4th Immport Ontology Group Web Conference

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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.