BioCartoon

BioCartoon is a free and open-source tool for creating biology figures with illustrations. It compiles existing open biology-focused illustration resources, along with its own illustrations, into a single database with a graphical interface for search and figure generation.

This package is the biocartoon command-line interface and MCP server, which search and download the database from a shell, a script, or an assistant such as Claude.

Usage

Web application: app.biocartoon.com

Install Desktop application: www.biocartoon.com/download

Resources

15,335 icons and 6 templates across 8 resources.

Command-Line Interface and MCP server

pip install biocartoon        # or: pipx install biocartoon / uv tool install biocartoon

The package is the compiled program alone, with no Python dependencies. The first command that needs the catalog downloads it; biocartoon sync updates it. This build searches icons; its MCP server also lists the shared slide templates. The BioCartoon desktop editor ships a fuller biocartoon that adds templates to search and the app command.

• biocartoon search "TERM": icons and templates matching TERM, best first. With no TERM it pages through everything.
  • --icons / --templates: only that kind
  • --source S: icons from one collection (a code or name from biocartoon --sources)
  • --category C: icons in one category (a slug from biocartoon --categories)
  • --sql: run TERM as read-only SQL on the catalog
• biocartoon get ID: everything about one icon: license, credit, PNG/SVG URLs, colour variants
• biocartoon fetch ID: download the PNG (--svg for the SVG, --out FILE|DIR, --max-side N)
• biocartoon sync: download the newest published catalog
• biocartoon upload FILE...: submit image files/folders to the database (approval required to merge in)
• biocartoon mcp: serve the same tools over MCP, mostly for agents (e.g., claude mcp add biocartoon -- biocartoon mcp)
• biocartoon --version: the program's version, and when the local catalog was published and downloaded
• biocartoon --sources: list icon sources for biocartoon search --source S
• biocartoon --categories: list icon categories for biocartoon search --category C

Run biocartoon --help for everything.

Examples

Find an icon, check its license, and download it:

$ biocartoon search mitochondria --icons --limit 2
bioart/353_641587                  bioart       Mitochondria  (Cells and Organelles; 2084x2084)  matched: title,description
bioart/101_628750                  bioart       Damaged Mitochondria  (Cells and Organelles; 1705x1174)  matched: title,tags,description

$ biocartoon get bioart/424_633913              # credit, license, PNG/SVG URLs, colour variants
$ biocartoon fetch bioart/424_633913 --svg --out ~/Desktop
$ biocartoon fetch bioart/424_633913 --max-side 512 --out neuron.png   # a smaller PNG

Contribute your own illustrations (held for review before they are published):

biocartoon upload figures/ --license CC-BY-4.0 --credit "Your Name" --dry-run   # check first
biocartoon upload figures/ --license CC-BY-4.0 --credit "Your Name" --category cells

Narrow a search by collection or category:

biocartoon --sources                                       # codes: BA, BI, SV, SD, HI, RE, OM, ...
biocartoon --categories                                    # slugs: cells, cells.cell_types, ...
biocartoon search "pyramidal neuron" --source BA           # NIH BioArt only
biocartoon search neuron --source BA --source SD           # BioArt or SciDraw
biocartoon search mitochondria --category cells.organelles_and_cell_components
biocartoon search --category viruses --sort az --limit 40 --offset 40   # page 2 of all viruses
biocartoon --categories --source SD                        # what SciDraw covers

Query the catalog with SQL (read-only):

biocartoon search --sql                                    # the schema
biocartoon search "select license, count(*) as n from assets group by license order by n desc"
biocartoon search --sql "select id, title from assets where svg_key is not null and title like '%ribosome%'"
biocartoon search "with dendrites" --no-sql                # words, even though it starts with WITH

From a script: every command takes --json, and search results come back as {"icons": [...], "templates": [...]}:

# download the SVG of the best match that has one (Servier and uploads are PNG only)
mkdir -p icons
for t in neuron astrocyte microglia; do
  id=$(biocartoon search "$t" --icons --limit 10 --json | jq -r '[.icons[] | select(.svg_url)][0].id')
  biocartoon fetch "$id" --svg --out icons/
done
biocartoon get bioart/424_633913 --json | jq -r .credit     # the attribution line to print

Keep the local catalog current, and connect an assistant:

biocartoon sync
claude mcp add biocartoon -- biocartoon mcp

The database schema is documented in the repository.

License

Copyright (c) 2026 Joseph Rich. The program is open source under the BSD 2-Clause License. Every illustration keeps its own upstream license (public domain, CC0, CC BY, CC BY-SA, ...): credit it as its credit field says. See NOTICE.md.

Other Links

Website: www.biocartoon.com

Database and CLI source code: github.com/josephrich98/biocartoon

Application and website source code: github.com/josephrich98/biocartoon-app

Icon SQLite database: assets.biocartoon.com/catalog/assets.sqlite.gz

Template SQLite database: assets.biocartoon.com/catalog/templates.sqlite.gz