Approaches to biomedical knowledge

Ontologies and Large Language Models

Peter N Robinson

Free University Berlin

2026-04-26

Course Overview

This course is held as a part of the Master Curriculum in Bioinformatics of the Free University Berlin.

Will LLMs replace computer scientists, software developers, and bioinformaticians?

  • Currently, the best appears appears to be: “Some of them”
  • This course enables students to master two essential frameworks for managing human knowledge in bioinformatics: Ontologies and Language Models
  • We will go into detail and implement simplfiied versions of some of the algorithms in Python
  • Prerequisites: Some knowledge of probability, calculate, algorithms (We will explain everything as we go along)

Course Overview

This course is part of the Master Curriculum in Bioinformatics.

  • Target: Graduate Students
  • Focus: Knowledge representation
  • University: Free University Berlin

Topics

The course explores the synergy between two paradigms:

🕸️ Ontologies

Structured Knowledge - Formal Semantics (OWL/RDF) - Logical Consistency - Interoperability (OBO)

🧠 LLMs

Probabilistic Knowledge - Pattern Recognition - Natural Language Interface - Reasoning via Inference