Skill Tracer
Skills › Scientific Agent Skills › database-lookup › encode.md

encode.md

49 lines · skills/database-lookup/references/encode.md at 5f2bc03

Open on GitHub
1# ENCODE (Encyclopedia of DNA Elements)
2

ENCODE (Encyclopedia of DNA Elements)

Raw lines 1 to 2
3## Base URL
4```
5https://www.encodeproject.org
6```
7

Base URL

https://www.encodeproject.org
Raw lines 3 to 7
8## Auth
9No auth required. Append `?format=json` or set `Accept: application/json`.

Auth

No auth required. Append ?format=json or set Accept: application/json.

Raw lines 8 to 10
11## Portal data objects and search support JSON; file download URLs return file content.

Portal data objects and search support JSON; file download URLs return file content.

Raw lines 11 to 12
13## Key Endpoints
15| Endpoint | Description |
16|----------|-------------|
17| `/search/?type=Experiment&format=json` | Search experiments |
18| `/experiments/{accession}/?format=json` | Specific experiment |
19| `/files/{accession}/?format=json` | File metadata |
20| `/biosamples/{accession}/?format=json` | Biosample info |
21| `/annotations/?format=json` | Search annotations |

Key Endpoints

EndpointDescription
/search/?type=Experiment&format=jsonSearch experiments
/experiments/{accession}/?format=jsonSpecific experiment
/files/{accession}/?format=jsonFile metadata
/biosamples/{accession}/?format=jsonBiosample info
/annotations/?format=jsonSearch annotations
Raw lines 13 to 22
23## Search Parameters
24- `type` — Experiment, File, Biosample, Annotation, etc.
25- `assay_title` — ChIP-seq, RNA-seq, ATAC-seq, etc.
26- `target.label` — target protein (e.g. CTCF, H3K27ac)
27- `biosample_ontology.term_name` — cell type
28- `limit` — results per page
29- `field` — specific fields to return

Search Parameters

  • type — Experiment, File, Biosample, Annotation, etc.
  • assay_title — ChIP-seq, RNA-seq, ATAC-seq, etc.
  • target.label — target protein (e.g. CTCF, H3K27ac)
  • biosample_ontology.term_name — cell type
  • limit — results per page
  • field — specific fields to return
Raw lines 23 to 30
31## Example Calls
32```
33# ChIP-seq experiments for CTCF
34https://www.encodeproject.org/search/?type=Experiment&assay_title=ChIP-seq&target.label=CTCF&format=json&limit=5
36# Specific experiment
37https://www.encodeproject.org/experiments/ENCSR000AAA/?format=json
39# Files for an experiment
40https://www.encodeproject.org/search/?type=File&dataset=/experiments/ENCSR000AAA/&format=json
41```

Example Calls

# ChIP-seq experiments for CTCF
https://www.encodeproject.org/search/?type=Experiment&assay_title=ChIP-seq&target.label=CTCF&format=json&limit=5

# Specific experiment
https://www.encodeproject.org/experiments/ENCSR000AAA/?format=json

# Files for an experiment
https://www.encodeproject.org/search/?type=File&dataset=/experiments/ENCSR000AAA/&format=json
Raw lines 31 to 42
43## Response Format
44JSON-LD. Search: `@graph` array + `total` + `facets`. Use `frame=object` or `frame=embedded` to control depth.

Response Format

JSON-LD. Search: @graph array + total + facets. Use frame=object or frame=embedded to control depth.

Raw lines 43 to 45
46## Rate Limits
47No published limits. Use `limit=` and `field=` to reduce payload.
49Search pagination uses `limit` and `from`; verify `@graph` length against `total`. Preserve file assembly, output_type, status and audit flags before selecting a download. Public reads need no key, while restricted/unreleased objects require authorized access.

Rate Limits

No published limits. Use limit= and field= to reduce payload.

Search pagination uses limit and from; verify @graph length against total. Preserve file assembly, output_type, status and audit flags before selecting a download. Public reads need no key, while restricted/unreleased objects require authorized access.

Raw lines 46 to 49