obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
Other
131 stars 29 forks source link

Remove replicates of HRA 3D models---use only latest version #3315

Closed emquardokus closed 1 month ago

emquardokus commented 1 month ago

Uberon term Affects all HuBMAP HRA organs in Uberon that are linked to HRA; there are male and female versions of most of the organs

Examples : this affects all of the HRA organs, these are only 3 examples; this is likely just something that can be corrected by a general code change? Use latest version rather than all versions.
Note that file naming schema changed over the 7 HRA releases, so if you are using unique file name, that will not work.

http://purl.obolibrary.org/obo/UBERON_0001264 pancreas http://purl.obolibrary.org/obo/UBERON_0000059 large intestine http://purl.obolibrary.org/obo/UBERON_0002108 small intestine

Bug description

Example of 3D models from HRA where every HRA released version is shown.

Screenshot 2024-07-20 at 10 22 06 PM

It should only show the latest from https://lod.humanatlas.io/

Screenshot 2024-07-20 at 10 24 13 PM

from here: https://lod.humanatlas.io/ref-organ/pancreas-female/latest/ You would use the latest version of the .glb file linked at bottom

Ellen Quardokus orcid: 0000-0001-7655-4833

aleixpuigb commented 1 month ago

Thank you @emquardokus. @anitacaron solved this last week in https://github.com/obophenotype/uberon/pull/3314. It should be only the latest in the next release.

anitacaron commented 1 month ago

This was finally fixed and is already available in the OLS.

Screenshot 2024-08-09 at 10 10 02

emquardokus commented 1 month ago

@anitacaron I just checked this out and kidney 3D models are gone now from uberon. I checked small intestine, large intestine, pancreas, heart, lung, skin of body, spleen, prostate gland---all good. I did not check all the organs we have models for, but this one stood out as it's one of our most popular. Can you check why this one is gone now?

anitacaron commented 1 month ago

@emquardokus I'll move your question to the ccf-validation-tools repo which is where I query the HRA KG and get the GLB files.