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Merge pull request #397 from monarch-initiative/lexmatch-revamp
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Lexmatch revamp
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@twhetzel
twhetzel authored Jan 29, 2024
2 parents 093c186 + f5203b7 commit 28166e2
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8 changes: 4 additions & 4 deletions docs/reports/mapped_deprecated.md
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# Mapped deprecated terms
| Ontology | Tot deprecated in Mondo |
|:--------------------------------------------|--------------------------:|
| [OMIM](./mapped_deprecated_omim.md) | 45 |
| [DOID](./mapped_deprecated_doid.md) | 2 |
| [NCIT](./mapped_deprecated_ncit.md) | 11 |
| [ORDO](./mapped_deprecated_ordo.md) | 0 |
| [OMIM](./mapped_deprecated_omim.md) | 43 |
| [DOID](./mapped_deprecated_doid.md) | 3 |
| [ORDO](./mapped_deprecated_ordo.md) | 225 |
| [NCIT](./mapped_deprecated_ncit.md) | 12 |
| [ICD10CM](./mapped_deprecated_icd10cm.md) | 0 |
| [ICD10WHO](./mapped_deprecated_icd10who.md) | 0 |
| [GARD](./mapped_deprecated_gard.md) | 0 |
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1 change: 1 addition & 0 deletions docs/reports/mapped_deprecated_doid.md
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|:--------------|:---------------------|:-------------------------|
| ID | A oboInOwl:hasDbXref | >A oboInOwl:source |
| MONDO:0002546 | DOID:955 | MONDO:equivalentObsolete |
| MONDO:0003333 | DOID:5209 | MONDO:equivalentObsolete |
| MONDO:0004398 | DOID:7922 | MONDO:equivalentObsolete |
1 change: 1 addition & 0 deletions docs/reports/mapped_deprecated_ncit.md
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| mondo_id | source_id | source |
|:--------------|:---------------------|:-------------------------|
| ID | A oboInOwl:hasDbXref | >A oboInOwl:source |
| MONDO:0002063 | NCIT:C6977 | MONDO:equivalentObsolete |
| MONDO:0003998 | NCIT:C40257 | MONDO:equivalentObsolete |
| MONDO:0004204 | NCIT:C4462 | MONDO:equivalentObsolete |
| MONDO:0004419 | NCIT:C39822 | MONDO:equivalentObsolete |
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2 changes: 0 additions & 2 deletions docs/reports/mapped_deprecated_omim.md
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| MONDO:0010859 | OMIM:600309 | MONDO:equivalentObsolete |
| MONDO:0011111 | OMIM:601563 | MONDO:equivalentObsolete |
| MONDO:0011543 | OMIM:605365 | MONDO:equivalentObsolete |
| MONDO:0011882 | OMIM:607655 | MONDO:equivalentObsolete |
| MONDO:0011910 | OMIM:607801 | MONDO:equivalentObsolete |
| MONDO:0012144 | OMIM:608890 | MONDO:equivalentObsolete |
| MONDO:0012461 | OMIM:610269 | MONDO:equivalentObsolete |
| MONDO:0012560 | OMIM:610799 | MONDO:equivalentObsolete |
| MONDO:0013596 | OMIM:614157 | MONDO:equivalentObsolete |
| MONDO:0013617 | OMIM:614192 | MONDO:equivalentObsolete |
| MONDO:0013701 | OMIM:614339 | MONDO:equivalentObsolete |
| MONDO:0014695 | OMIM:616568 | MONDO:equivalentObsolete |
| MONDO:0014849 | OMIM:616958 | MONDO:equivalentObsolete |
| MONDO:0017996 | OMIM:615057 | MONDO:equivalentObsolete |
| MONDO:0018138 | OMIM:103470 | MONDO:equivalentObsolete |
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231 changes: 228 additions & 3 deletions docs/reports/mapped_deprecated_ordo.md
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10 changes: 5 additions & 5 deletions docs/reports/unmapped.md
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| Ontology | Tot terms | Tot excluded | Tot deprecated | Tot deprecated unmapped | Tot mappable _(!excluded, !deprecated)_ | Tot mapped _(mappable)_ | Tot unmapped _(mappable)_ | % unmapped _(mappable)_ |
|:-----------------------------------|:------------|:---------------|:-----------------|:--------------------------|:------------------------------------------|:--------------------------|:----------------------------|:--------------------------|
| [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 | 1,160 | 79,235 | 98.6% |
| [NCIT](./unmapped_ncit.md) | 187,170 | 166,382 | 5,166 | 5,155 | 15,622 | 3,680 | 11,942 | 76.4% |
| [ICD10CM](./unmapped_icd10cm.md) | 95,847 | 15,452 | 0 | 0 | 80,395 | 1,161 | 79,234 | 98.6% |
| [NCIT](./unmapped_ncit.md) | 187,170 | 166,382 | 5,166 | 5,154 | 15,622 | 3,682 | 11,940 | 76.4% |
| [GARD](./unmapped_gard.md) | 12,004 | 0 | 0 | 0 | 12,004 | 0 | 12,004 | 100.0% |
| [ORDO](./unmapped_ordo.md) | 11,001 | 1,827 | 1,470 | 1,470 | 9,174 | 0 | 9,174 | 100.0% |
| [DOID](./unmapped_doid.md) | 13,863 | 2,642 | 2,477 | 2,469 | 11,219 | 11,088 | 131 | 1.2% |
| [OMIM](./unmapped_omim.md) | 29,054 | 19,096 | 1,359 | 1,314 | 8,600 | 8,518 | 82 | 1.0% |
| [DOID](./unmapped_doid.md) | 13,932 | 2,643 | 2,478 | 2,468 | 11,287 | 11,087 | 200 | 1.8% |
| [ORDO](./unmapped_ordo.md) | 10,915 | 1,724 | 1,391 | 1,166 | 9,191 | 9,025 | 166 | 1.8% |
| [OMIM](./unmapped_omim.md) | 29,164 | 19,168 | 1,359 | 1,316 | 8,638 | 8,522 | 116 | 1.3% |

`Ontology`: Name of ontology
`Tot terms`: Total terms in ontology
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