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

Critical attendance

• people from ImmPort community
• computational immunologists
• those interested in standards and ontologies in immunology

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 resources

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

1. What are the specific combinations of surface markers and internal proteins that reliably identify the same cell types? For instance CD19, B220, and the BCR (B cell receptor) are all found on B cells, and one can conceive of protocols that measure the presence of only one of these markers, yet give equal assurance that B cells are the cells being assayed. Can we push this paradigm further for more granular cell types?

2. What surface markers or internal proteins have reliable associations with biological processes, such that when we see a novel cell type or a variant of a known cell type we can predict the cell's function or (in other words the GO:Biological Processes it is capable of carrying out or participating in)? This question can obviously leverage existing GO annotations for particular proteins, some of which already have co-annotation with CL terms. But it can also lead to new terms for GO:Biological Processes and for CL cell types.

3. How do we determine what is really a new cell type rather than either a refinement of an existing cell type generated by additional markers, or (2) a transient activation state of some known cell type?

4. How can we leverage CyTOF to develop a true step-by-step picture of hematopoiesis? This is a question for both ontology and the experimental approach.

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