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Feature data release and patch for the lexmatch generation (#582)
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* Add confidence fill conditional in lexmatch compare

Currently the filter_redundant_rows in the sssom packages fails when

1. There is a confidence columns and
2. no single value is set

This needs to be fixed in sssom package.

In the meantime, this is a workaround.

* Update all data

* update ingest data files

* Delete src/ontology/check_me_out.sssom.tsv

* Another re-run
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matentzn authored Jun 24, 2024
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2 changes: 1 addition & 1 deletion docs/metrics/doid.md
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**IRI:** http://purl.obolibrary.org/obo/mondo/sources/doid.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-18/doid.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-22/doid.owl

### Entities and axioms

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2 changes: 1 addition & 1 deletion docs/metrics/gard.md
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**IRI:** http://purl.obolibrary.org/obo/mondo/sources/gard.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-18/gard.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-22/gard.owl

### Entities and axioms

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2 changes: 1 addition & 1 deletion docs/metrics/icd10cm.md
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**IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd10cm.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-18/icd10cm.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-22/icd10cm.owl

### Entities and axioms

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2 changes: 1 addition & 1 deletion docs/metrics/icd10who.md
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**IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd10who.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-18/icd10who.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-22/icd10who.owl

### Entities and axioms

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2 changes: 1 addition & 1 deletion docs/metrics/icd11foundation.md
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**IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd11foundation.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-18/icd11foundation.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-22/icd11foundation.owl

### Entities and axioms

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2 changes: 1 addition & 1 deletion docs/metrics/ncit.md
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**IRI:** http://purl.obolibrary.org/obo/mondo/sources/ncit.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-18/ncit.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-22/ncit.owl

### Entities and axioms

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2 changes: 1 addition & 1 deletion docs/metrics/omim.md
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**IRI:** http://purl.obolibrary.org/obo/mondo/sources/omim.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-18/omim.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-22/omim.owl

### Entities and axioms

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2 changes: 1 addition & 1 deletion docs/metrics/ordo.md
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**IRI:** http://purl.obolibrary.org/obo/mondo/sources/ordo.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-18/ordo.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-22/ordo.owl

### Entities and axioms

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4 changes: 2 additions & 2 deletions docs/reports/migrate.md
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| [GARD](./migrate_gard.md) | 9,370 |
| [DOID](./migrate_doid.md) | 34 |
| [NCIT](./migrate_ncit.md) | 2,209 |
| [OMIM](./migrate_omim.md) | 15 |
| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 12,409 |
| [ICD10WHO](./migrate_icd10who.md) | 119 |
| [ORDO](./migrate_ordo.md) | 10 |
| [ICD10CM](./migrate_icd10cm.md) | 1,889 |
| [OMIM](./migrate_omim.md) | 0 |
| [ORDO](./migrate_ordo.md) | 0 |

### Codebook
`Ontology`: Name of ontology
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21 changes: 3 additions & 18 deletions docs/reports/migrate_omim.md
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[Interactive FlatGithub table](https://flatgithub.com/monarch-initiative/mondo-ingest?filename=src/ontology/slurp/omim.tsv)

