4th Immport Ontology Group Web Conference: Difference between revisions
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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 | '''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? | ||
** | ** 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 | ||
| Line 17: | Line 17: | ||
* Understanding the SPARQL query | * Understanding the SPARQL query | ||
* The review step | * The review step | ||
* 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. | ||
** 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 | ||
== Adding markers to CL classes so that they can be computed on (instead of having them as comments) | == 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 | Alex Diehl, Alan Ruttenberg | ||
* 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 | ** 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 | ** Discussion of where different types of information go | ||
*** Distinguish CL from resource to support Immport experimental work | *** 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 | ||
| Line 49: | Line 49: | ||
* 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 and Yannick Pouliot | |||
*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. | ||
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
- Discussion of where different types of information go
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.
