Markdown Mermaid Writing

Markdown and Mermaid Writing

Overview

This skill creates structural diagrams as Markdown-native Mermaid source and applies a consistent layout to research artefacts. It owns diagram structure, not general prose drafting or data visualization.

The core bet: a relationship expressed as a Mermaid diagram inside a .md file is more valuable than any image. It is text, so it diffs cleanly in git. It requires no build step. It renders natively on GitHub, GitLab, Notion, VS Code, and any markdown viewer. It uses fewer tokens than a prose description of the same relationship. And it can always be converted to a polished image later — but the text version remains the source of truth.

"The more you get your reports and files in .md in just regular text, which mermaid is as well as being a simple 'script language'. This just helps with any downstream rendering and especially AI generated images (using mermaid instead of just long form text to describe relationships < tokens). Additionally mermaid can render along with markdown for easy use almost anywhere by humans or AI."

— Clayton Young (@borealBytes), K-Dense Discord, 2026-02-19

When to Use This Skill

Use this skill when:

• Producing structural diagrams such as workflows, screening flows, architectures, timelines, concept maps, or relationships
• Making an existing research artefact consistently structured and versionable in Markdown
• Someone asks to add a text-native diagram that must remain editable in git

Do not use this skill for general prose drafting, manuscript authorship, data-derived charts, or decorative image generation. Route those jobs to writing-skill or scientific-visualization.

🎨 The Source Format Philosophy

Why text-based diagrams win

Diagram routing

flowchart LR
    accTitle: Research Figure Routing
    accDescr: Structural relationships route to Mermaid while quantitative evidence routes to scientific visualization.

    need["Figure needed"]
    structure["Structural relationship"]
    data["Quantitative evidence"]
    p1["Mermaid in Markdown"]
    p2["scientific-visualization"]
    out["📊 Final Deliverable"]

    need --> structure --> p1 --> out
    need --> data --> p2 --> 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 optional
    class out output

Keep Mermaid source with the artefact whenever Mermaid is the selected representation.

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: 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 2: 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 3: Place the diagram in context

Apply the Markdown style guide and place the diagram beside the text it explains. Include a short prose interpretation and preserve the underlying evidence boundary.

Step 4: Validate and preserve the source

Check syntax in the target renderer when possible. Commit the .md file with embedded Mermaid as the editable source; any rendered image is supplementary.

⚠️ 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 writing-skill

When writing-skill produces a report or manuscript, use this skill for diagrams that show workflows, architectures, relationships, or screening logic. Keep the Mermaid source with the prose so both can be reviewed and versioned.

For data-derived charts or publication export requirements, use scientific-visualization instead.

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:

• 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

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

The style guides, diagram type guides, and example in this skill are adapted 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.

[^1]: GitHub Blog. (2022). "Include diagrams in your Markdown files with Mermaid." https://github.blog/2022-02-14-include-diagrams-markdown-files-mermaid/

[^2]: Mermaid. "Mermaid Diagramming and Charting Tool." https://mermaid.js.org/