Bug: Synonym Sync: Duplicate rows #684 - build

monarch-initiative · Dec 16, 2024 · 5d4cd99 · 5d4cd99
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diff --git a/docs/metrics/doid.md b/docs/metrics/doid.md
@@ -2,7 +2,7 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/doid.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-27/doid.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-12-16/doid.owl
 
 ### Entities and axioms
 

diff --git a/docs/metrics/icd10cm.md b/docs/metrics/icd10cm.md
@@ -2,7 +2,7 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd10cm.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-27/icd10cm.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-12-16/icd10cm.owl
 
 ### Entities and axioms
 

diff --git a/docs/metrics/icd10who.md b/docs/metrics/icd10who.md
@@ -2,7 +2,7 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd10who.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-27/icd10who.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-12-16/icd10who.owl
 
 ### Entities and axioms
 

diff --git a/docs/metrics/icd11foundation.md b/docs/metrics/icd11foundation.md
@@ -2,7 +2,7 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd11foundation.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-27/icd11foundation.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-12-16/icd11foundation.owl
 
 ### Entities and axioms
 

diff --git a/docs/metrics/ncit.md b/docs/metrics/ncit.md
@@ -2,7 +2,7 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/ncit.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-27/ncit.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-12-16/ncit.owl
 
 ### Entities and axioms
 

diff --git a/docs/metrics/omim.md b/docs/metrics/omim.md
@@ -2,16 +2,16 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/omim.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-27/omim.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-12-16/omim.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
-| Annotation properties | 21 |
-| Axioms | 358797 |
-| Logical axioms | 28211 |
-| Classes | 23596 |
+| Annotation properties | 23 |
+| Axioms | 373162 |
+| Logical axioms | 28241 |
+| Classes | 23606 |
 | Object properties | 7 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,18 +32,18 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 306964 |
+| AnnotationAssertion | 321287 |
 | SubAnnotationPropertyOf | 2 |
-| Declaration | 23620 |
-| SubClassOf | 28211 |
+| Declaration | 23632 |
+| SubClassOf | 28241 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| prefix_unknown | 22158 |
-| oboInOwl | 4 |
+| prefix_unknown | 22168 |
+| oboInOwl | 6 |
 | owl | 2 |
 | xsd | 1 |
 | skos | 1 |
@@ -62,8 +62,8 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 80013 |
-| ObjectSomeValuesFrom | 23248 |
+| Class | 80083 |
+| ObjectSomeValuesFrom | 23259 |
 
 
 More information about the source can be found [in the documentation](../sources.md). The raw data (ontology metrics) can be found [on GitHub](https://github.com/monarch-initiative/mondo-ingest/tree/main/src/ontology/metadata).

diff --git a/docs/metrics/ordo.md b/docs/metrics/ordo.md
@@ -2,16 +2,16 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/ordo.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-27/ordo.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-12-16/ordo.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 16 |
-| Axioms | 227556 |
-| Logical axioms | 42867 |
-| Classes | 15089 |
+| Axioms | 228273 |
+| Logical axioms | 43059 |
+| Classes | 15157 |
 | Object properties | 4 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,18 +32,18 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 169582 |
+| AnnotationAssertion | 170039 |
 | SubAnnotationPropertyOf | 1 |
-| Declaration | 15106 |
-| SubClassOf | 42867 |
+| Declaration | 15174 |
+| SubClassOf | 43059 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
 | dc11 | 1 |
-| prefix_unknown | 15089 |
+| prefix_unknown | 15157 |
 | oboInOwl | 6 |
 | owl | 2 |
 | rdf | 1 |
@@ -60,8 +60,8 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 100823 |
-| ObjectSomeValuesFrom | 6771 |
+| Class | 101275 |
+| ObjectSomeValuesFrom | 6799 |
 
 
 More information about the source can be found [in the documentation](../sources.md). The raw data (ontology metrics) can be found [on GitHub](https://github.com/monarch-initiative/mondo-ingest/tree/main/src/ontology/metadata).

diff --git a/docs/reports/mapped_deprecated.md b/docs/reports/mapped_deprecated.md
@@ -2,9 +2,9 @@
 | Ontology                                                  |   Tot deprecated in Mondo |
 |:----------------------------------------------------------|--------------------------:|
 | [NCIT](./mapped_deprecated_ncit.md)                       |                         5 |
-| [OMIM](./mapped_deprecated_omim.md)                       |                        47 |
+| [OMIM](./mapped_deprecated_omim.md)                       |                        48 |
 | [DOID](./mapped_deprecated_doid.md)                       |                         2 |
-| [ORDO](./mapped_deprecated_ordo.md)                       |                       169 |
+| [ORDO](./mapped_deprecated_ordo.md)                       |                       190 |
 | [ICD11FOUNDATION](./mapped_deprecated_icd11foundation.md) |                         0 |
 | [ICD10CM](./mapped_deprecated_icd10cm.md)                 |                         0 |
 | [ICD10WHO](./mapped_deprecated_icd10who.md)               |                         0 |

