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[ENQ-BUG-URGENT] EDAM not loading, terms changed? #129

Open ESapenaVentura opened 1 year ago

ESapenaVentura commented 1 year ago

@bvarner-ebi @zoependlington with the latest HCAO release (1.0.51), we have noticed that EDAM is no longer available ~(As you can see when we list the ontologies here https://ontology.archive.data.humancellatlas.org/ontologies)~ This is no longer the case as we have rolled back to 1.0.50

Also, we have noticed that in OLS, terms from the EDAM ontology have changed their obo_id (e.g. from data:3197 to EDAM:3197), which is a pretty big change that would affect our service greatly. Do you have any idea why this happened?

In the meantime, we will be rolling back to 1.0.50, but any help would be greatly appreciated

zoependlington commented 1 year ago

@bvarner-ebi I suspect this is because the get_mirrors.sh file refers to https://www.ebi.ac.uk/ols/ontologies/edam/download - can you replace it with the EDAM PURL (https://edamontology.org/EDAM.owl) and run a fake release that gets pushed to a branch so @ESapenaVentura can test the outcome please?

ghost commented 1 year ago

Thanks for checking this, @zoependlington. As discussed offline, this may be related to this comment.

@ESapenaVentura, I created an issue for EDAM and will advise once there is an update.

ESapenaVentura commented 1 year ago

Any news about this @zoependlington @bvarner-ebi ?

ghost commented 1 year ago

Hi @ESapenaVentura, thank you for the follow up. I am no longer overseeing the HCAO releases and unfortunately have not received any updates regarding the EDAM issue. @udp should be supporting the HCAO releases going forward, and I will ping him again on this.

jamesamcl commented 1 year ago

I'm working on porting HCAO to the ontology development kit (ODK) which will make it much easier to maintain going forwards.

I'm slightly confused because as far as I was concerned the HCAO repo was here: https://github.com/ebi-ait/ontology and I hadn't seen this repo until I was tagged in the issue.

Is there any reason there are two repos? The one I've been looking at has issues disabled and I don't have any admin rights for it, while this one has issues but seems out of date.

zoependlington commented 1 year ago

@udp https://github.com/ebi-ait/ontology is the current repo for development due to problems with this one a few years ago. Issues are still made here.

jamesamcl commented 1 year ago

Thanks @zoependlington . Do you remember what the problems are? I think we should be tracking issues in the same repo we develop in, and I don't like the fact there is an older version of the ontology here.

ESapenaVentura commented 1 year ago

@udp We are discussing internally, we are meeting on monday to discuss if we can "unify" the repos and just use the EBI-AIT one for both issues and development.

@zoependlington if you have any idea why this decision was taken, that would help us accelerate the process!

zoependlington commented 1 year ago

https://github.com/ebi-ait/hca-ebi-dev-team/issues/363 This is the release where the switch happened.