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

If your shell then says biocartoon: command not found, pip put the program in a folder that is not on your PATH (pip names it in a warning near the end of its output): add that folder to PATH, or install with pipx install biocartoon or uv tool install biocartoon, which handle PATH for you.

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
  • --tags T,...: icons and templates with one of these tags (a whole tag, any case)
  • --source S: icons from a collection (a code or name from biocartoon --sources)
  • --author A: icons by an author (part of the name, any case)
  • --category C: icons in a category (a slug from biocartoon --categories)
  • --subcategory S: icons in a subcategory (a slug from biocartoon --categories)
  • --source-category [S:]C: icons in a collection's own category (from biocartoon --source-categories)
  • --license L: icons under a license (CC-BY-4.0, CC0-1.0, ...)
  • --file-type svg|png: icons published as SVG, or as a PNG only

  Repeat a filter for several values: an icon matching any of them passes. An icon has to pass every filter given.

  • --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 SVG, or the PNG when the source publishes no SVG (--png or --svg for that type only, --out FILE|DIR, --max-side N for a smaller PNG)

• biocartoon sync: download the newest published catalog

• biocartoon bulk-download: the whole catalog into one folder with a README (contents, licenses, and the equivalent curl/sqlite3 commands, which it also prints as it goes); running it again fetches only what is missing

  • --files all|metadata|artwork|icons|templates: what to get (comma-separate several; artwork is icons and templates; default all)
  • --metadata-ext sqlite|csv|tsv|xlsx|json: the icon and template catalogs' format (default sqlite)
  • --artwork-ext png|svg: sets both of the next two (templates have no SVG, so they come as PNG)
  • --icons-ext svg|png: default svg, with a PNG where the source publishes no SVG
  • --templates-ext png|biocartoon: the thumbnail (default), or a .biocartoon file the editor opens
  • --output-dir DIR (default ./biocartoon-catalog), --jobs N (parallel downloads, default 8), --limit N (the first N of each, to try it out)

• biocartoon upload FILE...: submit image files/folders to the database (approval required to merge in); --tags T,... adds words to find them by

• 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

• biocartoon --source-categories: list the collections' own categories for biocartoon search --source-category S:C

Run biocartoon --help for everything.

Examples

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

$ biocartoon search mitochondria --icons --limit 2
BA001199                           bioart       Mitochondria  (Cells and Organelles; 2084x2084)  matched: title,description
BA000413                           bioart       Damaged Mitochondria  (Cells and Organelles; 1705x1174)  matched: title,tags,description

$ biocartoon get BA001505              # credit, license, PNG/SVG URLs, colour variants
$ biocartoon fetch BA001505 --out ~/Desktop               # the SVG
$ biocartoon fetch BA001505 --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 --tags "neuron, axon"

Narrow a search by collection, category, author, license or file type:

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
biocartoon search neuron --subcategory cell_types --file-type svg            # SVG cell types
biocartoon search --license CC0-1.0 --license PD --category cells            # free of attribution
biocartoon search --author kissinger --source BA --sort popular              # one illustrator
biocartoon search --source-category "BA:Cellular Processes" --source-category "BA:Proteins"

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 BA001505 --json | jq -r .credit     # the attribution line to print

Download the whole catalog (well over 1 GB), or parts of it:

biocartoon bulk-download                                   # everything, into ./biocartoon-catalog
biocartoon bulk-download --files metadata --metadata-ext xlsx       # the catalogs as spreadsheets
biocartoon bulk-download --files icons --icons-ext png --output-dir icons/
biocartoon bulk-download --files templates --templates-ext biocartoon   # templates to open in the editor

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