peterjc / thapbi-pict

Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool
https://thapbi-pict.readthedocs.io/
MIT License
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Remove 'Phytophthora austrocedri' workaround #584

Closed peterjc closed 8 months ago

peterjc commented 8 months ago

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:

$ grep 'Phytophthora austrocedr*' taxdmp_2024-01-01/names.dmp 
631361  |   Phytophthora austrocedrae Gresl. & E.M. Hansen 2007 |       |   authority   |
631361  |   Phytophthora austrocedrae   |       |   scientific name |
631361  |   Phytophthora austrocedri    |       |   synonym |

We've had a workaround in https://github.com/peterjc/thapbi-pict/blob/master/database/build_ITS1_DB.sh made in d4b0105a6f9a02e130fe1c0dee971abab12f1e5c and 4db494f77a0303854904d7d33ff9dbae3d09b1f5 (5 years ago) to flip this, with the comment:

Ad-hoc fix for NCBI taxonomy not yet having caught up with community consensus. At the 7th Meeting of the International Union of Forest Research Organisations Working Party (IUFRO) 7.02.09, Phytophthoras in forests and natural ecosystems, a decision was made to adhere to the original and correct version of the species name, Phytophthora austrocedri.

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.

peterjc commented 8 months ago

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:

$ grep 'Phytophthora .*austrocedr*' taxdmp_2024-02-01/names.dmp
631361  |       Phytophthora austrocedri Gresl. & E.M. Hansen 2007      |               |       synonym |
631361  |       Phytophthora austrocedri        |               |       scientific name |
631361  |       Phytophthora sp. austrocedrae   |               |       includes        |