biolink-model
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biolink
Schema and generated objects for biolink data model and upper ontology
**Is your feature request related to a problem? Please describe.** When ingesting Inxight:Drugs we encounter need for additional aspects **What working group (or team) did this request originate from?** MolePro...
bacterium is currently a sibling of cellular organism. If we keep it, we should make it a subclass. But why do we have it? It seems arbitrary. Why not prokaryote...
Ignoring mixins, this is the toplevel: Other than the highlighted, the others should have some kind of is-a organization, or the various outcome types could be made mixins
From @colleenXu : Some of the new "treats"-related predicates are mixins that the other predicates are mapped to: promotes condition, treats, treats or applied or studied to treat. I thought...
According to the [Biolink Model](https://github.com/biolink/biolink-model/blob/1698cf997785490304a617123d5e3a242c6b2bc0/src/biolink_model/schema/biolink_model.yaml#L27C13-L27C44) the `biolink` base namespace is `https://w3id.org/biolink/vocab/`. However while `https://w3id.org/biolink/vocab/Gene` does not resolve, `https://w3id.org/biolink/Gene` does (to `https://biolink.github.io/biolink-model/Gene/`). - [ ] `https://w3id.org/biolink/vocab/Gene` should resolve to `https://biolink.github.io/biolink-model/Gene/` -...
(This is a minor issue, so please feel free to close it as won't-fix if these issues aren't important to Biolink.) Here is the definition of `OMIM` in Biolink: https://github.com/biolink/biolink-model/blob/1698cf997785490304a617123d5e3a242c6b2bc0/project/prefixmap/biolink_model_prefix_map.json#L131...
**Describe the bug** The `biolink-model.yaml` file is currently recommending that the source relation `DRUGBANK:drug-interaction` should be mapped to the predicate `biolink:physically_interacts_with`. These seem rather semantically inequivalent. **To Reproduce** See the...
The NCBIGene concept IRI prefix in the Biolink Model prefix map is `http://identifiers.org/ncbigene/`: https://github.com/biolink/biolink-model/blob/ce4f70988e4141b50fe9e1161d696483094fe192/prefix-map/biolink-model-prefix-map.json#L121 However, Ubergraph thinks the concept IRI prefix should actually be `https://identifiers.org/ncbigene/` (i.e. `https` instead of `http`),...
https://biolink.github.io/ 404s (https://biolink.github.io/biolink-model/ works) I'm not actually sure which, if any, pages link to https://biolink.github.io/, but it shouldn't just 404
Add a new slot for **`mixins`** that distinguish between "important" user **`mixins`** (like 'treats') and purely internal **`mixins`** that simply facilitate sharing of model 'bits' (like shared slots).
