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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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[Update] retina-related bionetwork terms updates #2044

Closed ghost closed 1 year ago

ghost commented 1 year ago

Context: #1974

The following edits are derived from review of the Retina bionetwork and cellXgene references:

CL label Edit dbxref
Mueller cell Add "Muller cell" as exact syn with prop type MISSPELLING. doi:10.21769/BioProtoc.4179
amacrine cell Add "AC" as related syn, abbreviation. Add "ACs" as related syn, abbreviation, plural. doi:10.1038/s41598-020-66092-9
retinal bipolar neuron Add "BC" as related syn, abbreviation. Add "BCs" as related syn, abbreviation, plural. doi:10.1038/s41598-020-66092-9
retinal cone cell Add "cone" as related syn. doi:10.1038/s41598-020-66092-9
retina horizontal cell Add "HC" as related, abbreviation. Add "HCs" as related, abbreviation, plural. doi:10.1038/s41598-020-66092-9
macroglial cell Add "macroglia" as related, plural. doi:10.1152/physrev.2001.81.2.871
microglial cell CL has as exact synonym. EDIT "microglia" as related, plural. doi:10.1038/s41598-020-66092-9
retinal ganglion cell CL has "RGC" as exact synonym. EDIT "RGC" as related, abbreviation. Add "RGCs" as related, abbreviation, plural. doi:10.1038/s41598-020-66092-9
retinal rod cell Add "rod" as related syn. doi:10.1038/s41598-020-66092-9
H1 horizontal cell Add "H1" as related syn, abbreviation. doi:10.1038/s41598-020-66092-9
H2 horizontal cell Add "H2" as related syn, abbreviation. doi:10.1038/s41598-020-66092-9
dosumis commented 1 year ago

If we really need to refer to GEO IDs we should use https://bioregistry.io/registry/geo. => geo:GSE137537. Unless we can reliably tie the annotations to those on GEO, I don't think we should use GEO as a reference in cases like this. It would be better if we could use a standard CxG reference for the annotated matrix. It may be possible to use the UUID of the dataset, but we need some statement of official policy on IDs from CxG.

But in this case, we have DOI for all except one so I think we should use DOI alone for all except this and just drop the one with no DOI.