DataBiosphere / azul

Metadata indexer and query service used for AnVIL, HCA, LungMAP, and CGP
Apache License 2.0
7 stars 2 forks source link

Add antibody to AnVIL index #4440

Closed theathorn closed 8 months ago

theathorn commented 2 years ago

Add an outer and inner entity type called antibody using the table of the same name. Index that table's target column into a property of the same name in inner and outer entities of type antibody. Discover rows in that table by traversing the relation from the assayactivity table.

melainalegaspi commented 2 years ago

@hannes-ucsc to define details.

hannes-ucsc commented 2 years ago

This can be deprioritized since there currently is no snapshot in the corpus in which that table is not empty. Supposedly the upcoming ENCODE snapshot has a non-empty antibody table. Once we have that snapshot we can look into this. We need to also understand the cardinality of the target column in order to decide if we'll include it as a property of inner entities, and make it a facet.

hannes-ucsc commented 1 year ago

Spike to confirm that the antibody table is either empty or absent from all of the snapshots currently on the spreadsheet. If confirmed, we'll park this ticket with a request to be notified by the Broad when a snapshot is added that does have a non-empty antibody table.

nadove-ucsc commented 1 year ago

The antibody table is present but empty for every snapshot currently on the spreadsheet (rows 3-83).

achave11-ucsc commented 1 year ago

@bvizzier-ucsc to confirm point person at the Broad.

bvizzier-ucsc commented 1 year ago

Check with Nate Calvanese.

achave11-ucsc commented 1 year ago

Noa asked Nate here: https://ucsc-gi.slack.com/archives/C03TPJS54DC/p1691022243067239

hannes-ucsc commented 8 months ago

No response. We have too much else to do.