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evolgeniusteam / GMrepoProgrammableAccess

programmable access to GM repo
GNU General Public License v3.0
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taxonomy database for amplicon data #15

Open natashaklmnk opened 8 months ago

natashaklmnk commented 8 months ago

Could I please clarify one technical question. It is stated in the article (https://academic.oup.com/nar/article/50/D1/D777/6426060#authorNotesSectionTitle) that mapping to the GreenGenes database was used for amplicon data, while I see the NСBI taxonomy in the database itself. Could you please tell how the transition from the GreenGenes taxonomy to NСBI was made?

Thank you in advance!

whchenlab commented 8 months ago

thank you for using GMrepo. All taxonomic annotations were translated to NCBI taxonomy using in house R/Perl scripts. For GreenGenes, we did taxon name mapping followed by manual inspection.

natashaklmnk commented 8 months ago

Thank you very much for your answer! I also encountered in my work the need to transfer the GreenGenes taxonomy to NCBI and I was interested in how others solved this problem. It seems as if manual matching is one of the most common options. Thank you!