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KrishnaTO merged 9 commits into from
Aug 30, 2026
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[ARI:0001019, ARI:0001028, ARI:0001135, ARI:0001143] - mappings review #76

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36081ec
[ARI:0001135, ARI:0001143] - mappings review
aaronabend Aug 24, 2026
cda0410
[ARI:0001019, ARI:0001028, ARI:0001135, ARI:0001143] - mappings review
aaronabend Aug 27, 2026
16dd6a2
Update mappings/ari.equivalencies.tsv
KrishnaTO Aug 30, 2026
0fbe3e0
Update mappings/ari.equivalencies.tsv
KrishnaTO Aug 30, 2026
920d420
Update mappings/ari.sssom.tsv
KrishnaTO Aug 30, 2026
c559456
Update mappings/ari.sssom.tsv
KrishnaTO Aug 30, 2026
feb1edd
Update ARI_ChangeLog with confirmed OMOP ID for cross-reference review
KrishnaTO Aug 30, 2026
022ba66
Merge main and resolve PR #76 mapping review conflicts
KrishnaTO Aug 30, 2026
1f18f16
Refine ARI_OMOP and ARI_DXCODE entries in ari_t1d.owl for accuracy in…
KrishnaTO Aug 30, 2026
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23 changes: 23 additions & 0 deletions mappings/ari.equivalencies.tsv
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Expand Up @@ -500,6 +500,29 @@
ARI 0001143 Neuromyelitis optica skos:exactMatch ORPHA 71211 manual github:aaronabend
ARI 0001143 Neuromyelitis optica skos:exactMatch mesh D009471 manual github:aaronabend
ARI 0001143 Neuromyelitis optica skos:exactMatch OMIM NoTermFound manual-absent github:aaronabend
ARI 0001056 Birdshot chorioretinopathy skos:exactMatch ORPHA 179 manual github:KrishnaTO
ARI 0001028 Autoimmune encephalitis skos:exactMatch omop 4318558 manual github:aaronabend
ARI 0001028 Autoimmune encephalitis skos:exactMatch SNOMEDCT 95643007 manual github:aaronabend
ARI 0001028 Autoimmune encephalitis skos:exactMatch MONDO 0020640 manual github:aaronabend
ARI 0001019 Antisynthetase syndrome skos:exactMatch SNOMEDCT 445187004 manual github:aaronabend
ARI 0001019 Antisynthetase syndrome skos:exactMatch omop 40482477 manual github:aaronabend
ARI 0001019 Antisynthetase syndrome skos:exactMatch DOID 0080744 manual github:aaronabend
ARI 0001019 Antisynthetase syndrome skos:exactMatch MONDO 0019344 manual github:aaronabend
ARI 0001019 Antisynthetase syndrome skos:exactMatch ORPHA 81 manual github:aaronabend
ARI 0001135 Multiple sclerosis skos:exactMatch DOID 2377 manual github:aaronabend
ARI 0001135 Multiple sclerosis skos:exactMatch MONDO 0005301 manual github:aaronabend
ARI 0001135 Multiple sclerosis skos:exactMatch ncit C3243 manual github:aaronabend
ARI 0001135 Multiple sclerosis skos:exactMatch SNOMEDCT 128460000 manual-negative github:aaronabend
ARI 0001135 Multiple sclerosis skos:exactMatch SNOMEDCT 426373005 manual-negative github:aaronabend
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 github:aaronabend

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mappings/cross-file-drift 

ARI:1135 -> omop:374919 (confirmed, github:aaronabend) has no counterpart in mappings/ari.sssom.tsv. The two exports must stay identical row for row.
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-negative github:aaronabend

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mappings/cross-file-drift 

ARI:1135 -> omop:4027727 (flagged wrong, github:aaronabend) has no counterpart in mappings/ari.sssom.tsv. The two exports must stay identical row for row.
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
ARI 0001090 Essential mixed cryoglobulinemia skos:exactMatch MONDO 0007407 manual github:linikujp
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23 changes: 23 additions & 0 deletions mappings/ari.sssom.tsv
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Expand Up @@ -520,6 +520,29 @@
ARI:0001143 Neuromyelitis optica skos:exactMatch ORPHA:71211 ORPHA semapv:ManualMappingCuration github:aaronabend 2026-08-17
ARI:0001143 Neuromyelitis optica skos:exactMatch mesh:D009471 mesh semapv:ManualMappingCuration github:aaronabend 2026-08-17
ARI:0001143 Neuromyelitis optica skos:exactMatch sssom:NoTermFound OMIM semapv:ManualMappingCuration github:aaronabend 2026-08-17
ARI:0001056 Birdshot chorioretinopathy skos:exactMatch ORPHA:179 ORPHA semapv:ManualMappingCuration github:KrishnaTO 2026-08-20
ARI:0001028 Autoimmune encephalitis skos:exactMatch omop:4318558 omop semapv:ManualMappingCuration github:aaronabend 2026-08-27
ARI:0001028 Autoimmune encephalitis skos:exactMatch SNOMEDCT:95643007 SNOMEDCT semapv:ManualMappingCuration github:aaronabend 2026-08-27
ARI:0001028 Autoimmune encephalitis skos:exactMatch MONDO:0020640 MONDO semapv:ManualMappingCuration github:aaronabend 2026-08-27

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mappings/confirmed-not-stored 

MONDO:0020640 is confirmed for ARI:0001028 but is not stored on the disease in ontologies/ari_t1d.owl, so the confirmation is not reflected in what users see.
ARI:0001019 Antisynthetase syndrome skos:exactMatch SNOMEDCT:445187004 SNOMEDCT semapv:ManualMappingCuration github:aaronabend 2026-08-27
ARI:0001019 Antisynthetase syndrome skos:exactMatch omop:40482477 omop semapv:ManualMappingCuration github:aaronabend 2026-08-27
ARI:0001019 Antisynthetase syndrome skos:exactMatch DOID:0080744 DOID semapv:ManualMappingCuration github:aaronabend 2026-08-27
ARI:0001019 Antisynthetase syndrome skos:exactMatch MONDO:0019344 MONDO semapv:ManualMappingCuration github:aaronabend 2026-08-27

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mappings/confirmed-not-stored 

MONDO:0019344 is confirmed for ARI:0001019 but is not stored on the disease in ontologies/ari_t1d.owl, so the confirmation is not reflected in what users see.
ARI:0001019 Antisynthetase syndrome skos:exactMatch ORPHA:81 ORPHA semapv:ManualMappingCuration github:aaronabend 2026-08-27

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mappings/confirmed-not-stored 

ORPHA:81 is confirmed for ARI:0001019 but is not stored on the disease in ontologies/ari_t1d.owl, so the confirmation is not reflected in what users see.
ARI:0001135 Multiple sclerosis skos:exactMatch DOID:2377 DOID semapv:ManualMappingCuration github:aaronabend 2026-08-27
ARI:0001135 Multiple sclerosis skos:exactMatch MONDO:0005301 MONDO semapv:ManualMappingCuration github:aaronabend 2026-08-27

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mappings/confirmed-not-stored 

MONDO:0005301 is confirmed for ARI:0001135 but is not stored on the disease in ontologies/ari_t1d.owl, so the confirmation is not reflected in what users see.
ARI:0001135 Multiple sclerosis skos:exactMatch ncit:C3243 ncit semapv:ManualMappingCuration github:aaronabend 2026-08-27
ARI:0001135 Multiple sclerosis skos:exactMatch Not SNOMEDCT:128460000 SNOMEDCT semapv:ManualMappingCuration github:aaronabend 2026-08-27

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mappings/flagged-still-stored 

