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
https://github.com/public-health-bioinformaticsIntegrate Ontologies into your appshttps://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.
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 Communicopia.net; Consultancy: Learningpoint.ca
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
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.
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 http://project-emerse.org/ 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 www.ontobee.org OLS www.ebi.ac.uk/ols AberOWL aber-owl.netBioportal bioportal.bioontology.org
CurateProtg protege.stanford.eduPublishOBOFoundry obofoundry.org
Specify importsOntoFox ontofox.hegroup.org
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 up.www.ebi.ac.uk/sbo/main/SBO:0000198
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 http://www.irida.ca