galaxyproject / galaxyproject/brc-analytics

consider automatically pulling in all assemblies for an ncbi tax id

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#595 3 comments 0 reactions 1 assignee Claimed by @d-callan View on GitHub
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Description

this in partial response to a complaint we were made aware of about someone looking for a specific a fumigatus assembly and not finding it. @maximilianh suggested maybe only tracking ncbi tax ids we care about and pulling in all assemblies for it. thats a fun idea, but there are some implications we should discuss and consider what to do about. top three i see:
1. right now the tax ids we track are always associated w rank = species. theres some validation we do around this, and some annotations we hang off it. but id expect assemblies to be associated w tax ids of various ranks, like isolate. maybe the data catalog would learn to look for all assemblies for not just the provided species tax ids, but also for any child tax ids?
2. this could introduce a lot of assemblies very quickly, and ill guess @NoopDog might have some thoughts to share about whether were ready for that from a technical perspective
3. the more assemblies we have for an organism, the more important it is to differentiate them. so issues like #591 maybe become higher priority as well

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