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:
- explain the difference between continuant and occurrent
- summarize how this difference is handled in other ontologies (especially GO)
- list a set of properties that distinguish a cell type (continuant) from a transient state type (occurrent)
- what would it take to have an agreed process that would establish (a) that a hitherto unrecognized cell type exists or (b) that a hitherto unrecognized cell state exists?
- is it sufficient (for (a)) to interpret 'hitherto unrecognized' as meaning: 'not yet included in the CL'?
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)
- 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
