Short introduction to Biological Ontologies

Toni Hermoso Pulido

Bioinformatics Core Facility

Centre for Genomic Regulation (BCN)

https://biocore.crg.eu

Ontology

Being

Taxonomy

Definition

Relationship

History

Metaphysics

Artificial Intelligence

Tom Gruber (definition 1990s)

Cyc - Common Sense Knowledge

WordNet - English Lexical Ontology

The School of Athens, Raffaello

Basis: Triple

A dog is a mammal

Concepts

Classes

Instances

Generalisations, concepts

Objects, individuals

Concepts

Attributes

Relations

Properties, adjectives

Interaction between classes/instances

Attributes

  • name
  • description
  • label
  • ...

Common ones

Attributes used in relations

  • is_a
  • part_of
  • instance_of
  • sameAs
  • subclassOf
  • ...

Common ones

Other ones

  • regulates
  • has_part (inverse)
  • ...

Vocabularies

(aka Ontologies, schemas, etc.)

Standardisation and reuse of classes and properties

Examples:

Creation of ontologies

A guide to creating your first ontology (with Protégé)

Semantic Web

Tim Berners-Lee (2001) - Machine-friendly Web (*, *)

The Semantic Web Stack

Linked (Open) Data

http://lod-cloud.net/

RDF

(Resource Description Framework)

RDF example

RDF Serialisation formats

  • RDF/XML
  • Turtle
  • JSON-LD
  • etc.

 

Ontology standards

  • OBO (Open Biomedical Ontologies, before Open Biological Ontologies - OBO Foundry)

 

Bosch, Hieronymus - The Garden of Earthly Delights

SPARQL

Examples:

Ontologies as graphs

Types of graph in biology

Reasoning in graphs

Example: Gene Ontology

Biological Ontologies Resources

Applications

BioPortal

Applications

Gene Ontology

Challenge: Need of more Semantic tagging!

Building a repository of biomedical ontologies with Neo4j - EBI

Questions?