diff --git a/docs/reports/mapped_deprecated_omim.md b/docs/reports/mapped_deprecated_omim.md
@@ -17,6 +17,7 @@
 | MONDO:0008126 | OMIM:164891          | MONDO:equivalentObsolete |
 | MONDO:0008204 | OMIM:168850          | MONDO:equivalentObsolete |
 | MONDO:0008415 | OMIM:181515          | MONDO:equivalentObsolete |
+| MONDO:0008868 | OMIM:210550          | MONDO:equivalentObsolete |
 | MONDO:0009455 | OMIM:242870          | MONDO:equivalentObsolete |
 | MONDO:0009535 | OMIM:247440          | MONDO:equivalentObsolete |
 | MONDO:0009654 | OMIM:252700          | MONDO:equivalentObsolete |

diff --git a/docs/reports/mapped_deprecated_ordo.md b/docs/reports/mapped_deprecated_ordo.md
@@ -7,18 +7,26 @@
 | ID            | A oboInOwl:hasDbXref | >A oboInOwl:source       |
 | MONDO:0001153 | Orphanet:459690      | MONDO:equivalentObsolete |
 | MONDO:0001807 | Orphanet:79211       | MONDO:equivalentObsolete |
+| MONDO:0001971 | Orphanet:99906       | MONDO:equivalentObsolete |
+| MONDO:0005668 | Orphanet:99908       | MONDO:equivalentObsolete |
+| MONDO:0007744 | Orphanet:79506       | MONDO:equivalentObsolete |
 | MONDO:0007761 | Orphanet:413         | MONDO:equivalentObsolete |
 | MONDO:0007779 | Orphanet:306588      | MONDO:equivalentObsolete |
+| MONDO:0008401 | Orphanet:454821      | MONDO:equivalentObsolete |
 | MONDO:0009317 | Orphanet:1245        | MONDO:equivalentObsolete |
+| MONDO:0009971 | Orphanet:70587       | MONDO:equivalentObsolete |
 | MONDO:0010045 | Orphanet:2823        | MONDO:equivalentObsolete |
 | MONDO:0010994 | Orphanet:2641        | MONDO:equivalentObsolete |
+| MONDO:0011054 | Orphanet:1027        | MONDO:equivalentObsolete |
 | MONDO:0011910 | Orphanet:265         | MONDO:equivalentObsolete |
+| MONDO:0012839 | Orphanet:183713      | MONDO:equivalentObsolete |
 | MONDO:0015120 | Orphanet:101949      | MONDO:equivalentObsolete |
 | MONDO:0015163 | Orphanet:102373      | MONDO:equivalentObsolete |
 | MONDO:0015172 | Orphanet:103912      | MONDO:equivalentObsolete |
 | MONDO:0015173 | Orphanet:103916      | MONDO:equivalentObsolete |
 | MONDO:0015217 | Orphanet:108985      | MONDO:equivalentObsolete |
 | MONDO:0015218 | Orphanet:108987      | MONDO:equivalentObsolete |
+| MONDO:0015238 | Orphanet:1135        | MONDO:equivalentObsolete |
 | MONDO:0015255 | Orphanet:1256        | MONDO:equivalentObsolete |
 | MONDO:0015297 | Orphanet:137653      | MONDO:equivalentObsolete |
 | MONDO:0015343 | Orphanet:139420      | MONDO:equivalentObsolete |
@@ -29,13 +37,17 @@
 | MONDO:0015593 | Orphanet:163914      | MONDO:equivalentObsolete |
 | MONDO:0015594 | Orphanet:163918      | MONDO:equivalentObsolete |
 | MONDO:0015602 | Orphanet:163988      | MONDO:equivalentObsolete |
+| MONDO:0015637 | Orphanet:166295      | MONDO:equivalentObsolete |
+| MONDO:0015638 | Orphanet:166299      | MONDO:equivalentObsolete |
+| MONDO:0015639 | Orphanet:166302      | MONDO:equivalentObsolete |
 | MONDO:0015902 | Orphanet:181425      | MONDO:equivalentObsolete |
 | MONDO:0015919 | Orphanet:182073      | MONDO:equivalentObsolete |
 | MONDO:0015920 | Orphanet:182076      | MONDO:equivalentObsolete |
 | MONDO:0015937 | Orphanet:182214      | MONDO:equivalentObsolete |
 | MONDO:0015964 | Orphanet:183598      | MONDO:equivalentObsolete |
 | MONDO:0015965 | Orphanet:183601      | MONDO:equivalentObsolete |
 | MONDO:0015985 | Orphanet:1844        | MONDO:equivalentObsolete |
+| MONDO:0016022 | Orphanet:1935        | MONDO:equivalentObsolete |
 | MONDO:0016082 | Orphanet:2042        | MONDO:equivalentObsolete |
 | MONDO:0016111 | Orphanet:206659      | MONDO:equivalentObsolete |
