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Program in Detail

Aug 6 | Aug 7 | Aug 8 | Aug 9 | Aug 10 | Aug 11 | Aug 12

Venue

CH2M HILL Alumni Conference Center
725 SW 26th St,Corvallis, OR 97331,USA
Google map location | Venue Map

Program | At a glance | PDF

Monday, August 6, 2018 | Venue Map

Time Program Title Room #
8:00 AM
Registration  Alumni Center Foyer
8:00-9:00 am Breakfast  
9:00-9:15 am Welcome Willamette Room 115A-B
9:15-10:15 am

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

Willamette Room 115A-B
10:15-10:30 am Coffee Break  
10:30-12:30 pm Workshop-W01
Phenotype Ontologies Traversing All The Organisms (POTATO) (Session-2)
Aligning phenotype ontologies using design patterns
Willamette Room 115A-B
12:30-1:30 pm Lunch  
1:30-3:30 pm Workshop-W01
Phenotype Ontologies Traversing All The Organisms (POTATO) (Session-3)
Aligning phenotype ontologies using design patterns
Willamette Room 115A-B
3:30-4:00 pm Coffee Break  
4:00-5:30 pm Workshop-W01
Phenotype Ontologies Traversing All The Organisms (POTATO) (Session-4)
Aligning phenotype ontologies using design patterns
Willamette Room 115A-B
5:30 PM Dinner on your own  

 

Tuesday August, 7, 2018| Venue Map

Time Program Title Room #
8:00 AM Registration Alumni Center Foyer
8:00-9:00 am Breakfast + Poster setup and Vieweing Alumni Center Foyer
9:00-9:15 am

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

Cascade Ballroom 110
9:15-10:15 am

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

Cascade Ballroom 110
10:15-10:30 am Coffee Break + Poster setup and Vieweing Alumni Center Foyer
10:30-12:30 pm Workshop Group Session-1  
Workshop-W02
Ontology 101 (Part-I): A how-to guide to create, manage, and release an OBO ontology
Organizers: Nicole Vasilevsky, James A. Overton, Melissa Haendel, Chris Mungall, Rebecca Tauber
Cascade Ballroom 110

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

Johnson Lounge 102
Workshop-W04
Ontology-driven text-mining analysis and normalization of free-text specimen descriptions
Organizers: Damion Dooley, Gurinder Gosal, William Hsiao
Willamette Room 115A-B
Workshop-W05
Gramene Pathway Jamboree
Organizer: Suhma Naithani
Board Room Second floor
12:30-1:30 pm Lunch + Poster setup and Vieweing Alumni Center Foyer
1:30-3:30 pm Workshop Group Session-2  
Workshop-W02
Ontology 101 (Part-II): A how-to guide to create, manage, and release an OBO ontology
Organizers: Nicole Vasilevsky, James A. Overton, Melissa Haendel, Chris Mungall, Rebecca Tauber
Cascade Ballroom 110

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.)
Willamette Room 115A-B
Workshop-W07
Expanding the Informed CONSENT Ontology to support Specimen and Data Sharing
Organizers: Frank J. Manion and Jihad Obeid
Johnson Lounge 102
Workshop-W08
Data Standards and Knowledge Sharing in Biodiversity -Tools and Applications
Organizers: Laurel Cooper and Marie-Angélique Laporte
Elle Burlingham 111A-B
Workshop-W05
Gramene Pathway Jamboree
Board Room Second floor
3:30-4:00 pm Coffee Break + Poster setup and Vieweing Alumni Center Foyer
4:00-6:00 pm Workshop Group Session-3  
Workshop-W01
Phenotype Ontologies Traversing All The Organisms (POTATO) Session-5
Organizers: David Osumi-Sutherland, Nico Matentzoglu, Nicole Vasilevsky, Melissa Haendel, Chris Mungall, Jim Balhoff
Cascade Ballroom 110
Workshop-W09
Building Ontologies with Basic Formal Ontology
Organizer: Barry Smith
Willamette Room 115A-B

