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croissant.json

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+{
+  "@context": {
+    "@language": "en",
+    "@vocab": "http://schema.org/",
+    "sc": "http://schema.org/",
+    "cr": "http://mlcommons.org/croissant/",
+    "rai": "http://mlcommons.org/croissant/RAI/",
+    "dct": "http://purl.org/dc/terms/",
+    "annotation": "cr:annotation",
+    "conformsTo": "dct:conformsTo",
+    "containedIn": "cr:containedIn",
+    "data": {"@id": "cr:data", "@type": "@json"},
+    "dataType": {"@id": "cr:dataType", "@type": "@vocab"},
+    "field": "cr:field",
+    "fileObject": "cr:fileObject",
+    "fileSet": "cr:fileSet",
+    "recordSet": "cr:recordSet",
+    "source": "cr:source",
+    "subField": "cr:subField"
+  },
+  "@type": "sc:Dataset",
+  "name": "scShapeBench",
+  "description": "A benchmark dataset for single-cell shape analysis containing 2,547,517 cells across 105 real-world single-cell RNA-seq datasets stored in AnnData (.h5ad) format with precomputed PCA embeddings and Leiden clustering.",
+  "url": "https://huggingface.co/datasets/scShape-Benchmark/scShapeBench",
+  "conformsTo": "http://mlcommons.org/croissant/1.1",
+  "datePublished": "2026-05-05",
+  "keywords": ["single-cell", "RNA-seq", "scRNA-seq", "h5ad", "AnnData", "genomics", "benchmark", "shape-analysis"],
+
+  "distribution": [
+    {
+      "@type": "cr:FileSet",
+      "@id": "h5ad-files",
+      "name": "h5ad-files",
+      "description": "AnnData files containing single-cell gene expression data with PCA embeddings and Leiden clustering",
+      "containedIn": {"@id": "data-directory"},
+      "includes": "SCD-*.h5ad",
+      "encodingFormat": "application/x-hdf5"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "data-directory",
+      "name": "data-directory",
+      "description": "Directory containing all AnnData data files",
+      "contentUrl": "data/",
+      "encodingFormat": "application/x-directory"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "cell-metadata-csv",
+      "name": "cell_metadata.csv",
+      "description": "Combined cell-level metadata from all datasets: number of genes detected, Leiden cluster assignment, and source file identifier",
+      "contentUrl": "cell_metadata.csv",
+      "encodingFormat": "text/csv"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "gene-metadata-csv",
+      "name": "gene_metadata.csv",
+      "description": "Combined gene-level metadata from all datasets: gene IDs, feature types, dispersion statistics, and highly-variable flags",
+      "contentUrl": "gene_metadata.csv",
+      "encodingFormat": "text/csv"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "dataset-index-csv",
+      "name": "dataset_index.csv",
+      "description": "Per-file summary statistics: number of cells, number of genes, and file size",
+      "contentUrl": "dataset_index.csv",
+      "encodingFormat": "text/csv"
+    }
+  ],
+
+  "recordSet": [
+    {
+      "@type": "cr:RecordSet",
+      "name": "dataset_index",
+      "description": "Summary statistics for each of the 105 single-cell datasets in the benchmark",
+      "field": [
+        {
+          "@type": "cr:Field",
+          "name": "file_id",
+          "description": "Dataset identifier (e.g., SCD-0001)",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {"@id": "dataset-index-csv"},
+            "extract": {"column": "file_id"}
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "name": "filename",
+          "description": "Filename of the h5ad file",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {"@id": "dataset-index-csv"},
+            "extract": {"column": "filename"}
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "name": "n_cells",
+          "description": "Number of cells in the dataset",
+          "dataType": "sc:Integer",
+          "source": {
+            "fileObject": {"@id": "dataset-index-csv"},
+            "extract": {"column": "n_cells"}
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "name": "n_genes",
+          "description": "Number of genes in the dataset",
+          "dataType": "sc:Integer",
+          "source": {
+            "fileObject": {"@id": "dataset-index-csv"},
+            "extract": {"column": "n_genes"}
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "name": "file_size_bytes",
+          "description": "File size in bytes",
+          "dataType": "sc:Integer",
+          "source": {
+            "fileObject": {"@id": "dataset-index-csv"},
+            "extract": {"column": "file_size_bytes"}
+          }
+        }
+      ]
+    },
+    {
+      "@type": "cr:RecordSet",
+      "name": "cell_metadata",
+      "description": "Cell-level metadata across all 2,547,517 cells in the benchmark",
+      "field": [
+        {
+          "@type": "cr:Field",
+          "name": "cell_barcode",
+          "description": "Unique cell barcode identifier",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {"@id": "cell-metadata-csv"},
+            "extract": {"column": "cell_barcode"}
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "name": "n_genes",
+          "description": "Number of genes detected in the cell",
+          "dataType": "sc:Integer",
+          "source": {
+            "fileObject": {"@id": "cell-metadata-csv"},
+            "extract": {"column": "n_genes"}
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "name": "file_id",
+          "description": "Source dataset identifier (foreign key to dataset_index.file_id)",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {"@id": "cell-metadata-csv"},
+            "extract": {"column": "file_id"}
+          },
+          "references": {
+            "field": {"@id": "dataset_index/file_id"}
+          }
+        }
+      ]
+    },
+    {
+      "@type": "cr:RecordSet",
+      "name": "gene_metadata",
+      "description": "Gene-level metadata across all datasets including IDs, dispersion statistics, and highly-variable flags",
+      "field": [
+        {
+          "@type": "cr:Field",
+          "name": "gene_index",
+          "description": "Gene identifier (Ensembl ID or symbol)",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {"@id": "gene-metadata-csv"},
+            "extract": {"column": "gene_index"}
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "name": "gene_ids",
+          "description": "Ensembl gene identifier",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {"@id": "gene-metadata-csv"},
+            "extract": {"column": "gene_ids"}
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "name": "highly_variable",
+          "description": "Whether the gene is flagged as highly variable",
+          "dataType": "sc:Boolean",
+          "source": {
+            "fileObject": {"@id": "gene-metadata-csv"},
+            "extract": {"column": "highly_variable"}
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "name": "means",
+          "description": "Mean expression level",
+          "dataType": "sc:Float",
+          "source": {
+            "fileObject": {"@id": "gene-metadata-csv"},
+            "extract": {"column": "means"}
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "name": "n_cells",
+          "description": "Number of cells expressing this gene",
+          "dataType": "sc:Integer",
+          "source": {
+            "fileObject": {"@id": "gene-metadata-csv"},
+            "extract": {"column": "n_cells"}
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "name": "file_id",
+          "description": "Source dataset identifier (foreign key to dataset_index.file_id)",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {"@id": "gene-metadata-csv"},
+            "extract": {"column": "file_id"}
+          },
+          "references": {
+            "field": {"@id": "dataset_index/file_id"}
+          }
+        }
+      ]
+    }
+  ]
+}