ensembl-annotation skillA
ensembl-annotation is agent-read markdown (skill) from ammawla/encode-toolkit: 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 u.
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns 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. …
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How to install
mdr add ammawla/encode-toolkit/ensembl-annotation@git:20260312.665e731mdr add ammawla/encode-toolkit/ensembl-annotation@sha256:2bd15faafc685226Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_eudwlvv3z5lmvnwz)
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Audit of the latest version
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- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
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- pass: No base64 blob over 200 characters
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Source
ammawla/encode-toolkit · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · 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/2bd15faafc6852266bd0b0fe19f27bfd3d67ca7286017dbaa7de91203bd6dd25
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