babel - Babel v1.11

What's Changed

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

New Contributors

• @hyi made their first contribution in https://github.com/TranslatorSRI/Babel/pull/460

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/v1.10.0...v1.11

- Python
Published by gaurav 6 months ago

babel - v1.10.0

What's Changed

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

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/v1.9.1...v1.10.0

- Python
Published by gaurav 11 months ago

babel - Babel v1.9.1

What's Changed

• Try to fix an issue in anatomy by @gaurav in https://github.com/TranslatorSRI/Babel/pull/404
• Fix EFO issues by @gaurav in https://github.com/TranslatorSRI/Babel/pull/402
• Check duplicate prefixes by @gaurav in https://github.com/TranslatorSRI/Babel/pull/363
• Add support for icd11foundation in EFO by @gaurav in https://github.com/TranslatorSRI/Babel/pull/380
• Incorporate UMLS_UniProtKB mappings by @gaurav in https://github.com/TranslatorSRI/Babel/pull/361
• Keep Parquet files in own directory by @gaurav in https://github.com/TranslatorSRI/Babel/pull/397

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/v1.9.0...v1.9.1

- Python
Published by gaurav 12 months ago

babel - Babel v1.9.0

What's Changed

• Babel 1.8 (Translator Hammerhead) by @gaurav in https://github.com/TranslatorSRI/Babel/pull/351
• Added a check for duplicate CURIEs by @gaurav in https://github.com/TranslatorSRI/Babel/pull/342
• Added some additional manual concords by @gaurav in https://github.com/TranslatorSRI/Babel/pull/360
• inverted tradename by @cbizon in https://github.com/TranslatorSRI/Babel/pull/377
• Goumls by @cbizon in https://github.com/TranslatorSRI/Babel/pull/395
• Efo by @cbizon in https://github.com/TranslatorSRI/Babel/pull/396

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/v1.8.0...v1.9.0

- Python
Published by gaurav about 1 year ago

babel - Babel v1.8.0

What's Changed

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

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/v1.7.1...v1.8.0

- Python
Published by gaurav over 1 year ago

babel - Babel v1.7.1

What's Changed

• Adds a basic citation to Babel by @gaurav in https://github.com/TranslatorSRI/Babel/pull/347
• Improve BioMart downloads by @gaurav in https://github.com/TranslatorSRI/Babel/pull/297
• Babel 1.6 by @gaurav in https://github.com/TranslatorSRI/Babel/pull/279
• Add DrugBank labels by @gaurav in https://github.com/TranslatorSRI/Babel/pull/335

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/v1.6.0...v1.7.1

- Python
Published by gaurav over 1 year ago

babel - v1.6.0

What's Changed

• Create release notes for Babel by @gaurav in https://github.com/TranslatorSRI/Babel/pull/268
• Fix EFO labels and misc fixes by @gaurav in https://github.com/TranslatorSRI/Babel/pull/273
• Add manual concords for Disease to improve Opioid and Alcohol Use Disorder by @gaurav in https://github.com/TranslatorSRI/Babel/pull/274
• Removed special-cased Biolink prefixes by @gaurav in https://github.com/TranslatorSRI/Babel/pull/278
• Fix Reactome mapping by @gaurav in https://github.com/TranslatorSRI/Babel/pull/296
• Add Translator "Fugu" 2024jul13 release information by @gaurav in https://github.com/TranslatorSRI/Babel/pull/320
• Skip unresolvable DrugChemical conflation identifiers by @gaurav in https://github.com/TranslatorSRI/Babel/pull/325
• Cell wikidata by @cbizon in https://github.com/TranslatorSRI/Babel/pull/329

