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Babel v1.3 ongoing fixes#201

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gaurav merged 45 commits intomasterTranslatorSRI/Babel:masterfrom babel-1.3TranslatorSRI/Babel:babel-1.3Copy head branch name to clipboardJan 24, 2024

+333-15

Commits

Commits on Dec 9, 2023

• Add object normalization for PubChem IDs in drugchemical conflation.

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  55a8a79

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• Replaced exceptions with warnings.

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• Reverted one of the warnings back to an exception.

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• Prevent and log KeyError in anatomy.

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• Reverted anatomy hiding code.

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• Moved UniProtKB downloads into Snakefile as wget commands.

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• Improved progress output so it can be mixed with other logs better.

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• Deleted redundant output filename from pull_panther_pathways().

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• Took out --progress=dot as this somehow makes it even harder to read.

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• Added -k to gunzip so we keep the gzip file in case it's needed.

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• Upgraded UMLS and RxNorm versions.

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• Switched HGNC to HTTP from FTP.

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• Fixed FTP -> HTTP change for HGNC.

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• Added code to skip hgfemale_gene_ensembl.

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• Improved debugging.

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  c7e8e30

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• Removed unnecessary import.

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• Upgraded to the latest version of Biolink Model.

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• Updated version in the downloaded file.

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• First stab at a KGX exporter.

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• Added basic KGX export.

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  fa3b465

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• Improved logic.

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• Improved documentation.

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• Added export everything to KGX to the overall all rule.

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• Implemented get_all_compendia(), moved some code around as a result.

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• Increased Babel output PVC to accomodate KGX export.

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Commits on Dec 10, 2023

• Merge branch 'improve-uniprotkb-downloads' into babel-1.3

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• Objects not mapped to a RxCUI now warnings instead of skip.

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• Merge branch 'fix-infores-curies' into babel-1.3

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• First stab at choosing a better preferred name for NameRes cliques.

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• First stab at a more sophisticated preferred_name chooser.

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  6ace4cc

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• Upgraded RxNorm to 12042023.

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• Merge branch 'pick-better-preferred-names' into babel-1.3

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• Reduced log of empty synonym list to debug().

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• Changed warning for no preferred name to debug.

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• Fixed typo.

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• Removed unnecessary argument from get_panther_pathways.

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• Fixed bug in boost prefix sort, improve exception trace.

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Commits on Dec 11, 2023

• Added support for gzipped KGX files on the fly.

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• Increased batch size, suppressed per-batch log.

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Commits on Dec 13, 2023

• Moved PUBCHEM.COMPOUND to the back of the list.

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Commits on Dec 14, 2023

• Removed extraneous blank lines.

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Commits on Jan 2, 2024

• Upgraded Biolink Model to latest version.

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• Merge branch 'master' into babel-1.3

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Commits on Jan 5, 2024

• Uh oh, we're supposed to be on Biolink v3.6.0. Also updated RxNorm.

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Commits on Jan 23, 2024

• Merge branch 'master' into babel-1.3

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