Skeleton of docs for externally provided content

docs/editors-guide/externally-managed-content.md

@@ -0,0 +1,96 @@
+## Externally managed content
+
+- [Overview](#overview)
+- [Synchronisation system](#sync)
+- [List of external content providers](#providers)
+
+### Overview
+
+In 2024, we have begun outsourcing a few select dataypes to trusted external providers.
+We collaborate with these providers as follows:
+
+1. We agree on the content provided.
+1. The external provider provides the content in a table format that we can easily integrate (for example a ROBOT template TSV)
+1. We synchronize that content together with all other external content as part of the [Mondo Ingest pipeline](https://github.com/monarch-initiative/mondo-ingest)
+1. We periodically integrate the content into the Mondo ontology
+   **Note**: The content is integrated into Mondo without a detailed curation review.
+
+<a id="sync"></a>
+
+### Synchronisation system
+
+<a id="providers"></a>
+
+### List of external content providers
+
+**Providers**:
+
+- [ClinGen](#clingen)
+- [MedGen](#medgen)
+- [NORD](#nord)
+- [GARD](#gard)
+- [Orphanet](#orphanet)
+- [Open Targets](#otar)
+- [Nando](#nando)
+
+<a id="clingen"></a>
+
+#### Clinical Genome Resource (ClinGen)
+
+- ClinGen linkouts
+- ClinGen preferred names
+- ClinGen subset (terms used by ClinGen)
+
+<a id="medgen"></a>
+
+#### NCBI's Medical Genetics Portal (MedGen)
+
+MedGen is NCBI's portal to information about conditions and phenotypes related to Medical Genetics.
+
+- [Website](https://www.ncbi.nlm.nih.gov/medgen/)
+- Externally managed content:
+    - Mondo -  Medgen mappings
+    - Mondo - UMLS mappings
+    - Mondo - MESH mappings (currently on hold)
+
+<a id="nord"></a>
+
+#### National Organization for Rare Disorders (NORD)
+
+- NORD rare subset (Mondo IDs deemed "rare" by NORD)
+- NORD preferred names (report names)
+- NORD cross-references
+
+<a id="gard"></a>
+
+#### Genetic and Rare Diseases (GARD) Information Center
+
+- GARD rare subset
+- GARD cross-references
+
+<a id="orphanet"></a>
+
+#### Orphanet
+
+- Subsets for `disorder`, `group of disorders`, `subtype of a disorder`.
+- Rare subset (based on `disorder` subset above)
+
+<a id="otar"></a>
+
+#### Open Targets (OTAR)
+
+- Mondo - EFO mappings (managed by EBI)
+- Open Targets subset (terms used by Open Targets)
+
+<a id="nando"></a>
+
+#### NANDO
+
+- Mondo - Nando mappings (managed by DBCLS)
+- Nando rare subset
+
+#### OMIM
+
+- Mondo - OMIM phenotype associations
+- 
+

mkdocs.yml

@@ -70,6 +70,7 @@ nav:
       - Using Mondo for Data curation: editors-guide/using-mondo-for-curation.md
       - Sample code: editors-guide/sample-code.md
       - Rare disease subset: editors-guide/rare-disease-subset.md
+      - Externally managed content: editors-guide/externally-managed-content.md
     - Cite:
       - Cite Mondo: editors-guide/cite.md
     - Project management: