Babel v1.5.0

What's Changed

• Add clique identifier count to synonyms by @gaurav in #228
• Minor fixes by @gaurav in #253
• Normalize DrugChemical conflation IDs by @gaurav in #250
• Add PubMed IDs by @gaurav in #227
• Fix DrugChemical conflation typing by @gaurav in #266
• Read UNII file with Latin-1 character by @gaurav in #247

Full Changelog: v1.4.0...v1.5.0

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 #245
• Rename ncbi.nih.gov is now ncbi.nlm.nih.gov by @gaurav in #246

Full Changelog: v1.3.0...v1.4.0

Babel v1.3.0

What's Changed

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

Full Changelog: v1.2.0...v1.3.0

Babel v1.2.0

What's Changed

• Upgrade Biolink and RxNorm by @gaurav in #183
• Improve conflation by @cbizon in #181
• Remove HTML entities from GtoPDB by @gaurav in #184

Full Changelog: v1.1.0...v1.2.0

Babel v1.1.0

What's Changed

• Update requirements by @gaurav in #172
• Fix glom by @cbizon in #174
• Drugs by @cbizon in #173
• Emit CURIE suffixes in the synonym information by @gaurav in #179
• Drugs conflated synonyms by @gaurav in #180

Full Changelog: v1.0.1...v1.1.0

Babel v1.0.1

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

Full Changelog: v1.0.0...v1.0.1

Babel v1.0.0

What's Changed

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

Full Changelog: v0.9.1...v1.0.0

Babel v0.9.1

Full Changelog: v0.9...v0.9.1

Babel v0.9

What's Changed

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

New Contributors

• @Shalsh23 made their first contribution in #53
• @jdr0887 made their first contribution in #64

Full Changelog: 2022sep13...v0.9

Babel 2022dec2

What's Changed

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

New Contributors

• @Shalsh23 made their first contribution in #53
• @jdr0887 made their first contribution in #64

Full Changelog: 2022sep13...2022dec