huang-sh/deepscience/experimental-data

Experimental Data

Select by study design before retrieval. The resource tool discloses package metadata and instructions only after selection. Package-relative scripts, references, and assets support the Agent's task-specific execution; they are not fixed query functions.

Workflow

1. Define organism, biological system, condition, assay, study design, sample unit, required format,

processing level, and reuse constraints. This step is complete when every known constraint and every unresolved requirement is explicit.

1. Browse the closest modality and compare the complete leaf metadata:

resource({ action: "list", category: "experimental-data/transcriptomics" })

This step is complete when kind is resource_metadata and every returned candidate has been compared against the request.

1. Load each selected package with its exact exposed name:

resource({ action: "read", name: "biomarker-geo" })

This step is complete when each selected package's query interface, schema, access mode, and package-relative scripts, references, assets, and file conventions are known.

1. Accept a dataset only after verifying organism, assay, sample count, groups, processing state,

access conditions, file sizes, checksums when available, and repository version. This step is complete when every candidate has an explicit inclusion or exclusion reason and every selected file is accounted for.

1. Write manifests, raw responses, downloaded files, and normalized metadata to the Session

workspace. Report accession, retrieval date, selected files, sizes, checksums, and failures. This step is complete when every selected package has a result, a valid empty result, or a concrete failure and every artifact path is reported.

Use package directories as read-only sources; all generated output belongs in the Session workspace.