Think about how to handle genbank names with specified authority

fernphy / ftol

Pipeline to generate the Fern Tree of Life

https://fernphy.github.io/

MIT License

4 stars 1 forks source link

Think about how to handle genbank names with specified authority #9

Open joelnitta opened 2 years ago

joelnitta commented 2 years ago

In the /note="authority: field.

For example, https://www.ncbi.nlm.nih.gov/nuccore/1996759179

The original submission has /note="authority: Pteris inaequalis (Fee) Jenman", which is a valid name (maybe... valid synonym according to POW, illegal according to IPNI)

NCBI applies the name "Pteris inaequalis C.Presl", which is invalid.

For now, map Pteris inaequalis C.Presl to Pteris inaequalis (Fee) Jenman.

joelnitta commented 2 years ago

Since the workflow now uses fixed versions of both taxonomic data and genbank data (each downloaded from NCBI FTP servers), there is less uncertainty about how a given name might be treated between different accessions. So at least we can be confident in the treatment of a name for a given context.