Markdown and Mermaid Writing

Use this skill when:

• Creating any scientific document — reports, analyses, manuscripts, methods sections
• Writing any documentation — READMEs, how-tos, decision records, project docs
• Producing any diagram — workflows, data pipelines, architectures, timelines, relationships
• Generating any output that will be version-controlled — if it's going into git, it should be markdown
• Working with any other skill — this skill defines the documentation layer that wraps every other output
• Someone asks you to "add a diagram" or "visualize the relationship" — Mermaid first, always

Do NOT start with Python matplotlib, seaborn, or AI image generation for structural or relational diagrams. Those are Phase 2 and Phase 3 — only used when Mermaid cannot express what's needed (e.g., scatter plots with real data, photorealistic images).

🎨 The Source Format Philosophy

Why text-based diagrams win

The three-phase workflow

flowchart LR
    accTitle: Three-Phase Documentation Workflow
    accDescr: Phase 1 Mermaid in markdown is always required and is the source of truth. Phases 2 and 3 are optional downstream conversions for polished output.

    p1["📄 Phase 1<br/>Mermaid in Markdown<br/>(ALWAYS — source of truth)"]
    p2["🐍 Phase 2<br/>Python Generated<br/>(optional — data charts)"]
    p3["🎨 Phase 3<br/>AI Generated Visuals<br/>(optional — polish)"]
    out["📊 Final Deliverable"]

    p1 --> out
    p1 -.->|"when needed"| p2
    p1 -.->|"when needed"| p3
    p2 --> out
    p3 --> out

    classDef required fill:#dbeafe,stroke:#2563eb,stroke-width:2px,color:#1e3a5f
    classDef optional fill:#fef9c3,stroke:#ca8a04,stroke-width:2px,color:#713f12
    classDef output fill:#dcfce7,stroke:#16a34a,stroke-width:2px,color:#14532d

    class p1 required
    class p2,p3 optional
    class out output

Phase 1 is mandatory. Even if you proceed to Phase 2 or 3, the Mermaid source stays committed.

What Mermaid can express

Mermaid covers 24 diagram types. Almost every scientific relationship fits one:

💡 Pick the right type, not the easy one. Don't default to flowcharts for everything. A timeline beats a flowchart for chronological events. A sequence beats a flowchart for service interactions. Scan the table and match.

🔧 Core workflow

Step 1: Identify the document type

Check if a template exists before writing from scratch:

Step 2: Read the style guide

Before writing any .md file: read references/markdown_style_guide.md.

Key rules to internalize:

• One H1 per document — the title. Never more.
• Emoji on H2 headings only — one emoji per H2, none in H3/H4
• Cite everything — every external claim gets a footnote [^N] with full URL
• Bold sparingly — max 2-3 bold terms per paragraph, never full sentences
• Horizontal rule after every </details> — mandatory
• Tables over prose for comparisons, configurations, structured data
• Diagrams over walls of text — if it describes flow, structure, or relationships, add Mermaid

Step 3: Pick the diagram type and read its guide

Before creating any Mermaid diagram: read references/mermaid_style_guide.md.

Then open the specific type file (e.g., references/diagrams/flowchart.md) for the exemplar, tips, and copy-paste template.

Mandatory rules for every diagram:

accTitle: Short Name 3-8 Words
accDescr: One or two sentences explaining what this diagram shows.

• No %%{init} directives — breaks GitHub dark mode
• No inline style — use classDef only
• One emoji per node max — at the start of the label
• snake_case node IDs — match the label

Step 4: Write the document

Start from the template. Apply the markdown style guide. Place diagrams inline with related text — not in a separate "Figures" section.

Step 5: Commit as text

The .md file with embedded Mermaid is what gets committed. If you also generated a PNG or AI image, those are supplementary — the markdown is the source.

⚠️ Common pitfalls

Radar chart syntax (radar-beta)

WRONG:

radar
title Example
x-axis ["A", "B", "C"]
"Series" : [1, 2, 3]

CORRECT:

radar-beta
title Example
axis a["A"], b["B"], c["C"]
curve series["Series"]{1, 2, 3}
max 3

• Use radar-beta not radar (the bare keyword doesn't exist)
• Use axis to define dimensions, not x-axis
• Use curve to define data series, not quoted labels with colon
• No accTitle/accDescr — radar-beta doesn't support accessibility annotations; always add a descriptive italic paragraph above the diagram

XY Chart vs Radar confusion

Forgetting accTitle/accDescr on supported types

Only some diagram types support accTitle/accDescr. For those that don't, always place a descriptive italic paragraph directly above the code block:

Radar chart comparing three methods across five performance dimensions. Note: Radar charts do not support accTitle/accDescr.

radar-beta
...

🔗 Integration with other skills

With scientific-schematics

scientific-schematics generates AI-powered publication-quality images (PNG). Use the Mermaid diagram as the brief for the schematic:

Workflow:
1. Create the concept as Mermaid in .md (this skill — Phase 1)
2. Describe the same concept to scientific-schematics for a polished PNG (Phase 3)
3. Commit both — the .md as source, the PNG as a supplementary figure

With scientific-writing

When scientific-writing produces a manuscript, all diagrams and structural figures should use this skill's standards. The writing skill handles prose and citations; this skill handles visual structure.

Workflow:
1. Use scientific-writing to draft the manuscript
2. For every figure that shows a workflow, architecture, or relationship:
   - Replace placeholder with a Mermaid diagram following this skill's guide
3. Use scientific-schematics only for figures that truly need photorealistic/complex rendering

With literature-review

Literature review produces summaries with lots of relationship data. Use this skill to:

• Create concept maps (Mindmap) of the literature landscape
• Show publication timelines (Timeline or Gantt)
• Compare methodologies (Quadrant or Radar)
• Diagram data flows described in papers (Sequence or Flowchart)

With any skill that produces output documents

Before finalizing any document from any skill, apply this skill's checklist:

• Does the document use a template? If so, did I start from the right one?
• Are all diagrams in Mermaid with accTitle + accDescr?
• No %%{init}, no inline style, only classDef?
• Are all external claims cited with [^N]?
• One H1, emoji on H2 only?
• Horizontal rules after every </details>?

📚 Reference index

Style guides

Diagram type guides (24 types)

Each file contains: production-quality exemplar, tips specific to that type, and a copy-paste template.

references/diagrams/ — architecture, block, c4, class, complex_examples, er, flowchart, gantt, git_graph, kanban, mindmap, packet, pie, quadrant, radar, requirement, sankey, sequence, state, timeline, treemap, user_journey, xy_chart, zenuml

Document templates (9 types)

templates/ — decision_record, how_to_guide, issue, kanban, presentation, project_documentation, pull_request, research_paper, status_report

Examples

assets/examples/example-research-report.md — a complete scientific research report demonstrating proper heading hierarchy, multiple diagram types (flowchart, sequence, gantt), tables, footnote citations, collapsible sections, and all style guide rules applied.

📝 Attribution

All style guides, diagram type guides, and document templates in this skill are ported from the SuperiorByteWorks-LLC/agent-project repository under the Apache-2.0 License.

• Source: https://github.com/SuperiorByteWorks-LLC/agent-project
• Author: Clayton Young / Superior Byte Works, LLC (@borealBytes)
• License: Apache-2.0

This skill (as part of scientific-agent-skills) is distributed under the MIT License. The included Apache-2.0 content is compatible for downstream use with attribution retained, as preserved in the file headers throughout this skill.