4th Immport Ontology Group Web Conference: Difference between revisions

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** Arranging time with someone on Nolan team to prepare this set
** Arranging time with someone on Nolan team to prepare this set


== Protein Ontology ==
== Protein Ontology (PRO) ==
* How to use the PRO (Alex Diehl)
* How to use the PRO (Alex Diehl)
* Curating protein complexes  
* Curating protein complexes  


== Cell Ontology (CL) ==
'''Adding markers to CL classes so that they can be computed on (instead of having them as comments)'''
'''Adding markers to CL classes so that they can be computed on (instead of having them as comments)'''
Alex Diehl, Alan Ruttenberg
Alex Diehl, Alan Ruttenberg
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* https://bisc2012.atlassian.net/browse/ID-205  
* https://bisc2012.atlassian.net/browse/ID-205  
** Difference between initial spreadsheets and Dougall's
** Difference between initial spreadsheets and Dougall's
** Asserting surface marker appear on every instance of annotated-to cell type
** 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
** Asserting capability of secreting cytokine on every instance of annotated-to cell type
** Ignoring other types (e.g. transcription factors) for now  
** Ignoring other types (e.g. transcription factors) for now  
* https://bisc2012.atlassian.net/browse/OD-28
* https://bisc2012.atlassian.net/browse/OD-28
** Discussion of where different types of information goes.
** Discussion of where different types of information go
*** Distinguish CL from resource to support Immport experimental work (which includes CL) ?
*** Distinguish CL from CL-Provisional (resource to support Immport experimental work which extends CL)?
*** Antibodies used to detect cell type in different experimental paradigms
*** Antibodies used to detect cell type in different experimental paradigms
*** Extrinsic experimental properties such as side-scatter
*** Extrinsic experimental properties such as side-scatter
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== Next Steps ==
== Next Steps ==
Barry Smith
Barry Smith and Yannick Pouliot
*General issue of cell type versus cell state (why 'mature cell' is not a type of cell)
*General issue of cell type versus cell state (why 'mature cell' is not a type of cell)



Latest revision as of 12:30, 24 June 2013

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.