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:
- 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: train
    num_bytes: 162707
    num_examples: 333
  - name: validation
    num_bytes: 17988
    num_examples: 42
  - name: test
    num_bytes: 22287
    num_examples: 42
  download_size: 132594
  dataset_size: 202982
- config_name: cell6_literature
  features:
  - name: id
    dtype: string
  - name: source
    dtype: string
  - name: category
    dtype: string
  - name: pmid
    dtype: string
  - name: pmc_id
    dtype: string
  - name: doi
    dtype: string
  - name: core_id
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  - name: arxiv_id
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  - name: title
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  - name: abstract
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  - name: full_text
    dtype: string
  - name: section_hierarchy
    dtype: string
  - name: introduction
    dtype: string
  - name: methods
    dtype: string
  - name: results
    dtype: string
  - name: discussion
    dtype: string
  - name: authors
    dtype: string
  - name: author_count
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  - name: first_author
    dtype: string
  - name: last_author
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  - name: affiliations
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  - name: journal
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  - name: year
    dtype: int32
  - name: volume
    dtype: string
  - name: issue
    dtype: string
  - name: pages
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  - name: mesh_descriptors
    dtype: string
  - name: keywords
    dtype: string
  - name: publication_types
    dtype: string
  - name: grants
    dtype: string
  - name: grants_normalized
    dtype: string
  - name: chemicals
    dtype: string
  - name: tables
    dtype: string
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    dtype: int32
  - name: figures
    dtype: string
  - name: figure_count
    dtype: int32
  - name: is_open_access
    dtype: bool
  - name: oa_version
    dtype: string
  - name: oa_location
    dtype: string
  - name: has_pdf
    dtype: bool
  - name: has_fulltext
    dtype: bool
  - name: entities
    dtype: string
  - name: relations
    dtype: string
  - name: topics
    dtype: string
  - name: claims
    dtype: string
  - name: citation_count
    dtype: int32
  - name: references
    dtype: string
  - name: cited_by
    dtype: string
  - name: co_citations
    dtype: string
  - name: quality_score
    dtype: float32
  - name: completeness_score
    dtype: float32
  - name: word_count
    dtype: int32
  - name: timestamp
    dtype: string
  - name: version
    dtype: int32
  splits:
  - name: train
    num_bytes: 2898356
    num_examples: 184
  - name: validation
    num_bytes: 278624
    num_examples: 23
  - name: test
    num_bytes: 357639
    num_examples: 23
  download_size: 1963039
  dataset_size: 3534619
- config_name: cell7_1_stable_omics
  features:
  - name: id
    dtype: string
  - name: source
    dtype: string
  - name: category
    dtype: string
  - name: timestamp
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  - name: title
    dtype: string
  - name: description
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  - name: organism
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  - name: tax_id
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  - name: accession
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  - name: run_accession
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  - name: instrument
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  - name: read_count
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  - name: normalization_method
    dtype: string
  - name: units
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  - name: publication_date
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  - name: pubmed_ids
    dtype: string
  - name: gene_id
    dtype: string
  - name: gene_name
    dtype: string
  - name: gene_symbol
    dtype: string
  - name: biotype
    dtype: string
  - name: chromosome
    dtype: string
  - name: start
    dtype: int64
  - name: end
    dtype: int64
  - name: strand
    dtype: int8
  - name: transcripts_json
    dtype: string
  - name: variants_json
    dtype: string
  - name: regulatory_json
    dtype: string
  - name: file_url
    dtype: string
  - name: file_type
    dtype: string
  - name: file_size_mb
    dtype: float32
  - name: px_id
    dtype: string
  - name: file_name
    dtype: string
  - name: pride_file_url
    dtype: string
  - name: file_category
    dtype: string
  - name: ensembl_id
    dtype: string
  - name: uniprot_id
    dtype: string
  - name: sgd_id
    dtype: string
  - name: fungidb_id
    dtype: string
  - name: ortho_group_id
    dtype: string
  - name: ortho_level
    dtype: string
  - name: ortho_gene_count
    dtype: int32
  - name: homology_type
    dtype: string
  - name: target_species
    dtype: string
  - name: target_gene_id
    dtype: string
  - name: study_id
    dtype: string
  - name: study_type
    dtype: string
  - name: secondary_accessions
    dtype: string
  - name: feature_count
    dtype: int32
  - name: go_terms
    dtype: string
  - name: pathways
    dtype: string
  - name: expression_level
    dtype: float32
