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Zhongwei Li
403
skills/opentargets-database/scripts/query_opentargets.py
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403
skills/opentargets-database/scripts/query_opentargets.py
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#!/usr/bin/env python3
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"""
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Open Targets Platform GraphQL Query Helper
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This script provides reusable functions for querying the Open Targets Platform
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GraphQL API. Use these functions to retrieve target, disease, drug, and
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association data.
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Dependencies: requests (pip install requests)
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"""
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import requests
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import json
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from typing import Dict, List, Optional, Any
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# API endpoint
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BASE_URL = "https://api.platform.opentargets.org/api/v4/graphql"
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def execute_query(query: str, variables: Optional[Dict[str, Any]] = None) -> Dict[str, Any]:
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"""
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Execute a GraphQL query against the Open Targets Platform API.
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Args:
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query: GraphQL query string
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variables: Optional dictionary of variables for the query
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Returns:
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Dictionary containing the API response data
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Raises:
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Exception if the API request fails or returns errors
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"""
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payload = {"query": query}
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if variables:
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payload["variables"] = variables
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try:
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response = requests.post(BASE_URL, json=payload, timeout=30)
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response.raise_for_status()
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data = response.json()
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if "errors" in data:
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raise Exception(f"GraphQL errors: {data['errors']}")
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return data.get("data", {})
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except requests.exceptions.RequestException as e:
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raise Exception(f"API request failed: {str(e)}")
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def search_entities(query_string: str, entity_types: Optional[List[str]] = None) -> List[Dict[str, Any]]:
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"""
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Search for targets, diseases, or drugs by name or identifier.
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Args:
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query_string: Search term (e.g., "BRCA1", "alzheimer", "aspirin")
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entity_types: Optional list to filter by entity type ["target", "disease", "drug"]
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Returns:
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List of search results with id, name, entity type, and description
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"""
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query = """
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query search($queryString: String!, $entityNames: [String!]) {
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search(queryString: $queryString, entityNames: $entityNames, page: {size: 10}) {
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hits {
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id
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entity
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name
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description
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}
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}
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}
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"""
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variables = {"queryString": query_string}
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if entity_types:
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variables["entityNames"] = entity_types
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result = execute_query(query, variables)
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return result.get("search", {}).get("hits", [])
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def get_target_info(ensembl_id: str, include_diseases: bool = False) -> Dict[str, Any]:
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"""
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Retrieve comprehensive information about a target gene.
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Args:
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ensembl_id: Ensembl gene ID (e.g., "ENSG00000157764")
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include_diseases: Whether to include top associated diseases
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Returns:
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Dictionary with target information including tractability, safety, expression
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"""
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disease_fragment = """
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associatedDiseases(page: {size: 10}) {
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rows {
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disease {
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id
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name
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}
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score
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datatypeScores {
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componentId
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score
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}
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}
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}
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""" if include_diseases else ""
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query = f"""
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query targetInfo($ensemblId: String!) {{
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target(ensemblId: $ensemblId) {{
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id
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approvedSymbol
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approvedName
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biotype
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functionDescriptions
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tractability {{
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label
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modality
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value
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}}
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safetyLiabilities {{
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event
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effects {{
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dosing
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organsAffected
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}}
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biosamples {{
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tissue {{
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label
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}}
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}}
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}}
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geneticConstraint {{
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constraintType
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score
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exp
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obs
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}}
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{disease_fragment}
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}}
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}}
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"""
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result = execute_query(query, {"ensemblId": ensembl_id})
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return result.get("target", {})
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def get_disease_info(efo_id: str, include_targets: bool = False) -> Dict[str, Any]:
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"""
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Retrieve information about a disease.
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Args:
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efo_id: EFO disease identifier (e.g., "EFO_0000249")
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include_targets: Whether to include top associated targets
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Returns:
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Dictionary with disease information
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"""
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target_fragment = """
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associatedTargets(page: {size: 10}) {
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rows {
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target {
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id
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approvedSymbol
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approvedName
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}
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score
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datatypeScores {
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componentId
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score
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}
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}
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}
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""" if include_targets else ""
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query = f"""
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query diseaseInfo($efoId: String!) {{
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disease(efoId: $efoId) {{
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id
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name
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description
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therapeuticAreas {{
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id
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name
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}}
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synonyms {{
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terms
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}}
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{target_fragment}
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}}
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}}
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"""
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result = execute_query(query, {"efoId": efo_id})
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return result.get("disease", {})
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def get_target_disease_evidence(ensembl_id: str, efo_id: str,
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data_types: Optional[List[str]] = None) -> List[Dict[str, Any]]:
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"""
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Retrieve evidence linking a target to a disease.
