Added some manual mappings from cam-kp-api PR 640.

cam-kp-api PR 640: ExposuresProvider/cam-kp-api#640

scripts/generate_ro_biolink_mapping.sc

@@ -38,6 +38,27 @@ import io.circe.generic.auto._
  */
 
 object ROBiolinkMappingsGenerator extends ZIOAppDefault with LazyLogging {
+ /* Some manual annotations (we should try to move these into Biolink model so we don't need to deal with them ourselves. */
+
+ val manualPredicateMappingRows = Seq(
+ PredicateMappingRow(
+ predicate = "biolink:regulates", // Is this the best one?
+ `mapped predicate` = None,
+ `object aspect qualifier` = None,
+ `object direction qualifier` = Some("downregulated"),
+ `qualified predicate` = None,
+ `exact matches` = Some(Set("RO:0002305")), // causally upstream of, negative effect
+ ),
+ PredicateMappingRow(
+ predicate = "biolink:regulates", // Is this the best one?
+ `mapped predicate` = None,
+ `object aspect qualifier` = None,
+ `object direction qualifier` = Some("upregulated"),
+ `qualified predicate` = None,
+ `exact matches` = Some(Set("RO:0002304")), // causally upstream of, positive effect
+ )
+ )
+
  /* Configuration for this generator */
  case class Conf(
  outputFilename: String,
@@ -53,7 +74,7 @@ object ROBiolinkMappingsGenerator extends ZIOAppDefault with LazyLogging {
  githubPredicateMappings <- getPredicateMappingsFromGitHub(conf)
  _ = logger.info(s"Loaded ${githubBiolinkModel.length} mappings from the Biolink model and ${githubPredicateMappings.length} mappings from the predicate mappings file.")
 
- countPredsWritten <- writePredicates(githubBiolinkModel ++ githubPredicateMappings, conf.outputFilename)
+ countPredsWritten <- writePredicates(githubBiolinkModel ++ githubPredicateMappings ++ manualPredicateMappingRows, conf.outputFilename)
  _ = logger.info(s"Wrote out ${countPredsWritten} to ${conf.outputFilename}.")
  } yield ()