CELLxGENE Get Cell Metadata

Overview

Query cell metadata from CELLxGENE Census (50M+ human/mouse single cells). CRITICAL: obs_value_filter is REQUIRED - unfiltered queries will timeout. Common filters: tissue_general (brain, heart, lung, liver, blood, kidney, skin, eye, intestine), cell_type (T cell, B cell, neuron, macrophage, fibroblast), disease (normal, COVID-19, Alzheimer disease, cancer). Start with: obs_value_filter='tissue_general == "lung" and disease == "normal"'. Returns cell type, tissue, disease, donor info. Use for: finding cells by criteria, cohort selection, exploring cell populations.

Status

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

Last probed

1d ago

Last success

1d ago

Last latency

14517ms

Schema

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

{
  "properties": {
    "census_version": {
      "default": "stable",
      "description": "Census version to query. 'stable' (recommended, Long-Term Support release), 'latest' (newest data, may change), or specific date 'YYYY-MM-DD' (for reproducibility). Default 'stable' is best for production analyses.",
      "type": "string"
    },
    "column_names": {
      "description": "Specific columns to return (default: all columns)",
      "items": {
        "type": "string"
      },
      "type": "array"
    },
    "obs_value_filter": {
      "description": "REQUIRED - filter cells using SQL-like syntax. Unfiltered queries timeout (50M+ cells). Format: 'field == \"value\"'. Operators: ==, !=, in, <, >, <=, >=. Combine with 'and'/'or'. Common fields and values: tissue_general (brain, heart, lung, liver, blood, kidney, skin, eye, intestine, pancreas, bone marrow), cell_type (T cell, B cell, neuron, macrophage, fibroblast, epithelial cell, endothelial cell), disease (normal, COVID-19, Alzheimer disease, lung adenocarcinoma), assay (10x 3' v3, Smart-seq2), sex (male, female). Examples: 'tissue_general == \"lung\"', 'disease == \"COVID-19\" and tissue_general == \"blood\"', 'cell_type in [\"T cell\", \"B cell\"] and disease == \"normal\"'.",
      "type": "string"
    },
    "operation": {
      "default": "get_obs_metadata",
      "description": "Operation type",
      "enum": [
        "get_obs_metadata"
      ],
      "type": "string"
    },
    "organism": {
      "default": "Homo sapiens",
      "description": "Organism name",
      "enum": [
        "Homo sapiens",
        "Mus musculus"
      ],
      "type": "string"
    }
  },
  "required": [
    "operation",
    "obs_value_filter"
  ],
  "type": "object"
}

Examples (1)

{
  "column_names": [],
  "obs_value_filter": "",
  "operation": ""
}

Identifiers

Catalog ID

tu_CELLxGENE_get_cell_metadata

Tool name

CELLxGENE_get_cell_metadata

Added

2026-04-30 22:47Z

Tags

tooluniverse, slow