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.

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

• 7:00pm Dinner (Dutch treat, venue to be announced)

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 - Lindsay Cowell and Barry Smith

• 9:30am 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

Richard Scheuermann

ImmPort - Immunology Database and Analysis Portal

TBD

PRIME - Program for Research on Immune Modeling and Experimentation

• 11:00am Refreshment Break

• 11:30am Session 1 (continued)

Bruno Sobral

PATRIC - Pathosystems Resource Integration Center

PathogenPortal - Bioinformatics Resource Centers Portal

Pantelis Topalis

VectorBase - Invertebrate Vectors of Human Pathogens

• 12:30pm Lunch Break

• 2:00pm Session 1 (continued)

Alexander Diehl - comprehensive annotation system for infectious disease data

General discussion on the utility of IDO as Controlled Vocabulary

• 3:30pm Refreshment Break

• 4:00pm Session 2: 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 (Dutch treat, venue to be announced)

Day 2: Thursday, December 9

• 8:30am Continental Breakfast

• 9:00am Session 3: Data Integration Use Cases (Session chair: Goldfain)

Anna Maria Masci - CFAR

Stanley Schwartz - UB HIV project

Mélanie Courtot - PCIRN

Albert Goldfain - SABG

• 11:00am Refreshment Break

• 11:30am Session 4 IDO Extensions (Session chair: Ruttenberg)

Lindsay Cowell - SaIDO

Burke Squires - fluIDO

• 12:30pm Lunch Break

• 2:00pm session 4 continued

Oliver He - VIOLIN - VO

Yu Lin - BO

Pankaj Jaswal - Plant IDO

3:30

Lindsay Cowell - Next Steps

• 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]

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

• The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport.

• 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.)

Supriya Mahajan (University at Buffalo)

Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)

Anna Maria Masci (Duke University Medical Center)

Bjoern Peters (University of California at San Diego)

Jessica Reynolds (University at Buffalo)

Alan Ruttenberg (Science Commons / University at Buffalo)

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

Daniel Schober (Universität Freiburg, Germany)

Stanley D. Schwartz (University at Buffalo)

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)

Patricia Whetzel (NCBO, Stanford)

Ashley Xia (NIH/NIAID)

Allen Xiang (University of Michigan Medical Center)

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