diff --git a/docs/editors-guide/externally-managed-content.md b/docs/editors-guide/externally-managed-content.md new file mode 100644 index 0000000000..2edc3795bd --- /dev/null +++ b/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. + + + +### Synchronisation system + + + +### List of external content providers + +**Providers**: + +- [ClinGen](#clingen) +- [MedGen](#medgen) +- [NORD](#nord) +- [GARD](#gard) +- [Orphanet](#orphanet) +- [Open Targets](#otar) +- [Nando](#nando) + + + +#### Clinical Genome Resource (ClinGen) + +- ClinGen linkouts +- ClinGen preferred names +- ClinGen subset (terms used by ClinGen) + + + +#### 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) + + + +#### National Organization for Rare Disorders (NORD) + +- NORD rare subset (Mondo IDs deemed "rare" by NORD) +- NORD preferred names (report names) +- NORD cross-references + + + +#### Genetic and Rare Diseases (GARD) Information Center + +- GARD rare subset +- GARD cross-references + + + +#### Orphanet + +- Subsets for `disorder`, `group of disorders`, `subtype of a disorder`. +- Rare subset (based on `disorder` subset above) + + + +#### Open Targets (OTAR) + +- Mondo - EFO mappings (managed by EBI) +- Open Targets subset (terms used by Open Targets) + + + +#### NANDO + +- Mondo - Nando mappings (managed by DBCLS) +- Nando rare subset + +#### OMIM + +- Mondo - OMIM phenotype associations +- + diff --git a/mkdocs.yml b/mkdocs.yml index 8f6517ca82..1a8dfd3e6c 100644 --- a/mkdocs.yml +++ b/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: