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legumeinfo / microservices

A collection of microservices developed and maintained by the Legume Information System
https://legumeinfo.org/
Apache License 2.0
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eFP gene linkouts #615

Open jd-campbell opened 6 months ago

jd-campbell commented 6 months ago

@sammyjava

On SoyBase Classic Webpage we have a specific uBAR figure on gene model pages. This figure has the expression pattern for that specific gene model within multiple tissue types. The image can be seen under the Expression Patterns banner and I tool a screenshot of the uBAR figure I am referring to. We are currently bringing these figures using the uBAR API. We basically we bring in the figures by the subsequent URL (example).

Our question for you: Is there a way to add these figures to the gene model pages on GlycineMine?

Screen Shot 2024-01-18 at 14 34 03

sammyjava commented 6 months ago

The eFPs are pretty specific to particular curated tissue expression atlases for certain species (and are certainly cool). They aren't really appropriate to the mines, which are meant to provide a similar set of displayers for any species, if the data are present.

The better option is probably to add these linkouts to the linkout microservice which "knows" which genes are available at Toronto and which aren't. Eh what, @adf-ncgr ?

(It doesn't make sense to use the mine attribute linkouts because you'd get one for every Glycine gene, and I'm pretty sure Toronto does not have eFPs built for the 54 Glycine annotations we've got in GlycineMine at the moment.)

I'll move this to the microservices repo, as I think that's the appropriate place for it. (You'd also get those linkouts on the Jekyll gene search results, which is probably useful.)

adf-ncgr commented 6 months ago

Yes, I think your reasoning about making this a linkout is sensible, at least as an initial way of connecting things. There is some charm to having the eFP images embedded in the page as done at ThaleMine, but as you rightly noted it would not work for the vast majority of genes in our system so probably better to make it a linkout for those genes they support. I've just added one for glyma.Wm82.gnm4.ann1 genes though it's not immediately obvious to me whether they are using gnm2.ann1 or gnm4.ann1. I'll figure it out later, but let me know if you think I'm pointing to what you had in mind when you requested this, @jd-campbell