ImmPort Ontology Conference

Where: Stanford University

When: September 4-5, 2013

Audience: The conference is divided into two parts. Day 1 is intended for all those engaged in information-driven immunology research who have an interest in ontology and data standardization; Day 2 is intended to provide training for those interested in acquiring skills needed for working with ontologies to solve specific problems.

Participation: There is a limited number of places available for this meeting. If you are interested in attending please contact Barry Smith as soon as possible.

Goals (tentative): The goal of Day 1 is to survey the ontology work being done in support of NIAID-DAIT funded information-driven science, with special emphasis on

• identifying the ontology and data standardization needs of DAIT-funded experimental scientists,
• identifying ontologies to be used in submitting data from ImmPort,
• identifying strategies for data retrieval, including strategies based on natural language processing.

The goals of Day 2 are:

• to introduce those new to ontology to the tools and methods involved in ontology development and use,
• to provide an overview of ontology resources of particular interest to the ImmPort / HIPC and related communities,
• to work with immunologists who have data which pose special problems for handling in a resource such as ImmPort, and to develop detailed ontology-based strategies to address these problems that are designed to be of lasting utility.

Draft Schedule

Wednesday, September 4, 2013

8:30 Registration and Continental Breakfast

9:00 What Ontology Can Bring the DAIT Research Community

Overview by Barry Smith

10:30 Ontology, NLP and the Semantic Enhancement of Immunology Research Literature

Including presentation by Shai Shen-Orr (Technion Israel Institute of Technology)

12:00 Lunch

13:00 ImmPort Ontologies

An overview of ontologies proposed by ImmPort for use across the immunology research community. For background see here

• Anna Maria Masci: The Immunology Ontology
• Lindsay Cowell: The Infectious Disease Ontology

15:00 Flow Cytometry and CyTOF Data Using the Cell Ontology

• Courtot/Brinkman: http://ontology.buffalo.edu/pro/CytometryOntologyFramework.pdf The Cytometry-Ontology Framework]
• PRO, CL and CyTOF

Thursday, September 5, 2013

8:30 Continental Breakfast

9:00 An Introduction to Ontology for Immunology

10:00 Immunology in the Gene Ontology (Alexander Diehl)

10:30 VDJServer (Lindsay Cowell)

11:00 Further Use Cases

12:00 Lunch

13:00 Further Use Cases

16:00 Close

Participants (* = tentative)

Lindsay Cowell (UT Southwestern, Dallas)

• *Melanie Courtot / Ryan Brinkman (Vancouver, BC)

Alexander Diehl (ImmPort / Buffalo)

• *Anna Maria Masci (Duke)

Alan Ruttenberg (ImmPort / Buffalo) Shai Shen-Orr (ImmPort / Technion Institute) Barry Smith (ImmPort / Buffalo)

• *Christian Stoeckert (Penn)
• *Representatives of companies selling (for example) analytes

Very tentative:

• *James S. Cavenaugh (University of Rochester Medical Center)
• *Oliver Crespo (BD Biosciences, San Jose, CA)
• *Peter d'Eustachio (New York University)
• *Oliver He (University of Michigan)
• *Yu Lin (University of Michigan)
• *Darren Natale (Georgetown University)
• *Dave Parrish (Digital Infuzion)
• *Bjoern Peters (La Jolla Institute for Allergy and Immunology)
• *Veronica Shamovsky (NYU School of Medicine)
• *Cathy Wu (University of Delaware, Georgetown University)
• *Alex C. Yu (Seattle)

Plus participants from Stanford