This document merges the physical substrate-to-biology pathway (Particles → Taxa) with the nomenclature code taxonomy matrix. It flows from quarks through atoms, molecules, organisms, species, and the full taxonomic hierarchy, then details each nomenclature code’s taxonomy crosswalk.
Part I — Particle-to-Taxon Hierarchy
Particle-to-Taxon Directory Matrix
This directory maps physical and biological structure levels from fundamental particles up to species, showing how each connects to the UCLS ontology and taxonomy.
Quark — Particle
Built From: Elementary fermion
Connected To: Combines to form hadrons (protons, neutrons)
UCLS Role: Fundamental substrate; part of all baryonic matter anchoring biological systems
Lepton — Particle
Built From: Elementary fermion
Connected To: Electrons orbit nuclei; neutrinos interact weakly
UCLS Role: Electrons determine chemical bonding → molecule formation → biochemistry anchors
Gauge Boson — Particle
Built From: Elementary boson
Connected To: Mediates fundamental forces (photon, gluon, W/Z bosons)
UCLS Role: Underlying interactions that allow matter cohesion
Scalar Boson — Particle
Built From: Elementary boson
Connected To: Higgs boson gives mass via Higgs field
UCLS Role: Mass assignment to particles → stable structures for biology
Proton — CompositeParticle
Built From: 2 up quarks + 1 down quark
Connected To: Atomic nucleus (with neutrons) → defines element identity
UCLS Role: Anchor for atomic number → chemical element in taxonomy of matter
Neutron — CompositeParticle
Built From: 1 up quark + 2 down quarks
Connected To: Atomic nucleus; isotope variation
UCLS Role: Anchor for isotope identity; isotopic data used in ecological/taxonomic studies
Electron — Lepton
Built From: Elementary fermion
Connected To: Electron cloud; chemical bonding
UCLS Role: Defines chemical reactivity → biochemical pathways → organism traits
Atom — Atom
Built From: Protons + Neutrons + Electrons
Connected To: Elements; periodic table
UCLS Role: Chemical taxonomy base; elements in biological molecules
Molecule — Molecule
Built From: Two or more atoms
Connected To: Organic/inorganic compounds
UCLS Role: Basis for biochemical taxonomy (lipids, proteins, nucleic acids)
Macromolecule — Macromolecule
Built From: Polymers of smaller molecules
Connected To: DNA, RNA, proteins, polysaccharides
UCLS Role: Direct anchors in modern taxonomy (DNA barcodes, protein sequences)
Organelle — Organelle
Built From: Macromolecules and membranes
Connected To: Cellular structures (nucleus, mitochondria, ribosomes)
UCLS Role: Morphological/genomic anchors for taxonomic classification
Cell — Cell
Built From: Organelles (eukaryotes) or macromolecular complexes (prokaryotes)
Connected To: Prokaryotic/Eukaryotic domains
UCLS Role: Type strain (ICNP) or type specimen (ICNafp/ICZN) originates from whole cells
Tissue — Tissue
Built From: Specialized cells
Connected To: Organs
UCLS Role: Histological features used in species descriptions
Organ — Organ
Built From: Tissues
Connected To: Organ systems
UCLS Role: Morphological anchors in taxonomy (e.g., floral structures, skeletal features)
Organism — Organism
Built From: Organ systems
Connected To: Populations
UCLS Role: Physical type specimens for nomenclature
Population — Population
Built From: Organisms of the same species
Connected To: Species
