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obophenotype / human-phenotype-ontology

Ontology for the description of human clinical features
http://obophenotype.github.io/human-phenotype-ontology/
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Dead HPO links for "alternative_ids" #10643

Open JaneBrennan opened 1 month ago

JaneBrennan commented 1 month ago

HPO term Disproportionate short-limb short stature http://purl.obolibrary.org/obo/HP_0008873

Bug description If I select any of the 12 "alternative_ids" for this entry they lead nowhere. They are dead links. How can I trace what these IDs are?

Thank you!

Here are the links:

has_alternative_id

[HP:0001523](http://purl.obolibrary.org/obo/HP_0001523)
[HP:0003505](http://purl.obolibrary.org/obo/HP_0003505)
[HP:0003509](http://purl.obolibrary.org/obo/HP_0003509)
[HP:0008858](http://purl.obolibrary.org/obo/HP_0008858)
[HP:0008869](http://purl.obolibrary.org/obo/HP_0008869)
[HP:0008875](http://purl.obolibrary.org/obo/HP_0008875)
[HP:0008880](http://purl.obolibrary.org/obo/HP_0008880)
[HP:0008881](http://purl.obolibrary.org/obo/HP_0008881)
[HP:0008889](http://purl.obolibrary.org/obo/HP_0008889)
[HP:0008912](http://purl.obolibrary.org/obo/HP_0008912)
[HP:0008914](http://purl.obolibrary.org/obo/HP_0008914)
[HP:0008928](http://purl.obolibrary.org/obo/HP_0008928)

I have found a similar issue of dead "alternative_ids", for other HPO terms I have looked at. I am just wondering if I am doing something wrong - are these obsoleted links? I can find no reference to them anywhere except for in the corresponding UMLS terms.

matentzn commented 1 month ago

@pnrobinson this was always there, see https://github.com/obophenotype/human-phenotype-ontology/issues/8021

kanems commented 1 month ago

The links based on the "alternative ids" used to redirect to the new HPO ID, but the links haven't worked for a few months at least.

matentzn commented 1 month ago

I think there are two issues here:

https://hpo.jax.org/browse/term/HP:0001523

does not resolve to anything (because the ID does not exist). @iimpulse you might want to handle this a bit more gracefully saying that the ID does not exist?

The other issue is that HP:0001523 does not exist as a real term in the ontology. Basically:

HP:123 --[has alternative id]--> HP:0001523 means that HP:0001523 is intrinsically obsoleted, and replaced by HP:123. I looked back 2 years of HPO releases and this has not been correctly dealt with for a very long time (more than 6 years).

@pnrobinson If you like me to fix this issue, you will have to allow me to deal with #8021 which you previously put the lit on.

pnrobinson commented 1 month ago

Can we discuss this via zoom?

matentzn commented 1 month ago

Yes I put it on our (swelling) agenda!