4th Immport Ontology Group Web Conference: Difference between revisions

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


1. Status with CyTOF –CL workflow (Alan Ruttenberg)
== CyTOF –CL workflow ==
*https://bisc2012.atlassian.net/browse/OD-48


2. How to use the PRO (Alex Diehl)
Alan Ruttenberg - https://bisc2012.atlassian.net/browse/OD-48


3. Adding markers to CL classes so that they can be computed on (instead of having them as comments) (Alex Diehl)
Protocol for classifying and recording cell type/populations from CYTOF experiments (will be posted before Monday AM)
*https://bisc2012.atlassian.net/browse/ID-205
* Review proposed inputs
*https://bisc2012.atlassian.net/browse/OD-28
** Is information gathered adequate
** Is 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
* Reminder of the general issue of cell type versus state
* Caveats/Open issues
* 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


4. Immport Antibody Registry (Alex Diehl)
== Protein Ontology ==
* How to use the PRO (Alex Diehl)
* Curating protein complexes
 
== 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 surface marker appear 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 goes.
*** Distinguish CL from resource to support Immport experimental work (which includes 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


6:00pm (EST) Close
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.
Note that the originally planned discussion of [[HIPC Standards and Ontologies]] has been postponed, due to urgency of this workflow issue.

Revision as of 04:00, 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 (will be posted before Monday AM)

  • Review proposed inputs
    • Is information gathered adequate
    • Is 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
  • Reminder of the general issue of cell type versus state
  • Caveats/Open issues
  • 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

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

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 surface marker appear 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 goes.
      • Distinguish CL from resource to support Immport experimental work (which includes 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

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.

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