, not for style. Preserve the paper's structure, evidence, hedging, terminology, equations, units, and citation markers. Keep the output in prose paragraphs unless the source itself is tabular or list-like. Do not collapse the paper into keyword bullets or slide-style notes. The reading file should help a reader move between: - original text - translated text - source location - figure or table evidence Each substantive source block should have a stable anchor and a visible bilingual pair: ```markdown <a id="S001"></a> **Source:** p.1 S001 **Original:** [source paragraph] **中文:** [faithful Chinese translation] ``` For copyrighted publisher PDFs, keep chat responses short and point to the local artifact. In local `paper.md`, include the bilingual reader only for the user-provided source file or clearly lawful open-access content; avoid reproducing large copyrighted text directly in chat. ## Workflow ### 1. Identify the source and paper type Determine whether the source is: - selectable-text PDF - scanned PDF - publisher HTML - DOI or arXiv link - pasted text or notes Then identify the paper type at a high level: - discovery or mechanism paper - methods or algorithm paper - resource or dataset paper - conference paper - review or perspective This helps decide how tightly to couple text, figures, and captions. ### 2. Build a full-document source map before translating If the user provides a full paper, process the entire document. Do not stop at the abstract, introduction, or a few representative pages unless the user explicitly asks for a preview. Create stable IDs for source blocks: - `S001`, `S002`, ... for body text - `C001`, `C002`, ... for captions - `F001`, `F002`, ... for figures - `T001`, `T002`, ... for tables For each block, capture: - page number - block type - original text - translation - reading-order index - nearby figure or table references - first substantive figure/table mention when applicable - confidence level when extraction is uncertain Keep the source map stable so later questions can point back to the same IDs. For long papers, add a page index so the reader can jump across the whole document without losing location. ### 3. Translate conservatively Translate every extractable substantive block with these rules: - preserve technical terms unless a standard Chinese equivalent is clearly better - keep gene names, protein names, formulas, model names, and symbols intact - keep citations, superscripts, subscripts, and numeric values unchanged - do not collapse methods details into vague prose - keep paragraph order and section order unless the user asks for restructuring - mark uncertain text instead of guessing when OCR or layout extraction is weak - keep the source's paragraph form; do not convert dense prose into bullet-point keywords - do not silently skip Methods, limitations, data availability, code availability, competing interests, or extended captions - if the paper is too long for one pass, write `paper.md` incrementally by page/section and mark pending blocks rather than switching to summary mode If a sentence contains multiple claims, keep the translation readable but do not split away the original evidence chain. ### 4. Extract and place figures and tables near the relevant discussion Do not try to recreate the PDF pixel-for-pixel. Preserve semantic proximity instead. Default placement rule: - crop each figure/table into `assets/` and show it near its first substantive mention in the body text - keep the caption attached to the figure/table - show both original caption and Chinese caption translation - if the caption contains critical details, keep caption and figure together - if a table is central to the claim, keep it near the paragraph that interprets it - if a figure/table appears before the body discussion in PDF layout, still place it where it best supports the reading flow and add `Placed near: p.X SYYY` - if a later section mentions the same figure/table again, link back to the already inserted figure/table block instead of duplicating it If the paper has a complex multi-column layout, prefer a clean reading layout over exact visual mimicry. ### 4b. Crop figures and tables tightly When extracting a figure or table image: - crop only the figure or table content area, not the whole page - use the smallest rectangle that fully contains the visual object - exclude page headers, footers, surrounding prose, and unrelated margins - keep the caption separate unless the caption is part of the requested visual crop - if the crop box is uncertain, mark it as approximate instead of enlarging it Precision matters more than convenience here. A slightly smaller but correct crop is better than a wider crop that includes unrelated page content. Figure/table blocks in `paper.md` should use this shape: ```markdown <a id="F001"></a> ### Fig. 1. [short translated title] **Placed near:** p.3 S012 **Source:** p.4 C001  **Original caption:** [caption text] **中文图注:** [caption translation] **Reading note:** [brief explanation of what to inspect in the figure] ``` ### 5. Generate the Markdown file Default output is a single full-paper `paper.md` file. The Markdown must include: - metadata header - a short page/section index - page-level or section-level divisions for long papers - paragraph-level original/Chinese pairs for all extractable substantive text - figure and table blocks placed near the relevant discussion - source anchors on every substantive text, figure, caption, and table block - a terminology table for recurring technical terms - a short `阅读提示` / `critical reading notes` section only after the bilingual body, not as a replacement for it - short uncertainty notes only when extraction is weak Do not add an interactive Q&A panel or follow-up widget in the Markdown deliverable. If the user later asks a question, answer it in chat using the source map rather than embedding a conversational panel in the artifact. If a browser preview is explicitly requested, a companion `reader.html` can be generated as a secondary artifact, but the Markdown file remains the primary output. ### 6. Answer follow-up questions with source grounding When the user asks a question after the file is created: - identify the most relevant source blocks first - answer from the paper, not from memory - cite the exact block IDs and page numbers - if the answer depends on a figure or table, cite that too - if the paper does not support the claim, say so plainly Every substantive answer should include a source pointer such as: - `p.4 S012-S013` - `Fig. 2 caption` - `Table 1` If the answer is a synthesis across several blocks, list all supporting locations. ## Output contract Prefer these outputs: - `paper.md` for the full-paper Markdown artifact - `source_map.json` for stable source anchors - `translation_notes.md` for terminology, uncertainty, and layout notes - `assets/` for extracted figures or cropped snippets when needed - `reader.html` only when the user explicitly wants a browser preview Do not hide missing information. If the source is incomplete, label the output as draft mode. Before final response, verify: - `paper.md` contains `**Original:**` and `**中文:**` block pairs - every image/table link used in `paper.md` exists under `assets/` - every figure/table in `assets/` has a corresponding Markdown block and source pointer - `source_map.json` parses as JSON and includes source block IDs - `translation_notes.md` records skipped, uncertain, or draft-mode content ## Tooling guidance If the input is a PDF, load the `pdf` skill first for extraction and OCR guidance. If the user asks for a richer browser view, use `web-artifacts-builder` or `frontend-design` only as a preview layer on top of the Markdown workflow. If the user wants citation-level grounding to original text, keep the source map explicit and do not lose the page or block IDs. ## Quality bar Good output feels like a paper reader, not a machine translation dump. It should let a reader: - read the paper in two languages - see where a claim came from - inspect the nearby figure or table - move through a complete Markdown file without losing source traceability