skills.rest
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encode-skill

Query the ENCODE REST API for compact experiment and biosample metadata summaries.

5.3k|765|Updated Mar 4, 2026
Search Tags:#genomics#Search#Metadata#Research#ENCODE#bioSamples#REST api
One-click install
npx skills add https://github.com/openai/plugins --skill encode-skill
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: encode-skill
Source: https://github.com/openai/plugins/tree/main/plugins/life-science-research/skills/encode-skill
Command: npx skills add https://github.com/openai/plugins --skill encode-skill

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) components.

What problem does it solve?

Researchers querying the ENCODE portal often receive large, deeply nested JSON payloads that are hard to scan. This Skill submits compact ENCODE REST API requests and returns trimmed, readable summaries of experiments, biosamples, and other objects.

Core Features & Use Cases

  • Object Lookups: Fetch individual ENCODE objects by accession path, such as biosamples/ENCBS000AAA/, with compact JSON summaries.
  • Portal-Style Search: Run filtered searches (e.g., type=Experiment, assay_term_name=RNA-seq) with record extraction via record_path and item limits.
  • Raw Payload Saving: Optionally save full API responses to disk with save_raw for downstream inspection.
  • Use Case: A genomics researcher wants a quick list of RNA-seq experiments from ENCODE; the Skill queries the search endpoint, extracts the @graph records, and returns a concise markdown summary.

Quick Start

Ask the assistant to search ENCODE for RNA-seq experiments and summarize the first ten results.

Frequently Asked Questions about encode-skill

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I search the ENCODE database for experiments?▼

Send a JSON request to the search/ endpoint with filters like type=Experiment and assay_term_name=RNA-seq, plus limit=10 and format=json. The script extracts records from the @graph field and returns a compact summary.

How do I look up a specific ENCODE biosample by accession?▼

Use an accession path such as biosamples/ENCBS000AAA/ with params frame=object and format=json, and an Accept: application/json header. The response returns a compact summary of the object's metadata.

Can I save the full ENCODE API response instead of a summary?▼

Yes, set save_raw=true in the JSON input and optionally provide raw_output_path. The full JSON payload is written to disk and the output reports the saved file path.

What Python dependencies does the ENCODE REST client need?▼

The script requires the requests library for HTTP calls; everything else uses the Python standard library. If requests is missing, the script returns a missing_dependency error.

Why does my ENCODE request return an invalid_input error?▼

The input must be a single JSON object with required base_url and path fields, and optional fields must match expected types, such as positive integers for max_items and timeout_sec. Method is limited to GET or POST.

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