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 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

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