New required Terms for microbeMASST data submission

[raimofranke]

Hi Ming,

I would need a way to indicate clinical isolates and ideally also link to the NCBI BioSample database: Taxaname_file;NCBI_BioSample Pseudomonas aeruginosa isolate CH2682;https://www.ncbi.nlm.nih.gov/biosample/10564430 Pseudomonas aeruginosa isolate CH2690;https://www.ncbi.nlm.nih.gov/biosample/10564434 Pseudomonas aeruginosa isolate CH2706;https://www.ncbi.nlm.nih.gov/biosample/10564426 Pseudomonas aeruginosa isolate CH2860;https://www.ncbi.nlm.nih.gov/biosample/10564453 Pseudomonas aeruginosa isolate CH4528;https://www.ncbi.nlm.nih.gov/biosample/10564494 Pseudomonas aeruginosa isolate CH4591;https://www.ncbi.nlm.nih.gov/biosample/10564489 Pseudomonas aeruginosa isolate CH4681;https://www.ncbi.nlm.nih.gov/biosample/10564486 Pseudomonas aeruginosa isolate ESP027;https://www.ncbi.nlm.nih.gov/biosample/10564552 Pseudomonas aeruginosa isolate ESP046;https://www.ncbi.nlm.nih.gov/biosample/10565070 Pseudomonas aeruginosa isolate ESP058;https://www.ncbi.nlm.nih.gov/biosample/10565064 Pseudomonas aeruginosa isolate ESP067;https://www.ncbi.nlm.nih.gov/biosample/10565057 Pseudomonas aeruginosa isolate ESP083;https://www.ncbi.nlm.nih.gov/biosample/10565073 Pseudomonas aeruginosa isolate ESP088;https://www.ncbi.nlm.nih.gov/biosample/10565071 Pseudomonas aeruginosa isolate F1764;https://www.ncbi.nlm.nih.gov/biosample/10565128 Pseudomonas aeruginosa isolate F1864;https://www.ncbi.nlm.nih.gov/biosample/10565153 Pseudomonas aeruginosa isolate F1959;https://www.ncbi.nlm.nih.gov/biosample/12264259 Pseudomonas aeruginosa isolate F1997;https://www.ncbi.nlm.nih.gov/biosample/10565141 Pseudomonas aeruginosa isolate F2020;https://www.ncbi.nlm.nih.gov/biosample/10565165 Pseudomonas aeruginosa isolate F2030;https://www.ncbi.nlm.nih.gov/biosample/10565197 Pseudomonas aeruginosa isolate F2059;https://www.ncbi.nlm.nih.gov/biosample/10565188 Pseudomonas aeruginosa isolate F2165;https://www.ncbi.nlm.nih.gov/biosample/10565174 Pseudomonas aeruginosa isolate F2166;https://www.ncbi.nlm.nih.gov/biosample/10565173 Pseudomonas aeruginosa isolate F2224;https://www.ncbi.nlm.nih.gov/biosample/12264246 Pseudomonas aeruginosa isolate MHH16050;https://www.ncbi.nlm.nih.gov/biosample/10573928 Pseudomonas aeruginosa isolate MHH16563;https://www.ncbi.nlm.nih.gov/biosample/10573920 Pseudomonas aeruginosa isolate MHH16798;https://www.ncbi.nlm.nih.gov/biosample/10573917 Pseudomonas aeruginosa isolate MHH17546;https://www.ncbi.nlm.nih.gov/biosample/10573911 Pseudomonas aeruginosa isolate MHH17704;https://www.ncbi.nlm.nih.gov/biosample/12264239 Pseudomonas aeruginosa isolate MHH17767;https://www.ncbi.nlm.nih.gov/biosample/10573910 Pseudomonas aeruginosa isolate Psae1439;https://www.ncbi.nlm.nih.gov/biosample/10573901 Pseudomonas aeruginosa isolate Psae1837;https://www.ncbi.nlm.nih.gov/biosample/10573888 Pseudomonas aeruginosa isolate ZG302383;https://www.ncbi.nlm.nih.gov/biosample/10573932 Pseudomonas aeruginosa isolate ZG316717;https://www.ncbi.nlm.nih.gov/biosample/12264229 Pseudomonas aeruginosa isolate ZG8038581181;https://www.ncbi.nlm.nih.gov/biosample/10573957 Pseudomonas aeruginosa isolate ZG8510487;https://www.ncbi.nlm.nih.gov/biosample/10573956

Thanks and best wishes, Raimo

[alan-jarmusch]

to facilitate update can you please format with the NBCI number followed by the name "27334|Penicillium expansum"

[raimofranke]

Hi Alan, these are not NCBI taxonomy numbers, these are are all Pseudomonas aeruginosa samples, but each is a different clinical isolate with a unique NCBI biosample number - is it possible to use NCBI biosample numbers in ReDU? That would be super helpful! Thanks and best wishes, Raimo