### Migratable terms
| mondo_id | mondo_label | xref | xref_source | original_label | definition | parents |
|:--------------|:-------------------------------------------|:---------------------|:---------------------------|:-------------------------------------------|:--------------|:----------------------------|
| ID | LABEL | A oboInOwl:hasDbXref | >A oboInOwl:source SPLIT=| | | A IAO:0000115 | SC % |
| MONDO:0970998 | immunodeficiency 121 with autoinflammation | OMIM:620807 | MONDO:equivalentTo | immunodeficiency 121 with autoinflammation | | MONDO:0021094 |
| MONDO:0971002 | spermatogenic failure 94 | OMIM:620850 | MONDO:equivalentTo | spermatogenic failure 94 | | MONDO:0004983 |
| MONDO:0971004 | amyloidosis, hereditary systemic 1 | OMIM:105210 | MONDO:equivalentTo | amyloidosis, hereditary systemic 1 | | MONDO:0007100 |
| MONDO:0971005 | mhc class 2 deficiency 1 | OMIM:209920 | MONDO:equivalentTo | mhc class 2 deficiency 1 | | MONDO:0031520|MONDO:0008855 |
| MONDO:0971006 | mhc class 1 deficiency 1 | OMIM:604571 | MONDO:equivalentTo | mhc class 1 deficiency 1 | | MONDO:0011476 |
| MONDO:0971007 | neuroocular syndrome 1 | OMIM:619539 | MONDO:equivalentTo | neuroocular syndrome 1 | | MONDO:0859193 |
| MONDO:0971008 | amyloidosis, hereditary systemic 3 | OMIM:620657 | MONDO:equivalentTo | amyloidosis, hereditary systemic 3 | | MONDO:0007100 |
| MONDO:0971009 | amyloidosis, hereditary systemic 5 | OMIM:620658 | MONDO:equivalentTo | amyloidosis, hereditary systemic 5 | | MONDO:0007100 |
| MONDO:0971010 | amyloidosis, hereditary systemic 6 | OMIM:620659 | MONDO:equivalentTo | amyloidosis, hereditary systemic 6 | | MONDO:0007100 |
| MONDO:0971011 | mhc class 1 deficiency 2 | OMIM:620813 | MONDO:equivalentTo | mhc class 1 deficiency 2 | | MONDO:0011476 |
| MONDO:0971012 | mhc class 1 deficiency 3 | OMIM:620814 | MONDO:equivalentTo | mhc class 1 deficiency 3 | | MONDO:0011476 |
| MONDO:0971013 | mhc class 2 deficiency 2 | OMIM:620815 | MONDO:equivalentTo | mhc class 2 deficiency 2 | | MONDO:0008855 |
| MONDO:0971014 | mhc class 2 deficiency 3 | OMIM:620816 | MONDO:equivalentTo | mhc class 2 deficiency 3 | | MONDO:0008855 |
| MONDO:0971015 | mhc class 2 deficiency 4 | OMIM:620817 | MONDO:equivalentTo | mhc class 2 deficiency 4 | | MONDO:0008855 |
| MONDO:0971016 | mhc class 2 deficiency 5 | OMIM:620818 | MONDO:equivalentTo | mhc class 2 deficiency 5 | | MONDO:0008855 |
| mondo_id | mondo_label | xref | xref_source | original_label | definition | parents |
|:-----------|:--------------|:---------------------|:---------------------------|:-----------------|:--------------|:----------|
| ID | LABEL | A oboInOwl:hasDbXref | >A oboInOwl:source SPLIT=| | | A IAO:0000115 | SC % |
16 changes: 3 additions & 13 deletions docs/reports/migrate_ordo.md
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[Interactive FlatGithub table](https://flatgithub.com/monarch-initiative/mondo-ingest?filename=src/ontology/slurp/ordo.tsv)

