ImmPort Ontology Conference: Difference between revisions

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8:30 Continental Breakfast
8:30 Continental Breakfast


9:00 An Introduction to Ontology for Immunology
9:00 An Introduction to Ontology for CyTOF


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


10:30 VDJServer (Lindsay Cowell)
10:30 CL


11:00 Further Use Cases
11:00 PRO


12:00 Lunch
12:00 Lunch


13:00 Further Use Cases
13:00 CyTOF to CL Workflow


16:00 Close
16:00 Close


== '''Participants''' (* = tentative) ==
== '''Participants''' (* = tentative) ==

Revision as of 12:50, 18 June 2013

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 this meeting is to show how work in standards and ontologies can support NIAID-DAIT funded information-driven science. We will work with immunologists who have data which pose special problems for handling in a resource such as ImmPort, and develop strategies to address these problems.

Subgoals

  • providing examples of success stories in the use of standards and ontologies to support immunological research
  • identifying obstacles to the sharing of immunology research data and building strategies to overcome them
  • identifying the ontology and data standardization needs of DAIT-funded experimental scientists
  • provide an overview of ontology resources of particular interest to the ImmPort / HIPC and related communities
  • identifying strategies for data retrieval based on natural language processing

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

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