4th Immport Ontology Group Web Conference: Difference between revisions

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'''Draft Schedule'''
'''Draft Schedule'''


4:00pm (EST) Kei Cheung and Steve Kleinstein (Yale) on HIPC Standards and Ontology
4:00pm (EST) Discussion of CyTOF / PRO / CL workflow
:Discussion of HIPC templates (subjects, study design, samples, experiment, protocols, and reagents) and selection of ontologies to support their use.
:See background material here:


*[http://ncor.buffalo.edu/2013/Immunology/HIPC-Templates HIPC templates]
== CyTOF –CL workflow ==
*[http://ncor.buffalo.edu/2013/Immunology/HIPC-Example/ soluble proteins (including cytokines and chemokines) relevant to the HIPC templates]


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


4:15pm Meeting Planning
'''Protocol for classifying and recording cell type/populations from CYTOF experiments'''
:[http://ncorwiki.buffalo.edu/index.php/ImmPort_Ontology_Conference Immport Ontology Workshop] in Stanford, September 4-5, 2013
* Review proposed inputs
:HIPC Bioinformatics Meeting in Bethesda, September 11, 2013
** 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


5:00pm Discussion on CYTOF / PRO / CL workflow
* 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.

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.

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