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ZFIN / zebrafish-anatomical-ontology

Ontology describing the anatomy of Danio rerio from a single cell to adult fish. The namespace of the ontology is zebrafish_anatomical_ontology the prefix is ZFA. Updates to ZFA are released every other month. A subset of the ZFS http://purl.obolibrary.org/obo/zfs.obo is packaged with this ontology.
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Update zfa-edit.obo #166

Closed erik-whiting closed 1 year ago

erik-whiting commented 1 year ago

Related to https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2149

What this Does

Applies the annotation property has ontology root term (IAO:0000700) to ZFA:0100000

Why this is helpful

the Ontology Lookup Service uses this to help better display ontologies if the term mentioned above is ever aligned with an upper ontology like BFO, it still will be the thing shown on OLS as the "root" this will be generally useful for things like alignment with COB since it makes it easier to figure out where the work will be

cc @matentzn and @cthoyt

erik-whiting commented 1 year ago

@matentzn / @cthoyt did I do this right?

cthoyt commented 1 year ago

Yes, this is right!

But, it looks like you added two roots here where only one is corresponding to this ontology. Why did you include the ZFS one?

erik-whiting commented 1 year ago

@cthoyt when I looked here: https://www.ebi.ac.uk/ols/ontologies/zfa it looks like there are 2 roots in the ontology. Also, the original github issue listed zfa and zfs as needing to be updated in this repo but I didn't see a zfs-edit.obo file so I assumed zfa-edit.obo was the one to update for both. Should I remove the zfs line?

cthoyt commented 1 year ago

@erik-whiting that's a really interesting question - I think it's better to keep it focused on terms in the ontology itself, and not ones that are imported. If people want to browse ZFS terms, then I think it makes more sense to start with https://www.ebi.ac.uk/ols/ontologies/zfs.

The reason they're both showing up on OLS now is that neither are aligned with an upper level ontology at the moment. If they were, we'd see first owl:Thing then some BFO stuff then eventually the right terms (since they aren't annotated with IAO:700 yet)

erik-whiting commented 1 year ago

Updated to only change ZFA

cthoyt commented 1 year ago

@cerivs can you please review this?

@erik-whiting if we're not able to get in touch via github, you can use the contact information listed on OBO Foundry: https://github.com/OBOFoundry/OBOFoundry.github.io/blob/bfc8cd9756461ba92d24e6f076db4c4af3bc7043/ontology/zfa.md?plain=1#L10-L14

matentzn commented 1 year ago

It's an odd special case. I think having the ZFS root is probably fine, because in reality ZFS is Managed inside of ZFA and is extracted only after the fact..

cthoyt commented 1 year ago

🤯

then it makes sense to keep both

erik-whiting commented 1 year ago

updated to include both ZFA and ZFS

ybradford commented 1 year ago

@matentzn sorry to be dense but why do we need to change our root. looking at other AOs - root is not BFO.

matentzn commented 1 year ago

Yeah this is not changing the root, it's just making a statement: these 2 are the root classes of ZFA. This will help us in our grand plan to integrate with COB - it is not changing anything at all in the classification!

matentzn commented 1 year ago

I incorporated this in #168 to be correct.