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

4:00 - 4:05 pm Welcome
4:05 - 4:25 pm The Cell Line Ontology-based Representation, Integration and Analysis of Cell Lines Used in China (Hongjie Pan, Xiaocui Bian, Sheng Yang, Yongqun He, Yuqin Liu, and Xiaolin Yang) - full length paper
4:25 - 4:45 pm OSCI: Standardized stem cell ontology representation and use cases for stem cell investigation (Yongqun He, William D. Duncan, Daniel J. Cooper, Jens Hansen, Ravi Iyengar, Edison Ong, Kendal Walker, Omar Tibi, Sam Smith, Lucas Serra, Jie Zheng, Sirarat Sarntivijai, Stephan Schurer, K. Sue O’shea, and Alexander D. Diehl) - full length paper
4:45 - 5:05 pm The Cancer Cell Ontology (Lucas Serra, William Duncan and Alexander Diehl) - full length paper
5:05 - 5:15 pm Connecting cell population descriptions and gating definitions through ontologies (Randi Vita, James A. Overton, Alexander Diehl, Kei-Hoi Cheung, Patrick Dunn, Steven Kleinstein, and Bjoern Peters) - podium presentation
5:15 - 5:25 pm Semantic Interoperability: Challenges and Opportunities in Cell Type Knowledge Representation (Richard Scheuermann, Brian Aevermann, and Mohamed Keshk) - podium presentation
5:25 - 6:00 pm General discussion (coordinated by workshop organizers)
Theme: Design pattern representation of normal vs diseased conditions in cells 
  • What are the common design patterns for normal and diseased cells? 
  • Difference between normal and diseased cells, and how to ontologically represent the transformation from a normal cell to diseased cell?
  • How to represent additional information (e.g., gene markers) in ontology? 
Elle Burlingham 111A-B
Workshop-W05
Gramene Pathway Jamboree
Board Room Second floor
6:00-8:00 pm Poster and Demo Session-1 Cascade Ballroom 110
  Social and Mixer Alumni Center Foyer
6:30-7:00 pm Flash Talks (Posters and Demo) - PART I
Posters P01-P16 (See list)
Cascade Ballroom 110

 

Wednesday August 8, 2018 | Venue Map

8:00 AM Registration Alumni Center Foyer
8:00-9:00 am Breakfast + Poster setup and Vieweing Alumni Center Foyer
9:00-9:15 am Welcome
Cynthia Sagers, Vice President Research, Oregon State University
Cascade Ballroom 110
9:15-10:15 am

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

The Care and Feeding of Algorithms
Josh Clark, Big Medium

Cascade Ballroom 110
10:15-10:30 am Coffee Break + Poster setup and Vieweing Alumni Center Foyer
10:30-12:30 pm

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

Cascade Ballroom 110
10:30-12:30 pm Workshop-W05
Gramene Pathway Jamboree
Organizer: Sushma Naithani
Board Room Second floor
12:30-1:30 pm Lunch + Poster setup and Vieweing Alumni Center Foyer
1:30-3:30 pm

Plenary-2
Chair: Melissa Haendel, Oregon State University

Cascade Ballroom 110
1:30-3:30 pm Workshop-W05
Gramene Pathway Jamboree
Organizer: Sushma Naithani
Board Room Second floor
3:30-4:00 pm Coffee Break + Poster setup and Vieweing Alumni Center Foyer
4:00-6:00 pm

Plenary-3
Chair: Christian Stoeckert, University of Pennsylvania

Cascade Ballroom 110
4:00-6:00 pm Workshop-W05
Gramene Pathway Jamboree
Board Room Second floor
6:00-8:00 pm Poster and Demo Session-2 Cascade Ballroom 110
Social and Mixer Alumni Center Foyer
6:30-7:00 pm Flash Talks (Posters and Demo) - PART II
Posters P17-P33 (See list)
Cascade Ballroom 110

 

Thursday, August 9, 2018 | Venue Map

8:00 AM Registration Alumni Center Foyer
8:00-9:00 am Breakfast Alumni Center Foyer
9:00-9:15 am Welcome
Joyce Loper, Associate Dean, College of Agricultural Sciences, Oregon State University
Cascade Ballroom 110
9:15-10:15 am Keynote talk-3
Chairs: TBD

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

Cascade Ballroom 110
10:15-10:30 am Coffee Break Alumni Center Foyer
10:30-12:30 pm

