Source: https://github.com/aipoch/medical-research-skills

Mindmap HTML Generation

Overview

First organize input into a clear tree hierarchy, then call scripts/generate_mindmap_html.py to generate offline HTML. Prioritize reusing existing heading structure; do not modify visual code first — get structure correct, then let the script generate the output.

Tip: The generated HTML page now includes a top toolbar: Export PNG / Fullscreen. Content generation logic remains identical.

Workflow

1. Determine Input Source

• If the user has already provided Markdown headings or lists, render directly.
• If the user provides meeting notes, long text, or chat logs, first organize into Markdown hierarchy, then render.
• If the user provides a JSON tree, confirm fields are text / children, then render directly.

2. Organize Structure

• Prioritize preserving the user's original heading hierarchy.
• If the original text has no headings, first extract 1 main topic and several level-1 and level-2 branches.
• If the original is plain paragraphs or sentences, the script adaptively splits by blank lines, line breaks, colons, and periods.
• Recommended depth is 2-4 levels to avoid pages becoming hard to read.
• Keep node text as short phrases; do not stuff entire paragraphs into nodes.

Content Richness Requirements

• The default goal is not just "producing a map" but "complete information, clear hierarchy, usable for review, presentation, or reporting".
• Level-1 branches under root should typically be at least 6; if the topic is information-dense, expand to 8-12.
• Each level-1 branch should preferably have 3-6 level-2 nodes; do not force equal branch lengths for neatness.
• If a level-2 node contains methods, conditions, results, mechanisms, impacts, exceptions, or evidence, continue splitting to level-3 nodes.
• For information-dense paragraphs, prioritize splitting into more nodes rather than compressing into one summary sentence.
• For long texts, papers, and meeting notes, do not just keep section names — also include the actual information points under each section.
• Node text must be concise, but conciseness does not mean deleting details.

Information Extraction Priority

• Prioritize extracting: background, problem, objective, subject, method, materials, process, key variables, results, mechanism, conclusion, significance, limitations, applications.
• If the source text contains causal, conditional, parallel, or contrasting relationships, split into multiple nodes.
• If the source text contains proper nouns, core mechanisms, metrics, sample sizes, models, drugs, groups, or key conclusions, prioritize preserving them.
• If a level-1 node name is too abstract, add specific child nodes to carry the details.
• If content can be split into "subject / action / result / significance", prefer this structure.

Paper Input Enhancement Rules

• When processing papers, PDFs, or research abstracts, do not just extract section names — include information points within each section.
• Cover at minimum: research background, research question, experimental design, key results, mechanism chain, conclusions and implications.
• If paper information is sufficient, additionally include: research subject, sample size, model, groups, experimental methods, key molecules or pathways, intervention, efficacy, limitations.
• If PDF auto-extraction is too coarse, generate intermediate Markdown first, then restructure before rendering.

Prohibited Behaviors

• Do not distribute branches evenly just for neatness.
• Do not just restate headings without adding information beneath them.
• Do not write only one vague summary sentence for each of "Background, Methods, Results, Conclusion".
• Do not omit key numbers, key steps, key mechanisms, or key experimental subjects.
• Do not sacrifice information density for brevity.

3. Configure Script

• Edit the CONFIG block at the top of scripts/generate_mindmap_html.py.
• Common configuration options:
  • input_path: Input file path.
  • output_html_path: Output HTML path.
  • output_markdown_path: Intermediate Markdown path.
  • page_title: Page title.
  • fallback_title: Fallback title when no root heading exists.
  • auto_bold_levels: Heading levels to bold by default, recommend keeping [1, 2].
  • plain_text_root_max_children: Maximum level-1 branches when auto-splitting plain text.
  • plain_text_child_max_children: Maximum child items per level-1 branch when auto-splitting plain text.

4. Run Script

Run:

python scripts/generate_mindmap_html.py

The script will:

1. Read the input file.
2. Parse tree structure.
3. Generate intermediate Markdown.
4. Call npx markmap-cli to export offline HTML.
5. Inject fixed layout and color rules.

