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lincs-l1000.md

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1# LINCS L1000 (Clue.io) API Reference
2

LINCS L1000 (Clue.io) API Reference

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3## Overview
4The LINCS L1000 dataset is accessible via the **Connectivity Map (CMap) API** at clue.io.
5

Overview

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

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6## Base URL
7```
8https://api.clue.io/api
9```

Base URL

https://api.clue.io/api
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11## Authentication
12- **API key required** (free registration at clue.io)
13- Pass via header: `user_key: YOUR_API_KEY`

Authentication

  • API key required (free registration at clue.io)
  • Pass via header: user_key: YOUR_API_KEY
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15## Key Endpoints
17| Endpoint | Description |
18|---|---|
19| `GET /perts` | Query perturbagens (compounds, gene knockdowns, overexpression) |
20| `GET /genes` | Query genes (L1000 landmark + inferred) |
21| `GET /cells` | Query cell lines used in L1000 |
22| `GET /sigs` | Query connectivity signatures |
23| `GET /profiles` | Profile metadata (not the full level 5 expression matrix) |
24| `GET /pcls` | Perturbagen classes |

Key Endpoints

EndpointDescription
GET /pertsQuery perturbagens (compounds, gene knockdowns, overexpression)
GET /genesQuery genes (L1000 landmark + inferred)
GET /cellsQuery cell lines used in L1000
GET /sigsQuery connectivity signatures
GET /profilesProfile metadata (not the full level 5 expression matrix)
GET /pclsPerturbagen classes
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26## Query Parameters
27All endpoints support a `filter` parameter using Loopback-style JSON:
28- `where` — filter conditions
29- `fields` — select specific fields
30- `limit` / `skip` — pagination

Query Parameters

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

  • where — filter conditions
  • fields — select specific fields
  • limit / skip — pagination
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32## Example Calls
34```bash
35# Illustrative authenticated queries; JSON is encoded as one query parameter.
36curl --fail-with-body --get 'https://api.clue.io/api/perts' \
37 -H "user_key: $CLUE_API_KEY" \
38 --data-urlencode 'filter={"where":{"pert_iname":"vorinostat"},"limit":5}'
39curl --fail-with-body --get 'https://api.clue.io/api/genes' \
40 -H "user_key: $CLUE_API_KEY" \
41 --data-urlencode 'filter={"where":{"l1000_type":"landmark"},"limit":10}'
42curl --fail-with-body --get 'https://api.clue.io/api/sigs' \
43 -H "user_key: $CLUE_API_KEY" \
44 --data-urlencode 'filter={"where":{"pert_iname":"vorinostat"},"limit":5}'
45```

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}'
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47## Response Format
48JSON. Example (perturbagen):
49```json
51 {
52 "pert_id": "BRD-K81418486",
53 "pert_iname": "vorinostat",
54 "pert_type": "trt_cp",
55 "moa": ["HDAC inhibitor"],
56 "target": ["HDAC1","HDAC2","HDAC3","HDAC6"]
57 }
59```

Response Format

JSON. Example (perturbagen):

[
  {
    "pert_id": "BRD-K81418486",
    "pert_iname": "vorinostat",
    "pert_type": "trt_cp",
    "moa": ["HDAC inhibitor"],
    "target": ["HDAC1","HDAC2","HDAC3","HDAC6"]
  }
]
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61## Rate Limits
62- Free tier: moderate rate limiting (exact numbers not publicly documented)
63- Bulk data downloads available separately via clue.io data portal
65For expression matrices, obtain the versioned data release and join on signature
66and gene identifiers. Level 5 contains replicate-collapsed differential-expression
67signatures; it is not raw abundance. Official contract: https://clue.io/developer-resources

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

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