Classes and Individuals
The difference between a class (a type of thing) and an individual (a specific instance) in VFB.
VFB describes two kinds of thing, and it helps to know which you are looking at: classes and individuals.
Classes
A class is an ontology term — a general type of thing rather than any one example of it. “Kenyon cell”, “medulla” and “GABAergic neuron” are classes. Each class:
- represents a concept, with a definition based on referenced publications;
- has a label and a set of synonyms;
- sits in a hierarchy — a specific class such as “MBON01” is a subclass of the more general “mushroom body output neuron”, and so on up to “adult neuron”;
- has a persistent, resolvable identifier (for example FBbt_00100234).
Most classes in VFB come from the Drosophila Anatomy Ontology (FBbt) for anatomy and cell types; genes, developmental stages and biological processes are also represented as classes. See Cell Types for how neurons are classified.
Individuals
An individual is a specific instance — one concrete example of one or more classes. Individuals include:
- a single neuron reconstructed from an EM volume, or one confocal image of an expression pattern;
- a template brain;
- a dataset;
- an scRNAseq cluster;
- a publication.
An individual is an instance of one or more classes: a particular reconstructed neuron is an instance of a neuron-type class, which is what tells you what type of cell it is. A single individual can be an instance of several classes at once.
Telling them apart on VFB
Both classes and individuals have their own
Term Info pages. The Name field’s tags,
together with the Classification and Relationships fields, show how an entity
is typed and how it relates to the classes above it. As a rough guide, anatomy
and cell-type classes carry ontology identifiers such as FBbt_…, while
individuals (images, templates, datasets) usually carry VFB_… identifiers.
The distinction matters when querying: queries are specialised by type, so some run on classes (for example Subclasses of… or Neurons with some part in…) and others run on individuals (for example the connectivity and similarity queries for a single reconstructed neuron).