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Review/revise root classification strategy #14

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dosumis opened this issue Nov 21, 2024 · 2 comments
Open
Tracked by #8

Review/revise root classification strategy #14

dosumis opened this issue Nov 21, 2024 · 2 comments
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@dosumis
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dosumis commented Nov 21, 2024

First step: Document current behaviour in detail here:

Notes: IIRC, this was originally created as a way of managing general metadata + specifying where to start building hierarchy so that we could ignore the most general terms. It then become quite overloaded - including specification of relationship types to use to link to anatomy (this differs from neurons and non-neuronal + terms to use as genus in formal definition.

  • I think it makes more sense to switch to using directly curated CL mappings as genus.
  • Type of relation can be specified for each of 32 Classes most are neurons.
  • I think we can be conservative in choosing which roots to exclude.
@dosumis dosumis mentioned this issue Nov 21, 2024
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@dosumis dosumis added this to the WMBO 2.0 milestone Nov 21, 2024
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dosumis commented Dec 4, 2024

Update: The pipeline currently ignores configuration YAML root terms. Gross classification is coming from CAS ontology term mappings - but these don't cover all classes, so some currently have no classification. We need some sensible defaults. We will do this in CAS. See brain-bican/whole_mouse_brain_taxonomy#9

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dosumis commented Jan 6, 2025

Problem with using CAS is that we can't specify relation types as with root strategy, also we can't exclude any Classes, but we need to for some non-neural cell types. So - we may need a combined strategy after all.

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