{
  "graph_id": "schicar_external_open_discovery",
  "graph_type": "dataset_compatibility_network",
  "created_date": "2026-06-21",
  "seed_network": {
    "dataset": "scHiCAR",
    "paper_doi": "10.1038/s41587-026-03013-7",
    "accessions": ["GSE305889"],
    "organism": "mouse",
    "tissue_type": ["brain frontal cortex", "skeletal muscle"]
  },
  "legend": {
    "edge_style": {
      "solid": "same dataset or same paper internal modality relationship",
      "dashed": "compatibility/reference relationship between separate datasets"
    },
    "evidence_level": {
      "EXTRACTED": "directly extracted from paper, repository, or verified metadata",
      "INFERRED": "inferred compatibility from verified metadata",
      "AMBIGUOUS": "candidate or relationship requires additional verification"
    }
  },
  "nodes": [
    {
      "id": "scHiCAR.scRNA",
      "label": "scRNA",
      "type": "seed_modality",
      "dataset": "scHiCAR",
      "modality": "transcriptome",
      "organism": "mouse",
      "tissue_type": ["brain frontal cortex", "skeletal muscle"],
      "feature_space": "gene",
      "format_hint": "matrix_mtx_barcodes_features",
      "accession": "GSE305889",
      "evidence_level": "EXTRACTED",
      "evidence_source": "GEO GSE305889 file list and scHiCAR validation report",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "scHiCAR.scATAC",
      "label": "scATAC",
      "type": "seed_modality",
      "dataset": "scHiCAR",
      "modality": "open_chromatin",
      "organism": "mouse",
      "tissue_type": ["brain frontal cortex", "skeletal muscle"],
      "feature_space": "genomic_fragment",
      "format_hint": "filtered_fragment_tsv_gz",
      "accession": "GSE305889",
      "evidence_level": "EXTRACTED",
      "evidence_source": "GEO GSE305889 file list and scHiCAR validation report",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "scHiCAR.scHi-C",
      "label": "scHi-C",
      "type": "seed_modality",
      "dataset": "scHiCAR",
      "modality": "chromatin_contact",
      "organism": "mouse",
      "tissue_type": ["brain frontal cortex", "skeletal muscle"],
      "feature_space": "genomic_contact_pair",
      "format_hint": "dedup_filtered_pairs_gz",
      "accession": "GSE305889",
      "evidence_level": "EXTRACTED",
      "evidence_source": "GEO GSE305889 file list and scHiCAR validation report",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "AllenWMB.MERFISH",
      "label": "MERFISH",
      "type": "external_modality",
      "dataset": "Allen whole mouse brain atlas",
      "modality": "spatial_transcriptome",
      "organism": "mouse",
      "tissue_type": "whole brain",
      "feature_space": "gene",
      "observation_unit": "single_cell",
      "paper_doi": "10.1038/s41586-023-06812-z",
      "pmid": "38092916",
      "evidence_level": "EXTRACTED",
      "evidence_source": "PubMed ESummary for PMID 38092916",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "BICCN_MOp.scRNA",
      "label": "BICCN scRNA",
      "type": "external_modality",
      "dataset": "BICCN mammalian primary motor cortex census",
      "modality": "transcriptome",
      "organism": "mouse",
      "tissue_type": "primary motor cortex",
      "feature_space": "gene",
      "observation_unit": "single_cell_or_single_nucleus",
      "paper_doi": "10.1038/s41586-021-03950-0",
      "pmid": "34616075",
      "evidence_level": "EXTRACTED",
      "evidence_source": "PubMed ESummary for PMID 34616075",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "BICCN_MOp.scATAC",
      "label": "BICCN scATAC",
      "type": "external_modality",
      "dataset": "BICCN mammalian primary motor cortex census",
      "modality": "open_chromatin",
      "organism": "mouse",
      "tissue_type": "primary motor cortex",
      "feature_space": "peak_or_cCRE",
      "observation_unit": "single_cell_or_single_nucleus",
      "paper_doi": "10.1038/s41586-021-03950-0",
      "pmid": "34616075",
      "evidence_level": "EXTRACTED",
      "evidence_source": "PubMed ESummary for PMID 34616075",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "Takei2025.RNAseqFISH",
      "label": "RNAseqFISH",
      "type": "external_modality",
      "dataset": "Takei2025",
      "modality": "spatial_transcriptome",
      "organism": "mouse",
      "tissue_type": "adult mouse cerebellum",
      "feature_space": "gene_or_intron",
      "observation_unit": "spatial_cell",
      "paper_doi": "10.1038/s41586-025-08838-x",
      "accession": "zenodo:7693825",
      "evidence_level": "EXTRACTED",
      "evidence_source": "Takei 2025 validation report and Zenodo 7693825",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "Takei2025.DNAseqFISH",
      "label": "DNAseqFISH+",
      "type": "external_modality",
      "dataset": "Takei2025",
      "modality": "chromatin_spatial_position",
      "organism": "mouse",
      "tissue_type": "adult mouse cerebellum",
