Hello, I am using KEGGtranslator to generate models specifically for stoichiometric analyses. The tool fulfils most of my needs (although I am using version 2.5 downloaded here because it is still not clear to me how this repository is intended for use, see #5), but would like to obtain an encoding of maplink relations so that information on neighbouring pathways is also in the SBML (or extended format).
For example, KEGGconverter (which appears to be broken) does this by encoding neighbouring pathways as additional species and maplink relations as reactions between them and corresponding (e.g., metabolic) species. To quote directly from the paper:
"A core idea in this stage, is the conversion of the KGML elements, which point to other pathways, into additional SBML reactions. In this way, the map link information of the KGML pathway files is retained during this process."
Is there some way to achieve something similar using KEGGtranslator? If not identical to KEGGconverter framework (e.g. neighbouring as species), I don't mind post-processing the SBML files to achieve the specific stoichiometric model structure I want (I would have to do this anyway with KEGGconverter) so if you can just point me towards the best way to add this information in the output of the translator that would be great. Otherwise, if no such method for encoding the maplink relations is available, perhaps you could suggest an efficient way to combine the SBML with original KGML files and add this information myself? I apologise in advance if I have overlooked a simple solution to the problem, I am quite new to using the converters!
Hello, I am using KEGGtranslator to generate models specifically for stoichiometric analyses. The tool fulfils most of my needs (although I am using version 2.5 downloaded here because it is still not clear to me how this repository is intended for use, see #5), but would like to obtain an encoding of maplink relations so that information on neighbouring pathways is also in the SBML (or extended format).
For example, KEGGconverter (which appears to be broken) does this by encoding neighbouring pathways as additional species and maplink relations as reactions between them and corresponding (e.g., metabolic) species. To quote directly from the paper:
"A core idea in this stage, is the conversion of the KGML elements, which point to other pathways, into additional SBML reactions. In this way, the map link information of the KGML pathway files is retained during this process."
Is there some way to achieve something similar using KEGGtranslator? If not identical to KEGGconverter framework (e.g. neighbouring as species), I don't mind post-processing the SBML files to achieve the specific stoichiometric model structure I want (I would have to do this anyway with KEGGconverter) so if you can just point me towards the best way to add this information in the output of the translator that would be great. Otherwise, if no such method for encoding the maplink relations is available, perhaps you could suggest an efficient way to combine the SBML with original KGML files and add this information myself? I apologise in advance if I have overlooked a simple solution to the problem, I am quite new to using the converters!