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Extraction Example

This example demonstrates how to use the an LLM to extract data from a markdown file and create a data model. The data model used in example is the following:

classDiagram
    class ChemicalProject {
        string title
        Molecule[] molecules
        Reaction[] reactions
        Experiment[] experiments
    }

    class Molecule {
        string id
        string name
        string formula
    }

    class Experiment {
        string id
        Concentration[] initial_concentrations
    }

    class Concentration {
        string molecule_id
        number value
        string unit
    }

    class Reaction {
        string id
        string name
        Molecule[] educts
        Molecule[] products
    }

    ChemicalProject --> Molecule
    ChemicalProject --> Reaction
    ChemicalProject --> Experiment
    Experiment --> Concentration
    Concentration --> Molecule
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ChemicalProject

This object represents a chemical project and serves as the top-level container for managing various aspects of a research project. It organizes the project's title, associated molecules, reactions, and experiments, providing a structured overview of the entire chemical workflow.

  • title
    • Type: string
    • Description: The name/title of the project.
    • PK: True
  • molecules
    • Type: Molecule[]
    • Description: The molecules used in the project.
  • reactions
    • Type: Reaction[]
    • Description: The reactions in the project.
  • experiments
    • Type: Experiment[]
    • Description: The experiments in the project.

Molecule

  • name
    • Type: string
    • Description: The name of the molecule.
  • formula
    • Type: string
    • Description: The formula of the molecule.

Experiment

  • id
    • Type: string
    • Description: The identifier of the experiment.
  • initial_concentrations
    • Type: Concentration[]
    • Description: The initial concentrations of the molecules in the experiment.

Concentration

  • molecule_id
    • Type: string
    • Description: The identifier of the molecule.
  • value
    • Type: number
    • Description: The concentration of the molecule.
  • unit
    • Type: UnitDefinition
    • Description: The unit of the concentration.

Reaction

  • id
    • Type: string
    • Description: The identifier of the reaction.
  • name
    • Type: string
    • Description: The name of the reaction.
  • educts
    • Type: Element[]
    • Description: The reactants of the reaction.
  • products
    • Type: Element[]
    • Description: The products of the reaction.

Element

  • molecule_id
    • Type: string
    • Description: The identifier of the molecule.
  • stoichiometry
    • Type: number
    • Description: The stoichiometry of the reactant.