Merge pull request #554 from monarch-initiative/main-new

`main` <- `develop`

docs/developer/add-new-source.md

@@ -55,12 +55,11 @@ When `mondo-ingest-odk.yaml` is edited and `update_repo` is run, a new `componen
 `src/ontology/Makefile`. This essentially downloads a copy of the source. But, for it to be used in `mondo-ingest`, it 
 needs to be modified. This is done by creating a `$(COMPONENTSDIR)/omim.owl` goal in `mondo-ingest.Makefile` which runs 
 a composite `robot` command. Here are some sections you'll likely want to add that command:  
-- `rename --mappings config/SOURCE-property-map.sssom.tsv`: You'll notice that there are two other lines on most goals 
-for `property-map.sssom.tsv` and `property-map-2.sssom.tsv`. These handle some common renamings. However, 
-if your source has any properties that need to be renamed which are specific to that source, then you should create a 
-new file for that. While doing this, it might be useful to check any other `SOURCE-property-map.sssom.tsv` files to see 
-if they share any of the same property renamings. If so, it might be a good idea to move them to 
-`property-map.sssom.tsv` instead.
+- `rename --mappings config/SOURCE-property-map.sssom.tsv`: You'll notice that all components goals have a such a line 
+using `property-map.sssom.tsv`. This is for some common property renamings. However, if your source has any properties 
+that need to be renamed which are specific to that source, then you should create a new file for that. While doing this,
+ it might be useful to check any other `SOURCE-property-map.sssom.tsv` files to see if they share any of the same  
+property renamings. If so, it might be a good idea to move them to `property-map.sssom.tsv` instead.
 - `query --update ../sparql/SPARQL.ru`: There may be more complex modifications that need to be made to the ontology. If
  so, this can be done by 1 or more SPARQL queries.
 - `remove -T config/properties.txt --select complement --select properties --trim true`: `properties.txt` contains a 
@@ -78,4 +77,4 @@ all of the steps, but with modifications so that you're only running it for the
 For example, instead of `make slurp-all` you'd run `make slurp-*`.
 
 There are a few other files that will probably need to be added as well, such as `src/ontology/config/*_exclusions.tsv`.
-A full list of such things should be found in [this issue](https://github.com/monarch-initiative/mondo-ingest/issues/2).
+A full list of such things should be found in [this issue](https://github.com/monarch-initiative/mondo-ingest/issues/2).

docs/metrics/doid.md

@@ -2,17 +2,17 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/doid.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-28/doid.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-05/doid.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 27 |
-| Axioms | 115971 |
-| Logical axioms | 16110 |
-| Classes | 13099 |
-| Object properties | 2 |
+| Axioms | 110948 |
+| Logical axioms | 16161 |
+| Classes | 13124 |
+| Object properties | 0 |
 | Data properties | 0 |
 | Individuals | 0 |
 
@@ -32,11 +32,11 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 86733 |
+| AnnotationAssertion | 81636 |
 | SubAnnotationPropertyOf | 1 |
 | DisjointClasses | 26 |
-| Declaration | 13127 |
-| SubClassOf | 16084 |
+| Declaration | 13150 |
+| SubClassOf | 16135 |
 
 
 #### Entity namespaces: axiom counts by namespace
@@ -45,12 +45,11 @@
 | ------ | ----- |
 | oboInOwl | 12 |
 | owl | 2 |
-| DOID | 11552 |
+| DOID | 11577 |
 | HP | 118 |
 | xsd | 1 |
 | CL | 63 |
 | skos | 5 |
-| BFO | 2 |
 | rdfs | 2 |
 | FOODON | 24 |
 | NCBITaxon | 322 |
@@ -71,7 +70,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 45479 |
+| Class | 45606 |
 
 
 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).

docs/metrics/gard.md

@@ -2,7 +2,7 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/gard.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-28/gard.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-05/gard.owl
 
 ### Entities and axioms
 

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/2024-05-28/icd10cm.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-05/icd10cm.owl
 
 ### Entities and axioms
 

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/2024-05-28/icd10who.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-05/icd10who.owl
 
 ### Entities and axioms
 

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/2024-05-28/icd11foundation.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-05/icd11foundation.owl
 
 ### Entities and axioms
 

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/2024-05-28/ncit.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-05/ncit.owl
 
 ### Entities and axioms
 

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/2024-05-28/omim.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-05/omim.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 18 |
-| Axioms | 346016 |
-| Logical axioms | 22718 |
-| Classes | 19502 |
+| Axioms | 346108 |
+| Logical axioms | 22736 |
+| Classes | 19509 |
 | Object properties | 7 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,17 +32,17 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 303774 |
+| AnnotationAssertion | 303841 |
 | SubAnnotationPropertyOf | 1 |
-| Declaration | 19523 |
-| SubClassOf | 22718 |
+| Declaration | 19530 |
+| SubClassOf | 22736 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| prefix_unknown | 18056 |
+| prefix_unknown | 18063 |
 | oboInOwl | 4 |
 | owl | 2 |
 | xsd | 1 |
@@ -61,8 +61,8 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 64928 |
-| ObjectSomeValuesFrom | 17803 |
+| Class | 64971 |
+| ObjectSomeValuesFrom | 17811 |
 
 
 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).

docs/metrics/ordo.md

@@ -2,7 +2,7 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/ordo.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-28/ordo.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-05/ordo.owl
 
 ### Entities and axioms
 

docs/reports/migrate.md

@@ -2,7 +2,7 @@
 | Ontology                                        | Tot    |
 |:------------------------------------------------|:-------|
 | [GARD](./migrate_gard.md)                       | 9,370  |
-| [DOID](./migrate_doid.md)                       | 8      |
+| [DOID](./migrate_doid.md)                       | 34     |
 | [NCIT](./migrate_ncit.md)                       | 2,209  |
 | [OMIM](./migrate_omim.md)                       | 13     |
 | [ICD11FOUNDATION](./migrate_icd11foundation.md) | 12,409 |