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Ensembl Database: ID Mapping and Genomic Features · mkurman | DecimalAI

scienceby mkurman

Ensembl Database: ID Mapping and Genomic Features

mkurman/ensembl-database

Source mkurman/zorai ↗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).

NewMaintained

Automatic

Research pack

Last verified 8/21/2026

What it changes

4 of 22 test cases passed with the skill.

Pass-rate lift: —
Tokens: +67%
Agent turns: 0%
Response time: -33%

Model gemini-3.6-flashMeasured 8/21/2026v14 of 22 cases passed with skill · 4 comparable

Tokens, turns and time describe resource use, not a dollar price.

Lift withheld: 4 comparable cases; this report requires 8.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/mkurman-ensembl-database/SKILL.md https://app.decimal.ai/s/mkurman-ensembl-database/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add mkurman-ensembl-database, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/mkurman-ensembl-database/ and pins it in .decimal/skills.lock

decimalai skills add mkurman-ensembl-database

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/mkurman-ensembl-database/SKILL.md https://app.decimal.ai/s/mkurman-ensembl-database/SKILL.md

Raw file: /s/mkurman-ensembl-database/SKILL.md ↗ · machine-readable summary at /s/mkurman-ensembl-database.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

A test case the skill fixed. Same model, same prompt, with and without the skill.

Prompt

I am initializing the Ensembl database tool for the first time in a fresh environment. What pre-execution license check and file creation steps must be executed?

What was checked, without and with the skill
Checked	Without skill	With skill
The response specifies notifying the user of Ensembl terms if LICENSE_NOTIFICATION.txt does not exist.	Missed	Passed
The response specifies creating LICENSE_NOTIFICATION.txt recording notification text and timestamp.	Missed	Passed

case-14 · gemini-3.6-flash · 8/21/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md192 lines3 filesincludes scripts

Ensembl Database: ID Mapping and Genomic Features

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill 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 NCBI.
Canonical: Ensembl's representative transcript (used if MANE is not available or non-human).

Core Rules

Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully.
Default Species: If the species is absent or ambiguous in the prompt, default to "human". You MUST explicitly flag this default to the user to ensure they are aware.
Primary Transcripts: When listing transcripts for a gene, only return

Track record

Benchmark

4 / 22

test cases passed with the skill

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

mkurman / zorai

skills/scientific-skills-gdm/ensembl_database/SKILL.md

View on GitHub ↗

License MITImported 8/3/2026Version v1Bundled 2 files · scripts

Other skills for the same job

Published skills whose descriptions closely match this one, with their headline benchmark lift.

ensembl-databaseQuery Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.Close match+23 pp pass-rate lift

More skills from the same source and nearby in the registry, with their headline benchmark lift.

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See it in action

What's inside

Ensembl Database: ID Mapping and Genomic Features

Prerequisites

Overview

Core Rules

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

Related skills