4th Immport Ontology Group Web Conference - Revision history

Phismith: /* Next Steps */

2013-06-24T12:30:17Z

Next Steps

← Older revision		Revision as of 12:30, 24 June 2013
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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)

Phismith: /* Protein Ontology */

2013-06-24T12:29:39Z

Protein Ontology

Phismith: /* Adding markers to CL classes so that they can be computed on (instead of having them as comments) */

2013-06-24T12:27:20Z

Adding markers to CL classes so that they can be computed on (instead of having them as comments)

← Older revision		Revision as of 12:27, 24 June 2013
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	* Curating protein complexes		* Curating protein complexes

	== 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

Phismith: /* CyTOF –CL workflow */

2013-06-24T12:26:44Z

CyTOF –CL workflow

← Older revision		Revision as of 12:26, 24 June 2013
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	Alan Ruttenberg - https://bisc2012.atlassian.net/browse/OD-48		Alan Ruttenberg - https://bisc2012.atlassian.net/browse/OD-48

	Protocol for classifying and recording cell type/populations from CYTOF experiments ~~(now posted to [https://bisc2012.atlassian.net/browse/OD-48 JIRA])~~		'''Protocol for classifying and recording cell type/populations from CYTOF experiments'''
	* Review proposed inputs		* Review proposed inputs
	** Is information gathered adequate?		** Is information gathered adequate?

Phismith: /* Immport Antibody Registry */

2013-06-24T12:26:12Z

Immport Antibody Registry

← Older revision		Revision as of 12:26, 24 June 2013
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	* What to expect when		* What to expect when
	* Process for Identifying new antibodies to be included in registry		* Process for Identifying new antibodies to be included in registry

			== Next Steps ==
			Barry Smith
			*General issue of cell type versus cell state (why 'mature cell' is not a type of cell)

	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.

Phismith: /* CyTOF –CL workflow */

2013-06-24T12:25:27Z

CyTOF –CL workflow

← Older revision		Revision as of 12:25, 24 June 2013
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	Alan Ruttenberg - https://bisc2012.atlassian.net/browse/OD-48		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~~)		Protocol for classifying and recording cell type/populations from CYTOF experiments (now posted to [https://bisc2012.atlassian.net/browse/OD-48 JIRA])
	* Review proposed inputs		* Review proposed inputs
	** Is information gathered adequate		** Is information gathered adequate?
	** Is offering choices for input useful		** Are offering choices for input useful?
	* Splitting out into separate workflows:		* Splitting out into separate workflows
	** Registering/curating an antibody		** Registering/curating an antibody
	** Assigning qualitative marker levels		** Assigning qualitative marker levels
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	* Understanding the SPARQL query		* Understanding the SPARQL query
	* The review step		* The review step
	* Reminder of the general issue of cell type versus state
	* Caveats/Open issues
	* Identifying a data set for validating the workflow. -		* Identifying a data set for validating the workflow. -
	** is Bendall et al., 332 (6030): 687-696 a good source? Review.		** Is Bendall et al., 332 (6030): 687-696 a good source? Review.
	** Arranging time with someone on Nolan team to prepare this set		** Arranging time with someone on Nolan team to prepare this set

Alan Ruttenberg at 04:00, 24 June 2013

2013-06-24T04:00:09Z

@@ Line 3: / Line 3: @@
 :00pm (EST) Discussion of CyTOF / PRO / CL workflow
-. Status with CyTOF –CL workflow (Alan Ruttenberg)
+== CyTOF –CL workflow ==
-. How to use the PRO (Alex Diehl)
+Alan Ruttenberg - https://bisc2012.atlassian.net/browse/OD-48
-. 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
-. Immport Antibody Registry (Alex Diehl)
+== Protein Ontology ==
 :00pm (EST) Close
 Note that the originally planned discussion of [[HIPC Standards and Ontologies]] has been postponed, due to urgency of this workflow issue.

Phismith at 22:19, 22 June 2013

2013-06-22T22:19:25Z

← Older revision		Revision as of 22:19, 22 June 2013
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	*https://bisc2012.atlassian.net/browse/ID-205		*https://bisc2012.atlassian.net/browse/ID-205
	*https://bisc2012.atlassian.net/browse/OD-28		*https://bisc2012.atlassian.net/browse/OD-28

			4. Immport Antibody Registry (Alex Diehl)

	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.

Phismith at 16:35, 21 June 2013

2013-06-21T16:35:35Z

← Older revision		Revision as of 16:35, 21 June 2013
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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)
			*https://bisc2012.atlassian.net/browse/OD-48

			2. How to use the PRO (Alex Diehl)

			3. Adding markers to CL classes so that they can be computed on (instead of having them as comments) (Alex Diehl)
			*https://bisc2012.atlassian.net/browse/ID-205
			*https://bisc2012.atlassian.net/browse/OD-28

			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.

Phismith at 01:06, 20 June 2013

2013-06-20T01:06:47Z

← Older revision		Revision as of 01:06, 20 June 2013
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	'''Draft Schedule'''		'''Draft Schedule'''

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

	~~5:00pm Kei Cheung and Steve Kleinstein (Yale) on~~ HIPC Standards and ~~Ontology~~		Note that the originally planned discussion of [[HIPC Standards and Ontologies]] has been postponed, due to urgency of this workflow issue.
	~~: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]
	*[http://ncor.buffalo.~~edu/2013/Immunology/HIPC-Example/ soluble proteins (including cytokines and chemokines) relevant to the HIPC templates]~~

← Older revision		Revision as of 12:29, 24 June 2013
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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