BioHackathon 2025 progress

[slobentanzer]

Top-level issue to track hackathon tasks. Sub-issues for five distinct challenges:

Extend momapy to SBML (https://github.com/adrienrougny/momapy)

• clarify dependency structure: second package, separate module?
• add test suite?

SBGN adapter (momapy to BioCypher)

• in hackathon repo
• add adapter to load and transform momapy objects into tuples
• could use code from momapy_kg lib (https://github.com/adrienrougny/momapy_kb)

Schema config

• in this repo
• how do we use the schema configuration to drive the transformation from model to KG without duplicate effort?
• look at fieldz-kb (https://github.com/adrienrougny/fieldz_kb)

Export KG representation to SBGN (first)

• as BioCypher module (write submodule)

Benchmarking

• Augustin's generative code

[slobentanzer]

Mermaid of the processing:

flowchart TD
    %% Input Data Sources
    SBGN[SBGN Model Files<br/>.sbgn XML]
    SBML[SBML Model Files<br/>.xml]
    
    %% Adapters
    SBGNAdapter[SBGN Adapter<br/>MoMaPySBGNAdapter]
    SBMLAdapter[SBML Adapter<br/>SBMLAdapter]
    
    %% Data Extraction
    SBGNNodes[SBGN Nodes<br/>macromolecule, process,<br/>simple chemical, etc.]
    SBGNEdges[SBGN Edges<br/>consumption, production,<br/>inhibition, catalysis, etc.]
    
    SBMLNodes[SBML Nodes<br/>entity, process,<br/>compartment]
    SBMLEdges[SBML Edges<br/>reactant, product,<br/>modifier]
    
    %% BioCypher Core
    BioCypher[BioCypher<br/>Knowledge Graph Builder]
    
    %% Similarity Computation
    SimilarityModule[Similarity Scoring Module<br/>compute_pairwise_similarities]
    Embeddings[Semantic Embeddings<br/>SentenceTransformer<br/>all-mpnet-base-v2]
    SimilarityEdges[Similarity Edges<br/>weighted by:<br/>- names<br/>- annotations<br/>- db_ids<br/>- structure<br/>- process context]
    
    %% Output
    KnowledgeGraph[Knowledge Graph<br/>Neo4j Compatible<br/>CSV Export]
    
    %% Flow
    SBGN --> SBGNAdapter
    SBML --> SBMLAdapter
    
    SBGNAdapter --> SBGNNodes
    SBGNAdapter --> SBGNEdges
    
    SBMLAdapter --> SBMLNodes
    SBMLAdapter --> SBMLEdges
    
    SBGNNodes --> BioCypher
    SBGNEdges --> BioCypher
    SBMLNodes --> BioCypher
    SBMLEdges --> BioCypher
    
    %% Similarity computation flow
    SBGNNodes --> SimilarityModule
    SBGNEdges --> SimilarityModule
    SBMLNodes --> SimilarityModule
    SBMLEdges --> SimilarityModule
    
    SimilarityModule --> Embeddings
    Embeddings --> SimilarityEdges
    SimilarityEdges --> BioCypher
    
    BioCypher --> KnowledgeGraph
    
    %% Styling
    classDef inputStyle fill:#e1f5ff,stroke:#01579b,stroke-width:2px
    classDef adapterStyle fill:#fff3e0,stroke:#e65100,stroke-width:2px
    classDef dataStyle fill:#f3e5f5,stroke:#4a148c,stroke-width:2px
    classDef coreStyle fill:#e8f5e9,stroke:#1b5e20,stroke-width:3px
    classDef similarityStyle fill:#fce4ec,stroke:#880e4f,stroke-width:2px
    classDef outputStyle fill:#fff9c4,stroke:#f57f17,stroke-width:3px
    
    class SBGN,SBML inputStyle
    class SBGNAdapter,SBMLAdapter adapterStyle
    class SBGNNodes,SBGNEdges,SBMLNodes,SBMLEdges dataStyle
    class BioCypher coreStyle
    class SimilarityModule,Embeddings,SimilarityEdges similarityStyle
    class KnowledgeGraph outputStyle

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