Repository navigation
Add curated PHENOTYPE prefix for uphenotizer classes - #87
Open
kevinschaper wants to merge 3 commits into
Open
kevinschaper wants to merge 3 commits into
kevinschaper wants to merge 3 commits into
Conversation
uphenotizer mints phenotype classes under https://w3id.org/monarch-initiative/entity/PHENOTYPE_, and PHENIO imports them. No upstream source has this prefix, so CURIEs for these classes can't be expanded through the merged contexts, and their IRIs can't be compressed. Add it to the curated linked_data context. The generated CSVs are updated by hand-applied rows rather than a full ETL run, so this diff doesn't pull in unrelated upstream changes. Claude-Session: https://claude.ai/code/session_01GvqCPJKxcq1SNMtoHoMpYJ
|
Does it have to be this weird generic name? I was hoping more for something like monarch.phenotype or if you must monarchinitiative: and have phenotype be part of the id? |
This branch has not been deployed
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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Adds a curated
PHENOTYPEprefix forhttps://w3id.org/monarch-initiative/entity/PHENOTYPE_.uphenotizer mints pre-composed phenotype classes for FlyBase and SGD annotations under this namespace, and PHENIO imports them. They now appear in the Monarch KG, but no upstream source has the prefix, so
merged.monarchcan't expand or compress them. Consumers would each have to patch it locally.Changes
linked_data.curated.yaml.linked_data.csv,merged.csv,merged.monarch.csvandmerged.oak.csv.For reviewers
make etlwould refresh every upstream source and bury this change, so I added the rows with the package's own parser and writer.expansion_sourcewas then set tolinkmlby hand, to match other curated rows. A later refresh should produce the same rows.merged.monarch. They're all built from the same sources, somergedandmerged.oakget it too. No existing prefix or namespace conflicts with it, in any of the sources they merge, butPHENOTYPEis a fairly generic name to claim.Testing
pytest tests/test_corepasses, excludingtest_from_upstream, which needs network access to refresh from upstream.https://claude.ai/code/session_01GvqCPJKxcq1SNMtoHoMpYJ