From fb61081fb473181142c7ff57950058ac35f480e6 Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Tue, 7 Jul 2026 14:09:31 -0700 Subject: [PATCH] Fix PALLADIUM enum: CHEBI:33373 (promethium) -> CHEBI:33363 (palladium) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit MetalElementEnum.PALLADIUM was grounded to CHEBI:33373, which is actually "promethium atom" — one of a run of sequential CHEBI ids shared with the lanthanides, a copy-paste/off-by-one grounding error. The correct term is CHEBI:33363 ("palladium"), confirmed via OAK. - schema/communitymech.yaml: PALLADIUM meaning -> CHEBI:33363 - datamodel/communitymech.py: regenerated (just gen-python) - metal_extraction.py: fix parallel METAL_CHEBI_MAP key Community YAMLs already cited CHEBI:33363 in their term.{id,label} pairs, so no data records needed changing. validate-all clean; 197 tests pass. Co-Authored-By: Claude Opus 4.8 (1M context) --- src/communitymech/datamodel/communitymech.py | 4 ++-- src/communitymech/metal_extraction.py | 2 +- src/communitymech/schema/communitymech.yaml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/communitymech/datamodel/communitymech.py b/src/communitymech/datamodel/communitymech.py index 0bb5fba6..f773c5be 100644 --- a/src/communitymech/datamodel/communitymech.py +++ b/src/communitymech/datamodel/communitymech.py @@ -1,5 +1,5 @@ # Auto generated from communitymech.yaml by pythongen.py version: 0.0.1 -# Generation date: 2026-07-03T11:17:23 +# Generation date: 2026-07-07T13:23:20 # Schema: communitymech # # id: https://w3id.org/communitymech @@ -2440,7 +2440,7 @@ class MetalElementEnum(EnumDefinitionImpl): text="SILVER", description="Silver(1+) cation", meaning=CHEBI["30512"] ) PALLADIUM = PermissibleValue( - text="PALLADIUM", description="Palladium atom", meaning=CHEBI["33373"] + text="PALLADIUM", description="Palladium atom", meaning=CHEBI["33363"] ) GALLIUM = PermissibleValue( text="GALLIUM", description="Gallium(3+) cation", meaning=CHEBI["49631"] diff --git a/src/communitymech/metal_extraction.py b/src/communitymech/metal_extraction.py index 83a2d92e..a2db52f0 100644 --- a/src/communitymech/metal_extraction.py +++ b/src/communitymech/metal_extraction.py @@ -26,7 +26,7 @@ "CHEBI:49713": "LITHIUM", "CHEBI:29287": "GOLD", "CHEBI:30512": "SILVER", - "CHEBI:33373": "PALLADIUM", + "CHEBI:33363": "PALLADIUM", "CHEBI:49631": "GALLIUM", "CHEBI:49464": "INDIUM", "CHEBI:33341": "TITANIUM", diff --git a/src/communitymech/schema/communitymech.yaml b/src/communitymech/schema/communitymech.yaml index 40d80a7b..a1aa01f2 100644 --- a/src/communitymech/schema/communitymech.yaml +++ b/src/communitymech/schema/communitymech.yaml @@ -357,7 +357,7 @@ enums: meaning: CHEBI:30512 description: Silver(1+) cation PALLADIUM: - meaning: CHEBI:33373 + meaning: CHEBI:33363 description: Palladium atom GALLIUM: meaning: CHEBI:49631