CHEBI cleanup: fix 118 mislabeled id/label pairs across 105 files - #98
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… files OAK-verified sweep of every `id: CHEBI:* / label:` pair in kb/communities against the live ChEBI sqlite db. Found 133 mismatching unique pairs; fixed 118 (304 line occurrences across 105 files). Two fix kinds, both with labels taken from OAK's canonical string so id and label are guaranteed consistent: - REPOINT (65 rules): id resolved to a chemically unrelated compound; repointed to the correct id. Examples: chalcopyrite CHEBI:50885 (fludrocortisone) -> 86202; pyrite 51905 (calcein red-orange)/46627 -> 86471; chromate(2-) 48154 (sulfur oxide) -> 35404; vanadate(3-) 30019 (selenomethionine residue) -> 46442; the REE cations (Ce/La/Nd/Sm/Pr/ Y/Yb/Tb), uranium(IV)/(VI), zinc sulfate (zearalenone) -> 35176, sodium butyrate (a PI lipid) -> 64103, N-acyl-homoserine lactone (alkyloxynaphthalene) -> 55474, sulfur atom (selenium atom) -> 26833, xylan (alpha-D-allose) -> 37166, propane-1,3-diol -> 16109, etc. - RELABEL (53 rules): id was the correct compound but the label was a synonym/charge/stereo/hydrate/plural drift; relabeled to canonical (e.g. hydrogen -> dihydrogen, tryptophan -> L-tryptophan, cellulose -> (1->4)-beta-D-glucan, acetate -> acetic acid, calcium chloride -> calcium dichloride). 15 pairs left untouched (no clean CHEBI term): vanadyl cation, iron(II) sulfate (anhydrous), chromium(III) hydroxide, humic acid, uranyl(2+), organic matter, dysprosium(3+), three long-chain N-acyl-homoserine lactones, lead sulfide, zinc sulfide, sodium metasilicate, (2Z)-2-dodecenoic acid, yeast extract. These need a dedicated CHEBI term (or removal) and are flagged for manual follow-up. Tooling added under scripts/: - chebi_label_audit.py - reusable QC: reports id/label mismatches vs OAK - chebi_fix_apply.py - the one-time correction map applied here Test plan: just test (136 passed, 9 skipped); all 105 changed files validate clean; re-audit drops 133 -> 15 mismatches (all intentional). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Pull request overview
This PR performs a repo-wide data-quality sweep to ensure every CHEBI:* id: / label: pair in kb/communities/ matches OAK’s canonical ChEBI label, reducing accumulated CHEBI mislabels from prior backfill work and providing tooling to re-run the audit/correction process.
Changes:
- Add two scripts to (1) audit CHEBI
id/labelconsistency vs OAK canonical labels and (2) apply a curated correction map. - Apply bulk CHEBI repoints/relabels across a large set of community YAMLs to make
term.idandterm.labelconsistent.
Reviewed changes
Copilot reviewed 107 out of 107 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| scripts/chebi_label_audit.py | New audit script to report CHEBI id/label mismatches against OAK canonical labels. |
| scripts/chebi_fix_apply.py | New apply script to mass-correct known mismatching CHEBI id/label pairs across community YAMLs. |
| kb/communities/Wheat_Consortium_C6.yaml | Updates a CHEBI term id to the corrected violacein identifier while keeping label consistent. |
| kb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml | Relabels CHEBI terms to canonical strings (e.g., thiamine/pantothenate). |
| kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml | Relabels phosphate CHEBI label to canonical form. |
| kb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml | Relabels cellulose CHEBI label to canonical form across multiple occurrences. |
| kb/communities/Trichoderma_Lactate_Platform.yaml | Relabels cellulose CHEBI label to canonical form. |
| kb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml | Relabels cellulose CHEBI label to canonical form in metabolites and growth media. |
| kb/communities/Tinto_River_Iron_Cycling_Community.yaml | Repointer/relabler updates for sulfur and sulfide CHEBI terms. |
