Add sink reactions as pseudoreactions

[zakandrewking]

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 to EX_.

[aebrahim]

:+1: on using DM_

[nel3]

the older convention is for sink rxns to be reversible uptake/secretion and DM rxns are irreversible secretion

Nathan E. Lewis

Assistant Professor Department of Pediatrics University of California, San Diego Tel: (858) 997 - 5844 http://lewislab.ucsd.edu/

On Fri, Aug 14, 2015 at 4:35 PM, Zachary A. King notifications@github.com wrote:

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 to EX.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149.

[draeger]

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"?

[aebrahim]

IMHO A demand reaction should be "DM_". Anything that is "sink_" should be replaced in the database.

We shouldn't have source reaction... maybe "exchange reaction"? Those have the id "EX_"

On Wed, Sep 16, 2015 at 5:02 PM, Andreas Dräger notifications@github.com wrote:

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"?

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-140768510.

[nel3]

If we were to replace sinkXX reactions, what would we replace them to? They're not DM reactions because they differ in the reversibility and they're not EX reactions since they are within the cell

Nathan E. Lewis

Assistant Professor Department of Pediatrics University of California, San Diego Tel: (858) 997 - 5844 http://lewislab.ucsd.edu/

On Wed, Sep 16, 2015 at 8:06 AM, Ali Ebrahim notifications@github.com wrote:

IMHO A demand reaction should be "DM_". Anything that is "sink_" should be replaced in the database.

We shouldn't have source reaction... maybe "exchange reaction"? Those have the id "EX_"

On Wed, Sep 16, 2015 at 5:02 PM, Andreas Dräger notifications@github.com wrote:

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"?

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-140768510.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-140770031.

[aebrahim]

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 unintuitive. It almost seems like it's a bug. On Sep 18, 2015 07:30, "nel3" notifications@github.com wrote:

If we were to replace sinkXX reactions, what would we replace them to? They're not DM reactions because they differ in the reversibility and they're not EX reactions since they are within the cell

Nathan E. Lewis

Assistant Professor Department of Pediatrics University of California, San Diego Tel: (858) 997 - 5844 http://lewislab.ucsd.edu/

On Wed, Sep 16, 2015 at 8:06 AM, Ali Ebrahim notifications@github.com wrote:

IMHO A demand reaction should be "DM_". Anything that is "sink_" should be replaced in the database.

We shouldn't have source reaction... maybe "exchange reaction"? Those have the id "EX_"

On Wed, Sep 16, 2015 at 5:02 PM, Andreas Dräger < notifications@github.com> wrote:

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"?

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-140768510.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-140770031.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141349444.

[zakandrewking]

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 wrote:

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 unintuitive. It almost seems like it's a bug. On Sep 18, 2015 07:30, "nel3" notifications@github.com wrote:

If we were to replace sinkXX reactions, what would we replace them to? They're not DM reactions because they differ in the reversibility and they're not EX reactions since they are within the cell

Nathan E. Lewis

Assistant Professor Department of Pediatrics University of California, San Diego Tel: (858) 997 - 5844 http://lewislab.ucsd.edu/

On Wed, Sep 16, 2015 at 8:06 AM, Ali Ebrahim notifications@github.com wrote:

IMHO A demand reaction should be "DM_". Anything that is "sink_" should be replaced in the database.

We shouldn't have source reaction... maybe "exchange reaction"? Those have the id "EX_"

On Wed, Sep 16, 2015 at 5:02 PM, Andreas Dräger < notifications@github.com> wrote:

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"?

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-140768510.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-140770031.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141349444.

---

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[aebrahim]

What other instances do we expect of intracellular sources (out of curiosity)?

@Nate - For the handful of cases where we have "sink" are we sure that's not a bug that that was included as reversible? I can easily see it being an artifact of a simpheny export or something like that.

On Fri, Sep 18, 2015 at 7:42 AM, Zachary A. King notifications@github.com wrote:

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 wrote:

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 unintuitive. It almost seems like it's a bug. On Sep 18, 2015 07:30, "nel3" notifications@github.com wrote:

If we were to replace sinkXX reactions, what would we replace them to? They're not DM reactions because they differ in the reversibility and they're not EX reactions since they are within the cell

Nathan E. Lewis

Assistant Professor Department of Pediatrics University of California, San Diego Tel: (858) 997 - 5844 http://lewislab.ucsd.edu/

On Wed, Sep 16, 2015 at 8:06 AM, Ali Ebrahim notifications@github.com wrote:

IMHO A demand reaction should be "DM_". Anything that is "sink_" should be replaced in the database.

We shouldn't have source reaction... maybe "exchange reaction"? Those have the id "EX_"

On Wed, Sep 16, 2015 at 5:02 PM, Andreas Dräger < notifications@github.com> wrote:

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"?

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-140768510.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-140770031.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141349444.

---

Reply to this email directly or view it on GitHub: https://github.com/SBRG/BIGG2/issues/149#issuecomment-141350890

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141351266.

[zakandrewking]

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.

[aebrahim]

Can we ask Alex and Aarash if that's intentional? On Sep 18, 2015 6:20 PM, "Zachary A. King" notifications@github.com wrote:

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.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141497614.

