ImmPort Ontology Conference

Where: Paul Berg Hall A #230, Li Ka Shing Center for Learning and Knowledge, 291 Campus Drive West, Stanford School of Medicine, Stanford, CA 94305.

When: September 4-5, 2013

Audience

• Day 1 is intended for all those engaged in information-driven immunology research who have an interest in the work of ImmPort and/or in ontology and data standardization
• Day 2 (by invitation only) is intended primarily for those interested in CyTOF and related issues of data management in immunological science.

Background resources

• An overview of ontologies proposed by ImmPort for use across the immunology research community is provided here

If you are interested in attending please contact Barry Smith as soon as possible.

Wednesday, September 4, 2013

Schedule

8:30 Registration and Continental Breakfast

9:00 Barry Smith (Buffalo): Overview of ImmPort Ontologies Slides

9:15 Jeff Wiser (Northrop Grumman): Discussion on the Role of Ontologies in ImmPort

9:45 Atul Butte (Stanford / ImmPort): The Future of ImmPort Slides

10:00 Garry Nolan (Stanford): Goals for CyTOF

11:00 Break

11:15 Alex Diehl (Buffalo): PRO and CL Slides

11:45 Alan Ruttenberg (Buffalo): The Ontology for Biomedical Investigations (OBI) Slides

12:15 Lunch

13:00 Holden Maecker (Stanford):Flow Cytometry Standardization and the Problem of Cell Typing Slides

14:00 Ryan Brinkman (Vancouver): The Cytometry-Ontology Framework Supplementary data

14:45 Melanie Courtot (Vancouver): Enabling Faster and More Accurate Analysis of Vaccine Adverse Event Reports with Ontology Support

15:15 Break

15:30 Lindsay Cowell (Southwestern Medical Center): VDJ Repertoire and Ontology-Based Data Sharing Slides Slides 1 Slides 2

Thursday, September 5, 2013

Schedule

8:30 Continental Breakfast

9:00 Nikesh Kotecha (Stanford / Cytobank): Software Challenges for Cytometry

9:30 Yannick Pouliot, Alex Diehl, Chris Mungall: Symposium on the Cell Ontology (CL)

Cell types, cell stages, cell populations and CL terms and definitions.

10:30 Break

11:00 Alan Ruttenberg, Barry Smith: A Debate on Strategies for Use of Ontologies in ImmPort

12:00 Lunch

13:00 Open Discussion: Consequences for the Future of Immunological Science

Topics to be addressed

• The Cell Ontology as Canonical Ontology: The Case of OncoCL
• How do we create a Cell Stage / Cell State Ontology?
• Do we need a Cell System (Immune Cell System, Cancer Cell System, (Intercellular, Stroma ...)

15:00 Shai Shen-Orr (Tel Aviv): Ontology, NLP and the Semantic Enhancement of Immunology Research Literature

16:30

Major Questions for Discussion

1. Evaluation of the cell type definitions proposed in Maecker et al. (if possible do this prior to the meeting)

2. What should be the framework by which we can represent cell populations identified through given sorts of assays in such a way that we can later promote them to cell types recognized in the CL?

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?

• Subtasks:

Ontological Background

a. explain the difference between continuant and occurrent

b. summarize how this difference is handled in other ontologies (especially GO)

c. list a set of properties that distinguish a cell type (continuant) from a transient state type (occurrent)

Metadata

What metadata need to be captured in order to enable the downstream determination that a cell population identified by some assay is in fact either (a) a bona fide cell type that should be included in CL, or (b) a bona fide cell state type?

• Proposed:

a. composition of the antigen panel

b. antibodies used to probe each antigen (expressed as ImmPort Antibody Registry ID)

c. the type of flow experiment: traditional, phosphoflow, CyTOF

d. unique experiment ID

e. species of the cells being probed (NCBI Taxonomy ID)

f. type of sample (whole blood, PBCs)

g. combination of markers that define a cell type according to the experimenter

h. clinical status of subjects (affected, unaffected; vaccinated/unvaccinated)

i. interventions (e.g., which arm of a trial the subject belongs to)

(At least in the short-run, it is anticipated that these data will be obtained from ImmPort's store of flow data.)

More ambitious questions for discussion if time allows:

3. 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.

4. 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.

Participants

• Sanchita Bhattacharya (ImmPort / Stanford)
• Ryan Brinkman (Vancouver, BC)
• Atul Butte (ImmPort / Stanford)
• Quan Chen (NIH / NIAID)
• Lindsay Cowell (UT Southwestern, Dallas)
• Melanie Courtot (Vancouver, BC)
• Alexander Diehl (ImmPort / Buffalo)
• Nikesh Kotecha (Stanford)
• Suzanna Lewis (Berkeley)
• Holden Maecker (Stanford)
• Chris Mungall (Berkeley)
• Garry Nolan (Stanford)
• Yannick Pouliot (ImmPort / Stanford)
• Alan Ruttenberg (ImmPort / Buffalo)
• Nikolay Samusik (Stanford)
• Ravi Shankar (ImmPort / Stanford)
• Shai Shen-Orr (ImmPort / Technion Institute)
• Barry Smith (ImmPort / Buffalo)
• Nicole Vassilesky (OHSU, Oregon)
• Jeff Wiser (ImmPort / Northrop Grumman)
• Ashley Xia (NIH / NIAID)

Plus further participants from Stanford area.