SNOMEDCT:128460000 is flagged wrong for ARI:0001135 but is still stored on the disease (ARI_SNOMED or ARI_DXCODE, ontologies/ari_t1d.owl:13991) and is still served to users. Remove the id from the ontology in the same change.
ARI:0001135 Multiple sclerosis skos:exactMatch Not SNOMEDCT:426373005 SNOMEDCT semapv:ManualMappingCuration github:aaronabend 2026-08-27

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mappings/flagged-still-stored 

SNOMEDCT:426373005 is flagged wrong for ARI:0001135 but is still stored on the disease (ARI_SNOMED or ARI_DXCODE, ontologies/ari_t1d.owl:13992) and is still served to users. Remove the id from the ontology in the same change.
ARI:0001135 Multiple sclerosis skos:exactMatch Not SNOMEDCT:428700003 SNOMEDCT semapv:ManualMappingCuration github:aaronabend 2026-08-27

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mappings/flagged-still-stored 

SNOMEDCT:428700003 is flagged wrong for ARI:0001135 but is still stored on the disease (ARI_SNOMED or ARI_DXCODE, ontologies/ari_t1d.owl:13993) and is still served to users. Remove the id from the ontology in the same change.
ARI:0001135 Multiple sclerosis skos:exactMatch Not SNOMEDCT:49692006 SNOMEDCT semapv:ManualMappingCuration github:aaronabend 2026-08-27

Check failure on line 538 in mappings/ari.sssom.tsv

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mappings/flagged-still-stored 

SNOMEDCT:49692006 is flagged wrong for ARI:0001135 but is still stored on the disease (ARI_SNOMED or ARI_DXCODE, ontologies/ari_t1d.owl:13994) and is still served to users. Remove the id from the ontology in the same change.
ARI:0001135 Multiple sclerosis skos:exactMatch SNOMEDCT:24700007 SNOMEDCT semapv:ManualMappingCuration github:aaronabend 2026-08-27
ARI:0001135 Multiple sclerosis skos:exactMatch Not omop:374919 omop semapv:ManualMappingCuration github:aaronabend 2026-08-27

Check failure on line 540 in mappings/ari.sssom.tsv

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mappings/cross-file-drift 

ARI:1135 -> omop:374919 (flagged wrong, github:aaronabend) has no counterpart in mappings/ari.equivalencies.tsv. The two exports must stay identical row for row.
ARI:0001135 Multiple sclerosis skos:exactMatch Not omop:4178929 omop semapv:ManualMappingCuration github:aaronabend 2026-08-27
ARI:0001135 Multiple sclerosis skos:exactMatch Not omop:4145049 omop semapv:ManualMappingCuration github:aaronabend 2026-08-27
ARI:0001135 Multiple sclerosis skos:exactMatch Not omop:376970 omop semapv:ManualMappingCuration github:aaronabend 2026-08-27
ARI:0001135 Multiple sclerosis skos:exactMatch omop:4027727 omop semapv:ManualMappingCuration github:aaronabend 2026-08-27

Check failure on line 544 in mappings/ari.sssom.tsv

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mappings/cross-file-drift 

ARI:1135 -> omop:4027727 (confirmed, github:aaronabend) has no counterpart in mappings/ari.equivalencies.tsv. The two exports must stay identical row for row.
ARI:0001028 Autoimmune encephalitis skos:exactMatch sssom:NoTermFound icd10cm semapv:ManualMappingCuration github:aaronabend 2026-08-27
ARI:0001098 Hemophilia B Leyden skos:exactMatch MONDO:0850054 MONDO semapv:ManualMappingCuration github:linikujp 2026-08-21
ARI:0001098 Hemophilia B Leyden skos:exactMatch ORPHA:617930 ORPHA semapv:ManualMappingCuration github:linikujp 2026-08-21
ARI:0001090 Essential mixed cryoglobulinemia skos:exactMatch MONDO:0007407 MONDO semapv:ManualMappingCuration github:linikujp 2026-08-21
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8 changes: 6 additions & 2 deletions ontologies/ari_t1d.owl
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Expand Up @@ -3527,6 +3527,7 @@ The trigger for antisynthetase syndrome is unknown, but it may be associated wit
<ARI_SurveyCode rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ASY</ARI_SurveyCode>
<ARI_ChangeLog rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2026-06-15 10:37 | Importer | Imported from ARI core reports</ARI_ChangeLog>
<ARI_ChangeLog rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2026-08-21 17:35 | linikujp | Cross-reference review: confirmed MONDO 0019344; confirmed ORPHANET 81</ARI_ChangeLog>
<ARI_ChangeLog rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2026-08-27 17:57 | aaronabend | Cross-reference review: confirmed SNOMED 445187004; confirmed OMOP 40482477; confirmed DOID 0080744; confirmed MONDO 0019344; confirmed ORPHANET 81</ARI_ChangeLog>
</owl:NamedIndividual>