 | MONDO:0016124 | Orphanet:206985      | MONDO:equivalentObsolete |
@@ -47,6 +59,7 @@
 | MONDO:0016997 | Orphanet:263676      | MONDO:equivalentObsolete |
 | MONDO:0017036 | Orphanet:264955      | MONDO:equivalentObsolete |
 | MONDO:0017083 | Orphanet:268832      | MONDO:equivalentObsolete |
+| MONDO:0017199 | Orphanet:2787        | MONDO:equivalentObsolete |
 | MONDO:0017240 | Orphanet:280651      | MONDO:equivalentObsolete |
 | MONDO:0017336 | Orphanet:289527      | MONDO:equivalentObsolete |
 | MONDO:0017378 | Orphanet:2925        | MONDO:equivalentObsolete |
@@ -73,13 +86,17 @@
 | MONDO:0018110 | Orphanet:35064       | MONDO:equivalentObsolete |
 | MONDO:0018113 | Orphanet:35098       | MONDO:equivalentObsolete |
 | MONDO:0018138 | Orphanet:352740      | MONDO:equivalentObsolete |
+| MONDO:0018212 | Orphanet:36382       | MONDO:equivalentObsolete |
 | MONDO:0018239 | Orphanet:364817      | MONDO:equivalentObsolete |
 | MONDO:0018285 | Orphanet:371054      | MONDO:equivalentObsolete |
 | MONDO:0018286 | Orphanet:371064      | MONDO:equivalentObsolete |
+| MONDO:0018574 | Orphanet:436151      | MONDO:equivalentObsolete |
 | MONDO:0018627 | Orphanet:443287      | MONDO:equivalentObsolete |
 | MONDO:0018665 | Orphanet:448348      | MONDO:equivalentObsolete |
 | MONDO:0018718 | Orphanet:458827      | MONDO:equivalentObsolete |
 | MONDO:0018722 | Orphanet:458841      | MONDO:equivalentObsolete |
+| MONDO:0018932 | Orphanet:57777       | MONDO:equivalentObsolete |
+| MONDO:0018981 | Orphanet:64545       | MONDO:equivalentObsolete |
 | MONDO:0019116 | Orphanet:717         | MONDO:equivalentObsolete |
 | MONDO:0019348 | Orphanet:82004       | MONDO:equivalentObsolete |
 | MONDO:0019389 | Orphanet:83648       | MONDO:equivalentObsolete |
@@ -165,12 +182,16 @@
 | MONDO:0020282 | Orphanet:98714       | MONDO:equivalentObsolete |
 | MONDO:0020489 | Orphanet:99763       | MONDO:equivalentObsolete |
 | MONDO:0020524 | Orphanet:99878       | MONDO:equivalentObsolete |
+| MONDO:0020535 | Orphanet:99907       | MONDO:equivalentObsolete |
+| MONDO:0020537 | Orphanet:99909       | MONDO:equivalentObsolete |
 | MONDO:0020742 | Orphanet:1317        | MONDO:equivalentObsolete |
 | MONDO:0020871 | Orphanet:623         | MONDO:equivalentObsolete |
 | MONDO:0021062 | Orphanet:306539      | MONDO:equivalentObsolete |
 | MONDO:0022414 | Orphanet:1526        | MONDO:equivalentObsolete |
 | MONDO:0022921 | Orphanet:2861        | MONDO:equivalentObsolete |
 | MONDO:0023072 | Orphanet:1939        | MONDO:equivalentObsolete |
+| MONDO:0033672 | Orphanet:50817       | MONDO:equivalentObsolete |
 | MONDO:0043007 | Orphanet:330197      | MONDO:equivalentObsolete |
 | MONDO:0044683 | Orphanet:498700      | MONDO:equivalentObsolete |
+| MONDO:0044740 | Orphanet:500481      | MONDO:equivalentObsolete |
 | MONDO:0100343 | Orphanet:93604       | MONDO:equivalentObsolete |
diff --git a/docs/reports/migrate.md b/docs/reports/migrate.md
@@ -2,10 +2,10 @@
 | Ontology                                        | Tot   |
 |:------------------------------------------------|:------|
 | [DOID](./migrate_doid.md)                       | 73    |
+| [ORDO](./migrate_ordo.md)                       | 62    |
+| [OMIM](./migrate_omim.md)                       | 44    |
 | [ICD11FOUNDATION](./migrate_icd11foundation.md) | 4,593 |
-| [OMIM](./migrate_omim.md)                       | 39    |
 | [NCIT](./migrate_ncit.md)                       | 2,211 |
-| [ORDO](./migrate_ordo.md)                       | 13    |
 | [ICD10WHO](./migrate_icd10who.md)               | 119   |
 | [ICD10CM](./migrate_icd10cm.md)                 | 1,894 |
 

