Details : Day-1/Mon | Day-2/Tue | Day-3/Wed | Day-4/Thrs | Day-5/Fri (satellite meeting)

Day-1  Program Details (View at a glance)

Monday, August 1, 2016

8:00am onwards
Lobby/Foyer

Conference registration opens

8:00am-9:00am
Lobby/Foyer

Breakfast + Poster setup (Look for the Poster #)

9:00am-9:15am
Cascade Ballroom 110ABC

Welcome

Dr. Pankaj Jaiswal, ICBO 2016 Conference Chair & Associate Prof. Oregon State University
Prof. Joyce Loper, Associate Dean, College of Agricultural Sciences, Oregon State University

9:15am-10:15am
Cascade Ballroom 110ABC

Keynote Address

Chair: Kevin Cohen, University of Colorado School of Medicine

Information Retrieval and Text Mining Evaluation Must Go Beyond “Users”: Incorporating Real-World Context and Outcome
Prof. William (Bill) Hersh, MD, Oregon Health & Science University (OHSU)

10:15am-10:30am
Lobby/Foyer

Coffee Break + Poster setup (Look for the Poster #)

10:30am-12:30pm
Cascade Ballroom 110ABC

BioCreative Plenary Session #1

Text mining-facilitated models of curation

Chair: Lynette Hirschman

10:30am -10:50am BT101: SourceData: Making Data discoverable (Nancy George, EMBO, Germany)
10:50am -11:10am  BT102: Cycles of Scientific Investigation in Discourse - Machine Reading Methods for the Primary Research Contributions of a Paper (Gully Burns, USC-ISI, USA)
11:10am -11:30am  BT103: Collaborative Workspaces for Pathway Curation (Emek Demir, OHSU, USA)
11:30am -11:50am  BT104: Crowdsourcing Protein Family Database Curation (Matt Jeffryes,  EMBL-EBI, UK)
11:50am -12:20pm  BT105: Opportunities and challenges presented by Wikidata in the context of biocuration (Benjamin Good,  The Scripps Research Institute, USA)
12:20pm -12:30pm Discussion
10:30am-12:30pm
Elle Burlingham Room 111AB

ICBO Workshop W01 (More info)

Novel approaches to visualizing big data sets (Part I)

Organizers: Eugene Zhang and Yue Zhang

10:30am-11:30am W01-01: A Keynote talk on 'Big Data Visual Analysis' (Christopher Johnson)
11:30am-12:00pm W01-02: Topology-Driven Data Visualization of Large-Scale Tensor Fields (Yue Zhang)
12:00pm-12:30pm W01-03: Computer Vision for Next Generation Phenomics and Tree of Life (Sinisa Todorovic)

10:30am-12:30pm
Trysting Tree Room 114AB

ICBO Workshop W02 (More info)

OmniSearch and Beyond: Ontology-based biomedical information integration and knowledge acquisition for miRNAs

Organizer: Jingshan Huang
10:30am-12:30pm
Willamette Room 115

ICBO Workshop W03 (More info)

Integrating Ontological and Genomic Analysis with Galaxy

Organizer: Dave Clements

This is a hands on exercise. Please bring your laptops.
10:30am-12:30pm
Boardroom (Upstairs)

ICBO Workshop W04 (More info)

Representing social and legal entities in the biomedical domain (Part I)

Organizers:  Mathias Brochhausen and William Hogan

10:30am - 11:00am W04-01: Ontology of the Organigram (Barry Smith)
11:00am - 11:30am W04-02: Relations between Institutional roles and deontic roles in biomedical organizations (Neil Otte and Mathias Brochhausen)
11:30am - 12:00pm W04-03: An ontological study of healthcare corporations and their social entities (Mauricio Almeida)
12:00pm-12:30pm Open Discussion

12:30pm-1:30pm
Lobby/Foyer

Lunch + Poster setup (Look for the Poster #)

