From eb6d78c1cd728040cd32c01e822280a2509787c9 Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Mon, 7 Sep 2026 18:38:54 -0400 Subject: [PATCH 1/8] Review disease synonyms vs subtypes: batch 1 (ARI:0001001-0001044) 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 " | | " 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 Batch 1: 25 diseases, 69 synonym strings - 37 kept, 13 kept with a curator note, 19 withdrawn across 9 diseases (9 subtype, 4 broader, 4 distinct, 2 non-disease). Every withdrawn synonym already exists as an ARI_ClinicalSubtype on its disease, so no subtype lines were added or rewritten.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 --- .github/scripts/validate_mappings.py | 69 ++++++++++++++++++++++++++-- README.md | 5 ++ changelog.md | 36 +++++++++++++++ ontologies/ari_t1d.owl | 49 ++++++++++++-------- 4 files changed, 136 insertions(+), 23 deletions(-) diff --git a/.github/scripts/validate_mappings.py b/.github/scripts/validate_mappings.py index 63bb59c..982da62 100644 --- a/.github/scripts/validate_mappings.py +++ b/.github/scripts/validate_mappings.py @@ -861,6 +861,39 @@ def check_ontology_values(diseases: dict[str, Disease], report: Report) -> None: f"a {prefix} identifier (expected {ID_SHAPES[prefix]}).", ) + # An ARI_SynonymWithdrawn marker is what lets a synonym leave ARI_Synonym. + # It must be shaped " | | " with a known reason, and + # must not name a synonym that is still present (that is a contradiction, + # not a withdrawal). + live_synonyms = _values(disease, "ARI_Synonym") + for value, line in disease.annotations.get("ARI_SynonymWithdrawn", []): + parts = [p.strip() for p in value.split("|")] + if len(parts) < 3 or not parts[0] or not parts[2]: + report.error( + "withdrawn-synonym-shape", + ONTOLOGY_PATH, + line, + f"{disease.ari_id} has an ARI_SynonymWithdrawn value {value!r} that is not " + "' | | '.", + ) + continue + if parts[1] not in WITHDRAWAL_REASONS: + report.error( + "withdrawn-synonym-reason", + ONTOLOGY_PATH, + line, + f"{disease.ari_id} withdraws {parts[0]!r} with reason {parts[1]!r}; expected " + f"one of {sorted(WITHDRAWAL_REASONS)}.", + ) + if parts[0] in live_synonyms: + report.error( + "withdrawn-synonym-still-present", + ONTOLOGY_PATH, + line, + f"{disease.ari_id} still lists {parts[0]!r} as an ARI_Synonym but also marks " + "it withdrawn. Remove the ARI_Synonym line or the marker.", + ) + # ARI_DXCODE mirrors ARI_SNOMED. A DXCODE value with no SNOMED counterpart is how a # rejected SNOMED code survives removal, so it is worth surfacing; the reverse # (SNOMED recorded without a DXCODE copy) is common and harmless. @@ -921,11 +954,30 @@ def current_lines(path: str) -> list[str]: "ARI_Synonym": "synonym", "ARI_ClinicalSubtype": "clinical subtype", "ARI_ChangeLog": "changelog entry", + "ARI_SynonymWithdrawn": "withdrawn-synonym record", } +# A synonym may leave `ARI_Synonym` only when the same disease carries an +# `ARI_SynonymWithdrawn` marker naming it: " | | ", +# where is one of subtype / broader / distinct / non-disease. The marker +# is itself append-only, so the review that retired the synonym stays on record. +WITHDRAWAL_REASONS = {"subtype", "broader", "distinct", "non-disease"} # How many deleted values to name before the message just gives the count. DELETION_SAMPLE = 3 +def _withdrawn_synonyms(disease: Disease) -> set[str]: + """Synonym texts this disease has an ARI_SynonymWithdrawn marker for. + + Tokenised the same way as `_values` (comma-split) so the result lines up with + `_values(disease, "ARI_Synonym")` for set subtraction. + """ + out: set[str] = set() + for value, _ in disease.annotations.get("ARI_SynonymWithdrawn", []): + head = value.split("|", 1)[0] + out.update(part.strip() for part in head.split(",") if part.strip()) + return out + + def _values(disease: Disease, prop: str) -> set[str]: out = set() for value, _ in disease.annotations.get(prop, []): @@ -948,8 +1000,10 @@ def check_deletions(ref: str, sssom_rows: list[Row], report: Report) -> None: A cross-reference may legitimately go: flagging one wrong on the review page is exactly how a bad code is retired, and that judgment is in the mapping set. - Anything else -- a synonym, a subtype, a changelog entry, or an id no curator - ruled against -- has no decision behind its removal. + A synonym may go when an `ARI_SynonymWithdrawn` marker on the same disease + names it, which records why (subtype / broader / distinct / non-disease). + Anything else -- a subtype, a changelog entry, an unmarked synonym, or an id + no curator ruled against -- has no decision behind its removal. """ result = subprocess.run( ["git", "show", f"{ref}:{ONTOLOGY_PATH}"], @@ -986,14 +1040,21 @@ def check_deletions(ref: str, sssom_rows: list[Row], report: Report) -> None: for prop, noun in APPEND_ONLY_PROPERTIES.items(): lost = _values(was, prop) - _values(now, prop) + if prop == "ARI_Synonym": + lost -= _withdrawn_synonyms(now) if lost: + remedy = ( + "restore the value, or record an ARI_SynonymWithdrawn marker " + "saying why it is being withdrawn" + if prop == "ARI_Synonym" + else "restore the value, or say in review why it is being withdrawn" + ) report.error( "record-deleted", ONTOLOGY_PATH, 0, f"{ari_id} loses {len(lost)} {noun}(s) this branch did not add: " - f"{summarise(lost)}. {prop} is an append-only record — restore the " - f"value, or say in review why it is being withdrawn.", + f"{summarise(lost)}. {prop} is an append-only record — {remedy}.", ) for prefix, properties in ONTOLOGY_PROPERTIES.items(): diff --git a/README.md b/README.md index 434675b..7543476 100644 --- a/README.md +++ b/README.md @@ -101,6 +101,11 @@ What it catches: - Disagreement with the ontology — a disease id or label that does not match, a cross-reference the curators flagged wrong that is still stored and still served, or a confirmed one that was never stored. +- Curation that disappears without a decision — a synonym, clinical subtype or changelog + entry the branch drops rather than adds. A synonym may be retired only by pairing its + removal with an `ARI_SynonymWithdrawn` marker on the same disease, shaped + ` | | ` where `` is `subtype`, `broader`, `distinct` or + `non-disease`; the marker is itself append-only, so the review stays on record. ## Working rules diff --git a/changelog.md b/changelog.md index 3c660f1..b71191d 100644 --- a/changelog.md +++ b/changelog.md @@ -1,5 +1,41 @@ # Changelog +## disease-synonyms-subtypes + +- **Reviews `ARI_Synonym` strings against the disease's own concept and retires the ones + that are not synonyms.** Each disease's synonyms were checked against the exact-synonym + list and subclass hierarchy of the MONDO / DOID term it maps to (via EBI OLS), with + clinical judgement where no mapping exists. A string that names a narrower form, a + broader parent, a different disease, or a downstream finding is not a synonym. +- **New retirement mechanism.** `ARI_Synonym` stays append-only. A synonym is now retired + by removing its line **and** adding an `ARI_SynonymWithdrawn` marker on the same disease, + shaped ` | | ` with `` in + `subtype` / `broader` / `distinct` / `non-disease`. `validate_mappings.py` accepts a + synonym removal that carries a matching marker and still fails an unexplained one; it + also shape-checks the markers (`withdrawn-synonym-shape`, `-reason`, `-still-present`) + and treats `ARI_SynonymWithdrawn` as append-only itself. `ARI_ClinicalSubtype` and + `ARI_ChangeLog` are untouched — still strictly append-only. +- **Batch 1 — 25 diseases (ARI:0001001–0001044), 69 synonym strings.** 37 kept, 13 kept + with a note for a curator, **19 withdrawn across 9 diseases**: 9 name an existing + `ARI_ClinicalSubtype` (`subtype`), 4 a broader parent (`broader`), 4 a different disease + (`distinct`), 2 a downstream haematologic finding (`non-disease`). Every withdrawn + synonym maps to a subtype already listed on the disease, so no `ARI_ClinicalSubtype` + lines were added or rewritten. Each edited disease carries a dated `ARI_ChangeLog` line. +- Withdrawn: ADEM — *Nonvasculitic autoimmune inflammatory meningoencephalitis*, + *Hurst's disease*, *Weston-Hurst syndrome*; Addison's disease — *Adrenal Insufficiency*, + *Adrenal cortical hypofunction*; Ankylosing spondylitis — *Axial spondyloarthritis*, + *Spondyloarthritis*; Anti-CASPR2 encephalitis — *Morvan syndrome*; ANCA-associated + vasculitis — *Churg Strauss syndrome*, *Wegener's Granulomatosis*; Autoimmune inner-ear + disease — *Ménière's disease*; Autoimmune gastritis — *Megaloblastic Anemia*, + *Macrocytic Anemia*, *Eosinophilic gastritis*, *Autoimmune enteropathy*; Autoimmune + neutropenia — *Autoimmune neutropenia of infancy*, *Primary autoimmune neutropenia*; + Autoimmune pancreatitis — *Lymphoplasmocytic sclerosing pancreatitis*, *Nonalcoholic + destructive pancreatitis*. +- **One pre-existing bug noted for a curator, not fixed here:** ARI:0001031 is labelled + *Autoimmune gastritis* but its `rdfs:comment` describes autoimmune enteropathy. +- Batches 2+ (the remaining ~121 diseases with synonyms) follow once this rubric is + confirmed. + ## fix-ms-omop-and-lost-judgments - **Corrects an error `restore-overwritten-curation` introduced.** OMOP `4027727` is diff --git a/ontologies/ari_t1d.owl b/ontologies/ari_t1d.owl index e26add6..79802fb 100644 --- a/ontologies/ari_t1d.owl +++ b/ontologies/ari_t1d.owl @@ -184,6 +184,8 @@ + + @@ -1926,9 +1928,9 @@ 83942000, 72986009 Acute disseminated encephalomyelitis (ADEM) is caused when inflammation stemming from fever or immunization damages the myelin sheaths of nerves in the brain, spinal cord, and occasionally the optic nerves, leading to abnormal nerve function. Onset is brief but intense and occurs predominantly in children. Patients often experience complete recovery within 6 months and do not experience relapses. The risk of developing ADEM depends on several factors, including genetics, exposure to infectious organisms, immunization exposure, and lighter skin pigmentation. ADEM can affect people of all ethnic backgrounds globally. Between 50% to 85% of ADEM cases are linked to a prior infection or vaccination, with many following a viral or bacterial infection. Nonetheless, the specific pathogen causing ADEM is often unknown. ADEM - Nonvasculitic autoimmune inflammatory meningoencephalitis - Hurst's disease - Weston-Hurst syndrome + Nonvasculitic autoimmune inflammatory meningoencephalitis | distinct | NAIM/SREAT-spectrum steroid-responsive encephalopathy, a different entity from ADEM + Hurst's disease | subtype | eponym for acute haemorrhagic leukoencephalitis, the hyperacute haemorrhagic variant of ADEM (subtype "Hyperacute/Fulminant ADEM") + Weston-Hurst syndrome | subtype | eponym for acute haemorrhagic leukoencephalitis, the hyperacute haemorrhagic variant of ADEM (subtype "Hyperacute/Fulminant ADEM") Filippi and Rocca 2020; https://link.springer.com/chapter/10.1007/978-3-030-38621-4_5; Tenembaum 2002; https://pubmed.ncbi.nlm.nih.gov/12391351/ https://pubmed.ncbi.nlm.nih.gov/12391351/ Antibody @@ -1960,6 +1962,7 @@ 2026-07-13 03:09 | user | Edited: orphanet 374021 2026-08-30T20:37:56+00:00 | KrishnaTO | Cross-reference review: confirmed MONDO 0019383; confirmed ICD10 G04.0; confirmed ORPHANET 83597 + 2026-09-07 | Claude | Synonym review: withdrew "Nonvasculitic autoimmune inflammatory meningoencephalitis" (distinct entity) and "Hurst's disease" / "Weston-Hurst syndrome" (name the hyperacute haemorrhagic variant AHLE; covered by subtype "Hyperacute/Fulminant ADEM"). @@ -2334,8 +2337,8 @@ The cause of Kawasaki's Disease is uncertain but is believed to be autoimmune. C26689 Addison's disease is a hormonal disorder that occurs when the adrenal glands do not produce enough of certain hormones. The two hormones that tend to be affected the most are cortisol and aldosterone. Symptoms may occur slowly over several months, and most people do not realize these are symptoms of Addison’s and ignore them. Early symptoms include fatigue, dizziness or fainting due to low blood pressure, sweating due to low blood sugar, upset stomach, abdominal pain, and muscle cramps or weakness. If symptoms become worse quickly, then it can develop into an adrenal crisis, resulting in death if not treated quickly enough. Autoimmune adrenalitis - Adrenal Insufficiency - Adrenal cortical hypofunction + Adrenal Insufficiency | broader | umbrella term including secondary/tertiary and non-autoimmune adrenal insufficiency + Adrenal cortical hypofunction | broader | parent class of Addison's disease in the Disease Ontology; covers non-autoimmune causes Primary adrenal insufficiency Olaffson 2016; https://pubmed.ncbi.nlm.nih.gov/26437215/ https://pubmed.ncbi.nlm.nih.gov/26437215/ @@ -2371,6 +2374,7 @@ The cause of Kawasaki's Disease is uncertain but is believed to be autoimmune. 