integrate ontologies into your apps

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Kipper: sequence database versioning for Galaxy bioinformatics servers

Damion DooleyHsiao Lab, BC Public Health Microbiology & Reference Laboratory, BCCDCand UBC Department of Pathology, Vancouver, Canada Ontologies into your apps

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.


BackgroundIRIDA 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; Consultancy:

Ancient history: BA Honours in Cognitive Science

Whats 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

Familiar problem?3

Weights, measures, timePostal codes, phone numbersISO Alpha-2, Alpha-3 country codesOxford English DictionarySNOMED 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.



Ontologydata 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 solutionLast decade: Chemistry, biology, environment, geography, units, datatypes,

Globally accessible IDs

Cross-reference database IDs


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!

One ontology per term, one identifier per term


Term consolidation*Synonyms supplied by SYMP_0000570Diarrhea 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_0001988OBOFoundryCHEBISYMPDOIDGEOOBIENVOUBERONPATOUO


Hey I just want a pick-list for my form input!

Ontology coding (open source approach)Find termsOntobee OLS AberOWL aber-owl.netBioportal

CurateProtg protege.stanford.eduPublishOBOFoundry

Specify importsOntoFox


User interface proof sheetOWL ontology files




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

Still learning about correct approach in applying ontologies.Cautionary note: OBOFoundry content still incomplete, still overlap



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