In the current controlled vocabulary list, multiple species have a NCBI id which doesn't correspond to the authority species (for NCBI). This leads to unnecessary redundancy.
Example:
Penicillium expansum
The corresponding entry in the ReDU sheet is 1314791|Penicillium expansum.
However if we check the NCBI taxo list we have :
| tax_id |
name_txt |
unique_name |
name_class |
| 27334 |
Penicillium expansum Link, 1809 |
NaN |
authority |
| 27334 |
Penicillium expansum |
NaN |
scientific name |
| 1208580 |
Penicillium expansum NRRL 62431 |
NaN |
scientific name |
| 1314791 |
Penicillium expansum ATCC 24692 |
NaN |
scientific name |
| 1407458 |
Penicillium expansum T01 |
NaN |
scientific name |
It in fact it is Penicillium expansum ATCC 24692 which is listed.
Until a better solution is found see #241 for possible directions to explore, it might be good to at least limit entries to the NCBI id corresponding to the authority entry for a species. I understand from #241 that the idea is not to use a list of all possible species, however if this can help in the process here is a list of NCBI taxa restricted to "authority" entries (both the authority and the simpler scientific name are kept). Total is 629822 entries (instead of 3650056) ncbi_id_authority_list.tsv.gz
Gist of the treatment script https://gist.github.com/oolonek/c89fa6f078a771b5259d45d890bcd724
In the current controlled vocabulary list, multiple species have a NCBI id which doesn't correspond to the authority species (for NCBI). This leads to unnecessary redundancy.
Example:
Penicillium expansumThe corresponding entry in the ReDU sheet is
1314791|Penicillium expansum.However if we check the NCBI taxo list we have :
It in fact it is
Penicillium expansum ATCC 24692which is listed.Until a better solution is found see #241 for possible directions to explore, it might be good to at least limit entries to the NCBI id corresponding to the authority entry for a species. I understand from #241 that the idea is not to use a list of all possible species, however if this can help in the process here is a list of NCBI taxa restricted to "authority" entries (both the authority and the simpler scientific name are kept). Total is 629822 entries (instead of 3650056) ncbi_id_authority_list.tsv.gz
Gist of the treatment script https://gist.github.com/oolonek/c89fa6f078a771b5259d45d890bcd724