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.

The IDO is being considered for adoption 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 used

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

New Pre-Release Version of IDO

Following the workshop, we will release a new version of IDO. This version has only minor differences from the version released in May 2010 with respect to terms, definitions, and hierarchy. The primary difference is in the addition of OWL DL restrictions for many terms. This new version of IDO will be presented at the workshop and can be accessed via the following PURLs:

• Full IDO http://purl.obolibrary.org/obo/ido/2010-12-02/ido.owl
• Obsolete classes omitted http://purl.obolibrary.org/obo/ido/2010-12-02/ido-main.owl
• Axioms omitted http://purl.obolibrary.org/obo/ido/2010-12-02/ido-base.owl
• Asserted hierarchy only http://purl.obolibrary.org/obo/ido/2010-12-02/ido-asserted.owl
• OBO version, no axioms http://purl.obolibrary.org/obo/ido/2010-12-02/ido.obo

As always, comments, criticisms, and term requests are welcome. Please submit them on the issue tracker (http://code.google.com/p/infectious-disease-ontology/), email the discussion list (http://groups.google.com/group/ido-discuss), or email them directly to Lindsay Cowell (lindsay DOT cowell AT utsouthwestern DOT edu).

Schedule

Day 1: Wednesday, December 8

• 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 // Presentation

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

Richard Scheuermann

BRCs Overview: Virus Pathogen Resource (ViPR) and Influenza Research Database (IRD) // Presentation

Chris Stoeckert

EuPathDB - Eukaryotic Pathogen Database Resource // Presentation

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

Pantelis Topalis

VectorBase - Invertebrate Vectors of Human Pathogens // Presentation

Bruno Sobral

PATRIC - Pathosystems Resource Integration Center

PathogenPortal - Bioinformatics Resource Centers Portal

Presentation

• 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 // Presentation

Barry Smith

PRIME - Program for Research on Immune Modeling and Experimentation // Presentation

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

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

• 4:00pm Refreshment Break

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

Saul Lozano-Fuentes - Dengue/vector control // Presentation Runway Video

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

• 5:30pm End of Day 1

Day 2: Thursday, December 9

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

Alexander Diehl - Comprehensive Annotation System for Infectious Disease Data // Presentation

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

Albert Goldfain - Linking Vital Signs Data to IDO Disease Models // Presentation

Patricia Whetzel - NCBO Bioportal // Presentation

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

Yu Lin - Brucellosis Ontology // Presentation

Burke Squires - Flu-IDO // Presentation

• 2:00pm Session 2 continued

Oliver He - VIOLIN - VO // Presentation

Alan Zheng - OntoBee // Presentation

Pankaj Jaswal - Plant IDO

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

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 (University at Buffalo)

Saul Lozano-Fuentes (Colorado State University)

Andrei Gabrielian (NIAID / NIH)

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)

Alan Ruttenberg (Science Commons / University at Buffalo)

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

Daniel Schober (Universität Freiburg, Germany)

Barry Smith (NCBO / University at Buffalo)

Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)

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

Ram Sriram (National Institute of Science and Technology)

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)

Robert Williams (Uniformed Services University)

Allen Xiang (University of Michigan Medical Center)

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