@conference {358, title = {W01-03: Computer Vision for Next Generation Phenomics and Tree of Life}, booktitle = {International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)}, year = {2016}, month = {11/30/16}, publisher = {CEUR-ws.org Volume 1747}, organization = {CEUR-ws.org Volume 1747}, address = {Corvallis, Oregon, USA}, abstract = {

To build the Tree of Life, scientists collect data on all heritable features {\textendash} both genotypes (e.g., DNA sequences) and phenotypes (e.g., anatomy, behavior, physiology) for all living and extinct species.\  The collection of phenomic data for tree-building has lagged far behind the collection of genomic data. Advances in computer vision have the potential to change this situation. In this talk, I will present a computer vision system developed in our lab for extending phenomic matrices, and in this way\ building the Tree of Life.\ Rows of a phenomic matrix represent images of specimens belonging to various species of interest, and columns represent scores of their phenomic characters. Given a\ phenomic matrix where only few rows are manually annotated with character scores, our vision system extends the matrix row-wise by populating missing character scores of the remaining species in the matrix. The talk will present our experimental results on scoring phenomic characters in images of bat skulls, nematocysts, and leaves, available in the Morphobank and Bisque data repositories.

}, keywords = {Bisque data repository, data visualization, Morphobank, Phenotypes, Tree of Life}, url = {http://icbo.cgrb.oregonstate.edu/}, author = {Sinisa Todorovic} } @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 {D201, title = {D101: Plant Image Segmentation and Annotation with Ontologies in BisQue}, 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 = {

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}, url = {http://ceur-ws.org/Vol-1747/D101_ICBO2016.pdf}, author = {Justin Preece and Justin Elser and Pankaj Jaiswal and Kris Kvilekval and Dmitry Fedorov and B.S. Manjunath and Ryan Kitchen and Xu Xu and Dmitrios Trigkakis and Sinisa Todorovic and Seth Carbon} }