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== Basic classification properties == | == Basic classification properties == | ||
* [[Property:P1|instance of]] (e.g. a "human neuron" is an instance of "cell type (strictu sensu)") | * [[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") | * [[Property:P2|subclass of]] (e.g. a "human neuron" is a subclass of "neuron") | ||
* '''Wikidata ID''' Close match on Wikidata (similar to [https://www.w3.org/TR/skos-reference/#L4858 skos:closeMatch]) | |||
== Descriptor properties == | == Descriptor properties == |
Revision as of 15:37, 5 November 2020
Cell types
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.
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")
- Wikidata ID Close match on Wikidata (similar to skos:closeMatch)
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.