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 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

• 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

Sept 5 – restricted meeting – ImmPort and invitees only

Goals of this meeting: 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

• 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

• Courtot/Brinkman: http://ontology.buffalo.edu/pro/CytometryOntologyFramework.pdf The Cytometry-Ontology Framework]
• PRO, CL and CyTOF

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