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cite-encode SKILL.md skillA

cite-encode from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.

Install it, pinned

mdr add ammawla/encode-toolkit/cite-encode@git:20260920.6050003

Pins git:20260920.6050003 in mdr.lock. Pin the fingerprint instead.

Audit grade: A, 17 of 17 checks passed
Kind: SKILL.md skill
Repository: ammawla/encode-toolkit
Path: skills/cite-encode/SKILL.md
Versions recorded: 3
Latest version: git:20260920.6050003, committed Sep 20, 2026
First version recorded: Mar 8, 2026
Size: 33,177 bytes
Repository stars: 21
License: AGPL-3.0

Generate proper ENCODE citations for publications, grants, and presentations. Use when the user needs to cite ENCODE data, create bibliography entries, write acknowledgment sections, or ensure compliance with ENCODE data use policy.

Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.

What the file says

# Cite ENCODE Data Properly

## When to Use

- User wants to generate proper citations for ENCODE data, tools, and consortium papers
- User asks about "citing ENCODE", "BibTeX", "references", "bibliography", or "data citation"
- User needs to create a Key Resources Table (STAR Methods) for Cell-family journals
- User wants to export citations in BibTeX, RIS, or other reference manager formats
- Example queries: "cite the ENCODE experiments I used", "generate BibTeX for my tracked experiments", "how do I cite ENCODE in my paper?"

Help the user generate correct citations for ENCODE data following official guidelines. This is the definitive guide to citing ENCODE data in manuscripts, grants, presentations, and supplementary materials.

## ENCODE Citation Requirements

ENCODE data use policy requires citing data in publications. Data is freely available with **no embargo** -- unrestricted use upon release. However, proper attribution is both a scientific obligation and a practical necessity: reviewers will check that you have cited data sources correctly, and incomplete citations are a common reason for revision requests.

## Step 0: Assess Publication Trust Before Citing
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add ammawla/encode-toolkit/cite-encode@sha256:53ec7f9b40cc124c

The line at the top of this page pins the label git:20260920.6050003, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.

Badge

[![mdr](https://markdownregistry.com/badge/art_i4lcudqnzg775eun.svg)](https://markdownregistry.com/a/art_i4lcudqnzg775eun)

3 badge image fetches in 30 days. What the badge shows.

Versions

The registry has recorded 3 versions of this file, between Mar 8, 2026 and Sep 20, 2026, about one every 98 days.

version	committed	commit	size	audit
git:20260920.6050003 latest	2026-09-20	6050003	33,177 B	A	view · diff
git:20260920.992a807	2026-09-20	992a807	31,897 B	A	view · diff
git:20260308.ca46af5	2026-03-08	ca46af5	31,880 B	A	view

Audit of the latest version

A 17 of 17 checks passed. Fixed automatic checks with no AI involved, so the same checks give the same answer every run.

pass: Frontmatter block present
pass: Frontmatter declares a name
pass: Frontmatter declares a description
pass: Size between 200 bytes and 200 KB (33177 bytes)
pass: No zero-width or bidi control characters
pass: No instruction hidden inside an HTML comment
pass: No link to an exfiltration or paste host
pass: No credential-shaped string
pass: No instruction to send local credentials anywhere
pass: No text hidden with inline styles
pass: No prompt-injection phrasing
pass: No curl or wget piped into a shell
pass: No recursive delete of root, home or parent
pass: No instruction to read or print local credentials
pass: No base64 blob over 200 characters
pass: No link to a raw IP address
pass: No script tag

Source

GitHub

ammawla/encode-toolkit · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main

API

GET https://markdownregistry.com/api/v1/artifacts/art_i4lcudqnzg775eun
GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/cite-encode
GET https://markdownregistry.com/api/v1/blob/53ec7f9b40cc124c0667f7b1211b1e30524480da8baa7549b678b2775307b4b6

Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.

Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.

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