# Data and asset attribution This application ships three kinds of content with three different provenances. They are kept separate here, in the interface, and in the data model (every rendered piece carries a `provenance` of `source`, `adapted` or `schematic`). --- ## 1. Male anatomy — BodyParts3D (source-derived) BodyParts3D, © The Database Center for Life Science, licensed under CC Attribution 4.0 International. - License: https://dbarchive.biosciencedbc.jp/en/bodyparts3d/lic.html (updated 2025-02-27) - Dataset: https://dbarchive.biosciencedbc.jp/en/bodyparts3d/download.html - License terms: https://creativecommons.org/licenses/by/4.0/ - Source geometry: `isa_BP3D_4.0_obj_99.zip`, BodyParts3D 4.0. - English names and relationships: IS-A and PART-OF concept, element and inclusion tables from the same archive. - Publication: Mitsuhashi et al. (2009), BodyParts3D: 3D structure database for anatomical concepts. https://doi.org/10.1093/nar/gkn613 **Modifications:** axes and units converted from millimetres/Z-up to metres/Y-up; translated to rest at the stage; geometry simplified with meshoptimizer at a 0.2% relative error limit per structure; normals quantized to signed 16-bit; packed into binary chunks; curated display-system groupings and colours. The source contains 2,234 individual OBJ meshes; all remain represented. The combined hierarchy contains 3,432 named FMA concepts, which may reference multiple meshes. Original source identity is preserved in the manifest. Source OBJ comments mention an older CC BY-SA 2.1 Japan license. The official current database license linked above supersedes that legacy text and explicitly permits redistribution and adaptation under CC BY 4.0. **Scope and limitations:** BodyParts3D represents an adult male reference anatomy based on TARO MRI and anatomical illustration refinements. It is not a complete model of every possible human anatomical structure or variation. --- ## 2. Female anatomy — Human Reference Atlas / HuBMAP (source-derived) Kristen Browne and Heidi Schlehlein, Human Reference Atlas / HuBMAP, *3D Reference Organ Set for Female v1.5* (2023). Licensed CC BY 4.0. United assembly: - Source DOI: https://doi.org/10.48539/HBM352.BTSQ.586 - Dataset: https://lod.humanatlas.io/ref-organ/united-female/v1.5 - Original GLB: https://cdn.humanatlas.io/digital-objects/ref-organ/united-female/v1.5/assets/3d-vh-f-united.glb - Reference library: https://humanatlas.io/3d-reference-library - License terms: https://creativecommons.org/licenses/by/4.0/ - Conversion script in this repository: `scripts/convert-female.py` **Modifications:** translated native metre/Y-up coordinates onto the stage; coincident vertices welded and source normals averaged (HRA exports duplicate vertices at triangle boundaries); geometry simplified with a 0.2% per-structure relative error bound; normals quantized. Colours and display systems are curated for this interface. All 888 source meshes of the united assembly are represented, with 1,073 source nodes available as selectable individual or compound concepts. Ontology identifiers (UBERON, FMA) from the source are preserved as the atlas reference shown in the inspector. ### Additional reference organs merged into the assembly The `united-female` assembly omits organs that the Human Reference Atlas publishes as separate digital objects. Seven of those are acquired and merged by `scripts/fetch-female-organs.mjs`, adding 76 further meshes. Each is CC BY 4.0 and pinned by version: | Digital object | Version | Asset | | --- | --- | --- | | `ref-organ/mouth-female` | v1.0 | `3d-vh-f-mouth.glb` | | `ref-organ/sternum-female` | v1.0 | `3d-vh-f-sternum.glb` | | `ref-organ/manubrium-female` | v1.0 | `3d-vh-f-manubrium.glb` | | `ref-organ/intervertebral-disk-female` | v1.0 | `3d-vh-f-intervertebral-disk.glb` | | `ref-organ/omentum-female` | v1.0 | `3d-vh-f-omentum.glb` | | `ref-organ/epiploic-appendage-of-transverse-colon-female` | v1.0 | `3d-vh-f-epiploic-appendage-of-transverse-colon.glb` | | `ref-organ/adipose-female` | v1.0 | `3d-vh-f-adipose.glb` | All are served from `https://cdn.humanatlas.io/digital-objects///assets/`. `ref-organ/small-intestine-female` v1.2 is also downloaded but contributes no mesh: it is parsed only to verify registration, because every mesh it holds is already in the united assembly. **Registration verification.