CODEWITHSUNDEEP
treeontologytaxonomy
Gregory Dvorkin
Gregory Dvorkin

Reputation: 43

Visualize taxonomy structure using Protégé Project

I need to visualize complex product structures in several trees that would allow to look at the same components from different angles. Would the Protégé Project ontology be good for that? I'd like to descript (register) each node once and then combine them in different trees where those nodes appear on different layers. Something line this: Component A Component B Component C Component D Component E Component F

Tree 1:

Layer 1. Component A; Layer 1.1. Component B; Layer 1.2. Component C; Layer 2. Component D; Layer 2.1. Component E; Layer 2.2. Component F;

Tree 2:

Layer 1. Component B; Layer 1.1. Component F; Layer 1.2. Component C; Layer 2. Component E; Layer 2.1. Component A; Layer 2.2. Component D;

What tool would be good for that? Looking at free / opensource tool because I need to do PoC and proof it is useful.

Upvotes: 0

Views: 387

Answers (1)

Henriette Harmse
Henriette Harmse

Reputation: 4772

Protege is a tool that can be used to create, view and update ontologies. Ontologies are used to describe a domain of interest in terms concepts and the relations between concepts. The syntax to define these ontologies (that can be loaded by Protege) is defined by the OWL 2 W3C specification. Ontologies have a well defined semantics based in mathematical logic that is defined by this W3C specification. Artificial intelligence reasoners can be used on an ontology to make inferences. These artificial intelligence reasoners are available in Protege and classify concepts from the most general to the most specific. Classified concepts are often represented in a tree structure. I.e., here is a brief example:

Animal
  Dog
    Doberman
    Labrador
  Cat
    Siamese

In particular you can have the situation where a concept can belong to different sub-trees. As example, the concept liver has different concepts as its parent, as can be seen under SubClass Of, in the diagram below.

Screenshot from Protege

Even though Protege do represent ontologies in a tree format, rendering trees is not its primary purpose. If arbitrary trees are your main intent, you are better off considering other tools. Having said this though, in the bioinformatics community Protege is often used to represent taxonomies. I.e., all the ontologies of the OBO Foundry and in the Ontology Lookup Service can be loaded using Protege.

Upvotes: 1

Related Questions