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/v1.5.0...v1.6.0

- Python
Published by gaurav over 1 year ago

babel - Babel v1.5.0

What's Changed

• Add clique identifier count to synonyms by @gaurav in https://github.com/TranslatorSRI/Babel/pull/228
• Minor fixes by @gaurav in https://github.com/TranslatorSRI/Babel/pull/253
• Normalize DrugChemical conflation IDs by @gaurav in https://github.com/TranslatorSRI/Babel/pull/250
• Add PubMed IDs by @gaurav in https://github.com/TranslatorSRI/Babel/pull/227
• Fix DrugChemical conflation typing by @gaurav in https://github.com/TranslatorSRI/Babel/pull/266
• Read UNII file with Latin-1 character by @gaurav in https://github.com/TranslatorSRI/Babel/pull/247

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/v1.4.0...v1.5.0

- Python
Published by gaurav almost 2 years ago

babel - Babel v1.4.0

What's Changed

• Switched Dockerfile to Python 3.12 and upgraded Biolink Model to 4.16 and RxNorm to 03042024 by @gaurav in https://github.com/TranslatorSRI/Babel/pull/245
• Rename ncbi.nih.gov is now ncbi.nlm.nih.gov by @gaurav in https://github.com/TranslatorSRI/Babel/pull/246

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/v1.3.0...v1.4.0

- Python
Published by gaurav almost 2 years ago

babel - Babel v1.3.0

What's Changed

• Removed unique prefix for COMPLEXPORTAL since it is no longer needed by @gaurav in https://github.com/TranslatorSRI/Babel/pull/195
• Upgrade Panther to PTHR18.0 and SequenceAssociationPathway3.6.7.txt by @gaurav in https://github.com/TranslatorSRI/Babel/pull/197
• Skip writing synonyms that have no valid name by @gaurav in https://github.com/TranslatorSRI/Babel/pull/203
• Removed babel-private by @gaurav in https://github.com/TranslatorSRI/Babel/pull/207
• Improve UniProtKB downloads by @gaurav in https://github.com/TranslatorSRI/Babel/pull/202
• Fix CURIEs used for information content by @gaurav in https://github.com/TranslatorSRI/Babel/pull/218
• Babel v1.3 ongoing fixes by @gaurav in https://github.com/TranslatorSRI/Babel/pull/201
• Generate per-file reports for compendia files by @gaurav in https://github.com/TranslatorSRI/Babel/pull/221
• Add taxa to NCBIGene by @gaurav in https://github.com/TranslatorSRI/Babel/pull/211
• Move SAPBERT training data exporter into Babel by @gaurav in https://github.com/TranslatorSRI/Babel/pull/235

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/v1.2.0...v1.3.0

- Python
Published by gaurav almost 2 years ago

babel - Babel v1.2.0

What's Changed

• Upgrade Biolink and RxNorm by @gaurav in https://github.com/TranslatorSRI/Babel/pull/183
• Improve conflation by @cbizon in https://github.com/TranslatorSRI/Babel/pull/181
• Remove HTML entities from GtoPDB by @gaurav in https://github.com/TranslatorSRI/Babel/pull/184

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/v1.1.0...v1.2.0

- Python
Published by gaurav over 2 years ago

babel - Babel v1.1.0

What's Changed

• Update requirements by @gaurav in https://github.com/TranslatorSRI/Babel/pull/172
• Fix glom by @cbizon in https://github.com/TranslatorSRI/Babel/pull/174
• Drugs by @cbizon in https://github.com/TranslatorSRI/Babel/pull/173
• Emit CURIE suffixes in the synonym information by @gaurav in https://github.com/TranslatorSRI/Babel/pull/179
• Drugs conflated synonyms by @gaurav in https://github.com/TranslatorSRI/Babel/pull/180

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/v1.0.1...v1.1.0

- Python
Published by gaurav over 2 years ago

babel - Babel v1.0.1

Updated requirements to fix Docker image build issue seen in https://github.com/TranslatorSRI/Babel/actions/runs/5652234048.

