Molecular targets

Molecular Targets Platform Query Skill

Search the CCDI Molecular Targets Platform — an NCI-supported Open Targets instance focused on preclinical pediatric oncology data. Includes FDA Pediatric Molecular Target Lists and additional pediatric cancer datasets.

Entity Auto-Detection

Input Pattern	Detected As	Query Used
ENSG00000141510	Target (Ensembl gene)	target(ensemblId)
EFO_\d+, MONDO_\d+, Orphanet_\d+, HP_\d+, DOID_\d+	Disease / Phenotype	disease(efoId)
CHEMBL\d+	Drug / molecule	drug(chemblId)
anything else	Free text	search(queryString)

API

Function	Input	Returns
search(entity, size=10)	single entity string	dict (GraphQL data) or None
search_batch(entities)	list of strings	dict[str, dict|None] — uses batch GraphQL where possible
get_associations(entity, size=10)	Ensembl ID or EFO/MONDO ID	associated diseases (for target) or targets (for disease)
summarize(data, entity)	result dict + label	compact LLM-readable text
to_json(data)	result dict	list[dict] for pipeline output

Helper

Function	Purpose
detect_entity_type(entity)	returns 'target', 'disease', 'drug', or 'search'

Usage

See if __name__ == "__main__" block in 16_MolecularTargets.py for runnable examples covering:

1. Free-text search ("neuroblastoma")
2. Target lookup by Ensembl ID ("ENSG00000141510" → TP53)
3. Disease lookup by ontology ID ("MONDO_0005072")
4. Drug lookup by ChEMBL ID ("CHEMBL941" → imatinib)
5. Target → disease associations
6. Disease → target associations
7. Batch search (mixed entity types)
8. JSON pipeline output

Data Source

• Platform: NCI CCDI Molecular Targets Platform
• URL: https://moleculartargets.ccdi.cancer.gov
• API endpoint: https://moleculartargets.ccdi.cancer.gov/api/v4/graphql
• Method: HTTP POST, Content-Type: application/json, no auth required
• Upstream schema: Open Targets Platform GraphQL v4
• Focus: Pediatric oncology — FDA Pediatric Molecular Target Lists, preclinical data

Notes

• The API is optimised for single-entity queries. For bulk analyses consider Open Targets data downloads.
• Batch functions (search_batch) use the plural GraphQL fields (targets, diseases, drugs) to reduce round-trips where possible; free-text queries fall back to one-at-a-time.
• get_associations() returns scored target↔disease links ranked by overall evidence score (0–1). Use size to control how many rows are returned.
• Returns None / [] on HTTP errors — callers handle no-results gracefully.