### Migratable terms
| mondo_id | mondo_label | xref | xref_source | original_label | definition | parents | subset |
|:--------------|:-----------------------------------------------------|:---------------------|:---------------------------|:-----------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------|:----------------------|
| ID | LABEL | A oboInOwl:hasDbXref | >A oboInOwl:source SPLIT=| | | A IAO:0000115 | SC % | |
| MONDO:0968990 | genetic central precocious puberty in male | Orphanet:650097 | MONDO:equivalentTo | Genetic central precocious puberty in male | | MONDO:8000031|MONDO:0958356 | subtype of a disorder |
| MONDO:0968991 | non-genetic central precocious puberty in male | Orphanet:650102 | MONDO:equivalentTo | Non-genetic central precocious puberty in male | | MONDO:0958356|MONDO:8000031 | subtype of a disorder |
| MONDO:0970957 | terminal extramedullary conus spinal cord lipoma | Orphanet:645288 | MONDO:equivalentTo | Terminal extramedullary conus spinal cord lipoma | A rare form of extramedullary conus region spinal cord lipoma characterized by its location, extending from the poorly delineated tip of the conus. | MONDO:0968987|MONDO:8000031 | subtype of a disorder |
| MONDO:0970958 | transitional extramedullary conus spinal cord lipoma | Orphanet:645291 | MONDO:equivalentTo | Transitional extramedullary conus spinal cord lipoma | A rare form of extramedullary conus region spinal cord lipoma characterized by a location at the posterior surface of the conus and its tip. i.e-"transitional" between posterior and terminal conus region spinal cord lipoma. | MONDO:0968987|MONDO:8000031 | subtype of a disorder |
| MONDO:0970959 | posterior extramedullary conus spinal cord lipoma | Orphanet:645294 | MONDO:equivalentTo | Posterior extramedullary conus spinal cord lipoma | A rare form of conus region spinal cord lipoma characterized by its location where the interface between the lipoma and the spinal cord is strictcly above the level of the tip of the conus. The tip of the conus is readily delineated. | MONDO:0968987|MONDO:8000031 | subtype of a disorder |
| MONDO:0970960 | lipomatous non-saccular limited dorsal myeloschisis | Orphanet:645300 | MONDO:equivalentTo | Lipomatous non-saccular limited dorsal myeloschisis | A rare non-saccular limited dorsal myeloschisis histologically characterized by skin tissue with a jagged depression of squamous epithelium continued to subcutaneous mature adipose tissue with loose connective tissue. GFAP-immunopositive glial cells are embedded in the subcutaneous lipoma. The extradural and intradural stalk have cord-like fibrocollagenous tissue containing adipose tissue, peripheral nerve fibers, clusters of melanocytes, and skeletal muscle fibers. | MONDO:0968989|MONDO:8000031 | subtype of a disorder |
| MONDO:0970961 | fibroneural non-saccular limited dorsal myeloschisis | Orphanet:645310 | MONDO:equivalentTo | Fibroneural non-saccular limited dorsal myeloschisis | A rare non-saccular limited dorsal myeloschisis, in which the stalk histology is characterized by skin tissue with dermo-epidermal epithelium in continuity with a subcutaneous fibrocollagenous tract containing various ectopic tissues. | MONDO:8000031|MONDO:0968989 | subtype of a disorder |
| MONDO:0970962 | terminal myelocystocele | Orphanet:645337 | MONDO:equivalentTo | Terminal myelocystocele | A rare closed spinal dysraphism characterized by a myelocystocele at the termination of the spinal cord. It may be an isolated anomaly or be associated with other defects, including sacral agenesis, anorectal and genitourinary anomalies. The conus is not identifiable. The myelocystocele sac may have a significant lipomatous component (terminal lipomyelocystocele). | MONDO:0968988|MONDO:8000034|MONDO:8000030|MONDO:0017077 | disorder |
| MONDO:0970963 | saccular limited dorsal myeloschisis | Orphanet:645354 | MONDO:equivalentTo | Saccular limited dorsal myeloschisis | A rare form of limited dorsal myeloschisis (LDM), characterized by the stalk attached to the apex of a fully epithelialized meningocele. Chiari II malformation is not present. | MONDO:0968988|MONDO:8000034|MONDO:8000030 | disorder |
| MONDO:0970964 | myelic limited dorsal malformation | Orphanet:645378 | MONDO:equivalentTo | Myelic limited dorsal malformation | A rare intermediate form of open dysraphism between myelomeningocele and saccular limited dorsal myeloschisis without fulfilling the characteristics of one of these two diagnosis, characterized by stretched neurulated spinal cord attached at the dome of a sac. Partial cerebral signs of open dysraphism can be observed and the meningocele is usually poorly epithelialized. | MONDO:0968988|MONDO:8000034|MONDO:8000030 | disorder |
| mondo_id | mondo_label | xref | xref_source | original_label | definition | parents | subset |
|:-----------|:--------------|:---------------------|:---------------------------|:-----------------|:--------------|:----------|:---------|
| ID | LABEL | A oboInOwl:hasDbXref | >A oboInOwl:source SPLIT=| | | A IAO:0000115 | SC % | |
4 changes: 2 additions & 2 deletions docs/reports/unmapped.md
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| [NCIT](./unmapped_ncit.md) | 191,123 | 169,937 | 5,221 | 5,199 | 15,965 | 3,675 | 12,290 | 77.0% |
| [ICD11FOUNDATION](./unmapped_icd11foundation.md) | 100,382 | 30,335 | 6,587 | 6,587 | 64,451 | 0 | 64,451 | 100.0% |
| [GARD](./unmapped_gard.md) | 12,004 | 0 | 0 | 0 | 12,004 | 0 | 12,004 | 100.0% |
| [ORDO](./unmapped_ordo.md) | 15,402 | 6,212 | 1,391 | 1,165 | 9,190 | 9,127 | 63 | 0.7% |
| [ORDO](./unmapped_ordo.md) | 15,402 | 6,212 | 1,391 | 1,165 | 9,190 | 9,137 | 53 | 0.6% |
| [DOID](./unmapped_doid.md) | 14,058 | 2,655 | 2,483 | 2,468 | 11,401 | 11,367 | 34 | 0.3% |
| [OMIM](./unmapped_omim.md) | 29,362 | 19,260 | 1,364 | 1,318 | 8,739 | 8,724 | 15 | 0.2% |
| [OMIM](./unmapped_omim.md) | 29,362 | 19,260 | 1,364 | 1,318 | 8,739 | 8,739 | 0 | 0.0% |

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