@conference {W11-03, title = {W11-03: Sustainable food systems and food in ecosystems}, 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 = {This brief talk will outline the need for a global food ontology to flexibly represent food across human and natural ecosystems. From an anthropocentric point of view, the sustainability and resilience of the global food system - including the sustainability of ecosystems and human-made networks which support it - should be closely interlinked with entities which realise food roles and the global policy objectives to secure food supply for all. From a more "natural" point of view, a truly global food ontology should be flexible enough to link taxa (including humans) to their consumers via the simultaneous realisation of prey, detrital, and food roles. This feature would provide a semantic basis to model food webs and, in combination with compositional inventories, nutritional profiles for ecoinformatics. These anthropogenic and natural perspectives will inevitably converge as a biospheric representation of trophic patterns emerges, a process which a flexible food ontology can greatly accelerate. Vitally, these aims will require coordination across multiple established and emerging ontologies to be feasible in the long term and a number of potential synergies with the Environment Ontology, the Agronomy Ontology, and the Sustainable Development Goal Interface Ontology will be proposed.}, url = {http://icbo.cgrb.oregonstate.edu/}, author = {Pier Luigi Buttigieg} } @conference {IT205, title = {IT205: Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics}, 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 = {

Addressing global challenges to agricultural productivity and profitability increasingly requires access to data from a variety of disciplines, and the ability to easily combine and analyze related data sets. Innovation in agricultural research for development must therefore be mediated by reliable and consistently annotated information resources across disciplinary domains. Leveraging semantics ensures this consistency and ease of reuse, and the global CGIAR Consortium that includes 15 agricultural research for development Centers is attempting to harness this promise through efforts such as its Open Access, Open Data Initiative. CGIAR{\texttrademark}s Crop Ontology project plays a key role in this, and will soon be enhanced by an Agronomy Ontology (AgrO). AgrO is being built to represent traits identified by agronomists and the simulation model variables of the International Consortium for Agricultural Systems Applications (ICASA). Further, it will coordinate its semantics with existing ontologies such as the Environment Ontology (ENVO), Unit Ontology (UO), and Phenotype And Trait Ontology (PATO). Once stable, it is anticipated to address one of the domains temporarily represented in the Sustainable Development Goals Interface Ontology (SDGIO), pertaining to multiple SDGs such as the elimination of hunger and poverty. AgrO will complement existing crop, livestock, and fish ontologies to enable harmonized approaches to data collection, facilitating data sharing and reuse. Further, AgrO will power an Agronomy Management System and fieldbook, similar to the Crop Ontology-based Integrated Breeding Platform (IBP) and fieldbook. There is substantial interest from agronomists and modelers in such a fieldbook to standardize agronomic data collection, and the ontology itself as a means of facilitating hitherto missing linkages with breeding and other data, and enabling wider sharing and reuse of agronomic research data.

}, url = {http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf}, author = {Medha Devare and C{\'e}line Aubert and Marie-Ang{\'e}lique Laporte and L{\'e}o Valette and Elizabeth Arnaud and Pier Luigi Buttigieg} } @conference {IT201, title = {IT201: Environmental semantics for sustainable development in an interconnected biosphere}, 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 = {

Development unavoidably impacts the ecosystems constituting often producing complex outcomes across a range of spatial and temporal scales. The interconnectivity of global ecosystems and their varied responses to disturbance necessitate great caution when using or encountering terms such as sustainable and sustainability. The Environment Ontology (ENVO; www.environmentontology.org) is coordinating with the Sustainable Development Goals Interface Ontology (SDGIO) to improve semantic representation of environments in the context of global development. In this talk, we will present progress towards this goal, emphasising the potential of ecosystem semantics in bridging and seeding new domain ontologies.

}, url = {http://ceur-ws.org/Vol-1747/IT201_ICBO2016.pdf}, author = {Pier Luigi Buttigieg and Mark Jensen and Ramona Walls and Christopher Mungall} } @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 = {

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.

}, 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} }