ImmPort Ontology Conference

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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

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)

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