Ingest source terms into Mondo¶
There are three phases of ingesting source terms into Mondo:¶
- Mapping creates links between existing Mondo classes and external ids
- "Migrating" or "syncing" updates the content of Mondo in the light of changes to sources. For example a subclassOf axiom previously supported by ORDO may have been removed in the latest release. If ORDO was the only source supporting that axiom, we may want to also drop it.
- Slurping moves an entire term over from a source, if no suitable mapping was found. It is almost like migrating, but it involves some additional tasks, like “minting” a new Mondo ID, adding a candidate rdfs:label (during migration, we will never change the rdfs:label of a term).
Further instructions for the OMIM sync/slurp are documented here.
Definitions (Under development)¶
The approach to handling definitions is under development. Potential approaches are: 1. We could check if a definition is present, and if it is present choose not to migrate a definition from the source under consideration. This requires keeping some kind of if-else logic in the migration code. 2. Alternatively, we could create a new annotation property like "definitionAtSource" or something and add all definitions from each source.