| kb/communities/THOR_Rhizosphere_Model_Community.yaml | Repointer update for alkaloid-class CHEBI id used as placeholder. |
| kb/communities/Thermophilic_Pyrite_QS_Consortium.yaml | Repointer updates for pyrite/chalcopyrite and other CHEBI corrections. |
| kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml | Relabels benzoate CHEBI label to canonical acid form across sections. |
| kb/communities/Syntrophus_Benzoate_Degrader.yaml | Relabels benzoate CHEBI label to canonical acid form. |
| kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml | Repointer/relabel updates for multiple growth media CHEBI terms. |
| kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml | Repointer/relabel updates for multiple growth media CHEBI terms. |
| kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml | Relabels nitrogen CHEBI label to canonical dinitrogen in multiple places. |
| kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml | Repointer update for methylamine CHEBI id. |
| kb/communities/Soybean_N_Fixation_sfSynCom.yaml | Repointer/relabel updates for AHLs and several growth media CHEBI labels. |
| kb/communities/Soil_Corrinoid_B12_Reservoir_Community.yaml | Relabels cobalamin CHEBI label to canonical plural form. |
| kb/communities/SF356_Cellulose_Degrader.yaml | Relabels cellulose CHEBI label to canonical form across multiple occurrences. |
| kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml | Relabels lithium CHEBI label to canonical ionic form. |
| kb/communities/Saccharomyces_Acinetobacter_Lignocellulose_Detox_Coculture.yaml | Repointer update for 5-hydroxymethylfurfural CHEBI id/label alignment. |
| kb/communities/Saanich_Inlet_OMZ_Redox_Gradient_Community.yaml | Relabels nitrous oxide CHEBI label to canonical form. |
| kb/communities/Rifle_Uranium_Reducing_Community.yaml | Repointer updates for uranium oxidation-state CHEBI ids/labels across multiple sections. |
| kb/communities/Richmond_Mine_AMD_Biofilm.yaml | Repointer/relabel updates for pyrite/sulfur and selected growth media CHEBI labels. |
| kb/communities/Rice_Duckweed_Bacillus_SynCom.yaml | Relabels indole-3-acetic acid CHEBI label to canonical form. |
| kb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml | Relabels magnetite CHEBI label to canonical form across multiple occurrences. |
| kb/communities/Rammelsberg_Cobalt_Nickel_Tailings.yaml | Repointer update for sulfur atom CHEBI id. |
| kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml | Repointer/relabel updates for several growth media CHEBI ids/labels. |
| kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml | Relabels chloronitrobenzene CHEBI label to canonical IUPAC-style name in multiple sections. |
| kb/communities/Propanotrophic_Chlorinated_Ethene_Cometabolism_Enrichment.yaml | Repointer updates for chloroethene CHEBI ids. |
| kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml | Repointer updates for vanadate/vanadium dioxide CHEBI ids in multiple sections. |
| kb/communities/Phormidium_Alkaline_Consortium.yaml | Relabels thiamine CHEBI label to canonical ionic form. |
| kb/communities/Phenol_Carboxylation_Consortium.yaml | Relabels benzoate CHEBI label to canonical acid form. |
| kb/communities/PGM_Spent_Catalyst_Bioleaching.yaml | Repointer/relabel updates for palladium and other CHEBI terms used in the record. |
| kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml | Repointer/relabel updates for multiple growth media CHEBI terms. |
| kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml | Repointer updates for ACC and cellulose CHEBI term usage. |
| kb/communities/Ostreococcus_Dinoroseobacter_BVitamin_Mutualism.yaml | Relabels thiamine CHEBI label to canonical ionic form. |
| kb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml | Relabels fumarate CHEBI label to canonical acid form. |
| kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml | Repointer/relabel updates for cellulose/xylan and other CHEBI terms. |
| kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml | Repointer updates for uranium(VI) CHEBI id/label. |
| kb/communities/Ngawha_Geothermal_Mercury_Cycling_Community.yaml | Repointer update for methylmercury CHEBI id. |
| kb/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.yaml | Repointer updates for xylan CHEBI id across multiple occurrences. |
| kb/communities/Naica_Deep_Subsurface_Thermophilic.yaml | Relabels hydrogen CHEBI label to canonical dihydrogen. |
| kb/communities/MSC2_Model_Soil_Consortium.yaml | Repointer update for chitin CHEBI id. |
| kb/communities/MSC1_Dominant_Core.yaml | Repointer/relabel updates for chitin/chitooligosaccharide and other CHEBI terms. |
| kb/communities/Mixed_Gallium_LED_Recovery_Consortium.yaml | Relabels gallium CHEBI label to canonical form. |
| kb/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.yaml | Repointer update for coproporphyrin III CHEBI id. |
| kb/communities/Mercury_SFA_EFPC_Sediment_Community.yaml | Repointer update for methylmercury CHEBI id. |
| kb/communities/MAMC_M48_Lignocellulose.yaml | Repointer/relabel updates for cellulose/xylan CHEBI terms. |
| kb/communities/Lotus_LjSC3.yaml | Relabels calcium chloride CHEBI label to canonical form. |
| kb/communities/KBase_Synthetic_Bacterial_Community_R2A.yaml | Relabels purine CHEBI label to canonical plural form. |
| kb/communities/KBase_ORT_Workflow_Community_Model.yaml | Relabels multiple CHEBI labels to canonical forms (e.g., dinitrogen, glycine betaine). |
| kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml | Repointer update for dextrin CHEBI id. |
| kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml | Repointer/relabel updates for REE/phosphate CHEBI terms. |
| kb/communities/Industrial_Bioreactor_Consortium.yaml | Repointer update for chalcopyrite CHEBI id. |
| kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml | Repointer update for copper(II) sulfide CHEBI id. |
| kb/communities/High_Solids_Switchgrass_Methanogenic_Microbiome.yaml | Repointer/relabel updates for cellulose/xylan CHEBI terms. |
| kb/communities/Hanford_300_Area_Unconfined_Aquifer_Community.yaml | Repointer update for uranium(VI) CHEBI id/label. |
| kb/communities/GOM_Oil_Degrading_Consortium.yaml | Repointer updates for PAH/alkane CHEBI ids. |
| kb/communities/GLBRC_UFMP_Fermentation_Community.yaml | Relabels multiple organic acid CHEBI labels to canonical forms. |
| kb/communities/GLBRC_Populus_Variovorax_SynCom28.yaml | Relabels L-fucose CHEBI label to canonical form. |
| kb/communities/Geobacter_Methanosarcina_DIET.yaml | Repointer updates for cysteine and sodium sulfide CHEBI terms in growth media. |
| kb/communities/Geobacter_Methanosaeta_DIET.yaml | Repointer updates for cysteine and sodium sulfide CHEBI terms in growth media. |
| kb/communities/Geobacter_Clostridium_DIET.yaml | Repointer/relabel updates for multiple growth media and metabolite CHEBI terms. |
| kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml | Repointer/relabel updates for pyrite/chalcopyrite and other growth media CHEBI terms. |
| kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml | Relabels tryptophan CHEBI label to canonical L-tryptophan. |
| kb/communities/EcoFAB_Ring_Trial_SynCom17.yaml | Repointer/relabel updates for shikimate/coumarate CHEBI terms. |
| kb/communities/East_River_Floodplain_Core_Microbiome.yaml | Relabels thiosulfate CHEBI label to canonical charge form. |
| kb/communities/Drought_Rhizosphere_Iron_Actinobacteria_Community.yaml | Relabels iron CHEBI label to canonical form. |
| kb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml | Repointer/relabel updates for multiple growth media CHEBI terms. |
