ImmPort Ontology Conference: Difference between revisions

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== '''Goals''' ==
== '''Goals''' ==


<u>Day 1</u>
<u>Day 1: Sept 4</u>


*demonstrate to bench immunologists that their nomenclature schemes need to evolve to support enhanced discoverability and reusability (thus use of standards and ontologies)
*demonstrate to bench immunologists that their nomenclature schemes need to evolve to support enhanced discoverability and reusability (thus use of standards and ontologies)
Line 18: Line 18:
*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
*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


Sept 5 – restricted meeting – ImmPort and invitees only
<u>Day 2: Sept 5</u> – restricted meeting – ImmPort and invitees only


Goals of this meeting:
*go through the steps of the ontological process involved in handling CyTOF data
go through ontological process
address immunology science issues, e.g.,
address CyTOF --> CL mapping
how to deal with PPCs in an ontological manner, e.g., using a code to handle associated with protocol from which PPC was identified
Critical attendance:
people from CyTOF world
Draft schedule is here:
http://ncorwiki.buffalo.edu/index.php/ImmPort_Ontology_Conference
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'''
*identify immunology science issues for which new ontology content will be required; in particular:


*providing examples of success stories in the use of standards and ontologies to support immunological research
::address the workflow which leads from CyTOF data to identification of cell types using the CL ontology
*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
::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
*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
'''Critical attendance'''
*people from CyTOF world


'''Background'''
'''Background'''

Revision as of 17:10, 19 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

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

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

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