oboInOwl:hasOBONamespace 'uberon' not used consistently

[shawntanzk]

I know that I should avoid using oboInOwl:hasOBONamespace 'uberon' to filter out native terms, however, this is not super clear for people using the ontology without prior knowledge. I am guessing that oboInOwl:hasOBONamespace 'uberon' was added somewhere in the release make pipeline, however, this does not seem to be applied to DOSDP template terms (I think) that are suppose to be native to uberon too.

Running

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>

SELECT DISTINCT ?cls ?label
WHERE{
  ?cls a owl:Class .
  ?cls rdfs:label ?label . 
  FILTER (isIRI(?cls) && STRSTARTS(str(?cls), "http://purl.obolibrary.org/obo/UBERON_"))
  FILTER NOT EXISTS {?cls oboInOwl:hasOBONamespace 'uberon'}
} 

gives me 52 tooth terms

http://purl.obolibrary.org/obo/UBERON_8490001,right upper second secondary molar tooth http://purl.obolibrary.org/obo/UBERON_8490002,right upper first secondary molar tooth http://purl.obolibrary.org/obo/UBERON_8490003,right upper second secondary premolar tooth http://purl.obolibrary.org/obo/UBERON_8490012,right lower first secondary premolar tooth http://purl.obolibrary.org/obo/UBERON_8490004,right upper first secondary premolar tooth http://purl.obolibrary.org/obo/UBERON_8490013,right lower secondary canine tooth http://purl.obolibrary.org/obo/UBERON_8490005,right upper secondary canine tooth http://purl.obolibrary.org/obo/UBERON_8490014,right lower lateral secondary incisor tooth http://purl.obolibrary.org/obo/UBERON_8490006,right upper lateral secondary incisor tooth http://purl.obolibrary.org/obo/UBERON_8490015,right lower central secondary incisor tooth http://purl.obolibrary.org/obo/UBERON_8490007,right upper central secondary incisor tooth http://purl.obolibrary.org/obo/UBERON_8490016,right upper second primary molar tooth http://purl.obolibrary.org/obo/UBERON_8490017,right upper first primary molar tooth http://purl.obolibrary.org/obo/UBERON_8490018,right upper primary canine tooth http://purl.obolibrary.org/obo/UBERON_8490019,right upper lateral primary incisor tooth http://purl.obolibrary.org/obo/UBERON_8490010,right lower first secondary molar tooth http://purl.obolibrary.org/obo/UBERON_8490036,left lower first secondary molar tooth http://purl.obolibrary.org/obo/UBERON_8490011,right lower second secondary premolar tooth http://purl.obolibrary.org/obo/UBERON_8490037,left lower second secondary premolar tooth http://purl.obolibrary.org/obo/UBERON_8490038,left lower first secondary premolar tooth http://purl.obolibrary.org/obo/UBERON_8490039,left lower secondary canine tooth http://purl.obolibrary.org/obo/UBERON_8490030,left upper first secondary premolar tooth http://purl.obolibrary.org/obo/UBERON_8490008,right lower third secondary molar tooth http://purl.obolibrary.org/obo/UBERON_8490031,left upper secondary canine tooth http://purl.obolibrary.org/obo/UBERON_8490009,right lower second secondary molar tooth http://purl.obolibrary.org/obo/UBERON_8490032,left upper lateral secondary incisor tooth http://purl.obolibrary.org/obo/UBERON_8490033,left upper central secondary incisor tooth http://purl.obolibrary.org/obo/UBERON_8490034,left lower third secondary molar tooth http://purl.obolibrary.org/obo/UBERON_8490035,left lower second secondary molar tooth http://purl.obolibrary.org/obo/UBERON_8490024,right lower lateral primary incisor tooth http://purl.obolibrary.org/obo/UBERON_8490025,right lower central primary incisor tooth http://purl.obolibrary.org/obo/UBERON_8490026,left upper third secondary molar tooth http://purl.obolibrary.org/obo/UBERON_8490027,left upper second secondary molar tooth http://purl.obolibrary.org/obo/UBERON_8490028,left upper first secondary molar tooth http://purl.obolibrary.org/obo/UBERON_8490029,left upper second secondary premolar tooth http://purl.obolibrary.org/obo/UBERON_8490020,right upper central primary incisor tooth http://purl.obolibrary.org/obo/UBERON_8490021,right lower second primary molar tooth http://purl.obolibrary.org/obo/UBERON_8490022,right lower first primary molar tooth http://purl.obolibrary.org/obo/UBERON_8490048,left lower first primary molar tooth http://purl.obolibrary.org/obo/UBERON_8490023,right lower primary canine tooth http://purl.obolibrary.org/obo/UBERON_8490049,left lower primary canine tooth http://purl.obolibrary.org/obo/UBERON_8490040,left lower lateral secondary incisor tooth http://purl.obolibrary.org/obo/UBERON_8490041,left lower central secondary incisor tooth http://purl.obolibrary.org/obo/UBERON_8490042,left upper second primary molar tooth http://purl.obolibrary.org/obo/UBERON_8490043,left upper first primary molar tooth http://purl.obolibrary.org/obo/UBERON_8490044,left upper primary canine tooth http://purl.obolibrary.org/obo/UBERON_8490045,left upper lateral primary incisor tooth http://purl.obolibrary.org/obo/UBERON_8490046,left upper central primary incisor tooth http://purl.obolibrary.org/obo/UBERON_8490047,left lower second primary molar tooth http://purl.obolibrary.org/obo/UBERON_8490050,left lower lateral primary incisor tooth http://purl.obolibrary.org/obo/UBERON_8490051,left lower central primary incisor tooth http://purl.obolibrary.org/obo/UBERON_8490000,right upper third secondary molar tooth

Think making it all consistent (remove all or add it to the tooth terms too) would make it easier for end users :)

Thanks

[shawntanzk]

pinging @anitacaron & @matentzn - didnt assign anyone and I know this is low priority, just thought I'd open a ticket for it :) Thanks!

[matentzn]

Is there any reason we need to maintain this tag? Cant we just drop it?

cc @cmungall

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[shawntanzk]

btws same thing with oio:id :D https://api.triplydb.com/s/UzfGT0r5T

[matentzn]

Vote1: Retain oboInOwl:hasOBONamespace?

• 👍 Drop oboInOwl:hasOBONamespace tags from the ontology entirely and add QC that it never comes back
• 🎉 Add oboInOwl:hasOBONamespace tags consistently to every term that belongs to Uberon and add QC that this is never missed again

[matentzn]

@shawntanzk can you open a new issue about oboInOwl:id? I think there maybe some other concerns there than hasOBONamespace..

[wdduncan]

To be honest, I do not know what the purpose of the oboInOwl:hasOBONamespace annotation is.

[github-actions[bot]]

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.