Annotated SBGNML Generator

This code can generate random and syntactically valid SBGN PD diagrams and (optionally) annotate the entity glyphs. This could be used to a create a large collection of more consistently sized and annotated SBGN diagrams.

Run

uv run sbgnml_annotated_generator.py --output-dir annotated

Install (Playwright deps)

bash scripts/install_playwright_deps.sh

Uses

• SBGNML generator: https://sciluna.github.io/image-to-sbgn-analysis/dataset/index.html (https://github.com/sciluna/image-to-sbgn-analysis)
• Identifier service: https://grounding.indra.bio/
• playwright for browser automation