Cab biological regime map

config/cab_external_dataset_targets.yml

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+# CAB external dataset target manifest
+#
+# Purpose:
+#   Track external phenotype/death/family-history anchors without pretending they
+#   form one unified patient-level cohort.
+#
+# Categories:
+#   variant_death_anchor      -> variant + sudden death / SCD literature context
+#   variant_family_anchor     -> variant + family-history or cascade context
+#   phenotype_death_anchor    -> ECG/Holter/clinical phenotype + death outcome, no genetics
+#   phenotype_only_anchor     -> ECG phenotype without death/genetics
+#   closed_registry_reference -> strong clinical dataset, not downloadable now
+
+svad:
+  label: "SVAD / SCD-associated Variants Annotation Database"
+  category: "variant_death_anchor"
+  priority: "must_have_if_available"
+  expected_local_names:
+    - "data/raw/svad.tsv"
+    - "data/raw/svad.csv"
+    - "data/raw/svad.xlsx"
+  notes: "Variant-level SCD/death-context anchor. Original domain may be unavailable; manual mirror/supplement search may be required."
+
+color_data_v2:
+  label: "Color Data v2 / Color Genomics family-history anchor"
+  category: "variant_family_anchor"
+  priority: "candidate_if_public_table_found"
+  expected_local_names:
+    - "data/raw/color_data_v2.tsv"
+    - "data/raw/color_data_v2.csv"
+    - "data/raw/color_data_v2.xlsx"
+  notes: "Use only if a real public variant/family-history table is found. Do not use marketing pages or aggregate-only reports as data."
+
+physionet_scd_holter:
+  label: "PhysioNet Sudden Cardiac Death Holter Database"
+  category: "phenotype_death_anchor"
+  priority: "metadata_only_optional"
+  url_base: "https://physionet.org/files/sddb/1.0.0/"
+  small_files:
+    - "RECORDS"
+    - "ANNOTATORS"
+    - "SHA256SUMS.txt"
+  expected_local_dir: "data/raw/physionet_scd_holter"
+  notes: "Use as phenotype/death environment reference. Do not download waveform records unless doing signal processing."
+
+mit_bih_arrhythmia:
+  label: "MIT-BIH Arrhythmia Database"
+  category: "phenotype_only_anchor"
+  priority: "environment_reference_optional"
+  url_base: "https://physionet.org/files/mitdb/1.0.0/"
+  small_files:
+    - "RECORDS"
+    - "ANNOTATORS"
+    - "SHA256SUMS.txt"
+  expected_local_dir: "data/raw/mit_bih_arrhythmia"
+  notes: "Phenotype-observed ECG pole. No genetics and no death outcome."
+
+music:
+  label: "MUSIC SCD heart-failure cohort"
+  category: "phenotype_death_anchor"
+  priority: "already_integrated"
+  url_base: "https://physionet.org/files/music-sudden-cardiac-death/1.0.1/"
+  small_files:
+    - "subject-info.csv"
+    - "subject-info_codes.csv"
+    - "subject-info_definitions.csv"
+  expected_local_dir: "data/raw/music"
+  notes: "Already used as phenotype-first electrical-risk anchor. Do not download 43GB ZIP."
+
+lqts_lovd:
+  label: "Historical LQTS LOVD"
+  category: "variant_phenotype_anchor"
+  priority: "only_if_live_export_found"
+  expected_local_names:
+    - "data/raw/lqts_lovd.tsv"
+    - "data/raw/lqts_lovd.csv"
+    - "data/raw/lqts_lovd.xlsx"
+  notes: "Old genomed.org endpoint is currently domain-sale page, not data. Use only if a valid export/mirror is found."
+
+uk_biobank:
+  label: "UK Biobank"
+  category: "closed_registry_reference"
+  priority: "validation_horizon_not_dependency"
+  notes: "Best single patient-level resource, but controlled access. Treat as future validation horizon, not current dependency."
+
+ncvc_lqts_registry:
+  label: "NCVC LQTS Registry"
+  category: "closed_registry_reference"
+  priority: "discussion_reference"
+  notes: "Strong LQTS phenotype/genotype registry. Controlled access through NCVC. Not a current downloadable input."
+
+canadian_arvc_registry:
+  label: "Canadian National ARVC Registry"
+  category: "closed_registry_reference"
+  priority: "discussion_reference"
+  notes: "Strong structural-electrical ARVC reference. Controlled access. Use as conceptual support, not pipeline input."

data/processed/cab_clinvar_label_mining_by_environment.csv

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+

data/processed/cab_clinvar_label_mining_by_regime.csv

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+primary_regime,n_assertions,frac_syncope,frac_sudden_death,frac_sads,frac_cardiac_arrest,frac_familial,frac_provocation,frac_structural,frac_channelopathy,frac_any_death_context,frac_any_symptom_or_context,frac_disease_model_collision,frac_unanchored_assertion_state,frac_canonical_monogenic
+disease_model_collision,963,0.0010384215991692627,0.0,0.32191069574247144,0.0010384215991692627,0.016614745586708203,0.2720664589823468,0.01142263759086189,0.8494288681204569,0.3229491173416407,0.8982346832814122,1.0,0.7829698857736241,0.0
+unanchored_assertion_state,643,0.0,0.0,0.0,0.0,0.007776049766718507,0.0,0.007776049766718507,0.7465007776049767,0.0,0.7589424572317263,0.0,1.0,0.0
+canonical_monogenic,87,0.0,0.0,0.0,0.0,0.0,0.0,0.011494252873563218,0.6666666666666666,0.0,0.6781609195402298,0.0,0.0,1.0
+ancestry_concentrated,29,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.8275862068965517,0.0,0.8275862068965517,0.0,0.0,0.9655172413793104
+penetrance_boundary,8,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,0.0,1.0
+unknown_or_insufficient,1,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0

