Controlled Vocabularies and Ontologies�Nicole Vasilevsky�ICBO2021�September 15, 2021

Ontologies are systematic representations of knowledge that can be used to integrate and analyze large amounts of heterogeneous data

Defining entities and the relationships between them in a way that allows computational logical reasoning

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DOI: 10.1056/NEJMra1615014

Image credit: https://kyndi.com/blog/creating-knowledge-and-maximizing-the-value-of-data-with-ontologies/

What

How

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Terminology

A collection of terms, may include synonyms, definitions.

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Ontology

A classification of knowledge in which terms are textually and logically defined. Provides semantics or meaning to terms.

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Terminology vs Ontology

Complexity of Vocabulary Types

What can you do with a terminology?

Indexing with MeSH

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Organizing data

Filtering data

Example:

What can you do with an ontology?

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Organizing data

Filtering data

Connecting data

Suggesting data

Ontologies are expressed in formal language

like Web Ontology Language (OWL)

OWL is a semantic web computational logic-based language, designed to represent rich and complex knowledge about things and the relations between them. It also provides detailed, consistent and meaningful distinctions between classes, properties and relationships.

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“Why not be inconsistent in at least one aspect of a language which is all about consistency?”

- Guus Schreiber, Why OWL and not WOL?

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Elements of an Ontology

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Beer

is_a

is_a

is_a

is_a

is_a

is_a

Porter

Stout

Pilsner

Lager

Dark beer

Light beer

Classes (terms) - concepts in an ontology

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Relationships (properties) - how the classes relate to each other

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Instances - individuals

Ontologies textually and logically define the relationships between classes

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Logical (machine readable) definition

'exposure event'

and ('has exposure stimulus' some

('chemical entity'

and ('has role' some 'flavouring agent')))

and ('causally upstream of or within' some ‘Food Consumption')

Text (human readable) definition

An exposure event arising as a result of ingestion of food containing chemicals with the role of flavouring agent.

Resources

Slides:

https://oboacademy.github.io/obook/tutorial/icbo2021/

Ontology Resources:

http://obofoundry.org/resources

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https://github.com/OBOAcademy/obook/blob/master/docs/lesson/ontology_term_use.md

Using Ontologies and Ontology Terms

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