ontologically-aware automated gating
DESCRIPTION
Automatic the FLOCK tool, mapping results to the Cell Ontology and plotting the results using the Mondrian Cell PlotTRANSCRIPT
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Ontologically-Aware Automatic Gating
Yannick PouliotButte Laboratory
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FLOCKMapper: Goal
Identify the issues associated with automatically assigning ontological IDs to cell populations, whether identified programmatically or manually
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System Components• SDY1 “Casale” study• FLOCK1– FLOCKLaunch, FLOCKLoad
• Cell Ontology (CL)• ImmPort CL– 2011 (generated from previous BISC contract CL)– Processed into computable form; additional curation
• HIPC Lyoplate cell definitions, converted to computable form– Maecker, H., McCoy, J.P. & Nussenblatt, R. Standardizing immunophenotyping for the human
immunology project. Nature reviews Immunology 12, 191-200 (2012).
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Automating …- FCS conversion- Running FLOCK- Loading of results into DB
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Insanely High Level Systems View
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Mapping ProcessFor a given HIPC class:
1. identify CL class that is mappable using HIPC definitions, at least in principle
2. address mismatches, if possible3. codify as views and functions
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CL_0000236
CL_0002419
CL_0000815 CL_0000625
CL_0000624
CL_0000623
Six Cell Types Mapped So Far
(Authority source is HIPC Lyoplate definitions)
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Lots of Results
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DEMO
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Determining Optimal Number of Clusters
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Precision of Total T Cell Count Across Panels for Same Visit