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Babel v1.12

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@gaurav gaurav released this 15 Sep 23:09
v1.12
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gaurav Gaurav Vaidya
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gaurav Gaurav Vaidya
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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

Contributors

gaurav, hyi, and 2 other contributors
Assets 2
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