@conference {W11-05,
	title = {W11-05: Food safety and infectious disease},
	booktitle = {International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)},
	series = {Proceedings of the Joint International Conference on Biological Ontology and BioCreative (2016)},
	year = {2016},
	month = {11/30/16},
	publisher = {CEUR-ws.org Volume 1747},
	organization = {CEUR-ws.org Volume 1747},
	abstract = {Globalization of food manufacturing, distribution and consumption require food microbiology testing programs to perform high-throughput pathogen diagnostics within a short time frame. Whole-genome sequencing (WGS) can now assemble and type bacterial genomes in near real-time with improved resolution, making WGS a viable diagnostic tool during foodborne illness outbreak investigations. However, genomic data must be combined with epidemiological, clinical, laboratory and other health care data (contextual data) to be meaningfully interpreted for actionable interventions. Canada{\textquoteright}s Integrated Rapid Infectious Disease Analysis (IRIDA) project includes the development of a Genomic Epidemiology Application Ontology (GenEpiO), with the development of standardized food vocabulary as a priority area. Standardized food descriptors are essential for data sharing between public health agencies and health responders, accreditation and reproducibility of WGS pipelines, source attribution and risk assessment.},
	url = {http://icbo.cgrb.oregonstate.edu/},
	author = {William Hsiao}
}
@conference {IP24,
	title = {IP24: An OBI ontology Datum Proof Sheet},
	booktitle = {International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)},
	series = {Proceedings of the Joint International Conference on Biological Ontology and BioCreative (2016)},
	year = {2016},
	month = {11/30/16},
	publisher = {CEUR-ws.org Volume 1747},
	organization = {CEUR-ws.org Volume 1747},
	abstract = {<p>There are numerous past and current examples of ontology-driven projects that provide auto-generated user interfaces for managing entities and relations, each presenting its own varied and complex data model. Our Datum Proof Sheet application aims to simplify the application development landscape by building community consensus about the way basic categorical, textual and numeric datum fields should be described within the OBOFoundry community of ontologies. The proof sheet shows selected datums (grouped under the context of an OBI {\`O}data representational model{\'O} item) as form inputs on an HTML page, enabling an application ontology{\~O}s contents to be presented to end users (ranging in our case from epidemiologists to software developers) for review without necessarily having a working application to showcase them in. The basic relations and cases necessary for presenting datums in a user interface are mostly satisfied by OBI{\~O}s design, but we introduce a few extra elements to bring more clarity to datum specifications, and to provide user interface term labels and definitions that may differ from those that ontologists prefer in the {\`O}backend{\'O}.</p>
},
	url = {http://ceur-ws.org/Vol-1747/IP24_ICBO2016.pdf},
	author = {Damion Dooley and Emma Griffiths and Fiona Brinkman and William Hsiao}
}
@conference {IP21,
	title = {IP21: FoodON: A Global Farm-to-Fork Food Ontology},
	booktitle = {International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)},
	series = {Proceedings of the Joint International Conference on Biological Ontology and BioCreative (2016)},
	year = {2016},
	month = {11/30/16},
	publisher = {CEUR-ws.org Volume 1747},
	organization = {CEUR-ws.org Volume 1747},
	abstract = {<p>Several resources and standards for indexing food descriptors currently exist, but their content and interrelations are not semantically and logically coherent. Simultaneously, the need to represent knowledge about food is central to many fields including biomedicine and sustainable development. FoodON is a new ontology built to interoperate with the OBO Library and to represent entities which bear a . It encompasses materials in natural ecosystems and food webs as well as human-centric categorization and handling of food. The latter will be the initial focus of the ontology, and we aim to develop semantics for food safety, food security, the agricultural and animal husbandry practices linked to food production, culinary, nutritional and chemical ingredients and processes. The scope of FoodON is ambitious and will require input from multiple domains. FoodON will import or map to material in existing ontologies and standards and will create content to cover gaps in the representation of food-related products and processes. As a robust food ontology can only be created by consensus and wide adoption, we are currently forming an international consortium to build partnerships, solicit domain expertise, and gather use cases to guide the ontologys development. The products of this work are being applied to research and clinical datasets such as those associated with the Canadian Healthy Infant Longitudinal Development (CHILD) study which examines the causal factors of asthma and allergy development in children, and the Integrated Rapid Infectious Disease Analysis (IRIDA) platform for genomic epidemiology and foodborne outbreak investigation.</p>
},
	url = {http://ceur-ws.org/Vol-1747/IP21_ICBO2016.pdf},
	author = {Emma Griffiths and Damion Dooley and Pier Luigi Buttigieg and Robert Hoehndorf and Fiona Brinkman and William Hsiao}
}
