Much improved Qleverfile for PubChem #60
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
added 2 commits
August 19, 2024 00:13
The `get-data` command now does not only download the latest version of the PubChem data, but also of the associated ontologies. That is relatively little additional data but makes a big difference for usability. See the NOTEs in the new `Qleverfile.pubchem` for a longer explanation. TODO: Still testing whether this works as intended.
hannahbast
changed the title
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Outdated suggestions cannot be applied.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.
The
get-datacommand now does not only download the latest version of the PubChem data, but also of the associated ontologies. That is relatively little additional data but makes a big difference for usability. Also remove the fixing of the invalid IRIs in the PubChem data (usingsedandawk, which wasn't cheap) and instead rely on the new ad-freiburg/qlever#1448, which activates more relaxed parsing of IRI refs by default. I tried it and it worked like a charm. See the beginning of the newQleverfile.pubchemfor the resource requirements and a longer explanation.