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DO NOT MERGE: Address qc-duplicate-exact-synonym-no-abbrev failures in mondo - build #755

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DO NOT MERGE: Address qc-duplicate-exact-synonym-no-abbrev failures in mondo - build #755

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8c2c20d
Handle qc-duplicate-exact-synonym-no-abbrev failures in mondo
joeflack4 Jan 14, 2025
cd97eb9
Handle qc-duplicate-exact-synonym-no-abbrev failures in mondo
joeflack4 Jan 16, 2025
ef609cc
Handle qc-duplicate-exact-synonym-no-abbrev failures in mondo
joeflack4 Jan 16, 2025
5db2c39
Handle qc-duplicate-exact-synonym-no-abbrev failures in mondo
joeflack4 Jan 16, 2025
9c00b38
Handle qc-duplicate-exact-synonym-no-abbrev failures in mondo
joeflack4 Jan 16, 2025
016ff3e
Handle qc-duplicate-exact-synonym-no-abbrev failures in mondo - build
joeflack4 Jan 16, 2025
d7c2038
Handle qc-duplicate-exact-synonym-no-abbrev failures in mondo - build
joeflack4 Jan 23, 2025
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6 changes: 3 additions & 3 deletions docs/reports/mapped_deprecated.md
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Expand Up @@ -2,9 +2,9 @@
| Ontology | Tot deprecated in Mondo |
|:----------------------------------------------------------|--------------------------:|
| [NCIT](./mapped_deprecated_ncit.md) | 5 |
| [OMIM](./mapped_deprecated_omim.md) | 48 |
| [DOID](./mapped_deprecated_doid.md) | 2 |
| [ORDO](./mapped_deprecated_ordo.md) | 190 |
| [OMIM](./mapped_deprecated_omim.md) | 45 |
| [ORDO](./mapped_deprecated_ordo.md) | 171 |
| [DOID](./mapped_deprecated_doid.md) | 1 |
| [ICD11FOUNDATION](./mapped_deprecated_icd11foundation.md) | 0 |
| [ICD10CM](./mapped_deprecated_icd10cm.md) | 0 |
| [ICD10WHO](./mapped_deprecated_icd10who.md) | 0 |
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3 changes: 1 addition & 2 deletions docs/reports/mapped_deprecated_doid.md
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Expand Up @@ -5,5 +5,4 @@
| mondo_id | source_id | source |
|:--------------|:---------------------|:-------------------------|
| ID | A oboInOwl:hasDbXref | >A oboInOwl:source |
| MONDO:0011893 | DOID:0110578 | MONDO:equivalentObsolete |
| MONDO:0013209 | DOID:0080546 | MONDO:equivalentObsolete |
| MONDO:0011893 | DOID:0110578 | MONDO:equivalentObsolete |
3 changes: 0 additions & 3 deletions docs/reports/mapped_deprecated_omim.md
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Expand Up @@ -7,7 +7,6 @@
| ID | A oboInOwl:hasDbXref | >A oboInOwl:source |
| MONDO:0000911 | OMIM:613740 | MONDO:equivalentObsolete |
| MONDO:0007061 | OMIM:102590 | MONDO:equivalentObsolete |
| MONDO:0007066 | OMIM:102800 | MONDO:equivalentObsolete |
| MONDO:0007602 | OMIM:134700 | MONDO:equivalentObsolete |
| MONDO:0007659 | OMIM:137560 | MONDO:equivalentObsolete |
| MONDO:0007779 | OMIM:145410 | MONDO:equivalentObsolete |
Expand All @@ -31,10 +30,8 @@
| MONDO:0010527 | OMIM:301590 | MONDO:equivalentObsolete |
| MONDO:0010601 | OMIM:306500 | MONDO:equivalentObsolete |
| MONDO:0010666 | OMIM:309605 | MONDO:equivalentObsolete |
| MONDO:0010760 | OMIM:314800 | MONDO:equivalentObsolete |
| MONDO:0010804 | OMIM:600048 | MONDO:equivalentObsolete |
| MONDO:0010859 | OMIM:600309 | MONDO:equivalentObsolete |
| MONDO:0010996 | OMIM:601101 | MONDO:equivalentObsolete |
| MONDO:0011111 | OMIM:601563 | MONDO:equivalentObsolete |
| MONDO:0011543 | OMIM:605365 | MONDO:equivalentObsolete |
| MONDO:0011893 | OMIM:607683 | MONDO:equivalentObsolete |
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19 changes: 0 additions & 19 deletions docs/reports/mapped_deprecated_ordo.md
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Expand Up @@ -7,26 +7,18 @@
| 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 |
Expand All @@ -37,17 +29,13 @@
| 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 |
Expand All @@ -59,7 +47,6 @@
| 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 |
Expand All @@ -86,7 +73,6 @@
| 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 |
Expand All @@ -95,8 +81,6 @@
| 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 |
Expand Down Expand Up @@ -182,16 +166,13 @@
| 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 |
8 changes: 4 additions & 4 deletions docs/reports/unmapped.md
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Expand Up @@ -4,10 +4,10 @@
| [ICD10WHO](./unmapped_icd10who.md) | 12,542 | 0 | 0 | 0 | 12,542 | 18 | 12,524 | 99.9% |
| [ICD10CM](./unmapped_icd10cm.md) | 95,847 | 15,452 | 0 | 0 | 80,395 | 1,166 | 79,229 | 98.5% |
| [ICD11FOUNDATION](./unmapped_icd11foundation.md) | 57,713 | 0 | 5,594 | 5,594 | 52,119 | 4,108 | 48,011 | 92.1% |
| [NCIT](./unmapped_ncit.md) | 191,123 | 169,937 | 5,221 | 5,216 | 15,965 | 3,676 | 12,289 | 77.0% |
| [ORDO](./unmapped_ordo.md) | 15,632 | 6,310 | 1,444 | 1,254 | 9,322 | 9,195 | 127 | 1.4% |
| [DOID](./unmapped_doid.md) | 14,220 | 2,661 | 2,489 | 2,477 | 11,557 | 11,456 | 101 | 0.9% |
| [OMIM](./unmapped_omim.md) | 29,589 | 19,412 | 1,370 | 1,322 | 8,808 | 8,759 | 49 | 0.6% |
| [NCIT](./unmapped_ncit.md) | 191,123 | 169,937 | 5,221 | 5,216 | 15,965 | 3,732 | 12,233 | 76.6% |
| [ORDO](./unmapped_ordo.md) | 15,632 | 6,310 | 1,444 | 1,273 | 9,322 | 9,195 | 127 | 1.4% |
| [DOID](./unmapped_doid.md) | 14,220 | 2,661 | 2,489 | 2,478 | 11,557 | 11,455 | 102 | 0.9% |
| [OMIM](./unmapped_omim.md) | 29,596 | 19,414 | 1,370 | 1,325 | 8,813 | 8,759 | 54 | 0.6% |

`Ontology`: Name of ontology
`Tot terms`: Total terms in ontology
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3 changes: 2 additions & 1 deletion docs/reports/unmapped_doid.md
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Expand Up @@ -104,4 +104,5 @@
| DOID:0070620 | ring chromosome syndrome |
| DOID:0060989 | short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1 |
| DOID:0061007 | sideroblastic anemia 5 |
| DOID:0060998 | striatal degeneration 2 |
| DOID:0060998 | striatal degeneration 2 |
| DOID:0050706 | variable age at onset electroclinical syndrome |
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