5. Validate Results

• Open the generated HTML, confirm root node, level-1 branch order, and text display are correct.
• Confirm only level-1 and level-2 headings remain bold; level-3 and deeper are not bold.
• Confirm branch counts and child counts follow content variation, not mechanical equal lengths.
• Self-check that level-1 branches sufficiently cover the topic.
• Self-check that key numbers, mechanisms, subjects, and conclusions are not omitted.
• Self-check for multiple level-1 branches with identical structure but empty content.
• If nodes are too long, go back to compress input text, then re-run the script.
• If npx or markmap-cli is missing, install the Node.js environment first.

Input Rules

• Supports .md, .txt, .json.
• Markdown: prioritizes ATX headings (# to ######), then indented lists.
• Plain text prioritizes splitting by blank lines, line breaks, colons, periods, and other punctuation into unequal-length branches and children.
• JSON must be a single tree with fields text and children.
• Output path, page title, and fallback title go in CONFIG — do not pile CLI arguments.

Style Conventions

• The script has a built-in fixed final layout; manual style changes after HTML export are not recommended.
• Only # and ## level headings are bold by default; ### and below automatically remove bold.
• To adjust bold levels, modify CONFIG["auto_bold_levels"], but bolding level-3+ is not recommended.
• Exported HTML automatically assigns unified color groups per level-1 branch.
• Key parameter: MARKMAP_INIT_OPTIONS["colorFreezeLevel"] = 2. This freezes colors at "root + level-1 branch"; setting to 1 makes the entire map nearly monochrome.
• To adjust colors, modify MARKMAP_THEME — do not manually edit line colors in exported HTML.

Resources

scripts/generate_mindmap_html.py

Converts structured text to markmap source Markdown and generates offline HTML.

references/input-patterns.md

Read when deciding how to organize input — contains recommended structure templates and examples.

Execution Constraints

• All file I/O must explicitly use encoding="utf-8".
• When writing JSON, use ensure_ascii=False.
• Prefer modifying script top-level CONFIG; do not hide key parameters in long command lines.
• Generate offline pages by default; avoid online CDN dependencies.

When to Use

• Use this skill when the user explicitly needs to perform the core task of mindmap-html-generator and has provided the minimum executable input.
• Use this skill when you need a structured deliverable rather than general advice.
• Use this skill when the current task can be completed using this skill's bundled scripts, templates, or reference materials.

When Not to Use

• Do not proceed when required input files, identifiers, parameters, or context are missing — ask the user to provide them first.
• Do not assume capabilities beyond this skill's declared scope when the user requests external operations or inferences.
• Do not proceed without user confirmation when overwriting existing results, executing high-cost batch operations, or expanding task scope.

Required Inputs

Output Contract

• Primary output: Structured result or target file aligned with this skill's objective.
• Optional output: Intermediate check notes, issue list, supplementary suggestions, or generated file paths.
• Format requirement: Unless the user specifies otherwise, prefer stable, reviewable Markdown or JSON; if the skill's bundled script requires a fixed format, use that format.
• If partially complete: Must explicitly mark as PARTIAL and state which steps are completed and which remain.

Failure Handling

• Missing critical input: Explicitly state which fields, files, or identifiers are missing and pause.
• Script, template, or resource execution failure: Report the failing step, likely cause, and recovery suggestions — do not silently degrade.
• Partial completion only: Return the verified portion first, then list remaining blockers and suggested next steps.

User Checkpoints

• Before executing batch processing, overwriting files, long-running searches, or multi-stage generation, confirm scope and output format with the user.
• Before proceeding when a key judgment is ambiguous, evidence is insufficient, or the workflow is entering the next stage, confirm with the user.

Input Validation

This skill accepts requests that match the documented purpose of mindmap-html-generator and include enough context to complete the workflow safely.

Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions.

Quick Validation

• Check that key scripts, templates, or reference file paths this skill depends on exist.
• Check that the final output contains the core fields, sections, or files specified for this task.
• Check that results clearly mark assumptions, limitations, and incomplete items.