  - name: fold_change
    dtype: float32
  - name: p_value
    dtype: float32
  - name: quality_score
    dtype: float32
  - name: completeness_score
    dtype: float32
  - name: version
    dtype: int32
  splits:
  - name: train
    num_bytes: 28098
    num_examples: 47
  - name: validation
    num_bytes: 3058
    num_examples: 6
  - name: test
    num_bytes: 2913
    num_examples: 6
  download_size: 83632
  dataset_size: 34069
- config_name: cell7_specialized
  features:
  - name: id
    dtype: string
  - name: source
    dtype: string
  - name: category
    dtype: string
  - name: timestamp
    dtype: string
  - name: title
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  - name: description
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  - name: organism
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  - name: tax_id
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  - name: accession
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  - name: url
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  - name: experiment_accession
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  - name: run_accession
    dtype: string
  - name: library_strategy
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  - name: library_source
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    dtype: string
  - name: platform
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  - name: instrument_model
    dtype: string
  - name: read_count
    dtype: int64
  - name: base_count
    dtype: int64
  - name: normalization_method
    dtype: string
  - name: units
    dtype: string
  - name: gene_id
    dtype: string
  - name: gene_name
    dtype: string
  - name: biotype
    dtype: string
  - name: chromosome
    dtype: string
  - name: start
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  - name: end
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  - name: strand
    dtype: int8
  - name: transcripts_json
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  - name: variants_json
    dtype: string
  - name: regulatory_json
    dtype: string
  - name: file_url
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  - name: file_type
    dtype: string
  - name: file_size_mb
    dtype: float32
  - name: px_id
    dtype: string
  - name: file_name
    dtype: string
  - name: pride_file_url
    dtype: string
  - name: file_category
    dtype: string
  - name: ensembl_id
    dtype: string
  - name: uniprot_id
    dtype: string
  - name: sgd_id
    dtype: string
  - name: fungidb_id
    dtype: string
  - name: ortho_group_id
    dtype: string
  - name: ortho_level
    dtype: string
  - name: ortho_gene_count
    dtype: int32
  - name: homology_type
    dtype: string
  - name: target_species
    dtype: string
  - name: target_gene_id
    dtype: string
  - name: study_id
    dtype: string
  - name: study_type
    dtype: string
  splits:
  - name: validation
    num_bytes: 12414
    num_examples: 29
  - name: test
    num_bytes: 12172
    num_examples: 29
  - name: train
    num_bytes: 125258
    num_examples: 290
  download_size: 119112
  dataset_size: 149844
- config_name: cell7_specialized_omics
  features:
  - name: id
    dtype: string
  - name: source
    dtype: string
  - name: category
    dtype: string
  - name: timestamp
    dtype: string
  - name: title
    dtype: string
  - name: description
    dtype: string
  - name: organism
    dtype: string
  - name: tax_id
    dtype: int32
  - name: accession
    dtype: string
  - name: url
    dtype: string
  - name: study_accession
    dtype: string
  - name: sample_accession
    dtype: string
  - name: experiment_accession
    dtype: string
  - name: run_accession
    dtype: string
  - name: library_strategy
    dtype: string
  - name: library_source
    dtype: string
  - name: library_layout
    dtype: string
  - name: platform
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  - name: instrument
    dtype: string
  - name: read_count
    dtype: int64
  - name: base_count
    dtype: int64
  - name: sample_count
    dtype: int32
  - name: normalization_method
    dtype: string
  - name: units
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  - name: publication_date
    dtype: string
  - name: pubmed_ids
    dtype: string
  - name: gene_id
    dtype: string
  - name: gene_name
    dtype: string
  - name: gene_symbol
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  - name: biotype
    dtype: string
  - name: chromosome
    dtype: string
  - name: start
    dtype: int64
  - name: end
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  - name: strand
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  - name: transcripts_json
    dtype: string
  - name: variants_json
    dtype: string
  - name: regulatory_json
    dtype: string
  - name: file_url
    dtype: string
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  - name: px_id
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  - name: file_name
    dtype: string
  - name: pride_file_url
    dtype: string
  - name: file_category
    dtype: string
  - name: ensembl_id
    dtype: string
  - name: uniprot_id
    dtype: string
  - name: sgd_id
    dtype: string
  - name: fungidb_id
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  - name: ortho_group_id
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  - name: ortho_level
