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Babel 1.9#365

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gaurav wants to merge 54 commits intomasterTranslatorSRI/Babel:masterfrom babel-1.9TranslatorSRI/Babel:babel-1.9Copy head branch name to clipboard

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Commits on Oct 21, 2024

• Merge branch 'incorporate-umls-uniprotkb-mappings' into babel-1.9

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• Merge branch 'add-manual-concords' into babel-1.9

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• Updated Biolink and RxNorm versions.

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• Merge branch 'add-manual-concords' into babel-1.9

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Commits on Oct 22, 2024

• Merge branch 'add-manual-concords' into babel-1.9

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• Updated HGNC download URL.

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• Fixed URL.

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• Updated HGNC Family download.

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• Updated assert on file header.

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• Cleaned up SMILES extraction from GtoPDB ligand file.

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Commits on Oct 25, 2024

• Merge branch 'check-duplicate-prefixes' into babel-1.9

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• Merge branch 'check-duplicate-prefixes' into babel-1.9

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• Merge branch 'check-duplicate-prefixes' into babel-1.9

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• Merge branch 'check-duplicate-prefixes' into babel-1.9

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• Merge branch 'check-duplicate-prefixes' into babel-1.9

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Commits on Nov 4, 2024

• Minor bugfix in filtering labels.

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Commits on Dec 11, 2024

• Updated Biolink, UMLS, RxNorm versions.

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• Removed parquet directory as input.

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• Removed more Parquet paths from Snakemake file.

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Commits on Dec 13, 2024

• Improved error logging.

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• Fixed error message.

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Commits on Dec 14, 2024

• Improved error detection in util.get_prefix().

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• Improved error message.

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• Improve error message.

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• Trying to fix EFO icd11.foundation CURIEs.

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• Added CURIE check in Text.opt_to_curie().

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• Added icd11.foundation as prefix.

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• Fix bug.

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• Merge branch 'add-support-for-icd11foundation' into babel-1.9

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• Fixed test to ignore .nfs files.

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Commits on Dec 16, 2024

• Caught the new ValueError from Text.opt_to_curie().

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• Added another ValueError catch.

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• Merge branch 'add-support-for-icd11foundation' into babel-1.9

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Commits on Jan 10, 2025

• Merge branch 'master' into babel-1.9

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Commits on Jan 14, 2025

• Merge branch 'master' into babel-1.9

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• Merge branch 'keep-parquet-files-in-own-directory' into babel-1.9

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Commits on Jan 15, 2025

• Updated versions in config.json.

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• Updated Parquet output for compendia.

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• Fixed incorrect rule.

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Commits on Jan 18, 2025

• Replaced Parquet dir with Clique.parquet path.

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Commits on Jan 21, 2025

• Improved EFO code for catching CURIE parsing errors.

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• Try to fix anatomy issue.

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• Improved ORPHANET test.

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• Cleaned up NCBIGene label parsing code.

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Commits on Jan 22, 2025

• Improved how we handle Orphanet in EFO.

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Commits on Jan 25, 2025

• Moved Synonym.parquet into parquets directory.

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Commits on Jan 28, 2025

• Marked DuckDB files as temporary.

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• Merge branch 'keep-parquet-files-in-own-directory' into babel-1.9

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• Marked Parquet directories as dir().

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• Oops, that's not needed.

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• Improved DuckDB inputs.

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• Moved Parquet directory to params.

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• Merge branch 'master' into babel-1.9

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Commits on Jan 29, 2025

• Merge branch 'master' into babel-1.9

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