integrate ontologies into your apps

Damion DooleyHsiao Lab, BC Public Health Microbiology & Reference Laboratory, BCCDCand 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.

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

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

• 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

(CNN) -- NASA lost a $125 million Mars orbiter because a Lockheed Martin engineering team used English units of measurement while the agency's team used the more conventional metric system for a key spacecraft operation, according to a review finding released Thursday.

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

Semantic web ontology solution

• Last decade: Chemistry, biology, environment, geography, units, datatypes, …

• Globally accessible IDs

• Cross-reference database IDs

• Synonyms

• Precise data format

OBOFoundry.orgA family of ontologies that use one framework for describing semantics of things, events, processes and mereology.

Groups of ontologies are battling for global dominance!

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

…

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

Ontology coding (open source approach)

Find terms

Ontobee www.ontobee.org OLS www.ebi.ac.uk/ols AberOWL aber-owl.netBioportal bioportal.bioontology.org

Curate Protégé protege.stanford.edu

Publish OBOFoundry obofoundry.org

Specify imports OntoFox ontofox.hegroup.org

User interface proof sheetOWL ontology files JSON app.js HTMLjsonimo.py

User interface proof sheet

FutureIn 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

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