Pyrenoid Evolution Database

A community-curated database of pyrenoid presence, absence, and ultrastructure across the algae, built to pull 50+ years of scattered electron-microscopy literature into one place tied to phylogeny — so questions like when and how often did pyrenoids evolve? have an actual dataset behind them.

The pyrenoid is the carbon-concentrating organelle found in many algal chloroplasts. Reports of its presence, absence, and structure (shape, matrix organisation, starch sheath, thylakoid penetration, and more) are scattered across decades of taxonomic and ultrastructural papers, species by species. This project collects those species-level observations into a single searchable, phylogenetically-aware database.

How it works

• Submit — log a species-level observation from a paper, either via a quick form or a step-by-step guided version. Every submission records the presence/absence call, structural details, and the literature source.
• Browse — search reviewed, curated records by species, division, or reference.
• Guide — the classification guide defining the structural terms (shape, matrix, thylakoid arrangement, etc.) used when logging a record, so submissions stay consistent.
• To-do — the literature review backlog: papers found but not yet checked for pyrenoid data.

Submissions go through review before appearing in the browsable dataset. Full backend access (including in-review submissions and reference images) is available on request — contact james.barrett@york.ac.uk.

How it's built

• A static, no-build-step frontend (plain HTML/CSS/JS) for the home page, submission forms, browse view, guide, and to-do tracker.
• Supabase (Postgres) as the backend — schema and RPC functions live in supabase/migrations/.
• A scheduled GitHub Action (.github/workflows/literature-scan.yml) runs scripts/scan_literature.py weekly, querying Europe PMC and OpenAlex for new pyrenoid-related literature and adding anything unseen to the review queue.

Repository layout

index.html            Home page — overview and submission/database stats
submit/                Submission entry point, quick form, and guided form
browse/                Search and browse curated records
guide/                 Classification guide for structural terminology
todo/                  Literature review backlog
scripts/               Literature-scanning script run by the scheduled Action
supabase/migrations/   Database schema changes
.github/workflows/     Scheduled literature scan

Contributing

If you've come across a paper with pyrenoid ultrastructure data, the submission form is the way to add it — no account needed. Corrections to existing records or terminology questions can go to james.barrett@york.ac.uk.