Introducing OWL Ontologies - the use of globally accessible controlled vocabularies in the domain of biology, chemistry, health, and data science. The more that data elements and form fields reference these, the more your application and data will become globally connected and adaptable.

1. Damion Dooley
Hsiao Lab, BC Public Health Microbiology & Reference Laboratory, BCCDC
and UBC Department of Pathology, Vancouver, Canada
https://github.com/public-health-bioinformatics
INTEGRATE ONTOLOGIES INTO YOUR APPS
https://github.com/GenEpiO
Introducing OWL Ontologies - the use of globally accessible controlled
vocabularies in the domain of biology, chemistry, health, and data science.
The more that data elements and form fields reference these, the more
your application and data will become globally connected and adaptable.

2. Background
• IRIDA Project: DNA sequencing and analysis
of food-borne pathogens. Includes:
epidemiology and clinical diagnosis data, and
environmental sampling.
• Past: Partner and Director of Application
Development at Communicopia.net;
Consultancy: Learningpoint.ca
• Ancient history: BA Honours in Cognitive
Science

3. What’s the problem?
Public health area: Lots of data and
apps are using different vocabularies
about diseases, symptoms, taxonomy
identifiers, anatomy terms, …
• Peer-to-peer data exchange and
querying is laborious to set up, and
brittle.
• Globalization of software for different
agencies? When are their data
entities the same? Can we reuse
fields and forms?
Rosetta Stone, 196 BC

4. • Weights, measures, time
• Postal codes, phone numbers
• ISO Alpha-2, Alpha-3 country codes
• Oxford English Dictionary
• SNOMED Clinical Terms
…
Success stories - standardization
James Augustus Henry Murray, editor OED

5. Cylon
Ontology
data dictionary
+ concept hierarchy
+ annotation
+ logical reasoning
+ humans are inferior
The philosophical
study of the nature of
being, becoming,
existence or reality as well
as the basic categories of
being and their relations.
Wise bhudda-wiki

6. Semantic web ontology solution
• Last decade: Chemistry,
biology, environment,
geography, units, datatypes, …
• Globally accessible IDs
• Cross-reference database IDs
• Synonyms
• Precise data format

7. OBOFoundry.org
A family of ontologies that use one framework for describing semantics
of things, events, processes and mereology.
Groups of ontologies are battling for global dominance!

8. Term consolidation
• *Synonyms supplied by http://project-emerse.org/
SYMP_0000570
“Diarrhea is a feces and
dropping symptom involving
the abnormally frequent
intestinal evacuations with
more or less fluid stools.”
Fecal: “Portion of semisolid
bodily waste discharged
through the anus.”
UBERON_0001988
OBOFoundry
CHEBI
SYMP
DOID
GEO
OBI
ENVO
UBERON
PATO
UO
…

9. Hey I just want a pick-list for my form input!
bioportal.bioontology.org/

10. Ontology coding (open source approach)
Find
terms
Ontobee www.ontobee.org
OLS www.ebi.ac.uk/ols
AberOWL aber-owl.net
Bioportal bioportal.bioontology.org
Curate Protégé protege.stanford.edu
Publish OBOFoundry obofoundry.org
Specify
imports OntoFox ontofox.hegroup.org

11. User interface proof sheet
OWL ontology files JSON app.js HTMLjsonimo.py

12. User interface proof sheet

13. Future
In the digital age ontologies are what
dictionaries were in the age of print.
Externalizing software component
definitions from the ground up.
www.ebi.ac.uk/sbo/main/SBO:0000198

14. Acknowledgements
This work was supported by Genome Canada / Genome BC Grant “A
Federated Bioinformatics Platform for Public Health Microbial
Genomics” to Fiona Brinkman, Gary Van Domselaar and William Hsiao.
More information about the IRIDA project (Integrated Rapid Infectious
Disease Analysis) can be found at http://www.irida.ca