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Remove 'Phytophthora austrocedri' workaround #584

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peterjc opened this issue Jan 15, 2024 · 1 comment · Fixed by #594
Closed

Remove 'Phytophthora austrocedri' workaround #584

peterjc opened this issue Jan 15, 2024 · 1 comment · Fixed by #594

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@peterjc
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peterjc commented Jan 15, 2024

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 d4b0105 and 4db494f (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
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peterjc commented Feb 1, 2024

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        |

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?)
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