README.md

---
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:
  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: validation
    num_bytes: 50247
    num_examples: 50
  - name: test
    num_bytes: 26233
    num_examples: 25
  - name: train
    num_bytes: 181691
    num_examples: 98
  download_size: 778393
  dataset_size: 258171
configs:
- config_name: default
  data_files:
  - split: train
    path: cell3_semantic/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** | 3,836 |
| **Total Local Saved** | 3,836 |
| **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**: 1,000 records (local: 1,000)
- **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
```python
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
```python
# 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
```python
dataset = load_dataset("Milad96/Kluyveromyces-marxianus", data_dir='cell1_splits')
train = dataset['train']
val = dataset.get('validation')
test = dataset.get('test')
```

## Citation
```bibtex
@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