Cell designer only support SBML and BIOPAX file formats while Kegg contains KGML files.
Hej,
I am not entirely sure whether or not it is the same data, but some of the KEGG data have been transformed into SBML and are available in the Path2Models Database, a subbranch of BioModels Database:
http://www.ebi.ac.uk/biomodels-main/path2models
If you search for "translate KEGG into SBML", you even find software such as KEGGtranslator which lets you translate KEGGML into SBML:
http://www.ra.cs.uni-tuebingen.de/software/KEGGtranslator/
Does this help?
Dagmar
Thanks for your suggestion. I had already tried to convert the file using KEGGtranslator but the problem is although it successfully convert the file into SBML format but when i tried to upload the converted file in Cell-designer it's not able to capture the reaction mechanisms and therefore the model being formed by cell designer only shows compartments only without reactions so further simulation can't be done.
Yes, Path2Models Database provide files in SBML format but, it only provides SBML Level 3 Version-1 which is not compatible with Celldesigner. Is there any format converter that can convert one SBML version into another type?
Hi everyone! I have experienced the same problem. I am using the last version of CellDesigner (4.4) and I can not import SBML models from Path2Models.
This issue leads me to think if there is a better software for import the models and visualize/analyze them instead of CellDesigner (of course that supports SBML Level 3 version).
Can anyone help me with this problem?
Hello.
I am affraid I am having very related issues. I am not attached to any network software analysis yet so it will be great to find one that allow me to export the kegg networks and reduce them to it's functionally more connected components in a semi automatic way. Is there any winner to do so so far?
Hello everyone! Finally i got the answer for this. I have tried lot many things and today only i succeeded; bit happy about it :-).
So, to open the KEGG pathway file (KGML) there are following steps:
1. The very first thing is to download the KEGGtranslator software (http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/.) and perform the installation.
2. Open your file in KEGGtranslator (through browse option), also provide the FORMAT type to convert your file (for this select SBML_L2V4 from drop down option as other SMBL format will not work for it), and save the file from FILE > SAVE AS option.
3. But, this is not all the file you saved through KEGGtranslator is not ready to import into CellDesigner or any other simulation software; the reason is that when you open the file in any text-editor (notepad++ etc.) you will see some ambiguous characters (“ ,â€) in it.
4. So to make your SBML file ready please remove these characters (“ ,â€) through find and replace option in notepad++ and this is it. You can successfully upload it in CellDesigner.
Hello Miquel Oltra,
I am sorry as i am late to answer your question. I have imported models from Path2Models database and never faced any issues. But, i think the problem could be due to the use of older version SBML files (SBML_L1V3). You can do one thing "convert your older version SBML files to
SBML_L2V4 using KEGGtranslator and after the conversion edit the new SBML file by removing some anonymous characters (“ ,â€) through find and replace option.
Hello Ankita
I tried same method but it is still giving "file is unreadable".
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology