Programmatic obtention of SBML from a list of proteins
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Entering edit mode
5.5 years ago

Hi there!

I got a list of proteins (UniProt ID) from a proteomics experiment and i am trying to build a model containing all the routes where my proteins are implicated. To achieve this, my first idea is to extract the Reactome route identifier from all the Uniprot IDs and then obtain the SBML for each one of those routes.

Joining the models (SBMLs) is a problem for future me, but i actually dont know how to obtain the SBML from Reactome with a list of identifiers like this (R-HSA-112409). I obtained the list of identifiers with a small python script.

I'm trying to build the model, not to get the routes more represented within my list of proteins. Reactome provides this type of analysis, but the SBML resulting from the top routes does not contain the same information that those accesed from the UniProt identifiers.

This is my first contact with SBMLs, so i would like to ask for advice for constructing the model (other databases providing SBMLs given a list of proteins for example), and if it were possible, for a way to obtain the SBMLs from Reactome using the route identifiers!

SBML Reactome Proteomics Signaling • 1.3k views
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Entering edit mode

Wow, didn't know that API! It solves perfectly what i am trying to do! Thank you so much!

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Entering edit mode
5.5 years ago

I think you can get what you want with the REST API. For example, for R-HSA-112409:

curl http://reactome.org/ReactomeRESTfulAPI/RESTfulWS/sbmlExporter/112409 > R-HSA-112409.sbml

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Entering edit mode
5.5 years ago
mhucka ▴ 50

Hi, when you start to work with SBML more and have questions, please feel free to post them on the SBML forums or email the SBML Team directly. The team has set up monitors on Biostars.org for SBML-related questions, but we don't tend to subscribe to Biostars directly simply because it seems a bit more bioinformatics-focused. Consequently, we might miss questions posted here or not find out about them until long after.