Open targets

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

Query the Open Targets Platform for drug-target-disease associations. Use whenever the user asks about drug targets, gene-disease associations, drug indications, clinical trial phases, or wants to look up any entity (Ensembl gene ID, ChEMBL drug ID, or free-text gene/drug name) in Open Targets. Also trigger when the user mentions Open Targets, ENSG IDs, CHEMBL IDs, or asks about target prioritization for diseases.From its SKILL.md

Install

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

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

One thing to look at

no licenseNo license file was found in the repository. Code published without one is not open source by default, so using it at work is a question for whoever answers licensing questions where you are.

SKILL.md

2.3 KB, 576 tokens by cl100k_base, as published. Nobody here has run it

Open Targets Platform Query Skill

Query the Open Targets GraphQL API for drug, target, and disease association data. No API key required.

Entity Auto-Detection

Input Pattern	Detected As	Example
`ENSG00000...`	Target (Ensembl gene ID)	`ENSG00000146648` (EGFR)
`CHEMBL...`	Drug (ChEMBL ID)	`CHEMBL941` (Imatinib)
anything else	Free-text search	`BRCA1`, `aspirin`

API

Function	Input	Returns
`query(entity)`	single entity string	dict with type, name, associations
`query_batch(entities)`	list of entity strings	list[dict]
`summarize(result)`	query result dict	compact one-line text
`get_target_info(ensembl_id)`	Ensembl ID string	raw GraphQL response
`get_drug_info(chembl_id)`	ChEMBL ID string	raw GraphQL response
`search_entities(term)`	free-text string	raw GraphQL response

Return Format

Target result:

{"entity": "ENSG00000146648", "type": "target", "found": true,
 "symbol": "EGFR", "name": "epidermal growth factor receptor",
 "biotype": "protein_coding",
 "top_diseases": [{"disease": "lung carcinoma", "score": 0.78}]}

Drug result:

{"entity": "CHEMBL941", "type": "drug", "found": true,
 "name": "IMATINIB", "drug_type": "Small molecule",
 "max_phase": 4,
 "indications": [{"disease": "chronic myeloid leukemia", "phase": 4}]}

Search result:

{"entity": "BRCA1", "type": "search", "found": true,
 "hits": [{"id": "ENSG00000012048", "name": "BRCA1", "entity_type": "target"}]}

Usage

See if __name__ == "__main__" block in 12_Open_Targets_Platform.py for runnable examples covering: single target/drug/search query, batch query, and JSON output.

Source

Endpoint: https://api.platform.opentargets.org/api/v4/graphql
Docs: https://platform.opentargets.org/
Paper: https://doi.org/10.1093/nar/gkac1046

What ships with it: 5 files

21.9 KB alongside SKILL.md, 4 of them executable

example.pyruns6.8 KB
__init__.pyruns151 B
open_targets_skill.pyruns13.3 KB
README.md946 B
retrieve.pyruns770 B