Review disease synonyms vs subtypes (all 146 diseases) - #84
Merged
Conversation
Each ARI_Synonym string was checked against the exact-synonym list and subclass hierarchy of the disease's mapped MONDO/DOID term (EBI OLS), with clinical judgement where no mapping exists. Strings that name a narrower form, a broader parent, a different disease, or a downstream finding are not synonyms. Mechanism: ARI_Synonym stays append-only. A synonym is retired by removing its line AND adding an ARI_SynonymWithdrawn marker on the same disease, shaped "<synonym> | <reason> | <note>" with reason in subtype/broader/distinct/non-disease. validate_mappings.py now accepts a synonym removal carrying a matching marker, still fails an unexplained one, shape-checks the markers, and treats ARI_SynonymWithdrawn as append-only. ARI_ClinicalSubtype and ARI_ChangeLog are unchanged. Batch 1: 25 diseases, 69 synonym strings - 37 kept, 13 kept with a curator note, 19 withdrawn across 9 diseases (9 subtype, 4 broader, 4 distinct, 2 non-disease). Every withdrawn synonym already exists as an ARI_ClinicalSubtype on its disease, so no subtype lines were added or rewritten. Each edited disease gets a dated ARI_ChangeLog entry. Noted for a curator, not fixed: ARI:0001031 is labelled "Autoimmune gastritis" but its rdfs:comment describes autoimmune enteropathy. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…01067)
16 diseases, 181 synonym strings: 129 kept, 21 kept with a curator note,
31 withdrawn across 8 diseases via ARI_SynonymWithdrawn markers -
12 subtype (all already ARI_ClinicalSubtypes), 12 non-disease
("NON RARE IN EUROPE: ..." Orphanet classification labels that leaked in
as synonyms, on celiac disease and CFS), 4 distinct, 3 broader. No
ARI_ClinicalSubtype lines added or rewritten. One ARI_ChangeLog line per
edited disease.
Notable: "Chronic Lyme disease" carried the acute-infection terms
(Lyme borreliosis, Lyme arthritis, erythema migrans) as synonyms;
"Cataplexy and narcolepsy" carried NT1/NT2/genetic-locus subtype names.
Pre-existing, noted not fixed: ARI:0001065 definition describes the acute
tick-borne infection rather than the chronic syndrome.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
17 diseases, 125 synonym strings: 60 kept, 23 kept with a curator note, 42 withdrawn across 7 diseases via ARI_SynonymWithdrawn markers - 20 broader, 13 subtype (already ARI_ClinicalSubtypes), 7 distinct, 2 non-disease. One ARI_ChangeLog line per edited disease; no ARI_ClinicalSubtype lines added or rewritten. Notable: Cold agglutinin disease carried the whole autoimmune haemolytic anaemia synonym set (CAD is its cold-agglutinin subtype); Endometriosis' four synonyms all name adenomyosis, a separate diagnosis. Pre-existing, noted not fixed: ARI:0001076 definition describes discoid lupus rather than the cutaneous-lupus umbrella; ARI:0001069 / ARI:0001074 carry mis-imported sibling diseases in their subtype lists. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
18 diseases, 64 synonym strings: 40 kept, 4 kept with a curator note, 20 withdrawn across 5 diseases via ARI_SynonymWithdrawn markers - 17 subtype/manifestation, 2 distinct, 1 broader. No ARI_ClinicalSubtype lines added or rewritten. Notable: IgG4-related disease carried 14 organ-manifestation names (Riedel's thyroiditis, Kuttner's tumor, Mikulicz's syndrome, Ormond's disease, ...) as synonyms; Immune thrombocytopenia carried iTTP (a different disease). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
20 diseases, 70 synonym strings: 48 kept, 11 kept with a curator note, 11 withdrawn across 9 diseases via ARI_SynonymWithdrawn markers - 5 subtype, 3 broader, 3 distinct. Notable: MOG antibody disease carried anti-MAG neuropathy names (a different disease - MAG vs MOG); Mooren's ulcer carried the broader "peripheral ulcerative keratitis" / "corneal ulcer". Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
20 diseases, 98 synonym strings: 77 kept, 13 kept with a curator note, 8 withdrawn across 4 diseases via ARI_SynonymWithdrawn markers - 6 broader, 2 subtype. Notable: Paraneoplastic cerebellar degeneration carried the broad "paraneoplastic (neurological) syndrome"; PANDAS carried PANS (the wider umbrella). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
20 diseases, 70 synonym strings: 41 kept, 16 kept with a curator note, 13 withdrawn across 9 diseases via ARI_SynonymWithdrawn markers - 4 non-disease, 3 broader, 3 distinct, 3 subtype. Notable: two entities (Retinocochleocerebral vasculopathy, Rheumatoid aortitis) had one synonym each split into fragments on a comma during import; Sjogren's disease carried "SJS" (collides with Stevens-Johnson syndrome) and the broader "sicca syndrome" / "keratoconjunctivitis sicca". Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…01211) Final batch. 10 diseases, 31 synonym strings: 18 kept, 6 kept with a curator note, 7 withdrawn across 5 diseases via ARI_SynonymWithdrawn markers - 5 broader, 2 subtype. Review now covers all 146 diseases with synonyms: 708 strings reviewed, 450 kept, 107 kept with a note, 151 withdrawn across 56 diseases (63 subtype, 45 broader, 23 distinct, 20 non-disease). No ARI_ClinicalSubtype line added or rewritten; validate_mappings.py --since main clean. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…ms-subtypes-d11506 # Conflicts: # changelog.md # ontologies/ari_t1d.owl
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Reviews every
ARI_Synonymstring inontologies/ari_t1d.owlagainst the disease's own concept and retires the ones that are not synonyms — they name a narrower subtype, a broader parent, a different disease, or a downstream finding / import artefact.Method
For each disease, every synonym was checked against the exact-synonym list and subclass hierarchy of the MONDO / DOID term it maps to (via the EBI OLS4 API), with clinical judgement where no mapping exists. Done in 8 batches (one commit each), alphabetically.
New retirement mechanism (keeps
ARI_Synonymappend-only)ARI_Synonymstays append-only. A synonym is retired by removing its line and adding anARI_SynonymWithdrawnmarker on the same disease, shaped<synonym> | <reason> | <note>with<reason>insubtype/broader/distinct/non-disease.validate_mappings.py:ARI_Synonymremoval that carries a matching marker, still fails an unexplained one;withdrawn-synonym-shape/-reason/-still-present);ARI_SynonymWithdrawnas append-only itself.ARI_ClinicalSubtypeandARI_ChangeLogare untouched — still strictly append-only.Result
ARI_Synonymstrings reviewedsubtype)broader)distinct)non-disease)ARI_Synonym708 → 557. Every edited disease gets a datedARI_ChangeLogline. NoARI_ClinicalSubtypeline was added or rewritten — everysubtype-reason withdrawal already had a matching subtype (or a clearly narrower clinical form) on the disease.validate_mappings.py --since mainis clean.Representative catches
NON RARE IN EUROPE: …Orphanet labels; 2 terms split in half on a comma (Retinocochleocerebral vasculopathy, Rheumatoid aortitis).SJS(Stevens-Johnson),Carpenter syndrome.For a curator (not fixed here)
ARI:0001031(gastritis vs enteropathy),ARI:0001065(chronic vs acute Lyme),ARI:0001076(CLE vs discoid).ARI_ClinicalSubtypelists ofARI:0001069andARI:0001074.Per-string rationale for all 708 is in the batch findings tables shared with the reviewer.
Related: #79 (same validator / green-build workflow).
🤖 Generated with Claude Code