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Agent skill

Encode API

by aipoch in aipoch/medical-research-skills

Access the ENCODE Project REST API to search for and retrieve biological data (biosamples, experiments, etc.).

MITAuto-check passedBackend & APIs

Install Encode API

skills CLI
$ npx skills add aipoch/medical-research-skills --skill encode-api -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install aipoch/medical-research-skills encode-api --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Evidence Insight/encode-api' .claude/skills/encode-api && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
encode-api
GitHub stars
2k
Token cost
~1.4k tokens
SKILL.md length
652 words
Files
4 (incl. scripts)
Skills in repo
567
Repo updated
First seen
Licence
MIT

At a glance

Access the ENCODE Project REST API to search for and retrieve biological data (biosamples, experiments, etc.).

  • Works in 2 steps: Search for Objects → Get Object by Accession
  • The user needs to query ENCODE data
  • SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 10 more sections
  • Runs Python scripts from its folder; calls python and pip; reaches encodeproject.org

What it does

Encode API is an agent skill from aipoch/medical-research-skills. Access the ENCODE Project REST API to search for and retrieve biological data (biosamples, experiments, etc.). Use this skill when the user needs to query ENCODE data, search by keywords, or retrieve specific objects by accession ID.

Its SKILL.md is about 1.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files, including scripts (for example `encode-api_audit_result_v2.json` and `scripts/encode_client.py`).

It sits in Backend & APIs, covering REST APIs. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

  • The user needs to query ENCODE data
  • Search by keywords
  • Retrieve specific objects by accession ID

Example prompts

  • “/encode-api”

Requirements

  • Python 3

Workflow steps

2 steps, taken from the step headings in SKILL.md.

  1. Search for Objects
  2. Get Object by Accession

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 1 file in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python
    • pip

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Hosts in commands or code, which the agent is likely to contact:

    • encodeproject.org

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Encode API loads about 1.4k tokens when it runs. Until then it costs about 61 tokens; SKILL.md has 652 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~61
When it runs · the whole SKILL.md, loaded when a task matches
~1.4k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 652 words, ~1,436 tokens.

Download SKILL.mdSave it as .claude/skills/encode-api/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.
name
encode-api
description
Access the ENCODE Project REST API to search for and retrieve biological data (biosamples, experiments, etc.). Use this skill when the user needs to query ENCODE data, search by keywords, or retrieve specific objects by accession ID.
license
MIT
author
AIPOCH

Source: https://github.com/aipoch/medical-research-skills

ENCODE API Skill

This skill allows you to interact with the ENCODE Project database via its REST API.

When to Use

  • Use this skill when the request matches its documented task boundary.
  • Use it when the user can provide the required inputs and expects a structured deliverable.
  • Prefer this skill for repeatable, checklist-driven execution rather than open-ended brainstorming.

Key Features

  • Scope-focused workflow aligned to: Access the ENCODE Project REST API to search for and retrieve biological data (biosamples, experiments, etc.). Use this skill when the user needs to query ENCODE data, search by keywords, or retrieve specific objects by accession ID.
  • Packaged executable path(s): scripts/encode_client.py.
  • Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

  • requests (Install via pip install -r requirements.txt)

Example Usage

See ## Usage above for related details.

bash
cd "20260316/scientific-skills/Evidence Insight/encode-api"
python -m py_compile scripts/encode_client.py
python scripts/encode_client.py --help

Example run plan:

  1. Confirm the user input, output path, and any required config values.
  2. Edit the in-file CONFIG block or documented parameters if the script uses fixed settings.
  3. Run python scripts/encode_client.py with the validated inputs.
  4. Review the generated output and return the final artifact with any assumptions called out.

Implementation Details

  • Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
  • Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
  • Primary implementation surface: scripts/encode_client.py.
  • Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
  • Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.

Usage

You can use the provided Python script scripts/encode_client.py to perform searches or retrieve specific objects.

1. Search for Objects

To search for data using keywords:

python
from scripts.encode_client import search_encode

results = search_encode(term="bone chip", limit=10)
print(results)
2. Get Object by Accession

To retrieve a specific object (e.g., a Biosample or Experiment) by its accession ID:

python
from scripts.encode_client import get_object

data = get_object(accession="ENCBS000AAA")
print(data)

API Reference

  • Base URL: https://www.encodeproject.org/
  • Rate Limit: 10 requests/second
  • Authentication: Public data is accessible without keys. For private data, provide api_key and api_secret to the functions.

