gget-genomic-databases SKILL.md skillA
gget-genomic-databases from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/gget-genomic-databases@git:20260528.3e3f998Pins git:20260528.3e3f998 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/databases/gget-genomic-databases/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260528.3e3f998, committed May 28, 2026
- Size
- 21,051 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Unified CLI/Python interface to 20+ genomic databases. Gene lookups (Ensembl search/info/seq), BLAST/BLAT, AlphaFold, Enrichr enrichment, OpenTargets disease/drug, CELLxGENE single-cell, cBioPortal/COSMIC cancer, ARCHS4 expression. Spans genomics, proteomics, disease. For batch/advanced BLAST use biopython; for multi-DB Python SDK use bioservices.
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
# gget — Unified Genomic Database Access ## Overview gget is a command-line and Python package providing unified access to 20+ genomic databases and analysis methods. Query gene information, sequences, protein structures, expression data, and disease associations through a consistent interface. All modules work as both CLI tools and Python functions, returning DataFrames (Python) or JSON/CSV (CLI). ## When to Use - Looking up gene information (names, IDs, descriptions) across species from Ensembl - Retrieving nucleotide or protein sequences for Ensembl gene/transcript IDs - Running BLAST or BLAT searches against standard reference databases - Predicting protein 3D structures with AlphaFold2 from amino acid sequences - Performing gene set enrichment analysis (GO, KEGG, disease terms) via Enrichr - Querying single-cell RNA-seq datasets from CELLxGENE Census - Finding disease and drug associations for a gene target via OpenTargets - Downloading Ensembl reference genomes and annotations for a species - Finding cancer mutations and genomic alterations via cBioPortal or COSMIC - Getting tissue expression and correlated genes from ARCHS4 …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/gget-genomic-databases@sha256:3864142b01c34d1cThe line at the top of this page pins the label git:20260528.3e3f998, 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_v3jwjzcoabyeewzx)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on May 28, 2026.
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 (21051 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
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_v3jwjzcoabyeewzx GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/gget-genomic-databases GET https://markdownregistry.com/api/v1/blob/3864142b01c34d1c8c6c31666e9bebfca2c7754e4fb5def89854af6f617579ff
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.