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Overloaded usage of word term for output #1835

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Zethson opened this issue Aug 22, 2024 · 0 comments · Fixed by laminlabs/lamin-utils#84
Closed

Overloaded usage of word term for output #1835

Zethson opened this issue Aug 22, 2024 · 0 comments · Fixed by laminlabs/lamin-utils#84
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@Zethson
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Zethson commented Aug 22, 2024

 received 209 unique terms, 182666 empty/duplicated terms are ignored
✅ 36 terms (17.20%) are validated for name
❗ 173 terms (82.80%) are not validated for name: CAL62, MIAPACA2, LOVO, CAOV3, LUDLU1, SNU1105, DMS273, A375, NUGC3, LK2, HUCCT1, RH30, NCIH2126, SKMEL24, TE11, GP2D, G401, NCIH841, 769P, NCIH1693, ...
   detected 172 terms with inconsistent casing/synonyms: CAL62, MIAPACA2, LOVO, CAOV3, LUDLU1, SNU1105, DMS273, A375, NUGC3, LK2, HUCCT1, RH30, NCIH2126, SKMEL24, TE11, GP2D, G401, NCIH841, 769P, NCIH1693, ...
→  standardize terms via .standardize()

bt.CellLine.public(source=bt.Source.filter(name="depmap").one()).standardize(adata.obs["cell_line"], field="name")

-->

standardized 182577/182875 terms

So is a term now a value aka an instance of a term?

Above, we're stating 172 terms but later we mean all instances of this term. The language is confusing.
It should be UNIQUE terms in the output as we have once.

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