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README.md

@@ -1,1024 +1,14 @@
 ---
-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-*
+- cell8
 ---
 
-# 🧬 Kluyveromyces marxianus Quantum Dataset v10.0.0
+# Cell 8: Quantum Full-Text Mining
 
-## Overview
+## Data Access
 
-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')
+from datasets import load_dataset
+dataset = load_dataset("Milad96/Kluyveromyces-marxianus", name="cell8_data")
 ```
-
-### 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