data/processed/cab_clinvar_label_mining_summary.csv

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+flag,n_assertions,percent
+label_any_symptom_or_context_flag,1445,83.47775852108607
+label_channelopathy_flag,1389,80.24263431542461
+label_any_death_context_flag,311,17.966493356441365
+label_sads_flag,310,17.908723281340265
+label_provocation_flag,262,15.135759676487579
+label_familial_flag,21,1.2131715771230502
+label_structural_flag,17,0.9820912767186597
+label_syncope_flag,1,0.057770075101097634
+label_cardiac_arrest_flag,1,0.057770075101097634
+label_sudden_death_flag,0,0.0

data/processed/cab_single_model_stress_by_clinical_environment.csv

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+clinical_disease_group,n_assertions,repair_required_fraction,median_evidence_collision_index,mean_evidence_collision_index,fraction_multi_regime_required,death_context_label_fraction,provocation_label_fraction
+Brugada,181,1.0,4.0,4.204419889502763,0.425414364640884,0.0,0.0
+CPVT,258,1.0,5.0,5.228682170542636,0.7596899224806202,0.003875968992248062,1.0
+LQTS,883,0.8720271800679502,1.0,1.189127972819932,0.0,0.0,0.0
+SADS,310,1.0,6.0,5.819354838709677,0.9709677419354839,1.0,0.0
+SQTS,23,1.0,3.0,2.8260869565217392,0.0,0.0,0.0
+arrhythmia,50,0.92,2.0,1.7,0.0,0.0,0.0
+cardiomyopathy_overlap,17,1.0,4.0,4.176470588235294,0.4117647058823529,0.0,0.23529411764705882
+conduction,9,1.0,2.0,2.2222222222222223,0.0,0.0,0.0

data/processed/cab_single_model_stress_by_gene.csv

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+gene,n_assertions,repair_required_fraction,median_evidence_collision_index,mean_evidence_collision_index,dominant_primary_regime,svad_gene_context_flag_fraction,death_context_label_fraction,provocation_label_fraction
+RYR2,183,1.0,6.0,5.743169398907104,disease_model_collision,1.0,0.16393442622950818,0.8032786885245902
+SCN5A,394,1.0,6.0,5.180203045685279,disease_model_collision,1.0,0.6751269035532995,0.0
+CACNA1C,85,1.0,5.0,4.6,disease_model_collision,1.0,0.0,0.0
+CASQ2,65,1.0,4.0,4.4,disease_model_collision,0.0,0.046153846153846156,0.9538461538461539
+CALM1,15,1.0,5.0,4.4,disease_model_collision,0.0,0.2,0.6
+TRDN,51,1.0,4.0,4.392156862745098,disease_model_collision,0.0,0.13725490196078433,0.8627450980392157
+KCNJ2,29,1.0,3.0,2.8620689655172415,disease_model_collision,0.0,0.0,0.0
+ANK2,86,1.0,3.0,2.4767441860465116,disease_model_collision,0.0,0.0,0.0
+CALM3,8,1.0,2.0,2.375,disease_model_collision,0.0,0.125,0.0
+HCN4,18,1.0,2.0,2.2777777777777777,unanchored_assertion_state,0.0,0.0,0.0
+CALM2,13,1.0,2.0,2.076923076923077,disease_model_collision,0.0,0.07692307692307693,0.0
+CACNB2,1,1.0,2.0,2.0,ancestry_concentrated,1.0,0.0,0.0
+CACNA2D1,4,1.0,2.0,1.75,unanchored_assertion_state,0.0,0.0,0.0
+KCNQ1,286,0.8426573426573427,1.0,1.0454545454545454,unanchored_assertion_state,1.0,0.0,0.0
+AKAP9,1,1.0,1.0,1.0,unanchored_assertion_state,0.0,0.0,0.0
+KCNE1,14,0.6428571428571429,1.0,0.9285714285714286,unanchored_assertion_state,1.0,0.0,0.0
+KCNH2,478,0.8598326359832636,1.0,0.9225941422594143,unanchored_assertion_state,1.0,0.0,0.0

data/processed/cab_single_model_stress_by_regime.csv

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+primary_regime,n_assertions,repair_required_fraction,median_evidence_collision_index,mean_evidence_collision_index,fraction_single_model_compatible,fraction_moderate_tension,fraction_high_tension,fraction_multi_regime_required
+ancestry_concentrated,29,0.13793103448275862,1.0,1.1379310344827587,0.0,1.0,0.0,0.0
+canonical_monogenic,87,0.022988505747126436,0.0,0.022988505747126436,0.9770114942528736,0.022988505747126436,0.0,0.0
+disease_model_collision,963,1.0,5.0,4.670820353063344,0.0,0.09449636552440291,0.30218068535825543,0.6033229491173416
+penetrance_boundary,8,0.125,1.0,1.125,0.0,1.0,0.0,0.0
+unanchored_assertion_state,643,1.0,1.0,1.0295489891135303,0.0,0.995334370139969,0.004665629860031105,0.0
+unknown_or_insufficient,1,1.0,1.0,1.0,0.0,1.0,0.0,0.0

data/processed/cab_single_model_stress_summary.csv

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+total_assertions,repair_required_n,repair_required_percent,single_model_compatible_n,single_model_compatible_percent,moderate_tension_n,moderate_tension_percent,high_tension_n,high_tension_percent,multi_regime_required_n,multi_regime_required_percent,median_evidence_collision_index,mean_evidence_collision_index
+1731,1614,93.24090121317158,85,4.910456383593298,771,44.54072790294627,294,16.984402079722702,581,33.56441363373772,3.0,3.0069324090121317