Aims:
- Check CL term curation up to date
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Test flattening human BG tax + h5ad - for CAP Notes:
- It seems that everything is flattened. We should review this, it conflicts with option 2 here: cellannotation/cas-tools#111 Decision - we will stick with the status quo for now, but need to review. The flattened files are ugly, but we can offer unflattening. TODO - check what happens when we flatten annotation transfer.
- We are getting some warnings about hashes.
- TDT issue:
- Hierarchy merges down where two adjacent levels have the same name. Needs to be fixed. <-- v.high priority. Action item: Fix TDT issue and then share flattened human BG taxonomy with CAP. Action term: Review roundtripping - should we switch to mixed strategy?
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Add cell set level AT to Macaque BG tax
- Clusters get the most specific AT (homology subclass)
- Everything else gets most specific matching block - if one exists
- e.g. for
- cluster:
- 41_IN:Lamp5 Lhx6 gaba
- 42_IN:Lamp5 Lhx6 gaba
- 43_IN:Lamp5 gaba
- primate subclass:
- CCK-FBXL7: CTX-MGE GABA
- CCK-VIP-TAC3:vip Gaba
- CHAT:PAL-STR Gaba-Chol
- D1-ICj:OT D3 Folh1 Gaba
- primate-neighbourhood:
- Astroyctes: Astro-Epen
- CCK:CTX-MGE GABA
- TAC3:CTX-CGE GABA
- cholinergic: PAL-STR Gaba-Chol
If there are mutiple matches on the same level, we add all, again matching most specfic block
41_In : 287 + 288
CCK-FBKXL7 : 287 + 288
etc
Consider adding a gropuing mechanism in future
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Current schema:
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transferred_annotations
(list)transferred_cell_label
(string): Transferred cell label.source_taxonomy
(string): PURL of source taxonomy.source_node_accession
(string): accession of node that label was transferred from.algorithm_name
(string): .comment
(string): Free text comment on annotation transfer.
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Notes - we need a new field for labelset
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We need confirmation of algorithm and some text for the coment from Nelson
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Code with new CAS-LinkML lib.
- LinkML misfeature means that author annotation fields get stored as JSON_to_string which is a not a JSON string. Solution for now - we convert to JSON string before loading into CAS-LinkML instance. Convert back at end.
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(Test) Merge Macaque BG tax with new h5ad