Provide appropriate cell and tissue context using expression pattern curation

[vanaukenk]

Hi, This is a wish-list item, but the overall goal is to make use of additional curated data outside of GO for adding contextual information to a model.
WB generates an expression pattern GAF that lists the cell and anatomy ontology terms for which expression data has been reported for a given gene. It would be nice to incorporate this information into Noctua somehow such that the corresponding cell and anatomy terms would be available, with evidence, in a list for a given gene. Maybe this could be presented in the pop-up window where curators add edges and class expression to MF annotations? thx. --Kimberly

[kltm]

This sound like the kind of thing that may be site specific--the kind of thing that we tried to develop the plugin system for. We should touch bases, at some point, to figure out a way forward on this.

[cmungall]

We definitely don't want to make this site specific. We should standardize on an API that everyone can implement.

I would of course propose biolink as the standard, which provides simple routes for common queries such as this, e.g. /gene/{id}/expression.

The payload is essentially generalized GAF as JSON

A random worm gene and its expression in the monarch biolink implementation: WBGene00000004.

Monarch is getting all its expression from bgee, but there's nothing to stop something conforming to the same API and serving up different expression data.

This of course works for GO, phenotype, etc