Cell wikidata #329
Merged
Cell wikidata #329
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
Replaced GET -> POST, reformatted SPARQL query.
gaurav
added a commit
that referenced
this pull request
Sep 26, 2024
* Updated RxNorm from 07012024 to 08052024. * Updated ubergraph_iri_stem_to_prefix_map with additional IRI stems. * Bug fix: `chemicals.write_pubchem_ids()` was failing on reaching the end of the file. Rewrote the code to account for this possibility. * Updated the UMLS leftover output to include the `ic`, `clique_identifier_count`, `taxa`, `shortest_name_length` and `preferred_name` fields (still doesn't fix #126) * Changed PubChem Compound download from FTP to HTTPS (using wget). * Added a `--timestamping` option for wget recursive downloads to try to prevent re-downloading PubMed files if it hasn't changed. * Updated method to create a prefix map from `curies`. * Merged changes from #329 (this should go away once we merge the PRs before this and then merge it with master)
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Outdated suggestions cannot be applied.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 hits wikidata to find CL/UMLS concordances via wikidata IDs. It writes a concord table between CL and UMLS.
It could also bring in wikidata id's but not sure if that's terribly useful.
Does a pretty good job; there are still lots of nodes that are either Cl or UMLS but cleans up many unmerged cliques.