1:30pm-3:30pm
Cascade Ballroom 110ABC

BioCreative Plenary Session #2

Text mining in precision medicine

Chair: Donald Comeau

1:30pm-2:00pm  BT201: Text mining to enable routine personalized cancer therapy (Hua Xu, The University of Texas Health Science Center at Houston)
2:00pm-2:30pm BT202: Social Media Mining for Pharmacovigilance (Graciela Gonzalez, Arizona State University)
2:30pm-2:50pm BT203: MutD – A PubMed Scale Resource for Protein Mutation-Disease Relations through Bio-Medical Literature Mining (Ravikumar Komandur Elayavilli, Majid Rastegar-Mojarad and Hongfang Liu, Mayo Clinic)
2:50pm-3:10pm BT204: CancerMine: Knowledge base construction for personalised cancer treatment (Jake Lever, Martin Jones and Steven Jones, Canada's Michael Smith Genome Sciences Centre)
3:10pm-3:30pm BT205: Text Mining for Drug Development: Gathering Insights to Support Decision Making (Sherri Matis-Mitchell, DataStar Insights)
1:30pm-3:30pm
Elle Burlingham Room 111AB

ICBO Workshop W01 (More info)

Novel approaches to visualizing big data sets (Part II)

Organizers: Eugene Zhang and Yue Zhang

1:30pm-2:30pm W01-04: Telling a genome's story graphically (Suzanna Lewis)
2:30pm-3:00pm W01-05: Uncertainty analysis and visualization in Large-Scale Vector Fields (Eugene Zhang)
3:00pm-3:30pm Open Discussion
1:30pm-3:30pm
Boardroom (Upstairs)

ICBO Workshop W04 (More info)

Representing social and legal entities in the biomedical domain (Part II)

Organizers:  Mathias Brochhausen and William Hogan

1:30pm - 2:00pm W04-04: Who's paying and who's graying?  The organizations and roles associated with insurance policies, funding agencies, and national census data. (Amanda Hicks and William Hogan)
2:00pm - 2:30pm W04-05: Social and legal entities in the obstetric and neonatal domain (Fernanda Farinelli and Mauricio Almeida)
2:30pm - 3:15pm Open Discussion
3:15pm - 3:30pm Next Steps

1:30pm-3:30pm
Trysting Tree Room 114AB

ICBO Workshop W05 (More info)

Vaccine and Drug Ontology Studies (PART-I)

Organizers: Cui Tao, Yongqun (Oliver) He and Sivaram Arabandi

1:30pm-1:40pm Welcome
1:40pm-2:05pm W05-01: On Prescribing Drug Prescriptions (Ryeyan Taseen)
2:05pm-2:30pm W05-02: Therapeutic Indications and Other Use-case-driven Updates in the Drug Ontology Anti-malarials, Anti-hypertensives, Opioid Analgesics, and a Large Term Requset (William Hogan)
2:30pm-2:55pm W05-03: Modulated Evaluation Metrics For Drug-Based Ontologies (Tuan Amith)
2:55pm-3:20pm W05-04: LAERTES : An open scalable architecture for linking pharmacovigilance evidence sources with clinical data (Richard Boyce)
1:30pm-4:00pm
Willamette Room 115

ICBO Workshop W06 (More info)

OBO Tutorial: Open Biological and Biomedical Ontologies in Action

Organizer: James Overton

1:30pm-1:45pm W06-01: Introduction to Open Biomedical Ontologies (Barry Smith)
1:45pm-2:10pm W06-02: Using and Reusing Ontologies (James Overton)
2:10pm-2:35pm W06-03: Setting up an Ontology project (Chris Mungall)
2:35pm-2:43pm W06-04: Example: Biobanking (Chris Stoeckert)
2:43pm-2:52pm W06-05: Example: The Immune Epitope database (Randi Vita)
2:52pm-3:00pm W06-06: Example: ImmPort (Barry Smith)
3:00pm-3:10pm W06-07: Example: The Monarch Initiative (Melissa Haendel)
3:10pm-3:30pm W06-08: Ontology Communities (Melissa Haendel)

