De-Novol assembling metabolic pathway based on the metabolite structure clustering. This pathway assembler module is one of the metabolic network reconstruction model for biocad project.
Reconstruct of the metabolic pathway is based on the spectrum molecular networking method. For make the metabolic pathway de-novol assembling, the algorithm is implemeneted:
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Parse the molecule strcuture into graph data
A SMILES metabolite structure parser was implemented in mzkit package for parse the metabolite structure as network graph object. And the atom group node was sorted in duplicated number in asceding order for make a sequence.
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Make molecule structure graph embedding as vector
The SGT embedding algorithm was apply on the generated sequence data for make the vector embedding.
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Make knn network clustering of the embedding result
Make networking reconstruct via the knn networking method(UMAP implements algorithm).
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Generates the metabolic network reconstrction result based on the knn result
Export the umap graph as the metabolick network reconstruct result. And then make the reconstructed global metabolic network visualization.
Create metabolic network de-novol assembling based on 26K reference metabolites, get 421 pathways:
