Babel v1.14

What's Changed

• Pyoxigraph and test improvements by @gaurav in #590
• Increase length at which we demote labels from 15 to 25 characters by @gaurav in #600
• Replace requirements.txt with uv by @gaurav in #598
• Add code formatting for Python (ruff) and Snakemake (snakefmt) by @gaurav in #599
• Add a taxon_specific flag to the synonyms file output by @gaurav in #604
• Add support for UMLS level 0 subset by @gaurav in #605
• Replaced type-based DrugChemical conflation with prefix-based DrugChemical conflation by @gaurav in #626

Full Changelog: v1.13.1...v1.14

Babel v1.13.1

What's Changed

• Babel v1.13 by @gaurav in #511
• Reverted Python to 3.11 so that python-Levenshtein-wheels works again by @gaurav in #587

Full Changelog: v1.13...v1.13.1

Babel v1.13

What's Changed

• Add 2025mar31 release information by @gaurav in #435
• Improve NCBIGene labels, synonyms and descriptions by @gaurav in #436
• Collect common files in a single location by @gaurav in #438
• Add Translator documentation by @gaurav in #292
• Added database sizes for Babel 2025jan23 and 2025mar31, including NameRes Solr by @gaurav in #442
• Add a semantic type blocklist to write_umls_ids() by @gaurav in #444
• Remove CHEMBL labels identical to the CHEMBL ID by @gaurav in #446
• Expand NCBITaxon taxonomy synonyms by @gaurav in #425
• Using config.yaml to replace config.json (issue #275) by @hyi in #460
• Removed reference to renciorg/renci-python-image by @gaurav in #464
• Create get_biolink_model_toolkit() utility function by @gaurav in #465
• Fix information content comparisons (float instead of string) by @gaurav in #467
• Fix some UMLS bugs by @gaurav in #469
• Added option to generate prefix labels/synonyms files for some UberGraph prefixes by @gaurav in #470
• Fix BioMart downloads with more than ~10 attributes by @gaurav in #458
• Babel release changes by @gaurav in #455
• Detect duplicate curie leaders by @gaurav in #431
• Fixed bug in Snakemake file: dir() -> directory() by @gaurav in #474
• Setting PubChem Input encoding to ISO-8859-1 by @gaurav in #475
• Update encoding of CID-MeSH download by @gaurav in #476
• Conditionally apply overused xref filtering in combine_unichem by @cbizon in #508
• Add metadata by @gaurav in #459
• Remove redundant ENSEMBL gene ID code by @gaurav in #472
• Babel v1.11.0 by @gaurav in #471
• Add support for properties and use them to store ChEBI secondary IDs by @gaurav in #473
• Debug protein compendium slowdown by @gaurav in #477
• Slowdown fix and improved logging by @gaurav in #478
• Update TaxonFactory to use SQLite by @gaurav in #482
• Update factories to DuckDB by @gaurav in #481
• Fix chemical properties by @gaurav in #483
• Add GeneProtein conflated synonyms by @gaurav in #486
• Babel v1.12.0 by @gaurav in #485
• Added a UMLS concord to proteins by @gaurav in #495
• Rework DrugChemical conflation order by @gaurav in #506

New Contributors

• @hyi made their first contribution in #460

Full Changelog: v1.10.0...v1.13

Babel v1.12

Important bug fixes

• #467: We were previously sorting information content values alphanumerically instead of numerically, which means we were returning 100 for many nodes that should have had a lower IC value. This is now fixed. Thanks to @uhbrar for catching this!

What's Changed

• Add 2025mar31 release information by @gaurav in #435
• Improve NCBIGene labels, synonyms and descriptions by @gaurav in #436
• Collect common files in a single location by @gaurav in #438
• Add Translator documentation by @gaurav in #292
• Added database sizes for Babel 2025jan23 and 2025mar31, including NameRes Solr by @gaurav in #442
• Add a semantic type blocklist to write_umls_ids() by @gaurav in #444
• Remove CHEMBL labels identical to the CHEMBL ID by @gaurav in #446
• Expand NCBITaxon taxonomy synonyms by @gaurav in #425
• Using config.yaml to replace config.json (issue #275) by @hyi in #460
• Removed reference to renciorg/renci-python-image by @gaurav in #464
• Create get_biolink_model_toolkit() utility function by @gaurav in #465
• Fix information content comparisons (float instead of string) by @gaurav in #467
• Fix some UMLS bugs by @gaurav in #469
• Added option to generate prefix labels/synonyms files for some UberGraph prefixes by @gaurav in #470
• Fix BioMart downloads with more than ~10 attributes by @gaurav in #458
• Babel release changes by @gaurav in #455
• Detect duplicate curie leaders by @gaurav in #431
• Fixed bug in Snakemake file: dir() -> directory() by @gaurav in #474
• Setting PubChem Input encoding to ISO-8859-1 by @gaurav in #475
• Update encoding of CID-MeSH download by @gaurav in #476
• Conditionally apply overused xref filtering in combine_unichem by @cbizon in #508
• Add metadata by @gaurav in #459
• Remove redundant ENSEMBL gene ID code by @gaurav in #472
• Babel v1.11.0 by @gaurav in #471
• Add support for properties and use them to store ChEBI secondary IDs by @gaurav in #473
• Debug protein compendium slowdown by @gaurav in #477
• Slowdown fix and improved logging by @gaurav in #478
• Update TaxonFactory to use SQLite by @gaurav in #482
• Update factories to DuckDB by @gaurav in #481
• Fix chemical properties by @gaurav in #483
• Add GeneProtein conflated synonyms by @gaurav in #486

New Contributors

• @hyi made their first contribution in #460

Full Changelog: v1.10.0...v1.12

Babel v1.11

What's Changed

• Add 2025mar31 release information by @gaurav in #435
• Improve NCBIGene labels, synonyms and descriptions by @gaurav in #436
• Collect common files in a single location by @gaurav in #438
• Add Translator documentation by @gaurav in #292
• Added database sizes for Babel 2025jan23 and 2025mar31, including NameRes Solr by @gaurav in #442
• Add a semantic type blocklist to write_umls_ids() by @gaurav in #444
• Remove CHEMBL labels identical to the CHEMBL ID by @gaurav in #446
• Expand NCBITaxon taxonomy synonyms by @gaurav in #425
• Using config.yaml to replace config.json (issue #275) by @hyi in #460
• Removed reference to renciorg/renci-python-image by @gaurav in #464
• Create get_biolink_model_toolkit() utility function by @gaurav in #465
• Fix information content comparisons (float instead of string) by @gaurav in #467
• Fix some UMLS bugs by @gaurav in #469
• Added option to generate prefix labels/synonyms files for some UberGraph prefixes by @gaurav in #470
• Fix BioMart downloads with more than ~10 attributes by @gaurav in #458
• Babel release changes by @gaurav in #455
• Detect duplicate curie leaders by @gaurav in #431
• Fixed bug in Snakemake file: dir() -> directory() by @gaurav in #474
• Setting PubChem Input encoding to ISO-8859-1 by @gaurav in #475
• Update encoding of CID-MeSH download by @gaurav in #476
• Conditionally apply overused xref filtering in combine_unichem by @cbizon in #508
• Add metadata by @gaurav in #459
• Remove redundant ENSEMBL gene ID code by @gaurav in #472

New Contributors

• @hyi made their first contribution in #460

Full Changelog: v1.10.0...v1.11

v1.10.0

What's Changed

• Add release info for November 2024 and 2025jan23 by @gaurav in #411
• Babel 1.9.1 by @gaurav in #365
• Improve DrugChemical conflation leader using information content values by @gaurav in #362
• Added an in-file config for DrugChemicalSmaller.txt.gz by @gaurav in #418
• Clo by @cbizon in #419
• simple fma addition by @cbizon in #420
• Gzip synonyms files by @gaurav in #405
• Add additional manual conflations by @gaurav in #371
• Add PubMed Verifier by @gaurav in #432
• Replace file deletion with file truncation by @gaurav in #433
• Fix PubMed verification done-file output by @gaurav in #426
• Fix synonyms compression by @gaurav in #434
• Babel v1.10.0 by @gaurav in #424

Full Changelog: v1.9.1...v1.10.0

Babel v1.9.1

What's Changed

• Try to fix an issue in anatomy by @gaurav in #404
• Fix EFO issues by @gaurav in #402
• Check duplicate prefixes by @gaurav in #363
• Add support for icd11foundation in EFO by @gaurav in #380
• Incorporate UMLS_UniProtKB mappings by @gaurav in #361
• Keep Parquet files in own directory by @gaurav in #397

Full Changelog: v1.9.0...v1.9.1

Babel v1.9.0

What's Changed

• Babel 1.8 (Translator Hammerhead) by @gaurav in #351
• Added a check for duplicate CURIEs by @gaurav in #342
• Added some additional manual concords by @gaurav in #360
• inverted tradename by @cbizon in #377
• Goumls by @cbizon in #395
• Efo by @cbizon in #396

Full Changelog: v1.8.0...v1.9.0

Babel v1.8.0

What's Changed

• Babel 1.7 (Translator Guppy) by @gaurav in #336
• Load all compendia and synonym files into DuckDB by @gaurav in #290
• Add a manual concord for DrugChemicalConflation by @gaurav in #337
• Add Babel Guppy release information by @gaurav in #340
• Add taxon information to proteins by @gaurav in #349
• Reduce DrugChemical for load into SAPBERT by @gaurav in #330

Full Changelog: v1.7.1...v1.8.0

Babel v1.7.1

What's Changed

• Adds a basic citation to Babel by @gaurav in #347
• Improve BioMart downloads by @gaurav in #297
• Babel 1.6 by @gaurav in #279
• Add DrugBank labels by @gaurav in #335

Full Changelog: v1.6.0...v1.7.1