| --- |
| 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: 163976 |
| num_examples: 333 |
| - name: validation |
| num_bytes: 18452 |
| num_examples: 42 |
| - name: test |
| num_bytes: 20554 |
| num_examples: 42 |
| download_size: 133479 |
| dataset_size: 202982 |
| - 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_splits/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 |
| ```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 |
| |