** The per-organ exports and the united assembly both contain the mesh `VH_F_sphincter_of_heptopancreatic_ampulla`. After applying the same stage shift (0.794760942 m on Y, identical to `scripts/convert-female.py`), its bounding box agrees between the two sources to zero drift at six decimal places. The merge script performs this check on every run and refuses to write anything if it fails, so no organ is ever placed by guesswork. **Modifications to the merged organs:** glTF node transforms resolved through the full scene graph; the same stage shift applied; coincident vertices welded with averaged normals; simplified with meshoptimizer under the same 0.2% per-structure relative error bound as the rest of the atlas; normals quantized to signed 16-bit; packed into `female-extra-*.bin` chunks and gzipped. **Scope and limitations:** this is a reference assembly with a whole-body surface and selected organs, including a detailed female reproductive tract and mammary anatomy. Even with the merged organs, its skeleton coverage (93 meshes) and muscle coverage (16 meshes) are partial. It is not a complete model of every human structure and is not a single-person scan. Eight placenta and umbilical structures are classified under **Pregnancy reference** and hidden by default. **The collection contains no stomach**, in the united assembly or as a separate reference organ. Female mode therefore has none and no substitute was created. The collection also contains **no urethra, pelvic floor or external genitalia**. Those are supplied separately as authored schematics; see section 3. **Curated groupings (original, MIT).** The source names every piece at its finest level, so an organ such as the small intestine had no searchable name even though all of its parts were present. `app/female-groups.ts` adds about thirty grouping concepts over meshes that already exist, plus display-name corrections for typos carried in the source node names (`ginviva_of_upper_jaw`, `jejenum`, `fibria_of_uterine_tube`). No geometry and no anatomy is added by them. --- ## 3. Authored schematic and teaching geometry (original, MIT) Original geometry authored for this viewer. **None of it is scanned or derived from a third-party mesh, and none of it has been reviewed by an anatomist or a botanist.** It is released under the MIT License with the rest of the application code. Every piece is marked `provenance: 'schematic'` in the data and is labelled in the inspector as authored teaching geometry. ### 3a. Female pelvic supplement (`app/female-supplement.ts`) Eleven structures absent from the HRA source set: female urethra, external urethral orifice, levator ani, perineal body, left and right labium majus, left and right labium minus, clitoris and vaginal vestibule. They sit in their own **Schematic supplement** layer. **Placement method:** coordinates are computed at load time from the measured bounding boxes of the surrounding source meshes in the same dataset — the bladder neck (`VH_F_urinary_bladder_neck_smooth_muscle`), the vagina (`VH_F_vagina`) and the coccyx — rather than positioned by eye. The resulting urethral length is about 3.7 cm, consistent with the published adult female range. The shapes themselves are drawn, not measured. **Written from:** - OpenStax *Anatomy and Physiology 2e*, 27.2 Anatomy and Physiology of the Female Reproductive System (CC BY 4.0): https://openstax.org/books/anatomy-and-physiology-2e/pages/27-2-anatomy-and-physiology-of-the-female-reproductive-system - *Gray's Anatomy of the Human Body* (public domain): https://www.bartleby.com/lit-hub/anatomy-of-the-human-body/ **Limitations:** the levator ani is drawn as a single smooth sheet; in reality it is several named muscles with distinct attachments. Exact shapes are illustrative and should not be used for measurement or planning. ### 3b. Botany topics (`app/botany/`) 207 structures across seven topics, generated procedurally in the browser. Each topic declares on screen the plant type it represents and the scale at which it is drawn, and each structure carries its own description and references. **Written from OpenStax *Biology 2e* (CC BY 4.0):** - Ch. 30, Plant Form and Physiology: https://openstax.org/books/biology-2e/pages/30-introduction - 30.2 Stems: https://openstax.org/books/biology-2e/pages/30-2-stems - 30.3 Roots: https://openstax.org/books/biology-2e/pages/30-3-roots - 30.4 Leaves: https://openstax.org/books/biology-2e/pages/30-4-leaves - 30.5 Transport of Water and Solutes in Plants: https://openstax.org/books/biology-2e/pages/30-5-transport-of-water-and-solutes-in-plants - Ch. 32, Plant Reproduction: https://openstax.org/books/biology-2e/pages/32-introduction - 32.1 Reproductive Development and Structure: https://openstax.org/books/biology-2e/pages/32-1-reproductive-development-and-structure - 32.2 Pollination and Fertilization: https://openstax.org/books/biology-2e/pages/32-2-pollination-and-fertilization - 4.3 Eukaryotic Cells: https://openstax.org/books/biology-2e/pages/4-3-eukaryotic-cells - Ch. 8, Photosynthesis: https://openstax.org/books/biology-2e/pages/8-introduction Explanations are written originally for this project from those chapters; no text is copied. Ontology-style identifiers shown as the atlas reference (`PO:`, `GO:`, `CHEBI:`) point at the Plant Ontology, Gene Ontology and ChEBI terms that name each structure; they are labels, not imported data. **Stated model types.