3:30pm-4:00pm
Lobby/Foyer

Coffee Break + Poster setup (Look for the Poster #)

4:00pm-6:00pm
Room 110A/B

BioCreative Plenary Session #3

Domain portability or generalizability across medical literature

Chairs: Kevin Bretonnel Cohen and Donald Comeau

4:00pm-4:30pm BT301: NLP for the Institute: Developing and Deploying an NLP Capability to Accelerate Cancer Research (Aaron Cohen, Oregon Health & Science University, USA)
4:30pm-5:00pm BT302: Annotations for biomedical research and healthcare -- Bridging the gap (Olivier Bodenreider, LHNCBC, U.S. National Library of Medicine)
5:00pm-5:30pm BT303: PubAnnotation: a public shared platform for scientific literature annotation (Jin-Dong Kim, Database Center for Life Science, Japan)
5:30pm-6:00pm BT304: BioCconvert: A Conversion Tool Between BioC and PubAnnotation (Donald C. Comeau, Rezarta Islamaj Dogan, Sun Kim, Chih-Hsuan Wei, W. John Wilbur and Zhiyong Lu, NCBI, National Institutes of Health, USA)
4:00pm-6:00pm
Trysting Tree Room 114AB

ICBO Workshop W05 (More info)

Vaccine and Drug Ontology Studies (PART-II)

Organizers: Cui Tao, Yongqun (Oliver) He and Sivaram Arabandi

4:00pm-4:25pm W05-05: Co-occurrence Analysis of Adverse Events for Typhoid Fever Vaccines (Yuji Zhang)
4:25pm-4:50pm W05-06: Hierarchical Sentiment Analysis on HPV Vaccines Related Tweets Using Machine Learning Based Approaches (Cui Tao)
4:50pm-5:15pm W05-07: Ontology-based literature mining of E. coli vaccine-associated gene interaction networks (Junguk Hur)
5:15pm-5:30pm Closing
4:00pm-6:00pm
Elle Burlingham Room 111AB

ICBO Workshop W07 (More info)

Topics in OWL Reasoning for BFO-based Ontologies

Organizer: Alan Ruttenberg
4:00pm-6:00pm
Willamette Room 115

ICBO Workshop W08 (More info)

Noctua: An all in one solution for ontology development and annotation (Part I) (If required, to to be continued at the Demo Session #1 as Demo# D105)

Organizers: Suzanna Lewis and Chris Mungall

4:00pm-6:00pm
Boardroom (Upstairs)

ICBO Workshop W09 (More info)

OBI-ECO Interactions & Evidence

Organizers: Marcus Chibucos, Jie Zheng and Chris Stoeckert

6:00pm
Room 110A/B

ICBO and BioCreative Joint Posters and Demo Session #1

  • DEMO
    • D101: Plant Image Segmentation and Annotation with Ontologies in BisQue (Justin Preece)
    • D102: SPARQL2OWL: towards bridging the semantic gap between RDF and OWL (M Alsharani, Robert Hoendorf)
    • D103-W12-05: The Phenoscape Knowledgebase: tools and APIs for computing across phenotypes from evolutionary diversity and model organisms (James Balhoff)
    • D104: Updates to the AberOWL ontology repository (MÁ Rodríguez-García, LUke Slater, Robert Hoehndorf))
    • D105: Noctua An all in one solution for ontology development and annotation (Part II continued from ICBO Workshop W09) (Suzi Lewis and Chris Mungall)
    • D106-BP04: Enhancing Information Accessibility of Publications with Text Mining and Ontology (Weijia Xu and Amit Gupta)

6:00pm
Lobby/Foyer & Cacade BallCascade Ballroom 110ABC

ICBO and BioCreative Joint Evening Mixer