obophenotype / obophenotype/ncbitaxon
Include obsolete taxa
Open
@anitacaron is already working on this.
Since Feb 19, 2025.
enhancement
- Dominant language
- Python
- Stars
- 31
- Forks
- 7
- PR merge metrics
- No merged PRs in 30d
Description
As far as I can tell, we have never included obsolete taxa in our ncbitaxon.owl. (There's nothing obvious in the old code, and grep owl:deprecated ncbitaxon.owl returns nothing.)
taxdmp.zip includes tax_ids for merged and deleted nodes (merged.dmp and delnodes.dmp), but no other information. This is enough to add obsolete classes like this:
NCBITaxon:12 a owl:Class
; rdfs:label "obsolete taxon 12"^^xsd:string
; owl:deprecated "true"^^xsd:boolean
; IAO:0100001 NCBITaxon:74109 # term replaced by
.
NCBITaxon:2663962 a owl:Class
; rdfs:label "obsolete taxon 2663962"^^xsd:string
; owl:deprecated "true"^^xsd:boolean
.
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