GeneForge Language (GFL) Specification v0.1

GFL is a declarative YAML-based language for defining biological workflows.

Root Object

The root of any GFL file must be a plan object.

The plan Object

• goal (string, required): A high-level description of the scientific objective.
• steps (list, required): A list of one or more step objects to be executed.

Additional Top-Level Blocks

GFL also supports several optional top-level blocks that enhance its symbolic reasoning capabilities:

Rules Block

• rules (list, optional): A list of conditional rules that define biological relationships.
• Each rule must contain:
  • id (string): A unique identifier
  • if (object): Conditions for the rule
  • then (object): Consequences of the rule

Hypothesis Block

• hypothesis (object, optional): A scientific hypothesis to be tested.
• Must contain:
  • id (string): A unique identifier
  • description (string): Human-readable description
  • if (list): List of conditions
  • then (list): List of expected outcomes

Timeline Block

• timeline (object, optional): Temporal orchestration of experiments.
• Must contain:
  • events (list): List of temporal events
  • Each event must have:
  • at (string): Time specification
  • actions (list): Actions to perform

Biological Entities

• pathways (object, optional): Metabolic and signaling pathways
• complexes (object, optional): Protein complexes

Entity and Hypothesis References

Entity References

Entities defined in pathways and complexes blocks can be referenced in experiment parameters using the syntax: - pathway(entity_name) - complex(entity_name)

Hypothesis References

Experiment and analysis blocks can reference hypotheses using the validates_hypothesis field.