medsci-agent: Skill for OpenCode

Open Targets Platform

Overview

Open Targets integrates genetics, genomics, transcriptomics, drugs, and literature to score target-disease associations. It uses evidence from GWAS, differential expression, pathways, drugs, and more.

GraphQL API

import requests
OT_URL = "https://api.platform.opentargets.org/api/v4/graphql"
query = """
query target($id: String!) {
  target(ensemblId: $id) {
    approvedSymbol
    approvedName
    associatedDiseases(page: {index: 0, size: 5}) {
      rows {
        disease { id name }
        score
        datatypeScores { componentId score }
      }
    }
  }
}
"""
r = requests.post(OT_URL, json={"query": query, "variables": {"id": "ENSG00000141510"}})
data = r.json()["data"]["target"]

Search

search_q = 'query search($q: String!) { search(queryString: $q, entityNames: ["target"], page: {index: 0, size: 5}) { hits { id name entity } } }'
r = requests.post(OT_URL, json={"query": search_q, "variables": {"q": "BRAF"}})

Key Details

• Association score: 0-1 combining all evidence datatypes.
• Datatypes: genetic_association, somatic_mutation, known_drug, affected_pathway, literature, rna_expression, animal_model.
• Target IDs: Ensembl gene IDs (ENSG...). Disease IDs: EFO or MONDO IDs.
• No API key required; rate limit ~10 req/s.
• Use associatedTargets on disease nodes for reverse lookups.
• Genetics Portal provides variant-to-gene (V2G) and colocalisation data.