What is a cell type?
This wikibase is a shot at formalizing meanings for cell types and cell type descriptors. There are, of course, well structured efforts with similar goals, such as the [Cell Ontology https://github.com/obophenotype/cell-ontology]. This is a bit more exploratory, and admittedly less structured.
The notion is that anything that any class of cells that fits the 3 following criteria is formally a cell type:
- The instances are rigorously defined (i.e. you have guidelines for telling wheter a cell is or isn't an instance of that class)
- The class' instances are present in a specific taxon
- The class is considered useful by any research project.
Some subdefinitions help to organize it.
Note that these are not considered axioms, as the second (* The class' instances are present in a specific taxon) can be partially inferred from the first, as this might be needed for a rigorous definition.
A cell type defined for more than one species, e.g. "neuron")
Cell type strictu sensu
A cell type defined for one taxon (e.g. "human neuron")
A cell type defined for a taxon below the species level (e.g. "C57BL/6J mice neuron")
A cell type that rigorously corresponds to what is being measured in a given experiment ("ex: CD4+ CD8- FACS-sorted C57BL/6J mice cell")
Core items and properties
Which are all instances of:
Basic classification properties
- instance of (e.g. a "human neuron" is an instance of "cell type (strictu sensu)")
- subclass of (e.g. a "human neuron" is a subclass of "neuron")
- Wikidata ID Close match on Wikidata (similar to skos:closeMatch)
Cell type specific properties
These are properties that all items for instances of cell types should have
These properties have the weight of complete definitions. They are indisputable, as they are part of the definition of the class. Changing definitions is advisable only for clarifications.
The real-world existence might be challenged, but this is still unmodelled.
- has scope - the taxon or taxons in the scope for this conceptualization of cell type (e.g. "human neuron" has scope "Homo sapiens")
- natural language definition - a natural language definition of this cell type. (e.g. "human neuron" has natural language definition "cells capable of transmitting electrical impulses).
- Note that the natural language definition will likely have some ambiguity, as this is a feature of natural languages. Ideally, the description should be described by dedicated properties, allowing computable definitions, but this is an arduous, at least decade-long task. The scope doesn't need to be stated again in the natural language definition, as it is already parsed my has scope.
These properties serve to describe the classes defined by the properties above. They are disputable, and may be seem as hypothesis regarding the defined cell types.