Hello, I was following the clawback tutorial (Understanding q2-clawback weights learning) to build wheighted classifiers from Annelida gut habitats (assuming that worm habitats might differ from mammalian habitats).
My idea was to start with ´´´redbiom search metadata "where host_taxid==6340" ´´´ to get a list of sample ids from Annelida. Since the output is empty, I am wondering whether taxids can be used in the same way as at NCBI (where txid 6340 specifies Annelida and all taxonomic groups within Annelida), or whether taxids in redbiom are not hierarchically stored (only the specific taxid is stored)?
Hi @arwqiime ,
I have recategorized your question as "other bioinformatics tools" as it is rather a question about how Qiita and/or redbiom handles taxids. This is a pre-clawback step so I also changed the title for clarity.
I am not 100% certain, but I think that you are correct, that Qiita and redbiom probably do not store hierarchical taxid info, it is most likely just the specific taxon linked to that taxid, since I belive that this is just stored in a sample metadata file in Qiita (but maybe redbiom handles this differently, I am not sure). You could search directly on Qiita for more specific taxids in Annelida to confirm (or maybe search via common names).
provided you can find a workaround (maybe a list of specific taxids or sample ids?) and pull up enough records, this indeed sounds like a good approach. I would still recommend comparing vs. the uniform classifier to make sure that results look reasonable, as you would probably only recover a small number of records (if any).