4th Immport Ontology Group Web Conference

Draft Schedule

4:00pm (EST) Discussion of CyTOF / PRO / CL workflow

CyTOF –CL workflow

Protocol for classifying and recording cell type/populations from CYTOF experiments

Review proposed inputs
- Is information gathered adequate?
- Are offering choices for input useful?
Splitting out into separate workflows
- Registering/curating an antibody
- Assigning qualitative marker levels
- Clustering/gating
Understanding the SPARQL query
The review step

Identifying a data set for validating the workflow. -
- Is Bendall et al., 332 (6030): 687-696 a good source? Review.
- Arranging time with someone on Nolan team to prepare this set

Adding markers to CL classes so that they can be computed on (instead of having them as comments) Alex Diehl, Alan Ruttenberg

https://bisc2012.atlassian.net/browse/ID-205
- Difference between initial spreadsheets and Dougall's
- Asserting that a surface marker appears on every instance of annotated-to cell type
- Asserting capability of secreting cytokine on every instance of annotated-to cell type
- Ignoring other types (e.g. transcription factors) for now
https://bisc2012.atlassian.net/browse/OD-28
- Discussion of where different types of information go
  - Distinguish CL from CL-Provisional (resource to support Immport experimental work which extends CL)?
  - Antibodies used to detect cell type in different experimental paradigms
  - Extrinsic experimental properties such as side-scatter

Alex Diehl

Barry Smith and Yannick Pouliot

General issue of cell type versus cell state (why 'mature cell' is not a type of cell)

6:00pm (EST) Close

Note that the originally planned discussion of HIPC Standards and Ontologies has been postponed, due to urgency of this workflow issue.