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feat: 'native cell' -> 'unknown' on geneformer label_blocklist #999

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merged 1 commit into from
Mar 26, 2024

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danieljhegeman
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@danieljhegeman danieljhegeman commented Feb 16, 2024

Fixes #1019

Schema 5.0 will use an updated ontology that does not include CL:0000003 - native cell. We will accept instead "unknown" for the cell_type_ontology_term_id, and accordingly we will annotate cell_type (label) as "unknown".

This should (probably) be merged once we migrate. @mlin let me know if you foresee any issues.

@danieljhegeman danieljhegeman changed the title feat: 'native cell' -> 'unknown' on geneformer label_blocklist -- DO NOT MERGE feat: 'native cell' -> 'unknown' on geneformer label_blocklist -- DO NOT MERGE (yet) Feb 16, 2024
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codecov bot commented Feb 17, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (cd0c6df) 86.01% compared to head (8e3fc1f) 86.01%.

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #999   +/-   ##
=======================================
  Coverage   86.01%   86.01%           
=======================================
  Files          71       71           
  Lines        5647     5647           
=======================================
  Hits         4857     4857           
  Misses        790      790           
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unittests 86.01% <ø> (ø)

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metakuni commented Mar 1, 2024

@ebezzi ebezzi merged commit 3ac2135 into main Mar 26, 2024
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@ebezzi ebezzi deleted the dan/647-deprecate-native-cell branch March 26, 2024 23:21
@ebezzi ebezzi changed the title feat: 'native cell' -> 'unknown' on geneformer label_blocklist -- DO NOT MERGE (yet) feat: 'native cell' -> 'unknown' on geneformer label_blocklist Mar 26, 2024
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[misc] native cell obsolescence (GeneFormer config)
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