WikiPathways RDF IRIs are now dereferenceable

[marvinm2]

WikiPathways RDF IRIs are now dereferenceable

The WikiPathways RDF IRI resolver is live at rdf.wikipathways.org/about. Every http://rdf.wikipathways.org/ IRI — pathways, interactions, complexes — now resolves via standard HTTP with content negotiation.

What does this mean?

Until now, WikiPathways RDF IRIs (like http://rdf.wikipathways.org/Pathway/WP4846_r140186) existed in the triplestore but returned nothing when you tried to dereference them in a browser or with curl. That breaks a core Linked Data principle: IRIs should be dereferenceable.

The resolver fixes this by acting as a transparent SPARQL proxy. When you request an IRI, it issues a DESCRIBE <IRI> query against the WikiPathways Virtuoso endpoint and returns the result in whatever format you ask for.

How to use it

In a browser

Just visit any WikiPathways RDF IRI and you'll get a syntax-highlighted HTML view with clickable links:

• rdf.wikipathways.org/Pathway/WP4846_r140186
• rdf.wikipathways.org/Pathway/WP4846_r140186/WP/Interaction/a273b
• rdf.wikipathways.org/Pathway/WP4846_r140186/Complex/a4fdf

From the command line

Via Accept header:

# Turtle
curl -H "Accept: text/turtle" https://rdf.wikipathways.org/Pathway/WP4846_r140186

# JSON-LD
curl -H "Accept: application/ld+json" https://rdf.wikipathways.org/Pathway/WP4846_r140186

# RDF/XML
curl -H "Accept: application/rdf+xml" https://rdf.wikipathways.org/Pathway/WP4846_r140186

# N-Triples
curl -H "Accept: application/n-triples" https://rdf.wikipathways.org/Pathway/WP4846_r140186

Via file extension (overrides Accept header):

curl https://rdf.wikipathways.org/Pathway/WP4846_r140186.ttl
curl https://rdf.wikipathways.org/Pathway/WP4846_r140186.jsonld
curl https://rdf.wikipathways.org/Pathway/WP4846_r140186.rdf
curl https://rdf.wikipathways.org/Pathway/WP4846_r140186.nt

Supported formats

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

Browsers and clients sending */* get HTML by default.

Operational details

The service caches responses in memory (5 min TTL) and supports HTTP caching via ETag, If-None-Match (304), and Cache-Control headers. CORS is open (Access-Control-Allow-Origin: *). Prometheus metrics are at /metrics, health check at /_health. Rate limit is 60 requests/minute per IP, configurable.

Links

• https://rdf.wikipathways.org/about
• https://github.com/wikipathways/wikipathways-iri-resolver

The resolver is a single-file Flask app deployed with Gunicorn in Docker. MIT licensed. If you hit a bug or have questions, open an issue in the GitHub repo!