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 an ontology-based strategy to address these 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)
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
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
