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: 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

• 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

Major Questions for Discussion:

Notes on topics and goals: The ontological landscape of immunology: perusing terms, concepts and protocol descriptions

• Extreme case: no nomenclature standard for cytokines
• Less extreme case: "standard" principal name in immunology frequently not the principal name used in the rest of biology --> consequence

How other areas of biology have handled some of these issues: from funcky gene names to coherent naming schemes. Surely immunology can do the same

• Why bother? When terms are so ill-defined or mis-used as in immunology, synonyms aren't necessarily a solution

Provide example use cases compromised by nomenclature chaos: relating FCM phenotyping to gene expression: hard to relate CD86 on the FCM measurement side to integrin XXX on the gene expression side, because no repository follows immuno principal naming. And that's not taking into account all the synonyms on the immunological side How key ontologies can help immunology CL, PRO: assigning cell populations to well-defined concepts to facilitate exchange and enable computation OBI: describing protocols and assays other?

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)
• Yannick Pouliot (ImmPort / Stanford)
• Alan Ruttenberg (ImmPort / Buffalo)
• Ravi Shankar (ImmPort / Stanford)
• Shai Shen-Orr (ImmPort / Technion Institute)
• Barry Smith (ImmPort / Buffalo)

• *Representatives of institutions supplying data to ImmPort
• *Representatives of companies selling (for example) analytes

Plus participants from Stanford area