envo_bridge is injecting a problematic IAO annotation

[cmungall]

We have a bridge module that performs injections into some classes to avoid things hanging at root. Eventually this can be replaced but for now we should remove things one at a time (see this ticket for injection https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1443)

In particular, See this line:

https://github.com/EnvironmentOntology/envo/blame/da9456c8fd9d022f7fdd677d0a0d7a9d148cf949/src/envo/imports/envo_bridge.owl#L87

(Note: I am 100% responsible for this.)

What is this line doing?

It is injecting a triple on

IAO:0000111 'editor preferred term'

specifically it is saying

IAO:0000111 IAO:0000111 'editor preferred term~editor preferred label'

specifically that the 'editor preferred term' for 'editor preferred term' is the weird string 'editor preferred term~editor preferred label', which is definitely not the editor preferred term for editor preferred term!

we can see how this looks in OLS: https://www.ebi.ac.uk/ols/ontologies/envo/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000111

it gets worse. Other ontologies import ENVO modules, and ontologies import these ontologies. In general annotations end up getting included (because SLME). So we see this junk propagated all over OBO.

e.g. if we try this SPARQL on ontobee:

SELECT ?v ?g WHERE {
  GRAPH ?g {
  <http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/IAO_0000111> ?v} .
  FILTER (regex(?v,"~"))}

we see the following ontologies are infected:

ditor preferred term~editor preferred label,obomerged:OSCI
editor preferred term~editor preferred label,obomerged:VO
editor preferred term~editor preferred label,obomerged:MCO
editor preferred term~editor preferred label,obomerged:PCO
editor preferred term~editor preferred label,obomerged:VICO
editor preferred term~editor preferred label,obomerged:CLO
editor preferred term~editor preferred label,obomerged:OBI
editor preferred term~editor preferred label,obomerged:ICDC
editor preferred term~editor preferred label,obomerged:CIDO
editor preferred term~editor preferred label,obomerged:SWO
editor preferred term~editor preferred label,obomerged:OPMI
editor preferred term~editor preferred label,obomerged:OLAM
editor preferred term~editor preferred label,obomerged:HTN
editor preferred term~editor preferred label,obomerged:PSDO
editor preferred term~editor preferred label,obomerged:CTCAE-OAEview
editor preferred term~editor preferred label,obomerged:OHMI
editor preferred term~editor preferred label,obomerged:OAE
editor preferred term~editor preferred label,obomerged:OVAE
editor preferred term~editor preferred label,obomerged:STATO
editor preferred term~editor preferred label,obomerged:UPHENO
editor preferred term~editor preferred label,obomerged:ECOCORE
editor preferred term~editor preferred label,obomerged:BCO
editor preferred term~editor preferred label,obomerged:OHPI
editor preferred term~editor preferred label,obomerged:LTHIDO
editor preferred term~editor preferred label,obomerged:TSO
editor preferred term~editor preferred label,obomerged:CTO
editor preferred term~editor preferred label,obomerged:OCVDAE
editor preferred term~editor preferred label,obomerged:OCMR
editor preferred term~editor preferred label,obomerged:ODAE
editor preferred term~editor preferred label,obomerged:ONS
editor preferred term~editor preferred label,obomerged:KTAO
editor preferred term~editor preferred label,obomerged:VIO
editor preferred term~editor preferred label,obomerged:ICEO
editor preferred term~editor preferred label,obomerged:VIO-ImmPort

One might say that this is not such a big deal, as it is just an annotation property, it doesn't affect logic or structure. However, this kind of virally propagated junk makes our ontologies confusing to users and lessens their confidence, so I regard it as high priority.

I will fix ASAP as I am responsible

[cmungall]

in my defence, one one seems to agree on what the editor preferred term is for editor preferred term, with some saying

• editor preferred term editor preferred term editor preferred term

and others saying

• editor preferred label editor preferred label editor preferred label

the irony...

[cthoyt]

[anitacaron]

I came across this issue from the issue https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1443 and found out that this annotation is still there when I clicked on the OLS link, which shouldn't work anymore.

All this time, it's also in the envo-edit.owl L47508