Cortexa research tool·chemistry·hubmap

HuBMAP Search Datasets

Search HuBMAP (Human BioMolecular Atlas Program) published datasets by organ, assay type, or free text. HuBMAP provides spatial biology and single-cell atlas datasets across 43 human organs with data types including scRNA-Seq, CODEX, MALDI, LC-MS, snATAC-Seq, and more. Organ codes: LK=Left Kidney, RK=Right Kidney, LI=Large Intestine, SI=Small Intestine, HT=Heart, LV=Liver, LU=Lung, SP=Spleen, TH=Thymus, LY=Lymph Node, BL=Bladder, PA=Pancreas, SK=Skin, BR=Brain, BM=Bone Marrow, MU=Muscle.

Livelast probed 2026-04-30 23:07Z· 424msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 424ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "dataset_type": {
      "description": "Filter by assay/data type (e.g., 'RNAseq', 'CODEX', 'MALDI', 'snATACseq', 'LC-MS', 'scRNAseq-10xGenomics-v3')",
      "type": "string"
    },
    "limit": {
      "default": 10,
      "description": "Maximum number of results (1-50, default 10)",
      "type": "integer"
    },
    "organ": {
      "description": "Organ code to filter by (e.g., 'LK' for left kidney, 'HT' for heart, 'LV' for liver, 'LU' for lung, 'BR' for brain, 'SP' for spleen). Use HuBMAP_list_organs to see all codes.",
      "type": "string"
    },
    "query": {
      "description": "Free text search across title, description, and anatomy fields",
      "type": "string"
    },
    "status": {
      "default": "Published",
      "description": "Dataset status filter. Default: 'Published'",
      "type": "string"
    }
  },
  "required": [],
  "type": "object"
}

Examples (1)

Default HuBMAP Search Datasets call

public-safeinput

{
  "limit": 3,
  "query": "BRCA1"
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_HuBMAP_search_datasets
Tool name: HuBMAP_search_datasets
Added: 2026-04-30 22:47Z
Tags: tooluniverse

HuBMAP Search Datasets

Livelast probed 2026-04-30 23:07Z· 424msCortexa

Schema

JSON Schema the agent (or your API call) must match.

{ "properties": { "dataset_type": { "description": "Filter by assay/data type (e.g., 'RNAseq', 'CODEX', 'MALDI', 'snATACseq', 'LC-MS', 'scRNAseq-10xGenomics-v3')", "type": "string" }, "limit": { "default": 10, "description": "Maximum number of results (1-50, default 10)", "type": "integer" }, "organ": { "description": "Organ code to filter by (e.g., 'LK' for left kidney, 'HT' for heart, 'LV' for liver, 'LU' for lung, 'BR' for brain, 'SP' for spleen). Use HuBMAP_list_organs to see all codes.", "type": "string" }, "query": { "description": "Free text search across title, description, and anatomy fields", "type": "string" }, "status": { "default": "Published", "description": "Dataset status filter. Default: 'Published'", "type": "string" } }, "required": [], "type": "object" }