1. The document discusses automatically assigning ontological IDs to cell populations identified in studies using FLOCKMapper. 2. It describes the system components used, including a study dataset, FLOCK for analysis, the Cell Ontology and ImmPort ontologies for IDs, and HIPC definitions converted to a computable form. 3. It explains the mapping process involves identifying an ontological class that maps to a given HIPC class definition, addressing mismatches, and codifying the mappings as views and functions.

1. Ontologically-Aware Automatic
Gating
Yannick Pouliot
Butte Laboratory

2. FLOCKMapper: Goal
Identify the issues associated with automatically
assigning ontological IDs to cell populations,
whether identified programmatically or
manually

3. 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).

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

5. Insanely High Level Systems View

6. Mapping Process
For a given HIPC class:
1. identify CL class that is mappable using HIPC definitions,
at least in principle
2. address mismatches, if possible
3. codify as views and functions

7. Six Cell Types
Mapped So Far
CL_0002419
CL_0000815
CL_0000625
CL_0000624
CL_0000236
(Authority source is HIPC Lyoplate
definitions)
CL_0000623

8. Lots of Results

9. DEMO

11. Determining Optimal Number of Clusters

12. Precision of
Total T Cell
Count Across
Panels for
Same Visit