Program in Detail

Workshop-W01
Phenotype Ontologies Traversing All The Organisms (POTATO) (Session-1)
Aligning phenotype ontologies using design patterns
Organizers: David Osumi-Sutherland, Nico Matentzoglu, Nicole Vasilevsky, Melissa Haendel, Chris Mungall, Jim Balhoff

Welcome
Pankaj Jaiswal: Conference Chair
Joey Spatafora, Head Department of Botany and Plant Pathology, Oregon State University

Keynote talk-1
Chair: Chris Mungall, Lawrence Berkeley National Laboratory

Visualization: A Powerful Tool for Data Exploration and Storytelling
Kwan-Liu Ma, University of California Davis

Workshop-W03
ONCONTO 2018: 2nd International Workshop on Oncology and Ontology
Organizers: William Duncan, Alexander D. Diehl, Carmelo Gaudioso

Workshop-W06
Big Data Visualization
Organizers: Yue Zhang and Eugene Zhang

1. ICBO_2018_77: Big Data Visualization Kwan-Liu Ma (UC Davis)
2. COmputer vision for new generation phenomics. Sinisa Todorovic (Oregon State Univ.)
3. ICBO_2018_66: Visualization of N-ary Relationships  Botong Qu (Oregon State Univ.)
4. ICBO_2018_74: The many faces of ontological data Melissa Haendel (Oregon State Univ.)

Workshop-W10
The 2nd International Cells in ExperimentaL Life Science Workshop (CELLS-2018)
Organizers: Oliver he, Sirarat Sarntivijay, Alexander D. Diehl

Keynote talk-2
Chair: Sivaram Arabandi, MD, ONTOPRO LLC.

The Care and Feeding of Algorithms
Josh Clark, Big Medium

Plenary-1
Chair: Chris Mungall, Lawrence Berkeley National Laboratory

• Taking a Dive: Experiments in Deep Learning for Automatic Ontology-based Annotation of Scientific Literature (Prashanti Manda)-25 minutes
• A Quality Assurance Methodology for ChEBI Ontology Focusing on Uncommonly Modeled Concepts (Ling Zheng) -25 minutes
• Transforming and Unifying Research with Biomedical Ontologies: The Penn TURBO project (Chris Stoeckert) -25 minutes
• Domain Informational Vocabulary Extraction Experiences with Publication Pipeline Integration and Ontology Curation (Amit Gupta) -20 minutes
• ELIXIR Interoperability: Standardisation of identifiers, schemas, and ontologies for scientific communities (Sirarat Samtivijail) -20 minutes

Plenary-2
Chair: Melissa Haendel, Oregon State University

• The Identity and Mereology of Pathological Dispositions (Adrien Barton) -20 minutes
• TOCSOC: A temporal ontology for comparing the survival outcomes of clinical trials in oncology (Deendayal Dinakarpandian) -20 minutes
• On the statistical sensitivity of semantic similarity metrics (Prashanti Manda) -15 minutes
• Phenotype Ontology workshop report (Phenotype Ontology Group) -15 minutes
• Flash Talks (Posters and Demo) - PART I
  Posters P01-P16 (See list)

Plenary-3
Chair: Christian Stoeckert, University of Pennsylvania

• KTAO: A kidney tissue atlas ontology to support community-based kidney knowledge base development and data integration (Yongqun He)-21 minutes
• Ontology-Enhanced Representations of Non-image Data in The Cancer Image Archive (Jonathan Bona)-20 minutes
• Does the Foundational Model of Anatomy ontology provide a knowledgebase for learning and assessment in anatomy education? (Melissa Clarkson)-21 minutes
• The New SNOMED CT International Medicinal Product Model (Olivier Bodenreider) -21 minutes
• An (ontological) patient perspective (Melissa Haendel) -18 minutes
• Planteome & BisQue: Automating Image Annotation with Ontologies using Deep-Learning Networks (Justin Preece/Dimitri Trigkakis)-18 minutes

Changing Face of Agriculture: Data-driven opportunities for nutrition and health
Parag Chitnis, NIFA

Plenary-4
Chairs: Mark Lieberman and Karl Mundorff, Oregon State University Advantage Accelerator

• Affordable Multiple Environment Sensors for Agriculture (Austin Meier, Sensiplicity LLC.) – 20 minutes
• Amit Dhingra, Phytelligence Inc. and Washington State Univ. – 20 minutes
• What if? Voice-Driven Food & Ag Traceability (Bruce Rasa, AgVoice Inc.) – 20 minutes
• Innovation discussion - 15 minutes
• Innovation Challenge - 45 minutes
  • Hands on Innovation idea exercise

Plenary-5
Chair: Pankaj Jaiswal

• Invited talk: Taxa, metacoder, poppr and vcfR: Four packages for parsing, visualization, and manipulation of genetic, genomic and metagenomic data in R. (Nik Grunwald, USDA ARS) - 25 minutes
• Invited talk: Vocabularies, Ontologies, APIs, and Formats for Heterogeneous High Throughput Crop Phenotyping Data (David LeBauer) - 25 minutes
• Invited talk: GO-MAP Implements CAFA Tools: Improved Automated Gene Function Annotation for Plants (Carolyn Lawrence) - 25 minutes
• Invited talk: Designing and Building the IC-FOODS Foundry: Community, Technology, and Standards for a Semantic Web of Food (Matthew Lange) - 25 minutes
• Reference Ontologies for plants, standardized annotations and helping accelerated plant breeding efforts (Pankaj Jaiswal) - 20 minutes

Plenary-6
Chairs: William Duncan

• Formalizing the Representation of Immune Exposures for Human Immunology Studies (Randi Vita)-20 minutes
• Quality Assurance of Ontology Content Reuse (Michael Halper)-20 minutes
• Can a Convolutional Neural Network Support Auditing of NCI Thesaurus Neoplasm Concepts? (Hao Liu)-20 minutes

Plenary-7
Chairs: Damion Dooley and William Hsiao

• Test-driven Ontology Development in Protégé (Patrick Rodler)-20 minutes
• Standardizing Ontology Workflows Using ROBOT (Rebecca Tauber)-20 minutes
• Formal Ontological Framework for representation of Food Phenotype, Sensation, Perception Tractable Flavor (Tarini Naravane)-20 minutes
• OOPS: The Ontology of Plant Stress, A semi-automated standardization methodology (Austin Meier)-20 minutes

CLOSING remarks

Workshop-W12
Vaccine and Drug Ontology VDOS Studies
Organizers: Cui Tao, Oliver He, Junguk Hur