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Public Bioinformatics Data Access · xuzhougeng | DecimalAI

scienceby xuzhougeng

Public Bioinformatics Data Access

xuzhougeng/public-data-access

Source xuzhougeng/wisp-science ↗License AGPL-3.0

Plan, configure, validate, and document portable public-bioinformatics data acquisition.

SkillScore68Maintained

Automatic

Data Engineer pack

Last verified 9/24/2026

What it changes

Passed 10 of 14 test cases with the skill, and 5 of 14 without it.

Without skill36%

With skill68%

Checks it passed that the model alone missed

Sets default resume parameter to true
Sets default overwrite parameter to false
Places output under data/public/<provider>/

and 5 more in the full report

7 fixed8 passed either way7 still failing0 broke

Pass-rate lift: +32 pp
Tokens: +19%
Agent turns: 0%
Response time: -64%

Model gemini-3.6-flashMeasured 9/24/2026v115 of 22 cases passed with skill · 14 comparable

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

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/xuzhougeng-public-data-access/SKILL.md https://app.decimal.ai/s/xuzhougeng-public-data-access/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add xuzhougeng-public-data-access, 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/xuzhougeng-public-data-access/ and pins it in .decimal/skills.lock

decimalai skills add xuzhougeng-public-data-access

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

curl -fsSL --create-dirs -o .claude/skills/xuzhougeng-public-data-access/SKILL.md https://app.decimal.ai/s/xuzhougeng-public-data-access/SKILL.md

Raw file: /s/xuzhougeng-public-data-access/SKILL.md ↗ · machine-readable summary at /s/xuzhougeng-public-data-access.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 6 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 6

Prompt

What should the system do if a user requests a transport or provider capability that the current provider adapter cannot perform?

What was checked, without and with the skill
Checked	Without skill	With skill
Stops execution after producing the validated plan when a capability is missing	Missed	Passed
Explicitly reports the missing adapter capability to the user	Passed	Passed

case-20 · gemini-3.6-flash · 9/24/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md115 lines4 filesincludes scripts

Public Bioinformatics Data Access

Build a reproducible acquisition plan before downloading. Treat GEO, SRA/ENA, GDC, GTEx, and DepMap as independent providers behind one provider-neutral workflow. Do not require a provider-specific toolkit or machine-specific checkout.

Workflow

Clarify the dataset contract. Identify the provider, accession/project, release, modality, smallest useful data product, filters, target directory, expected scale, and downstream analysis.
Inspect before transfer. Use available MCP/connectors or official metadata endpoints to list releases, files, samples, sizes, and checksums. Do not start a bulk transfer during discovery.
Write a provider-neutral plan. Run scripts/public_data_plan.py init. Store the plan next to the future dataset as download-plan.json.
Validate and review. Run validate, show the user the resolved provider, transport, filters, limits, output location, and known size. Wait for explicit confirmation before a large, paid, authenticated, or overwrite-capable job.
Select the adapter at runtime. Prefer an already available Wisp MCP tool for metadata and small queries. Prefer official HTTPS/FTP or provider clients for bulk files. Use an external project only when it is installed and record its version in the plan/manifest.
Acquire safely. Reuse existing valid files, resume partial transfers when supported, keep raw files immutable, and never place credentials in the plan.
Verify and hand off. Check expected files, byte sizes, checksums when available, and sample/file counts. Generate manifest.json with the script.

Provider routing

Provider	Discovery and small queries	Bulk acquisition	Typical products
GEO	GEO metadata connector, NCBI E-utilities	NCBI GEO HTTPS/FTP	series matrix, SOFT, supplementary files
SRA/ENA	RunInfo or ENA Portal API	ENA HTTPS/FTP or SRA Toolkit	FASTQ, run metadata
GDC	GDC files/cases API	manifest + `gdc-client`, or HTTPS for bounded files	expression, mutation, CNV, clinical, methylation
GTEx	GTEx expression connector/API	official release files for matrices	gene/tissue queries, median or sample expression
DepMap	DepMap model/release metadata	official release file endpoint	model metadata, expression, mutation, dependency
custom	User-provided catalog/API	explicit HTTPS/FTP URLs	provider-specific files

Read references/provider-routing.md before implementing or changing a

Track record

Benchmark

10 / 14

test cases passed, vs 5 / 14 without

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 v5 — 8/17/2026

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

xuzhougeng / wisp-science

skills/public-data-access/SKILL.md

View on GitHub ↗

License AGPL-3.0Imported 8/17/2026Version v1Bundled 3 files · scripts

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

Ready to supercharge your AI agents?

See it in action

What's inside

Public Bioinformatics Data Access

Workflow

Provider routing

Track record

Benchmark

Adoption

SkillSafety

Source

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