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Molecular targets

Skill BioTender-max/awesome-bio-agent-skills/skills/drugclaw/molecular_targets

A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.

Install

npx -y skills add BioTender-max/awesome-bio-agent-skills --skill molecular_targets

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Query the NCI CCDI Molecular Targets Platform (pediatric oncology) for targets (genes), diseases, drugs, and target-disease associations via its public GraphQL API. Auto-detects entity type from input string.

SKILL.md

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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:

Free-text search ("neuroblastoma")
Target lookup by Ensembl ID ("ENSG00000141510" → TP53)
Disease lookup by ontology ID ("MONDO_0005072")
Drug lookup by ChEMBL ID ("CHEMBL941" → imatinib)
Target → disease associations
Disease → target associations
Batch search (mixed entity types)
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.

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