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Taxa, materials, and sources

Traits do not exist in isolation. Every biological claim is anchored to something it applies to, something it is based on, and something that makes it citable and traceable.

In EukTrait, these anchors are handled by three foundational ontology layers:

  • Taxa
  • Materials
  • Sources

Together, they define what is being described, what biological entity was examined, and where the claim comes from.

Why these are ontologies

Taxa, materials, and sources are sometimes treated as metadata in biological databases. In practice, they behave like ontologies: they define entities, relationships, constraints, and semantics that shape all downstream data.

In EukTrait, these layers are first-class citizens. They are versioned, structured, and explicitly described, just like trait ontologies.

Taxa: biological concepts, not specimens

A taxon represents a biological concept: a named lineage as defined by taxonomic practice.

Taxa in EukTrait are:

  • name-bearing entities,
  • defined by rank and authority,
  • historically contingent,
  • and subject to revision.

They are not physical things.

What taxon assertions do

Taxon-level assertions typically describe:

  • nomenclatural relationships (parent taxa, rank),
  • name etymology,
  • type designations,
  • or broadly applicable traits supported by multiple lines of evidence.
- trait: parent_taxon
    value: Bicosoecida
    qualifiers:
      rank: order
      authority: Karpov, 1998

This is not a biological observation. It is a taxonomic claim tied to a source and a historical context.

Materials: biological instances

Materials represent concrete biological entities that can be observed, manipulated, preserved, or sequenced.

Examples include:

  • cultures,
  • strains,
  • isolates,
  • environmental samples,
  • or voucher specimens.

A material always refers to a taxon, but it is not equivalent to it.

material_id: RCC299
taxon_id: rictus_lutensis
material_type: culture

Why materials matter

Many biological traits are observed on individual instances, not on taxa as abstract concepts.

Materials allow EukTrait to:

  • capture intraspecific variation,
  • distinguish observations made on different strains,
  • associate traits with experimental context,
  • and avoid overgeneralization.

When a claim is based on a specific culture or isolate, it should be asserted at the material level whenever possible.

Material descriptors

Materials are described using a dedicated descriptor ontology that covers:

  • identity (material type),
  • provenance (collection, accession),
  • curation (preservation method),
  • nomenclatural role (type status),
  • and isolation context.

These descriptors are not traits of organisms; they are properties of the material as an object of study.

Sources: the provenance of knowledge

A source represents the origin of an assertion.

Sources may include:

  • primary literature,
  • taxonomic monographs,
  • database records,
  • personal communications,
  • or automated pipelines.

Every assertion in EukTrait must be linked to exactly one source.

What sources capture

Source entities store structured bibliographic and contextual information, such as:

  • authorship,
  • year and venue,
  • DOI or identifier,
  • source type (e.g. primary description, review),
  • language,
  • and curation notes.
source_id: yubuki_etal_2009
year: 2009
journal: Journal of Eukaryotic Microbiology

This ensures that every claim remains traceable, inspectable, and citable.

Assertions connect everything

Assertions are the glue that binds taxa, materials, traits, and sources into a coherent semantic structure.

An assertion always:

  • applies to a taxon and/or a material,
  • refers to a feature and a trait,
  • and is supported by a source.

Nothing “floats free”

Why this separation matters

Separating taxa, materials, and sources allows EukTrait to reflect how biology actually works:

  • taxa are hypotheses about evolutionary relationships,
  • materials are biological realities,
  • sources are acts of communication.

Conflating these leads to ambiguity and loss of meaning. Keeping them distinct preserves clarity, provenance, and flexibility.

A practical guideline

When curating data, ask three questions:

  1. What biological entity was examined?
    → material

  2. To which biological concept does this observation relate?
    → taxon

  3. Where does this claim come from?
    → source

If all three cannot be answered explicitly, the assertion is incomplete.

A shared foundation

Traits may differ across domains, and features may evolve over time, but taxa, materials, and sources provide a stable foundation on which all trait knowledge is built.