2026-07-22 15:39 | user | Edited: orphanet 363732003 2026-08-30T20:37:56+00:00 | KrishnaTO | Cross-reference review: confirmed ORPHANET 85138 + 2026-09-07 | Claude | Synonym review: withdrew "Adrenal Insufficiency" and "Adrenal cortical hypofunction" as broader parent concepts of the autoimmune disease. @@ -3008,8 +3012,8 @@ However, based on the research available at this time, there is no evidence that 437082 9631008 Ankylosing spondylitis, a form of arthritis, triggers inflammation in the spine's joints and ligaments, potentially extending to peripheral joints such as knees, ankles, and hips. Typically, these spinal joints and ligaments facilitate movement and flexibility. However, in ankylosing spondylitis, inflammation can induce stiffness. In severe instances, this inflammation may prompt the vertebrae to fuse together, resulting in a rigid and immobile spine. Although there's no cure, various treatments can manage symptoms effectively. These may encompass exercises, physical or occupational therapy to enhance mobility and posture, and medications to alleviate pain, reduce inflammation, improve posture, and slow disease progression. With appropriate treatment, individuals with ankylosing spondylitis can lead fulfilling lives. - Axial spondyloarthritis - Spondyloarthritis + Axial spondyloarthritis | broader | parent concept; ankylosing spondylitis is the radiographic subtype of axial spondyloarthritis + Spondyloarthritis | broader | disease family (includes psoriatic, reactive, enteropathic and peripheral spondyloarthritis) Bakland 2005 ; https://onlinelibrary.wiley.com/doi/full/10.1002/art.21577 Unconfirmed Unconfirmed @@ -3037,6 +3041,7 @@ However, based on the research available at this time, there is no evidence that 2026-07-10 18:09 | KrishnaTO | Cross-reference review: flagged ICD10 720.0 825 2026-07-22 15:42 | user | Edited: orphanet + 2026-09-07 | Claude | Synonym review: withdrew "Axial spondyloarthritis" and "Spondyloarthritis" as broader parent concepts. @@ -3165,7 +3170,8 @@ However, based on the research available at this time, there is no evidence that 1 Nervous System 2026-07-02 15:40 | Krishna Udaiwal | Edited: age_range, clinical_subtypes, def_source, definition, demographic_bias, disease_category, doid, evidence_quality, icd10, incidence_rate, mesh, mondo, name, nci, obsolete, omop, prevalence_desc, prevalence_per_100k, prevalence_value, snomed, synonyms, umls - Morvan syndrome + Morvan syndrome | subtype | a specific CASPR2-antibody phenotype (encephalopathy + peripheral nerve hyperexcitability + dysautonomia); already an ARI_ClinicalSubtype + 2026-09-07 | Claude | Synonym review: withdrew "Morvan syndrome" — a CASPR2-antibody phenotype already listed as an ARI_ClinicalSubtype. @@ -3330,10 +3336,10 @@ However, based on the research available at this time, there is no evidence that 722191003, 82275008, 195353004 Anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is a group of diseases characterized by destruction and inflammation of small vessels. The clinical signs vary and affect several organs, such as the kidney, stomach, intestine, and lung. Skin symptoms like purpura (small purple spots) may appear when small blood vessels leak under the skin. AAV occurs when the immune system produces ANCAs, which mistakenly activate neutrophils, a type of white blood cell. These activated neutrophils damage the lining of blood vessels. Though the mechanism of damage is understood, the triggers that lead to AAV are unknown. Anti-neutrophil cytoplasmic antibody-associated vasculitis - Churg Strauss syndrome + Churg Strauss syndrome | subtype | eosinophilic granulomatosis with polyangiitis (EGPA); already an ARI_ClinicalSubtype + Wegener's Granulomatosis | subtype | granulomatosis with polyangiitis (GPA); already an ARI_ClinicalSubtype ANCA-associated vasculitis ANCA vasculitis - Wegener's Granulomatosis Berti 2017; https://pubmed.ncbi.nlm.nih.gov/28881446/; Mohammad 2007; https://pubmed.ncbi.nlm.nih.gov/17553910/ https://pubmed.ncbi.nlm.nih.gov/28881446/ https://pubmed.ncbi.nlm.nih.gov/17553910/ @@ -3364,6 +3370,7 @@ However, based on the research available at this time, there is no evidence that D056648 2026-07-22 15:49 | user | Edited: mesh 2026-07-22 16:03 | KrishnaTO | Cross-reference review: flagged DOID 3049 + 2026-09-07 | Claude | Synonym review: withdrew "Churg Strauss syndrome" (EGPA) and "Wegener's Granulomatosis" (GPA) — subtypes of ANCA-associated vasculitis already listed as ARI_ClinicalSubtypes. @@ -3916,7 +3923,7 @@ The trigger for antisynthetase syndrome is unknown, but it may be associated wit 4337463, 79833 232308006, 13445001 Autoimmune inner ear disease (AIED) is a condition characterized by inflammation of the inner ear. It happens when the immune system mistakenly targets cells in the inner ear as if they were a virus or bacteria. AIED is uncommon, affecting fewer than one percent of the 28 million Americans with hearing loss. The symptoms of AIED are sudden hearing loss in one ear progressing rapidly to the second ear. The hearing loss can progress over weeks or months. It can happen alone or in addition to other systemic autoimmune disorders. - Ménière's disease + Ménière's disease | distinct | separate clinical entity (idiopathic endolymphatic hydrops); autoimmune inner-ear disease is a different diagnosis Vambutas 2016; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5113311/ Immune-mediated Autoimmune @@ -3930,6 +3937,7 @@ The trigger for antisynthetase syndrome is unknown, but it may be associated wit 2024-04 AIE 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Ménière's disease" — a distinct clinical entity, not a synonym for autoimmune inner-ear disease. @@ -4272,12 +4280,12 @@ When the NMDA receptor antibodies attack the NMDA receptors in the brain, certai 192667, 4341626, 432295 84568007, 235728001, 84027009 Autoimmune enteropathy is an extremely rare disease characterized by diarrhea that does not respond to treatment and may require intravenous feeding to sustain the patient. It is diagnosed most frequently in infants, and it is marked by the presence of antibodies to the enzyme tryptophan hydroxylase, which performs a number of functions in human biology, Autoimmune enteropathy is increasingly being diagnosed in adults, but the symptoms are the same as many more common diseases, so correct diagnosis is difficult. It is more frequently diagnosed in patients already diagnosed with other autoimmune diseases such as autoimmune polyendocrine syndrome 1. - Megaloblastic Anemia + Megaloblastic Anemia | non-disease | downstream haematologic consequence of B12 deficiency, not a name for the gastritis + Macrocytic Anemia | non-disease | downstream haematologic consequence of B12 deficiency, not a name for the gastritis + Eosinophilic gastritis | distinct | separate disease in the eosinophilic gastrointestinal disease spectrum + Autoimmune enteropathy | distinct | separate small-bowel disease with anti-enterocyte antibodies Autoimmune atrophic gastritis Atrophic gastritis - Macrocytic Anemia - Eosinophilic gastritis - Autoimmune enteropathy Ruemmele 2015; https://www.sciencedirect.com/topics/immunology-and-microbiology/autoimmune-enteropathy; Toh 1997; https://pubmed.ncbi.nlm.nih.gov/9358143/ https://pubmed.ncbi.nlm.nih.gov/9358143/ Antibody @@ -4293,6 +4301,7 @@ When the NMDA receptor antibodies attack the NMDA receptors in the brain, certai 2025-02 AG 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Megaloblastic Anemia" / "Macrocytic Anemia" (B12-deficiency consequences) and "Eosinophilic gastritis" / "Autoimmune enteropathy" (distinct diseases). @@ -4781,8 +4790,8 @@ Primary neutropenia is diagnosed when there are no other conditions diagnosed. S Primary neutropenia most often appears in infants and children. The cause may be unrelated to autoimmune disease. Most cases of childhood primary neutropenia that are autoimmune are not serious and the disease goes away in 3 to 5 years with no long term effects. However, in a relatively small number of patients, the disease becomes chronic. Adults, mostly women, can also develop primary autoimmune neutropenia after childhood. These cases are almost always chronic. In chronic autoimmune neutropenia the body produces IgG antibodies that target and destroy the body's own white blood cells (“neutrophils”), which leads to a lowered white blood cell count and leaves patients with weakened immune systems susceptible to bacterial and other infections. - Autoimmune neutropenia of infancy - Primary autoimmune neutropenia + Autoimmune neutropenia of infancy | subtype | the benign primary form of infancy/childhood; covered by ARI_ClinicalSubtype "Autoimmune Neutropenia, Primary" + Primary autoimmune neutropenia | subtype | primary/idiopathic form; already an ARI_ClinicalSubtype ("Autoimmune Neutropenia, Primary") Chaudhari 2020; https://pubmed.ncbi.nlm.nih.gov/32809736/ https://pubmed.ncbi.nlm.nih.gov/32809736/ Antibody @@ -4797,6 +4806,7 @@ In chronic autoimmune neutropenia the body produces IgG antibodies that target a 2025-02 AN 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Autoimmune neutropenia of infancy" and "Primary autoimmune neutropenia" — the primary subtype, already an ARI_ClinicalSubtype. @@ -5038,9 +5048,9 @@ In chronic autoimmune neutropenia the body produces IgG antibodies that target a 40490446, 36716715, 37162896 448542008, 722872000, 1197740007 Autoimmune pancreatitis is a rare autoimmune disorder characterized by inflammation of the pancreas that may be acute or chronic. It is thought to be caused by the body's immune system attacking healthy cells of the pancreas. There are two subtypes of AIP, known as type 1 and type 2. Type 1 is the most common and it affects the pancreas, along with other organs, such as the liver, salivary glands, kidneys, lymph nodes, and gallbladder. Type 2 seems to only affect the pancreas but is associated with inflammatory bowel disease. Symptomatic patients often experience yellowing of the eyes (jaundice) and weight loss, but many patients are asymptomatic. Autoimmune pancreatitis is a non-cancerous condition, but it is often mistaken for pancreatic cancer due to similar signs and symptoms. There is no cure, but the condition is well-managed with treatment. - Lymphoplasmocytic sclerosing pancreatitis + Lymphoplasmocytic sclerosing pancreatitis | subtype | histopathological name for type 1 (IgG4-related) AIP; already an ARI_ClinicalSubtype + Nonalcoholic destructive pancreatitis | subtype | idiopathic duct-centric pancreatitis = type 2 AIP; already an ARI_ClinicalSubtype Tumefactive pancreatitis - Nonalcoholic destructive pancreatitis Cai 2017; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5288542/ Immune-mediated Autoimmune @@ -5057,6 +5067,7 @@ In chronic autoimmune neutropenia the body produces IgG antibodies that target a 2024-09 AP 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Lymphoplasmocytic sclerosing pancreatitis" (type 1 AIP) and "Nonalcoholic destructive pancreatitis" (type 2 AIP) — subtypes already listed as ARI_ClinicalSubtypes. From 8cd34b2a54049824c5a09a5afdb1883e9f0e11f9 Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Mon, 7 Sep 2026 18:57:57 -0400 Subject: [PATCH 2/8] Review disease synonyms vs subtypes: batch 2 (ARI:0001036, 0001048-0001067) 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 --- changelog.md | 24 ++++++++++++--- ontologies/ari_t1d.owl | 70 +++++++++++++++++++++++------------------- 2 files changed, 59 insertions(+), 35 deletions(-) diff --git a/changelog.md b/changelog.md index b71191d..39a1b19 100644 --- a/changelog.md +++ b/changelog.md @@ -31,10 +31,26 @@ neutropenia — *Autoimmune neutropenia of infancy*, *Primary autoimmune neutropenia*; Autoimmune pancreatitis — *Lymphoplasmocytic sclerosing pancreatitis*, *Nonalcoholic destructive pancreatitis*. -- **One pre-existing bug noted for a curator, not fixed here:** ARI:0001031 is labelled - *Autoimmune gastritis* but its `rdfs:comment` describes autoimmune enteropathy. -- Batches 2+ (the remaining ~121 diseases with synonyms) follow once this rubric is - confirmed. +- **Batch 2 — 16 diseases (ARI:0001036, 0001048–0001067), 181 synonym strings.** 129 kept, + 21 kept with a note, **31 withdrawn across 8 diseases**: 12 name an existing + `ARI_ClinicalSubtype` (`subtype`), 12 are `NON RARE IN EUROPE: …` Orphanet + epidemiological-classification labels that leaked in as synonyms (`non-disease`), 4 name a + different disease (`distinct`), 3 a broader parent (`broader`). No `ARI_ClinicalSubtype` + lines added or rewritten. +- Batch 2 withdrawn: Autoimmune urticaria — *Chronic idiopathic urticaria*, + *Chronic urticaria* (broader), *Physical urticaria* (distinct); Behçet's syndrome — + *Hughes-Stovin syndrome* ×2 (a rare vascular variant); Benign mucous membrane pemphigoid — + *Ocular pemphigoid*; Cataplexy and narcolepsy — 8 NT1 / NT2 / HCRT-locus / *narcolepsy 1* + strings; Celiac disease — 9 *NON RARE IN EUROPE: …* strings; Chronic Fatigue Syndrome — + 3 *NON RARE IN EUROPE: …* strings; Chronic interstitial cystitis — *ulcerative cystitis*; + Chronic Lyme disease — *Lyme Borreliosis*, *Lyme Arthritis*, *Erythema Migrans with + Polyarthritis* (the active infection), *Lyme disease* (broader). +- **Pre-existing bugs noted for a curator, not fixed here:** ARI:0001031 is labelled + *Autoimmune gastritis* but its `rdfs:comment` describes autoimmune enteropathy; ARI:0001065 + *Chronic Lyme disease* has a definition describing the acute tick-borne infection; several + large synonym lists (celiac, CFS, CIDP, cold agglutinin) carry dozens of MeSH permuted + forms that are kept but add little. +- Batches 3+ (the remaining ~120 diseases with synonyms) follow in the same style. ## fix-ms-omop-and-lost-judgments diff --git a/ontologies/ari_t1d.owl b/ontologies/ari_t1d.owl index 79802fb..52a10d3 100644 --- a/ontologies/ari_t1d.owl +++ b/ontologies/ari_t1d.owl @@ -5563,9 +5563,9 @@ Several names are used for autoimmune thyroiditis. When it is known to be autoim Autoimmune urticaria occurs when the immune system attacks the normal tissues of the body, resulting in hives. The condition becomes chronic when the lesions persists longer than 6 weeks. Chronic autoimmune urticaria has been found to be associated with autoimmune thyroid disease. Urticaria can also be caused by allergic reaction to plants like poison ivy, dyes found in clothing, and cosmetics. An allergic reaction is not an autoimmune disease because there is no involvement by the adaptive immune system and auto-antibodies that attack your own cells are not involved. There are antibodies (IgE antibodies), but they target the invading molecules (e.g., poison ivy), not the cells in the skin. In autoimmune urticaria, the antibodies created are attacking the skin itself, not an invading molecule. - Chronic idiopathic urticaria - Physical urticaria - Chronic urticaria + Chronic idiopathic urticaria | broader | chronic spontaneous/idiopathic urticaria is the parent category; autoimmune urticaria is a subset with functional autoantibodies + Physical urticaria | distinct | the inducible/physical urticarias (dermographism, cold, cholinergic, pressure) are a mechanistically separate category, not autoimmune urticaria + Chronic urticaria | broader | umbrella term (DOID:0080747) with chronic spontaneous and chronic inducible urticaria as children Zuberbier 2010; https://pubmed.ncbi.nlm.nih.gov/20456386/ https://pubmed.ncbi.nlm.nih.gov/20456386/ Antibody @@ -5590,6 +5590,7 @@ Urticaria can also be caused by allergic reaction to plants like poison ivy, dye C1304191 2026-07-11 04:10 | user | Edited: umls 2026-07-11 04:34 | KrishnaTO | Cross-reference review: confirmed SNOMED 402397006; confirmed OMOP 4224623; flagged DOID 0080747; flagged MESH D000080223 + 2026-09-07 | Claude | Synonym review: withdrew "Chronic idiopathic urticaria" and "Chronic urticaria" (broader parent categories) and "Physical urticaria" (the inducible urticarias, a separate category). @@ -5958,8 +5959,8 @@ There are many types of vasculitis, and most of them are rare. Vasculitis might This disease is not well understood but is believed to be autoimmune in nature since the symptoms are due to vasculitis. Researchers have also found several genes to be associated with Behçet’s and believe that those with these genes can trigger Behçet’s if they are exposed to a virus or bacterium. Morbus Adamandiades-Behçet - Hughes-Stovin syndrome - Hughes Stovin syndrome + Hughes-Stovin syndrome | subtype | rare vascular variant of Behcet disease (pulmonary artery aneurysms with venous thrombosis); has its own nosologic status but is described as within the Behcet spectrum + Hughes Stovin syndrome | subtype | rare vascular variant of Behcet disease (pulmonary artery aneurysms with venous thrombosis); has its own nosologic status but is described as within the Behcet spectrum Behçet's disease Behcet's syndrome Calamia 2009 and Mohammad 2013. ; https://pubmed.ncbi.nlm.nih.gov/19405011/ @@ -5989,6 +5990,7 @@ This disease is not well understood but is believed to be autoimmune in nature s 2026-07-11 16:53 | KrishnaTO | Cross-reference review: confirmed SNOMED 310701003; confirmed OMOP 436642; confirmed DOID 13241; confirmed NCI C34416; confirmed ICD10 M35.2; confirmed UMLS C0004943; confirmed MESH D001528; flagged SNOMED 721226005; flagged OMOP 36715522 310701003 436642 + 2026-09-07 | Claude | Synonym review: withdrew "Hughes-Stovin syndrome" / "Hughes Stovin syndrome" - a rare vascular variant of Behcet disease, not a synonym for it. @@ -6155,7 +6157,7 @@ This disease is not well understood but is believed to be autoimmune in nature s Cicatricial pemphigoid is a rare autoimmune disease, discovered in 2002, that causes blistering of the mucous membranes. This blistering is due to autoantibodies binding to anchoring filaments of the epidermis. A common mucous membrane that is affected is the conjunctiva of the eye. Other areas that can be affected include the skin, nose, mouth, and genitals. Cicatricial pemphigoid is usually not chronic, and most patients symptoms disappear within 3 years. - Ocular pemphigoid + Ocular pemphigoid | subtype | the eye-restricted form (ocular cicatricial pemphigoid); covered by existing subtype "Benign Mucous Membrane Pemphigoid, Ocular" Cicatricial pemphigoid Scarring pemphigoid Mucous membrane pemphigoid @@ -6180,6 +6182,7 @@ Cicatricial pemphigoid is usually not chronic, and most patients symptoms disapp 2026-07-11 16:53 | KrishnaTO | Cross-reference review: confirmed SNOMED 34250006; confirmed OMOP 4142060; confirmed DOID 11656; confirmed NCI C34907; confirmed ICD10 L12.1; confirmed UMLS C0030804; confirmed MESH D010390; flagged SNOMED 314757003; flagged OMOP 4152707 34250006 4142060 + 2026-09-07 | Claude | Synonym review: withdrew "Ocular pemphigoid" - the eye-restricted form, already an ARI_ClinicalSubtype. @@ -6456,7 +6459,14 @@ Cicatricial pemphigoid is usually not chronic, and most patients symptoms disapp Narcolepsy is a neurologic condition that causes a person to experience extreme sleepiness during the day without warning. When combined with cataplexy, a similar onset of muscle weakness, the condition is sometimes called narcolepsy type 1 and is suspected of being caused when the immune system attacks an important chemical in brain cells called hypocretin. The destruction of this chemical leads to the symptoms experienced by patients. The first reports of narcolepsy being an autoimmune disease came in 2013, but retraction of that paper in 2014 put its status in doubt. Subsequent research and identification of the molecular mechanism by Mahoney et al. provides evidence and justifies classification as an autoimmune disease. - Narcolepsy type 1 + Narcolepsy type 1 | subtype | NT1 (narcolepsy with cataplexy / hypocretin deficiency); already an ARI_ClinicalSubtype "Narcolepsy Type 1" + Narcolepsy, without cataplexy | subtype | NT2; already an ARI_ClinicalSubtype "Narcolepsy Type 2" + narcolepsy with cataplexy | subtype | = NT1; already an ARI_ClinicalSubtype "Narcolepsy Type 1" + narcolepsy-cataplexy syndrome | subtype | maps to the NT1 concept (MONDO:0016158) and is already an ARI_ClinicalSubtype + Hypocretin/orexin deficiency syndrome | subtype | defines NT1 specifically (low CSF hypocretin-1); already covered by ARI_ClinicalSubtype "Narcolepsy Type 1" + narcolepsy caused by mutation in HCRT | subtype | narcolepsy 7 (HCRT gene); already an ARI_ClinicalSubtype "narcolepsy 7" + HCRT narcolepsy | subtype | narcolepsy 7 (HCRT gene); already an ARI_ClinicalSubtype "narcolepsy 7" + narcolepsy 1 | subtype | the classic HLA-associated locus; already an ARI_ClinicalSubtype "narcolepsy 1" Scheer 2017; https://pubmed.ncbi.nlm.nih.gov/31004158/ https://pubmed.ncbi.nlm.nih.gov/31004158/ Antibody @@ -6510,18 +6520,12 @@ The first reports of narcolepsy being an autoimmune disease came in 2013, but re D009290 193042000 437854 - Narcolepsy, without cataplexy - narcolepsy with cataplexy narcolepsy Narcolepsy-cataplexy - narcolepsy-cataplexy syndrome - Hypocretin/orexin deficiency syndrome paroxysmal sleep Gelineau's syndrome Gelineau disease Gelineau syndrome - narcolepsy caused by mutation in HCRT - HCRT narcolepsy Narcoleptic Syndrome Syndrome, Gelineau's Syndromes, Gelineau's @@ -6531,7 +6535,6 @@ The first reports of narcolepsy being an autoimmune disease came in 2013, but re Gelineau's Syndromes Narcoleptic Syndromes Syndrome, Gelineau - narcolepsy 1 Sleep, Paroxysmal Syndromes, Narcoleptic narcolepsy 7 - subtype of Cataplexy and narcolepsy (MONDO:0013652) @@ -6541,6 +6544,7 @@ The first reports of narcolepsy being an autoimmune disease came in 2013, but re Gelineau Syndrome Gelineau's Syndrome narcolepsy-cataplexy syndrome - subtype of Cataplexy and narcolepsy (MONDO:0016158) + 2026-09-07 | Claude | Synonym review: withdrew 8 strings naming narcolepsy subtypes (NT1 / NT2 / HCRT-locus / narcolepsy 1) that are already listed as ARI_ClinicalSubtypes; kept the umbrella synonyms (narcolepsy, Gelineau syndrome, etc.). @@ -6678,25 +6682,25 @@ CD is generally treated by eliminating gluten from the diet. Patients with an e 396331005 194992 Sprue, Nontropical - NON RARE IN EUROPE: Nontropical sprue - NON RARE IN EUROPE: Coeliac sprue + NON RARE IN EUROPE: Nontropical sprue | non-disease | Orphanet epidemiological-classification label that leaked in as a synonym + NON RARE IN EUROPE: Coeliac sprue | non-disease | Orphanet epidemiological-classification label that leaked in as a synonym + NON RARE IN EUROPE: Coeliac disease | non-disease | Orphanet epidemiological-classification label that leaked in as a synonym + NON RARE IN EUROPE: Gluten intolerance | non-disease | Orphanet epidemiological-classification label that leaked in as a synonym + NON RARE IN EUROPE: Celiac disease | non-disease | Orphanet epidemiological-classification label that leaked in as a synonym + NON RARE IN EUROPE: Celiac sprue | non-disease | Orphanet epidemiological-classification label that leaked in as a synonym + NON RARE IN EUROPE: Idiopathic steatorrhea | non-disease | Orphanet epidemiological-classification label that leaked in as a synonym + NON RARE IN EUROPE: Gluten-sensitive enteropathy | non-disease | Orphanet epidemiological-classification label that leaked in as a synonym + NON RARE IN EUROPE: Gluten-induced enteropathy | non-disease | Orphanet epidemiological-classification label that leaked in as a synonym coeliac sprue Enteropathy, Gluten-Sensitive Sprue, Celiac - NON RARE IN EUROPE: Coeliac disease - NON RARE IN EUROPE: Gluten intolerance Enteropathies, Gluten-Sensitive idiopathic steatorrhea Disease, Celiac Sprue gluten intolerance - NON RARE IN EUROPE: Celiac disease - NON RARE IN EUROPE: Celiac sprue Gluten-Sensitive Enteropathies - NON RARE IN EUROPE: Idiopathic steatorrhea Gluten Enteropathies - NON RARE IN EUROPE: Gluten-sensitive enteropathy - NON RARE IN EUROPE: Gluten-induced enteropathy Enteropathies, Gluten non tropical sprue Gluten Enteropathy @@ -6707,6 +6711,7 @@ CD is generally treated by eliminating gluten from the diet. Patients with an e Latent Celiac Disease - subtype of Celiac disease (NCIT:C45425) 2026-08-15 22:37 | KrishnaTO | Cross-reference review: confirmed SNOMED 396331005; confirmed OMOP 194992; confirmed DOID 10608; confirmed MONDO 0005130; confirmed NCI C26714; confirmed ICD10 K90.0; confirmed ORPHANET 555; confirmed UMLS C0007570; confirmed MESH D002446; flagged SNOMED 91867008; flagged OMOP 4241413; flagged ICD10 579.0 2026-08-15 22:38 | KrishnaTO | Enrichment from confirmed cross-references: +24 synonym(s), +4 clinical subtype(s) + 2026-09-07 | Claude | Synonym review: withdrew 9 "NON RARE IN EUROPE: ..." strings - Orphanet epidemiological-classification labels that leaked in as synonyms. Real synonyms (celiac sprue, coeliac disease, gluten-sensitive enteropathy, etc.) kept. @@ -6966,7 +6971,9 @@ The cause of this syndrome is unknown, however, researchers believe that it may Fatigue Syndrome, Postviral Infectious Mononucleosis-Like Syndrome, Chronic Fatigue Syndrome, Chronic - NON RARE IN EUROPE: Myalgic encephalomyelitis + NON RARE IN EUROPE: Myalgic encephalomyelitis | non-disease | Orphanet epidemiological-classification label that leaked in as a synonym + NON RARE IN EUROPE: Chronic fatigue syndrome | non-disease | Orphanet epidemiological-classification label that leaked in as a synonym + NON RARE IN EUROPE: Chronic fatigue immune dysfunction syndrome | non-disease | Orphanet epidemiological-classification label that leaked in as a synonym Postviral Fatigue Syndromes Chronic Fatigue Syndromes Myalgic encephalitis @@ -6978,17 +6985,16 @@ The cause of this syndrome is unknown, however, researchers believe that it may chronic fatigue immune dysfunction syndrome Postviral fatigue syndrome Fatigue Disorder, Chronic - NON RARE IN EUROPE: Chronic fatigue syndrome Fatigue Syndromes, Chronic Fatigue-Fibromyalgia Syndromes, Chronic Chronic Fatigue Disorder Myalgic encephalomyelitis/chronic fatigue syndrome CFS Chronic Fatigue Disorders - NON RARE IN EUROPE: Chronic fatigue immune dysfunction syndrome Encephalomyelitis, Myalgic 0005404 1983 + 2026-09-07 | Claude | Synonym review: withdrew 3 "NON RARE IN EUROPE: ..." strings - Orphanet epidemiological-classification labels that leaked in as synonyms. @@ -7239,7 +7245,7 @@ Currently, the cause of interstitial cystitis is unknown. There are two main the 0018301 37202 C27189 - ulcerative cystitis + ulcerative cystitis | subtype | the classic (Hunner-lesion) form of interstitial cystitis; covered by existing subtype "Chronic Interstitial Cystitis, Hunner's Lesions" IC/BPS IC/PBS Interstitial Cystitides @@ -7249,6 +7255,7 @@ Currently, the cause of interstitial cystitis is unknown. There are two main the interstitial cystitis/bladder pain syndrome Cystitis, Interstitial interstitial cystitis, chronic + 2026-09-07 | Claude | Synonym review: withdrew "ulcerative cystitis" - the Hunner-lesion form, already an ARI_ClinicalSubtype. @@ -7344,10 +7351,10 @@ Currently, the cause of interstitial cystitis is unknown. There are two main the If the disease is detected and treated (with antibiotics) recovery is usually complete and symptoms like Bell’s disappear completely. In these cases, there is no autoimmune disease. However, in some people, the Lyme disease triggers symptoms similar to rheumatoid arthritis. This is called “chronic Lyme disease” and is suspected of being an autoimmune disease. - Lyme Borreliosis - Lyme disease - Lyme Arthritis - Erythema Migrans with Polyarthritis + Lyme Borreliosis | distinct | the active tick-borne Borrelia infection; a different disease from the post-treatment/chronic syndrome this entity represents + Lyme disease | broader | the infection itself (DOID:11729); chronic/post-treatment Lyme is a sequela of it, not a synonym + Lyme Arthritis | distinct | a late manifestation of the Borrelia infection, not the post-treatment syndrome + Erythema Migrans with Polyarthritis | distinct | describes early/disseminated active Lyme disease (the rash plus arthritis), not the chronic syndrome No studies found; CONFIRMED NO DATA Sept 2021 Unconfirmed Unconfirmed @@ -7410,6 +7417,7 @@ However, in some people, the Lyme disease triggers symptoms similar to rheumatoi 19137845 37365579 2026-08-31T02:09:20+00:00 | KrishnaTO | Cross-reference review: confirmed OMOP 19137845; flagged OMOP 440638, 4141757; flagged SNOMED 23502006, 33937009 + 2026-09-07 | Claude | Synonym review: withdrew "Lyme Borreliosis", "Lyme Arthritis", "Erythema Migrans with Polyarthritis" (the active infection / its manifestations) and "Lyme disease" (broader). Kept the post-treatment Lyme disease syndrome synonyms (PTLDS, post-Lyme disease syndrome, etc.). From 73b7101df41b941ffef9fc4324184c34bfade00c Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Mon, 7 Sep 2026 19:03:41 -0400 Subject: [PATCH 3/8] Review disease synonyms vs subtypes: batch 3 (ARI:0001068-0001093) 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 --- changelog.md | 25 ++++++++++-- ontologies/ari_t1d.owl | 91 +++++++++++++++++++++++------------------- 2 files changed, 70 insertions(+), 46 deletions(-) diff --git a/changelog.md b/changelog.md index 39a1b19..700d46f 100644 --- a/changelog.md +++ b/changelog.md @@ -45,12 +45,29 @@ 3 *NON RARE IN EUROPE: …* strings; Chronic interstitial cystitis — *ulcerative cystitis*; Chronic Lyme disease — *Lyme Borreliosis*, *Lyme Arthritis*, *Erythema Migrans with Polyarthritis* (the active infection), *Lyme disease* (broader). +- **Batch 3 — 17 diseases (ARI:0001068–0001093), 125 synonym strings.** 60 kept, 23 kept + with a note, **42 withdrawn across 7 diseases**: 20 name a broader parent (`broader`), + 13 name an existing `ARI_ClinicalSubtype` (`subtype`), 7 name a different disease + (`distinct`), 2 are `NON RARE IN EUROPE: …` / complication strings (`non-disease`). +- Batch 3 withdrawn: Cold agglutinin disease — 16 strings naming autoimmune haemolytic + anaemia in general (CAD is its cold-agglutinin subtype); Complex regional pain syndrome — + *Amplified musculoskeletal pain syndrome* (distinct) and the CRPS type-1/type-2 names + (*Causalgia*, *CRPS I*, …); Crohn's disease — the location forms (*Crohn's colitis*, + *Ileocolitis*, *Gastroduodenal Crohn's disease*, *Illeitis*), *Crohn disease-associated + growth failure*, *NON RARE IN EUROPE: Crohn disease*; Cryptogenic organizing pneumonia — + broader interstitial-pneumonia terms and two names for IPF (*Idiopathic fibrosing + alveolitis*, *Diffuse idiopathic pulmonary fibrosis*); Cutaneous lupus erythematosus — + the *Discoid lupus* strings (a subtype); Endometriosis — all four synonyms, which name + *adenomyosis* (a separate diagnosis); Erythema nodosum — *Idiopathic erythema nodosum*. - **Pre-existing bugs noted for a curator, not fixed here:** ARI:0001031 is labelled *Autoimmune gastritis* but its `rdfs:comment` describes autoimmune enteropathy; ARI:0001065 - *Chronic Lyme disease* has a definition describing the acute tick-borne infection; several - large synonym lists (celiac, CFS, CIDP, cold agglutinin) carry dozens of MeSH permuted - forms that are kept but add little. -- Batches 3+ (the remaining ~120 diseases with synonyms) follow in the same style. + *Chronic Lyme disease* has a definition describing the acute tick-borne infection; + ARI:0001076 *Cutaneous lupus erythematosus* has a definition describing discoid lupus; + ARI:0001069 and ARI:0001074 carry many mis-imported sibling diseases in their + `ARI_ClinicalSubtype` lists (whole AIHA / interstitial-pneumonia families); several large + synonym lists (celiac, CFS, CIDP, cold agglutinin) carry dozens of MeSH permuted forms + that are kept but add little. +- Batches 4+ (the remaining ~110 diseases with synonyms) follow in the same style. ## fix-ms-omop-and-lost-judgments diff --git a/ontologies/ari_t1d.owl b/ontologies/ari_t1d.owl index 52a10d3..31ef357 100644 --- a/ontologies/ari_t1d.owl +++ b/ontologies/ari_t1d.owl @@ -8163,7 +8163,22 @@ More study is needed. Cold agglutinin disease is a type of autoimmune hemolytic anemia in which the body's immune system attacks and destroys its own red blood cells. Unlike warm autoimmune hemolytic anemia, the autoimmune destruction of cells occurs when a person is exposed to cold, or their body temperature is below normal. Some patients experience heart problems because the heart has to work harder to make sure the body gets enough healthy red blood cells CAD Cold autoimmune hemolytic anemia - Anemia + Anemia | broader | bare 'anemia' is the broad category, not a name for cold agglutinin disease + autoimmune hemolytic anemia | broader | AIHA is the parent; cold agglutinin disease is its cold-antibody subtype (warm AIHA is the other main type) + autoimmune hemolytic anemia, cold type | broader | cold-type AIHA (MONDO:0016450) also covers paroxysmal cold haemoglobinuria and mixed-type; broader than cold agglutinin disease proper + autoimmune hemolytic anaemia | broader | AIHA is the parent category, not a synonym of cold agglutinin disease + autoimmune haemolytic anemia | broader | AIHA is the parent category, not a synonym of cold agglutinin disease + Autoimmune haemolytic anaemia | broader | AIHA is the parent category, not a synonym of cold agglutinin disease + AIHA | broader | abbreviation for autoimmune haemolytic anaemia, the parent category + AHA | broader | abbreviation for autoimmune haemolytic anaemia, the parent category + Anaemia, Autoimmune Haemolytic | broader | permuted AIHA, the parent category + Anemia, Autoimmune Hemolytic | broader | permuted AIHA, the parent category + Anemia, Hemolytic, Autoimmune | broader | permuted AIHA, the parent category + Anemia, Hemolytic, Acquired Autoimmune | broader | permuted AIHA, the parent category + Hemolytic Anemia, Autoimmune | broader | permuted AIHA, the parent category + Haemolytic Anaemia, Autoimmune | broader | permuted AIHA, the parent category + Autoimmune Hemolytic Anemias | broader | permuted/plural AIHA, the parent category + Autoimmune Haemolytic Anaemias | broader | permuted/plural AIHA, the parent category Cold antibody disease hemolytic cold antibody Cold antibody hemolytic anemia @@ -8219,21 +8234,6 @@ More study is needed. cold agglutinin syndrome cold AIHA chronic cold agglutinin disease - autoimmune hemolytic anemia, cold type - Anaemia, Autoimmune Haemolytic - autoimmune hemolytic anemia - Anemia, Hemolytic, Acquired Autoimmune - Anemia, Autoimmune Hemolytic - autoimmune hemolytic anaemia - autoimmune haemolytic anemia - Anemia, Hemolytic, Autoimmune - Hemolytic Anemia, Autoimmune - Autoimmune Hemolytic Anemias - Haemolytic Anaemia, Autoimmune - AHA - Autoimmune haemolytic anaemia - AIHA - Autoimmune Haemolytic Anaemias Primary Cold Agglutinin Disease - subtype of Cold agglutinin disease (NCIT:C199387) paroxysmal cold hemoglobinuria - subtype of Cold agglutinin disease (MONDO:0019533) mixed-type autoimmune hemolytic anemia - subtype of Cold agglutinin disease (MONDO:0019534) @@ -8243,6 +8243,7 @@ More study is needed. drug-induced autoimmune hemolytic anemia - subtype of Cold agglutinin disease (MONDO:0019535) neonatal autoimmune hemolytic anemia - subtype of Cold agglutinin disease (MONDO:0018358) autoimmune hemolytic anemia, cold type - subtype of Cold agglutinin disease (MONDO:0016450) + 2026-09-07 | Claude | Synonym review: withdrew 16 strings that name autoimmune haemolytic anaemia in general (AIHA and its permutations), cold-type AIHA (broader than CAD), or bare 'anemia'. Cold agglutinin disease is the chronic cold-agglutinin subtype of AIHA; kept the CAD-specific synonyms (CAD, CAS, cold agglutinin syndrome, chronic cold agglutinin disease, etc.). @@ -8420,7 +8421,11 @@ More study is needed. D020918 C206547 Complex regional pain syndrome (CRPS) and amplified musculoskeletal pain syndromes (AMPS) are chronic pain conditions lasting at least 6 months. CRPS is often triggered by an injury followed by immobilization, and is marked by pain that does not diminish in a manner typical for the injury. Patients experience unreasonably intense pain in the arms, legs, hands, or feet, both in response to painful and non-painful triggers. Pain can include burning, tingling, or squeezing sensations. Redness and swelling are often present in the affected area. There are two types of CRPS. Patients with CRPS-I/Reflex Sympathetic Dystrophy do not have a confirmed nerve injury, whereas patients with CRPS-II/Causalgia do have an associated, confirmed nerve injury. CRPS usually occurs after an injury that caused damage to the nervous system. The cause is unknown but there are correlations with immune processes that result in swelling surrounding injury. Treatments are available to manage symptoms, which help some patients, but not all. Younger patients are more likely to recover than older patients, whose pain may persist and lead to disability.There is no known cause, and autoimmunity is suspected, but no evidence of autoimmunity has been definitively linked to CRPS. - Amplified musculoskeletal pain syndrome + Amplified musculoskeletal pain syndrome | distinct | AMPS is a separate (largely paediatric) chronic-pain construct; the ARI definition itself lists 'CRPS and AMPS' as two conditions + Causalgia | subtype | the historical name for CRPS type 2 (pain with a defined nerve lesion); already an ARI_ClinicalSubtype 'CRPS Type 2' + Complex regional pain syndrome I | subtype | CRPS type 1; already an ARI_ClinicalSubtype 'CRPS Type 1' + complex regional pain syndrome type 1 | subtype | CRPS type 1; already an ARI_ClinicalSubtype 'CRPS Type 1' + CRPS I | subtype | CRPS type 1; already an ARI_ClinicalSubtype 'CRPS Type 1' Sandroni 2003; https://pubmed.ncbi.nlm.nih.gov/12749974/ https://pubmed.ncbi.nlm.nih.gov/12749974/ Unconfirmed @@ -8472,20 +8477,17 @@ More study is needed. algoneurodystrophy Complex regional pain syndromes CRPS (Complex Regional Pain Syndromes) - Causalgia CRPS Sudeck's atrophy Algodystrophy - Complex regional pain syndrome I - complex regional pain syndrome type 1 reflex neurovascular dystrophy - CRPS I reflex sympathetic dystrophy syndrome complex regional pain syndrome type 2 - subtype of Complex regional pain syndrome (MONDO:0020572) Complex Regional Pain Syndrome I - subtype of Complex regional pain syndrome (NCIT:C85042) Complex Regional Pain Syndrome II - subtype of Complex regional pain syndrome (NCIT:C121572) complex regional pain syndrome type 1 - subtype of Complex regional pain syndrome (MONDO:0011441) M89.0 + 2026-09-07 | Claude | Synonym review: withdrew 'Amplified musculoskeletal pain syndrome' (a separate pain construct) and the CRPS-type-1 / CRPS-type-2 names ('Causalgia', 'CRPS I', etc.) that are already ARI_ClinicalSubtypes. Kept the historical whole-disease names (reflex sympathetic dystrophy, Sudeck's atrophy, algodystrophy). @@ -8630,12 +8632,13 @@ Both UC and CD are caused by an autoimmune response that reflects the involvemen 1110689.0 15-35 years ARI:0001073 - Gastroduodenal Crohn's disease + Gastroduodenal Crohn's disease | subtype | the upper-GI (L4) location form; already an ARI_ClinicalSubtype 'Crohn’s Disease, Gastroduodenal' and a DOID child + Crohn's colitis | subtype | the colonic (L2) location form; already an ARI_ClinicalSubtype 'Crohn’s Disease, Colonic' and a MONDO/DOID child + Ileocolitis | subtype | the ileocolonic (L3) location form; a DOID child of Crohn's disease + Illeitis | subtype | misspelling of 'ileitis', the ileal (L1) location form; a DOID child of Crohn's disease + Crohn disease-associated growth failure | non-disease | a paediatric complication of Crohn's disease, not a name for it + NON RARE IN EUROPE: Crohn disease | non-disease | Orphanet epidemiological-classification label that leaked in as a synonym Crohn's granulomatous - Ileocolitis - Illeitis - Crohn's colitis - Crohn disease-associated growth failure Granulomatous Colitis inflammatory bowel disease caused by mutation in NOD2 inflammatory bowel disease 1, Crohn disease @@ -8649,7 +8652,6 @@ Both UC and CD are caused by an autoimmune response that reflects the involvemen inflammatory bowel disease type 1 paediatric Crohn's disease Crohn disease - NON RARE IN EUROPE: Crohn disease Crohn's Enteritis Crohns Disease Inflammatory Bowel Disease 1 @@ -8710,6 +8712,7 @@ Both UC and CD are caused by an autoimmune response that reflects the involvemen 266600 206 2026-09-03T00:46:11+00:00 | KrishnaTO | Removed flagged cross-reference: UMLS C0156147 + 2026-09-07 | Claude | Synonym review: withdrew the location-based forms ('Gastroduodenal Crohn's disease', 'Crohn's colitis', 'Ileocolitis', 'Illeitis') which are subtypes/children, 'Crohn disease-associated growth failure' (a complication), and the 'NON RARE IN EUROPE:' Orphanet label. Kept 'regional enteritis', the IBD1 genetic-locus names, and 'pediatric Crohn's disease' (a MONDO exact synonym). @@ -8805,16 +8808,16 @@ Both UC and CD are caused by an autoimmune response that reflects the involvemen 27506.0 40-60 years ARI:0001074 - Interstitial pneumonia + Interstitial pneumonia | broader | the whole interstitial-pneumonia category; cryptogenic organizing pneumonia is one member + idiopathic interstitial pneumonia | broader | the idiopathic interstitial pneumonia (IIP) group; COP is one of its members + idiopathic interstitial pneumonitis | broader | variant spelling of the IIP group name + noninfectious pneumonia | broader | a very broad category, not a synonym for cryptogenic organizing pneumonia + Idiopathic fibrosing alveolitis | distinct | an old name for idiopathic pulmonary fibrosis (IPF), a different idiopathic interstitial pneumonia + Diffuse idiopathic pulmonary fibrosis | distinct | idiopathic pulmonary fibrosis (IPF), a different idiopathic interstitial pneumonia Bronchiolitis obliterans with organizing pneumonia - idiopathic interstitial pneumonia organising pneumonia cryptogenic organizing pneumonitis - Idiopathic fibrosing alveolitis - idiopathic interstitial pneumonitis - noninfectious pneumonia COP - Diffuse idiopathic pulmonary fibrosis Organizing Pneumonia bronchiolitis obliterans organizing pneumonia BOOP @@ -8865,6 +8868,7 @@ Both UC and CD are caused by an autoimmune response that reflects the involvemen COP 1302 2026-09-03T00:46:11+00:00 | KrishnaTO | Removed flagged cross-reference: NCI C35806; ICD10 J84.114; UMLS C0085786; MESH D000080203 + 2026-09-07 | Claude | Synonym review: withdrew broader category terms ('Interstitial pneumonia', 'idiopathic interstitial pneumonia/pneumonitis', 'noninfectious pneumonia') and two names for IPF ('Idiopathic fibrosing alveolitis', 'Diffuse idiopathic pulmonary fibrosis'), a different interstitial pneumonia. Kept COP / BOOP / organising pneumonia. @@ -8926,9 +8930,9 @@ Both UC and CD are caused by an autoimmune response that reflects the involvemen 7119001 0050169 Discoid lupus erythematosus, also referred to as DLE, is a chronic but localized skin condition where sores (lesions) form on the scalp, face, elbow, or fingertips. In DLE, the autoimmune system attacks connective tissue. The lesions are red, inflamed patches with a scaling and crusting appearance. If present in areas with a significant amount of hair, the lesions can cause scarring and hair loss in that area. Because the symptoms are similar to other skin diseases and other types of lupus, a skin biopsy must be performed to confirm a diagnosis. The primary difference between discoid lupus erythematosus (DLE) and systemic lupus erythematosus (SLE) is that DLE mainly affects the skin, while SLE also affects the organs, such as the heart, blood vessels, nervous system, and kidneys. Patients can have both DLE and SLE. - Discoid lupus erythematosus of oral mucosa - Discoid lupus - Discoid lupus erythematosus + Discoid lupus erythematosus | subtype | discoid LE = chronic cutaneous lupus, a subtype of cutaneous lupus erythematosus; already an ARI_ClinicalSubtype 'Cutaneous Lupus, Discoid' and a MONDO child + Discoid lupus | subtype | discoid LE = chronic cutaneous lupus, a subtype; already an ARI_ClinicalSubtype 'Cutaneous Lupus, Discoid' + Discoid lupus erythematosus of oral mucosa | subtype | the oral-mucosa form of discoid LE, a narrow subtype of cutaneous lupus erythematosus Gauzere 2019; https://pubmed.ncbi.nlm.nih.gov/30041816/ https://pubmed.ncbi.nlm.nih.gov/30041816/ Antibody @@ -8977,6 +8981,7 @@ Both UC and CD are caused by an autoimmune response that reflects the involvemen C0024137 0005282 535 + 2026-09-07 | Claude | Synonym review: withdrew the discoid-lupus strings - discoid LE is a subtype of cutaneous lupus erythematosus (already an ARI_ClinicalSubtype), not a synonym for the umbrella. NB the entity's definition text describes discoid lupus - a pre-existing label/definition mismatch for a curator. @@ -9499,10 +9504,10 @@ When mastocytosis is not limited to the skin, it is called systemic mastocytosis 433527 129103003 A disorder where the tissue that normally lines the uterus grows outside of the uterus. The tissue can grow on the ovaries, fallopian tubes, outer wall of the uterus, intestines, or other organs in the belly. - Adenomysis uteri - Endometriosis Uterina - Adenomyometritis - Adenomyosis + Adenomyosis | distinct | adenomyosis (endometrial tissue within the myometrium) is a separate diagnosis from endometriosis (endometrial tissue outside the uterus) + Adenomysis uteri | distinct | misspelling of 'adenomyosis uteri' - adenomyosis, a separate diagnosis from endometriosis + Adenomyometritis | distinct | an old term for adenomyosis, a separate diagnosis from endometriosis + Endometriosis Uterina | distinct | 'endometriosis interna' = adenomyosis in historical usage; a separate diagnosis from endometriosis Eisenberg 2017; https://pubmed.ncbi.nlm.nih.gov/28444957/ https://pubmed.ncbi.nlm.nih.gov/28444957/ Unconfirmed @@ -9522,6 +9527,7 @@ When mastocytosis is not limited to the skin, it is called systemic mastocytosis 2024-09 ENDO 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew all four synonyms - they name adenomyosis (endometrial tissue within the myometrium), a separate diagnosis from endometriosis. Clear import error; the entity is left with no synonyms. @@ -10086,8 +10092,8 @@ When mastocytosis is not limited to the skin, it is called systemic mastocytosis 32861005 Erythema nodosum is a condition that causes the fat layer just beneath the skin to become inflamed, forming swollen bumps 1 to 5 cm across. These bumps most frequently occur on the shins, and sometimes the thighs and forearms as well. The degree of inflammation may vary by day over a period of 3 to 6 weeks, after which time the bumps finally fade. The affected area may appear bruised for a period of up to a few months afterward, but most patients experience a full recovery with no scars. The cause is uncertain but is correlated with an over-reactive immune response following infection, medication, pregnancy, inflammatory conditions, vaccines, and autoimmune or other medical conditions. Treatments are available to relieve discomfort. EN - Idiopathic erythema nodosum - Erythema nodosum of unknown etiology + Idiopathic erythema nodosum | subtype | the idiopathic form; already an ARI_ClinicalSubtype 'Erythema Nodosum, Idiopathic' + Erythema nodosum of unknown etiology | subtype | the idiopathic form; already an ARI_ClinicalSubtype 'Erythema Nodosum, Idiopathic' Requena 2001; https://pubmed.ncbi.nlm.nih.gov/11464178/ https://pubmed.ncbi.nlm.nih.gov/11464178/ Unconfirmed @@ -10106,6 +10112,7 @@ When mastocytosis is not limited to the skin, it is called systemic mastocytosis 2024-09 EN 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew 'Idiopathic erythema nodosum' and 'Erythema nodosum of unknown etiology' - the idiopathic form, already an ARI_ClinicalSubtype. From 041c4ca8d321da2dd363145efe237676bd381f28 Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Mon, 7 Sep 2026 19:06:30 -0400 Subject: [PATCH 4/8] Review disease synonyms vs subtypes: batch 4 (ARI:0003, 0001094-0001114) 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 --- changelog.md | 14 ++++++++++++- ontologies/ari_t1d.owl | 45 +++++++++++++++++++++++------------------- 2 files changed, 38 insertions(+), 21 deletions(-) diff --git a/changelog.md b/changelog.md index 700d46f..497d132 100644 --- a/changelog.md +++ b/changelog.md @@ -67,7 +67,19 @@ `ARI_ClinicalSubtype` lists (whole AIHA / interstitial-pneumonia families); several large synonym lists (celiac, CFS, CIDP, cold agglutinin) carry dozens of MeSH permuted forms that are kept but add little. -- Batches 4+ (the remaining ~110 diseases with synonyms) follow in the same style. +- **Batch 4 — 18 diseases (ARI:0003, 0001094–0001114), 64 synonym strings.** 40 kept, 4 kept + with a note, **20 withdrawn across 5 diseases**: 17 name a manifestation/subtype + (`subtype`), 2 a different disease (`distinct`), 1 a broader parent (`broader`). +- Batch 4 withdrawn: Graves' disease — *Thyrotoxicosis* (broader); Guillain-Barré syndrome — + *Miller-Fisher syndrome* / *MFS* / *Fisher syndrome* (a variant, already a subtype); + Hemophilia B Leyden — *Autoimmune hemophilia B* (acquired haemophilia B, a different + disease); Immune thrombocytopenia — *Immune-mediated thrombotic thrombocytopenic purpura + (iTTP)* (a different disease); Immunoglobulin G4 related disease — 14 organ-manifestation + names (*Riedel's thyroiditis*, *Küttner's tumor*, *Mikulicz's syndrome*, *retroperitoneal + fibrosis* / *Ormond's disease*, *periaortitis*, *inflammatory pseudotumor*, …). +- **Pre-existing note for a curator:** ARI:0001098 *Hemophilia B Leyden* is a genetic + F9-promoter variant; its place in an autoimmune registry is questionable. +- Batches 5+ (the remaining ~90 diseases with synonyms) follow in the same style. ## fix-ms-omop-and-lost-judgments diff --git a/ontologies/ari_t1d.owl b/ontologies/ari_t1d.owl index 31ef357..1edb3ca 100644 --- a/ontologies/ari_t1d.owl +++ b/ontologies/ari_t1d.owl @@ -10808,7 +10808,7 @@ ASA is not a concern except for people trying to conceive. Autoimmune hyperthyroidism Parry disease Graves' hyperthyroidism - Thyrotoxicosis + Thyrotoxicosis | broader | thyrotoxicosis is excess thyroid hormone from any cause (toxic nodular goitre, thyroiditis, factitious, etc.); Graves' disease is one cause Basedow disease Thyrotoxicosis due to Graves' disease Eaton 2011; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717015/ @@ -10840,6 +10840,7 @@ ASA is not a concern except for people trying to conceive. 2026-08-04 18:23 | user | Edited: omim 2026-08-04 18:26 | Jennyzeng25 | Cross-reference review: confirmed SNOMED 353295004; confirmed OMOP 4232076; confirmed DOID 12361; confirmed MONDO 0005364; confirmed NCI C3071; confirmed ICD10 E05.0; confirmed OMIM 275000; confirmed MESH D006111 353295004 + 2026-09-07 | Claude | Synonym review: withdrew "Thyrotoxicosis" - a broader term (excess thyroid hormone from any cause), not a synonym of Graves' disease. Kept the Graves-specific names (toxic diffuse goitre, Basedow disease, Parry disease, autoimmune hyperthyroidism, etc.). @@ -11006,10 +11007,10 @@ ASA is not a concern except for people trying to conceive. D020275 C116345 Acute motor axonal neuropathy (AMAN) is an acute, rare, and variant form of Guillain–Barré syndrome. Guillain–Barré syndrome (GBS) can be divided into demyelinating and axonal subtypes. The axonal subtype is referred to as AMAN. AMAN is characterized pathologically by motor nerve fiber degeneration of variable severity and by sparing of sensory fibers. Therefore, it is a rapid onset of muscle weakness and loss of reflexes. There is little demyelination or lymphocytic inflammation involved. Potential pathophysiological reasons for this paradox may involve axonal conduction failure triggered by antibody assault without actual axonal loss, and axonal abnormalities restricted to the nerve terminal area. - Miller-Fisher syndrome + Miller-Fisher syndrome | subtype | the ophthalmoplegia/ataxia/areflexia variant of GBS; already an ARI_ClinicalSubtype 'GBS, Miller Fisher Syndrome' + MFS | subtype | abbreviation for Miller-Fisher syndrome, a GBS variant; already an ARI_ClinicalSubtype + Fisher syndrome | subtype | = Miller-Fisher syndrome, a GBS variant; already an ARI_ClinicalSubtype Guillain-Barre Syndrome - MFS - Fisher syndrome GBS Martinez-Agredano 2016; https://n.neurology.org/content/78/1_Supplement/P06.148; Sejvar 2011; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5703046/ Antibody @@ -11034,6 +11035,7 @@ ASA is not a concern except for people trying to conceive. 2026-06-15 10:37 | Importer | Imported from ARI core reports 353295004, 40956001 4164770 + 2026-09-07 | Claude | Synonym review: withdrew "Miller-Fisher syndrome" / "MFS" / "Fisher syndrome" - a GBS variant already listed as an ARI_ClinicalSubtype. Kept 'GBS' and the label variant. @@ -11195,13 +11197,14 @@ ASA is not a concern except for people trying to conceive. 1336117005 1076202 NR - Autoimmune hemophilia B + Autoimmune hemophilia B | distinct | acquired haemophilia B (factor IX autoantibodies) is a different disease; haemophilia B Leyden is a genetic F9 promoter variant, not autoimmune 1% of all cases of hemophilia B; NR 2.1 2026-06-15 10:37 | Importer | Imported from ARI core reports 2026-08-21 17:35 | linikujp | Cross-reference review: confirmed MONDO 0850054; confirmed ORPHANET 617930 0850054 617930 + 2026-09-07 | Claude | Synonym review: withdrew "Autoimmune hemophilia B" - that names acquired (autoantibody) haemophilia B, a different disease; haemophilia B Leyden is a genetic F9-promoter variant. NB the entity's autoimmune classification is itself questionable - for a curator. @@ -11744,7 +11747,7 @@ Note that thrombotic thrombocytopenic purpura, TTP, is a ***genetic*** disease t Autoimmune thrombocytopenic purpura ITP Idiopathic thrombocytopenic purpura - Immune-mediated thrombotic thrombocytopenic purpura (iTTP) + Immune-mediated thrombotic thrombocytopenic purpura (iTTP) | distinct | iTTP is caused by ADAMTS13 autoantibodies and is a thrombotic microangiopathy - a different disease from immune thrombocytopenia (ITP) Segal 2006; https://pubmed.ncbi.nlm.nih.gov/16869934/ https://pubmed.ncbi.nlm.nih.gov/16869934/ Antibody @@ -11782,6 +11785,7 @@ Note that thrombotic thrombocytopenic purpura, TTP, is a ***genetic*** disease t 4103532 C0242584 2026-09-01T00:10:35+00:00 | KrishnaTO | Cross-reference review: confirmed UMLS C0398650 + 2026-09-07 | Claude | Synonym review: withdrew "Immune-mediated thrombotic thrombocytopenic purpura (iTTP)" - a different disease (ADAMTS13-autoantibody thrombotic microangiopathy), not a synonym for immune thrombocytopenia. @@ -12020,23 +12024,23 @@ This condition is usually temporary (4-6 weeks) with a full recovery for most pa Immunoglobulin G4 is a type of antibody normally found in humans. However, in some persons, the level of this antibody is elevated and it plays a role in the development of several autoimmune diseases, including myasthenia gravis, pemphigus, autoimmune thrombocytopenic purpura and autoimmune pancreatitis. IgG4-related diseases (IgG4-RD) are complex fibro-inflammatory disorder that can affect any organ. Medical practitioners assign a diagnosis based on symptoms and the organ affected. The primary clinical feature in IgG4-RD entails a tumor-like presentation coupled with tissue-destructive lesions.For more information, see the pages on specific diseases. At this time, not all IgG4 diseases are documented, and many are very rare. However, as this disease profile shows, IgG4-related disease has 19 synonyms and subtypes, so it may be more common as a class than thought. - Idiopathic hypocomplementemic tubulointerstitial nephritis - Mediastinal fibrosis - Periaortitis - Idiopathic retroperitoneal Fibrosis + Idiopathic hypocomplementemic tubulointerstitial nephritis | subtype | the renal (tubulointerstitial nephritis) manifestation of IgG4-related disease + Mediastinal fibrosis | subtype | the fibrosing-mediastinitis manifestation of IgG4-related disease + Periaortitis | subtype | the IgG4-related periaortitis manifestation + Idiopathic retroperitoneal Fibrosis | subtype | = Ormond disease, the retroperitoneal-fibrosis manifestation of IgG4-related disease + Inflammatory pseudotumor | subtype | the IgG4-related inflammatory-pseudotumor (mass-forming) manifestation + Ormond's disease | subtype | = retroperitoneal fibrosis, an IgG4-related disease manifestation + Eosinophilic angiocentric fibrosis | subtype | the sinonasal/orbital manifestation of IgG4-related disease + Retroperitoneal fibrosis | subtype | an IgG4-related disease manifestation (a proportion of cases) + Riedel's thyroiditis | subtype | the thyroid (Riedel/fibrosing thyroiditis) manifestation of IgG4-related disease + Küttner's tumor | subtype | = IgG4-related sialadenitis of the submandibular gland + Periarteritis | subtype | the IgG4-related periarteritis/periaortitis manifestation + Inflammatory aortic aneurysm | subtype | the IgG4-related (inflammatory) aortic-aneurysm manifestation + IgG4-related retroperitoneal fibrosis | subtype | the retroperitoneal-fibrosis manifestation of IgG4-related disease + Mikulicz's syndrome | subtype | = IgG4-related dacryoadenitis and sialadenitis Multifocal fibrosclerosis Hyper-IgG4 disease - Inflammatory pseudotumor - Ormond's disease IgG4-related systemic disease - Eosinophilic angiocentric fibrosis - Retroperitoneal fibrosis - Riedel's thyroiditis - Küttner's tumor - Periarteritis - Inflammatory aortic aneurysm - IgG4-related retroperitoneal fibrosis - Mikulicz's syndrome IgG4-related diseases Opriţă 2017; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5771249/ Antibody @@ -12067,6 +12071,7 @@ At this time, not all IgG4 diseases are documented, and many are very rare. Howe 36717255 D89.84 C4087124 + 2026-09-07 | Claude | Synonym review: withdrew 14 strings naming organ-specific manifestations of IgG4-related disease (Riedel's thyroiditis, Kuttner's tumor, Mikulicz's syndrome, retroperitoneal fibrosis / Ormond disease, periaortitis, inflammatory pseudotumor, etc.) - these are subtypes/manifestations, not synonyms for the whole disease. Kept the whole-disease synonyms (multifocal fibrosclerosis, hyper-IgG4 disease, IgG4-related systemic disease). From 2ebcac56289aadab4528b0d0ad728ca2cf19710a Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Mon, 7 Sep 2026 19:09:38 -0400 Subject: [PATCH 5/8] Review disease synonyms vs subtypes: batch 5 (ARI:0002, 0001115-0001142) 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 --- changelog.md | 12 +++++++++++- ontologies/ari_t1d.owl | 31 ++++++++++++++++++++----------- 2 files changed, 31 insertions(+), 12 deletions(-) diff --git a/changelog.md b/changelog.md index 497d132..d028b2b 100644 --- a/changelog.md +++ b/changelog.md @@ -79,7 +79,17 @@ fibrosis* / *Ormond's disease*, *periaortitis*, *inflammatory pseudotumor*, …). - **Pre-existing note for a curator:** ARI:0001098 *Hemophilia B Leyden* is a genetic F9-promoter variant; its place in an autoimmune registry is questionable. -- Batches 5+ (the remaining ~90 diseases with synonyms) follow in the same style. +- **Batch 5 — 20 diseases (ARI:0002, 0001115–0001142), 70 synonym strings.