[nel3]

I've always disagreed with the sink definition since I felt it was opposite of what it should be (sinks are usually the flow out of a model), but it was a convention set sometime around 2000-2004 in the Palsson lab which was propagated into SimPheny. Thus, caution should be taken in changing the definition, without a clear disclaimer somewhere.

Ines describes them here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125167/ but it has been used and mentioned in the lab papers since at least 2007 http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030192 and in Recon1

Nathan E. Lewis

Assistant Professor Department of Pediatrics University of California, San Diego Tel: (858) 997 - 5844 http://lewislab.ucsd.edu/

On Fri, Sep 18, 2015 at 9:29 AM, Ali Ebrahim notifications@github.com wrote:

Can we ask Alex and Aarash if that's intentional? On Sep 18, 2015 6:20 PM, "Zachary A. King" notifications@github.com wrote:

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.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141497614.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141499419.

[zakandrewking]

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:

I've always disagreed with the sink definition since I felt it was opposite of what it should be (sinks are usually the flow out of a model), but it was a convention set sometime around 2000-2004 in the Palsson lab which was propagated into SimPheny. Thus, caution should be taken in changing the definition, without a clear disclaimer somewhere. Ines describes them here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125167/ but it has been used and mentioned in the lab papers since at least 2007 http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030192 and in Recon1 Nathan E. Lewis Assistant Professor Department of Pediatrics University of California, San Diego Tel: (858) 997 - 5844 http://lewislab.ucsd.edu/ On Fri, Sep 18, 2015 at 9:29 AM, Ali Ebrahim notifications@github.com wrote:

Can we ask Alex and Aarash if that's intentional? On Sep 18, 2015 6:20 PM, "Zachary A. King" notifications@github.com wrote:

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.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141497614.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141499419.

---

Reply to this email directly or view it on GitHub: https://github.com/SBRG/BIGG2/issues/149#issuecomment-141504556

[nel3]

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, other than to make it look like DM or EX?

Nathan E. Lewis

Assistant Professor Department of Pediatrics University of California, San Diego Tel: (858) 997 - 5844 http://lewislab.ucsd.edu/

On Fri, Sep 18, 2015 at 10:06 AM, Zachary A. King notifications@github.com wrote:

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:

I've always disagreed with the sink definition since I felt it was opposite of what it should be (sinks are usually the flow out of a model), but it was a convention set sometime around 2000-2004 in the Palsson lab which was propagated into SimPheny. Thus, caution should be taken in changing the definition, without a clear disclaimer somewhere. Ines describes them here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125167/ but it has been used and mentioned in the lab papers since at least 2007

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030192 and in Recon1 Nathan E. Lewis Assistant Professor Department of Pediatrics University of California, San Diego Tel: (858) 997 - 5844 http://lewislab.ucsd.edu/ On Fri, Sep 18, 2015 at 9:29 AM, Ali Ebrahim notifications@github.com wrote:

Can we ask Alex and Aarash if that's intentional? On Sep 18, 2015 6:20 PM, "Zachary A. King" notifications@github.com wrote:

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.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141497614.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141499419.

---

Reply to this email directly or view it on GitHub: https://github.com/SBRG/BIGG2/issues/149#issuecomment-141504556

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141508832.

[aebrahim]

I think it won't look like a bug is important... Like you said Nate sink strongly implies one direction.

Are we sure the modelers using sink reactions were even aware of the counterintuitive convection? On Sep 18, 2015 7:11 PM, "nel3" notifications@github.com wrote:

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, other than to make it look like DM or EX?

Nathan E. Lewis

Assistant Professor Department of Pediatrics University of California, San Diego Tel: (858) 997 - 5844 http://lewislab.ucsd.edu/

On Fri, Sep 18, 2015 at 10:06 AM, Zachary A. King < notifications@github.com> wrote:

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:

I've always disagreed with the sink definition since I felt it was opposite of what it should be (sinks are usually the flow out of a model), but it was a convention set sometime around 2000-2004 in the Palsson lab which was propagated into SimPheny. Thus, caution should be taken in changing the definition, without a clear disclaimer somewhere. Ines describes them here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125167/ but it has been used and mentioned in the lab papers since at least 2007

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030192

and in Recon1 Nathan E. Lewis Assistant Professor Department of Pediatrics University of California, San Diego Tel: (858) 997 - 5844 http://lewislab.ucsd.edu/ On Fri, Sep 18, 2015 at 9:29 AM, Ali Ebrahim <notifications@github.com

wrote:

Can we ask Alex and Aarash if that's intentional? On Sep 18, 2015 6:20 PM, "Zachary A. King" notifications@github.com wrote:

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.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141497614.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141499419.

---

Reply to this email directly or view it on GitHub: https://github.com/SBRG/BIGG2/issues/149#issuecomment-141504556

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141508832.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141509777.

