4th Immport Ontology Group Web Conference

Draft Schedule

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

CyTOF –CL workflow

Alan Ruttenberg - https://bisc2012.atlassian.net/browse/OD-48

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

Protein Ontology (PRO)

• How to use the PRO (Alex Diehl)
• Curating protein complexes

Cell Ontology (CL)

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

Immport Antibody Registry

Alex Diehl

• What is planned/should be recorded
• How to host work in progress (triple store?)
• Do we need indications of status of curation?
• What to expect when
• Process for Identifying new antibodies to be included in registry

Next Steps

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.