Experimental research software · Synthetic data · Not for clinical use · Not scientifically validated

Source: docs/evidence_review/anatomy_nodes_v2.md @ e3d560e · Source SHA-256 0f1520fb949f95d912938138ea25868678b8c8ee46b23f6b1341a9ccd030e47e · Markdown source

Anatomical node specification v2 (2026-11-01)

Established under the user's directive that nodes be built from the latest knowledge. This page is the current node list for the Smith 2004 semantic layer. Propagated on 2026-11-01 to the SHACL shapes, fixtures and the workspace 267 translation (shacl/, rules S7 and the v2 identifier check); the project registry uses the v2 identifiers for the nodes it refers to (blood, heart, both ventricles and ventricular cavities, the four valves) and keeps its peripheral compartments local (decisions.md, "Node specification v2 applied to the registry"). Machine-readable copy: anatomy_nodes_v2.json.

Principles and their sources

1. Identifier: Uberon first, FMA where Uberon lacks the structure, and always both. Current physiology infrastructure works this way. NIH SPARC: "our core anatomical ontology is UBERON, a pan-species anatomical ontology", supplemented with FMA and EMAPA (S23). SCKAN 2025: "UBERON … forms the “backbone” of its anatomical terminology efforts. Species-specific ontologies such as FMA … are used to supplement as necessary" (S23). HRA 2023 states the rule this specification adopts: the identifier "was based on the UBERON ID if possible. If the vessel was not in UBERON, we used an FMA ID if it existed" (S23). A 2024 OMEX-style annotation of a CellML circulation model from the Auckland group, described by its README as preliminary, writes blood in the LV cavity as UBERON:0000178 part of UBERON:0016514 (S23). Counter-evidence is recorded: OMEX metadata v1.2 (2021) recommends FMA and does not mention Uberon, and Physiome repository practice up to 2023 is FMA-based (S16, S23). Status: Uberon release 2026-10-01, active, CC BY 3.0; FMA 5.1.0 released 2026-05-15, CC BY 4.0, listed "inactive" by the OBO Foundry. Equivalence: 25 of 30 structures have a Uberon term carrying the same FMA cross-reference (docs/evidence/d_uberon_fma_map.json); Uberon's bridge file defines each FMA class as the Uberon class restricted to Homo sapiens (S23).
2. Bearer form unchanged. Blood is part of a cavity or lumen (decisions.md, C5). Heart chambers use Uberon cavity terms. Vessels use FMA lumen terms, because Uberon has no vessel-specific lumen, only "lumen of blood vessel" UBERON:0010161.
3. Compartment meaning comes from the source paper. The manuscript says the peripheral circulation is "modelled using elastic chambers, simulating the arteries and veins, and resistances, simulating blood flow through the capillaries" (S6P pp. 12-13). The "aorta", "vena cava", "pulmonary artery" and "pulmonary vein" chambers are therefore lumped arterial and venous beds named after a representative vessel, and Smith-derived models describe them as systemic and pulmonary arteries and veins (S12, S24). This is an interpretation of the paper's wording; the pressure targets still refer to aortic and pulmonary-artery pressure (S6P p. 17).
4. Which structures are nodes. (a) Every structure a variable, process or equation refers to (decisions.md, valves). (b) Structures the model lumps: the atria, as parts of the venous compartments (decisions.md, atria). (c) Catalogue nodes, with identifiers but no assertions in the Smith graph, for heart structures current adult closed-loop models do not represent. All surveyed general-purpose models since 2018 represent four chambers and four valves; none of the adult models surveyed includes the valve of the inferior vena cava or of the coronary sinus, and the foramen ovale appears only in fetal and neonatal models (S24). Recent reviews describe the Eustachian valve as becoming "irrelevant" after the foramen ovale closes and the coronary sinus valve as a vestigial remnant (S24).

Node table

primary names the ontology of the primary identifier. Classes: modelled (referred to by the model), lumped part, catalogue (identifier only), reference (organ-level term for registry and context).

What changes when v2 is propagated

• 27 of the 31 nodes take a Uberon primary identifier; the four vessel-lumen nodes keep FMA. FMA remains on every node as the cross-reference.
• The four peripheral compartments change meaning: the "aorta" compartment becomes the systemic arterial tree lumen (v1: Lumen of aorta) and the "vena cava" compartment the systemic venous tree lumen plus the right atrial cavity (v1: Set of lumens of vena cava trunks). This brings Smith's compartments closer to the project's local sa and sv concepts (R6, R8, R10).
• The workspace 267 split of P_pa (Lumen of pulmonary trunk) and V_pa (Lumen of pulmonary arterial tree) is resolved: both use the pulmonary arterial tree lumen.
• The septum node is the interventricular septum (UBERON:0002094 / FMA:7133), not "Cardiac septum".
• The minor valves, the venae cavae and the coronary sinus are catalogue nodes.

Not established

• No COMBINE document from 2022-2026 formally recommends Uberon over FMA; the identifier rule rests on SPARC, SCKAN and HRA practice (S23).
• Uberon quirks to watch: the aortic valve has no "connects" relation, the pulmonary valve connects to the generic cardiac ventricle, and the valve of foramen ovale sits under "anatomical conduit space" (S23, S24).
• The entity for the thoracic-cavity contents (source of P_th, sink of P_pcd) is still not selected.
• Principle 3 and the atrial lumping are interpretations of the paper, recorded as such.