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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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[Logical def] erythrocyte capable of --> blood circulation has multiple meanings #2306

Open lubianat opened 6 months ago

lubianat commented 6 months ago

CL term

http://purl.obolibrary.org/obo/CL_0000232 (erythrocyte) and

UBERON term

http://purl.obolibrary.org/obo/UBERON_0007100 (primary circulatory organ

Suggested revision of logical definition

Not sure on how to represent that precisely, but currently both "heart" and "erythrocyte" are capable of --> blood circulation . That does not seem precise, as they are "capable of" in very different fashions, one is directing circulation and blood flow and the other is just going with the flow.

This does not seem precise, though. I wonder if there is a way to represent that a cell circulates on the blood image

dosumis commented 6 months ago

We've discussed this pattern in the recent past. It doesn't make any sense for cells and should be removed. I believe it is used to classify 'circulating cell' - itself a rather dubious category. The advantage of capable_of is it doesn't have to apply all the time (and may never apply for an individual cell - classic example is sperm capable_of fertilization). part_of OTOH, should always apply, so we can't use part_of blood. We do need a pattern we can reliably use for some grouping terms that the community needs - e.g. PBMC.

As far as possible, these links to GO should make sense in terms of shared molecular/genetic mechanisms. The GO annotations then provide an important link to experimentally supported gene expression & gene programs for the transcriptomics community. "oxygen transport" fits that a bit better - there are haemoglobin annotations to this.

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