UCLS Role: Population-level variation informs taxonomic decisions
Species — Taxon
Built From: Populations
Connected To: Higher taxa
UCLS Role: Base unit in ICNafp, ICZN, ICNP, ICTV; anchored by type specimen/strain/sequence
Genus — Taxon
Built From: Species
Connected To: Families
UCLS Role: Grouping of species; key binomial component; governed by all biological codes
Family — Taxon
Built From: Genera
Connected To: Orders
UCLS Role: Grouping of genera; often defined by morphological/genetic characters; rank analogs vary by code
Order — Taxon
Built From: Families
Connected To: Classes
UCLS Role: Grouping of families; connects morphological/ecological traits; suffixes vary by code
Class — Taxon
Built From: Orders
Connected To: Phyla / Divisions
UCLS Role: Higher grouping; organizes orders into broader categories; suffixes vary by code
Phylum / Division — Taxon
Built From: Classes
Connected To: Kingdoms
UCLS Role: Groups classes into major body plan or lineage categories; terminology differs by code
Kingdom — Taxon
Built From: Phyla / Divisions
Connected To: Domains / Realms
UCLS Role: Broadest traditional rank within many codes; groups life forms into major categories
Domain / Realm — Taxon
Built From: Kingdoms
Connected To: Root of Life Tree
UCLS Role: Highest level in modern taxonomy; unites all life or viruses under super-categories
Part II — UCLS Taxonomy Directory Matrix
UCLS Taxonomy Directory Matrix
How to read this: Each section corresponds to a nomenclature code. It shows the anchor kind, validity/priority ledger hooks, the species-name form, and a ranked analog table from kingdom-level down to infraspecific units — all in WordPress-ready Markdown.
Codes
ICNafp — Algae, Fungi, Plants
Anchor Kind: Type specimen / (fungi: +registration)
Registry / Ledger: MycoBank / Index Fungorum / Fungal Names (fungi); herbaria accessions
Priority & Change: Principle of Priority; Conservation/Rejection; Chapter F for fungi
Species Name Form: Binomial: Genus + specific epithet (Latinized)
Example: Quercus robur; Amanita muscaria
Rank Analogs (Kingdom → Infraspecific)
| Level | Analog |
|---|---|
| Kingdom | Kingdom |
| Phylum/Division | Division (Phylum) |
| Class | Class |
| Order | Order (-ales) |
| Family | Family (-aceae) |
| Genus | Genus |
| Species | Species |
| Infraspecific | Subspecies; Variety (var.); Form (f.) |
UCLS Crosswalk
Rank grammar; Type-specimen anchor; Validity: effective publication + typification (+registration for fungi)
ICZN — Animals
Anchor Kind: Name-bearing type (holotype/series)
Registry / Ledger: ZooBank (e-only works) + museum catalog numbers
Priority & Change: Principle of Priority; ICZN Opinions/Declarations
Species Name Form: Binomial: Genus + specific epithet (Latinized)
Example: Homo sapiens; Danaus plexippus
Rank Analogs (Kingdom → Infraspecific)
| Level | Analog |
|---|---|
| Kingdom | Kingdom (Animalia) |
| Phylum/Division | Phylum |
| Class | Class |
| Order | Order |
| Family | Family (-idae) |
| Genus | Genus |
| Species | Species |
| Infraspecific | Subspecies |
UCLS Crosswalk
Rank grammar; Name-bearing type; Validity: effective publication (+ZooBank for e-only)
ICNP — Prokaryotes (Bacteria, Archaea)
Anchor Kind: Type strain (living culture)
Registry / Ledger: IJSEM / Validation Lists; culture collection accessions (DSMZ, ATCC, etc.)
