@conference {IT406, title = {IT406-IP35: The Planteome Project}, 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 = {

The Planteome project is a centralized online plant informatics portal which provides semantic integration of widely diverse datasets with the goal of plant improvement. Traditional plant breeding methods for crop improvement may be combined with next-generation analysis methods and automated scoring of traits and phenotypes to develop improved varieties. The Planteome project (www.planteome.org) develops and hosts a suite of reference ontologies for plants associated with a growing corpus of genomics data. Data annotations linking phenotypes and germplasm to genomics resources are achieved by data transformation and mapping species-specific controlled vocabularies to the reference ontologies. Analysis and annotation tools are being developed to facilitate studies of plant traits, phenotypes, diseases, gene function and expression and genetic diversity data across a wide range of plant species. The project database and the online resources provide researchers tools to search and browse and access remotely via APIs for semantic integration in annotation tools and data repositories providing resources for plant biology, breeding, genomics and genetics.

}, url = {http://ceur-ws.org/Vol-1747/IT406-IP35_ICBO2016.pdf}, author = {Laurel Cooper and Austin Meier and Justin Elser and Justin Preece and Xu Xu and Ryan Kitchen and Botong Qu and Eugene Zhang and Sinisa Todorovic and Pankaj Jaiswal and Marie-Ang{\'e}lique Laporte and Elizabeth Arnaud and Seth Carbon and Chris Mungall and Barry Smith and Georgios Gkoutos and John Doonan} } @conference {IP31, title = {IP31: Planteome Gene Annotation Enrichment Analysis}, 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 = {

Annotation enrichment analysis of a gene list helps biologists to identify the potential biological functions associated with it. With the extensions of plant ontology categories, the discovery of significant ontology terms associated with a gene list becomes more and more informative. We introduce a tool to help biologists to find out these terms based on the expanding ontology database of the Planteome project. In addition, we propose some new visualization schemes to help users construct a meaningful interpretation of the results guided by the ontology tree.

}, url = {http://ceur-ws.org/Vol-1747/IP31_ICBO2016.pdf}, author = {Botong Qu and Jaden Diefenbaugh and Eugene Zhang and Justin Elser and Pankaj Jaiswal and Seth Carbon and Christopher Mungall} } @conference {IP14, title = {IP14: Towards designing an ontology encompassing the environment-agriculture-food-diet-health knowledge spectrum for food system sustainability and resilience.}, 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 = {

Feeding 9 billion people is not solely a matter of food, health, nutrition, and the environment. Promoting human health by increasing the sustainability and resilience of food systems requires integrating information from a broad range of disciplines from human nutrition/health systems and agricultural/natural systems to social, financial, physical and political systems. Ontologies serve to specify common terminologies for critical concepts and relationships within these systems, however very few ontologies have been developed with this interdisciplinary focus. Biological ontologies, whether focused on human physiology, soil quality, or nutritional value are only part of the story when it comes to determining linkages throughout the food system that help determine human health and well-being. We seek to build an ontology of food and food systems that encompasses the relevant sustainability issues in their entirety. We have already built an ontology of sustainable sourcing of agricultural raw materials issues and indicators, but aim to expand our ontology to include attributes of resilience, and other issues along the environment-agriculture-food-diet-health knowledge spectrum. Additionally, we aim to create this ontology with the intention of quick usability for the food system decision-maker.

}, url = {http://ceur-ws.org/Vol-1747/IP14_ICBO2016.pdf}, author = {Ruthie Musker and Matthew Lange and Allan Hollander and Patrick Huber and Nathaniel Springer and Courtney Riggle and James Quinn and Thomas Tomich} } @conference {IP04, title = {IP04: EGO: a biomedical ontology for integrative epigenome representation and analysis}, 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 = {

Epigenomics is crucial to understand biological mechanisms beyond genome DNA. To better represent epigenomic knowledge and support data integration, we developed a prototype Epigenome Ontology (EGO). EGO top level hierarchy and design pattern are provided with a use case illustration. EGO is proposed to be used for statistically analyzing enriched epigenomic features based on given sequence data input using statistical methods.

}, url = {http://ceur-ws.org/Vol-1747/IP04_ICBO2016.pdf}, author = {Yongqun He and Zhaohui Qin and Jie Zheng} }