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NCATSTranslator / Babel Public

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GeneProtein synonym conflation#185

Draft

gaurav wants to merge 21 commits intomasterNCATSTranslator/Babel:masterfrom

conflate-gene-protein-synonymsNCATSTranslator/Babel:conflate-gene-protein-synonymsCopy head branch name to clipboard

Conversation Commits21 (21)Checks Files changed

Draft

GeneProtein synonym conflation#185
gaurav wants to merge 21 commits intomasterfrom
conflate-gene-protein-synonyms

Commits

Commits on Dec 2, 2023

Add object normalization for PubChem IDs in drugchemical conflation.
gaurav
committed
Replaced exceptions with warnings.
gaurav
committed
Reverted one of the warnings back to an exception.
gaurav
committed
Prevent and log KeyError in anatomy.
gaurav
committed
Reverted anatomy hiding code.
gaurav
committed
Moved UniProtKB downloads into Snakefile as wget commands.
gaurav
committed
Improved progress output so it can be mixed with other logs better.
gaurav
committed
Deleted redundant output filename from pull_panther_pathways().
gaurav
committed
Took out --progress=dot as this somehow makes it even harder to read.
gaurav
committed
Added `-k` to gunzip so we keep the gzip file in case it's needed.
gaurav
committed
Removed babel-private.
gaurav
committed
Upgraded UMLS and RxNorm versions.
gaurav
committed
Switched HGNC to HTTP from FTP.
gaurav
committed
Fixed FTP -> HTTP change for HGNC.
gaurav
committed
Added code to skip hgfemale_gene_ensembl.
gaurav
committed
Improved debugging.
gaurav
committed
Removed unnecessary import.
gaurav
committed

Commits on Dec 3, 2023

First stab at generating a GeneProtein conflation.
gaurav
committed
Improved output variable name.
gaurav
committed
Fixed typos.
gaurav
committed
Fixed requirement for conflations to be a list.
gaurav
committed

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