NAMO Rare-Disease Experimental Models

Goal

Bridge dismech's disease-centric curation model to Monarch NAMO without importing the full NAMO schema into dismech.

The immediate target is a small set of disease-level experimental_models entries that are: - first-class inside dismech disorder files - explicitly mapped to NAMO classes with namo_type - focused on high-signal rare-disease examples

Initial Scope

• Cystic Fibrosis
• Stargardt Disease
• Noonan Syndrome
• Crohn Disease as an IBD-adjacent host-microbiome/barrier test case

Current Bridge Pattern

Use a narrow disease-level experimental_models slot in dismech rather than a full study-centric import of NAMO.

Each model should capture: - experimental_model_type for local coarse typing - namo_type for crosswalk to NAMO classes - cell_source and culture_system for translational interpretation - disease-relevant findings and evidence

NAMO Classes In Scope

• namo:Organoid
• namo:OrganOnChip
• namo:CellLineModel
• namo:TwoDCellCulture

These class CURIEs were verified against the current NAMO schema snapshot used for this bridge spike.

These cover the current bridge cases better than a direct wholesale import because dismech remains disease-centric while NAMO is model-centric.

Disease Anchors

Cystic Fibrosis

• Patient-derived airway organoid theratyping
• CF airway-on-chip microphysiological model
• NuLi/CuFi airway epithelial cell-line model

Stargardt Disease

• Patient-derived retinal organoid model
• STGD1 iPSC-derived RPE disease-in-a-dish model

Noonan Syndrome

• Noonan cortical organoid model
• Noonan iPSC-cardiomyocyte model

Crohn Disease / IBD Bridge

• Primary human small-intestinal monolayer barrier model from UNC

Ulcerative Colitis

• Biopsy-derived UC colonoid air-liquid interface model
• Cytokine-conditioned hiPSC-derived colon organoid UC model
• Human colon-on-chip mucus barrier model

Aadra Bhatt / UNC Note

The user's requested UNC lead appears to be Aadra P. Bhatt.

Current curation stance: - UNC public profile language points to primary human cells plus representative human intestinal bacteria as a lab direction. - The strongest immediately curatable Bhatt anchor is PMID:29094594, a primary human small-intestinal monolayer platform paper. - That paper is not Crohn_Disease-specific, so it is curated as SUPPORT whose explanation records the indirect bridge ("remaining an indirect bridge rather than direct disease evidence"), not as direct Crohn Disease evidence. It predates the retirement of PARTIAL from EvidenceItem.supports (issue #7439) and does not yet set an explicit directness: INDIRECT.

This is the right level of confidence for now. Stronger Crohn_Disease-specific curation should wait for a directly attributable host-microbe coculture, organoid, or microbiome paper tied to Crohn Disease or broader IBD.

Next Expansion Targets

• Add Cystic Fibrosis intestinal organoid-monolayer as a separate bridge case if we want explicit coverage of organoid-derived 2D systems.
• Consider a follow-on schema refinement for functional_assays and concordance if we decide to track more of NAMO's richer comparison model.