** 48 kept, 11 kept + with a note, **11 withdrawn across 9 diseases**: 5 `subtype`, 3 `broader`, 3 `distinct`. +- Batch 5 withdrawn: Juvenile RA — *Pediatric rheumatic disease* (broader); Lichen sclerosus — + *Balanitis xerotica obliterans* (the male genital form); Linear IgA dermatosis — + *Chronic bullous dermatosis of childhood* (the childhood form); Lipomatosis dolorosa — + *Juxta-Articular adiposis dolorosa*; Mooren's ulcer — *Peripheral Ulcerative Keratitis*, + *Corneal Ulcer* (broader); MOG antibody disease — *Anti-MAG disease* and its full name + (anti-MAG neuropathy is a different disease — MAG vs MOG); Myocarditis due to autoimmune + disease — *Coxsackie myocarditis* (viral); Myositis — *Juvenile myositis*; Neonatal lupus — + *Congenital heart block due to maternal anti-Ro/SSA and anti-La/SSB* (the cardiac form). +- Batches 6+ (the remaining ~70 diseases with synonyms) follow in the same style. ## fix-ms-omop-and-lost-judgments diff --git a/ontologies/ari_t1d.owl b/ontologies/ari_t1d.owl index 1edb3ca..5d4800c 100644 --- a/ontologies/ari_t1d.owl +++ b/ontologies/ari_t1d.owl @@ -12484,7 +12484,7 @@ Some patients experience full relief from symptoms with medical attention, while JRA Juvenile chronic arthritis Juvenile arthritis - Pediatric rheumatic disease + Pediatric rheumatic disease | broader | covers paediatric lupus, dermatomyositis, vasculitis, etc., not only juvenile arthritis JIA Juvenile idiopathic arthritis Harrold 2017; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5657479/ @@ -12505,6 +12505,7 @@ Some patients experience full relief from symptoms with medical attention, while 2024-09 JRA 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Pediatric rheumatic disease" - a broad category, not a synonym for juvenile idiopathic arthritis. @@ -12687,7 +12688,7 @@ Most papers on lichen planus assume all cases of the disease are autoimmune or d 619430, 4119189 895454001, 25674000 Lichen sclerosus causes patches of skin to look white, thickened and crinkly. It most often affects the skin around the vulva or anus.There is circumstantial evidence that lichen sclerosus is autoimmune but no clear evidence to support it. - Balanitis xerotica obliterans + Balanitis xerotica obliterans | subtype | the male genital (glans/foreskin) form of lichen sclerosus; a subtype (existing 'Lichen Sclerosus, Genital'), has its own DOID term Melnick 2020; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7522895/ Immune-mediated Autoimmune @@ -12706,6 +12707,7 @@ Most papers on lichen planus assume all cases of the disease are autoimmune or d 2024-09 LS 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Balanitis xerotica obliterans" - the male genital form of lichen sclerosus, a subtype rather than a synonym for the whole. @@ -13030,7 +13032,7 @@ Most papers on lichen planus assume all cases of the disease are autoimmune or d 95330001 Linear IgA disease causes blisters to form deep in the skin. It can affect the skin and mucus membranes such as the mouth and genitals. Its name comes from the image produced during a skin biopsy in which a line of IgA antibodies can be found just below the outer layer of skin (the epidermis). Linear IgA bullous disease - Chronic bullous dermatosis of childhood + Chronic bullous dermatosis of childhood | subtype | the childhood form of linear IgA disease; already an ARI_ClinicalSubtype 'Linear IgA Dermatosis, Childhood (Chronic Bullous Disease of Childhood)' Linear IgA disease Fortuna 2012; https://pubmed.ncbi.nlm.nih.gov/22137225/ https://pubmed.ncbi.nlm.nih.gov/22137225/ @@ -13045,6 +13047,7 @@ Most papers on lichen planus assume all cases of the disease are autoimmune or d 2024-09 LID 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Chronic bullous dermatosis of childhood" - the childhood form, already an ARI_ClinicalSubtype. @@ -13190,7 +13193,7 @@ Most papers on lichen planus assume all cases of the disease are autoimmune or d 4324974 71404003 Adiposis dolorosa is characterized by the slow formation of multiple, painful growths consisting of fatty tissue (lipomas) that are found just below the surface of the skin. Pain may vary from mild discomfort when a growth is pressed or touched to severe pain that is disproportionate to the physical findings. - Juxta-Articular adiposis dolorosa + Juxta-Articular adiposis dolorosa | subtype | the juxta-articular type, one of the classical clinical subtypes of adiposis dolorosa (Dercum disease) Fatty tissue rheumatism Adiposis dolorosa Dercum's disease @@ -13210,6 +13213,7 @@ Most papers on lichen planus assume all cases of the disease are autoimmune or d 2024-09 LD 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Juxta-Articular adiposis dolorosa" - a clinical subtype of Dercum disease, not a synonym for the whole. @@ -14135,8 +14139,8 @@ It is under debate whether collagenous and lymphocytic colitis are different pha 435271 22440001 Mooren's Ulcer is a chronic eye condition that causes inflammation where the eye's covering (cornea) joins with the white part of the eye (sclera). This type of inflammation is called Peripheral Ulcerative Keratitis (PUK). These persistent peripheral ulcers of the cornea often spread into and around the eye. There are several variants of this disorder: Aggressive Bilateral Mooren's Ulcers patients usually have an ulcer in one eye and congestion or discharge in the other eye. Pain is milder, and grey patches may develop within 2 mm of the border between the cornea and the white of the eye (limbus). Bilateral Indolent Mooren's Ulcers affect both eyes, with one eye typically showing more severity. Discomfort may occur with minimal inflammation. Unilateral Mooren's ulcers can occur in one or both eyes and is excessively painful. Redness and congestion are apparent, but inflammation is seen within 3 mm of the limbus. Mooren's Ulcer is believed to be an autoimmune disorder, but more research is needed. The condition can be benign, with few symptoms and low risk of complications, or malignant, with severe symptoms. Without medical care, malignant cases may lead to vision loss, but treatments are available to prevent this. - Peripheral Ulcerative Keratitis - Corneal Ulcer + Peripheral Ulcerative Keratitis | broader | PUK is a category with many causes (rheumatoid arthritis, GPA, relapsing polychondritis, infection, ...); Mooren's ulcer is the idiopathic form + Corneal Ulcer | broader | any ulcerative keratitis, most often infectious - far broader than Mooren's ulcer No studies found; CONFIRMED NO DATA Sept 2021 Unconfirmed Unconfirmed @@ -14152,6 +14156,7 @@ It is under debate whether collagenous and lymphocytic colitis are different pha 2024-09 MU 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Peripheral Ulcerative Keratitis" and "Corneal Ulcer" - broader categories; Mooren's ulcer is idiopathic peripheral ulcerative keratitis. @@ -14868,10 +14873,10 @@ Although this rare disease most commonly affects children, adults may have this 1237194006, 718213001 Myelin oligodendrocyte glycoprotein disease (MOG) is a recently recognized condition marked by the presence of antibodies against myelin oligodendrocyte glycoprotein (MOG). The disease differs from multiple sclerosis (MS), aquaporin-4 (AQP4) antibody disease, and neuromyelitis optica spectrum disorders (NMOSD). MOG symptoms can range from those of neuromyelitis optica to acute demyelinating encephalomyelitis and cortical encephalitis. A correct diagnosis requires both specific and sensitive assays for the antibody. In brain images MOG overlaps with AQP4 antibody NMOSD but can be usually distinguished from MS. In particular, the silent lesions typical of MS that progressively increase lesion volume are rare in MOG antibody disease. Medium-term immunosuppression appears to be protective. Permanent disability, particularly severe ambulatory and visual disability, is less frequent than in AQP4 antibody NMOSD and usually results from the onset attack. MOG - Anti-MAG disease + Anti-MAG disease | distinct | anti-MAG (myelin-associated glycoprotein) neuropathy is a paraproteinaemic demyelinating peripheral neuropathy (IgM MGUS) - a different disease from MOG antibody disease (a CNS demyelinating disease) + Polyneuropathy associated with monoclonal immunoglobulin M antibodies to myelin-associated glycoprotein | distinct | the full name of anti-MAG neuropathy, a different disease from MOG antibody-associated disease Anti-MOG disease Myelin oligodendrocyte glycoprotein disease - Polyneuropathy associated with monoclonal immunoglobulin M antibodies to myelin-associated glycoprotein MOG antibody disease Flanagan 2019; https://onlinelibrary.ectrims-congress.eu/ectrims/2019/stockholm/278755/eoin.flanagan.the.epidemiology.of.myelin.oligodendrocyte.glycoprotein.antibody.html Antibody @@ -14887,6 +14892,7 @@ Although this rare disease most commonly affects children, adults may have this 2024-09 MOG 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Anti-MAG disease" and its full name - anti-MAG neuropathy is a paraproteinaemic peripheral neuropathy, a different disease from MOG antibody-associated disease (MAG vs MOG). @@ -14984,7 +14990,7 @@ Although this rare disease most commonly affects children, adults may have this Myocarditis is an inflammation of the heart wall. Myocarditis can affect both the heart's muscle cells and the heart's electrical system, leading to problems with the heart's pumping function and irregular heart rhythms. Myocarditis can also be caused by viral infections or systemic inflammatory conditions such as additional autoimmune disorders. In severe cases of myocarditis, the heart muscle weakens and cannot pump blood effectively to other parts of your body. There are 3 types of myocarditis: acute, chronic, and lymphocytic. Autoimmune myocarditis Autoimmune cardiomyopathy - Coxsackie myocarditis + Coxsackie myocarditis | distinct | coxsackievirus myocarditis is infectious (viral) myocarditis, not autoimmune myocarditis Lancet 2018; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227754/ Antibody Autoimmune @@ -14998,6 +15004,7 @@ Although this rare disease most commonly affects children, adults may have this 2025-05 MYC 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Coxsackie myocarditis" - viral (infectious) myocarditis, a different disease from myocarditis due to autoimmune disease. @@ -15082,7 +15089,7 @@ Although this rare disease most commonly affects children, adults may have this 36716807, 37396156, 45765443, 73001 722991004, 715863001, 702380008, 26889001 Myositis and "inflammatory myopathy" both mean inflammation of the muscles, which may in turn cause muscle weakness, swelling, and pain. Polymyositis, dermatomyositis, inclusion body myositis, and juvenile myositis are all specific types of myositis that are autoimmune. However, myositis and "inflammatory myopathy" are broad terms that means muscle inflammation, and not all forms are autoimmune, and not all individuals diagnosed with myositis or inflammatory myopathy have an autoimmune form of disease. If a cause cannot be acertained, the patient may be diagnosed with an "idiopathic" condition, which simply means that the cause of the inflammation has not been found; such patients could eventually be found to have an autoimmune form of the disease. - Juvenile myositis + Juvenile myositis | subtype | the paediatric idiopathic inflammatory myopathies (mostly juvenile dermatomyositis), a distinct age-defined group narrower than 'myositis' Idiopathic inflammatory myopathies Meyer 2014; https://pubmed.ncbi.nlm.nih.gov/25065005/ https://pubmed.ncbi.nlm.nih.gov/25065005/ @@ -15103,6 +15110,7 @@ Although this rare disease most commonly affects children, adults may have this 2025-02 MYS 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Juvenile myositis" - the paediatric inflammatory-myopathy group, a subtype narrower than myositis. Kept 'Idiopathic inflammatory myopathies'. @@ -15328,9 +15336,10 @@ The specific location of vasculitis inflammation determines what tissue or organ ARI:0001141 95609003 4316373 - Congenital heart block due to maternal anti-Ro/SSA and anti-La/SSB + Congenital heart block due to maternal anti-Ro/SSA and anti-La/SSB | subtype | the cardiac manifestation of neonatal lupus (~2% of cases); neonatal lupus also presents as rash, cytopenias or hepatitis, often without heart block 2.1 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Congenital heart block due to maternal anti-Ro/SSA and anti-La/SSB" - the cardiac manifestation of neonatal lupus, not a synonym for the whole syndrome. The entity is left with no synonyms. From 1aa6c7df19aa00c54a421e98d587ff4679326417 Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Mon, 7 Sep 2026 19:12:26 -0400 Subject: [PATCH 6/8] Review disease synonyms vs subtypes: batch 6 (ARI:0001143-0001173) 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 --- changelog.md | 10 +++++++++- ontologies/ari_t1d.owl | 20 ++++++++++++-------- 2 files changed, 21 insertions(+), 9 deletions(-) diff --git a/changelog.md b/changelog.md index d028b2b..8ec99fb 100644 --- a/changelog.md +++ b/changelog.md @@ -89,7 +89,15 @@ (anti-MAG neuropathy is a different disease — MAG vs MOG); Myocarditis due to autoimmune disease — *Coxsackie myocarditis* (viral); Myositis — *Juvenile myositis*; Neonatal lupus — *Congenital heart block due to maternal anti-Ro/SSA and anti-La/SSB* (the cardiac form). -- Batches 6+ (the remaining ~70 diseases with synonyms) follow in the same style. +- **Batch 6 — 20 diseases (ARI:0001143–0001173), 98 synonym strings.