<owl:NamedIndividual rdf:about="#Sym_0001019_176">
Expand Down Expand Up @@ -3977,6 +3978,7 @@ The trigger for antisynthetase syndrome is unknown, but it may be associated wit
<ARI_AuthorDate rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2025-02</ARI_AuthorDate>
<ARI_SurveyCode rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AE</ARI_SurveyCode>
<ARI_ChangeLog rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2026-06-15 10:37 | Importer | Imported from ARI core reports</ARI_ChangeLog>
<ARI_ChangeLog rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2026-08-27 17:57 | aaronabend | Cross-reference review: confirmed OMOP 4318558; confirmed SNOMED 95643007; confirmed MONDO 0020640; no term in ICD10</ARI_ChangeLog>
</owl:NamedIndividual>

<owl:NamedIndividual rdf:about="#Sym_0001028_215">
Expand Down Expand Up @@ -13997,8 +13999,8 @@ 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">374919, 4178929, 4145049, 376970, 4027727</ARI_OMOP>
<ARI_DXCODE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">24700007, 428700003, 426373005, 49692006, 128460000</ARI_DXCODE>
<ARI_OMOP rdf:datatype="http://www.w3.org/2001/XMLSchema#string">4027727</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>
<ARI_Synonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MS</ARI_Synonym>
Expand Down Expand Up @@ -14032,6 +14034,7 @@ Although this rare disease most commonly affects children, adults may have this
<ARI_AuthorDate rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2024-09</ARI_AuthorDate>
<ARI_SurveyCode rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MS</ARI_SurveyCode>
<ARI_ChangeLog rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2026-06-15 10:37 | Importer | Imported from ARI core reports</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>
</owl:NamedIndividual>

<owl:NamedIndividual rdf:about="#Sym_0001135_1241">
Expand Down Expand Up @@ -14930,6 +14933,7 @@ The specific location of vasculitis inflammation determines what tissue or organ
<ARI_SurveyCode rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMO</ARI_SurveyCode>
<ARI_ChangeLog rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2026-06-15 10:37 | Importer | Imported from ARI core reports</ARI_ChangeLog>
<ARI_ChangeLog rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2026-08-17 18:32 | aaronabend | Cross-reference review: confirmed SNOMED 25044007; confirmed OMOP 380995; confirmed DOID 8869; confirmed MONDO 0019100; confirmed NCI C84934; confirmed ICD10 G36.0; confirmed ORPHANET 71211; confirmed MESH D009471; no term in OMIM</ARI_ChangeLog>
<ARI_ChangeLog rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2026-08-27 17:57 | aaronabend | Cross-reference review: confirmed SNOMED 25044007; confirmed OMOP 4027727; confirmed DOID 8869; confirmed MONDO 0019100; confirmed NCI C84934; confirmed ICD10 G36.0; confirmed ORPHANET 71211; confirmed MESH D009471; no term in OMIM</ARI_ChangeLog>
</owl:NamedIndividual>

<owl:NamedIndividual rdf:about="#Sym_0001143_1338">
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