Skip to content

Correct the Multiple sclerosis OMOP concept, restore six lost IPEX judgments #81

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
KrishnaTO merged 1 commit into from
Sep 1, 2026
Merged

Correct the Multiple sclerosis OMOP concept, restore six lost IPEX judgments #81

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
38 changes: 38 additions & 0 deletions changelog.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,43 @@
# Changelog

## fix-ms-omop-and-lost-judgments

- **Corrects an error `restore-overwritten-curation` introduced.** OMOP `4027727` is
"Systemic sclerosis, diffuse" (SNOMED 128460000); OMOP `374919` is "Multiple sclerosis"
(SNOMED 24700007). The SSSOM rows for ARI:0001135 had the two verdicts swapped,
`ari.equivalencies.tsv` had them the right way round, and the earlier branch resolved that
disagreement in favour of the SSSOM side without checking either concept's label. So `main`
stored the systemic sclerosis concept on Multiple sclerosis and had dropped the correct one.
The curator's own SNOMED verdicts settle it: they confirmed 24700007 and flagged 128460000,
which are exactly 374919 and 4027727. Both exports and `ARI_OMOP` now say 374919.
- The lesson generalises: a mapping row is not self-validating. Every stored OMOP concept was
re-checked against the SNOMED code it carries and the SNOMED codes its disease stores. Five
more diseases hold an OMOP concept broader or narrower than their SNOMED one — ARI:0001057
(Pemphigoid vs Bullous pemphigoid), ARI:0001117 (Juvenile idiopathic vs Juvenile Rheumatoid
Arthritis), ARI:0001138, ARI:0001144 and ARI:0001196 (Lupus erythematosus vs SLE). Those are
pre-existing curation questions, not errors introduced here, and are **left for a curator**.
- **Restored six confirmations on ARI:0001106** (IPEX). AnjaliRH recorded nine judgments on
2026-08-03; `02938dd` wiped every row for the disease on the 4th, and her next publish on the
7th restored four. The six confirmations — MONDO:0010580, OMIM:304790, ORPHA:37042,
mesh:C580192, ncit:C131009, umls:C0342288 — never came back, though every id is still stored
on the disease and her changelog entry still names them. The review page therefore showed six
cells as never reviewed when they had been.
- This is the first confirmed loss of *mapping rows*, as opposed to ontology records. The
earlier branch checked only back to PR #69 and found the mapping set additive over that
window; the loss is older, from the 2026-08-04 save.
- **Added `umls:C0398650` on ARI:0001107** (Immune thrombocytopenia). The id is stored and a
changelog entry names AnjaliRH confirming it on 2026-08-10, but no row was ever written.
This creates the record that entry implies rather than restoring a deleted one.
- Audited every disease for the same shape — an id stored, or a changelog entry naming it, with
no judgment in the mapping set. What remains is deliberate: 11 ICD-9 codes whose rows the
ICD-9 retirement removed on purpose, and one entry on ARI:0003 whose row exists under the
repaired `MONDO:0014523` spelling.
- **One finding needs a curator, not a fix.** ARI:0001143 (Neuromyelitis optica) carries a
changelog entry from 2026-08-27 confirming OMOP `4027727` — systemic sclerosis again, on a
third disease. The mapping set holds the correct `omop:380995`, so the data is right and only
the note is wrong; but the same wrong concept reaching two diseases in one session suggests a
mis-click worth knowing about.

