1. Particle–Subparticle Organizational Schema
A) Fundamental Level (Ontology Class: Particle)
| Ontology Node | Description | Subclass Of | Connected To |
|---|---|---|---|
| Quark | Elementary fermions with fractional electric charge; come in six flavors (up, down, charm, strange, top, bottom). | Particle | Combine to form hadrons (protons, neutrons) |
| Lepton | Elementary fermions not subject to strong interaction; includes electron, muon, tau, neutrinos. | Particle | Electrons orbit nuclei; neutrinos interact weakly |
| Gauge Boson | Force carriers (photon, gluon, W/Z bosons, gluons). | Particle | Mediate fundamental forces |
| Scalar Boson | Higgs boson; gives mass via Higgs field. | Particle | Coupled to fermions/bosons |
B) Composite Level (Ontology Class: Composite Particle)
| Ontology Node | Description | Built From | Connected To |
|---|---|---|---|
| Proton | Baryon of two up quarks + one down quark. | Quarks, gluons | Atomic nucleus (taxonomy anchor for elements) |
| Neutron | Baryon of one up quark + two down quarks. | Quarks, gluons | Atomic nucleus |
| Meson | Quark–antiquark pairs. | Quarks, antiquarks | Short-lived intermediaries in nuclear force |
C) Atomic Level (Ontology Class: Atom)
| Ontology Node | Description | Connected To |
|---|---|---|
| Nucleus | Protons + neutrons bound by strong force. | Defines isotope identity (taxonomy in chemistry) |
| Electron cloud | Electrons in quantized orbitals. | Determines chemical behavior |
| Isotope | Atoms with same protons, different neutrons. | Chemistry → molecular biology |
D) Molecular Level
| Ontology Node | Description | Connected To |
|---|---|---|
| Molecule | Stable chemical compound of atoms. | Basis for biochemical taxonomy |
| Macromolecule | Large polymers (proteins, nucleic acids, polysaccharides, lipids). | DNA, RNA, proteins — anchors for ICNP/ICNafp/ICZN |
| Supramolecular assembly | Virus capsids, ribosomes, cell membranes. | Links to ICTV (viruses), ICPN (ecosystems) |
E) Biological Structures
- Cellular Level (Ontology:
Cell):- Prokaryotic cell — anchor for ICNP taxa
- Eukaryotic cell — anchor for ICNafp/ICZN
- Tissue / Organ / Organism (Taxonomy nodes in ICNafp, ICZN, etc.)
- Population → Species → Higher Taxa (Already in UCLS Taxonomy)
2. How They Connect to UCLS Ontology
- Particle classes →
Ontology:PhysicalSubstratebranch of UCLS - Atomic & molecular nodes → connect as foundational anchors for chemical taxonomy
- Macromolecules:
- DNA/RNA: primary anchors for ICTV (sequence) and often ICNP (genomic reference)
- Proteins: functional anchors for phenotypic definitions in many taxa
- Cell structures → map directly to Domain Anchoring Layer (e.g., type strain in ICNP anchored by a cell culture)
- Higher biological levels → already structured in the taxonomy matrix
3. Linking to Taxonomy
Here’s the vertical integration from particle physics → biological taxonomy in UCLS:
Quark/Lepton → Proton/Neutron/Electron → Atom (Element, Isotope)
→ Molecule (Organic/Inorganic) → Macromolecule (DNA, Protein)
→ Organelle → Cell (Prokaryote/Eukaryote)
→ Tissue → Organ → Organism → Population → Taxon (ICNafp/ICZN/ICNP/ICTV/etc.)
Anchor Connection:
- At particle/atomic level: supports isotopic/geochemical data used in taxonomy (e.g., isotopic fingerprinting in species delimitation).
- At molecular level: DNA sequences as direct anchors for ICTV and modern species definitions (DNA barcoding).
- At cell/organism level: Type specimens, type strains, reference sequences.
4. WordPress Directory Matrix Layout (Particles → Taxa)
Example entry:
## Proton — Composite Particle
**Ontology Class:** CompositeParticle
**Built From:** 2 up quarks + 1 down quark
**Connected To:** Atomic nucleus → Element taxonomy → Chemistry anchor for biological molecules
**UCLS Role:** Foundational substrate; indirectly anchors all matter-based taxonomy.
UCLS Taxonomy Directory Matrix – SolveForce Communications