ensembl-database SKILL.md skillA
ensembl-database from pengqianhan/ai-human-research-os is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pengqianhan/ai-human-research-os/ensembl-database@git:20260715.38d79bePins git:20260715.38d79be in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pengqianhan/ai-human-research-os
- Path
research-skills-hub/science-skills/ensembl_database/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260715.38d79be, committed Jul 15, 2026
- Size
- 8,827 bytes
- Repository stars
- 3
- License
- MIT
Query the Ensembl database to resolve gene, transcript, and protein IDs, fetch genomic or protein sequences, retrieve gene structures (exons), and get variant consequence and effect predictions (VEP). Use this skill as a primary ID translator, genomic sequence database and variant effect prediction tool.
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
# Ensembl Database: ID Mapping and Genomic Features
## Prerequisites
1. **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
`uv` is installed and on PATH.
2. **User Notification**: If .licenses/ensembl_database_LICENSE.txt does not
already exist in the workspace root directory then (1) prominently notify
the user to check the terms at https://useast.ensembl.org/index.html and
https://github.com/Ensembl/ensembl-rest/wiki, then (2) create the file
recording the notification text and timestamp.
## Overview
The Ensembl database is a resource for genome annotation. This skill allows you
to interact with the Ensembl REST API to resolve ambiguous symbols,
cross-reference IDs (RefSeq, HGNC, UniProt, ENSG), fetch raw sequences, and
retrieve detailed transcript structures.
**Key Concepts:**
- **ENSG (Gene):** Stable identifier for a human gene. Other species will have
different three-letter species codes.
- **ENST (Transcript):** Stable identifier for a transcript (splicing
isoform).
- **ENSP (Protein):** Stable identifier for a translated protein.
- **MANE Select:** The consensus primary transcript agreed upon by Ensembl and
…Read the whole file at its exact version.
How to install
mdr add pengqianhan/ai-human-research-os/ensembl-database@sha256:aff4c6f7c86268afThe line at the top of this page pins the label git:20260715.38d79be, 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.
[](https://markdownregistry.com/a/art_grndw2s6ygqssjot)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Jul 15, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (8827 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
pengqianhan/ai-human-research-os · 3 stars · license MIT · pushed 2026-11-06 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_grndw2s6ygqssjot GET https://markdownregistry.com/api/v1/resolve?ref=pengqianhan/ai-human-research-os/ensembl-database GET https://markdownregistry.com/api/v1/blob/aff4c6f7c86268afaacd8a56a88771f536f263602b895cb360603bb7bbf0487f
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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