Medical-research-skills ensembl-database

Access Ensembl REST API for vertebrate genomic data; use when you need gene/ID lookups, sequence retrieval, variant effect prediction (VEP), or homology/assembly coordinate mapping.

install

source · Clone the upstream repo

git clone https://github.com/aipoch/medical-research-skills

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/aipoch/medical-research-skills "$T" && mkdir -p ~/.claude/skills && cp -r "$T/scientific-skills/Evidence Insight/ensembl-database" ~/.claude/skills/aipoch-medical-research-skills-ensembl-database && rm -rf "$T"

manifest: scientific-skills/Evidence Insight/ensembl-database/SKILL.md

source content

Source: https://github.com/aipoch/medical-research-skills

Ensembl Database Skill

When to Use

Use this skill when you need access ensembl rest api for vertebrate genomic data; use when you need gene/id lookups, sequence retrieval, variant effect prediction (vep), or homology/assembly coordinate mapping in a reproducible workflow.
Use this skill when a evidence insight task needs a packaged method instead of ad-hoc freeform output.
Use this skill when the user expects a concrete deliverable, validation step, or file-based result.
Use this skill when
```
scripts/query_ensembl.py
```
is the most direct path to complete the request.
Use this skill when you need the
```
ensembl-database
```
package behavior rather than a generic answer.

Key Features

Scope-focused workflow aligned to: Access Ensembl REST API for vertebrate genomic data; use when you need gene/ID lookups, sequence retrieval, variant effect prediction (VEP), or homology/assembly coordinate mapping.
Packaged executable path(s):
```
scripts/query_ensembl.py
```
.
Reference material available in
```
references/
```
for task-specific guidance.
Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

```
Python
```
:
```
3.10+
```
. Repository baseline for current packaged skills.
```
Third-party packages
```
:
```
not explicitly version-pinned in this skill package
```
. Add pinned versions if this skill needs stricter environment control.

Example Usage

cd "20260316/scientific-skills/Evidence Insight/ensembl-database"
python -m py_compile scripts/query_ensembl.py
python scripts/query_ensembl.py --help

Example run plan:

Confirm the user input, output path, and any required config values.
Edit the in-file
```
CONFIG
```
block or documented parameters if the script uses fixed settings.
Run
```
python scripts/query_ensembl.py
```
with the validated inputs.
Review the generated output and return the final artifact with any assumptions called out.

Implementation Details

Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
Primary implementation surface:
```
scripts/query_ensembl.py
```
.
Reference guidance:
```
references/
```
contains supporting rules, prompts, or checklists.
Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.

1. When to Use

Gene-centric queries: When you need to resolve a gene symbol or region to Ensembl identifiers and basic annotations (e.g.,
```
BRCA2
```
in human).
Sequence extraction: When you need DNA/cDNA/protein sequences for a known Ensembl gene/transcript/protein ID in FASTA or JSON.
Variant interpretation: When you need to predict functional consequences of variants using VEP from HGVS notation.
Comparative genomics: When you need ortholog/paralog relationships across vertebrate species.
Assembly/coordinate mapping: When you need to map coordinates between assemblies (e.g., GRCh37 ↔ GRCh38).

2. Key Features

Query Ensembl REST endpoints for:
- Gene lookup by symbol, Ensembl ID, or genomic region
- Sequence retrieval (DNA, cDNA, protein) in FASTA/JSON
- Variant Effect Predictor (VEP) analysis from HGVS inputs
- Homology retrieval (orthologs/paralogs)
- Assembly/coordinate mapping between common human assemblies
CLI helper script for repeatable queries:
- ```
scripts/query_ensembl.py
```
  (wrapper around an
```
ensembl_rest
```
  client)
Reference documentation for endpoints:
- ```
references/api_endpoints.md
```
- Ensembl REST base URL: https://rest.ensembl.org

3. Dependencies

Python
```
>=3.8
```
```
ensembl_rest
```
(Python client; version depends on your environment)
Network access to
```
https://rest.ensembl.org
```

4. Example Usage

CLI: Gene lookup by symbol

python scripts/query_ensembl.py --action lookup --species human --symbol BRCA2

CLI: Retrieve sequence by Ensembl ID

python scripts/query_ensembl.py --action sequence --id ENSG00000139618

CLI: Variant effect prediction (VEP) by HGVS

python scripts/query_ensembl.py --action vep --species human --hgvs "ENST00000380152.8:c.68_69delAG"

5. Implementation Details

Script entry point

Tool:
```
scripts/query_ensembl.py
```
Purpose: Provide a simple command-line interface that dispatches to Ensembl REST calls via an
```
ensembl_rest
```
client.

Core parameters

```
--action
```
: Operation selector.
- Supported values:
```
lookup
```
  ,
```
sequence
```
  ,
```
vep
```
```
--species
```
: Target species name used by Ensembl REST (e.g.,
```
human
```
).
```
--symbol
```
: Gene symbol used for lookup actions (e.g.,
```
BRCA2
```
).
```
--id
```
: Ensembl stable ID used for sequence retrieval (e.g.,
```
ENSG...
```
,
```
ENST...
```
,
```
ENSP...
```
).
```
--hgvs
```
: HGVS notation string used for VEP (e.g.,
```
ENST...:c.123A>G
```
).

Data types and outputs

Lookup: Returns gene/transcript metadata as provided by Ensembl REST.
Sequence: Returns DNA/cDNA/protein sequence; format depends on the endpoint/options (commonly FASTA or JSON).
VEP: Returns consequence annotations and (when available) population frequency fields as provided by Ensembl VEP REST responses.

Endpoint reference

For the exact REST paths, required parameters, and response schemas, see:

```
references/api_endpoints.md
```
https://rest.ensembl.org