ImmPort Ontology Conference

Where: Stanford University

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

Goals

• Work out with bench immunologists how nomenclature schemes can evolve to support enhanced discoverability and reusability through 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

Schedule

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

We will begin by going through the steps of the ontological process involved in handling CyTOF data in order to address the following:

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. 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.

Schedule (Very Tentative)

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 Consequences for the Future of Immunology Science (See questions above)

16:00 Close

Participants

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

Plus participants from Stanford area