{
  "name": "aggregated_config_3.json",
  "description": "Aggregated config 3 to transform several public datasets",
  "data": {
    "file_type": "h5ad",
    "biosample_metadata": {
      "metadata_keys": {
        "obs": "metadata"
      },
      "biosample_column_name": "sample_id",
      "sample": {
        "create_new_group": false,
        "template_id": null,
        "linking_group": null,
        "columns_to_export": [
          "Condition",
          "self_reported_ethnicity_ontology_term_id",
          "tissue_type"
        ],
        "columns_renaming_map": {
          "Condition": "Condition Group",
          "self_reported_ethnicity_ontology_term_id": "Donor Ethnicity Term ID",
          "tissue_type": "Cell Source"
        },
        "columns_to_fill_missing_values": null,
        "columns_to_curate_values": {
          "Sample Source ID": {
            "AM031": "Liver-32",
            "AM042": "Liver-13",
            "AM048": "Liver-14",
            "AM061": "Liver-18",
            "AM062": "Liver-33",
            "AM072": "Liver-34"
          }
        }
      },
      "library": {
        "create_new_group": null,
        "template_id": null,
        "linking_group": null,
        "columns_to_export": null,
        "columns_to_fill_missing_values": null,
        "columns_to_curate_values": null
      }
    },
    "cell_metadata": {
      "metadata_keys": {
        "obs": "metadata",
        "obsm": "embedding",
        "obsp": "pairwise"
      },
      "linking_group": null,
      "columns_to_drop": [
        "barcode",
        "Sex",
        "Age",
        "batch",
        "organism_ontology_term_id",
        "donor_id",
        "development_stage_ontology_term_id",
        "sex_ontology_term_id",
        "disease_ontology_term_id",
        "tissue_ontology_term_id"
      ],
      "columns_renaming_map": {
          "_index": "barcode",
          "sample_id": "batch",
          "log10GenesPerUMI_injured": "log10_genes_per_umi_injured",
          "CellType_injured": "cell_type_injured",
          "log10GenesPerUMI_healthy": "log10_genes_per_umi_healthy",
          "CellType_healthy": "cell_type_healthy",
          "cell_type_ontology_term_id": "cell_type"
      },
      "columns_to_fill_missing_values": null,
      "columns_to_curate_values": {
        "batch": {
          "AM031": "Liver-32",
          "AM042": "Liver-13",
          "AM048": "Liver-14",
          "AM061": "Liver-18",
          "AM062": "Liver-33",
          "AM072": "Liver-34"
        }
      },
      "set_column_value": null,
      "columns_to_preserve_name": null,
      "add_qc_metrics": true
    },
    "feature_metadata": {
      "metadata_keys": {
        "var": "metadata",
        "varm": "embedding",
        "varp": "pairwise"
      },
      "columns_to_drop": null,
      "columns_renaming_map": {
        "_index": "gene"
      },
      "columns_to_fill_missing_values": null,
      "columns_to_curate_values": null,
      "set_column_value": null,
      "columns_to_preserve_name": null,
      "map_gene_ids_to_names": true
    },
    "cell_expression": {
      "compression_level": null,
      "chunk_size": null,
      "max_buffer_size": null,
      "data_class": "Single-cell transcriptomics",
      "number_format": "float32",
      "columns_to_drop": null,
      "columns_renaming_map": null,
      "set_column_value": null,
      "source_file_metadata": true
    }
  }
}