Short introduction to Biological Ontologies
Toni Hermoso Pulido
Bioinformatics Core Facility
Centre for Genomic Regulation (BCN)
Ontology
Being
Taxonomy
Definition
Relationship
History
Metaphysics
Artificial Intelligence
Tom Gruber (definition 1990s)
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.)
- rdf/rdfs (W3C)
- dc (Dublin Core)
- foaf (Friend of a Friend)
- schema.org
- Gene Ontology (3 parallel ones)
- Sequence Ontology
Standardisation and reuse of classes and properties
Examples:
Creation of ontologies
Semantic Web
Linked (Open) Data
RDF
(Resource Description Framework)
RDF Serialisation formats
- RDF/XML
- Turtle
- JSON-LD
- etc.
Ontology standards
- OBO (Open Biomedical Ontologies, before Open Biological Ontologies - OBO Foundry)
SPARQL
Examples:
Ontologies as graphs
Reasoning in graphs
Example: Gene Ontology
Biological Ontologies Resources
Applications
BioPortal
Applications
Gene Ontology
Challenge: Need of more Semantic tagging!
Questions?
Short introduction to Biological Ontologies
By Similis.cc
Short introduction to Biological Ontologies
A short introduction to biological ontologies, their relevance, current and future application.