[zakandrewking]

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:

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, other than to make it look like DM or EX? Nathan E. Lewis Assistant Professor Department of Pediatrics University of California, San Diego Tel: (858) 997 - 5844 http://lewislab.ucsd.edu/ On Fri, Sep 18, 2015 at 10:06 AM, Zachary A. King notifications@github.com wrote:

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:

I've always disagreed with the sink definition since I felt it was opposite of what it should be (sinks are usually the flow out of a model), but it was a convention set sometime around 2000-2004 in the Palsson lab which was propagated into SimPheny. Thus, caution should be taken in changing the definition, without a clear disclaimer somewhere. Ines describes them here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125167/ but it has been used and mentioned in the lab papers since at least 2007

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030192 and in Recon1 Nathan E. Lewis Assistant Professor Department of Pediatrics University of California, San Diego Tel: (858) 997 - 5844 http://lewislab.ucsd.edu/ On Fri, Sep 18, 2015 at 9:29 AM, Ali Ebrahim notifications@github.com wrote:

Can we ask Alex and Aarash if that's intentional? On Sep 18, 2015 6:20 PM, "Zachary A. King" notifications@github.com wrote:

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.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141497614.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141499419.

---

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— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141508832.

---

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[aebrahim]

Let's really not call it sink though. That's super misleading. Demand reactions are actual sinks.

As we learned from mongoose, non obvious conventions are kind of just asking for trouble. On Sep 18, 2015 19:36, "Zachary A. King" notifications@github.com wrote:

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:

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, other than to make it look like DM or EX? Nathan E. Lewis Assistant Professor Department of Pediatrics University of California, San Diego Tel: (858) 997 - 5844 http://lewislab.ucsd.edu/ On Fri, Sep 18, 2015 at 10:06 AM, Zachary A. King < notifications@github.com> wrote:

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:

I've always disagreed with the sink definition since I felt it was opposite of what it should be (sinks are usually the flow out of a model), but it was a convention set sometime around 2000-2004 in the Palsson lab which was propagated into SimPheny. Thus, caution should be taken in changing the definition, without a clear disclaimer somewhere. Ines describes them here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125167/ but it has been used and mentioned in the lab papers since at least 2007

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030192

and in Recon1 Nathan E. Lewis Assistant Professor Department of Pediatrics University of California, San Diego Tel: (858) 997 - 5844 http://lewislab.ucsd.edu/ On Fri, Sep 18, 2015 at 9:29 AM, Ali Ebrahim < notifications@github.com> wrote:

Can we ask Alex and Aarash if that's intentional? On Sep 18, 2015 6:20 PM, "Zachary A. King" <notifications@github.com

wrote:

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.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141497614.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141499419.

---

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— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141508832.

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— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-141515531.

[zakandrewking]

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 Sink_ is used (Sink_f6p) and sometimes lowercase sink_ is used (sink_dna_c). And some have a compartment, and some don't (e.g. Sink_f6p). Therefore, the existing standardization is somewhat lacking.

(a) I think it makes sense to rename all sink reactions to look like:

SK_f6p_e

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:

Sink reactions are similar to demand reactions but are defined to be reversible and thus provide the network with metabolites (see Figure 7 for examples). These sink reactions are of great use for compounds that are produced by non-metabolic cellular processes but need to be metabolized. Adding too many sink reactions may enable the model to grow without any resources in the medium. Therefore, sink reactions have to be added with care. As for demand reactions, sink reactions are mostly used during the debugging process. They help to identify the origin of a problem (e.g., why a metabolite cannot be produced). These sink reactions are functionally replaced by filling the identified gap. Thiele, I. & Palsson, B. Ø. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat. Protoc. 5, 93–121 (2010). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125167/

[draeger]

It actually seems that sink reactions can also be seen as source reactions, while demand reactions are actual sinks.

[zakandrewking]

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.

[nel3]

The sink name has always bothered me. Is there a place where we could annotate the change in the models if we rename them since they are only in a couple models?

Sent from my Android phone. On Sep 23, 2015 11:56 AM, "Zachary A. King" notifications@github.com wrote:

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.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-142696760.

[zakandrewking]

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:

The sink name has always bothered me. Is there a place where we could annotate the change in the models if we rename them since they are only in a couple models? Sent from my Android phone. On Sep 23, 2015 11:56 AM, "Zachary A. King" notifications@github.com wrote:

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.

— Reply to this email directly or view it on GitHub https://github.com/SBRG/BIGG2/issues/149#issuecomment-142696760.

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Reply to this email directly or view it on GitHub: https://github.com/SBRG/BIGG2/issues/149#issuecomment-142752221

[zakandrewking]

Are there any objections to using SK_ for source/sink reactions? The pull request is ready to go.

For clarity, I also added a subsystem label for these reactions: "Intracellular source/sink"

[aebrahim]

Fine by me, especially with the subsystem label clarifying it's both a source and sink.

On Wed, Sep 30, 2015 at 10:51 AM, Zachary A. King notifications@github.com wrote:

Are there any objections to using SK_ for source/sink reactions? The pull request is ready to go.

For clarity, I also added a subsystem label for these reactions: "Intracellular source/sink"

— Reply to this email directly or view it on GitHub https://github.com/SBRG/bigg_models/issues/149#issuecomment-144489567.