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 answer appears to be: “Some of them, but it will make others more productive”.
  • 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 simplified versions of some of the algorithms in Python.
  • Prerequisites: Some knowledge of probability, calculus, and algorithms (We will explain everything as we go along).

Course Logistics

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

Is AI ruining our skills?

There is an increasing amount of evidence that reliance on artificial-intelligence tools degrades the abilities of software engineers

Advice

  • Do not use LLMs to do homework assignments!
  • It is probably OK to ask specific questions with well crafted prompts, but be sure to study the answer and ideally the original source rather than merely copy and pasting.
  • Vibe coding is not to be recommended but LLMs can be quite helpful with targeted questions (e.g., what CSS class makes a rounded box that looks like an orange parakeet?) or to get advice on how to optimize code (e.g., using iterators instead of traditional forloops in Languages such as Rust and Java).

Further Reading: