D-lyxose — MIM

Ontology mapping

Primary identifier: CHEBI:62318
Notes: Imported from microbedecoder (source_id=kgmicrobe.trait:2_d_lyxose); no CAS-RN or CHEBI/NCIT match. Curator review needed.

Synonyms (3)

Synonym	Type	Source
(2)-D-lyxose	RAW_TEXT	microbedecoder
D-(-)-lyxose	RAW_TEXT	MERGED_FROM (#398)
D-lyxo-pentose	EXACT_SYNONYM	MERGED_FROM D-(-)-lyxose (#398)

Evidence (2)

DATABASE_MATCH via microbedecoder residual free normalized/fuzzy pass (recovered from closed PR #201) + local CHEBI verification

(2)-D-lyxose parse artifact of D-lyxose; exact match to CHEBI:62318.

DATABASE_MATCH via MIM curation (#322)

mapping_quality EXACT_MATCH -> SYNONYM_MATCH. CHEBI:62318 carries no structural definition, so it is a class rather than an individual, and the record's label '(2)-D-lyxose' does not equal the term label 'D-lyxose'. EXACT_MATCH therefore asserted an identity the pair does not have. Re-graded because a corrupted numeric prefix on the same sugar.

Occurrence statistics

Total occurrences

Distinct media

Source occurrences

Source
microbedecoder
Count
1
Source columns
BacDive_Metabolite_utilization

Curation history

Timestamp	Curator	Action	New status	Changes
2026-08-04T02:54:09.684805+00:00	audit_import_ingredients[microbedecoder]	CREATED_AS_UNMAPPED	UNMAPPED	Imported from microbedecoder (source_id=kgmicrobe.trait:2_d_lyxose); no CAS-RN or CHEBI/NCIT match. Curator review needed.
2026-08-04T00:00:00+00:00	promote_resolved_unmapped	PROMOTED_TO_MAPPED	MAPPED	Promoted UNMAPPED_0783 -> CHEBI:62318 "D-lyxose" (EXACT_MATCH); mapping_status UNMAPPED -> MAPPED, SSSOM row added.
2026-08-13T00:00:00+00:00	regrade_class_overstatements	REGRADED_CLASS_OVERSTATEMENT		mapping_quality EXACT_MATCH -> SYNONYM_MATCH (#322); a corrupted numeric prefix on the same sugar.
2026-08-18T00:00:00+00:00	correct_labels_keep_raw	CORRECTED_PREFERRED_TERM		Corrected preferred_term '(2)-D-lyxose' -> 'D-lyxose'. The '(2)' is a mangled character from the microbedecoder ingest (source_id=kgmicrobe.trait:2_d_lyxose) and carries no recoverable information — the sibling record 'D-(-)-lyxose' suggests it was a '(-)' optical-rotation descriptor, but that is inference, not evidence, so it is dropped rather than reconstructed. The corrected label is CHEBI:62318's own label, which the record already maps to at exactMatch. The original is kept as a RAW_TEXT synonym so any source string still resolves. Applied under the rule agreed for #396: MIM's subject_label became the KG's canonical name for the mapped ontology term when kg-microbe made MIM the naming authority, so a damaged or source-language label is published as that term's name. Correct the label; keep the raw one.
2026-08-18T00:00:00+00:00	merge_aldehydo_duplicates	MERGED_FROM		Absorbed 'D-(-)-lyxose' (CHEBI:16789 aldehydo- form) into CHEBI:62318 (#398). Both records name the same substance — the muramic pair carry an identical CAS and formula — split across a ChEBI class term and its open-chain aldehydo- form. The class term wins because the identifier optimises for how the node READS in the knowledge graph: no catalogue sells an 'aldehydo-' tautomer, and MIM is kg-microbe's naming authority, so grounding here would rename the ChEBI node after a minor solution-equilibrium component. ChEBI does hang the commercial CAS (1114-34-7) on the aldehydo- term, which is why the earlier reading of the orderability rule pointed the other way; that CAS is now carried in supplied_form and republished as a synonym, so nothing purchasable is lost from the identity. Occurrences 0/0 + 0/0 -> 0/0.
2026-08-18T00:00:00+00:00	merge_aldehydo_duplicates	FOLDED_MERGED_SYNONYMS		Folded 1 synonym(s) from 'D-(-)-lyxose': ['D-lyxo-pentose']. The merge kept the loser's LABEL but left its own synonyms on the tombstone. They still resolved via label_index, which publishes REJECTED rows, but the tombstone's SSSOM row was dropped — so they no longer reached KGX. These are real chemical names (D-Lyx, D-lyxo-pentose, the systematic forms), not notation noise.