Session Descriptions

Research Highlights

In a series of oral presentations, this session will showcase new scientific findings and impactful research being undertaken across BD2K, highlighting the breadth of activities ranging from molecules to populations.

Presenters on November 29, 2016, are:

1. Soojin Park: Predicting Vasospasm After Subarachnoid Hemorrhage Using High-Frequency Physiological Data
2. Anders Dohlman: Predicting Adverse Cardiovascular Events for Tyrosine Kinase Inhibitors From Molecular Features
3. Alexander Tropsha: Hypothesis Fusion to Improve the Odds of Successful Drug Repurposing
4. David Haussler: BD2K and Global Genomic Data Sharing
5. Vikas Singh: Multi-resolution Analysis of Brain Connectivity: Associations With PET-Based Alzheimer’s Pathology
6. Paul Avillach: Identification of Genotype-Phenotype Associations in Phelan-McDermid Syndrome Using Patient-Sourced Data

Presenters on November 30, 2016, are:

1. Clark Glymour: Toward a Causome of the Brain
2. Wilbert Van Panhuis: Integrating Data With Epidemic Simulators to Improve Pandemic Preparedness: Chikungunya in Colombia
3. Amin Emad: Knowledge-Guided Prioritization of Genes Determinant of Drug Resistance Using ProGENI
4. Eni Halilaj: Predicting Phenotypes of Osteoarthritis Progression
5. Quynh Nguyen: Geotagged Tweets as Predictors of County-Level Health Outcomes
6. Peipei Ping: Understanding Cardiovascular Health and Revealing Pathogenic Insights via Text-Mining Approaches

Moderator: Jennie Larkin

Data Commons Session (11/29)

This session will commence with an overview of the “Data Commons” and will provide updates on four major ongoing activities: the Commons Framework pilots, the Cloud Credits Model, the Reference Datasets and Resource Indexing.

This session will also serve as a launching pad for discussion about other BD2K research activities that could synergize with the Data Commons to enable the development and implementation of a biomedical data ecosystem

Presenters are:

1. Vivien Bonazzi: NIH Data Commons Overview

A panel discussion will follow with NIH staff involved the Data Commons development including:

Vivien Bonazzi (NIH Data Commons, Reference Datasets); Valentina Di Francesco (Commons Framework); George Komatsoulis (Cloud Credits Model); Ian Fore, Dawei Lin, Ron Margolis, and Alison Yao (Resource Indexing).

Moderator: Vivien Bonazzi

Standards Development

Using appropriate data-related standards is critical for effectively transmitting, sharing, reusing, and harmonizing or integrating data. This session will focus on emerging topics in data-related standards and highlight tools or resources that address gaps, such as finding appropriate content standards to use in research; facilitating development and reuse of Common Data Elements; facilitating traversal across connected datasets through a Commons for Identifiers; and creating a flexible, extensible, expressive exchange format to represent phenotypic features.

Time will be allowed for discussion. Topics are:

1. Susanna-Assunta Sansone: An Informative and Educational Service for Community-Developed Standards (Biosharing)
2. Mark Musen: Use of Standard Common Data Elements (CDEs) in CEDAR
3. Julie McMurry: An Urban Dictionary of Identifier Syntax for the Data Integration Jungle (Prefix Commons)
4. Melissa Haendel : Making Phenotypic Data FAIR++ for Disease Diagnosis and Discovery (Phenotype Exchange Format)

Moderator: Sherri de Coronado

Training & Workforce Development

This session will showcase the wide variety of awards and activities in the BD2K Initiative aimed at training current and future scientists to use biomedical Big Data. These activities range from support for individual early career researchers to the development of resources, such as short courses, open educational resources, and infrastructure for the discovery of educational resources. Presenters and their topics are:

1. Jack Van Horn: Training Coordination Center’s Efforts to Foster New Collaborations Through the ROAD-Trip Program, Innovation Labs, and the BD2K Guide to the Fundamentals in Data Science Lecture Series
2. Jose-Luis Ambite: ERuDIte, the Educational Resource Discovery Index
3. Vivek Shetty: An example of One Center’s (MD2K’s) Training Efforts
4. Kevin Read: Curricula to Prepare Medical Librarians to Understand and Teach Data Management
5. Patricia Ordonez: Efforts at the University of Puerto Rico, Rio Pedras That Increase Didactic and Research Opportunities for Undergraduates and Their Instructors
6. Daniela Witten: University of Washington’s R25 Short Course
7. Rafael Irizarry: A BD2K-Funded MOOC and How It Influenced Classroom Instruction
8. Jonathan Chen: A Career Development Awardee Who Will Describe the Work That a BD2K K01 Allowed Him to Pursue

Moderator: Michelle Dunn

BioCADDIE & Resource Indexing

This session will explore digital object indexing drawing from the experiences of the bioCADDIE Data Discovery Index prototype (DataMed) and alternative/complementary indexing models and will address technical issues that contribute to “FIND.”

