Medical-research-skills gget

Unified CLI/Python interface for querying genomic, proteomic, structure, and expression data across 20+ bioinformatics databases; use when you need fast, scriptable retrieval by gene/protein IDs or keywords.

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 "$T/scientific-skills/Evidence Insight/gget" ~/.claude/skills/aipoch-medical-research-skills-gget && rm -rf "$T"

manifest: scientific-skills/Evidence Insight/gget/SKILL.md

source content

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

When to Use

You need to search genes/proteins by keyword and species across common databases (e.g., Ensembl/UniProt/NCBI).
You want to fetch detailed metadata for one or many Ensembl/UniProt/NCBI identifiers.
You need to retrieve nucleotide/protein sequences for downstream analysis or pipelines.
You want to obtain or predict protein structures (PDB download or AlphaFold prediction) from a sequence.
You need to query expression resources (e.g., ARCHS4, CELLxGENE, Bgee) or run enrichment analysis (Enrichr).

Key Features

Unified wrapper (
```
scripts/wrapper.py
```
) exposing multiple
```
gget
```
subcommands through a consistent interface.
Gene/protein search and identifier resolution across multiple databases.
Rich gene/protein information retrieval (annotations and metadata).
Sequence retrieval for provided IDs.
Structure workflows: PDB retrieval and AlphaFold-based prediction (optional plotting).
Expression querying across popular expression atlases.
Enrichment analysis via Enrichr.
Backed by the upstream
```
gget
```
Python library.

Dependencies

Python 3.9+ (recommended)
```
gget
```
(latest compatible version)
```
pandas
```
(latest compatible version)

Install:

uv pip install gget pandas

Example Usage

The skill is accessed via the unified wrapper script:

1) Search for genes by keyword

python scripts/wrapper.py search --keywords "insulin" --species "human"

2) Retrieve gene information by Ensembl ID

python scripts/wrapper.py info --ids "ENSG00000034713"

3) Fetch sequences by Ensembl ID

python scripts/wrapper.py seq --ids "ENSG00000034713"

4) Predict protein structure with AlphaFold (optional plotting)

python scripts/wrapper.py alphafold --sequence "MKWMFK..." --plot

Implementation Details

Wrapper entrypoint:
```
scripts/wrapper.py
```
acts as a dispatcher that maps subcommands (e.g.,
```
search
```
,
```
info
```
,
```
seq
```
,
```
alphafold
```
) to the corresponding
```
gget
```
library functions, normalizing CLI arguments and output behavior.
Supported modules/functions:
- ref: Download reference genomes/annotations.
- search: Keyword-based gene/protein lookup (Ensembl/UniProt/NCBI).
- info: Detailed gene/protein metadata retrieval for one or multiple IDs.
- seq: Nucleotide/protein sequence retrieval for provided IDs.
- structure: Structure retrieval (PDB) and AlphaFold prediction.
- expression: Expression queries (ARCHS4, CELLxGENE, Bgee).
- enrichment: Enrichr-based enrichment analysis.
Notes on AlphaFold: The
```
alphafold
```
subcommand requires additional setup depending on the environment (e.g., model/data availability). Use
```
--plot
```
to request visualization output when supported.
Further reference: See
```
references/module_reference.md
```
for detailed module-level documentation and parameters.