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
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 :
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