Presenters and their topics are:

1. Lucila Ohno-Machado: bioCADDIE: Progress and Next Steps
2. Henning Hermjakob: Omics Discovery Index – Discovering and Linking Public ‘Omics’ Datasets
3. Denis Torre: Datasets2Tools: Enriching DataMed With Canned Analyses
4. Susanna-Assunta Sansone: The DataMed DATS Model, Annotated With Schema.org
5. Tim Clark: The bioCADDIE Data Citation Implementation Pilot

Moderator: Ian Fore

Software, Analysis & Methods Development

This extended session will feature presentations of software tools and analysis methods developed by BD2K awardees.

1. Peter Rose: Compressive Structural Bioinformatics: Large-Scale Analysis and Visualization of the PDB Archive
2. Olgica Milenkovic: New Algorithms for RNA-Seq and ChiP-Seq Data Compression
3. Joseph Picone: EEG Event Detection Using Deep Learning
4. Chunlei Wu: BioThings APIs: Linked High-Performance APIs for Biological Entities
5. Jun Zhu: Curate Patient-Centric Multi-Omics Data for Precision Medicine
6. Satya Sahoo: Scientific Reproducibility Using the Provenance for Clinical and Healthcare Research Framework
7. Haixu Tang: Enabling Privacy-Preserving Biomedical Data Analytics in the Cloud and Across Institutions
8. Griffin Weber: Visualizing Healthcare System Dynamics in Biomedical Big Data
9. T.M. Murali: Using Crowds to Design Biological Network Visualizations
10. Avi Ma’ayan: GEN3VA: Aggregation and Analysis of Gene Expression Signatures From Related Studies
11. Gregory Cooper: Fast, Accurate Causal Search Algorithms From the Center for Causal Discovery (CCD)
12. David Page: Mining Electronic Health Records for Possible Drug Repositioning Opportunities
13. Charles Blatti: KnowEnG: Cloud-Based Environment for Scalable Analyses of Genomic Signatures
14. Martin O’Connor: A Standards-Based Model for Metadata Exchange

Moderator: Dave Miller

Initial Implementation of the Commons Session (11/30)

This session will build on the Day 1 “Data Commons” session with more detailed discussions of the Commons Framework pilots and Cloud Credits Model. The goal of this session is to develop new ideas for implementing a Data Commons.

Presenters are:

1. Neil McKenna & Michel Dumontier – Development of FAIR-ness Metrics
2. Michel Dumontier – API Interoperability
3. Umberto Ravaioli & Brian O’Connor – Workflow Sharing & Docker Registry
4. Lucila Ohno-Machado, Wei Wang, & Michel Dumontier – Data-Object Registry
5. Owen White & Ian Foster – A Roadmap for the Commons
6. George Komatsoulis – Cloud Credits Model

Following the presentation, there will be time allotted for interactive discussion and questions regarding the Data Commons.

Moderators: Valentina Di Francesco & Owen White

Collaborative Presentations

The BD2K Initiative aims to encourage collaborations, both among BD2K grantees and between BD2K grantees and others. By taking advantage of the consortium-based organization of the BD2K effort, such collaborations create synergies and accelerate progress beyond the abilities of individual research efforts to achieve the ambitious goals of the initiative.

Presenters and their topics are:

1. Pablo Roman-Garcia: ELIXIR; A European Distributed Infrastructure for Life-Science Information
2. Tim Clark: PREFIX: ACCESSION Compact Identifier Resolution: An EBI/CDL Collaboration
3. Mark Musen: When the World Beats a Path to Your Door: Collaboration in the Era of Big Data
4. Paul Thompson: Worldwide Big Data Collaborations: Examples From ENIGMA, Spanning 35 Countries
5. Ida Sim: Count Everything: Secure Count Query Framework Across Big Data Centers
6. Ben Heavner: Annual California BD2K Centers Regional Meetings – Building Connections Across Centers
7. Elvira Mitraka: Revisions to the Disease Ontology to Support the Alliance of Genome Resources

Moderator: TBD

Sustainability

This session will focus on metrics and measures of success for data preservation. Sustainable data preservation is critical to biomedical research communities and to funders of the sciences. Researcher needs should drive data lifecycle governance, with the selection of appropriate models to improve data management and longer term maintenance varying by the particular research community. This session will start with an introduction, a summary of the recent RFI on metrics to assess value of biomedical digital repositories (NOT-OD-16-133) ,and a series of short presentations and a panel discussion to initiate open dialogue on the emerging issues and strategies in this area, including archiving, preservation, and certification. Planned agenda:

1. Introduction: Allen Dearry
2. Results From Metrics RFI: Juli Klemm and/or Betsy Hsu
3. Panel Presentations and Discussion: Susan Gregurick, Moderator
4. David Giaretta: The Role of Trustworthy Digital Repositories in Sustainability
5. George Alter: The Stewardship Gap
6. Melissa Landrum: Archiving Interpretations of Variants in ClinVar
7. Cathy Wu: Interoperability, Sustainability, and Impact: A UniProt Case Study