ImmPort Ontology Conference

From NCOR Wiki
Jump to navigationJump to search

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

Day 1: Sept 4

  • demonstrate to bench immunologists that their nomenclature schemes need to evolve to support enhanced discoverability and reusability (thus use of standards and ontologies)
  • provide arguments and success stories that will help to achieve buy-in from bench immunologists as to the importance of standards and ontologies
  • provide examples of ontology content and of good practice use of ontologies which will help immunologists to rationalize their nomenclature and help them understand how ontologies are applied

Day 2: Sept 5 – restricted meeting – ImmPort and invitees only

  • go through the steps of the ontological process involved in handling CyTOF data
  • identify immunology science issues for which new ontology content will be required; in particular:
address the workflow which leads from CyTOF data to identification of cell types using the CL ontology
address how to deal with PPCs in an ontological manner, e.g., using a code to handle the experimental protocol through which the PPC was identified

Critical attendance

  • people from CyTOF world

Background

An overview of ontologies proposed by ImmPort for use across the immunology research community

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

12:00 Lunch

13:00 Flow Cytometry

15:00 Break

15:30 Shai Shen-Orr: Ontology, NLP and the Semantic Enhancement of Immunology Research Literature

16:30 Lindsay Cowell: Immunology Ontology and NLP

Thursday, September 5, 2013

8:30 Continental Breakfast

9:00 An Introduction to Ontology for CyTOF

9:30 An Introduction to Immunology for CyTOF

10:00 Immunology in the Gene Ontology (Alexander Diehl)

10:30 CL

11:00 PRO

12:00 Lunch

13:00 CyTOF to CL Workflow

16:00 Close

Participants (* = tentative)

  • Ryan Brinkman (Vancouver, BC)
  • Lindsay Cowell (UT Southwestern, Dallas)
  • Melanie Courtot (Vancouver, BC)
  • Alexander Diehl (ImmPort / Buffalo)
  • Sanda Harabagiu (UT Southwestern, Dallas)
  • 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