plan: FMA bake v4 — the address layer, not the mesh

.claude/docs/anatomy-substrate-prior-art.md

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+# Anatomy substrate — prior art and sources
+
+> Reference companion to `claude-notes/plans/2026-09-06-fma-bake-v4-plan.md`.
+> Descriptive: what each source is, what it establishes, and which finding in
+> that plan it bears on. No verdicts here — the plan owns those.
+
+## Attribution (required, and already carried in-tree)
+
+The body geometry is **BodyParts3D**, and its licence requires attribution
+wherever the data is used. The bake tools already carry it
+(`crates/osint-bake/tools/bake_torso_mesh.py:22`,
+`bake_body_v3.py:25`); restated here so a reader of this doc does not have to
+go find it:
+
+> BodyParts3D, © The Database Center for Life Science, licensed under
+> CC Attribution-Share Alike 2.1 Japan.
+
+Data archive DOI: `10.18908/lsdba.nbdc00837-000`.
+
+---
+
+## 1. BodyParts3D — the geometry and the two relation tables
+
+**Mitsuhashi N, Fujieda K, Tamura T, Kawamoto S, Takagi T, Okubo K.**
+*BodyParts3D: 3D structure database for anatomical concepts.*
+Nucleic Acids Research 2009 Jan;37(Database issue):D782-5.
+doi:[10.1093/nar/gkn613](https://doi.org/10.1093/nar/gkn613) ·
+PMC[2686534](https://pmc.ncbi.nlm.nih.gov/articles/PMC2686534/)
+
+Project page: http://lifesciencedb.jp/bp3d/
+
+Mirror used in this session: `AdaWorldAPI/BodyParts3D` (STL conversion of the
+**3.0 / 20110915** release + a Julia interface). Our bakes read **4.0**
+(`bake_body_v3.py:139-140` → `isa_BP3D_4.0_obj_99`, `partof_BP3D_4.0_obj_99`).
+
+The tables under `assets/BodyParts3D_data/`, measured:
+
+| file | lines | schema | bears on |
+|---|---|---|---|
+| `conventional_part_of.txt` | 2,359 | `id ⇥ name ⇥ part id ⇥ part name` | **F-3** — 2,358 edges / 1,523 nodes / **536 multi-parent** / single root `FMA20394` "human body" |
+| `FMA.csv` | 104,724 | `FMAID, Preferred Label, Parent FMAID` | **F-5** — the is_a table; max FMAID 270,201 = 19 bits, which is why **F-1**'s 16-bit identity slot is a forced choice |
+| `composite_parts.txt` | 12,531 | `composite id ⇥ composite name ⇥ primitive id ⇥ primitive name` | **F-4** — 8,265 of 12,530 edges add an axis word to the composite name |
+| `parts_list_e.txt` | 1,524 | FMAID → English name | label slab |
+
+Axis-word census over `composite_parts.txt` (the laterality that is *not*
+consumed by any bake):
+
+    right 3871  left 3849  proximal 311  distal 310  lateral 287  posterior 256
+    anterior 250  superior 248  lower 239  upper 236  medial 196  inferior 192
+    dorsal 34
+
+The mirror's README also records, in upstream's own words, why it ships 3.0:
+*"The latest version 4.0, although more complete, was not chosen as it appears
+to have intersecting skin/muscle areas."* Bears on **F-7**; the plan treats a
+shared cause with our 20260629b/c re-bakes as CONJECTURE pending **P-5**.
+
+---
+
+## 2. VOXEL-MAN / InnerOrgans — the spatial/symbolic split
+
+**Pommert A, Höhne KH, Pflesser B, Richter E, Riemer M, Schiemann T,
+Schubert R, Schumacher U, Tiede U.** *Creating a high-resolution
+spatial/symbolic model of the inner organs based on the Visible Human.*
+Medical Image Analysis 5(3), 2001.
+PDF: https://www.virtual-body.org/media/pommert-medical-image-analysis-2001.pdf
+Gallery: https://www.virtual-body.org/gallery/visible-human/torso-and-internal-organs/
+Institute of Mathematics and Computer Science in Medicine (IMDM),
+University Hospital Hamburg-Eppendorf.
