Add query-genomic-intelligence skill - #46
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Wrap Genomic Intelligence's hosted DNA-sequence models (promoter, splice, enhancer, chromatin, expression, annotation, plus a find-genes-then-expression composite) over the REST /v1 API and the keyless hosted MCP server. Single SKILL.md with inline requests, mirroring the query-ensembl skill. Skill-only change, no source files touched.
fetch_ensembl_sequence takes gene (fetch_region handles coordinates), load_demo_sequence requires name, and find_genes / find_genes_and_predict_expression take a sequence handle rather than a region. The annotation task is find_genes; there is no predict_annotation and no load_local_fasta on the hosted server. Also drop dangling references/errors.md pointers, add the 422 validation_failed case, and state the 9,198 bp window consistently.
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query-genomic-intelligenceskillAdds a runtime skill wrapping Genomic Intelligence (GI), a set of hosted
transformer DNA language models that predict regulatory features, gene structure,
and expression directly from DNA sequence. No local GPU or model weights are
needed; the skill is a thin client over a hosted, versioned inference API.
Per
CONTRIBUTING.md, new capabilities arrive as skills. This is a runtime skillunder
container/skills/, modelled onquery-ensembl: a singleSKILL.mdwithinline
requests.What it does
Give it a gene symbol, a genomic region, or a DNA/FASTA sequence and it returns
structured predictions across six tasks, plus a composite:
promoter: promoter regionssplice: donor/acceptor splice sitesenhancer: developmental and housekeeping activitychromatin: chromatin state across hundreds of tracksexpression: sequence to expression, log(TPM+1)annotation: de-novo gene/transcript annotationHow it connects
The REST
/v1API needs aGI_API_KEYbearer and is called asPOST /v1/tasks/{task}/predict. The hosted MCP server athttps://mcp.genomicintelligence.ai/mcpworks keyless against a public demoquota, with the key optional.
The skill documents both paths, the Ensembl-based sequence acquisition (including
the exact 9,198 bp TSS-centred window the
expressionmodel requires), and theasync annotation poll.
Scope
This is a skill-only change. It adds one file,
container/skills/query-genomic-intelligence/SKILL.md, and touches no sourcefiles, so the skills-only PR check passes. Verified with
git diff --name-only upstream/main...HEAD, which lists that path alone.No secrets are committed; the key is read from the
GI_API_KEYenvironmentvariable. The keyless MCP path was verified against the live endpoint: an
anonymous Streamable HTTP session with no
Authorizationheader completesinitializeand returns a realpredict_promoterresult.Notes
For research and development use, not clinical or diagnostic decisions.
Docs: https://docs.genomicintelligence.ai