| kb/communities/Cyprus_Copper_Sulphide_Bioleaching_Consortium.yaml | Repointer updates for chalcopyrite/chalcocite CHEBI ids. |
| kb/communities/Coscinodiscus_Synthetic_Community.yaml | Repointer/relabel updates for multiple growth media and metabolite CHEBI terms. |
| kb/communities/Copper_Biomining_Heap_Leach.yaml | Repointer/relabel updates for chalcopyrite and multiple growth media CHEBI terms. |
| kb/communities/Coniochaeta_Sphingobacterium_Citrobacter_Wheat_Straw_Consortium.yaml | Repointer/relabel updates for cellulose/xylan CHEBI terms. |
| kb/communities/Clostridium_Thermocellum_Saccharoperbutylacetonicum_Cellulosic_Butanol_Coculture.yaml | Relabels cellulose CHEBI label to canonical form in multiple sections. |
| kb/communities/Clostridium_Thermoanaerobacterium_JN4_GD17_Cellulosic_Biofuel_Coculture.yaml | Relabels cellulose CHEBI label to canonical form in multiple sections. |
| kb/communities/Clostridium_Thermoanaerobacter_Cellulosic_Bioethanol_Coculture.yaml | Relabels cellulose CHEBI label to canonical form in multiple sections. |
| kb/communities/Clostridium_Saccharomyces_Cellulose_Ethanol_Coculture.yaml | Relabels cellulose CHEBI label to canonical form in multiple sections. |
| kb/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.yaml | Relabels citrate CHEBI label to canonical acid form. |
| kb/communities/Clostridium_Ljungdahlii_Kluyveri_Syngas_Alcohol_Coculture.yaml | Relabels hydrogen and organic acid CHEBI labels to canonical forms across sections. |
| kb/communities/Clostridium_Cellulovorans_Rhodopseudomonas_Cellulose_Biohydrogen_Coculture.yaml | Relabels cellulose CHEBI label to canonical form in multiple sections. |
| kb/communities/Clostridium_Cellulovorans_Methanosarcina_Cellulose_Methane_Coculture.yaml | Relabels cellulose CHEBI label to canonical form in multiple sections. |
| kb/communities/Clostridium_Cellulolyticum_Geobacter_Cellulose_MFC_Coculture.yaml | Relabels cellulose CHEBI label to canonical form across multiple occurrences. |
| kb/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.yaml | Relabels hexanoate CHEBI label to canonical acid form. |
| kb/communities/Clostridium_Caldicellulosiruptor_Minimal_Medium_Coculture.yaml | Repointer/relabel updates for cellulose/xylan CHEBI terms in multiple sections. |
| kb/communities/Cinnamate_Degradation_Consortium.yaml | Relabels cinnamate/benzoate and hydrogen CHEBI terms to canonical ids/labels. |
| kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml | Repointer/relabel updates for chromate/chromium/sulfur and thiosulfate CHEBI terms. |
| kb/communities/Chlorella_Ecoli_Mixotrophic_Biofuel_Coculture.yaml | Relabels D-glucose CHEBI label to canonical form across multiple occurrences. |
| kb/communities/Chlorella_Azospirillum_Synthetic_Mutualism.yaml | Relabels thiamine CHEBI label to canonical ionic form. |
| kb/communities/Chlamydomonas_Methylobacterium_Mutualism.yaml | Relabels Tris CHEBI label to canonical form. |
| kb/communities/Chlamydomonas_Bacterial_H2_Consortium.yaml | Repointer/relabel updates for hydrogen/Tris/mannitol CHEBI terms. |
| kb/communities/Cellulomonas_Rhodobacter_Cellulose_Photohydrogen_Coculture.yaml | Relabels cellulose CHEBI label to canonical form in multiple sections. |
| kb/communities/Caldicellulosiruptor_TwoSpecies_Hydrogen_Coculture.yaml | Relabels hydrogen CHEBI label to canonical dihydrogen. |
| kb/communities/Caldibacillus_Clostridium_Aerotolerant_Cellulose_Coculture.yaml | Relabels cellulose CHEBI label to canonical form in multiple sections. |
| kb/communities/BioModels_MODEL2209060002_DPigrum_SAureus_Community.yaml | Relabels lactate CHEBI label to canonical stereospecific acid form. |
| kb/communities/BioModels_MODEL2204300001_Kefir_Community_Model.yaml | Relabels lactate CHEBI label to canonical stereospecific acid form across occurrences. |
