ontologically-aware automated gating

Ontologically-Aware Automatic Gating

Yannick PouliotButte Laboratory

FLOCKMapper: Goal

Identify the issues associated with automatically assigning ontological IDs to cell populations, whether identified programmatically or manually

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).

Automating …- FCS conversion- Running FLOCK- Loading of results into DB

Insanely High Level Systems View

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

CL_0000236

CL_0002419

CL_0000815 CL_0000625

CL_0000624

CL_0000623

Six Cell Types Mapped So Far

(Authority source is HIPC Lyoplate definitions)

Lots of Results

DEMO

Determining Optimal Number of Clusters

Precision of Total T Cell Count Across Panels for Same Visit