GO_Flow_LLM/mirna_curation_flowchart_author_intent.json at main · RNAcentral/GO_Flow_LLM · GitHub

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{
    "nodes": {
      "experimental_evidence": {
        "type": "conditional_prompt_boolean",
        "data": {
          "desc": "Experimental Evidence?",
          "condition": "hasExperimentalEvidence"
        },
        "transitions": {
          "true": "functional_interaction",
          "false": "no_annotation"
        }
      },
      "functional_interaction": {
        "type": "conditional_prompt_boolean",
        "data": {
          "desc": "Functional interaction by reporter assay?",
          "condition": "hasFunctionalInteraction"
        },
        "transitions": {
          "true": "effect_endogenous_1",
          "false": "mirna_mrna_binding"
        }
      },
      "mirna_mrna_binding": {
        "type": "conditional_prompt_boolean",
        "data": {
          "desc": "miRNA-mRNA binding assay?",
          "condition": "hasBindingAssay"
        },
        "transitions": {
          "true": "effect_endogenous_2",
          "false": "computational_prediction"
        }
      },
      "effect_endogenous_1": {
        "type": "conditional_prompt_boolean",
        "data": {
          "desc": "Effect on endogenous target gene expression?",
          "condition": "hasEndogenousEffect"
        },
        "transitions": {
          "true": "mirna_changes",
          "false": "validated_binding_only"
        }
      },
      "disease_model_1": {
        "type": "conditional_tool_use",
        "data": {
          "desc": "Are the experiments being done in a disease context?",
          "condition": "diseaseModel",
          "tools": ["search_cellosaurus", "search_wikipedia"]
        },
        "transitions": {
          "false" : "validated_binding_only",
          "true": "validated_binding_mrna"
        }
      },
      "disease_model_2": {
        "type": "conditional_tool_use",
        "data": {
          "desc": "Are the experiments being done in a disease context?",
          "condition": "diseaseModel",
          "tools": ["search_cellosaurus", "search_wikipedia"]
        },
        "transitions": {
          "false" : "validated_binding_only",
          "true": "validated_binding_translation"
        }
      },
      "effect_endogenous_2": {
        "type": "conditional_prompt_boolean",
        "data": {
          "desc": "Effect on endogenous target gene expression?",
          "condition": "hasEndogenousEffect"
        },
        "transitions": {
          "true": "mirna_changes",
          "false": "no_annotation"
        }
      },
      "computational_prediction": {
        "type": "conditional_prompt_boolean",
        "data": {
          "desc": "Computational target prediction?",
          "condition": "hasComputationalPrediction"
        },
        "transitions": {
          "true": "effect_endogenous_3",
          "false": "no_annotation"
        }
      },
      "effect_endogenous_3": {
        "type": "conditional_prompt_boolean",
        "data": {
          "desc": "Effect on endogenous target gene expression?",
          "condition": "hasEndogenousEffect"
        },
        "transitions": {
          "true": "no_validated_binding",
          "false": "no_annotation"
        }
      },
      "mirna_changes": {
        "type": "conditional_prompt_boolean",
        "data": {
          "desc": "miRNA inhibition or addition changes endogenous target mRNA level?",
          "condition": "hasMiRNAEffect"
        },
        "transitions": {
          "true": "disease_model_1",
          "false": "disease_model_2"
        }
      },


      "no_annotation": {
        "type": "terminal_short_circuit",
        "data": {
          "desc": "No annotation",
          "terminal": "no_annotation"
        }
      },

      "validated_binding_only": {
        "type": "terminal_full",
        "data": {
          "desc": "Validated binding only",
          "terminal" : "validated_binding_only"

        }
      },
      "validated_binding_mrna": {
        "type": "terminal_full",
        "data": {
          "desc": "Validated binding + evidence of mRNA destabilization",
          "terminal" : "validated_binding_plus_destabilisation"
        }
      },
      "validated_binding_translation": {
        "type": "terminal_full",
        "data": {
          "desc": "Validated binding + evidence of inhibition of translation",
          "terminal" : "validated_binding_plus_trans_inhibition"
        }
      },
      "no_validated_binding": {
        "type": "terminal_conditional",
        "data": {
          "desc": "No validated binding. Decreased expression of target",
          "terminal" : "validated_binding_plus_decreased_expression"
        }
      }
    },
    "startNode": "experimental_evidence"
  }