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thortiede / sbml4j

Load SBML Files and persist them in Neo4j
MIT License
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Load more databases #24

Open thortiede opened 5 years ago

thortiede commented 5 years ago

load wikipathways load recon3d

thortiede commented 5 years ago

Recon3D uses fbc-extension has multiple compartments -> need to check that they are alll created and the link from the entities works. species do NOT have an id filed, but a metaid field. Need to use that one (same for reaction)

thortiede commented 5 years ago

Recon3D has additonal lists in the model


flux balance constraints:
<fbc:listOfObjectives fbc:activeObjective="obj">
<fbc:listOfGeneProducts>
groups extension:
<groups:listOfGroups>
thortiede commented 3 years ago

There are issues with multiple species with the same name but different id. This needs work on #30 to properly load the other databases besides KEGG.

thortiede commented 3 years ago

I can load the Recon3D model, but creating a metabolic Mapping requires a LOT of Heap Space. More than I can currently provide on my local instance

thortiede commented 3 years ago

I managed to load some Models (Logical Models) from Biomodels, but due to lacking SBO Terms I cannot create network mappings.

thortiede commented 3 years ago

Grunwald2008 (https://www.ebi.ac.uk/biomodels/MODEL1403120000) can be loaded but fails to build a metabolic mapping, as there is a duplicate symbol (a species and a reaction have the same name) Something has to be done about that.