WikiPathways IRI Resolver

A lightweight Flask app that makes http://rdf.wikipathways.org/ IRIs resolvable by proxying requests as SPARQL DESCRIBE queries against the WikiPathways Virtuoso endpoint.

Features

• HTTP content negotiation (HTML for browsers, RDF serializations for clients)
• Syntax-highlighted HTML view with clickable IRIs
• Multiple RDF formats: Turtle, JSON-LD, RDF/XML, N-Triples
• File extension overrides (.ttl, .jsonld, .rdf, .nt)
• In-memory response caching with configurable TTL
• HTTP caching (ETag, If-None-Match → 304, Cache-Control, Vary: Accept)
• CORS headers (Access-Control-Allow-Origin: *)
• Prometheus metrics endpoint
• Rate limiting per IP
• Health check endpoint

Quick Start

pip

pip install -r requirements.txt
python app.py
# Dev server running on http://localhost:3000

Docker

docker build -t wpiri . && docker run -p 3000:3000 wpiri

Docker Compose

docker compose up

Usage

Browse in a browser

Open any IRI path to get a syntax-highlighted HTML view with clickable links:

• Pathway/WP4846_r140186 — a pathway
• Pathway/WP4846_r140186/WP/Interaction/a273b — an interaction
• Pathway/WP4846_r140186/Complex/a4fdf — a protein complex

Fetch RDF from the command line

# Turtle via Accept header
curl -H "Accept: text/turtle" http://localhost:3000/Pathway/WP4846_r140186/WP/Interaction/a273b

# Turtle via file extension
curl http://localhost:3000/Pathway/WP4846_r140186/WP/Interaction/a273b.ttl

# JSON-LD
curl http://localhost:3000/Pathway/WP4846_r140186/Complex/a4fdf.jsonld

# RDF/XML
curl http://localhost:3000/Pathway/WP4846_r140186.rdf

# N-Triples
curl http://localhost:3000/Pathway/WP4846_r140186.nt

Content Negotiation

Format	Accept Header	File Extension
HTML (default)	text/html	—
Turtle	text/turtle	.ttl
JSON-LD	application/ld+json	.jsonld
RDF/XML	application/rdf+xml	.rdf
N-Triples	application/n-triples	.nt

Environment Variables

Variable	Default	Description
SPARQL_ENDPOINT	https://sparql.wikipathways.org/sparql	Virtuoso SPARQL endpoint URL
BASE_IRI	http://rdf.wikipathways.org	IRI prefix prepended to request path
SPARQL_TIMEOUT	30	SPARQL request timeout in seconds
CACHE_TTL	300	In-memory cache TTL in seconds
CACHE_MAXSIZE	1024	Maximum number of cached responses
CACHE_CONTROL_MAX_AGE	300	HTTP Cache-Control max-age in seconds
RATE_LIMIT	60/minute	Rate limit per IP address

API Endpoints

Endpoint	Description
/	Landing page with documentation and examples
/<path>	Resolve an IRI and return RDF data
/_health	Health check (returns 200 OK)
/metrics	Prometheus metrics

Development

# Install dev dependencies
pip install -r requirements.txt
pip install pytest responses ruff

# Run tests
pytest -v

# Lint
ruff check .

Built With

This service was built with the help of Claude Code.

License

MIT