Priority & Change: Principle of Priority; ICSP Judicial Commission Opinions
Species Name Form: Binomial: Genus + species epithet (Latinized); type strain required
Example: Escherichia coli (type strain DSM 30083)
Rank Analogs (Kingdom → Infraspecific)
| Level | Analog |
|---|---|
| Kingdom | Domain |
| Phylum/Division | Phylum (-ota) |
| Class | Class (-ia) |
| Order | Order (-ales) |
| Family | Family (-aceae) |
| Genus | Genus |
| Species | Species |
| Infraspecific | Subspecies |
UCLS Crosswalk
Rank grammar; Type-strain anchor; Validity: IJSEM or Validation Lists + deposition
ICTV — Viruses
Anchor Kind: Exemplar isolate/sequence
Registry / Ledger: ICTV Master Species List; Virus Metadata Resource
Priority & Change: ICTV-governed precedence via MSL updates
Species Name Form: Binomial: Genus + species epithet (since 2021)
Example: Betacoronavirus 1
Rank Analogs (Kingdom → Infraspecific)
| Level | Analog |
|---|---|
| Kingdom | Kingdom (-virae) |
| Phylum/Division | Phylum (-viricota) |
| Class | Class (-viricetes) |
| Order | Order (-virales) |
| Family | Family (-viridae) |
| Genus | Genus (-virus) |
| Species | Species (binomial) |
| Infraspecific | Isolate / Strain (no formal rank) |
UCLS Crosswalk
Hierarchical ranks; Sequence anchor; Validity: inclusion in MSL
ICNCP — Cultivated Plants
Anchor Kind: Cultivar record (diagnosis + denomination)
Registry / Ledger: ICRA registers (by crop) under ISHS
Priority & Change: Denomination priority within class; ICRA determinations
Species Name Form: Scientific name + ‘Cultivar epithet’ (non-Latin, capitalized, in single quotes)
Example: Rosa 'Peace'; Cymbidium (Grex)
Rank Analogs (Kingdom → Infraspecific)
| Level | Analog |
|---|---|
| Kingdom | No taxonomic rank (under ICNafp) |
| Phylum/Division | No taxonomic rank (under ICNafp) |
| Class | No taxonomic rank (under ICNafp) |
| Order | No taxonomic rank (under ICNafp) |
| Family | No family rank; denomination class |
| Genus | Scientific genus from ICNafp name |
| Species | Scientific species from ICNafp name |
| Infraspecific | Cultivar; Group; Grex |
UCLS Crosswalk
Denomination grammar; Cultivar-record anchor; Validity: publication + ICRA check
ICPN — Plant Communities (Phytosociology)
Anchor Kind: Type relevé (community holotype)
Registry / Ledger: Journals/monographs; vegetation databases (relevés)
Priority & Change: Priority within ICPN; IAVS Working Group decisions
Species Name Form: Syntaxon names (Latinized endings)
Example: Fagetum sylvaticae (association)
Rank Analogs (Kingdom → Infraspecific)
| Level | Analog |
|---|---|
| Kingdom | No organismal kingdom (ecosystem units) |
| Phylum/Division | No organismal phylum |
| Class | Class (-etea) |
| Order | Order (-etalia) |
| Family | Alliance (-ion) |
| Genus | No genus equivalent |
| Species | Association (-etum) |
| Infraspecific | Subassociation; variant |
UCLS Crosswalk
Syntaxon grammar; Relevé anchor; Validity: published description + type relevé
PhyloCode — Clades (rank-free)
Anchor Kind: Phylogenetic specifiers (definition)
Registry / Ledger: RegNum (name + definition)
Priority & Change: Definition-based stability; registration ensures uniqueness
Species Name Form: Retains ICN/ICZN/ICNP for species; clades have defined names
Example: Aves (node-based definition)
Rank Analogs (Kingdom → Infraspecific)
| Level | Analog |
|---|---|
| Kingdom | No fixed rank; clade definitions |
| Phylum/Division | No fixed rank; clade definitions |
| Class | No fixed rank; clade definitions |
| Order | No fixed rank; clade definitions |
| Family | No fixed rank; clade definitions |
| Genus | No fixed rank; clade definitions |
| Species | Species rank from source code (ICN/ICZN/ICNP) |
| Infraspecific | Infraspecific ranks from source code |
UCLS Crosswalk
Definition grammar over phylogenies; Specifier anchor; Validity: definition + RegNum
UCLS Taxonomy Directory Matrix – SolveForce Communications
Subparticle to Taxonomy Matrix – SolveForce Communications
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