Merge pull request #44 from DARPA-ASKEM/3964-model-enrichment

3964 model enrichment

gollm/openai/prompts/petrinet_config.py

@@ -6,15 +6,33 @@
       Return the different sets of initial parameters for the petri net model file like so:
 	  {{"conditions": {{"condition_1": "description of condition_1", "condition_2": "description of condition_2", ...}},
 	  "parameters": [{{
-      "id": "beta",
-      "value": {{'condition_1': 0.1, 'condition_2': 0.2}},
+		"id": "beta",
+		"name": "β",
+		"value": {{'condition_1': 0.1, 'condition_2': 0.2}},
+		"description": "infection rate",
+		"units": {{ "expression": "1/(person*day)", "expression_mathml": "<apply><divide/><cn>1</cn><apply><times/><ci>person</ci><ci>day</ci></apply></apply>" }}
+		"distribution": {{
+			"type": "Uniform1",
+			"parameters": {{
+				"minimum": 2.6e-7,
+				"maximum": 2.8e-7
+			}}
+		}},
       ....
       }}
 	  ],
       }}
       If a condition is not mentioned in the following text body, then the value should be set to the string "null". Be sure to use consistent naming conventions for the conditions.
       Instead of 'condition_1' and 'condition_2'.. use names that are descriptive of the conditions.
-      Only use parameters found in the reference petrinet file provided above.
+
+	  For each parameter, following below instructions, fill the value for `name`, `description`, `units`, and `distribution` fields if not provided in the petrinet file.
+	  - For the name, extract from the user provided text or derive it from the id whenever possible. Here are some examples of id to name mappings: {{ id: "beta", name: "β" }}, {{ id: "gamma", name: "γ" }}, {{ id: "S0", name: "S₀" }}, {{ id: "I0", name: "R₀" }}. If a name can't be generated, omit the field.
+	  - For the description, provide long-form description of the parameter. If the description can not be found, set it to an empty string "",
+	  - For units, provide both "units.expression" (a unicode string) and "units.expression_mathml" (MathML format). Ensure both units are valid and represent the same unit. If the unit is not found or not valid, omit the units field.
+	  - For the distribution, if present, provide 'distribution.type' and 'distribution.parameters' using 'name' and 'parameters' from the following probability distribution ontology JSON. If a valid distribution is not found, omit the distribution field. Make sure following JSON content is only used for the distribution field and must not affect other fields. --START PROBABILITY DISTRIBUTION ONTOLOGY JSON-- {pb} --END PROBABILITY DISTRIBUTION ONTOLOGY JSON--
+
+  	  Only use parameters found in the reference petrinet file provided above.
+
       Ensure that the output follows the above petri net format and can be serialized as a JSON. Specifically populate parameters and initials. Use the following
       text body to answer the user's query: --START USER PROVIDED TEXT-- {research_paper}--END USER PROVIDED TEXT--\n\n Answer:
          {{