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obophenotype / ncbitaxon

Build for NCBITaxon
BSD 3-Clause "New" or "Revised" License
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NCBITaxon should depend on latest archived NCBI release, rather than latest release #78

Closed matentzn closed 1 year ago

matentzn commented 1 year ago

Right now, NCBI taxon depends on the latest working release in

https://ftp.ncbi.nih.gov/pub/taxonomy/.

The problem with that is that we never know which version of NCBI we are actually aligning with. @jamesaoverton told me that only some, not all of the "latest" versions are being properly archived and versioned.

I would like to suggest to obtain the latest archived version of NCBITaxon rather than the latest snapshot, thereby having a clear provenance trail to which NCBI taxon version was used. As a second benefit, people that do not use the owl or OBO versions can still be in sync with the latest release of the ontology when they obtain the corresponding archived ncbitaxon from the source!

anitacaron commented 1 year ago

It might be a good time to do this.

I was running a new release to update taxslim-disjoint-over-in-taxon.owl, and I noticed some differences in synonyms.

Screenshot 2023-09-18 at 11 54 21

This is reflected in the latest taxdmp.zip:

Screenshot 2023-09-18 at 11 56 23

But in the 2023-09-01 taxdmp.zip release, we have:

Screenshot 2023-09-18 at 11 56 05

Note the changes from authority to synonym.