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/v1.0.0...v1.0.1

- Python
Published by gaurav over 2 years ago

babel - Babel v1.0.0

What's Changed

• Unpinned more-iterutils to help find solutions by @gaurav in https://github.com/TranslatorSRI/Babel/pull/146
• Fix GtoPdb ligands.tsv header by @gaurav in https://github.com/TranslatorSRI/Babel/pull/132
• Add run scripts to Babel by @gaurav in https://github.com/TranslatorSRI/Babel/pull/97
• Generate descriptions for all identifiers from UberGraph by @gaurav in https://github.com/TranslatorSRI/Babel/pull/121
• Fix UNII download by @gaurav in https://github.com/TranslatorSRI/Babel/pull/139
• Download UMLS using a UMLSAPIKEY environmental variable by @gaurav in https://github.com/TranslatorSRI/Babel/pull/133
• Download information content values for Ubergraph terms directly from Ubergraph by @gaurav in https://github.com/TranslatorSRI/Babel/pull/135
• Fix - synonyms in NCBIGene by @gaurav in https://github.com/TranslatorSRI/Babel/pull/166
• Fix synonym uniquification by @gaurav in https://github.com/TranslatorSRI/Babel/pull/171

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/v0.9.1...v1.0.0

- Python
Published by gaurav over 2 years ago

babel - Babel v0.9.1

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/v0.9...v0.9.1

- Python
Published by gaurav over 2 years ago

babel - Babel v0.9

What's Changed

• Add complex portal by @Shalsh23 in https://github.com/TranslatorSRI/Babel/pull/53
• Paginate UberGraph results and remove EFO by @gaurav in https://github.com/TranslatorSRI/Babel/pull/49
• Save intermediate files into babel_outputs by @gaurav in https://github.com/TranslatorSRI/Babel/pull/57
• Add macromolecular complex compendium by @Shalsh23 in https://github.com/TranslatorSRI/Babel/pull/55
• Improve kegg requests by @jdr0887 in https://github.com/TranslatorSRI/Babel/pull/64
• Add UMLS IDs to taxon by @gaurav in https://github.com/TranslatorSRI/Babel/pull/60
• Improve UMLS coverage by @gaurav in https://github.com/TranslatorSRI/Babel/pull/50
• Fix misplaced continue by @gaurav in https://github.com/TranslatorSRI/Babel/pull/80
• Fix CHEBI:CHEBI: bug (#69) by @gaurav in https://github.com/TranslatorSRI/Babel/pull/78
• Added relation from UMLS/synonyms into synonyms/umls.txt by @gaurav in https://github.com/TranslatorSRI/Babel/pull/92
• Split cliques that contain both MolecularMixtures and SmallMolecules by @gaurav in https://github.com/TranslatorSRI/Babel/pull/91
• Fix ChemicalEntity identifier prefix order bug by @gaurav in https://github.com/TranslatorSRI/Babel/pull/94
• Improve Dockerfile by @gaurav in https://github.com/TranslatorSRI/Babel/pull/74
• Treat ENSEMBL versioned identifier as identical to their non-versioned representation by @gaurav in https://github.com/TranslatorSRI/Babel/pull/79
• Added a filter for numerical values in UMLS synonyms by @gaurav in https://github.com/TranslatorSRI/Babel/pull/95
• Fix bug in HMDB metabolites with a single synonym by @gaurav in https://github.com/TranslatorSRI/Babel/pull/104
• Replaced UberGraph's closure graph with the redundant graph by @gaurav in https://github.com/TranslatorSRI/Babel/pull/118
• Fix UniChem by @gaurav in https://github.com/TranslatorSRI/Babel/pull/108
• Replace MacromolecularComplexMixin with MacromolecularComplex by @gaurav in https://github.com/TranslatorSRI/Babel/pull/117
• Returned EFO identifiers to disease/phenotypes by @cbizon in https://github.com/TranslatorSRI/Babel/pull/120
• change syn file format by @cbizon in https://github.com/TranslatorSRI/Babel/pull/113
• Fix capitalization bug in SynonymFactory by @gaurav in https://github.com/TranslatorSRI/Babel/pull/130
• Make synonym outputs explicit inputs to other rules in Snakemake by @gaurav in https://github.com/TranslatorSRI/Babel/pull/124
• Add a GitHub Action to generate Docker images from this repo for all releases by @gaurav in https://github.com/TranslatorSRI/Babel/pull/106
• Move UNII out of private and back into Downloads by @gaurav in https://github.com/TranslatorSRI/Babel/pull/96

