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Generate test data #620

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@gaurav gaurav commented Feb 7, 2023

This PR adds a utility for generating test data for CAM-KP-API -- this will likely be in JSONL format initially, with an additional script that can transform it into the format for SRI Testing.

Closes #556.

Should be merged after PR #635.

WIP: once this has been implemented, this should be added to x-trapi as per #556

WIP: needs to transform into the final format, need to update this for Biolink 3. Also, while the algorithm probably works well to ensure that all the subject and objects are included, it currently just queries biolink:related_to for the predicate. This means that the predicates returned are inconsistent. Here is the current predicate distribution in test-edges.jsonl as of eb0d266:

   2 "biolink:entity_positively_regulates_entity"
   2 "biolink:has_output"
   2 "biolink:produces"
   4 "biolink:location_of"
   5 "biolink:enables"
   5 "biolink:process_regulates_process"
   6 "biolink:negatively_regulates"
   7 "biolink:interacts_with"
   9 "biolink:active_in"
   9 "biolink:located_in"
  10 "biolink:entity_regulates_entity"
  11 "biolink:has_input"
  12 "biolink:caused_by"
  14 "biolink:preceded_by"
  16 "biolink:positively_regulates"
  16 "biolink:precedes"
  17 "biolink:acts_upstream_of_or_within_positive_effect"
  24 "biolink:acts_upstream_of"
  37 "biolink:affects_activity_of"
  43 "biolink:actively_involved_in"
  47 "biolink:enabled_by"
  51 "biolink:occurs_in"
  58 "biolink:capable_of"
  61 "biolink:has_participant"
  62 "biolink:molecularly_interacts_with"
  66 "biolink:related_to"
  84 "biolink:has_part"
  99 "biolink:participates_in"
 142 "biolink:overlaps"
 189 "biolink:part_of"

@gaurav gaurav mentioned this pull request Mar 28, 2023
@gaurav gaurav changed the base branch from master to replace-predicate-mapping March 28, 2023 16:34
We should now have everything we need to make this work. Unfortunately,
of course, it doesn't. So now we need to figure out why.
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