Genbank Fixer Upper - Genbank Taxonomic Updater

[jhpoelen]

Related to NCBI Taxonomy / Accession - names in Genbank are sometimes outdates and may not "corrected" over time - Asellia tridens haplotype DF1 cytochrome b (cytb) gene, complete cds; mitochondrial - This accession is classified as Asellia tridens, but is used in the paper: Benda,P., Vallo,P. and Reiter,A. 2011. Acta Chiropt. Taxonomic revision of the genus Asellia (Chiroptera:Hipposideridae) with a description of a new species from southern Arabia Acta Chiropt. 13 (2), 245-270 (2011)

describing the accession at Asellia arabica: https://www.ncbi.nlm.nih.gov/nuccore/JF439015 .

Prototype Idea: index genbank and make searchable annotations by individuals that make claims on how name associated to genbank accessions should be interpreted.
Initially at the level of Chiroptera Could then do all mammals – and other taxa

Kendra claims that https://www.ncbi.nlm.nih.gov/nuccore/JF439015 should be identified as Asellia arabica instead of Asellia tridens as documented in Benda,P., Vallo,P. and Reiter,A. 2011.

[jhpoelen]

Also suggested to republish genbank mammals with applied name changes.

[jhpoelen]

see also:

https://www.ncbi.nlm.nih.gov/genbank/wgs_update/

[jhpoelen]

for the flat file publications - https://ftp.ncbi.nlm.nih.gov/genbank/

[jhpoelen]

@n8upham shared an appendix from published research[1] that describe ncbi records and suggested interpretations.

UphamEtAl_MamPhy_IUCN-to-NCBI_matchup_Sept2015.csv

First 10 lines -

Source	ID	MasterTax_Order	MasterTax_Family	MasterTax_SciName	matched_name	matching_source	NCBI_SciName	NCBI_Rank	NCBI_ID	COMMENT	PUBLICATION		_2
IUCN	42641	RODENTIA	MURIDAE	Abditomys_latidens	0	0	0	0	0	NA	NA
IUCN	17879	RODENTIA	MURIDAE	Abeomelomys_sevia	Abeomelomys_sevia	IUCN	Abeomelomys_sevia	Species	491870	NA	NA
IUCN	17879	RODENTIA	MURIDAE	Abeomelomys_sevia	_Matched-manually-to-NCBI	MSW3	Abeomelomys_sevia_tatei	Subspecies	491889	NA	NA
IUCN	16	RODENTIA	CRICETIDAE	Abrawayaomys_ruschii	Abrawayaomys_ruschii	IUCN	Abrawayaomys_ruschii	Species	1258732	NA	NA
IUCN	42656	RODENTIA	ABROCOMIDAE	Abrocoma_bennettii	Abrocoma_bennettii	IUCN	Abrocoma_bennettii	Species	108855	NA	NA
IUCN	42656	RODENTIA	ABROCOMIDAE	Abrocoma_bennettii	Abrocoma_bennettii	MSW3	Abrocoma_bennettii_bennettii	Subspecies	126352	NA	NA
IUCN	18	RODENTIA	ABROCOMIDAE	Abrocoma_boliviensis	_Matched-manually-to-NCBI	REF--Upham and Patterson 2015	MANUAL ADDING	0	0	KJ742657	Upham, N. S. and Patterson, B.D. 2015. Evolution of caviomorph rodents: a complete phylogeny and timetree for living genera. Pp. 63-120 In: Biology of caviomorph rodents: diversity and evolution (A.I. Vassallo and D. Antenucci, eds.). SAREM Series A, Buenos Aires, Argentina.
IUCN	136334	RODENTIA	ABROCOMIDAE	Abrocoma_budini	0	0	0	0	0	NA	NA

references

[1] Upham NS, Esselstyn JA, Jetz W (2019) Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLoS Biol 17(12): e3000494. https://doi.org/10.1371/journal.pbio.3000494