** 77 kept, 13 kept with + a note, **8 withdrawn across 4 diseases**: 6 `broader`, 2 `subtype`. +- Batch 6 withdrawn: Opsoclonus-myoclonus syndrome — *Paraneoplastic opsoclonus-myoclonus* + (×2, the cancer-associated subtype); Paraneoplastic cerebellar degeneration — + *Paraneoplastic neurological syndrome* / *PNS* / *Paraneoplastic syndrome* (broader + categories); PANDAS — *PANS* / *Pediatric Acute-onset Neuropsychiatric Syndrome* (the + broader umbrella); Primary idiopathic dilated cardiomyopathy — bare *Dilated + cardiomyopathy*. +- Batches 7+ (the remaining ~50 diseases with synonyms) follow in the same style. ## fix-ms-omop-and-lost-judgments diff --git a/ontologies/ari_t1d.owl b/ontologies/ari_t1d.owl index 5d4800c..53fe406 100644 --- a/ontologies/ari_t1d.owl +++ b/ontologies/ari_t1d.owl @@ -15868,14 +15868,14 @@ Patients with GO experience swelling in the tissues, muscles, and fat in the eye Opsoclonus-myoclonus syndrome is a rare autoimmune disorder that affects the nervous system. Inflammation in the neurological system causes this disorder. OMS typically occurs with tumors (neuroblastomas) or after a viral or bacterial infection. The immune reaction to the tumor or infection makes the body attack the nervous system. In some cases, the cause is unknown. POMA syndrome OMA syndrome - Paraneoplastic opsoclonus-myoclonus + Paraneoplastic opsoclonus-myoclonus | subtype | the cancer-associated (mostly neuroblastoma) form; already an ARI_ClinicalSubtype 'Opsoclonus-Myoclonus, Paraneoplastic' + Paraneoplastic opsoclonus-myoclonus-ataxia syndrome | subtype | the cancer-associated form; already an ARI_ClinicalSubtype 'Opsoclonus-Myoclonus, Paraneoplastic' Dancing eye-dancing feet syndrome Ataxo-opso-myoclonus syndrome Opsoclonus-myoclonus-ataxia syndrome Dancing eye syndrome Opsoclonus myoclonus syndrome OMS - Paraneoplastic opsoclonus-myoclonus-ataxia syndrome Kinsbourne syndrome Pranzatelli 2017; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5604058/#:~:text=anti%2DHu%20syndrome-,Introduction,per%20million%20children%20(2). Immune-mediated @@ -15890,6 +15890,7 @@ Patients with GO experience swelling in the tissues, muscles, and fat in the eye 2024-09 OMS 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew the two 'paraneoplastic opsoclonus-myoclonus...' strings - the cancer-associated form, already an ARI_ClinicalSubtype. Kept the whole-syndrome synonyms (Kinsbourne syndrome, dancing eye syndrome, OMS, POMA, etc.). @@ -16094,10 +16095,10 @@ Patients with GO experience swelling in the tissues, muscles, and fat in the eye Paraneoplastic cerebellar degeneration (PCD) is a rare autoimmune disorder that occurs in patients with carcinoma. PCD results when the immune system does not differentiate between tumor cells and healthy cells in the cerebellum and attacks both, causing damage. Cancer is often undetected in these patients until symptoms of PCD emerge. Disease progresses quickly, and patients will experience motor and cognitive difficulties that become disabling within less than a few weeks. Treatments are available to manage symptoms, but prognosis is usually poor. PCD PCA - Paraneoplastic neurological syndrome - PNS + Paraneoplastic neurological syndrome | broader | the whole family of paraneoplastic neurological syndromes (limbic encephalitis, LEMS, sensory neuronopathy, opsoclonus-myoclonus, ...); PCD is one member + PNS | broader | abbreviation for paraneoplastic neurological syndrome, the whole family + Paraneoplastic syndrome | broader | the entire paraneoplastic category (endocrine, haematologic, dermatologic, neurologic, ...) Paraneoplastic cerebellar ataxia - Paraneoplastic syndrome Vogrig 2019; https://pubmed.ncbi.nlm.nih.gov/31552550/ https://pubmed.ncbi.nlm.nih.gov/31552550/ Antibody @@ -16111,6 +16112,7 @@ Patients with GO experience swelling in the tissues, muscles, and fat in the eye 2024-09 PCD 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew 'Paraneoplastic neurological syndrome' / 'PNS' / 'Paraneoplastic syndrome' - broader categories; paraneoplastic cerebellar degeneration is one paraneoplastic neurological syndrome. Kept PCD / PCA / paraneoplastic cerebellar ataxia. @@ -16353,8 +16355,8 @@ Patients with GO experience swelling in the tissues, muscles, and fat in the eye 446682003 Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcus (PANDAS) affect children, adolescents, and young adults who may present with acute onset of obsessive-compulsive disorder (OCD) and/or tics following strep infection. PANDAS is a subset of Pediatric Acute-Onset Neuropsychiatric Syndrome (PANS) in which similar symptoms result from a misguided immune response following other infectious or environmental triggers such as the flu, COVID, or tick-borne diseases. PANDAS - PANS - Pediatric Acute-onset Neuropsychiatric Syndrome + PANS | broader | Pediatric Acute-onset Neuropsychiatric Syndrome is the umbrella - acute-onset OCD/tics from any trigger; PANDAS is the streptococcus-specific subset + Pediatric Acute-onset Neuropsychiatric Syndrome | broader | the PANS umbrella; PANDAS is its streptococcus-associated subset No studies found; CONFIRMED NO DATA Sept 2021 Antibody Suspected Autoimmune @@ -16374,6 +16376,7 @@ Patients with GO experience swelling in the tissues, muscles, and fat in the eye 2024-09 PAN 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew 'PANS' / 'Pediatric Acute-onset Neuropsychiatric Syndrome' - the broader umbrella; PANDAS is the streptococcus-associated subset of PANS. @@ -17980,7 +17983,7 @@ To date, there is no direct or indirect evidence that post-pericardiotomy syndro 4203149 53043001 A disease in which the immune system attacks the heart muscle causing inflammation, normally beginning in the heart's left ventricle (the heart's main pumping chamber). The ventricle stretches and thins and is unable to pump blood as a healthy heart can. Not all patients experience symptoms, but for some it can be life-threatening. - Dilated cardiomyopathy + Dilated cardiomyopathy | broader | DCM is the whole category (ischaemic, genetic/familial, alcoholic, peripartum, idiopathic, autoimmune, ...); this entity is the primary idiopathic / autoimmune subset Idiopathic dilated cardiomyopathy Codd 1989; https://pubmed.ncbi.nlm.nih.gov/2766509/ https://pubmed.ncbi.nlm.nih.gov/2766509/ @@ -17998,6 +18001,7 @@ To date, there is no direct or indirect evidence that post-pericardiotomy syndro 2024-09 PIDC 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew bare 'Dilated cardiomyopathy' - the whole DCM category, broader than primary idiopathic dilated cardiomyopathy. Kept 'Idiopathic dilated cardiomyopathy' (essentially the label). From b9ab2176a4fa772fbff87e84c9cf579271efd2dd Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Mon, 7 Sep 2026 19:15:50 -0400 Subject: [PATCH 7/8] Review disease synonyms vs subtypes: batch 7 (ARI:0001176-0001199) 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 --- changelog.md | 18 +++++++++++++++++- ontologies/ari_t1d.owl | 35 ++++++++++++++++++++++------------- 2 files changed, 39 insertions(+), 14 deletions(-) diff --git a/changelog.md b/changelog.md index 8ec99fb..8a04909 100644 --- a/changelog.md +++ b/changelog.md @@ -97,7 +97,23 @@ categories); PANDAS — *PANS* / *Pediatric Acute-onset Neuropsychiatric Syndrome* (the broader umbrella); Primary idiopathic dilated cardiomyopathy — bare *Dilated cardiomyopathy*. -- Batches 7+ (the remaining ~50 diseases with synonyms) follow in the same style. +- **Batch 7 — 20 diseases (ARI:0001176–0001199), 70 synonym strings.** 41 kept, 16 kept with + a note, **13 withdrawn across 9 diseases**: 4 `non-disease`, 3 `broader`, 3 `distinct`, + 3 `subtype`. +- Batch 7 withdrawn: Relapsing polychondritis — *Relapsing polyneuropathy* (a nerve disease); + Retinocochleocerebral vasculopathy — *retinal and encephalic tissue* / *Small infarctions + of cochlear* (one term split on a comma); Rheumatic fever — *Acute rheumatic myocarditis*; + Rheumatoid aortitis — *non-vasculitic)* / *Autoimmune aortitis (isolated* (one term split + on a comma); Secondary Raynaud's phenomenon — bare *Raynaud's phenomenon*; Sjögren's + disease — *Sicca syndrome*, *Keratoconjunctivitis sicca* (broader), *SJS* (Stevens-Johnson + collision); Subacute bacterial endocarditis — *Subacute native valve endocarditis*; + Systemic sclerosis — *Diffuse Systemic sclerosis*; SSc with limited cutaneous involvement — + *dcSSc* (the diffuse form). +- **Pre-existing notes for a curator:** the comma-split imports on ARI:0001180 and ARI:0001183 + (the whole terms should be re-added); ARI:0001176 conflates primary and secondary Raynaud's; + ARI:0001194 (subacute bacterial endocarditis, an infection) sits oddly in an autoimmune + registry. +- Batches 8+ (the remaining ~30 diseases with synonyms) follow in the same style. ## fix-ms-omop-and-lost-judgments diff --git a/ontologies/ari_t1d.owl b/ontologies/ari_t1d.owl index 53fe406..143b089 100644 --- a/ontologies/ari_t1d.owl +++ b/ontologies/ari_t1d.owl @@ -18835,7 +18835,7 @@ A third type of PRCA, Diamond-Blackfan syndrome, is due to genetic mutation and Secondary Raynaud's is a symptom experienced (and reported) by patients with autoimmune diseases. Primary Raynaud's is when the symptoms appear without any other disease. Therefore, primary Raynaud's is not an autoimmune disease. However, a person suffering from Raynaud's could have an undiagnosed autoimmune disease. Raynaud's disease Secondary Raynaud's - Raynaud's phenomenon + Raynaud's phenomenon | broader | Raynaud's phenomenon is the sign itself (primary or secondary); this entity is the secondary form Raynaud disease Garner 2015; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4368987/ Unconfirmed @@ -18853,6 +18853,7 @@ Secondary Raynaud's is a symptom experienced (and reported) by patients with aut 2024-09 RAY 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew bare "Raynaud's phenomenon" - the sign itself, broader than secondary Raynaud's phenomenon. NB the entity conflates primary and secondary (it carries a 'Primary' subtype) - for a curator. @@ -19112,7 +19113,7 @@ In cases where the cartilage is not visible, RP can cause heart valve abnormalit Systemic chondromalacia Chronic atrophic polychondritis Recurrent polychondritis - Relapsing polyneuropathy + Relapsing polyneuropathy | distinct | a peripheral-nerve disease (cf. chronic relapsing polyneuropathy = CIDP); an error for 'relapsing polychondritis' Atrophic polychondritis Meyenburg-Altherr-Uehlinger syndrome Kent 2004; https://pubmed.ncbi.nlm.nih.gov/14673390/ @@ -19131,6 +19132,7 @@ In cases where the cartilage is not visible, RP can cause heart valve abnormalit 2024-09 RP 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Relapsing polyneuropathy" - a peripheral-nerve disease, not a synonym for relapsing polychondritis (likely a transcription error). @@ -19320,10 +19322,10 @@ In cases where the cartilage is not visible, RP can cause heart valve abnormalit The severity of cases may vary, with mild cases resolving in under a year and severe cases having longer duration and causing irreparable damage. During the course of the disease, some patients may experience symptoms in a flare-remission pattern, while others are consistently symptomatic until time of recovery. Treatment is available to prevent permanent damage, and most patients under medical care can expect to experience complete or near complete recovery. RED-M SICRET - retinal and encephalic tissue + retinal and encephalic tissue | non-disease | a fragment of 'small infarctions of cochlear, retinal and encephalic tissue' split on a comma during import + Small infarctions of cochlear | non-disease | a fragment of 'small infarctions of cochlear, retinal and encephalic tissue' split on a comma during import Retinopathy-encephalopathy-deafness associated microangiopathy Susac's syndrome - Small infarctions of cochlear Susac syndrome Dörr 2013; https://pubmed.ncbi.nlm.nih.gov/23628737/ https://pubmed.ncbi.nlm.nih.gov/23628737/ @@ -19339,6 +19341,7 @@ The severity of cases may vary, with mild cases resolving in under a year and se 2024-09 RCV 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "retinal and encephalic tissue" and "Small infarctions of cochlear" - two halves of one term (the SICRET expansion) split on a comma during import. The whole phrase should be re-added by a curator. @@ -19614,7 +19617,7 @@ Note: scarlet fever is another symptom of a strep infection but is not a separat Acute rheumatic fever Rheumatic arthritis Inflammatory rheumatism - Acute rheumatic myocarditis + Acute rheumatic myocarditis | subtype | names the cardiac manifestation (rheumatic carditis) of rheumatic fever, not the whole disease Orphanet; https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=3099 Antibody Autoimmune @@ -19632,6 +19635,7 @@ Note: scarlet fever is another symptom of a strep infection but is not a separat 2024-09 RF 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Acute rheumatic myocarditis" - the cardiac manifestation of rheumatic fever, not a synonym for the whole disease. @@ -19738,10 +19742,11 @@ Note: scarlet fever is another symptom of a strep infection but is not a separat ARI:0001183 38877003 4306357 - non-vasculitic) - Autoimmune aortitis (isolated + non-vasculitic) | non-disease | a fragment of 'Autoimmune aortitis (isolated, non-vasculitic)' split on a comma during import + Autoimmune aortitis (isolated | non-disease | a fragment of 'Autoimmune aortitis (isolated, non-vasculitic)' split on a comma during import 2.1 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "non-vasculitic)" and "Autoimmune aortitis (isolated" - two halves of one term split on a comma during import. The whole phrase 'Autoimmune aortitis (isolated, non-vasculitic)' should be re-added by a curator; the entity is left with no synonyms. @@ -20500,9 +20505,9 @@ Patients with Schnitzler syndrome typically experience chronic rash, relapsing f Sjogren's disease Sjögrens disease Sjögren's syndrome - Sicca syndrome - Keratoconjunctivitis sicca - SJS + Sicca syndrome | broader | dry eyes + dry mouth from any cause (drugs, age, radiation, other diseases); the ARI definition itself says it is called Sjögren's disease only when autoimmune + Keratoconjunctivitis sicca | broader | dry eye disease from any cause; a component of Sjögren's, not a synonym + SJS | distinct | 'SJS' overwhelmingly denotes Stevens-Johnson syndrome, a different and dangerous disease; too ambiguous to keep as a Sjögren's synonym Narváez 2020; https://pubmed.ncbi.nlm.nih.gov/32606345/ https://pubmed.ncbi.nlm.nih.gov/32606345/ Antibody @@ -20523,6 +20528,7 @@ Patients with Schnitzler syndrome typically experience chronic rash, relapsing f 2025-02 SJ 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Sicca syndrome" and "Keratoconjunctivitis sicca" (broader dryness terms from any cause) and "SJS" (collides with Stevens-Johnson syndrome). Kept Sjögren's syndrome / disease spelling variants. @@ -21273,7 +21279,7 @@ SBE is not an autoimmune disease, but patients are at increased risk of developi This condition most frequently occurs following surgery to a region of the body infected with streptococcal bacteria. Invasive surgery in the infected tissue facilitates the spread of the bacteria to the heart valves by way of the blood. The infection normally develops slowly during the two weeks after surgery and may persist for months. SBE typically only occurs in patients who already have damage to their heart valves from other health conditions. SBE is difficult to diagnosis because initial symptoms consist almost exclusively of feelings of malaise, which are also common in many other disorders. SBE may trigger the onset of autoimmune conditions, such as vasculitis. If left untreated, complications can be fatal; however, positive outcomes are expected with early medical care. Subacute infective endocarditis - Subacute native valve endocarditis + Subacute native valve endocarditis | subtype | the native-valve form; already an ARI_ClinicalSubtype 'Subacute Bacterial Endocarditis, Native Valve' Cahill 2017; https://pubmed.ncbi.nlm.nih.gov/28104075/ https://pubmed.ncbi.nlm.nih.gov/28104075/ Unconfirmed @@ -21291,6 +21297,7 @@ This condition most frequently occurs following surgery to a region of the body 2024-09 SBE 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Subacute native valve endocarditis" - the native-valve form, already an ARI_ClinicalSubtype. NB this infectious disease's place in an autoimmune registry is questionable - for a curator. @@ -21810,7 +21817,7 @@ When mastocytosis is limited to the skin, it is called cutaneous mastocytosis, a 89155008 Scleroderma is an autoimmune, rheumatic, and chronic disease that affects the body by hardening connective tissue. This disease may also cause issues in the blood vessels, organs, and digestive tract. Scleroderma is characterized as limited or diffuse, referring to the degree of skin involvement, but can both involve any vascular or organ symptoms. These symptoms occur when the body produces too much collagen, which builds up the body’s connective tissues. People who usually get scleroderma are those between the ages of 30 and 50 and tend to be female at birth. Scleroderma - Diffuse Systemic sclerosis + Diffuse Systemic sclerosis | subtype | the diffuse cutaneous form (dcSSc); MONDO hasNarrowSynonym, and already an ARI_ClinicalSubtype 'Systemic Sclerosis, Diffuse' Systemic scleroderma Barnes 2012; https://pubmed.ncbi.nlm.nih.gov/22269658/ https://pubmed.ncbi.nlm.nih.gov/22269658/ @@ -21831,6 +21838,7 @@ When mastocytosis is limited to the skin, it is called cutaneous mastocytosis, a 2025-02 SS 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Diffuse Systemic sclerosis" - the diffuse cutaneous subtype (MONDO narrow synonym), already an ARI_ClinicalSubtype. Kept 'Scleroderma' and 'Systemic scleroderma'. @@ -21992,7 +22000,7 @@ S - Sclerodactyly: thick and tight skin on the fingers, caused by an excess of c T - Telangiectasia: small red spots on the hands and face that are caused by the swelling of tiny blood vessels. To be diagnosed with CREST, you must have 3 out of the 5 symptoms. - dcSSc + dcSSc | distinct | diffuse cutaneous systemic sclerosis - the opposite form to this entity (limited cutaneous) lcSSc CREST syndrome Efrimescu 2023; https://pubmed.ncbi.nlm.nih.gov/36686888/ @@ -22021,6 +22029,7 @@ To be diagnosed with CREST, you must have 3 out of the 5 symptoms.2026-07-07 20:44 | KrishnaTO | Cross-reference review: confirmed SNOMED 298285004; confirmed OMOP 4185187; confirmed ICD10 M34.1; flagged SNOMED 128461001, 31848007; flagged OMOP 4135937, 4027230; flagged NCI C70646; flagged UMLS C1527226, C0206138; flagged MESH D017675 298285004 4185187 + 2026-09-07 | Claude | Synonym review: withdrew "dcSSc" - diffuse cutaneous systemic sclerosis, the opposite of this entity (limited cutaneous involvement). Kept 'lcSSc' and 'CREST syndrome'. From b7baa11c7f1e3a3c6f1018db755683d261f34cf0 Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Mon, 7 Sep 2026 19:18:21 -0400 Subject: [PATCH 8/8] Review disease synonyms vs subtypes: batch 8 (ARI:0001080, 0001200-0001211) 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 --- changelog.md | 26 +++++++++++++++++++++++++- ontologies/ari_t1d.owl | 19 ++++++++++++------- 2 files changed, 37 insertions(+), 8 deletions(-) diff --git a/changelog.md b/changelog.md index 8a04909..5b23a91 100644 --- a/changelog.md +++ b/changelog.md @@ -113,7 +113,31 @@ (the whole terms should be re-added); ARI:0001176 conflates primary and secondary Raynaud's; ARI:0001194 (subacute bacterial endocarditis, an infection) sits oddly in an autoimmune registry. -- Batches 8+ (the remaining ~30 diseases with synonyms) follow in the same style. +- **Batch 8 — 10 diseases (ARI:0001080, 0001200–0001211), 31 synonym strings.** 18 kept, 6 kept + with a note, **7 withdrawn across 5 diseases**: 5 `broader`, 2 `subtype`. +- Batch 8 withdrawn: TIF1-gamma positive dermatomyositis — *Cancer-associated myositis* + (broader); Transverse myelitis — *Secondary acute transverse myelitis*; Uveitis — + *Idiopathic intermediate uveitis*; Vitiligo — *Leukoderma* (broader); Warm autoimmune + haemolytic anaemia — *Immune hemolytic anemia*, *Acquired autoimmune hemolytic anemia*, + *Immunohemolytic anemia* (broader — the whole AIHA / immune-haemolysis family, mirroring the + cold-agglutinin-disease finding in batch 3). + +### Review complete — all 146 diseases with synonyms + +- **708 `ARI_Synonym` strings reviewed. 450 kept, 107 kept with a curator note, + 151 withdrawn across 56 diseases** — 63 name an existing or clear clinical subtype + (`subtype`), 45 a broader parent (`broader`), 23 a different disease (`distinct`), + 20 an import artefact / downstream finding / split fragment (`non-disease`). +- `ARI_Synonym` 708 → 557; every removal carries an `ARI_SynonymWithdrawn` marker and its + disease a dated `ARI_ChangeLog` line. No `ARI_ClinicalSubtype` line was added or rewritten — + every `subtype`-reason withdrawal already had a matching subtype (or a clearly narrower + clinical form) on the disease. `validate_mappings.py --since main` is clean. +- The 107 "kept (noted)" strings are left in place with a rationale in the findings tables for + a curator: ambiguous broader/near-synonymous terms, historical eponyms, misspellings kept + pending a spelling pass, and dangerous homonyms (e.g. *SJS*, *Carpenter syndrome*). +- Pre-existing issues surfaced but not fixed: label/definition mismatches (ARI:0001031, + 0001065, 0001076), comma-split imports (ARI:0001180, 0001183), and mis-imported sibling + diseases in some `ARI_ClinicalSubtype` lists (ARI:0001069, 0001074). ## fix-ms-omop-and-lost-judgments diff --git a/ontologies/ari_t1d.owl b/ontologies/ari_t1d.owl index 143b089..18f9c8f 100644 --- a/ontologies/ari_t1d.owl +++ b/ontologies/ari_t1d.owl @@ -22474,9 +22474,10 @@ Early symptoms may include fever, night sweats, fatigue, joint pain, and chest d TIF1-gamma positive dermatomyositis false ARI:0001202 - Cancer-associated myositis + Cancer-associated myositis | broader | cancer-associated myositis also covers anti-NXP2 and seronegative cases, and not all anti-TIF1-gamma patients have cancer; a broader category 2.1 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Cancer-associated myositis" - a broader category; anti-TIF1-gamma dermatomyositis is one (cancer-enriched) serologic subtype. The entity is left with no synonyms. @@ -22584,7 +22585,7 @@ Early symptoms may include fever, night sweats, fatigue, joint pain, and chest d 443904 16631009 Inflammation of the spinal cord with neurological effects that go in a transverse (horizontal or bandlike) manner across the body, as opposed to going up or down the spinal cord. - Secondary acute transverse myelitis + Secondary acute transverse myelitis | subtype | the acute form secondary to a defined cause (MS, NMO, infection, SLE, ...); narrower than transverse myelitis Holroyd 2018; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6078000/ Antibody Autoimmune @@ -22605,6 +22606,7 @@ Early symptoms may include fever, night sweats, fatigue, joint pain, and chest d 2024-09 TM 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Secondary acute transverse myelitis" - a subtype (acute, secondary to a defined cause), narrower than transverse myelitis. The entity is left with no synonyms. @@ -23249,7 +23251,7 @@ Urticaria can also be caused by allergic reaction to plants like poison ivy, dye The most common form of autoimmune uveitis is intermediate uveitis. Idiopathic uveitis - Idiopathic intermediate uveitis + Idiopathic intermediate uveitis | subtype | doubly narrow (idiopathic + intermediate = pars planitis); a subtype - ARI has both an 'Uveitis, Intermediate' subtype and a separate 'Intermediate uveitis' entity (ARI:0001115) Autoimmune uveitis Acharya 2013; https://pubmed.ncbi.nlm.nih.gov/24008391/ https://pubmed.ncbi.nlm.nih.gov/24008391/ @@ -23282,6 +23284,7 @@ The most common form of autoimmune uveitis is intermediate uveitis.2026-07-07 20:44 | KrishnaTO | Cross-reference review: confirmed SNOMED 128473001; confirmed OMOP 4028363; confirmed DOID 0040088; flagged SNOMED 231947004; flagged OMOP 4335981 128473001 4028363 + 2026-09-07 | Claude | Synonym review: withdrew "Idiopathic intermediate uveitis" - the pars planitis subtype, narrower than uveitis. Kept 'Autoimmune uveitis' and 'Idiopathic uveitis'. @@ -23354,7 +23357,7 @@ The most common form of autoimmune uveitis is intermediate uveitis.Vitiligo is a disease that causes the loss of skin color in blotches. The extent and rate of color loss from vitiligo is unpredictable. It can affect the skin on any part of your body. It may also affect hair, the inside of the mouth, and even the eyes. Normally, the color of hair, skin, and eyes is determined by melanin. Vitiligo occurs when the cells that produce melanin die or stop functioning. - Leukoderma + Leukoderma | broader | leukoderma is any white skin (post-inflammatory, chemical, halo nevus, piebaldism, tinea versicolor, ...); vitiligo is one cause. Commonly used loosely for vitiligo but not listed as a synonym by MONDO or DOID Zhang 2016; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5038943/ Antibody Autoimmune @@ -23376,6 +23379,7 @@ Normally, the color of hair, skin, and eyes is determined by melanin. Vitiligo o 2023-01 VIT 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Leukoderma" - a broader term for white skin of any cause; vitiligo is one cause. The entity is left with no synonyms (its subtypes carry the segmental/non-segmental split). @@ -23545,9 +23549,9 @@ Normally, the color of hair, skin, and eyes is determined by melanin. Vitiligo o Some cases of this disease are caused by medications and are not autoimmune. Idiopathic autoimmune hemolytic anemia - Immune hemolytic anemia - Acquired autoimmune hemolytic anemia - Immunohemolytic anemia + Immune hemolytic anemia | broader | includes warm AIHA, cold agglutinin disease, paroxysmal cold haemoglobinuria, drug-induced and alloimmune haemolysis + Acquired autoimmune hemolytic anemia | broader | acquired AIHA covers warm, cold, mixed and drug-induced types; this entity is the warm type + Immunohemolytic anemia | broader | = immune haemolytic anaemia, the broad category Eaton 2011; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892249/ Antibody Autoimmune @@ -23563,6 +23567,7 @@ Some cases of this disease are caused by medications and are not autoimmune.2023-01 WAHA 2026-06-15 10:37 | Importer | Imported from ARI core reports + 2026-09-07 | Claude | Synonym review: withdrew "Immune hemolytic anemia", "Acquired autoimmune hemolytic anemia" and "Immunohemolytic anemia" - broader categories; warm AIHA is one type. Kept the warm-specific synonyms (wAIHA, warm AIHA, etc.) and 'Idiopathic autoimmune hemolytic anemia' (noted).