Re: [Sbfc-devel] No biopax "control" class in biomodels and getting pathway information
Nicolas Rodriguez
Hi Nicolas,
I haven't been able to look into the pathway model for a few weeks. I did unzip the distribution but don't know how to use it. Can you please give me a detailed step by step instruction on how to run it?
Once you unzip the distribution (http://lenoverelab.org/perso/rodrigue/sbfc-1.3.8-SNAPSHOT.zip) somewhere, you can use the script sbml2biopax3.sh (on Linux and MacOS) or sbml2biopax3.bat (on windows) by passing either a folder that contain SBML files (*.xml) or a single SBML file and the biopax conversion will be created. If you pass a folder, every SBML file in it will be converted to biopax. In order to do that, you will have to open a terminal on Linux or MacOS or a ms-dos command prompt on windows.
You can also use a small GUI to run the different converters. The GUI can be started with the script sbfConverterGUI.sh (on Linux and MacOS) or sbfConverter.bat (on windows) or by running the "big jar" ("java -jar sbfc-1.3.8-SNAPSHOT-standalone.jar" or just double click on the jar file on some OS). If using the GUI, the right converter to select is called "SBML2BioPAX". In the build I have made, you have three older versions of the converter that I am using to compare and that will not be present in the future official release, you can ignore them.
If you have the newly converted files for all the models in biomodels it would be great if you could share it. If not, I would need to run the sbml2biopax3 converted to get the required file and iterate through all of them to get the reaction values.
As indicated above, the script can take a folder of the downloaded biomodels release and convert all the models in one go.
I have found some problems in the converter so I will try to re-generate all the biomodels models during next week. I can send an email with the download link when it is done.
Again, thank you so much for your help. Appreciate it. Also let me know if there's anyway I can contribute to your efforts in the future or if I can help you and your team in anyway.
Thanks you, I think using/testing the converter and reporting problem/error is already a good help.
Nico
On Fri, May 25, 2018 at 6:58 AM, Nicolas Rodriguez <rodr...@ebi.ac.uk> wrote:
Hi Rashid,
I think I managed to fix the new sbml2biopax converter and it is now working properly.
You can download the sample biopax files there: http://lenoverelab.org/perso/rodrigue/biopax-gsoc2016.tar.gz
And the distribution to use the converter: http://lenoverelab.org/perso/rodrigue/sbfc-1.3.8-SNAPSHOT.zip
Once you unzip it, you can run the converter using the script sbml2biopax3.sh (or sbml2biopax3.bat). You can also launch a GUI with the script sbfconverterGUI.sh (or sbfconverterGUI.bat on windows, you can also start it by 'running' the jar file 'java -jar sbfc-1.3.8-SNAPSHOT-standalone.jar').
Let me know if the biopax if good for you. For the sample files, I have selected biomodels models with proper annotation but most of them will miss the annotation to tell if it is an activation or inihibition. So you will just have a Control class without a controlType. Not sure if you are already familiar with paxtools/biopax but what you want to do could be done easily directly on the SBML files using a library like JSBML.
cheers,
Nico
On 21/05/18 17:07, Nicolas Rodriguez wrote:
The problem is that we did not yet took the time to properly cleanup, test and releases the new biopax converters so the converters at https://www.ebi.ac.uk/biomodels/tools/converters/ are still and old version.
I could either generate you few biopax models with the new converter to see if there are better for you or provide you with a zip file where you can run the converter locally ?
If you are satisfied I could then re-generate the whole biomodels biopax files. Are you interested by both the curated and uncurated models ?
We are planning a new release of sbfc for this summer where the new biopax converters will be included.
For the pathway name, it seems that we forgot to set it up and the new converter is missing completely the pathway element at the moment ! Might be due to the support of the SBML comp package, I will have to have a look at it.
Thanks,
Nico
On 18/05/18 16:14, Rashid Saadman wrote:
Hello,
I have been trying to use rbiopaxparser(R package) to parse biopax models that I got from biomodels (https://www.ebi.ac.uk/biomodels-main/ <https://www.ebi.ac.uk/biomodels-main/> <https://www.ebi.ac.uk/biomodels-main/ <https://www.ebi.ac.uk/biomodels-main/>>). I wanted the ACTIVATION/INHIBITION data(adjacency matrix) from the models for pathways and as far as I have read in the documenation for biopax, there has to be a "control" class which I don't get from biopax models in the biomodels database. How do I get the ACTIVATION/INHIBITION data?
I found this slide http://co.mbine.org/events/COMBINE_2016/agenda?q=system/files/tramy-combine-2016.pdf which mentioned about the different conversion tools from SBML to biopax. What I did was convert one of the SBML files from biomodels database to a biopax model using SBML2Biopax web tool:https://www.ebi.ac.uk/biomodels/tools/converters/
I didn't get the control class in the new biopax model. Maybe it doesn't have/create the control object at all? I don't have much idea on how to go about solving this or creating my own controls. Previously I used biopax models from NCI_pid, NCI_reactome, NCI_kegg to get the activation/inhibition data and I was trying to do the same thing with the biopax model in biomodels and I still haven't been able to figure out how to solve this.
Also, how can I get the actual pathway names from the biopax models in biomodels database? They don't have a NAME identifier for the pathway and it's encoded based on MIRIAM.
Thank you.
Rashid
University of Cincinnati
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Nicolas Rodriguez
I fixed most of the issues and all of the models should be converted.