Schema Elements Associated with NAMs
The schema elements a New Approach Methodology touches, as two trees: the fields on a ModelMechanismLink and the four places such a link can live. Written 2026-10-13.
Disease
├── name string
├── pathophysiology: [Pathophysiology]
│ ├── name ◄────────────────────────────────────────┐ string; the pathograph node
│ └── biological_scale │ BiologicalScaleEnum (optional)
│ │ MOLECULAR | CELLULAR | TISSUE | ORGANISM
│ │ compared against the link's model_scale
└── experimental_models: [ExperimentalModel] │
├── name │ string; the NAM
└── modeled_mechanisms: [ModelMechanismLink] │
├── target ───────────────────────────────────┤ string, required; = pathophysiology[].name
├── relationship │ ModelMechanismRelationshipEnum
│ │ RECAPITULATES | PARTIALLY_RECAPITULATES |
│ │ FAILS_TO_RECAPITULATE | PERTURBS | MEASURES | RESCUES
├── fidelity │ ModelFidelityEnum
│ │ HIGH | MODERATE | LOW | UNKNOWN
├── limitations │ string; the translational caveat as prose
├── model_scale │ BiologicalScaleEnum; the scale the model OBSERVES
├── divergences: [ModelDivergence] │
│ ├── divergence_type │ ModelDivergenceTypeEnum
│ │ │ BOUNDARY_OMISSION | PROXY_QUANTITY |
│ │ │ CALIBRATION_PROVENANCE | CAUSE_UNREPRESENTED |
│ │ │ STRUCTURAL_IDEALIZATION | TEMPORAL_SCOPE |
│ │ │ CONTESTED_ASSUMPTION | SCALE_EXTRAPOLATION |
│ │ │ SPECIES_MISMATCH | POPULATION_MISMATCH | OTHER
│ ├── materiality │ ModelDivergenceMaterialityEnum
│ │ │ INVALIDATING | QUALIFYING | IMMATERIAL | UNKNOWN
│ ├── description │ string, required; says why it applies HERE
│ └── evidence: [EvidenceItem] │
├── readouts: [ExperimentalReadout] │
│ ├── name │ string; the outcome measure
│ ├── target ───────────────────────────────┘ string, required; must repeat the link's target
│ ├── direction ModelReadoutDirectionEnum
│ │ INCREASED | DECREASED | UNCHANGED |
│ │ RESTORED | ABOLISHED | ALTERED
│ ├── interpretation string
│ ├── (phenotype_term | biomarker_term | optional ontology grounding of the measure
│ │ biological_processes | assays) (HP / biomarker / GO / OBI)
│ └── evidence: [EvidenceItem] layer 2: "this measurement was made"
└── evidence: [EvidenceItem] layer 1: "this model is informative for this node"
├── reference PMID / DOI / …
├── supports EvidenceItemSupportEnum
│ SUPPORT | REFUTE | NO_EVIDENCE
├── evidence_source EvidenceSourceEnum (IN_VITRO for NAMs)
├── snippet exact quote from the reference
└── explanation string
Disease
├── pathophysiology: [Pathophysiology]
│ └── name ◄──────────────────────────────────────────────┐ the pathograph node
│ │
├── experimental_models: [ExperimentalModel] NAMs │ 600 entries use it
│ ├── name │
│ ├── experimental_model_type ORGANOID | ORGAN_ON_CHIP | IPSC_DERIVED_MODEL |
│ │ CELL_LINE | PRIMARY_CELL_CULTURE | CO_CULTURE | …
│ ├── namo_type · cell_source · culture_system · cell_types · tissue_term
│ └── modeled_mechanisms: [ModelMechanismLink] ───────────┤
│ │
├── animal_models: [AnimalModel] whole organisms │ 1,206 entries use it
│ ├── name (optional; recommended once linked)
│ ├── species · genotype · background · genes · alleles │
│ ├── associated_phenotypes │
│ └── modeled_mechanisms: [ModelMechanismLink] ───────────┤
│ │
├── computational_models: [ComputationalModel] in silico │ 56 entries use it
│ ├── name │
│ ├── model_type BOOLEAN_NETWORK | KINETIC | AGENT_BASED | FLUX_BALANCE_ANALYSIS |
│ │ GENOME_SCALE_METABOLIC | PHYSIOLOGICAL | DIGITAL_TWIN | MACHINE_LEARNING |
│ │ PERTURBATION_PREDICTION | FOUNDATION_MODEL | STRUCTURAL_PREDICTION |
│ │ MOLECULAR_DOCKING | BIOMECHANICAL
│ ├── model_id · repository_url · model_format · variables · perturbations · findings
│ └── modeled_mechanisms: [ModelMechanismLink] ───────────┤
│ │
└── discussions: [Discussion] │
└── proposed_experiments: [Experiment] │
├── model_systems: [ExperimentalModel] 4th home │
│ └── modeled_mechanisms: [ModelMechanismLink] ───┤
└── controls: [ExperimentalControl] │
└── model_systems: [ExperimentalModel] │
└── modeled_mechanisms ─────────────────────┘
ModelMechanismLink is the same class in every home: target · relationship · fidelity · limitations · model_scale · divergences · readouts · evidence