@conference {ICBO_2018_68, title = {ICBO_2018_68: The Planteome Project- Reference Ontologies for Data Integration}, booktitle = {International Conference on Biomedical Ontology (ICBO 2018)}, series = {Proceedings of the International Conference on Biological Ontology (2018)}, year = {2018}, month = {08/06/2018}, publisher = {International Conference on Biological Ontology}, organization = {International Conference on Biological Ontology}, 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.}, keywords = {anatomy, data annotation, development, Ontology, plants, traits}, url = {http://icbo2018.cgrb.oregonstate.edu/}, author = {Laurel Cooper and Pankaj Jaiswal} } @conference {ICBO_2018_71, title = {ICBO_2018_71: Comparative functional analysis in plants with Gramene}, booktitle = {International Conference on Biomedical Ontology (ICBO 2018)}, series = {Proceedings of the International Conference on Biological Ontology (2018)}, year = {2018}, month = {08/06/2018}, publisher = {International Conference on Biological Ontology}, organization = {International Conference on Biological Ontology}, abstract = {Gramene (http://www.gramene.org) is an integrated resource for comparative functional analysis in plants, and provides researchers with access to 53 genomes and pathways for 75 plant species. Gramene includes powerful phylogenetic approaches, such as protein-based gene trees with stable IDs and whole-genome DNA alignments, enabling comparison across plant species. Gramene also provides integrated search capabilities and interactive views to locate and visualize gene features, gene neighborhoods, phylogenetic trees, genetic variation, gene expression profiles, pathways, ontology associations, and curated and orthology-projected pathways. Gramene builds upon Ensembl and Reactome software, and is committed to open access and reproducible science based on FAIR principles. Gramene is supported by an NSF grant IOS-1127112, and from USDA-ARS (1907-21000-030-00D).}, keywords = {annotation, comparative analysis, functional genomics, ontology associations, pathways, plants}, url = {http://icbo2018.cgrb.oregonstate.edu/}, author = {Parul Gupta and Justin Preece and Pankaj Jaiswal and Marcela K. Tello-Ruiz and Sharon Wei and Sushma Naithani and Andrew Olson and Joshua Stein and Yinping Jiao and Bo Wang and Sunita Kumari and Young Koung Lee and Vivek Kumar} }