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Update Bgee ingest #414

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cmungall opened this issue Feb 9, 2023 · 3 comments
Open

Update Bgee ingest #414

cmungall opened this issue Feb 9, 2023 · 3 comments
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@cmungall
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cmungall commented Feb 9, 2023

Talking to @fbastian

  • They have an RDF dump and also JSON but it may be fine to keep using TSV although we may need to switch to their H5AD
  • they have someone actively working on improving the FDR calculation
  • let's try and get all the cool species they have in; platypus (cc @mellybelly), veterinary species...
  • they are working on a post composition model for cell type - tissue tuples. We definitely want the single cell data! (cc @dosumis)
    • currently they only have some human/mouse smartseq
    • next release will have drosophila and a lot more
@putmantime putmantime mentioned this issue Feb 10, 2023
@kevinschaper
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This is implemented

@kevinschaper
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oops, I'll re-open, I don't think we have nearly everything that's enumerated in the issue

@kevinschaper kevinschaper reopened this Jun 27, 2023
@kevinschaper kevinschaper changed the title Bgee ingest Update Bgee ingest Jun 27, 2023
@kevinschaper kevinschaper reopened this Jun 27, 2023
@monicacecilia
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  • We do not yet get all the cool species they have. Which species do we want to add now? (#DWRNATO?)
  • Has there been any progress on the ingestion of single-cell data? Is this still needed?

👀 👆🏽
@cmungall
@dosumis
@kevinschaper

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