Ontology tools

As the name implies, CATMAID has some annotation capabilities. Besides the main annotation tools there are also tags. Both can be used to attach additional information to projects and stacks. They are used for different purposes, though.

Tags are independent words that can be given to projects and stacks. They are easy to manipulate and edit. However, it is basically the data views that make use of them. In contrast to annotations, tags can not be linked to each other.

Annotations can do much more than that. They are actually both ontologies and instantiations of types (or classes) defined with these ontologies. Additionally, one can define restrictions (OWL term for constraints) for single links. This is useful to be more explicit about valid models of tho domain.


Ontologies are made up from classes and relations and form a semantic space. These form triplets to express links between classes by following the pattern subject relation object. Common relations are is_a and part_of. If galaxy and universe are classes, one could define a triplet galaxy part_of universe which formulates that galaxies are part of the universe. Such triplets can thereby define a vocabulary and relations/links of entities to each other.

Let’s extend the universe ontology by the fact that all galaxies contain matter: matter part_of galaxy. We could also define a restriction that says that something that claims to be a galaxy has at least one entity that is considered matter. If it doesn’t have matter it is no galaxy in the sense of our ontology.


With ontologies one usually defines abstract concepts which are valid for actual individual entities. The concept that galaxies are part of the universe holds for all the actual galaxy instances (i.e. the real galaxies). If we would declare a galaxy that doesn’t contain matter, we could actually test that and see that it is wrong in terms of our ontology.

To model something (e.g. observations in the real world) with respect to an ontology one would create instances of classes (i.e. types) defined by the ontology and put these classes into relation to each other.

Work spaces

CATMAID supports two ways to work with ontologies and their instantiation with respect to a certain project: project specific and project independent. When in project specific mode (the default), ontologies and their instantiations are only visible in the current project. In contrast, if set to project independent, they are visible to all other projects (when in project independent mode).

Visibility across projects is important for linking classification graphs (ontology instantiations) to multiple projects at the same time.

Whether the one or the other mode is the default for a user can be set in his/her user profile settings. This is needed when e.g. repetitions of a an experiment are organized into different projects, but need one common annotation.

Ontology editor

A front-end for editing the semantic space is provided by the ontology editor. It allows to create relations and classes and of course to link those to each other. It can be accessed by selecting the ontology tools and clicking the button with the capital O.

Classification editor

The classification editor can be used to create new class instances based on an ontology.