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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 10 months ago

natashaklmnk commented 10 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 10 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 10 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!