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Knowledge-Graph-Hub / kg-phenio

A Graph for experiments doing ML on ontologies.
BSD 3-Clause "New" or "Revised" License
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Include WBbt & FBbt anatomy ontologies #64

Open kevinschaper opened 1 year ago

kevinschaper commented 1 year ago

This will help to connect 400k & 100k gene expression edges respectively into MonarchKG.

https://obofoundry.org/ontology/fbbt.html https://obofoundry.org/ontology/wbbt.html

matentzn commented 1 year ago

This issue is better placed in phenio, not KG phenio. Its odd though because both are in there:

https://github.com/monarch-initiative/phenio/blob/main/src/ontology/phenio-odk.yaml#L91 https://github.com/monarch-initiative/phenio/blob/main/src/ontology/phenio-odk.yaml#L93

matentzn commented 1 year ago

YOu dont see them in KG phenio?

caufieldjh commented 1 year ago

I also don't see them among the KG-Phenio nodes - just AnnotationProperty types like OBO:fbbt#part_of and OBO:wbbt#part_of

I had the prefix wrong - the FBBT nodes are prefixed with OBO:FBbt_ and the WBBT nodes are, irritatingly, prefixed with both OBO:WBbt_ and WBbt:. Both are present in the graph.

matentzn commented 1 year ago

Yes it is very very important that we all use the same prefix map in monarch

@kevinschaper I would suggest you use https://github.com/linkml/prefixmaps in all Monarch related projects!

kevinschaper commented 1 year ago

I think @caufieldjh is saying that they're OBO:FBbt in the Phenio graph? The edges I'm dropping right now due to missing nodes have FBbt: and WBbt: prefixes - but I do see the OBO:FBbt and OBO:WBbt_ nodes! Is that something you'll fix in KG Phenio? or should I fix them in our import preprocessing of KG Phenio?

I'll keep an eye out for were we can use prefixmaps. The case we have most often is that we're ingesting files that don't have an ID prefix, or have an ID prefix that we need to change - would it work to use prefixmaps almost like an enumeration to add guard rails?

matentzn commented 1 year ago

In this case it's probably KG phenio that needs to adapt the prefixmap library:)

caufieldjh commented 1 year ago

Yes, +1 to integrating prefixmaps here. There should be more consistent prefix usage within phenio.owl, too