The Raras Knowledge Graph

Overview

The graph integrates Orphanet, the Human Phenotype Ontology (HPO), OMIM, MONDO, ClinVar, Open Targets, PubMed and ClinicalTrials.gov with Brazilian public-health data (DATASUS, CEAF, SIGTAP, PNTN, PCDT). Every disease carries Portuguese clinical content and crosswalks to international ontologies, so the data is usable both for Brazilian care pathways and for global federation (ERN, EJP RD, GA4GH, NCATS Translator).

The data is dedicated to the public domain under CC0 1.0 for Raras-originated triples, with upstream sources keeping their own open licenses (see Data sources & licensing). Full license terms are on the license page.

Quick start

No authentication, no API key. Every endpoint is public and CORS-enabled.

1 — Query with SPARQL

curl -G https://raras.org/api/sparql \
  --data-urlencode 'query=SELECT ?orphaCode ?name WHERE {
    ?d a rnc:Disease ;
       rnp:orphaCode ?orphaCode ;
       rdfs:label ?name .
  } LIMIT 5' \
  -H 'Accept: application/sparql-results+json'

2 — Get one disease as RDF

curl 'https://raras.org/api/rdf?type=Disease&format=turtle' | head -40

3 — Query with GraphQL

curl https://raras.org/api/graphql \
  -H 'Content-Type: application/json' \
  -d '{"query":"{ disease(orphaCode:\"166\"){ name mondoId genes{ symbol } } }"}'

Data model

The graph has 8 entity classes and 45 properties. Classes are aligned with the Biolink Model, schema.org and OBO ontologies, so the same vocabulary works across SPARQL, GraphQL and TRAPI. Every term dereferences to its own RDF definition — see /class/Disease and /property/orphaCode, or browse the full vocabulary at /ontology.

Entity classes

Disease properties

Relationships

Biolink aliases (e.g. biolink:has_phenotype, biolink:treats) are accepted as synonyms for TRAPI/Translator compatibility.

Identifiers & cross-references

Like Wikidata, every entity has a persistent, dereferenceable identifier. Resources live under https://raras.org/id/ and resolve to RDF via content negotiation (HTTP 303 to HTML, or Turtle / JSON-LD with the matching Accept header).

Each disease emits owl:sameAs links to external authorities, enabling round-trip integration with the wider Linked Open Data cloud:

• Orphanet — http://www.orpha.net/ORDO/Orphanet_{code}
• MONDO — http://purl.obolibrary.org/obo/MONDO_{id}
• OMIM — https://omim.org/entry/{id}
• HPO — http://purl.obolibrary.org/obo/HP_{id}
• Wikidata — http://www.wikidata.org/entity/{QID}
• HGNC (genes) — https://www.genenames.org/.../HGNC:{id}

Auditability & the Disease Twin

The graph is not a one-off import. Every one of the 10,468 diseases is continuously maintained by an autonomous “Disease Twin” agent that verifies facts against official sources, keeps the data fresh, discovers new sources, and proposes research hypotheses. This is what makes the dataset auditable: every fact is traceable to a source and a verification timestamp.

Each release is stamped with provenance (dcterms:publisher, prov:wasAttributedTo) and a unique fingerprint (dcterms:hasVersion), so any copy stays traceable. See the license page for attribution terms, and the live Disease Twin transparency dashboard for real-time coverage and freshness across all diseases.

Access methods

The same data is exposed through multiple open protocols — pick the one that fits your use case.

SPARQL support

Supported: SELECT (DISTINCT, aggregates COUNT/SUM/AVG/MIN/MAX), ASK, CONSTRUCT, DESCRIBE, OPTIONAL, FILTER (=, !=, <, >, CONTAINS, STRSTARTS, STRENDS, REGEX, BOUND), ORDER BY, GROUP BY, LIMIT, OFFSET. Not yet supported (returns HTTP 501): UNION, MINUS, SERVICE, subqueries, property paths. Rate limit: 120 requests/min per IP; 15s query timeout. The bare endpoint (no query) returns a machine-readable service description.

Namespaces

Default prefixes are pre-declared on the SPARQL endpoint, so you can use them without a PREFIX header.

SPARQL examples

Diseases linked to a specific HPO phenotype

SELECT ?orphaCode ?name WHERE {
  ?d a rnc:Disease ;
     rnp:orphaCode ?orphaCode ;
     rdfs:label ?name ;
     rnp:hasPhenotype ?p .
  ?p rnp:hpoId "HP:0001250" .
}

Count diseases with active clinical trials

SELECT (COUNT(?d) AS ?count) WHERE {
  ?d a rnc:Disease ;
     rnp:activeTrialCount ?n .
  FILTER(?n > 0)
}

CONSTRUCT RDF for one disease

CONSTRUCT {
  ?d rdfs:label ?name ;
     rnp:orphaCode ?orphaCode ;
     rnp:mondoId ?mondoId .
} WHERE {
  ?d a rnc:Disease ;
     rnp:orphaCode "166" ;
     rdfs:label ?name .
  OPTIONAL { ?d rnp:mondoId ?mondoId }
}

Check existence (ASK)

ASK { ?d rnp:orphaCode "166" }

GraphQL

The GraphQL endpoint at /api/graphql has introspection enabled. Key queries: searchDiseases, disease(orphaCode), diseaseByMondo, diseasesByPhenotypes (differential-diagnosis ranking), similarDiseases (vector similarity), searchPhenotypes, referenceCenters, stats and serviceInfo.

{
  disease(orphaCode: "166") {
    name
    mondoId
    cid10
    phenotypes(limit: 5) { phenotype { hpoId name } frequency }
    genes { symbol hgncId }
    susCoverage { coverageScore ceafMedicationCount }
  }
}

Formats & content negotiation

RDF endpoints negotiate by Accept header or a ?format= query parameter:

Data sources & licensing

Per-partition licensing follows the Wikidata / Open Targets convention: the Raras-originated layer is CC0, upstream sources keep their licenses. The combined dataset / bulk dump is distributed under CC-BY 4.0 (it embeds CC-BY sources, so attribution is required), while Raras-originated triples remain CC0. These terms are emitted machine-readably in the VOID descriptor as void:subset + dcterms:license. See the license page for details.

Rate limits & versioning

• Rate limit: 120 requests/min per IP on the SPARQL endpoint; 15s query timeout.
• CORS: all read endpoints send Access-Control-Allow-Origin: *.
• Versioning: dataset version and last-modified date are published in the VOID descriptor (dcterms:modified).
• Read-only: SPARQL UPDATE (INSERT/DELETE/LOAD) is rejected with HTTP 403.

How to cite

When reusing the dataset, please cite:

Raras — Brazilian Rare Disease Knowledge Graph (RarasNet).
https://raras.org — Raras-originated triples CC0 1.0; combined dataset CC-BY 4.0.
Upstream sources retain their own licenses (see /license).

Questions, federation requests or data corrections: [email protected]. Full license terms: /license.