uberon
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obophenotype
Make the Allen Ontologies more discoverable
[close if we think this is not Uberon's responsibility]
It's good that Allen are producing the OWL themselves. I wish that they provided a central source of truth with table of downloads
Right now one has to navigate to individual repos like https://github.com/brain-bican/developing_human_brain_atlas_ontology/, test the URLs in the README, discover they don't work, then fall back on the uberon makefile as SoT
Bioportal has this from 2009 https://bioportal.bioontology.org/ontologies/ABA-AMB
Nothing in OLS
Bioregistry has entries for all of them
https://bioregistry.io/registry/dhba
But they have no links to the Allen repos, or to the PURLs we use (which are not resolvable). It seems to resolve to an internal bioregistry ontology browser?? https://biopragmatics.github.io/providers/dhba/10153/
This is not really our mess but we may be the best ones to fix. The simplest thing would be to register in OBO but it's not worth trying to make these conform to principles that are not relevant (this falls under the databases-as-ontologies pattern)
Originally posted by @cmungall in https://github.com/obophenotype/uberon/issues/3133#issuecomment-2083533796
Another thing to sort out
A lot of the raw github URLs suggest the prefix has an O in it, e.g. dhbao
https://github.com/brain-bican/developing_human_brain_atlas_ontology/raw/main/dhbao-base.owl
However we have historically used this without the o. In retrospect, having the O is better to increase global uniqueness but this will take some coordinating to change
Looks like @haideriqbal has submitted HBA and DHBA
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https://github.com/EBISPOT/ols4/pull/747
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https://www.ebi.ac.uk/ols4/ontologies/dhba
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https://www.ebi.ac.uk/ols4/ontologies/hba
These use the same class PURLs that we use in the bridge files, so it looks like this is all being coordinated, e.g
https://purl.brain-bican.org/ontology/dhbao/DHBA_11218
Note the class PURLs are still not resolvable, neither are the ontology PURLs (latest or versioned), the bioregistry entry goes nowhere and the ontologies are still not very resolvable outside of OLS
No mouse/NHPA yet
@hkir-dev - can you update the brain-bican PURLs to make terms resolvable to OLS? We also need to add the mouse (adult and dev) to OLS.
I guess we also need to look at updating bioregistry CURIE mappings.
Not sure of status of NHP as, AFAIK, it is not used for any atlases and new hierarchy and parcellations for Macaque and Marmoset are coming soon.
@patrick-lloyd-ray - is there progress on new atlas infrastructure in BICAN we should be co-ordinating with? We discussed plans for compliance with the 'atom' standard previously. Maybe we should meet to discuss?
OLS resolution issue fixed:
- https://purl.brain-bican.org/ontology/hbao/HBA_4697
- https://purl.brain-bican.org/ontology/dhbao/DHBA_11218
Wow, happy to see them in OLS and glad the purls resolve now!
is there progress on new atlas infrastructure in BICAN we should be co-ordinating with? We discussed plans for compliance with the 'atom' standard previously. Maybe we should meet to discuss?
We (BICAN) have a new mouse spinal atlas that we are looking to start ontologizing in Q4, and some updates on a unified DHBA atlas as well. It would be great to standardize infrastructure all at once, if we could, and try to bring these in compliance (with ATOM and other standards as well). The updated BICAN atlases for NHP (macaque and marmoset) are in progress now, but it would be good to grease the gears in advance of their publication.
Happy to meet to discuss these more.
