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Pull requests: NCATSTranslator/Babel

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Pull requests list

chore(deps): bump snakemake from 9.25.1 to 9.25.2 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#1056 opened Aug 23, 2026 by dependabot Bot Loading…
chore(deps-dev): bump rumdl from 0.2.55 to 0.2.58 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#1055 opened Aug 23, 2026 by dependabot Bot 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
Fix SAPBERT training data synonym duplication
#1043 opened Aug 19, 2026 by hyi Contributor Loading…
4
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
Add the NCATS GARD rare-disease registry to Disease.txt, joined to existing cliques through MONDO's and DOID's GARD mappings documentation Improvements or additions to documentation enhancement New feature or request new data source A new data source to include in Babel Priority: High testing Related to the test suite or testing infrastructure
#980 opened Jul 28, 2026 by SkyeAv Member Loading…
1 of 7 tasks
1
18
feat: add LOINC clinical terms as a biolink:ClinicalFinding compendium discussion needed documentation Improvements or additions to documentation enhancement New feature or request new data source A new data source to include in Babel Priority: Low testing Related to the test suite or testing infrastructure
#979 opened Jul 28, 2026 by SkyeAv Member Loading…
@SkyeAv
feat: add GTDB as a biolink:OrganismTaxon source in the taxon pipeline discussion needed documentation Improvements or additions to documentation enhancement New feature or request new data source A new data source to include in Babel Priority: Low testing Related to the test suite or testing infrastructure
#978 opened Jul 28, 2026 by SkyeAv Member Loading…
@SkyeAv
1
feat: add Transcript and SequenceVariant compendia (gene2ensembl + ClinVar) Data Source: Ensembl discussion needed documentation Improvements or additions to documentation enhancement New feature or request new data source A new data source to include in Babel Priority: Low testing Related to the test suite or testing infrastructure
#977 opened Jul 28, 2026 by SkyeAv Member Loading…
@SkyeAv
1
feat: add an opt-in MyGene.info backend for the Ensembl pull Data Source: Ensembl discussion needed documentation Improvements or additions to documentation enhancement New feature or request New mappings Priority: Medium testing Related to the test suite or testing infrastructure
#976 opened Jul 28, 2026 by SkyeAv Member Loading…
@SkyeAv
chore: swap build backend from setuptools to maturin dependencies Pull requests that update a dependency file developer tooling Tooling & workflow that helps develop, debug, and validate Babel without changing pipeline outputs enhancement New feature or request github_actions Pull requests that update GitHub Actions code Priority: Critical python:uv Pull requests that update python:uv code structural Changes to the structure of Babel in order to apply DRY and to make future development easier. testing Related to the test suite or testing infrastructure
#975 opened Jul 27, 2026 by SkyeAv Member Loading…
@SkyeAv
15
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
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