EFO URL error

[henrietteharmse]

This issue was originally logged on RT: https://helpdesk.ebi.ac.uk/Ticket/Display.html?id=431577

I'm seeing an issue with links to EFO terms. For example, assay:

https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0000070

In the right-hand column the EFO URI is given as http://www.ebi.ac.uk/efo/EFO_0001455 however clicking on that brings me to https://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_0001455 which gives an error.

[paolaroncaglia]

Notes for self: copying relevant comments from our Slack thread: H: "To me this seems to be a case where OBI has an incorrect annotation referencing a non-existent term in EFO." P: "EFO:0001455 doesn’t seem to exist, even as an obsolete term. On the other hand, the original OBI entry doesn’t seem to have any mapping to EFO. I’m not sure where the error comes from. It could be as you say, an incorrect annotation, or possibly EFO:0001455 was created a long time ago to represent ‘assay’ and then replaced with the OBI term without leaving any trace." P: "I can’t access RT, the submitter mentions “issue with links to EFO terms”, i.e. more than one link, are there others that need fixing as far as you know?" H: "He said there are others, but he did not give the examples of them. I replied and pointed him to the ticket I opened on EFO and suggested he open tickets for the others on github as this need to be dealt with probably on an individual basis." T: "I took a look at this also and there are others. For example, if you review the usages of this property in Protege the handful I checked all had this issue. I gather there was some historical reason this existed, but don't know what it is"

[paolaroncaglia]

Note for self: expanding on the last comment above, the EFO_URI annotation property is used 1276 times in EFO (including self-usage). At a quick glance, lots of chemicals including roles, plus some measurement units. I spot-checked a couple and they too point to EFO terms that seem dead. This issue may be due to an obsoletion policy that in the past was different than what we have now. In which case I’m not sure we’d want to remove trace of the EFO term entirely, and anyway we may want to have a global resolution and act on all 1275 cases.

• [ ] Gain some "historical" EFO perspective
• [ ] Figure out if all EFO_URIs point to dead terms
• [ ] Establish a global strategy and fix.

[zoependlington]

I believe in the past anything that was imported into EFO from an external ontology was given a placeholder EFO URI. It may be useful for us to create obsolete versions of these EFO URIs and remove the EFO_URI annotations and instead implement replaced by links from the obsolete term to the existing term. This could be done through ROBOT (to create the obsolete terms) and ROBOT/SPARQL to remove the annotation. I will assign myself.