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The NCBI taxonomy database is a database, not an ontology. As such that automatic translation includes various things that are not ideal from an ontology modeling perspective
If we were to make the…
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### Prefix
ncbiprotein
### Explanation
I was digging/cleaning into DrugBank data. They have things like this
```
GenBank Protein Database
33150626
```
I had to try/guess th…
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For example the [bioregistry](https://bioregistry.io) saves it's ontologies in the `.obo` format.
It would be nice to allow the parsing/loading of such files into Archivo, but currently rapper/rdf…
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Thank you for your ontologies, especially ncbislim.obo.
It uses the prefix "NCBITaxon:". This does not conform to the standard for CURIEs, which should be lower case, and is not the one used by ide…
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Hi!
As many species will likely appear soon on ReDU and the coverage of NCBI taxonomy even if very good will not be enough, I would suggest adding the possibility to add taxa through the [Bioregist…
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**Describe the bug**
PyDantic update causes pip dependency's imcompatibility.
with pydantic=2.5 (default pip behavior) raise error like:
`
... ...
File "/home/rnalab/zfdeng/miniconda3/envs/tm…
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gombo (https://obofoundry.github.io/obo-nor.github.io/dashboard/gombo/dashboard.html) and epso (https://obofoundry.github.io/obo-nor.github.io/dashboard/epso/dashboard.html) both contain in the `Info:…
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Here's the OLS page for the Cell Ontology's term for [osteoblast (CL:0000062)](
https://www.ebi.ac.uk/ols4/ontologies/cl/classes?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000062).
The Biore…
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In the Ontology Quality Assessment, I found that there was an unknown prefix `oma` (see https://cthoyt.com/oquat/unknowns/prefix/oma). This apparently only appears in definition xrefs in PRO entries t…
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**Question:**
What is the appropriate Biolink Model slot for a URL associated with a node?
MolePro encountered a data item called "reaction_url" (e.g., https://reactome.org/PathwayBrowser/#/R-MMU-…