My apologies for spamming the list on this problem. But in order to figure out how many gbCdna entries have a discrepancy between their actual tax id and that of the Organism id, you may have to create a table by mapping the EST/mRNA accessions to their real taxonomy id, and the tax id that corresponds to the Organism from the Organism table. Would it be possible to provide me with such a table, so I may correct my version of gbCdnaInfo?
Thanks so much, Charu G. Kumar, Ph.D. , UIUC ________________________________ From: Kumar, Charu Gupta Sent: Tuesday, April 03, 2012 11:07 AM To: [email protected] Subject: Problems with Organism Info in gbCdnaInfo, e.g.AU194514 Hi, Upon further checks, it looks like that the Organism id is not the same as taxonomy id. Once that assumption is removed, then all is good. So, my request is if it is possible to include the taxonomy id in the Organism table. That would be a great help and will clarify the distinction between the actual taxonomy id versus just a primary identifier to link with the Organism table. Thanks, Charu G. Kumar, Ph.D. ________________________________ From: Kumar, Charu Gupta Sent: Monday, April 02, 2012 6:18 PM To: [email protected] Subject: Problems with Organism Info in gbCdnaInfo, e.g.AU194514 Hi, I am noticing problems in 'gbCdnaInfo' table in the Organism field. E.g. take the acc, AU194514. In NCBI it belongs to Porphyra yezoenis (taxid:2788), but in gbCdnaInfo table, the Organism field has taxid as 623 (Shigella) for this acc. This is not limited to just one record. It would be great if you could help me out with this. These discrepancies are significantly affecting my work. Thanks, Charu Charu G. Kumar, Ph.D., UIUC _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
