It Is Possible To Obtain A Sbml Model From Ec Numbers Or Kegg Reactions Identifiers?

Question

[mgalactus]

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

Answer 1

[Michael Schubert]

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.

Answer 2

[Sudeep]

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.

[mgalactus]

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?

[Sudeep]

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"

[mgalactus]

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).