{
  "format_version": "uniprot_fot_graphified_v0",
  "raw_manifest": {
    "raw_root": "/home/iska/Documents/amelie/bio/iska-net/data/raw_hf_bio_scale",
    "datasets": [
      {
        "name": "dna_coding_regions_train",
        "path": "/home/iska/Documents/amelie/bio/iska-net/data/raw_hf_bio_scale/dna_coding_regions_train",
        "parquet_files": 24,
        "readable_parquet_files": 24,
        "unreadable_files": [],
        "bytes": 5448417115,
        "rows": 1677609,
        "schema": [
          {
            "name": "accession",
            "type": "string"
          },
          {
            "name": "organism",
            "type": "string"
          },
          {
            "name": "sequence",
            "type": "string"
          },
          {
            "name": "introns",
            "type": "list<element: struct<after: string, before: string, end: int64, gene: string, sequence: string, start: int64>>"
          },
          {
            "name": "exons",
            "type": "list<element: struct<after: string, before: string, end: int64, gene: string, sequence: string, start: int64>>"
          },
          {
            "name": "proteins",
            "type": "list<element: struct<end: int64, gene: string, sequence: string, start: int64>>"
          }
        ]
      },
      {
        "name": "pubchem10m_selfies_train",
        "path": "/home/iska/Documents/amelie/bio/iska-net/data/raw_hf_bio_scale/pubchem10m_selfies_train",
        "parquet_files": 5,
        "readable_parquet_files": 5,
        "unreadable_files": [],
        "bytes": 555511826,
        "rows": 9999999,
        "schema": [
          {
            "name": "SELFIES",
            "type": "string"
          }
        ]
      },
      {
        "name": "rfam_sequence_train",
        "path": "/home/iska/Documents/amelie/bio/iska-net/data/raw_hf_bio_scale/rfam_sequence_train",
        "parquet_files": 1,
        "readable_parquet_files": 1,
        "unreadable_files": [],
        "bytes": 726072383,
        "rows": 20051822,
        "schema": [
          {
            "name": "id",
            "type": "string"
          },
          {
            "name": "sequence",
            "type": "string"
          },
          {
            "name": "family",
            "type": "string"
          },
          {
            "name": "clan",
            "type": "string"
          },
          {
            "name": "description",
            "type": "string"
          }
        ]
      },
      {
        "name": "rnacentral_8192_sequence_train",
        "path": "/home/iska/Documents/amelie/bio/iska-net/data/raw_hf_bio_scale/rnacentral_8192_sequence_train",
        "parquet_files": 7,
        "readable_parquet_files": 7,
        "unreadable_files": [],
        "bytes": 2432802851,
        "rows": 7340032,
        "schema": [
          {
            "name": "upi",
            "type": "string"
          },
          {
            "name": "sequence",
            "type": "string"
          },
          {
            "name": "type",
            "type": "string"
          },
          {
            "name": "description",
            "type": "string"
          }
        ]
      },
      {
        "name": "uniprot_function_text_train",
        "path": "/home/iska/Documents/amelie/bio/iska-net/data/raw_hf_bio_scale/uniprot_function_text_train",
        "parquet_files": 1,
        "readable_parquet_files": 1,
        "unreadable_files": [],
        "bytes": 237633233,
        "rows": 464395,
        "schema": [
          {
            "name": "entry",
            "type": "string"
          },
          {
            "name": "entry_name",
            "type": "string"
          },
          {
            "name": "protein_name",
            "type": "string"
          },
          {
            "name": "sequence",
            "type": "string"
          },
          {
            "name": "function",
            "type": "string"
          }
        ]
      },
      {
        "name": "uniprot_uniref50_sequence_train",
        "path": "/home/iska/Documents/amelie/bio/iska-net/data/raw_hf_bio_scale/uniprot_uniref50_sequence_train",
        "parquet_files": 130,
        "readable_parquet_files": 129,
        "unreadable_files": [
          {
            "path": "/home/iska/Documents/amelie/bio/iska-net/data/raw_hf_bio_scale/uniprot_uniref50_sequence_train/default/train/0109.parquet",
            "error": "ArrowInvalid: Parquet magic bytes not found in footer. Either the file is corrupted or this is not a parquet file."
