tatonetti-lab/onsides: OnSIDES v3.1.1

Le résumé fourni par la source

Updated April 2026 with the latest drug labels from all four regulatory sources. Summary | Type | v3.1.0 | v3.1.1 | | --- | --- | --- | | Products | 42,268 | 41,119 | | Adverse effects | 5,472,613 | 6,928,666 | | Ingredients | 1,955 | 1,866 | Labels processed | Source | Labels parsed | Labels in database | Adverse effects | | --- | --- | --- | --- | | US (DailyMed) | 51,026 | 35,340 | 6,540,259 | | UK (EMC) | 7,578 | 2,874 | 81,978 | | EU (EMA) | 1,782 | 1,021 | 76,869 | | JP (KEGG) | 8,924 | 1,884 | 229,560 | Japan labels are scored by string matching only (no BERT model). Of ~20,000 JP labels downloaded, 8,924 contained a side-effects section; the remainder are supplements, diagnostics, and other products without listed adverse reactions. Pipeline fixes This release includes several fixes to the data pipeline discovered during the update process: Japanese filename handling: Reduced the filename byte-length limit from 240 to 220 bytes to prevent ENAMETOOLONG errors when the parse step appends derived suffixes (e.g. .side_effects.table.NN.csv) to Japanese multi-byte filenames. Japanese labels without side effects: Labels lacking a side-effects section (par-11) now produce an empty output file instead of crashing, allowing the pipeline to continue gracefully. MRCONSO.RRF encoding: Added ignore_errors = true to DuckDB's CSV reader for the UMLS MRCONSO file, which contains some non-UTF-8 bytes in non-English rows (e.g. Swedish). The skipped rows do not affect English or Japanese MedDRA vocabulary extraction. MRCONSO.RRF filename case: Fixed all references from lowercase mrconso.rrf to uppercase MRCONSO.RRF to match the actual file distributed by UMLS. MedDRA vocabulary deduplication: Fixed a UNIQUE constraint violation in the MedDRA vocab table by using ROW_NUMBER() to select one entry per meddra_id when the same ID maps to multiple name/type combinations across OMOP and MRCONSO sources. New documentation Added AI-assisted update guides for running future data releases with an AI coding agent (e.g. Claude Code): HUMAN_UPDATE_GUIDE.md — operator-facing guide AGENT_UPDATE_GUIDE.md — technical reference for the AI agent

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