## restore-overwritten-curation

- Restores curation that the editor app's saves reverted, and re-applies the cleanups they
Expand Down
11 changes: 9 additions & 2 deletions mappings/ari.equivalencies.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -515,11 +515,11 @@ ARI 0001135 Multiple sclerosis skos:exactMatch SNOMEDCT 426373005 manual-negativ
ARI 0001135 Multiple sclerosis skos:exactMatch SNOMEDCT 428700003 manual-negative github:aaronabend
ARI 0001135 Multiple sclerosis skos:exactMatch SNOMEDCT 49692006 manual-negative github:aaronabend
ARI 0001135 Multiple sclerosis skos:exactMatch SNOMEDCT 24700007 manual github:aaronabend
ARI 0001135 Multiple sclerosis skos:exactMatch omop 374919 manual-negative github:aaronabend
ARI 0001135 Multiple sclerosis skos:exactMatch omop 374919 manual github:aaronabend
ARI 0001135 Multiple sclerosis skos:exactMatch omop 4178929 manual-negative github:aaronabend
ARI 0001135 Multiple sclerosis skos:exactMatch omop 4145049 manual-negative github:aaronabend
ARI 0001135 Multiple sclerosis skos:exactMatch omop 376970 manual-negative github:aaronabend
ARI 0001135 Multiple sclerosis skos:exactMatch omop 4027727 manual github:aaronabend
ARI 0001135 Multiple sclerosis skos:exactMatch omop 4027727 manual-negative github:aaronabend
ARI 0001028 Autoimmune encephalitis skos:exactMatch icd10cm NoTermFound manual-absent github:aaronabend
ARI 0001098 Hemophilia B Leyden skos:exactMatch MONDO 0850054 manual github:linikujp
ARI 0001098 Hemophilia B Leyden skos:exactMatch ORPHA 617930 manual github:linikujp
Expand Down Expand Up @@ -549,3 +549,10 @@ ARI 0001065 Chronic Lyme disease skos:exactMatch omop 440638 manual-negative git
ARI 0001065 Chronic Lyme disease skos:exactMatch omop 4141757 manual-negative github:KrishnaTO
ARI 0001065 Chronic Lyme disease skos:exactMatch SNOMEDCT 23502006 manual-negative github:KrishnaTO
ARI 0001065 Chronic Lyme disease skos:exactMatch SNOMEDCT 33937009 manual-negative github:KrishnaTO
ARI 0001106 Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked Syndrome skos:exactMatch MONDO 0010580 manual github:AnjaliRH
ARI 0001106 Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked Syndrome skos:exactMatch OMIM 304790 manual github:AnjaliRH
ARI 0001106 Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked Syndrome skos:exactMatch ORPHA 37042 manual github:AnjaliRH
ARI 0001106 Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked Syndrome skos:exactMatch mesh C580192 manual github:AnjaliRH
ARI 0001106 Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked Syndrome skos:exactMatch ncit C131009 manual github:AnjaliRH
ARI 0001106 Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked Syndrome skos:exactMatch umls C0342288 manual github:AnjaliRH
ARI 0001107 Immune thrombocytopenia skos:exactMatch umls C0398650 manual github:AnjaliRH
11 changes: 9 additions & 2 deletions mappings/ari.sssom.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -535,11 +535,11 @@ ARI:0001135 Multiple sclerosis skos:exactMatch Not SNOMEDCT:426373005 SNOMEDCT s
ARI:0001135 Multiple sclerosis skos:exactMatch Not SNOMEDCT:428700003 SNOMEDCT semapv:ManualMappingCuration github:aaronabend 2026-08-27T00:00:00+00:00
ARI:0001135 Multiple sclerosis skos:exactMatch Not SNOMEDCT:49692006 SNOMEDCT semapv:ManualMappingCuration github:aaronabend 2026-08-27T00:00:00+00:00
ARI:0001135 Multiple sclerosis skos:exactMatch SNOMEDCT:24700007 SNOMEDCT semapv:ManualMappingCuration github:aaronabend 2026-08-27T00:00:00+00:00
ARI:0001135 Multiple sclerosis skos:exactMatch Not omop:374919 omop semapv:ManualMappingCuration github:aaronabend 2026-08-27T00:00:00+00:00
ARI:0001135 Multiple sclerosis skos:exactMatch omop:374919 omop semapv:ManualMappingCuration github:aaronabend 2026-08-27T00:00:00+00:00
ARI:0001135 Multiple sclerosis skos:exactMatch Not omop:4178929 omop semapv:ManualMappingCuration github:aaronabend 2026-08-27T00:00:00+00:00
ARI:0001135 Multiple sclerosis skos:exactMatch Not omop:4145049 omop semapv:ManualMappingCuration github:aaronabend 2026-08-27T00:00:00+00:00
ARI:0001135 Multiple sclerosis skos:exactMatch Not omop:376970 omop semapv:ManualMappingCuration github:aaronabend 2026-08-27T00:00:00+00:00
ARI:0001135 Multiple sclerosis skos:exactMatch omop:4027727 omop semapv:ManualMappingCuration github:aaronabend 2026-08-27T00:00:00+00:00
ARI:0001135 Multiple sclerosis skos:exactMatch Not omop:4027727 omop semapv:ManualMappingCuration github:aaronabend 2026-08-27T00:00:00+00:00
ARI:0001028 Autoimmune encephalitis skos:exactMatch sssom:NoTermFound icd10cm semapv:ManualMappingCuration github:aaronabend 2026-08-27T00:00:00+00:00
ARI:0001098 Hemophilia B Leyden skos:exactMatch MONDO:0850054 MONDO semapv:ManualMappingCuration github:linikujp 2026-08-21T00:00:00+00:00
ARI:0001098 Hemophilia B Leyden skos:exactMatch ORPHA:617930 ORPHA semapv:ManualMappingCuration github:linikujp 2026-08-21T00:00:00+00:00
Expand Down Expand Up @@ -570,3 +570,10 @@ ARI:0001065 Chronic Lyme disease skos:exactMatch Not omop:440638 omop semapv:Man
ARI:0001065 Chronic Lyme disease skos:exactMatch Not omop:4141757 omop semapv:ManualMappingCuration github:KrishnaTO 2026-08-31T02:09:20+00:00
ARI:0001065 Chronic Lyme disease skos:exactMatch Not SNOMEDCT:23502006 SNOMEDCT semapv:ManualMappingCuration github:KrishnaTO 2026-08-31T02:09:20+00:00
ARI:0001065 Chronic Lyme disease skos:exactMatch Not SNOMEDCT:33937009 SNOMEDCT semapv:ManualMappingCuration github:KrishnaTO 2026-08-31T02:09:20+00:00
ARI:0001106 Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked Syndrome skos:exactMatch MONDO:0010580 MONDO semapv:ManualMappingCuration github:AnjaliRH 2026-08-03T00:00:00+00:00
ARI:0001106 Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked Syndrome skos:exactMatch OMIM:304790 OMIM semapv:ManualMappingCuration github:AnjaliRH 2026-08-03T00:00:00+00:00
ARI:0001106 Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked Syndrome skos:exactMatch ORPHA:37042 ORPHA semapv:ManualMappingCuration github:AnjaliRH 2026-08-03T00:00:00+00:00
ARI:0001106 Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked Syndrome skos:exactMatch mesh:C580192 mesh semapv:ManualMappingCuration github:AnjaliRH 2026-08-03T00:00:00+00:00
ARI:0001106 Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked Syndrome skos:exactMatch ncit:C131009 ncit semapv:ManualMappingCuration github:AnjaliRH 2026-08-03T00:00:00+00:00
ARI:0001106 Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked Syndrome skos:exactMatch umls:C0342288 umls semapv:ManualMappingCuration github:AnjaliRH 2026-08-03T00:00:00+00:00
ARI:0001107 Immune thrombocytopenia skos:exactMatch umls:C0398650 umls semapv:ManualMappingCuration github:AnjaliRH 2026-08-10T00:00:00+00:00
5 changes: 4 additions & 1 deletion ontologies/ari_t1d.owl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11677,6 +11677,7 @@ ASA is not a concern except for people trying to conceive.</rdfs:comment>
<ARI_UMLS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C0342288</ARI_UMLS>
<ARI_MESH rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C580192</ARI_MESH>
<ARI_DOID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0090110</ARI_DOID>
<ARI_ChangeLog rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2026-09-01T00:10:35+00:00 | KrishnaTO | Cross-reference review: restored confirmed MONDO 0010580; OMIM 304790; ORPHANET 37042; MESH C580192; NCI C131009; UMLS C0342288</ARI_ChangeLog>
</owl:NamedIndividual>