diff --git a/docs/reports/migrate_omim.md b/docs/reports/migrate_omim.md
@@ -28,7 +28,7 @@
 | MONDO:0975831 | blood group, anton system                                                                                 | OMIM:620975          | MONDO:equivalentTo         | blood group, anton system                                                                                 |               |               |
 | MONDO:0975832 | immunodeficiency 127                                                                                      | OMIM:620977          | MONDO:equivalentTo         | immunodeficiency 127                                                                                      |               | MONDO:0021094 |
 | MONDO:0975833 | leukodystrophy, hypomyelinating, 28                                                                       | OMIM:620978          | MONDO:equivalentTo         | leukodystrophy, hypomyelinating, 28                                                                       |               | MONDO:0019046 |
-| MONDO:0975834 | immunodeficiency 128                                                                                      | OMIM:620983          | MONDO:equivalentTo         | immunodeficiency 128                                                                                      |               |               |
+| MONDO:0975834 | immunodeficiency 128                                                                                      | OMIM:620983          | MONDO:equivalentTo         | immunodeficiency 128                                                                                      |               | MONDO:0021094 |
 | MONDO:0975835 | bronchiectasis and nasal polyposis                                                                        | OMIM:620984          | MONDO:equivalentTo         | bronchiectasis and nasal polyposis                                                                        |               |               |
 | MONDO:0975836 | karayol-borroto-haghshenas neurodevelopmental syndrome                                                    | OMIM:620985          | MONDO:equivalentTo         | karayol-borroto-haghshenas neurodevelopmental syndrome                                                    |               |               |
 | MONDO:0975837 | neurodegeneration, infantile-onset, with optic atrophy and brain abnormalities                            | OMIM:620987          | MONDO:equivalentTo         | neurodegeneration, infantile-onset, with optic atrophy and brain abnormalities                            |               |               |
@@ -43,4 +43,9 @@
 | MONDO:0975847 | autoimmune disease with susceptibility to mycobacterium tuberculosis                                      | OMIM:621004          | MONDO:equivalentTo         | autoimmune disease with susceptibility to mycobacterium tuberculosis                                      |               |               |
 | MONDO:0975848 | morimoto-ryu-malicdan neuromuscular syndrome                                                              | OMIM:621010          | MONDO:equivalentTo         | morimoto-ryu-malicdan neuromuscular syndrome                                                              |               |               |
 | MONDO:0975874 | neurodevelopmental disorder with dysmorphic facies, absent speech and ambulation, and brain abnormalities | OMIM:621012          | MONDO:equivalentTo         | neurodevelopmental disorder with dysmorphic facies, absent speech and ambulation, and brain abnormalities |               |               |
-| MONDO:0975875 | basal ganglia calcification, idiopathic, 10, autosomal recessive                                          | OMIM:621018          | MONDO:equivalentTo         | basal ganglia calcification, idiopathic, 10, autosomal recessive                                          |               |               |
+| MONDO:0975875 | basal ganglia calcification, idiopathic, 10, autosomal recessive                                          | OMIM:621018          | MONDO:equivalentTo         | basal ganglia calcification, idiopathic, 10, autosomal recessive                                          |               | MONDO:0008947 |
+| MONDO:0975877 | spastic paraplegia, mitochondrial                                                                         | OMIM:500018          | MONDO:equivalentTo         | spastic paraplegia, mitochondrial                                                                         |               |               |
+| MONDO:0975878 | neurodevelopmental disorder with variable familial hypercholanemia                                        | OMIM:621016          | MONDO:equivalentTo         | neurodevelopmental disorder with variable familial hypercholanemia                                        |               |               |
+| MONDO:0975879 | cerebral cavernous malformations 5                                                                        | OMIM:621032          | MONDO:equivalentTo         | cerebral cavernous malformations 5                                                                        |               | MONDO:0031037 |
+| MONDO:0975880 | anemia, congenital, nonspherocytic hemolytic                                                              | OMIMPS:300908        | MONDO:equivalentTo         | Anemia, congenital, nonspherocytic hemolytic                                                              |               |               |
+| MONDO:0975881 | autoinflammation, panniculitis, and dermatosis syndrome                                                   | OMIMPS:617099        | MONDO:equivalentTo         | Autoinflammation, panniculitis, and dermatosis syndrome                                                   |               |               |