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AIRR Community Data Standards
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Change CellExpression property_type to enum? #733

Closed bcorrie closed 6 months ago

bcorrie commented 7 months ago

In #699 we added the property_type field to CellExpression as a string with documented preferred values.

We noted that we probably should change this to an enum.

bcorrie commented 7 months ago

Currently we have this describing the text field:

               Keyword describing the property type and detection method used to measure the property value.
                The following keywords are recommended, but custom property types are also valid:
                "mrna_expression_by_read_count",
                "protein_expression_by_fluorescence_intensity", "antigen_bait_binding_by_fluorescence_intensity",
                "protein_expression_by_dna_barcode_count" and "antigen_bait_binding_by_dna_barcode_count".
bcorrie commented 7 months ago

Can we come up with a set of enum values for this? Outside of my area of expertise... 8-)

scharch commented 7 months ago

I feel like an enum would be very brittle for this, and as we are aiming to move to a maintenance mode it's better to leave it free text.

bcorrie commented 7 months ago

@bussec @javh any objections to leaving this as a string with "suggested values". If no objections I will close this issue.

schristley commented 7 months ago

These seem like things that belong or should be in OBI ontology? Though more specialized terms might be desired there is protein expression assay (OBI:0000615) and mRNA expression assay (OBI:0001926) as parent terms.

bussec commented 6 months ago

@schristley I would also prefer to have an ontology, but then we would have to split the field again, as I doubt that there is an ontology that would capture both components of our keywords (i.e., what was measured and how it was measured) and we decided a while ago, that having two components is potentially confusing to curators.

bussec commented 6 months ago

For the call: Leave the field as it is, i.e. free text with suggested keywords. This is clearly not perfect, but better than having a solution that is more formalized but less flexible.