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laminlabs / bionty-base

Access public biological ontologies.
https://bionty-base.lamin.ai
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Add GENCODE to `Gene` source #527

Closed sunnyosun closed 3 months ago

sunnyosun commented 9 months ago

https://www.gencodegenes.org/

Zethson commented 3 months ago

We looked into it.

Summary:

  1. GENCODE IDs are ENSEMBL IDs.
  2. GENCODE IDs are a subset of ENSEMBL with a focus on human and mouse genes. These genes are manually reviewed and more curated.
  3. We may consider using GENCODE as a source which is just a subset of ensembl.
  4. A boolean column implying whether a ENSEMBL ID is a part of GENCODE is currently not planned because different users might not set it at the same time