Default mechanism family taxonomy

[
  {
    "domain": "neurodegeneration",
    "description": "Protein misfolding and aggregation (amyloid, tau, alpha-synuclein, TDP-43).",
    "family_label": "proteinopathy",
    "tag_patterns": [
      "protein_misfolding",
      "amyloid",
      "tauopathy",
      "alpha_synuclein",
      "TDP-43",
      "aggregation"
    ],
    "kg_predicates": [
      "invokes_mechanism"
    ]
  },
  {
    "domain": "neurodegeneration",
    "description": "Impaired mitochondrial function, oxidative phosphorylation, or mitophagy.",
    "family_label": "mitochondrial_dysfunction",
    "tag_patterns": [
      "mitochondria",
      "oxidative_stress",
      "mitophagy",
      "ROS",
      "OXPHOS"
    ],
    "kg_predicates": [
      "invokes_mechanism"
    ]
  },
  {
    "domain": "neurodegeneration",
    "description": "Microglial activation, astrocyte reactivity, cytokine signaling.",
    "family_label": "neuroinflammation",
    "tag_patterns": [
      "microglia",
      "neuroinflammation",
      "cytokine",
      "astrocyte",
      "inflammation"
    ],
    "kg_predicates": [
      "invokes_mechanism"
    ]
  },
  {
    "domain": "neurodegeneration",
    "description": "Blood-brain barrier breakdown, cerebral hypoperfusion, vascular pathology.",
    "family_label": "vascular",
    "tag_patterns": [
      "vascular",
      "BBB",
      "blood_brain_barrier",
      "hypoperfusion",
      "hemorrhage"
    ],
    "kg_predicates": [
      "invokes_mechanism"
    ]
  },
  {
    "domain": "neurodegeneration",
    "description": "Synaptic loss, neurotransmitter dysfunction, synaptic plasticity impairment.",
    "family_label": "synaptic",
    "tag_patterns": [
      "synaptic",
      "synapse",
      "neurotransmitter",
      "glutamate",
      "GABA",
      "dopaminergic"
    ],
    "kg_predicates": [
      "invokes_mechanism"
    ]
  },
  {
    "domain": "neurodegeneration",
    "description": "DNA methylation, histone modification, chromatin remodeling in neurodegeneration.",
    "family_label": "epigenetic",
    "tag_patterns": [
      "epigenetic",
      "methylation",
      "histone",
      "chromatin",
      "non_coding_RNA"
    ],
    "kg_predicates": [
      "invokes_mechanism"
    ]
  },
  {
    "domain": "neurodegeneration",
    "description": "Monogenic or polygenic risk variants driving neurodegenerative disease.",
    "family_label": "genetic",
    "tag_patterns": [
      "genetic",
      "mutation",
      "variant",
      "GWAS",
      "familial",
      "SNP"
    ],
    "kg_predicates": [
      "invokes_mechanism"
    ]
  },
  {
    "domain": "neurodegeneration",
    "description": "Metabolic pathway disruption (glucose metabolism, lipid metabolism, iron homeostasis).",
    "family_label": "metabolic",
    "tag_patterns": [
      "metabolic",
      "glucose",
      "lipid",
      "iron",
      "homeostasis",
      "insulin"
    ],
    "kg_predicates": [
      "invokes_mechanism"
    ]
  },
  {
    "domain": "neurodegeneration",
    "description": "Adaptive and innate immune responses in neurodegeneration (distinct from neuroinflammation).",
    "family_label": "immune",
    "tag_patterns": [
      "immune",
      "T_cell",
      "B_cell",
      "autoimmune",
      "complement",
      "antibody"
    ],
    "kg_predicates": [
      "invokes_mechanism"
    ]
  },
  {
    "domain": "neurodegeneration",
    "description": "Impaired autophagic clearance, lysosomal dysfunction, proteostasis failure.",
    "family_label": "autophagy",
    "tag_patterns": [
      "autophagy",
      "lysosomal",
      "proteostasis",
      "clearance",
      "ubiquitin"
    ],
    "kg_predicates": [
      "invokes_mechanism"
    ]
  }
]