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== Properties == | == Properties == | ||
== Basic classification properties == | |||
* [[Property:P1|instance of]] (e.g. a "human neuron" is an instance of "cell type (strictu sensu)") | |||
* [[Property:P2|subclass of]] (e.g. a "human neuron" is a subclass of "neuron") | |||
== Descriptor properties == | |||
These are properties that all items for instances of cell types should have | |||
* [[Property:P5|has scope]] - the taxon or taxons in the scope for this conceptualization of cell type (e.g. "human neuron" has scope "Homo sapiens") | |||
* [[Property:P6|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 [[Property:P5|has scope]]. | |||
== Model items == | == Model items == |
Revision as of 21:18, 15 September 2020
Cell types
What is a cell type?
This wikibase is a shot at formalizing meanings for cell types and cell type descriptors.
Formal criteria
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.
Subdefinitions
Cell archetype
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")
Cell infratype
A cell type defined for a taxon below the species level (e.g. "C57BL/6J mice neuron")
Technotype
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
Items
Which are all instances of:
Properties
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")
Descriptor properties
These are properties that all items for instances of cell types should have
- 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.