IDO Workshop 2010

Background

A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for Biomedical Ontology (NCBO).

The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, including diseases of bacterial, viral, and eukaryotic origin.

Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to serve integration of a broad array of -omics, epidemiological and clinical data.

For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.

This NCBO Workshop on the Infectious Disease Ontology is funded by the United States National Institutes of Health through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028. Its content is solely the responsibility of the organizers and presenters and does not necessarily represent the official views of the National Human Genome Research Institute or the National Institutes of Health. Information on the National Centers for Biomedical Computing can be found at http://nihroadmap.nih.gov/bioinformatics.

Goals of the Meeting

• The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency.

• We will explore the benefits of the IDO controlled vocabulary, especially in advancing the work of the Bioinformatics Resource Centers, in areas such as:

clinical data integration

text and data mining

genetic susceptibility to infectious disease

disease surveillance

plant infectious disease

• The meeting will also address relations between IDO and other parallel initiatives, including PRIME, DebugIT, and the various IDO extension ontologies.

• To address these goals, speakers are asked to address the following points
  • The goals of their project

biological questions for research projects

content and functions for computational resource projects

• • The tasks for which terminologies are needed
  • The terminologies currently being using

brief description of any terminologies developed specifically for the project

description of the ways in which current terminologies are inadequate for the project’s needs

Schedule

Tuesday, December 7

• 7:00-9:00pm Welcome Reception (Sponsored by the University of Texas Southwestern Medical Center at Dallas; Cash Bar)

Day 1: Wednesday, December 8

• 8:30am Registration & Continental Breakfast

• 9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research (Session chair: Smith)

Lindsay Cowell: Scope and Content of IDO

Barry Smith: How use of IDO creates information integration across multiple domains

• 10:00am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)

Richard Scheuermann

BRCs Overview

ViPR - Virus Pathogen Resource

IRD - Influenza Research Database

Chris Stoeckert

EuPathDB - Eukaryotic Pathogen Database Resource

• 11:00am Refreshment Break

• 11:30am Session 1 continued (Session chair: Sobral)

Pantelis Topalis

VectorBase - Invertebrate Vectors of Human Pathogens

Bruno Sobral

PATRIC - Pathosystems Resource Integration Center

PathogenPortal - Bioinformatics Resource Centers Portal

• 12:30pm Lunch Break

• 2:00pm Session 2: Additional large data and information repositories relevant for infectious disease research (Session chair: Scheuermann)

Richard Scheuermann

ImmPort - Immunology Database and Analysis Portal

TBD

PRIME - Program for Research on Immune Modeling and Experimentation

• 3:00pm Session 3: General discussion of the Utility of IDO as a Controlled Vocabulary (Session chair: Smith)

• 4:00pm Refreshment Break

• 4:30pm Session 4: Decision Support Use Cases (Session chair: Fuentes)

Saul Lozano-Fuentes - Dengue/vector control

Daniel Schober - DeBugIT - Detecting and Eliminating Bacteria using Information Technology

• 5:30pm End of Day 1

• 6:00pm Dinner (for interested participants; No-host/Dutch treat)

Day 2: Thursday, December 9

• 8:30am Continental Breakfast

• 9:00am Session 1: Data Integration Use Cases (Session chair: Goldfain)

Alexander Diehl - Comprehensive Annotation System for Infectious Disease Data

Anna Maria Masci - CFAR - Centers for AIDS Research

Stanley Schwartz - UB HIV project

Mélanie Courtot - PCIRN - Public Health Agency of Canada / Canadian Institutes of Health Research Influenza Research Network

Albert Goldfain - The Staphylococcus aureus IDO Extension

• 11:00am Refreshment Break

• 11:30am Session 2: IDO Extensions (Session chair: Ruttenberg)

Yu Lin - Brucellosis Ontology

Burke Squires - Flu-IDO

• 12:30pm Lunch Break

• 2:00pm Session 2 continued

Oliver He - VIOLIN - VO

Pankaj Jaswal - Plant IDO

• 3:00pm Session 3: Next Steps Lindsay Cowell

• 4:00pm Close of NCBO/IDO 2010 Workshop

Format

Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.

Venue

A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:

Hilton Baltimore BWI Airport 1739 West Nursery Road Linthicum Heights, MD 21090

To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name: NCBO – IDO 2010 / Group Code: NCBO.

To access our online reservation link, click [1]

• The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport, and complimentary internet access in the lobby-area.

• NCBO–IDO 2010 attendees will also receive complimentary internet access in their guest room.

• To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation no later than November 15, 2010.

Driving directions for local participants can be found here [2]

Participants

Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)

Sivaram Arabandi (Case Western Reserve University)

Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)

Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)

Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)

Alexander Diehl (Gene Ontology / The Jackson Laboratory)

Saul Lozano-Fuentes (Colorado State University)

Albert Goldfain (University at Buffalo)

Yongqun "Oliver" He (University of Michigan Medical Center)

Pankaj Jaiswal (Plant Ontology / Oregon State University)

Jessica Kissinger (Center for Tropical & Emerging Global Diseases / University of Georgia)

Yu Lin (University of Michigan Medical Center)

Joanne Luciano (Predictive Medicine, Inc. and Rensselaer Polytechnic Institute (RPI))

Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)

Anna Maria Masci (Duke University Medical Center)

Alan Ruttenberg (Science Commons / University at Buffalo)

Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)

Daniel Schober (Universität Freiburg, Germany)

Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)

Barry Smith (NCBO / University at Buffalo)

Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)

Burke Squires (University of Texas Southwestern Medical Center at Dallas)

Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)

Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)

Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)

Miguel H. Torres-Urquidy (CDC / OID/ NCIRD)

Patricia Whetzel (NCBO, Stanford)

Allen Xiang (University of Michigan Medical Center)

Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)