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serratus-bio / open-virome

monorepo for data explorer UI and APIs
http://openvirome.com/
GNU Affero General Public License v3.0
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sOTU based queries return all sOTU in "match" bioProjects #58

Open ababaian opened 1 month ago

ababaian commented 1 month ago

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I have a query here for sOTU u145189 and u183036 with the purpose of retrieving the following component I have in R

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The current Open Virome returns a more complex network image

What appears to be happening is that all runs which have those sOTU are being matched (correctly), and then what the Virome Module is displaying is all sOTU in the matching runs, including those not specificed in the query are being displayed.

I think both behaviours are/can be technically correct, but the expected behaviour upfront I think should be to return/display only matching sOTU. Otherwise it's unclear why co-associated sOTU are being shown. This certainly will be neccesary when moving towards palm-palm networks to avoid pulling down huge clusters of unrelated sequences when querying by sOTU/Sequence.

lukepereira commented 1 month ago

I noticed this as well. I think there is more complexity when the user mixes multiple filters and the runs overlap, but it should be possible to filter out irrelevant sOTUs based on sOTU filters as a post-processing step

ababaian commented 1 month ago

Ingrida but maybe the issue is i am getting more than needed; or this is also as expected? See at the top: Virus Family: Polycipiviridae while in the graph: you have many different +ssRNA viruses, not just picorna-like

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ababaian commented 1 week ago

Please add a Time Estimate: for this issue.