ImmPort Ontology Conference

Where: Stanford University

When: September 4-5, 2013

Goals (tentative): The conference is divided into two parts.

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 an ontology-based strategy to address these problems.

Audience: 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.

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)ImmPort Ontologies

12:00 Lunch

13:00 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:

Thursday, September 5, 2013

8:30 Continental Breakfast

9:00 An Introduction to Ontology for Immunology

10:00 VDJServer (Lindsay Cowell)

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 (

Plus participants from Stanford