Closes #747 (data normalization inconsistencies)#748
Merged
galtay merged 13 commits intobigscience-workshop:mainfrom Nov 19, 2022
Merged
Closes #747 (data normalization inconsistencies)#748galtay merged 13 commits intobigscience-workshop:mainfrom
galtay merged 13 commits intobigscience-workshop:mainfrom
Conversation
…rtchner/biomedical into fix_data_inconsistencies
davidkartchner
requested review from
debajyotidatta,
galtay,
hakunanatasha,
jason-fries,
leonweber,
ruisi-su,
sg-wbi and
sunnnymskang
as code owners
galtay
reviewed
Nov 19, 2022
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This dataset closes Issue #747, which identifies multiple inconsistencies in the normalization entities across datasets. Specifically, it does the following:
ncbi_diseaseinto a list rather than concatenating them into a single normalization stringnlm_geneandgnormplusto have the same name for the linked ontology (NCBIGene) rather than different names for this ontologyncbi_diseaseandbc5cdrto use same casing forMESHontologydb_idvalues inmedmentions_st21pvnormalizations are a UMLS CUI with no prependedUMLS:Justification for this PR were further discussed with @galtay and @phlobo on slack.