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 also 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.

Wednesday, September 4, 2013

8:30 Registration and Continental Breakfast

9:00 What Benefits Can Ontology Bring to the DAIT Research Community?

Overview by Barry Smith

10:15 Break

10:30 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

12:00 Lunch

13:00 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

15:00 Break

15:30 Ontology, NLP and the Semantic Enhancement of Immunology Research Literature

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

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)

• Ryan Brinkman (Vancouver, BC)
• Lindsay Cowell (UT Southwestern, Dallas)
• Melanie Courtot (Vancouver, BC)
• Alexander Diehl (ImmPort / Buffalo)
• Nikesh Kotecha (Stanford)
• *Anna Maria Masci (Duke)
• Yannick Pouliot (ImmPort / Stanford)
• Alan Ruttenberg (ImmPort / Buffalo)
• Ravi Shankar (ImmPort / Stanford)
• Shai Shen-Orr (ImmPort / Technion Institute)
• Barry Smith (ImmPort / Buffalo)
• *Christian Stoeckert (Penn)

• *Representatives of institutions supplying data to ImmPort
• *Representatives of companies selling (for example) analytes

Plus participants from Stanford area