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NCATSTranslator / testing

Materials and tools for testing Translator components
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Disease (MONDO:0004496) <located_in> NamedThing #195

Open sstemann opened 2 years ago

sstemann commented 2 years ago

Query: location.json PK: 054272f9-cf05-4a2f-9a9b-ca4b79cf927c

Looking for the cells that PLP1 is located in. Should be all neuronal cells.

image

brettasmi commented 2 years ago

I'm a little confused which query is actually in play here. The query in the linked PK results is (disease OR gene) - located in - (cell) query, but this issue title and the linked json seems to concern a (disease) - located in - (named thing).

I suspect we're looking at the query in the linked PK. If that's the case we do have such information, but it's not exposed correctly due to some ongoing modeling challenges between SPOKE and biolink.

I've attached the results that can be imported into ARAX here. A big caveat is that there is an attribute level that describes the level of expression represented by that edge. For most of the results, the level is "Not detected," so it could be confusing to interpret without reviewing the attributes of each edge. To save everyone the trouble, here are the positive results:

UBERON:0000479/CL:2000032: peripheral nerve in soft tissue 1
UBERON:0000956/CL:0000125: glial cells in cerebral cortex
UBERON:0000956/CL:0000775: neuropil in cerebral cortex
UBERON:0001873/CL:0002319: neuronal cells in caudate
UBERON:0002305/CL:0002319: neuronal cells in hippocampus

We haven't tried to clean this up much because it hasn't been exposed. Hopefully we'll get that biolink issue resolved soon.

gene-expression-location.txt