add gene column to variant tabs on non-gene pages

monarch-initiative / monarch-legacy

Monarch web application and API

BSD 3-Clause "New" or "Revised" License

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add gene column to variant tabs on non-gene pages #746

Open nlwashington opened 9 years ago

nlwashington commented 9 years ago

it would be convenient if there was a gene column (as an attribute of the variant) added to the variant tables. it would help with interpretation. @ccondit, this will require additional fields in the golr schema.

cmungall commented 9 years ago

This could be useful on other object categories, such as genotype and disease too

On 8 Jun 2015, at 5:40, Nicole Washington wrote:

it would be convenient if there was a gene column (as an attribute of the variant) added to the variant tables. it would help with interpretation. @ccondit, this will require additional fields in the golr schema.

Reply to this email directly or view it on GitHub: https://github.com/monarch-initiative/monarch-app/issues/746

nlwashington commented 9 years ago

@cmungall should we really have genes here for disease? can you clarify what you want populated in that case?

ccondit commented 9 years ago

After discussing this with @nlwashington here's what needs to happen:

Add subject_gene, subject_chromosome, object_gene, object_chromosome and subject_gene_label, subject_chromosome_label, object_gene_label, and object_chromosome_label to the oban model as Golr closures.
Any subject or object that is a gene, variant, or genotype should add a gene and / or phenotype when available.

ccondit commented 9 years ago

This is loaded on geoffrey

kshefchek commented 9 years ago

Thanks @ccondit! Will update the oban config and then add these to the variant pages.

kshefchek commented 9 years ago

some kinks to be worked out, assigning back to Chris.

ccondit commented 9 years ago

Does this seem resolved with the latest Golr load?

jmcmurry commented 8 years ago

This doesn't appear fixed yet (on non-Gene pages). screen shot 2015-10-13 at 20 47 19

On gene pages, all looks to be in order. screen shot 2015-10-13 at 20 44 46

@nlwashington do you anticipate that this will be fixed with next golr load?

nlwashington commented 8 years ago

i think the data is ready to go; just has to be added to the app code to leverage it in a new column of those tabs.

jmcmurry commented 8 years ago

Great! Sounds easy enough. What is your preferred column header in this (non-gene-page) context? Also do you want just the gene, or also the relationship (eg. is allele of).

kshefchek commented 8 years ago

I'm not able to get this information from the current golr instances. There may be an issue at load time.

cmungall commented 8 years ago

We have this in the latest golr load on persei, I suggest we deploy this first, then we can add the column to the config

jmcmurry commented 8 years ago

The column is there, but the content is not (both beta and prod). @kshefchek please describe what needs to be done, thanks.

kshefchek commented 8 years ago

I think https://github.com/SciGraph/golr-loader/commit/c88693a2d7ec64a20011f215292d098fddfd7f68 should fix it, but let's leave open to make sure.

jmcmurry commented 8 years ago

ok; will flag with 'revisit in testing'.