New Contributors

• @Shalsh23 made their first contribution in https://github.com/TranslatorSRI/Babel/pull/53
• @jdr0887 made their first contribution in https://github.com/TranslatorSRI/Babel/pull/64

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/2022sep13...v0.9

- Python
Published by gaurav over 2 years ago

babel - Babel 2022dec2

What's Changed

• Add complex portal by @Shalsh23 in https://github.com/TranslatorSRI/Babel/pull/53
• Paginate UberGraph results and remove EFO by @gaurav in https://github.com/TranslatorSRI/Babel/pull/49
• Save intermediate files into babel_outputs by @gaurav in https://github.com/TranslatorSRI/Babel/pull/57
• Add macromolecular complex compendium by @Shalsh23 in https://github.com/TranslatorSRI/Babel/pull/55
• Improve kegg requests by @jdr0887 in https://github.com/TranslatorSRI/Babel/pull/64
• Add UMLS IDs to taxon by @gaurav in https://github.com/TranslatorSRI/Babel/pull/60
• Improve UMLS coverage by @gaurav in https://github.com/TranslatorSRI/Babel/pull/50
• Fix misplaced continue by @gaurav in https://github.com/TranslatorSRI/Babel/pull/80
• Fix CHEBI:CHEBI: bug (#69) by @gaurav in https://github.com/TranslatorSRI/Babel/pull/78
• Added relation from UMLS/synonyms into synonyms/umls.txt by @gaurav in https://github.com/TranslatorSRI/Babel/pull/92
• Split cliques that contain both MolecularMixtures and SmallMolecules by @gaurav in https://github.com/TranslatorSRI/Babel/pull/91
• Fix ChemicalEntity identifier prefix order bug by @gaurav in https://github.com/TranslatorSRI/Babel/pull/94
• Improve Dockerfile by @gaurav in https://github.com/TranslatorSRI/Babel/pull/74
• Treat ENSEMBL versioned identifier as identical to their non-versioned representation by @gaurav in https://github.com/TranslatorSRI/Babel/pull/79

New Contributors

• @Shalsh23 made their first contribution in https://github.com/TranslatorSRI/Babel/pull/53
• @jdr0887 made their first contribution in https://github.com/TranslatorSRI/Babel/pull/64

Full Changelog: https://github.com/TranslatorSRI/Babel/compare/2022sep13...2022dec2

- Python
Published by gaurav about 3 years ago

babel - Babel 2022sep13

What's Changed

• Many source databases have been updated.
• Overhaul by @cbizon in https://github.com/TranslatorSRI/Babel/pull/27
• Biolink2 by @cbizon in https://github.com/TranslatorSRI/Babel/pull/30
• Umls chem by @cbizon in https://github.com/TranslatorSRI/Babel/pull/31
• Add Dockerfile by @gaurav in https://github.com/TranslatorSRI/Babel/pull/37
• Umls mesh by @cbizon in https://github.com/TranslatorSRI/Babel/pull/46
• Increased babel-downloads size by @gaurav in https://github.com/TranslatorSRI/Babel/pull/47
• Greatly expanded the OrganismTaxon compendium with identifiers from UMLS.
• A new "leftover UMLS" compendium includes all UMLS concepts that are not included elsewhere in Babel, with a few exceptions.

New Contributors

• @cbizon made their first contribution in https://github.com/TranslatorSRI/Babel/pull/27

Differences to previous versions

• Differences from the January 1, 2022 Babel release, which is currently deployed: summary
• Differences from the September 6, 2022 Babel release, which was never released: summary

Full Changelog: https://github.com/TranslatorSRI/Babel/commits/2022sep13

- Python
Published by gaurav over 3 years ago