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
Cascade Ballroom 110
10:30-12:30 pm Workshop-W05
Gramene Pathway Jamboree
Organizer: Sushma Naithani
Board Room Second floor
12:30-1:30 pm Lunch Alumni Center Foyer
Innovation Challenge continues in last 30 minutes of lunch Cascade Ballroom 110
1:30-3:30 pm

Plenary-5
Chair: Pankaj Jaiswal

Cascade Ballroom 110
1:30-3:30 pm Workshop-W05
Gramene Pathway Jamboree
Board Room Second floor
3:30-4:00 pm Coffee Break  
4:00-5:00 pm Panel Discussion (Future needs, Directions, Projects, Collaborations, Deficiencies) Cascade Ballroom 110
  Workshop-W05
Gramene Pathway Jamboree
Board Room Second floor
5:00-6:00 pm Poster and Demo Session-3 Cascade Ballroom 110
6:00-6:30 pm Drop your belongings in your room and/or assemble in the conference venue Lobby -
6:30 PM Depart for Conference Dinner (Transport will be provided) Alumni center front enterance
6:45-9:00 Conference Dinner Off Campus

 

Friday, August 10, 2018 | Venue Map

8:00 AM Registration Alumni Center Foyer
8:00-9:00 am Breakfast Alumni Center Foyer
9:00-9:15 am Welcome Cascade Ballroom 110
9:15-10:15 am

Plenary-6
Chairs: William Duncan

Cascade Ballroom 110
9:15-10:15 am Workshop-W05
Gramene Pathway Jamboree
Board Room Second floor
10:15-10:30 am Coffee Break  
10:30-12:00 pm

Plenary-7
Chairs: Damion Dooley and William Hsiao

CLOSING remarks

Cascade Ballroom 110
10:30-12:00 pm Workshop-W05
Gramene Pathway Jamboree
Board Room Second floor
12:00-1:00 pm Lunch  
12:15-3:15 pm Workshop Group Session-4  
12:15-3:15 pm Workshop-W11
Biomedical Health Knowledge Integration and Dissemination : Human Disease Ontology (BIG-DATA DISEASE Part-I & II)
Organizers: Lynn Schriml and Michelle Giglio
Trysting Tree 114A-B
1:00-3:00 pm

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

Willamette Room 115A-B
3:00-3:30 pm Coffee Break  
3:30-6:00 pm Workshop Group Session-5  
  Workshop-W13
Machine Learning (Preworkshop + Registration)
Willamette Room 115A-B
6:00 PM Dinner on your own  

 

Saturday, August 11, 2018 | Venue Map

8:00 AM Registration Alumni Center Foyer
8:00-9:00 am Breakfast Alumni Center Foyer
9:00-9:15 am Welcome  
9:15-10:15 am Workshop-W13
Machine Learning (Session-1)
Willamette Room 115A-B
10:15-10:30 am Coffee Break  
10:30-12:30 pm Workshop-W13
Machine Learning (Session-2)
Willamette Room 115A-B
12:30-1:30 pm Lunch  
1:30-3:30 pm Workshop-W13
Machine Learning (Session-3)
Willamette Room 115A-B
3:30-4:00 pm Coffee Break  
4:00-5:30 pm Workshop-W13
Machine Learning (Session-4)
Willamette Room 115A-B
5:30 PM Dinner on your own  

 

Sunday, August 12, 2018| Venue Map

8:00 AM Doors Open  
8:00-9:00 am Breakfast Alumni Center Foyer
9:00-9:15 am Remarks and Q&A Willamette Room 115A-B
9:15-10:15 am Workshop-W13
Machine Learning (Session-5)
10:15-10:30 am Coffee Break  
10:30-12:30 pm Workshop-W13
Machine Learning (Session-6)
Willamette Room 115A-B
12:30-1:30 pm Lunch  
1:30-3:30 pm Workshop-W13
Machine Learning (Session-7)
Willamette Room 115A-B
3:30-4:00 pm Coffee Break  
4:00-5:30 pm Workshop-W13
Machine Learning (Session-8)
Discussion and CLOSING
Willamette Room 115A-B
5:30 PM Dinner on your own