Add sink reactions as pseudoreactions #149
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👍 on using DM_ |
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the older convention is for sink rxns to be reversible uptake/secretion and Nathan E. Lewis Assistant Professor On Fri, Aug 14, 2015 at 4:35 PM, Zachary A. King notifications@github.com
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Ok, so what is the solution now? Will we continue using both, sink and demand reactions? While I am aware of demand reactions and use the new specific SBO term 628 to highlight their role, I am not sure how sink reactions could be automatically recognized. Are there also certain prefixes or infixes in the BiGG id that can be used to recognize those? I am asking because Zak mentioned that we are using a certain nomenclature. Of course, I am already checking the number of products and reactions to see if the reaction is either a source or a sink. Furthermore, should we request two specific SBO terms for "source reaction" and "sink reaction"? |
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IMHO A demand reaction should be "DM_<met_id>". Anything that is We shouldn't have source reaction... maybe "exchange reaction"? Those have On Wed, Sep 16, 2015 at 5:02 PM, Andreas Dräger notifications@github.com
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If we were to replace sink_XX reactions, what would we replace them to? Nathan E. Lewis Assistant Professor On Wed, Sep 16, 2015 at 8:06 AM, Ali Ebrahim notifications@github.com
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Could we allow EX_ to be intracellular? The compartment is still at the end so it would be clear. Having a reaction called sink bringing flux into a cell is super
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Perhaps a new convention for intracellular source, e.g. SR_? -zak On Thu, Sep 17, 2015 at 10:40 PM, Ali Ebrahim notifications@github.com
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What other instances do we expect of intracellular sources (out of @nate - For the handful of cases where we have "sink" are we sure that's On Fri, Sep 18, 2015 at 7:42 AM, Zachary A. King notifications@github.com
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FYI .There are around 60 of them in BiGG right now: http://bigg.ucsd.edu/search?query=sink_ Many are in the RBC and PLT models. |
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Can we ask Alex and Aarash if that's intentional?
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I've always disagreed with the sink definition since I felt it was opposite Ines describes them here: Nathan E. Lewis Assistant Professor On Fri, Sep 18, 2015 at 9:29 AM, Ali Ebrahim notifications@github.com
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Ines's description is very clear—I support keeping these. It would be nice to formalize this as we have done with DM and EX, including a SBO term. I vote for a new prefix in line with our other standards. Maybe SN_ac_c or SK_ac_c Zak On Fri, Sep 18, 2015 at 9:45 AM, nel3 notifications@github.com wrote:
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yeah, I wish it hadn't been clearly defined... but it is. Is there a reason why we need to change it from sink_ to something else, Nathan E. Lewis Assistant Professor On Fri, Sep 18, 2015 at 10:06 AM, Zachary A. King notifications@github.com
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I think it won't look like a bug is important... Like you said Nate sink Are we sure the modelers using sink reactions were even aware of the
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Yeah, I like the idea that all of these 3 types look the same, so it's obvious that sinks are pseudoreactions. We can make it a formal specification, so, for instance, exported modes could include the SBO term for sink reactions and users will know exactly what they are. However, we can do that even if they are still called sink_ On Fri, Sep 18, 2015 at 10:11 AM, nel3 notifications@github.com wrote:
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Let's really not call it sink though. That's super misleading. Demand As we learned from mongoose, non obvious conventions are kind of just
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OK. Because this has been defined so clearly in the literature, I think we are stuck with the term "sink reaction." However, we have the opportunity to (a) rename the reactions, and (b) define a SBO term that very clearly delineates what these reactions do. As a note, sometimes capital (a) I think it makes sense to rename all sink reactions to look like:
In conjunction with #84, we can enforce that the sink BiGG ID includes the full metabolite BiGG ID. (b) Let's come up with text to best describe sink reactions, and to help resolve the misleading name for these reaction. Text from the protocol paper:
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It actually seems that sink reactions can also be seen as source reactions, while demand reactions are actual sinks. |
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Yeah, that's what Ali was saying. My solution is to keep the titles sink and demand because they are widely used and to clarify the meanings in the SBO terms and in help boxes on the BiGG Models website. |
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The sink name has always bothered me. Is there a place where we could Sent from my Android phone.
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We can annotate the model files with both the original reaction ID from the published model—we already do this—and the SBO term for explanation. On Wed, Sep 23, 2015 at 3:45 PM, nel3 notifications@github.com wrote:
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- Standardized names for biomass, sink, exchange, atpm, and demand reactions - Uses the prefixes EX_, DM_, SK_, BIOMASS_, and ATPM - If pseudoreactions have gpr's, then log a warning - If pseudoreactions have coefficients not 1 or -1, then log a warning - Closes SBRG/bigg_models#84, SBRG/bigg_models#149, SBRG/bigg_models#175
- Standardized names for biomass, sink, exchange, atpm, and demand reactions - Uses the prefixes EX_, DM_, SK_, BIOMASS_, and ATPM - If pseudoreactions have gpr's, then log a warning - If DM_, SK_, or EX_ have coefficients not 1 or -1, then log a warning - Closes SBRG/bigg_models#84, SBRG/bigg_models#149, SBRG/bigg_models#175
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Are there any objections to using For clarity, I also added a subsystem label for these reactions: "Intracellular source/sink" |
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Fine by me, especially with the subsystem label clarifying it's both a On Wed, Sep 30, 2015 at 10:51 AM, Zachary A. King notifications@github.com
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These are also valid pseudoreactions.
Is there any real distinction between sink and demand reactions? Can we just convert to using one nomenclature? I definitely prefer
DM_because it is analogous toEX_.The text was updated successfully, but these errors were encountered: