'''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.