ensembl-annotation SKILL.md skillA
ensembl-annotation from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add ammawla/encode-toolkit/ensembl-annotation@git:20260920.6050003Pins 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
plugin/skills/ensembl-annotation/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 12, 2026
- Size
- 15,321 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Query the Ensembl REST API for regulatory feature annotations, variant effect prediction (VEP), coordinate liftover, gene lookups, and cross-references. Use when the user needs to annotate variants with VEP (consequence, CADD, REVEL, SpliceAI), check Ensembl Regulatory Build overlap for ENCODE regions, convert coordinates between GRCh37 and GRCh38, resolve gene IDs (Ensembl ↔ symbol ↔ RefSeq), look up gene phenotype associations, or cross-reference ENCODE targets with Ensembl annotations. Also…
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
# Query the Ensembl REST API ## When to Use - User wants to annotate variants with Ensembl VEP (Variant Effect Predictor) consequences - User asks about "VEP", "Ensembl", "variant annotation", "regulatory build", or "gene annotation" - User needs to convert coordinates between assemblies using Ensembl's liftover API - User wants to check the Ensembl Regulatory Build for overlap with ENCODE elements - Example queries: "run VEP on my variant list", "annotate SNPs with regulatory consequences", "check Ensembl regulatory build for my peaks" Annotate variants, look up regulatory features, convert coordinates, and resolve gene identifiers using the Ensembl REST API. ## Scientific Rationale **The question**: "What does the Ensembl Regulatory Build say about this region, and what is the predicted effect of this variant?" The Ensembl Regulatory Build integrates ENCODE, Roadmap Epigenomics, and Blueprint data into a unified annotation of regulatory features across human cell types. The Variant Effect Predictor (VEP) is the standard tool for variant consequence prediction, integrating 50+ annotation sources including CADD, REVEL, SpliceAI, and AlphaMissense. …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/ensembl-annotation@sha256:f050e3e8365bde6aThe 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.
[](https://markdownregistry.com/a/art_eudwlvv3z5lmvnwz)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between Mar 12, 2026 and Sep 20, 2026, about one every 96 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 15,321 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 14,756 B | A | view · diff |
| git:20260312.665e731 | 2026-03-12 | 665e731 | 14,751 B | A | view |
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 (15321 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
ammawla/encode-toolkit · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_eudwlvv3z5lmvnwz GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/ensembl-annotation GET https://markdownregistry.com/api/v1/blob/f050e3e8365bde6a688c311ae832ce66adaaadc8188b1cdad20c33434df1de6c
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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