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Pull requests: NCATSTranslator/Babel

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Pull requests list

feat: add NCATS GARD rare-disease registry as a biolink:Disease source 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: High testing Related to the test suite or testing infrastructure
#980 opened Jul 28, 2026 by SkyeAv Member Loading…
2
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
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
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: High 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
1
Correct the compendium format docs and link out to NodeNorm instead of restating it
#973 opened Jul 27, 2026 by gaurav Collaborator Loading… Babel v1.19
1
Bump duckdb from 1.5.4 to 1.5.5 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#970 opened Jul 26, 2026 by dependabot Bot Loading…
Bump tqdm from 4.68.4 to 4.69.1 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#969 opened Jul 26, 2026 by dependabot Bot Loading…
Bump rumdl from 0.2.30 to 0.2.43 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#968 opened Jul 26, 2026 by dependabot Bot Loading…
Bump ruff from 0.15.21 to 0.16.0 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#967 opened Jul 26, 2026 by dependabot Bot Loading…
Bump actions/setup-python from 6 to 7 dependencies Pull requests that update a dependency file github_actions Pull requests that update GitHub Actions code
#966 opened Jul 26, 2026 by dependabot Bot Loading…
Bump gitpython from 3.1.50 to 3.1.54 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#965 opened Jul 24, 2026 by dependabot Bot Loading…
Babel 1.18.1
#958 opened Jul 21, 2026 by gaurav Collaborator Loading…
1 task
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
feat: add unstable manual compendium for hand-curated cliques, EUPATH seed term, and source docs documentation Improvements or additions to documentation enhancement New feature or request new data source A new data source to include in Babel Priority: Medium 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
#887 opened Jul 1, 2026 by SkyeAv Member Loading… Babel v1.19
@SkyeAv
3
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
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