Class BioPAXBridge

java.lang.Object
org.episteme.natural.biology.loaders.biopax.BioPAXBridge
public class BioPAXBridge extends Object
Bridge for converting BioPAX DTOs to core Episteme biological pathway objects.

BioPAX (Biological Pathway Exchange) is the standard ontology for biological pathway data. This bridge converts parsed BioPAX data to Episteme domain objects.

Architecture

BioPAX OWL/XML → BioPAXReader → BioPAX DTOs → BioPAXBridge → Core Objects
                                                             ├── Pathway
                                                             ├── BioChemicalReaction
                                                             ├── Protein
                                                             └── Molecule
Since:
1.0
Author:
Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

  • Constructor Details

    • BioPAXBridge

      public BioPAXBridge()

  • Method Details

    • toPathway

      public Pathway toPathway(BioPAXPathway biopaxPathway)
      Converts BioPAX pathway to Episteme Pathway.
      Parameters:
      biopaxPathway - the parsed BioPAX pathway
      Returns:
      a Pathway object with reactions and participants

    • convertReaction

      public BioChemicalReaction convertReaction(BioPAXBiochemicalReaction biopaxReaction)
      Converts BioPAX biochemical reaction to Episteme BioChemicalReaction.

    • convertSmallMolecule

      public Molecule convertSmallMolecule(BioPAXPhysicalEntity entity)
      Converts BioPAX small molecule to Episteme Molecule.

    • convertProtein

      public Protein convertProtein(BioPAXPhysicalEntity entity)
      Converts BioPAX protein to Episteme Protein.

    • toPathways

      public List<Pathway> toPathways(BioPAXModel model)
      Extracts all pathways from a BioPAX model.