| kb/communities/BioModels_MODEL1806250005_Cicada_Sulcia_Hodgkinia.yaml | Relabels nitrogen CHEBI label to canonical atom form across occurrences. |
| kb/communities/BioModels_MODEL1806250004_Sharpshooter_Sulcia_Baumannia.yaml | Relabels nitrogen CHEBI label to canonical atom form across occurrences. |
| kb/communities/BioModels_MODEL1806250003_Spittlebug_Sulcia_Sodalis.yaml | Relabels nitrogen CHEBI label to canonical atom form across occurrences. |
| kb/communities/Bifidobacterium_Ruminococcus_Infant_HMO_CrossFeeding.yaml | Repointer/relabel updates for 2'-fucosyllactose and lactose CHEBI terms. |
| kb/communities/Bayan_Obo_REE_Tailings_Consortium.yaml | Repointer/relabel updates for REE terms and relabels lactic acid CHEBI label to canonical form. |
| kb/communities/Bacteroides_Eubacterium_Gnotobiotic_Gut_Model.yaml | Repointer update for glycoprotein CHEBI id used for mucin glycans. |
| kb/communities/Australian_Lead_Zinc_Polymetallic.yaml | Repointer updates for ferrihydrite and chalcopyrite CHEBI ids. |
| kb/communities/AMD_Acidophile_Heterotroph_Network.yaml | Relabels phosphate CHEBI label to canonical charge form. |
| kb/communities/Acetobacterium_Clostridium_CO2_Electrolysis_Coculture.yaml | Relabels hexanoate CHEBI label to canonical acid form. |
| kb/communities/Aalborg_East_Full_Scale_EBPR_Community.yaml | Relabels phosphate CHEBI label to canonical charge form. |
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Closer OAK search resolved 4 of the 15 previously-residual pairs: - iron(II) sulfate (anhydrous) CHEBI:31437 -> 75832 - (2Z)-2-dodecenoic acid (BDSF) CHEBI:87659 -> 38372 (cis-2-dodecenoic acid) - vanadyl cation CHEBI:30320 -> 30046 (oxidovanadium(2+)) - dysprosium(3+) CHEBI:49782 -> 33377 (dysprosium atom; no 3+ cation term exists) 9 line occurrences across 6 files. Re-audit now 133 -> 11 mismatches. The remaining 11 have no clean CHEBI term and need a minted term or removal: lead sulfide, zinc sulfide, sodium metasilicate, chromium(III) hydroxide, humic acid, uranyl(2+), organic matter, three long-chain N-acyl-homoserine lactones (C14 / 3-OH-C12 / 3-OH-C14), yeast extract. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This was referenced Jun 3, 2026
realmarcin
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Jun 9, 2026
Closes the metals-cohort tail (gallium/vanadium/lithium/pyrite-QS/mercury). CHEBI ids verified live via OAK; snippets verbatim from cached abstracts. related_ingredients adoption: 80/265 -> 86/265. | Community | Ingredients (CHEBI-verified) | |---|---| | Mixed_Gallium_LED_Recovery_Consortium | gallium(3+) | | Polaromonas_Vanadium_Reduction_Community | vanadate(3-), oxidovanadium(2+) | | Salar_Atacama_Lithium_Brine_Community | lithium chloride, lithium(1+), sodium chloride, magnesium dichloride | | Thermophilic_Pyrite_QS_Consortium | pyrite, chalcopyrite, iron(2+), cis-11-Methyl-2-dodecenoic acid (DSF) | | Mercury_SFA_EFPC_Sediment_Community | mercury(2+), methylmercury(1+), sulfide, secondary alcohol | | Ngawha_Geothermal_Mercury_Cycling_Community | mercury(2+), mercury(0), methylmercury(1+), sulfur atom | Mixed_Gallium got only 1 ingredient (its sole reference has no cached abstract body, only the title) and also has pre-existing fabricated snippets unrelated to gallium - flagged for a separate evidence-repair pass. Pre-existing CHEBI bugs flagged here overlap with those already fixed in the chebi-cleanup PR (#98); these files' metabolites blocks will be corrected when that merges. New finding: vanadyl cation CHEBI:30320 (currently unmapped) has a valid id CHEBI:30046 (oxidovanadium(2+)) - worth folding into a CHEBI-cleanup follow-up. Test plan: just test (136 passed, 9 skipped), all 6 files validate clean. Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
realmarcin
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Jun 9, 2026