      "feature_space": "25kb_genomic_locus",
      "observation_unit": "spatial_cell",
      "paper_doi": "10.1038/s41586-025-08838-x",
      "accession": "zenodo:7693825",
      "evidence_level": "EXTRACTED",
      "evidence_source": "Takei 2025 validation report and Zenodo 7693825",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "MuscleRegen.scRNA",
      "label": "MuscleRegen scRNA",
      "type": "candidate_modality",
      "dataset": "skeletal muscle regeneration candidates",
      "modality": "transcriptome",
      "organism": "mouse",
      "tissue_type": "skeletal muscle",
      "feature_space": "gene",
      "status": "needs_accession_check",
      "evidence_level": "AMBIGUOUS",
      "evidence_source": "PubMed search result count for mouse skeletal muscle regeneration single-cell RNA-seq",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "MuscleRegen.scATAC",
      "label": "MuscleRegen scATAC",
      "type": "candidate_modality",
      "dataset": "skeletal muscle regeneration candidates",
      "modality": "open_chromatin",
      "organism": "mouse",
      "tissue_type": "skeletal muscle",
      "feature_space": "peak_or_cCRE",
      "status": "needs_accession_check",
      "evidence_level": "AMBIGUOUS",
      "evidence_source": "Open-discovery validation candidate family",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "sc3DGenome.RNA3D",
      "label": "RNA + 3D genome",
      "type": "candidate_modality",
      "dataset": "droplet-based single-cell 3D genome plus transcriptomics",
      "modality": "transcriptome_and_3d_genome",
      "paper_doi": "10.1038/s41421-025-00770-8",
      "pmid": "39837831",
      "status": "weak_or_method_reference",
      "evidence_level": "EXTRACTED",
      "evidence_source": "PubMed ESummary for PMID 39837831",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "NeuronHiC.megadomain",
      "label": "Neuron Hi-C",
      "type": "candidate_modality",
      "dataset": "neuron-specific chromosomal megadomain organization",
      "modality": "chromatin_contact",
      "paper_doi": "10.1038/s41467-021-26862-z",
      "pmid": "34903713",
      "status": "weak_or_contact_reference",
      "evidence_level": "EXTRACTED",
      "evidence_source": "PubMed ESummary for PMID 34903713",
      "evidence_date": "2026-06-21"
    }
  ],
  "edges": [
    {
      "id": "edge_schicar_rna_atac",
      "source": "scHiCAR.scRNA",
      "target": "scHiCAR.scATAC",
      "type": "same_cell",
      "style": "solid",
      "display_label": "paired frontal cortex or skeletal muscle cells",
      "integration_strength": "seed_internal",
      "evidence_level": "EXTRACTED",
      "evidence_source": "scHiCAR validation report",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "edge_schicar_rna_hic",
      "source": "scHiCAR.scRNA",
      "target": "scHiCAR.scHi-C",
      "type": "same_cell",
      "style": "solid",
      "display_label": "paired frontal cortex or skeletal muscle cells",
      "integration_strength": "seed_internal",
      "evidence_level": "EXTRACTED",
      "evidence_source": "scHiCAR validation report",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "edge_schicar_atac_hic",
      "source": "scHiCAR.scATAC",
      "target": "scHiCAR.scHi-C",
      "type": "same_cell",
      "style": "solid",
      "display_label": "paired frontal cortex or skeletal muscle cells",
      "integration_strength": "seed_internal",
      "evidence_level": "EXTRACTED",
      "evidence_source": "scHiCAR validation report",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "edge_schicar_rna_allen_merfish",
      "source": "scHiCAR.scRNA",
      "target": "AllenWMB.MERFISH",
      "type": "spatial_anchor",
      "style": "dashed",
      "display_label": "spatial anchor / shared mouse brain genes",
      "integration_strength": "strong",
      "compatibility_basis": ["organism", "tissue_type", "feature_space", "task"],
      "evidence": "same organism and brain context; gene-level spatial transcriptome can anchor scHiCAR RNA-derived states",
      "enabled_question": "Map scHiCAR-derived regulatory programs onto whole-brain spatial regions.",
      "evidence_level": "INFERRED",
      "evidence_source": "PubMed ESummary plus compatibility rule",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "edge_schicar_rna_biccn_rna",
      "source": "scHiCAR.scRNA",
      "target": "BICCN_MOp.scRNA",
      "type": "label_transfer",
      "style": "dashed",
      "display_label": "label transfer / cortical taxonomy",
      "integration_strength": "strong",
      "compatibility_basis": ["organism", "tissue_type", "feature_space", "task"],
      "evidence": "same organism and cortical brain context; gene feature space supports label transfer",
      "enabled_question": "Compare scHiCAR frontal cortex cells with BICCN cortical cell taxonomy.",
      "evidence_level": "INFERRED",
      "evidence_source": "PubMed ESummary plus compatibility rule",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "edge_schicar_atac_biccn_atac",
