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FAIRsharing / domain-ontology

A project supporting the DRAO application ontology, a hierarchy of specific research domains and descriptors which imports subsets of terms from over 50 publicly-available ontologies.
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Mesh hierarchy issues #33

Closed allysonlister closed 5 years ago

allysonlister commented 5 years ago

At the moment, we have a significant number of mesh terms in DRAO. These terms are, in themselves, good. However they bring with them the Mesh hierarchy which creates a duplicated / parallel hierarchy within DRAO. Additionally, although the main hierarchy for each of the leaf terms is not visible to our users, the labels for these hierarchies can be confusing if we ever wish to expose the hierarchies of DRAO to aid searching, for example. I think we need to mesh I think we need to

  1. Go through those terms originating from Mesh, which themselves are being important from various external ontologies.
  2. Look for ones that have sensible alternatives and use them
  3. Those which cannot be refactored must change their hierarchy via the Ontofox configuration file.

The ultimate goal would be to remove the Mesh hierarchy from DRAO to have an integrated hierarchy for our domain tags.

allysonlister commented 5 years ago

This covers all OMIT terms imported into DRAO as part of the mesh hierarchy. After confirmation from @Drosophilic I can progress to the refactoring

allysonlister commented 5 years ago

Notes on the changes:

allysonlister commented 5 years ago

@Drosophilic - please could you answer the following outstanding questions related to the above list of Mesh terms?

Drosophilic commented 5 years ago

Thanks Ally.

Yes. We should move to SRAO.

Yes. Please make an issue.

allysonlister commented 5 years ago

Great thanks - will add two to SRAO, and create an issue for STATO.

allysonlister commented 5 years ago

Please see https://github.com/ISA-tools/stato/issues/80 for the STATO issue related to this.

allysonlister commented 5 years ago

STATO are happy to add gene frequency with the next release (as an alternative term). Therefore I will go ahead with removing the OMIT gene frequency term. There is only one record annotated with this term (bsg-d000004) and the term "allele frequency" is appropriate, so I have updated the curation on that record and deletion of the OMIT term can proceed.

allysonlister commented 5 years ago

It seems that, due to the forest that was the MeSH hierarchy, I missed out a final few OMIT terms that were lurking within. The following should be the final hierarchy / refactoring changes required by this ticket:

Please can you confirm you are OK with these solutions @Drosophilic ? Thanks!

Drosophilic commented 5 years ago

These are all fine apart from 'Teaching Material', as some teaching material may be media e.g. video etc. I'm not sure where it should go though.

allysonlister commented 5 years ago

Yes, the "document" label is counter intuitive, which is why I put the definition in. In theory, document fits because the definition stipulates a collection of ICEs. However, the label ("document") is one that many people would interpret very differently from the stated definition.

Theoretically, I could see it as a role or quality - it could be any ICE that has the role of being teaching materials. Perhaps as a child of role then @Drosophilic ?

Drosophilic commented 5 years ago

I'm not sure users would understand 'teaching materials' to be a role, although I see the point your making. I wonder if there is anywhere else?

allysonlister commented 5 years ago

Otherwise, I would just suggest as a child of ICE, as multimedia / video etc are.

allysonlister commented 5 years ago

Cool - I shall interpret your thumbs up as approving of me placing it under ICE :)