SemMedDB V43 update #8
Merged
Conversation
This file contains 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
…mat checking; specify csv reading options
…se matching operation to accelarate
…retired predication dtype to Pyarrow string before concatenation; add the client to query Node Normalizer
…CUIs; add a function to determine the document ID for each predication; change node normalizer parameter conflate to True
…ent NCBIGene ID row location algorithm (reducing running time from 24min to 40sec
…usage from 3x dataframe size to 2x
Merged
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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 PR update the SemMedDB API per biothings/pending.api#63.
It also fixes the following issues towards piped CUIs, retired CUI, and equivalent NCBIGene IDs:
semmedVER43_2022_R_PREDICATION.csv#2semmedVER43_2022_R_PREDICATION.csv#3conflateparameter of Node Normalizer #7