      "source": "scHiCAR.scATAC",
      "target": "BICCN_MOp.scATAC",
      "type": "regulatory_reference",
      "style": "dashed",
      "display_label": "regulatory reference / cortical accessibility",
      "integration_strength": "strong",
      "compatibility_basis": ["organism", "tissue_type", "feature_space", "task"],
      "evidence": "same organism and cortical brain context; accessibility feature space can support regulatory comparison after genome-build and peak-space harmonization",
      "enabled_question": "Compare scHiCAR accessible regions with cortical regulatory programs.",
      "evidence_level": "INFERRED",
      "evidence_source": "PubMed ESummary plus compatibility rule",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "edge_schicar_rna_takei_rna",
      "source": "scHiCAR.scRNA",
      "target": "Takei2025.RNAseqFISH",
      "type": "spatial_anchor",
      "style": "dashed",
      "display_label": "spatial anchor / adult mouse cerebellum genes",
      "integration_strength": "medium",
      "compatibility_basis": ["organism", "brain_context", "feature_space", "task"],
      "evidence": "same organism and brain, but cerebellum differs from frontal cortex; gene feature space can support cross-region comparison",
      "enabled_question": "Test whether scHiCAR brain states have spatial-transcriptomic analogs in cerebellum.",
      "evidence_level": "INFERRED",
      "evidence_source": "Takei 2025 validation plus compatibility rule",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "edge_schicar_hic_takei_dna",
      "source": "scHiCAR.scHi-C",
      "target": "Takei2025.DNAseqFISH",
      "type": "contact_reference",
      "style": "dashed",
      "display_label": "contact reference / spatial 3D genome",
      "integration_strength": "medium",
      "compatibility_basis": ["organism", "genomic_locus", "3d_genome_task"],
      "evidence": "both represent 3D genome information, but scHiCAR stores contact pairs whereas DNAseqFISH measures spatial locus positions",
      "enabled_question": "Compare contact-derived and imaging-derived 3D genome organization across mouse brain contexts.",
      "evidence_level": "INFERRED",
      "evidence_source": "Takei 2025 validation plus compatibility rule",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "edge_schicar_rna_muscle_rna",
      "source": "scHiCAR.scRNA",
      "target": "MuscleRegen.scRNA",
      "type": "label_transfer",
      "style": "dashed",
      "display_label": "candidate / skeletal muscle regeneration",
      "integration_strength": "candidate",
      "evidence_level": "AMBIGUOUS",
      "evidence_source": "Open PubMed candidate search; accession not yet verified",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "edge_schicar_atac_muscle_atac",
      "source": "scHiCAR.scATAC",
      "target": "MuscleRegen.scATAC",
      "type": "regulatory_reference",
      "style": "dashed",
      "display_label": "candidate / skeletal muscle regeneration",
      "integration_strength": "candidate",
      "evidence_level": "AMBIGUOUS",
      "evidence_source": "Open-discovery candidate family; accession not yet verified",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "edge_schicar_hic_sc3d",
      "source": "scHiCAR.scHi-C",
      "target": "sc3DGenome.RNA3D",
      "type": "method_reference",
      "style": "dashed",
      "display_label": "method reference / single-cell 3D genome",
      "integration_strength": "weak",
      "evidence_level": "AMBIGUOUS",
      "evidence_source": "PubMed title indicates modality fit; tissue context not verified",
      "evidence_date": "2026-06-21"
    },
    {
      "id": "edge_schicar_hic_neuron_hic",
      "source": "scHiCAR.scHi-C",
      "target": "NeuronHiC.megadomain",
      "type": "contact_reference",
      "style": "dashed",
      "display_label": "contact reference / neuron chromatin domains",
      "integration_strength": "weak",
      "evidence_level": "AMBIGUOUS",
      "evidence_source": "PubMed title indicates contact reference; observation level and resolution require verification",
      "evidence_date": "2026-06-21"
    }
  ],
  "excluded_candidates": [
    {
      "dataset": "scHiCAR",
      "ids": ["doi:10.1038/s41587-026-03013-7", "GSE305889"],
      "status": "exclude",
      "reason": "seed dataset; do not add as an external node",
      "evidence_level": "EXTRACTED",
      "evidence_source": "seed network metadata",
      "evidence_date": "2026-06-21"
    }
  ],
  "uncertainties": [
    "This graph is a prototype extracted from validation outputs, not a completed systematic review.",
    "Skeletal muscle regeneration candidates need accession, format, genome build and assay verification.",
    "Some dashed compatibility edges are task hypotheses and should be treated as INFERRED, not direct evidence of shared cells or samples."
  ]
}