Adds a KGX exporter #206
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Adds a KGX exporter #206
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This PR includes several minor fixes needed to build Babel: - Upgrade: - UMLS to 2023AB - RxNorm to 01022024 - Biolink Model to 3.6.0 - Reduced log level of empty synonym list from warning to debug to reduce the size of the overall log. - I accidentally merged #206 into this branch instead of `master`, so it has a bunch of changes, including: - Adding `genefamily_outputs`, `umls_outputs` and `macromolecularcomplex_outputs`. - Adding the KGX export to the `all` target. - Expanding babel_outputs to 500Gi to accommodate KGX files. - A bug fix for #197 - KGX export now produces gzipped files. - #207 - #202 - #218 - Includes some code from PR #217, but only produces a warning instead of skipping mappings.
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This PR moves the KGX exporter from NodeNorm (specifically, https://github.com/TranslatorSRI/NodeNormalization/blob/68096b2f16e6c2eedb699178ace71cea98dc794f/node_normalizer/loader.py#L70-L208) into this repo and sets up Snakemake to generate the KGX files with every Babel run.
Closes #61. Closes TranslatorSRI/NodeNormalization#95.