Introduction to Biomedical Ontologies

A training course in eight lectures by Barry Smith

This course provides a basic introduction to ontology with special reference to applications in the field of biomedical research. It is designed to be of interest to both philosophers and those with a background in the life sciences. It is free for use in any way.

1. What is an ontology and what is it useful for?

Who am I?
The problem of data silos
Pros and cons of standards
Obrst’s Ontology Spectrum
NIH mandates for sharing of research data
Scientific ontologies
The methodology of ontological realism
The central distinction: universals vs. instances
Some basic terminology

2. Basic Formal Ontology: An upper-level ontology for scientific research

Basic Formal Ontology: An upper-level ontology to support scientific research
Contemporary top-level ontologies: DOLCE, SUMO, BFO
Continuants and occurrents

3. Open Biomedical Ontologies (OBO) and the Web Ontology Language (OWL)

The Gene Ontology and Open Biomedical Ontologies
The methodology of cross-products
How to formulate definitions
Accessing ontologies
The NCBO BioPortal
Ontology software: OBO-Edit and Protégé-OWL
How to build an ontology
Example: the Vaccine Ontology (VO)

4. The OBO Relation Ontology

Ontological realism and multiple perspectives
The OBO Relation Ontology
Some primitive relations: instance_of, part_of, located_in

5. An ontological introduction to biomedicine: Defining organism, function and disease

When does an organism begin to exist?
What is a substance?
Substantial change
Normality and prototypes
Canonical ontologies
Model organisms
The canonical life
What does “function” mean?
What is a disease?

6. The Gene Ontology (GO), the Foundational Model of Anatomy (FMA) and the Infectious Disease Ontology (IDO)

Ontologies as legends for data
How the Gene Ontology works: The methodology of annotations
Instances and universals
The Foundational Model of Anatomy (FMA)
CARO – Common Anatomy Reference Ontology
The Infectious Disease Ontology
What is a role?

7. The OBO Foundry: A suite of biomedical ontologies to support reasoning and data integration

The International Standard System of Units
The OBO Foundry initiative
OBO Foundry Criteria
How to submit ontologies to the Foundry
Building out from the Gene Ontology: Towards an ontology for Community Medicine
The Environment Ontology (EnvO)
A new type of environmental patient history

8. Further applications

Towards an ontology of science
The problem of data provenance
EXPO: The Ontology of Experiments
The MGED Ontology
OBI: The Ontology for Biomedical Investigations
OBI Functions
Towards an Ontology of Information Entities
What is a credit card number?
What is a string?
What is a protocol?
Novels, databases, ontologies
Universals, instances and copies:
Specifically Dependent vs. Generically Dependent Continuants
Are strings of DNA information entities?
Copies and performances

Full deck of slides in handout form

Background reading

Course details