It Is Possible To Obtain A Sbml Model From Ec Numbers Or Kegg Reactions Identifiers?
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9.3 years ago
mgalactus ▴ 760

Hi all,

I was wondering if some tools exist to build a SBML model starting from EC numbers or KEGG reaction IDs. I've seen tools like KEGGtranslator, but i have no access to KGML files, just a list of EC numbers or Reaction IDs (also RPairs or pathway IDs).

Thanks a lot, Marco

kegg pathway • 3.7k views
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Entering edit mode
9.3 years ago

You can search the BioModels database with EC numbers, and it will find SBML models if they have been annotated with the corresponding terms.

BioModels Database serves as a reliable repository of computational models of biological processes. It hosts models described in peer-reviewed scientific literature and models generated automatically from pathway resources (Path2Models). A large number of models collected from literature are manually curated and semantically enriched with cross-references from external data resources. The resource allows scientific community to store, search and retrieve mathematical models of their interest. In addition, features such as generation of sub-models, online simulation, conversion of models into different representational formats, and programmatic access via web services, are provided.

For instance, searching for 3.4.11.4 (N-terminal cleavage of tripeptides) yields:

• Thiele2013 - Human metabolism global reconstruction (Recon 2)
• Hoppe2012 - Predicting changes in metabolic function using transcript profiles

Also, there was a large-scale conversion of KEGG models into SBML. You can find the details in this article.

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Entering edit mode
9.3 years ago
Sudeep ★ 1.7k

If you have pathway IDs, then you can use KEGG Rest API to retrieve the kgml file and probably convert it into SBML models using KEGGtranslator or KEGG CONVERTER, although I have to say that I haven't tried converting a kgml file to an SBML model.

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Thanks for the info, but what if i have just a list of EC numbers? There is really no way you can produce a SBML file from that?

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Then you probably want this EC number to pathway mapping, how to do it is here in KEGG Rest API documentation under the section "Linked entries"

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Thanks, but i was looking for a way to obtain a SBML model from just EC numbers, without the use of the KEGG API (otherwise i would just have used the KGML format).