| { |
| "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." |
| ] |
| } |