          }
        ],
        "bytes": 18112483652,
        "rows": 59604946,
        "schema": [
          {
            "name": "id",
            "type": "string"
          },
          {
            "name": "name",
            "type": "string"
          },
          {
            "name": "updated",
            "type": "string"
          },
          {
            "name": "member_count",
            "type": "int32"
          },
          {
            "name": "common_taxon",
            "type": "string"
          },
          {
            "name": "common_taxon_id",
            "type": "int32"
          },
          {
            "name": "seed_id",
            "type": "string"
          },
          {
            "name": "go_mf",
            "type": "list<element: string>"
          },
          {
            "name": "go_bp",
            "type": "list<element: string>"
          },
          {
            "name": "go_cc",
            "type": "list<element: string>"
          },
          {
            "name": "member_ids",
            "type": "list<element: string>"
          },
          {
            "name": "rep_member_id",
            "type": "string"
          },
          {
            "name": "rep_member_id_type",
            "type": "string"
          },
          {
            "name": "rep_organism",
            "type": "string"
          },
          {
            "name": "rep_organism_tax_id",
            "type": "int32"
          },
          {
            "name": "rep_protein_name",
            "type": "string"
          },
          {
            "name": "rep_accessions",
            "type": "list<element: string>"
          },
          {
            "name": "rep_uniparc_id",
            "type": "string"
          },
          {
            "name": "rep_uniref90_id",
            "type": "string"
          },
          {
            "name": "rep_uniref100_id",
            "type": "string"
          },
          {
            "name": "rep_is_seed",
            "type": "bool"
          },
          {
            "name": "sequence",
            "type": "large_string"
          },
          {
            "name": "sequence_length",
            "type": "int32"
          },
          {
            "name": "sequence_crc64",
            "type": "string"
          },
          {
            "name": "sequence_xxh128",
            "type": "string"
          }
        ]
      }
    ],
    "totals": {
      "datasets": 6,
      "parquet_files": 168,
      "readable_parquet_files": 167,
      "bytes": 27512921060,
      "rows": 99138803
    },
    "raw_links": [
      {
        "dataset": "dna_coding_regions_train",
        "path": "data/uniprot_fot/raw_sources/dna_coding_regions_train",
        "mode": "symlink",
        "source": "/home/iska/Documents/amelie/bio/iska-net/data/raw_hf_bio_scale/dna_coding_regions_train"
      },
      {
        "dataset": "pubchem10m_selfies_train",
        "path": "data/uniprot_fot/raw_sources/pubchem10m_selfies_train",
        "mode": "symlink",
        "source": "/home/iska/Documents/amelie/bio/iska-net/data/raw_hf_bio_scale/pubchem10m_selfies_train"
      },
      {
        "dataset": "rfam_sequence_train",
        "path": "data/uniprot_fot/raw_sources/rfam_sequence_train",
        "mode": "symlink",
        "source": "/home/iska/Documents/amelie/bio/iska-net/data/raw_hf_bio_scale/rfam_sequence_train"
      },
      {
        "dataset": "rnacentral_8192_sequence_train",
        "path": "data/uniprot_fot/raw_sources/rnacentral_8192_sequence_train",
        "mode": "symlink",
        "source": "/home/iska/Documents/amelie/bio/iska-net/data/raw_hf_bio_scale/rnacentral_8192_sequence_train"
      },
      {
        "dataset": "uniprot_function_text_train",
        "path": "data/uniprot_fot/raw_sources/uniprot_function_text_train",
        "mode": "symlink",
        "source": "/home/iska/Documents/amelie/bio/iska-net/data/raw_hf_bio_scale/uniprot_function_text_train"
      },
      {
        "dataset": "uniprot_uniref50_sequence_train",
        "path": "data/uniprot_fot/raw_sources/uniprot_uniref50_sequence_train",
        "mode": "symlink",
        "source": "/home/iska/Documents/amelie/bio/iska-net/data/raw_hf_bio_scale/uniprot_uniref50_sequence_train"
      }
    ]
  },
  "derived": {
    "jsonl": "data/uniprot_fot/derived/uniprot_fot_graphified_sample.jsonl",
    "parquet": "data/uniprot_fot/derived/uniprot_fot_graphified_sample.parquet",
    "records": 48,
    "sample_per_dataset": 8,
    "counts_by_dataset": {
      "dna_coding_regions_train": 8,
      "pubchem10m_selfies_train": 8,
      "rfam_sequence_train": 8,
      "rnacentral_8192_sequence_train": 8,
      "uniprot_function_text_train": 8,
      "uniprot_uniref50_sequence_train": 8
    },
    "schema": [
      {
        "name": "record_id",
        "type": "string"
      },
      {
        "name": "dataset",
        "type": "string"
      },
      {
        "name": "source_file",
        "type": "string"
      },
      {
        "name": "source_row_index",
        "type": "int64"
      },
      {
        "name": "entry_id",
        "type": "string"
      },
      {
        "name": "task_family",
        "type": "string"
      },
      {
        "name": "sequence",
        "type": "large_string"
      },
      {
        "name": "annotation_text",
        "type": "large_string"
      },
      {
        "name": "text",
        "type": "large_string"
      },
      {
        "name": "graph_json",
        "type": "large_string"
      },
      {
        "name": "forest_json",
        "type": "large_string"
      },
      {
        "name": "metadata_json",
        "type": "large_string"
      },
      {
        "name": "content_hash",
        "type": "string"
      },
      {
        "name": "group_hash",
        "type": "string"
      },
      {
        "name": "split",
        "type": "string"
      },
      {
        "name": "split_cluster",
        "type": "string"
      },
      {
        "name": "quality_flags_json",
        "type": "string"
      }
    ]
  },
  "notes": [
    "This is a deterministic graphification sample, not the final authored reasoning corpus.",
    "Raw sources are symlinked by default to avoid duplicating 26GB on a nearly full filesystem.",
    "Use --raw-link-mode move only after confirming no other workflow depends on the old raw path."
  ]
}