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 (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? | ||
** | ** 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 | ||
Revision as of 12:25, 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 (now posted to JIRA)
- 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
- 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
- Discussion of where different types of information goes.
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.
