医学公开数据库查询与登记｜个人思维图谱小站

医学公开数据库查询与登记

使用有明确接口的公开数据库查询方法保存请求、筛选、分页与来源，可用于医学文献、临床试验及药物资料检索。

正文

references/lincs-l1000.md

Overview

The LINCS L1000 dataset is accessible via the Connectivity Map (CMap) API at clue.io.

Base URL

https://api.clue.io/api

Authentication

API key required (free registration at clue.io)
Pass via header: user_key: YOUR_API_KEY

Key Endpoints

Endpoint	Description
`GET /perts`	Query perturbagens (compounds, gene knockdowns, overexpression)
`GET /genes`	Query genes (L1000 landmark + inferred)
`GET /cells`	Query cell lines used in L1000
`GET /sigs`	Query connectivity signatures
`GET /profiles`	Profile metadata (not the full level 5 expression matrix)
`GET /pcls`	Perturbagen classes

Query Parameters

All endpoints support a filter parameter using Loopback-style JSON:

where — filter conditions
fields — select specific fields
limit / skip — pagination

Example Calls

# Illustrative authenticated queries; JSON is encoded as one query parameter.
curl --fail-with-body --get 'https://api.clue.io/api/perts' \
  -H "user_key: $CLUE_API_KEY" \
  --data-urlencode 'filter={"where":{"pert_iname":"vorinostat"},"limit":5}'
curl --fail-with-body --get 'https://api.clue.io/api/genes' \
  -H "user_key: $CLUE_API_KEY" \
  --data-urlencode 'filter={"where":{"l1000_type":"landmark"},"limit":10}'
curl --fail-with-body --get 'https://api.clue.io/api/sigs' \
  -H "user_key: $CLUE_API_KEY" \
  --data-urlencode 'filter={"where":{"pert_iname":"vorinostat"},"limit":5}'

Response Format

JSON. Example (perturbagen):

[
  {
    "pert_id": "BRD-K81418486",
    "pert_iname": "vorinostat",
    "pert_type": "trt_cp",
    "moa": ["HDAC inhibitor"],
    "target": ["HDAC1","HDAC2","HDAC3","HDAC6"]
  }
]

Rate Limits

Free tier: moderate rate limiting (exact numbers not publicly documented)
Bulk data downloads available separately via clue.io data portal

For expression matrices, obtain the versioned data release and join on signature and gene identifiers. Level 5 contains replicate-collapsed differential-expression signatures; it is not raw abundance. Official contract: https://clue.io/developer-resources