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OntoZoo / ontobee

Ontobee is a linked data server for ontologies. See: http://www.ontobee.org.
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Part-of should be treated as a hierarchical relationship #160

Open cmungall opened 2 years ago

cmungall commented 2 years ago

When ontologies such as GO, Uberon, ENVO are viewed in ontobee there is no visual indication of the partonomy

ontobee should show part-ofs (formally A subClassOf part-of some B) in the hierarchy, as OLS and Bioportal do

I also recommend standardizing with OLS on various kinds of ontology metadata that drive configuration:

https://www.ebi.ac.uk/ols/docs/installation-guide

yongqunh commented 2 years ago

This is a good suggestion. We will consider it carefully. Thanks.

cmungall commented 2 years ago

I don't suppose there are any plans to implement this? I am happy to help with providing a more detailed specification, with testing, etc. I also have both python and java code that will do the necessary transform.

I can't over-emphasize how important this feature is for a lot of ontologies. Seeing the ontology without the partonomy is really misleading for users.

yongqunh commented 2 years ago

Hi Chris, sorry that we do not have a timeline to implement it yet since our previous effort was to update the automatic ontobee updating program. Given the automatic updating program is basically done, we may come back to focus on this issue. Probably we can schedule a meeting to discuss this? Thanks!

cmungall commented 2 years ago

I'm happy to schedule a meeting, but maybe we should do as much prelim work as possible async ahead of time?

I think the first part is coming up with requirements and specification of intended behavior. this should be easy as we can look to OLS and bioportal. I like to think of it in terms of graphs - consider a graph G with edges:

We would only do this for select values of R, typically part_of, but this could be configurable

Then figure the best way to implement this is in the context of ontobee. I can help given some documentation. E.g. for the current method to draw the hierarchy, do you use SPARQL property paths, do you cache graphs in advance, etc