+
+Scale: >1000 cryosections + congruent fresh/frozen CT of the male Visible
+Human; a 573×330×1049 mm³ volume; **650 anatomical constituents, >2000
+relations**. (For calibration: BodyParts3D's part_of table is 1,523 nodes /
+2,358 edges — same order, independent lineage.)
+
+Three things it establishes, each with a direct counterpart in the plan:
+
+**(a) Views as attributes of relations — bears on F-3, D-2b.** Verbatim:
+
+> the kidneys can be seen according to structural or functional criteria:
+> • regional anatomy — the kidneys are shown as part of the **abdominal viscera**
+> • systemic anatomy — part of the **urogenital system**
+> • relation to peritoneum — part of the **primary retroperitoneal organs**
+>
+> *"Views are represented as attributes of relations."*
+
+One object under three part_of parents, the view selecting the reading. This
+is the multi-parent case the cascade currently collapses, solved in 2001 by
+naming the view rather than picking a winner. It is also, in one sentence, what
+`ClassView` does — arrived at independently.
+
+**(b) A separate `branching from` relation type — bears on F-3, and on the
+arterial-convergence episode.** Verbatim: *"our model also contains a
+'branching from' type, **modeling the arterial blood flow**."* Arterial
+branching was not forced into the part hierarchy; it got its own relation.
+
+**(c) `hidden part of` — bears on F-4.** Where a constituent is several
+segmented objects with individual labels, this relation hides the technical
+ones so it *"appears as one single entity."* Structurally the job
+`composite_parts.txt` does upstream.
+
+Also relevant to the vessel work (§6.4) — their segmentation is codebook +
+connected-component, the same two operations in the same order as
+`fill_body_soa.py`:
+
+> *"this cluster is approximated by a **parameterized ellipsoid**, which is
+> described by its center and three axis vectors."*
+> *"there are other regions present in the volume which also match this
+> colour-space description. If they are not connected to the target organ, it
+> can be **isolated easily by a 3D connected component analysis**."*
+
+And the scope line our bake inherits without stating: *"we decided to **model
+non-segmentable objects like nerves and small blood vessels artificially** on
+the basis of landmarks… their size and contrast is too small."*
+
+Sources cited inside Pommert that matter for the symbolic half: Höhne et al.
+1995 (the semantic-network knowledge base); Rosse et al. 1998 (Digital
+Anatomist symbolic knowledge base); Schiemann et al. 1997 (colour-space
+classification); Federative Committee on Anatomical Terminology 1998
+(standardised nomenclature).
+
+---
+
+## 3. Gagvani & Silver — the volumetric skeleton
+
+**Gagvani N, Silver D.** *Animating the Visible Human Dataset.*
+Dept. of Electrical and Computer Engineering & CAIP Center, Rutgers.
+
+A skeleton computed **directly from the Visible Human voxels**, imported into a
+commercial animation package for skeletal animation. Their own framing of what
+the artifact is:
+
+> *"an advanced data structure for referencing all of the voxels in a
+> volumetric model."*
+
+Bears on **§6.3's explicit volumetric trie**: an address spine over a volume,
+extracted rather than authored — the same role HHTL plays for us, from voxels
+instead of a mesh hierarchy.
+
+Pommert (§2) cites this work and states its limit, which is the argument for
+having an address at all: per-voxel transparency *"fails to display internal
+structures properly. In addition, **organ borders are not explicitly
+indicated**, thus making the removal or exclusive display of an organ
+impossible."* A skeleton that references every voxel still cannot answer
+"show me only the liver."
+
+---
+
+## 4. Visible Human Project
+
+https://www.nlm.nih.gov/research/visible/visible_human.html — NLM. The
+cryosection + CT/MRI source underlying §2 and §3.
+
+**Lineage caution.** VOXEL-MAN and Gagvani are both **voxel** models over the
+Visible Human. BodyParts3D is **surface mesh**, from DBCLS/Anatomography,
+independent. Our bake is on the mesh line. The convergence recorded in §2 is in
+the **addressing**, not the geometry; no code path linking the lineages has
+been measured, and none is claimed.