Backfills the substrate-chemistry-bearing subset of the agricultural / SynCom files (denitrification, nitrification, bioremediation, P-uptake, methane-Cr coupling, straw/lignocellulose degradation). CHEBI ids verified live via OAK; snippets verbatim from cached abstracts. related_ingredients adoption: 87/265 -> 97/265. | Community | Ingredients (CHEBI-verified) | |---|---| | Aerobic_Denitrification_QQ_SynCom | nitrate, nitrite, N-(3-oxododecanoyl)-L-homoserine lactone, pyocyanine | | ENIGMA_Denitrifying_SynCom | nitrate, nitrite, nitric oxide, dinitrogen oxide | | Urine_Nitrification_SynCom | urea, ammonium, nitrate | | Rice_P_Uptake_Intercropping_SynCom4 | phosphorus atom, phosphate, phosphate ion | | Tribromophenol_Anaerobic_Bioremediation_SynCom | 2,4,6-tribromophenol, phenol, glucose | | Methane_Oxidation_CrVI_Reduction_SynCom | methane, chromate(2-) | | Multiomics_Corn_Straw_Degradation_SynCom | lignocellulose, cellulose, hemicellulose, lignin | | Coniochaeta_..._Wheat_Straw_Consortium | lignocellulose, cellulose, xylan, hemicellulose | | Wheat_Straw_Biogas_Pretreatment_SynCom | lignocellulose, cellulose, hemicellulose | | Bacillus_Bradyrhizobium_Straw_Humification_SynCom | lignocellulose, cellulose, lignin, xylan | 2 of the 12 attempted yielded 0 (abstracts too generic): the Aerobic_Denitrification_Disturbance and Phylogenetically_Diverse denitrifying SynComs name no N-cycle compound verbatim. The remaining ~38 agri/biocontrol SynComs (Banana/Pepper/Watermelon/nematode etc.) are expected to be similarly thin and were not attempted in this batch. Pre-existing CHEBI bugs in Coniochaeta growth_media/metabolites (CHEBI:37686 "xylan"=alpha-D-allose; CHEBI:18246 label "cellulose") are already fixed in the chebi-cleanup PR (#98). Test plan: just test (136 passed, 9 skipped), all 10 files validate clean. Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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OAK-verified sweep of every
id: CHEBI:* / label:pair inkb/communities/against the live ChEBI sqlite db. Found 133 mismatching unique pairs; fixed 118 (304 line occurrences across 105 files). This clears the CHEBI-mislabel backlog accumulated across the #30related_ingredientsbackfill PRs (#90–#97).Labels are always taken from OAK's canonical string, so id and label are guaranteed consistent after the fix.
Fix kinds
REPOINT (65 rules) — id resolved to a chemically unrelated compound; repointed to the correct id:
CHEBI:50885"chalcopyrite" (fludrocortisone) →86202;CHEBI:51905/46627"pyrite" (calcein red-orange / hydrogen muonium) →86471CHEBI:48154"chromate(2-)" (sulfur oxide) →35404;CHEBI:30019"vanadate(3-)" (selenomethionine residue) →46442CHEBI:10106"zinc sulfate" (zearalenone) →35176CHEBI:88613"sodium butyrate" (a PI lipid) →64103;CHEBI:48850"N-acyl-homoserine lactone" (alkyloxynaphthalene) →55474CHEBI:27568"sulfur atom" (selenium atom) →26833;CHEBI:37686"xylan" (alpha-D-allose) →37166;CHEBI:16775"propane-1,3-diol" →16109; and moreRELABEL (53 rules) — id was the right compound; label was a synonym/charge/stereo/hydrate/plural drift; relabeled to canonical:
hydrogen→dihydrogen,tryptophan→L-tryptophan,cellulose→(1->4)-beta-D-glucan,acetate→acetic acid,calcium chloride→calcium dichloride, etc.Left untouched (15 pairs, no clean CHEBI term)
vanadyl cation, iron(II) sulfate (anhydrous), chromium(III) hydroxide, humic acid, uranyl(2+), organic matter, dysprosium(3+), three long-chain N-acyl-homoserine lactones, lead sulfide, zinc sulfide, sodium metasilicate, (2Z)-2-dodecenoic acid, yeast extract. These need a dedicated CHEBI term (or removal) — flagged for manual follow-up.
Tooling (added under
scripts/)chebi_label_audit.py— reusable QC tool: reports every id/label mismatch vs OAKchebi_fix_apply.py— the one-time correction map applied here (full provenance of the edits)Test plan
just test→ 136 passed, 9 skippedlinkml-validate)🤖 Generated with Claude Code