bio-geo-data SKILL.md skillA
bio-geo-data from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-geo-data@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-database-access-geo-data/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 17,934 bytes
- Repository stars
- 662
- License
- MIT
Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror. Use when finding expression datasets, navigating SuperSeries vs SubSeries, choosing between series-matrix (submitter-normalized) and raw supplementary files, downloading via GEOparse (Python) or GEOquery (R/Bioconductor), linking GEO to SRA for raw reads, or distinguishing GSE/GSM/GPL/GDS record types. Encodes the SuperSeries trap, the series-matrix normalization-trust caveat, GEOmetadb…
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
## Version Compatibility
Reference examples tested with: BioPython 1.83+, GEOparse 2.0+, R Bioconductor GEOquery 2.70+, pandas 2.2+
Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show biopython geoparse` then introspect signatures
- R: `packageVersion('GEOquery')`
If the GSE structure doesn't match expectations (missing fields, malformed series matrix), re-fetch from FTP directly and inspect the SOFT or MINiML file as source of truth.
# GEO Data
**"Pull expression data from GEO accession GSE..."** -> GEO stores Series (GSE), Samples (GSM), Platforms (GPL), and curated DataSets (GDS, frozen 2018). The single most consequential decision is **processed (series matrix) vs raw (supplementary files / linked SRA)** — the answer turns on how much trust the submitter's normalization deserves.
The single most-missed gotcha: **SuperSeries**. A GSE may be a meta-container (`!Series_relation = SuperSeries of: GSExxxxx`) holding multiple sub-studies on different platforms. Naively pulling samples from a SuperSeries gives mixed Affymetrix + Illumina + RNA-seq, mis-batched.
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-geo-data@sha256:8cf6edf58ee48466The line at the top of this page pins the label git:20260821.2d1b678, 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_g4i7usiapqwa5mtj)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_g4i7usiapqwa5mtj GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-geo-data GET https://markdownregistry.com/api/v1/blob/8cf6edf58ee48466a0c2ecd22ae417eb2caf0405f689e1306791ead0313b29b1
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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.