** Whole plant: a generalized flowering eudicot, not a named species. Flower: a complete perfect generalized eudicot flower with a Polygonum-type embryo sac. Leaf: a simple dorsiventral eudicot foliage leaf. Root: a young eudicot root, tetrarch. Stem: a young eudicot and a monocot section, kept as two separate models and never combined. Seed: *Phaseolus vulgaris* and *Zea mays* as separate models; the germination sequence is the bean's epigeal pattern and does not apply to maize. Cell: a mature photosynthetic mesophyll cell, one representative plant cell type. **Limitations:** teaching animations are aids to understanding direction and sequence, not quantitative simulations. Particle-style markers in the water transport animation represent a continuous column under tension and are explicitly labelled as schematic. Timescales are compressed and each animation states by how much. ### 3c. Human teaching animations (`app/human-animations.ts`) Cardiac cycle, thoracic-pump breathing, lung expansion and the ovulation-to-implantation route. These animate meshes that already exist in the loaded dataset; they add no geometry. They are schematic teaching aids, not physiological simulations: chamber and lung volume changes are drawn as uniform scaling of whole meshes, breathing movement is exaggerated to be visible, valve motion is not modelled, and no timing is quantitative. The oocyte animation models no oocyte, follicle or embryo, because the dataset contains none; it moves a marker between the measured centres of real meshes. Each animation states its own simplifications on screen. Written from OpenStax *Anatomy and Physiology 2e* (CC BY 4.0): 19.3 Cardiac Cycle, 22.3 The Process of Breathing, 28.2 Embryonic Development. **Data correction.** Five meshes in the published BodyParts3D male atlas are filed under the Heart display system but are cerebral ventricles: FMA78454 (third ventricle), FMA78469 (fourth ventricle), FMA78450 and FMA78449 (lateral ventricles) and FMA75351 (interventricular foramen). They are moved to the nervous system when the atlas loads. The published data file is not modified; the correction lives in code so that it stays visible and reviewable. ### 3d. Classification data (`app/taxonomy.ts`) Lineages for *Homo sapiens* and for each botany topic, compiled from ITIS, NCBI Taxonomy and the APG IV classification (Angiosperm Phylogeny Group, 2016, https://doi.org/10.1111/boj.12385) and Plants of the World Online. Ranks above family for flowering plants are labelled "clade", which is what APG IV uses, rather than being presented as formal divisions or classes. ### 3e. Translations (`app/i18n.ts`) Interface strings in fourteen languages: English, Tamil, Hindi, Bengali, Telugu, Marathi, Gujarati, Kannada, Malayalam, Punjabi, Odia, Urdu, Assamese and Sanskrit. Tamil and Hindi additionally translate layer names, organ names, botanical structure names and taxonomic ranks; Tamil is the most complete. **No translation has been reviewed by a subject-matter translator.** This is stated in the language picker and in the About sheet. Untranslated names fall back to English and the interface says so rather than implying coverage that does not exist. Scientific names, ontology identifiers and source citations are never translated. --- ## Build attribution This build is extended by **Kalviyogi** under the **369 Tesla** name, from the open-source Human Atlas by Ashe Magalhaes (https://github.com/ashemag/human-atlas), with thanks to that source project. The build branding is a name only: it carries no scientific claim, asserts no endorsement by any dataset provider, and forms no part of the CC BY 4.0 attributions above, which must be preserved on their own terms. --- ## Educational use notice This application is an educational reference. It is not a diagnostic, surgical, clinical or plant identification tool. It makes no claim of patient-specific or specimen-specific accuracy, and no content in it has been validated by a domain expert for teaching or clinical use. ## Redistribution The MIT license on the application code does **not** cover the BodyParts3D or Human Reference Atlas geometry. Those datasets remain CC BY 4.0 and must keep their attribution when redistributed. Do not relabel them as MIT.