Immunology Ontologies and Their Applications in Processing Clinical Data

The National Center for Biomedical Ontology (NCBO) in collaboration with the Protein Ontology (PRO) and the Infectious Disease Ontology (IDO) will host a three-day dissemination workshop in Buffalo, NY on June 11-13, 2012. Day 1 will provide a survey of current ontology-based research in immunology and infectious disease; Day 2 will be focused on flow cytometry; Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, and a session on the Ontology for General Medical Science.

Goals

Provisional goals of the meeting are:

To identify and coordinate activities on-going in immunology ontology and related fields, with special attention to the use of ontologies to support clinical data analysis in flow cytometry and other fields.

Registration

This meeting is free for registered participants. Space is limited and those interested in participating should contact Barry Smith as soon as possible.

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Draft Schedule

Day 1: Monday, June 11, 2012: 9:00am-5:00pm

An Overview of Ontologies to Support Research in Immunology and Infectious Disease

Morning: GO, PRO, CL, IO, IEO

Topics to be discussed will include:

Immune pathway representations

Representation of cells used in experiments such as: PBMCs, splenocytes, adherent cells

Representation of immunology experiments using OBI

Representing epitope mapping experiments for Immune Epitope Database (IEDB)

Lunchtime talk: Atul Butte (Stanford): Discovery of a novel inflammatory receptor and related drug for type 2 diabetes from integration of publicly-available microarray data

Afternoon: The Infectious Disease Ontology (IDO) and Its Extensions

Lindsay Cowell (Dallas): Update on IDO-Core

simplified definitions

new approach to MIREOTing

new terms/definitions/relations deriving from the work with Saul and potentially the work with Plant IDO

A Template for Creating an IDO Extension

Updates on IDO Extensions

Staph Aureus (Sa) IDO

A lattice of Sa IDO ontologies

Sa IDO as a tool for creating interoperable clinical case report forms

Sa IDO and Common Data Elements

IDO flu

IDO Bru

IDO HIV

IDO Mal

Day 2: Tuesday, June 12, 2012: 9:00am-5:00pm

Ontologies and Flow Cytometry Informatics

Morning: Flow cytometry typing of normal and malignant cell types

Alexander Diehl (Buffalo)

Overview of Hematopoietic Cell Types in the Cell Ontology

An Ontological Treatment of Protein Marker Expression on Multiple Myeloma Subtypes

Representative of Euroflow Consortium (to be identified): Overview of Euroflow Typing Panels

(To be identified): Clinical Flow Cytometry in HIV

Discussion of the ontological treatment of typing panels.

Afternoon: Automated gating of Flow Cytometry results and linking to the Cell Ontology

Ryan Brinkman (Vancouver):

1. Overview of the representation of flow cytometry assays in OBI

2. Overview of Flow Cap Competition & flowMeans

Richard Scheuermann (Dallas): Connecting results from automated FCM analysis systems with the Cell Ontology

Cliburn Chan (Duke): Flow cytometry analysis system

Topics to be discussed will include:

Methods to automatically link flow cytometry results to cell type identification.

Day 3: Wednesday, June 13, 2012:9:00am-6:00pm

9am-noon: TBD

noon-1pm: Lunch

1pm-3pm SESSION OPEN TO THE PUBLIC: Practical Applications of Ontologies in Clinical Research

Topics to be discussed will include:

Current work on Neurological Disease Ontology

Protein Ontology and the treatment of protein isoforms, mutations, and aggregates of relevance to Alzheimer's Disease

The HIV Ontology

3pm-6pm: Working Session on the Ontology for General Medical Science (OGMS)

Albert Goldfain (Blue Highway / Syracuse)

An update on OGMS

Close: 6:00pm

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Relevant ontology efforts

GO-IP Gene Ontology -- Immunological Process (Alex Diehl)

CL Cell ontology immune branches (e.g. for dendritic cells)

PRO Protein Ontology

IO Immunology Ontology (Lindsay Cowell and Alex Diehl)

IEO Immune Epitope Ontology (Bjoern Peters)

MHC Major Histocompatibility Complex Ontology (Bjoern Peters)

OGMS Ontology for General Medical Science (Albert Goldfain)

IDO Infectious Disease Ontology (Lindsay Cowell)

Vaccine Ontology (Oliver He)

AO Allergy Ontology (Alex C. Yu)

ND Neurological Disease Ontology (Alex Diehl)

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Participants will include

Ryan Brinkman (University of British Columbia, June 11-12)

Atul Butte (Stanford University)

Cliburn Chan (Duke University, June 11-12)

Lindsay Cowell (University of Texas Southwestern Medical Center)

Peter d'Eustachio (New York University, June 11-12)

Alex Diehl (University at Buffalo)

Albert Goldfain (University at Buffalo, Syracuse University and Blue Highway, Inc.)

Oliver He (University of Michigan)

Anna Maria Masci (Duke University)

Darren Natale (Georgetown University)

Dave Parrish (Digital Infuzion)

Bjoern Peters, (University of California at San Diego)

Alan Ruttenberg (University at Buffalo)

Richard Scheuermann (University of Texas Southwestern Medical Center)

Stanley A. Schwartz (University at Buffalo)

Barry Smith (University at Buffalo)

Cathy Wu (University of Delaware, Georgetown University)

Alex C. Yu (University at Buffalo)