When Not to Use

  • Do not use this skill when the required source data, identifiers, files, or credentials are missing.
  • Do not use this skill when the user asks for fabricated results, unsupported claims, or out-of-scope conclusions.
  • Do not use this skill when a simpler direct answer is more appropriate than the documented workflow.
Show full SKILL.md (276 more words)Show less

Required Inputs

  • A clearly specified task goal aligned with the documented scope.
  • All required files, identifiers, parameters, or environment variables before execution.
  • Any domain constraints, formatting requirements, and expected output destination if applicable.
  1. Validate the request against the skill boundary and confirm all required inputs are present.
  2. Select the documented execution path and prefer the simplest supported command or procedure.
  3. Produce the expected output using the documented file format, schema, or narrative structure.
  4. Run a final validation pass for completeness, consistency, and safety before returning the result.

Output Contract

  • Return a structured deliverable that is directly usable without reformatting.
  • If a file is produced, prefer a deterministic output name such as encode_api_result.md unless the skill documentation defines a better convention.
  • Include a short validation summary describing what was checked, what assumptions were made, and any remaining limitations.

Validation and Safety Rules

  • Validate required inputs before execution and stop early when mandatory fields or files are missing.
  • Do not fabricate measurements, references, findings, or conclusions that are not supported by the provided source material.
  • Emit a clear warning when credentials, privacy constraints, safety boundaries, or unsupported requests affect the result.
  • Keep the output safe, reproducible, and within the documented scope at all times.

Failure Handling

  • If validation fails, explain the exact missing field, file, or parameter and show the minimum fix required.
  • If an external dependency or script fails, surface the command path, likely cause, and the next recovery step.
  • If partial output is returned, label it clearly and identify which checks could not be completed.

Quick Validation

Run this minimal verification path before full execution when possible:

bash
python scripts/encode_client.py --help

Expected output format:

text
Result file: encode_api_result.md
Validation summary: PASS/FAIL with brief notes
Assumptions: explicit list if any

© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 3 other files (scripts) in scientific-skills/Evidence Insight/encode-api of aipoch/medical-research-skills.

  • SKILL.md
  • encode-api_audit_result_v2.json
  • requirements.txt
  • scripts/encode_client.py

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Encode API next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

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Encode API this skillaipoch/medical-research-skills2k—~1.4kAutomated safety check: PassMIT
API DesignerJeffallan/claude-skills12k2 repos~2kAutomated safety check: PassMIT
Paperclippaperclipai/paperclip99k—~9.6kAutomated safety check: PassMIT
Nodejs Backend Patternsever-works/ever-works15818 repos~4kAutomated safety check: PassAGPL-3.0
OpenAPI to MCP Servermcp-use/mcp-use11k—~5.2kAutomated safety check: PassApache-2.0
Use Yaakmountain-loop/yaak19k—~1.9kAutomated safety check: PassMIT

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Categories

Questions about Encode API

What does Encode API do?

Access the ENCODE Project REST API to search for and retrieve biological data (biosamples, experiments, etc.). Encode API is an agent skill from aipoch/medical-research-skills.).

When should I use Encode API?

Encode API fits situations like: the user needs to query ENCODE data; search by keywords; retrieve specific objects by accession ID.

How do I install Encode API in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill encode-api -a claude-code`. Or copy the skill folder (scientific-skills/Evidence Insight/encode-api in aipoch/medical-research-skills) into .claude/skills/encode-api in your project. Claude Code loads it when a task matches its description.

How do I install Encode API in Codex?

Run `npx skills add aipoch/medical-research-skills --skill encode-api -a codex`. Or copy the skill folder (scientific-skills/Evidence Insight/encode-api in aipoch/medical-research-skills) into .agents/skills/encode-api in your project. Codex loads it when a task matches its description.

Can I use Encode API in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aipoch/medical-research-skills --skill encode-api -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/encode-api, .gemini/skills/encode-api, .github/skills/encode-api and .opencode/skills/encode-api in your project.

What does Encode API need to run?

Going by SKILL.md and its folder, Encode API needs Python for the scripts in its folder and the command-line tools its instructions call (python and pip). Our summary lists: Python 3.

Does Encode API access the network?

SKILL.md names 1 domain. In commands or code: encodeproject.org; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.

Is Encode API safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Encode API use?

Encode API is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Encode API use?

About 1.4k tokens (SKILL.md is roughly 5.7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Encode API?

Skills that share tags, products or a category with Encode API: API Designer (Jeffallan/claude-skills, 12k stars), Paperclip (paperclipai/paperclip, 99k stars), Nodejs Backend Patterns (ever-works/ever-works, 158 stars) and OpenAPI to MCP Server (mcp-use/mcp-use, 11k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Encode API?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.