Skip to content

Pull requests: NCATSTranslator/Babel

New pull request New
38 Open 358 Closed
38 Open 358 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Reviews
Filter by reviews
No reviews Review required Approved review Changes requested
Assignee
Filter by who’s assigned
Assigned to nobody Loading
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Pull requests list

chore(deps-dev): bump ruff from 0.16.3 to 0.16.5 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#1082 opened Sep 6, 2026 by dependabot Bot Loading…
chore(deps-dev): bump rumdl from 0.2.55 to 0.2.63 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#1081 opened Sep 6, 2026 by dependabot Bot Loading…
chore(deps): bump snakemake from 9.25.1 to 9.26.1 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#1080 opened Sep 6, 2026 by dependabot Bot Loading…
chore(deps): bump pyoxigraph from 0.5.9 to 0.5.11 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#1079 opened Sep 6, 2026 by dependabot Bot Loading…
Document how to check a BabelTest assertion, and stop duplicating the assertion list
#1075 opened Sep 1, 2026 by gaurav Collaborator Loading…
Build the Publication compendium from the pubmed2db NDJSON export instead of parsing PubMed XML
#1050 opened Aug 21, 2026 by gaurav Collaborator Loading…
7 tasks
Verify #948 against a real build, and record what that clique diff cost
#1030 opened Aug 17, 2026 by gaurav Collaborator Loading… Babel v1.19
Update setuptools requirement from >=83.0.0 to >=84.0.0 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#1025 opened Aug 16, 2026 by dependabot Bot Loading…
Time a failed job from when it died, not from when the run gave up
#1020 opened Aug 13, 2026 by gaurav Collaborator • Draft
Document the long-term archiving strategy for past runs
#1001 opened Jul 31, 2026 by gaurav Collaborator • Draft
1
Stop redoing per-call setup work, and hand the untyped compendium over as JSONL
#992 opened Jul 30, 2026 by gaurav Collaborator • Draft Babel v1.19
Read concord files through one shared function
#986 opened Jul 30, 2026 by gaurav Collaborator • Draft Babel v1.19
Stop conflate_synonyms computing output it then discards
#985 opened Jul 30, 2026 by gaurav Collaborator • Draft Babel v1.19
Parse PubMed with iterparse and release each article as it is written
#984 opened Jul 30, 2026 by gaurav Collaborator • Draft Babel v1.19
Detect encoding damage in labels and synonyms
#953 opened Jul 21, 2026 by gaurav Collaborator Loading…
Distribute compendia as .txt.gz
#947 opened Jul 20, 2026 by gaurav Collaborator Loading…
Type foods from their NCIt classification, beyond DrugBank (#935)
#936 opened Jul 13, 2026 by gaurav Collaborator • Draft
clique-diff: report the incoming side of cross-compendium moves
#915 opened Jul 10, 2026 by gaurav Collaborator Loading…
Write UberGraph concords in a deterministic order
#901 opened Jul 9, 2026 by gaurav Collaborator • Draft
5 tasks
Babel v1.19
1
Document what Ubergraph's SPARQL results actually contain
#899 opened Jul 9, 2026 by gaurav Collaborator Loading…
Activate glom's MONDO close-match guard, with concord-reader symmetry tests
#888 opened Jul 2, 2026 by gaurav Collaborator Loading… Not urgent
1
drugchemical: record dropped conflation pairs to a retained exclusion report (#754)
#874 opened Jun 24, 2026 by gaurav Collaborator • Draft
fixed issue #827 with DRUGBANK:DB10626 preferred name
#872 opened Jun 23, 2026 by hyi Contributor Loading… Babel v1.19
1
Estimate drugprotein
#848 opened Jun 9, 2026 by gaurav Collaborator • Draft
Add protein/chemical overlap report
#830 opened Jun 4, 2026 by gaurav Collaborator • Draft
ProTip! Updated in the last three days: updated:>2026-09-03.