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Following the discussion during the pre-SAB at OICR (https://docs.google.com/document/d/1svWXeINuRYvJpTnYRpsVwkyvcZQV7LUgmsJ3eSQ6-ac/edit?tab=t.0), the following changes have been made in this pull request:

  • added doRelease to Event (_doRelease at gk_central)
  • added modifiedList to DatabaseObject (originally modified. Right now modified is used to keep the last IE. Avoided "edit" since it may be confused with "edited")
  • Added StableIdentifier class and link it to DatabaseObject as in gk_central
  • Moved GO_Term as a subclass to ExternalOntology (See note below)
  • Added PathwayDiagram class
  • Added RetractionStatus class and retractionStatus attribute to LiteratureReference

Note: In the current version of GO_Term, which is NOT a subclass to ExternalOntology, GO identifiers are called "accession". However, after changing GO_Term as a subclass to ExternalOntology, to make the data model consistent, they are now called "identifier". To make it work, some code in the graph import has to be updated. Please see an example what may need to be changed here: https://github.com/reactome/graph-importer/blob/dd7431b725c2dddf09032ae142c17ab4a0b5ba45/src/main/java/org/reactome/server/graph/batchimport/ReactomeAllInstancesImporter.java#L888.

The following has not been done yet:

  • Add a root node called "ReactomeRoot"
  • Add a new AnnotationType for the attribute type: Mandatory, Required, Optional, NonManualEdit

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