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
8:30 Continental Breakfast
9:00 An Introduction to Ontology 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)
- *Anna Maria Masci (Duke)
- Yannick Pouliot (ImmPort / Stanford)
- Alan Ruttenberg (ImmPort / Buffalo)
- Ravi Shankar (ImmPort / Stanford)
- Shai Shen-Orr (ImmPort / Technion Institute)
- Barry Smith (ImmPort / Buffalo)
- *Christian Stoeckert (Penn)
- *Representatives of institutions supplying data to ImmPort
- *Representatives of companies selling (for example) analytes
Plus participants from Stanford area
