-
Notifications
You must be signed in to change notification settings - Fork 2
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Remove 'Phytophthora austrocedri' workaround #584
Comments
Curiously in the interim they dropped Phytophthora austrocedrae as a synonym, but added Phytophthora sp. austrocedrae as an includes - both on the website and in the Feb dump:
|
peterjc
added a commit
that referenced
this issue
Feb 1, 2024
This changes more species names than usual, and many are missing the older name as a defined synonym. Closes #584. txid631361 Phytophthora austrocedrae -> Phytophthora austrocedri (without synonym defined) txid565288 Phytophthora hydropathica -> Phytophthora honggalleglyana (with synonym defined) txid572928 Phytophthora citricola III -> Phytophthora aff. citricola III (without synonym defined) txid132615 Phytophthora glovera -> Phytophthora gloveri (without synonym defined) txid977911 Phytophthora citricola E -> Phytophthora cf. citricola group E (with synonym defined) txid4795 Phytophthora megakarya -> changed in Jan to invalid -> returned txid187986 Phytophthora bisheria -> txid1880901 Phytophthora bishii (in taxdmp_2024-02-01/merged.dmp) (without synonym defined) Phytophthora nicotianae taxid=4790 -> Phytophthora nicotianae taxid=4792 Phytophthora parasitica taxid=4792 -> Phytophthora nicotianae taxid=4792 (in taxdmp_2024-02-01/merged.dmp) (with synonym) (given they merged Phytophthora parasitica into nicotianae, why not keep 4790?)
peterjc
added a commit
that referenced
this issue
Feb 5, 2024
This changes more species names than usual, and many are missing the older name as a defined synonym. Closes #584. txid631361 Phytophthora austrocedrae -> Phytophthora austrocedri (without synonym defined) txid565288 Phytophthora hydropathica -> Phytophthora honggalleglyana (with synonym defined) txid572928 Phytophthora citricola III -> Phytophthora aff. citricola III (without synonym defined) txid132615 Phytophthora glovera -> Phytophthora gloveri (without synonym defined) txid977911 Phytophthora citricola E -> Phytophthora cf. citricola group E (with synonym defined) txid4795 Phytophthora megakarya -> changed in Jan to invalid -> returned txid187986 Phytophthora bisheria -> txid1880901 Phytophthora bishii (in taxdmp_2024-02-01/merged.dmp) (without synonym defined) Phytophthora nicotianae taxid=4790 -> Phytophthora nicotianae taxid=4792 Phytophthora parasitica taxid=4792 -> Phytophthora nicotianae taxid=4792 (in taxdmp_2024-02-01/merged.dmp) (with synonym) (given they merged Phytophthora parasitica into nicotianae, why not keep 4790?)
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Until recently and as of the taxdump_2024-01-01 files the NCBI had this species as Phytophthora austrocedrae with Phytophthora austrocedri as a synonym:
We've had a workaround in https://github.com/peterjc/thapbi-pict/blob/master/database/build_ITS1_DB.sh made in d4b0105 and 4db494f (5 years ago) to flip this, with the comment:
Checking today, the NCBI taxonomy https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=631361 now has species Phytophthora austrocedri with Phytophthora austrocedrae as a synonym.
So, once we update to the 2024-02-01 taxonomy (next release), we should be able to drop our workaround.
The text was updated successfully, but these errors were encountered: