Erica Wood

From @saramsey: > Oh yes, so on a related note, but motivated by a different issue, we will need to start developing a file of Biolink predicates that have been...

[v3.2.0](https://github.com/biolink/biolink-model/releases/tag/v3.2.0): I don't see anything we have to change. [v3.2.1](https://github.com/biolink/biolink-model/releases/tag/v3.2.1): There's a change with KGX, but I don't think this impacts us. [v3.2.2](https://github.com/biolink/biolink-model/releases/tag/v3.2.2): - UniProt PURLs [v3.2.3](https://github.com/biolink/biolink-model/releases/tag/v3.2.3): This doesn't impact...

> @ecwood Thank you! Any thoughts about the 3.3.X and 3.4.X releases? @saramsey Yes! I updated the comment with information about the other releases.

I expected that we'd need to change the UniProt URL. However, `run-validation-tests.sh` on the master branch is not failing. @saramsey Do you know why it (specifically `validate_curies_to_urls_map_yaml.py`) wouldn't fail despite...

@acevedol Some of the changes have already been made (#306), and all of that has been done in `kg2.8.4-prep`, so let's stick with that. > we are also addressing issue...

While testing out bc079cf (to ensure the validation scripts are using the correct version of biolink), we got this error: ``` Reading ontology JSON file: /home/ubuntu/kg2-build/biolink-model.owl.json; size: 2213.82 KiB Traceback...

With [8a63bbc](https://github.com/RTXteam/RTX-KG2/commit/8a63bbc2110cab025165afdb7e722c78a8da6862), the validator is not failing anymore. That being said, there are still hundreds (possibly thousands) of errors like this: ```2023-07-05 20:34:47,913 ERROR (OWLAnnotationPropertyTransformer:98) Attempt to transform an axiom...

Per @saramsey, `validate_curies_to_urls_map_yaml.py` is validating CURIEs only, not the URLs. In an enhancement, we should have the script compare the URLs to what is in Biolink.

Now that [#319](https://github.com/RTXteam/RTX-KG2/issues/319) and [#320](https://github.com/RTXteam/RTX-KG2/issues/320) have been finished, tested, and are passing, do we need to do anything else to verify that we are Biolink 3.5.0 compliant? Do we need...

New error: ``` + /home/ubuntu/kg2-venv/bin/python3 -u /home/ubuntu/kg2-code/filter_kg_and_remap_predicates.py --dropNegated --dropSelfEdgesExcept interacts_with,regulates,inhibits,increase /home/ubuntu/kg2-code/predicate-remap.yaml /home/ubuntu/kg2-code/kg2-provided-by-curie-to-infores-curie.yaml /home/ubuntu/kg2-code/curies-to-urls-map.yaml /home/ubuntu/kg2-build/kg2.json /home/ubuntu/kg2-build/kg2-simplified.json /home/ubuntu/kg2-build/kg2-version.txt /home/ubuntu/kg2-venv/lib/python3.7/site-packages/rdflib_jsonld/__init__.py:12: DeprecationWarning: The rdflib-jsonld package has been integrated into rdflib as of rdflib==6.0.0. Please...