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Args:
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ensembl_id: Ensembl gene ID
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efo_id: EFO disease identifier
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data_types: Optional filter for evidence types (e.g., ["genetic_association", "known_drug"])
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Returns:
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List of evidence records with scores and sources
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"""
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query = """
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query evidences($ensemblId: String!, $efoId: String!, $dataTypes: [String!]) {
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disease(efoId: $efoId) {
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evidences(ensemblIds: [$ensemblId], datatypes: $dataTypes, size: 100) {
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rows {
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datasourceId
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datatypeId
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score
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targetFromSourceId
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studyId
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literature
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cohortPhenotypes
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}
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}
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}
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}
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"""
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variables = {"ensemblId": ensembl_id, "efoId": efo_id}
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if data_types:
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variables["dataTypes"] = data_types
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result = execute_query(query, variables)
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return result.get("disease", {}).get("evidences", {}).get("rows", [])
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def get_known_drugs_for_disease(efo_id: str) -> Dict[str, Any]:
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"""
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Get drugs known to be used for a disease.
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Args:
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efo_id: EFO disease identifier
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Returns:
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Dictionary with drug information including phase, targets, and status
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"""
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query = """
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query knownDrugs($efoId: String!) {
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disease(efoId: $efoId) {
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knownDrugs {
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uniqueDrugs
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uniqueTargets
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rows {
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drug {
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id
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name
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drugType
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maximumClinicalTrialPhase
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}
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targets {
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id
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approvedSymbol
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}
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phase
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status
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mechanismOfAction
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}
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}
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}
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}
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"""
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result = execute_query(query, {"efoId": efo_id})
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return result.get("disease", {}).get("knownDrugs", {})
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def get_drug_info(chembl_id: str) -> Dict[str, Any]:
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"""
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Retrieve information about a drug.
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Args:
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chembl_id: ChEMBL identifier (e.g., "CHEMBL25")
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Returns:
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Dictionary with drug information
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"""
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query = """
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query drugInfo($chemblId: String!) {
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drug(chemblId: $chemblId) {
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id
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name
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synonyms
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drugType
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maximumClinicalTrialPhase
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hasBeenWithdrawn
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withdrawnNotice {
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reasons
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countries
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}
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mechanismsOfAction {
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actionType
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mechanismOfAction
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targetName
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targets {
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id
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approvedSymbol
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}
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}
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indications {
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disease
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efoId
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maxPhaseForIndication
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}
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}
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}
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"""
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result = execute_query(query, {"chemblId": chembl_id})
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return result.get("drug", {})
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def get_target_associations(ensembl_id: str, min_score: float = 0.0) -> List[Dict[str, Any]]:
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"""
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Get all disease associations for a target, filtered by minimum score.
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Args:
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ensembl_id: Ensembl gene ID
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min_score: Minimum association score (0-1) to include
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Returns:
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List of disease associations with scores
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"""
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query = """
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query targetAssociations($ensemblId: String!) {
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target(ensemblId: $ensemblId) {
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associatedDiseases(page: {size: 100}) {
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count
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rows {
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disease {
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id
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name
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}
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score
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datatypeScores {
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componentId
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score
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}
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}
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}
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}
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}
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"""
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result = execute_query(query, {"ensemblId": ensembl_id})
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associations = result.get("target", {}).get("associatedDiseases", {}).get("rows", [])
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# Filter by minimum score
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return [assoc for assoc in associations if assoc.get("score", 0) >= min_score]
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# Example usage
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if __name__ == "__main__":
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# Example 1: Search for a gene
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print("Searching for BRCA1...")
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results = search_entities("BRCA1", entity_types=["target"])
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for result in results[:3]:
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print(f" {result['name']} ({result['id']})")
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# Example 2: Get target information
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if results:
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ensembl_id = results[0]['id']
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print(f"\nGetting info for {ensembl_id}...")
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target_info = get_target_info(ensembl_id, include_diseases=True)
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print(f" Symbol: {target_info.get('approvedSymbol')}")
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print(f" Name: {target_info.get('approvedName')}")
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# Show top diseases
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diseases = target_info.get('associatedDiseases', {}).get('rows', [])
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if diseases:
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print(f"\n Top associated diseases:")
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for disease in diseases[:3]:
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print(f" - {disease['disease']['name']} (score: {disease['score']:.2f})")
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# Example 3: Search for a disease
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print("\n\nSearching for Alzheimer's disease...")
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disease_results = search_entities("alzheimer", entity_types=["disease"])
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if disease_results:
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efo_id = disease_results[0]['id']
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print(f" Found: {disease_results[0]['name']} ({efo_id})")
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# Get known drugs
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print(f"\n Known drugs for {disease_results[0]['name']}:")
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drugs = get_known_drugs_for_disease(efo_id)
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for drug in drugs.get('rows', [])[:5]:
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print(f" - {drug['drug']['name']} (Phase {drug['phase']})")
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