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Kluyveromyces-marxianus

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metadata 
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
        dtype: string
      - name: arxiv_id
        dtype: string
      - name: title
        dtype: string
      - name: abstract
        dtype: string
      - 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
        dtype: int32
      - name: first_author
        dtype: string
      - name: last_author
        dtype: string
      - name: affiliations
        dtype: string
      - name: journal
        dtype: string
      - name: year
        dtype: int32
      - name: volume
        dtype: string
      - name: issue
        dtype: string
      - name: pages
        dtype: string
      - 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
      - name: table_count
        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
        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
        dtype: string
      - 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
        dtype: string
      - name: publication_date
        dtype: string
      - 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
        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
        dtype: string
      - 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
        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
    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
        dtype: string
      - 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
        dtype: string
      - name: publication_date
        dtype: string
      - 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: 8816
        num_examples: 9
    download_size: 28761
    dataset_size: 8816
  - config_name: cell7_ultimate
    features:
      - name: id
        dtype: string
      - name: source
        dtype: string
      - name: category
        dtype: string
      - name: accession
        dtype: string
      - 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
        dtype: string
      - name: title
        dtype: string
      - name: description
        dtype: string
      - name: biotype
        dtype: string
      - name: status
        dtype: string
      - name: chromosome
        dtype: string
      - name: start
        dtype: int64
      - name: end
        dtype: int64
      - name: strand
        dtype: int32
      - name: sequence
        dtype: string
      - name: platform
        dtype: string
      - name: library_strategy
        dtype: string
      - name: platform_type
        dtype: string
      - name: normalization_method
        dtype: string
      - name: expression_unit
        dtype: string
      - name: log_transformed
        dtype: bool
      - name: instrument
        dtype: string
      - name: ptm_count
        dtype: int32
      - name: peptide_count
        dtype: int32
      - name: protein_count
        dtype: int32
      - name: orthology_type
        dtype: string
      - name: target_species
        dtype: string
      - name: target_gene_id
        dtype: string
      - name: percent_identity
        dtype: float32
      - name: organism
        dtype: string
      - name: tax_id
        dtype: int32
      - name: sample_count
        dtype: int32
      - name: total_spots
        dtype: int64
      - name: total_bases
        dtype: int64
      - name: timestamp
        dtype: string
      - name: version
        dtype: int32
    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
        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: 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 

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