<owl:NamedIndividual rdf:about="https://diseases.autoimmuneregistry.org/disease/ARI_0001107">
Expand Down Expand Up @@ -11752,6 +11753,7 @@ Note that thrombotic thrombocytopenic purpura, TTP, is a ***genetic*** disease t
<ARI_DXCODE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2897005</ARI_DXCODE>
<ARI_OMOP rdf:datatype="http://www.w3.org/2001/XMLSchema#string">4103532</ARI_OMOP>
<ARI_UMLS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C0242584</ARI_UMLS>
<ARI_ChangeLog rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2026-09-01T00:10:35+00:00 | KrishnaTO | Cross-reference review: confirmed UMLS C0398650</ARI_ChangeLog>
</owl:NamedIndividual>

<owl:NamedIndividual rdf:about="#Sym_0001107_335">
Expand Down Expand Up @@ -14505,7 +14507,7 @@ Although this rare disease most commonly affects children, adults may have this
<ARI_ICD10 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">G35</ARI_ICD10>
<ARI_MESH rdf:datatype="http://www.w3.org/2001/XMLSchema#string">D009103</ARI_MESH>
<ARI_NCI rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C3243</ARI_NCI>
<ARI_OMOP rdf:datatype="http://www.w3.org/2001/XMLSchema#string">4027727</ARI_OMOP>
<ARI_OMOP rdf:datatype="http://www.w3.org/2001/XMLSchema#string">374919</ARI_OMOP>
<ARI_DXCODE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">24700007</ARI_DXCODE>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Multiple Sclerosis (MS) is a central nervous system disease that occurs when the immune system attacks the myelin, which is a protective covering around the nerves. The nerves may then suffer permanent damage. The cause of the abnormal immune system action is unknown, but there seems to be some genetic link. The most common form of MS is relapsing-remitting which occurs when a patient has symptom-free periods, but the patient may develop a progressive form where the symptoms worsen over time. Women are affected twice as often as men. MS varies in severity, with some people losing the ability to walk.</rdfs:comment>
<ARI_Synonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Disseminated sclerosis</ARI_Synonym>
Expand Down Expand Up @@ -14544,6 +14546,7 @@ Although this rare disease most commonly affects children, adults may have this
<ARI_ChangeLog rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2026-08-27 17:57 | aaronabend | Cross-reference review: confirmed DOID 2377; confirmed MONDO 0005301; confirmed NCI C3243; confirmed SNOMED 128460000, 426373005, 428700003, 49692006, 24700007; confirmed OMOP 374919, 4178929, 4145049, 376970, 4027727</ARI_ChangeLog>
<ARI_ChangeLog rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2026-08-27 17:57 | aaronabend | Cross-reference review: confirmed DOID 2377; confirmed MONDO 0005301; confirmed NCI C3243; confirmed SNOMED 24700007; confirmed OMOP 4027727</ARI_ChangeLog>
<ARI_MONDO rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0005301</ARI_MONDO>
<ARI_ChangeLog rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2026-09-01T00:10:35+00:00 | KrishnaTO | Cross-reference review: confirmed OMOP 374919; flagged OMOP 4027727</ARI_ChangeLog>
</owl:NamedIndividual>

<owl:NamedIndividual rdf:about="#Sym_0001135_1241">
Expand Down
Loading