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  - name: ortho_gene_count
    dtype: int32
  - name: homology_type
    dtype: string
  - name: target_species
    dtype: string
  - name: target_gene_id
    dtype: string
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  - name: p_value
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  - name: quality_score
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  - name: completeness_score
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  - name: version
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  splits:
  - name: train
    num_bytes: 8816
    num_examples: 9
  download_size: 28761
  dataset_size: 8816
- config_name: cell7_ultimate
  features:
  - name: id
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  - name: source
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  - name: category
    dtype: string
  - name: accession
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  - name: gene_id
    dtype: string
  - name: protein_id
    dtype: string
  - name: uniprot_id
    dtype: string
  - name: study_id
    dtype: string
  - name: sample_id
    dtype: string
  - name: run_accession
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  - name: title
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  - name: biotype
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  - name: status
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  - name: start
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  - name: strand
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  - name: sequence
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  - name: platform
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  - name: library_strategy
    dtype: string
  - name: platform_type
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  - name: normalization_method
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  - name: protein_count
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  - name: orthology_type
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  - name: target_species
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  - name: sample_count
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  - name: timestamp
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  - name: version
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  splits:
  - name: train
    num_bytes: 39832
    num_examples: 148
  download_size: 20300
  dataset_size: 39832
- config_name: cell8_fulltext_nlp
  features:
  - name: record_id
    dtype: string
  - name: source
    dtype: string
  - name: cell
    dtype: string
  - name: title
    dtype: string
  - name: authors
    list: string
  - name: year
    dtype: int32
  - name: publication
    dtype: string
  - name: doi
    dtype: string
  - name: pmid
    dtype: string
  - name: pmcid
    dtype: string
  - name: arxiv_id
    dtype: string
  - name: abstract
    dtype: string
  - name: full_text
    dtype: string
  - name: sections
    list: string
  - name: keywords
    list: string
  - name: mesh_terms
    list: string
  - name: references
    list: string
  - name: citations_count
    dtype: int32
  - name: reference_count
    dtype: int32
  - name: language
    dtype: string
  - name: word_count
    dtype: int32
  - name: sentence_count
    dtype: int32
  - name: url
    dtype: string
  - name: pdf_url
    dtype: string
  - name: open_access
    dtype: bool
  - name: collection_timestamp
    dtype: string
  - name: version
    dtype: string
  splits:
  - name: validation
    num_bytes: 15997
    num_examples: 7
  - name: test
    num_bytes: 16656
    num_examples: 8
  - name: train
    num_bytes: 248579
    num_examples: 125
  download_size: 32317036
  dataset_size: 281232
- 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
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    dtype: string
  - name: sequence
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  splits:
  - name: train
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    num_examples: 425
  - name: validation
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    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_splits/train-*
  - split: validation
    path: cell5_splits/validation-*
  - split: test
    path: cell5_splits/test-*
- config_name: cell6_literature
  data_files:
  - split: train
    path: cell6_splits/train-*
  - split: validation
    path: cell6_splits/validation-*
  - split: test
    path: cell6_splits/test-*
- config_name: cell7_1_stable_omics
  data_files:
  - split: train
    path: cell7_1_splits/train-*
  - split: validation
    path: cell7_1_splits/validation-*
  - split: test
    path: cell7_1_splits/test-*
- config_name: cell7_specialized
  data_files:
  - split: train
    path: cell7_data/train-*
  - split: validation
    path: cell7_splits/validation-*
  - split: test
    path: cell7_splits/test-*
- config_name: cell7_specialized_omics
  data_files:
  - split: train
    path: cell7_splits/train-*
- config_name: cell7_ultimate
  data_files:
  - split: train
    path: cell7_data/train-*
- config_name: cell8_fulltext_nlp
  data_files:
  - split: train
    path: cell8_data/train-*
  - split: validation
    path: cell8_splits/validation-*
  - split: test
    path: cell8_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
```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