-
Notifications
You must be signed in to change notification settings - Fork 46
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
fix: subSystems field #11
Comments
@demilappa maybe you can shed some light here? I remember you told me you managed to do this once, if so which version of Yeast did you use for it? |
@BenjaSanchez I have added the rxnECNumbers & subSystems to other GEMs of bacterial species with semi-automated scripts, not the yeast one. Unfortunately, for multiple EC Numbers per reaction it involved manual input in case the Subsytems were different. In my case the source of reconstruction was http://kbase.us/metabolic-modeling-in-kbase/. In their Git repository they already had a preliminary mapping among rxns and external DBs, where for the vast majority of the cases they had soecified compartments. As for the EC Numbers, you can still have multiple ones in your structure. |
@demilappa thanks for the info! @hongzhonglu as you mentioned that you checked previous versions of the model with no luck, I will close this issue. |
@BenjaSanchez, about two weeks ago, I did some mapping according to the reaction name to obtain the subsystem for each reaction. The model used in the mapping are iMM904, iTO980 and the latest human model Recon3D. All the transport reaction are clarified as transport+compartment. So based on such mapping and the present subsystem in the yeast7.6, I hope each reaction can has a unique subsystem, just like the latest human and E.coli GEMs. |
@hongzhonglu interesting! how much coverage did you achieve with said mapping? which pathway names are you getting back? from KEGG or another database? I have now re-opened this issue with a changed goal: to eliminate the duplicates in subsystems. Looking forward to your contribution! |
@BenjaSanchez I have updated the subsystem. You can check it now! |
as discussed in person, a new branch |
Discussed today:
|
I would like to reignite this issue. In From the comments above, it seemed there was consensus that single subsystems are preferred, but we ended up with multiple subystems anyway. A few points to consider:
Having single subSystems and Expected feature/value/output:Single subSystems, e.g. in the case of Current feature/value/output:Many reactions have multiple subSystems, e.g. in the case of |
Hi Ed, @edkerk actually, we now already has single subsystem for each rxns. I like your idea to have "both single subSystems and rxnKEGGpathway annotations". |
@hongzhonglu, that's great, but where can I find those single subsystems? Both in |
Hi Ed, @edkerk, i don't yet upload them as we did not know how to handle it before. |
Update: I have opened #253 moving the KEGG pathway ids to the proper field. After it is merged, |
Nice! I will try to further update the group classifications. |
- run model=rmfield(model,'subSystems') before running saveYeastModel, until subSystems are added (see #11)
What is the status of this? I was about to make a few curations to Hongzhong's proposed list of subsytems, but then I noticed that MetabolicAtlas also has subsystems defined . @mihai-sysbio should we try to adhere to the MetabolicAtlas maps whenever possible/suitable? Or will these just be re-drawn when we here have settled the subsystems in yeast-GEM? |
I now noticed the maps on https://github.com/SysBioChalmers/Yeast-maps/, should we try to adhere to these? How have they been defined? |
This is a bit of a thorny issue. I don't think I can remember all the details accurately (please correct me @edkerk @pecholleyc @hongzhonglu):
With all of the above in mind my suggestion going forward is to add 1 |
I should have mentioned this, but Metabolic Atlas is relying on the |
But it makes sense that this information is sourced from |
Hi all, I am sorry that in past months, i have no time to further curate subsystem used for our model and maps. But I will try to update it in following months. |
@edkerk I'm following up on your questions below.
I guess we can also change how the reaction to subsytem association is parsed from the
Indeed - the SVG maps are already created and they won't be changed. They would need to be updated, as @hongzhonglu says above, but it will take a long time until that happens, so for the near future we should think that they won't be changed.
What is expected is that in the
To my knowledge, this is part of the normal export to yaml that has been recently included in Raven. |
My intonation probably didn't come across as I intended, I do think it makes sense to do it that way, so I do no propose any changes. My confusion was based on whether subsystem assignment is actively used to assign reactions to different maps, so that if subsystems would be changed this would directly alter the maps. But I now understand that this is not the case, the maps were once assigned based on subsystems that were specified in that version of the yeast model. Any changes to the subsystems in new model versions do not automatically translate in changes in maps on Metabolic Atlas (the same reactions will still be linked) but if we'd want to have the maps truly reflect the subsystems then it would have to be done manually. Alright, so just to make sure I understand it correctly, we should:
And to see the existing mapping of reactions to Metabolic Atlas maps, one should look at the |
I agree with the two points @edkerk |
Very well laid out @edkerk!
On Metabolic Atlas will will look into automatic generation of 2D maps, so perhaps don't put too much weight on the current assignment, as we intend to find a way of always having fully accurate maps.
That's right. In the case of some existing maps not mapping well with a definition of a subsystem (ie many reactions from other subsystems), there is already support for |
@edkerk Hi Ed, now I added miss subsystem information for the remaining rxns. It will be better to combine this into dev version for further update. In the following, the newly added reactions should have a unique subsystem definition. |
I rebased it to the For the subsystems that are based on KEGG pathways maps, this should be removed from the end of the subsystem name ( |
Currently the fields
rxnECNumbers
&subSystems
are retrieved from KEGG & Swissprot, using an automatic script. However, this leads to many cases in which there is more than one match, undesired in the case of subsystems. At some previous version of the Yeast model, this information was indeed present, but someone deleted those fields. @hongzhonglu could you look further into this? The desired data should be available in the original sourceForge repositoryThe text was updated successfully, but these errors were encountered: