Datasets:

Milad96
/

Kluyveromyces-marxianus

language:
  - en
license: cc-by-4.0
task_categories:
  - text-generation
  - token-classification
  - question-answering
tags:
  - biology
  - kluyveromyces-marxianus
  - yeast
  - genomics
  - proteomics
  - bioinformatics
size_categories:
  - 10K<n<100K
dataset_info:
  - config_name: cell5_metabolomics
    features:
      - name: id
        dtype: string
      - name: source
        dtype: string
      - name: category
        dtype: string
      - name: gene_id
        dtype: string
      - name: gene_name
        dtype: string
      - name: gene_symbol
        dtype: string
      - name: protein_id
        dtype: string
      - name: protein_name
        dtype: string
      - name: sequence
        dtype: string
      - name: title
        dtype: string
      - name: abstract
        dtype: string
      - name: full_text
        dtype: string
      - name: pmid
        dtype: string
      - name: doi
        dtype: string
      - name: authors
        dtype: string
      - name: journal
        dtype: string
      - name: year
        dtype: string
      - name: timestamp
        dtype: string
      - name: cid
        dtype: string
      - name: chembl_id
        dtype: string
      - name: chebi_id
        dtype: string
      - name: hmdb_id
        dtype: string
      - name: lm_id
        dtype: string
      - name: bigg_id
        dtype: string
      - name: rhea_id
        dtype: string
      - name: ec_number
        dtype: string
      - name: inchikey
        dtype: string
      - name: inchi
        dtype: string
      - name: canonical_smiles
        dtype: string
      - name: isomeric_smiles
        dtype: string
      - name: molecular_formula
        dtype: string
      - name: molecular_weight
        dtype: float32
      - name: charge
        dtype: int32
      - name: hbond_donor
        dtype: int32
      - name: hbond_acceptor
        dtype: int32
      - name: rotatable_bonds
        dtype: int32
      - name: heavy_atoms
        dtype: int32
      - name: xlogp
        dtype: float32
      - name: tpsa
        dtype: float32
      - name: complexity
        dtype: float32
      - name: smiles_valid
        dtype: bool
      - name: mapped_pubchem_ids
        dtype: string
      - name: mapped_chembl_ids
        dtype: string
      - name: mapped_chebi_ids
        dtype: string
      - name: pathway_ids
        dtype: string
      - name: reaction_ids
        dtype: string
      - name: enzyme_ec
        dtype: string
      - name: metabolic_role
        dtype: string
      - name: completeness_score
        dtype: float32
    splits:
      - name: validation
        num_bytes: 18452
        num_examples: 42
      - name: test
        num_bytes: 20554
        num_examples: 42
      - name: train
        num_bytes: 20394
        num_examples: 70
    download_size: 256274
    dataset_size: 59400
  - config_name: default
    features:
      - name: id
        dtype: string
      - name: source
        dtype: string
      - name: category
        dtype: string
      - name: gene_id
        dtype: string
      - name: gene_name
        dtype: string
      - name: gene_symbol
        dtype: string
      - name: protein_id
        dtype: string
      - name: protein_name
        dtype: string
      - name: sequence
        dtype: string
      - name: title
        dtype: string
      - name: abstract
        dtype: string
      - name: full_text
        dtype: string
      - name: pmid
        dtype: string
      - name: doi
        dtype: string
      - name: authors
        dtype: string
      - name: journal
        dtype: string
      - name: year
        dtype: string
      - name: timestamp
        dtype: string
    splits:
      - name: train
        num_bytes: 449948
        num_examples: 425
      - name: validation
        num_bytes: 56299
        num_examples: 50
      - name: test
        num_bytes: 25214
        num_examples: 25
    download_size: 431437
    dataset_size: 531461
configs:
  - config_name: cell5_metabolomics
    data_files:
      - split: train
        path: cell5_data/train-*
      - split: validation
        path: cell5_splits/validation-*
      - split: test
        path: cell5_splits/test-*
  - config_name: default
    data_files:
      - split: train
        path: cell2_splits/train-*
      - split: validation
        path: cell2_splits/validation-*
      - split: test
        path: cell2_splits/test-*

🧬 Kluyveromyces marxianus Quantum Dataset v10.0.0

Overview

Comprehensive multi-omics dataset for Kluyveromyces marxianus collected using quantum-grade async streaming pipeline, fully integrated with Cell 0's structured directory system.

Statistics

Metric	Value
Total Collected	3,835
Total Local Saved	3,835
Version	v10.0.0
Collection Date	2025-11-10

Data Categories & Local Storage

Literature: 1,417 records (local: 1,417)
Proteins: 1,001 records (local: 1,001)
PMC Full-Text: 999 records (local: 999)
SRA Sequencing: 352 records (local: 352)
GEO Expression: 48 records (local: 48)
Nucleotide Sequences: 18 records (local: 18)

Cell 0 Integration

This dataset strictly respects Cell 0's directory structure. Only folders actively used by collectors:

km_dataset/
├── genomic/          # Genes, nucleotide sequences
├── protein/          # Protein sequences
├── literature/       # PubMed, PMC articles
├── expression/       # GEO, SRA sequencing data
└── checkpoints/
    └── cell1_quantum/  # Collection checkpoints

Note: Cell 0 also creates pathway/, interaction/, structure/, repository/ folders, but current collectors don't produce data for these categories yet.

HuggingFace Organization

Data is organized by phase using data_dir to prevent overwrites:

cell1_genes - Gene data
cell1_proteins - Protein sequences
cell1_literature - PubMed articles
cell1_pmc - PMC full-text articles
cell1_sequences - Nucleotide sequences
cell1_geo - GEO expression data
cell1_sra - SRA sequencing data
cell1_splits - Train/validation/test splits

Usage

Load All Data

from datasets import load_dataset, concatenate_datasets

# Load all phases (FIXED: correct data_dir names)
all_data = []
for phase in ['cell1_genes', 'cell1_proteins', 'cell1_literature',
              'cell1_pmc', 'cell1_sequences', 'cell1_geo', 'cell1_sra']:
    try:
        ds = load_dataset("Milad96/Kluyveromyces-marxianus", split='train', data_dir=phase)
        all_data.append(ds)
    except:
        pass

combined = concatenate_datasets(all_data)

Load Specific Phase

# Load only genes
genes = load_dataset("Milad96/Kluyveromyces-marxianus", split='train', data_dir='cell1_genes')

# Load only literature
literature = load_dataset("Milad96/Kluyveromyces-marxianus", split='train', data_dir='cell1_literature')

Load Splits

dataset = load_dataset("Milad96/Kluyveromyces-marxianus", data_dir='cell1_splits')
train = dataset['train']
val = dataset.get('validation')
test = dataset.get('test')

Citation

@dataset{km_quantum_v10_0_0,
  title={Kluyveromyces marxianus Quantum Dataset},
  version={v10.0.0},
  year={2025},
  url={https://huggingface.co/datasets/Milad96/Kluyveromyces-marxianus}
}

Status: ✅ Production Ready Quality: 🌟 Quantum Grade Pipeline: Async Streaming v10.0 + Cell 0 Full Integration Local Storage: ✅ All records saved in structured folders Overwrite Protection: ✅ Phase-specific data_dirs