drawing membrane transport

[Egon Willighagen]

Hi all,

following up from our discussion on enzymatic reactions, we discussed a membrane transport facilitated by a (membrane) protein. I asked Augustin Luna on the COVID19 Disease Maps Slack channel and he quickly replied. They already answered this question [0]:

So, the answer is "necessary stimulation" :)

If everyone is happy with this, I will continue along that road. I quite like this representation. We already have the glyph in PathVisio (and we did not remove it in the simplification?).

Egon

0.https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005740

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E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
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[Kristina Hanspers]

I like it!

Kristina

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[Alex Pico]

From the 2010 MIM spec, https://discover.nci.nih.gov/mim/formal_mim_spec.pdf (bolding is mine):

This specification also does not support several features of interest including: compartmentalization of entities, the transport of entities, and representation of stoichiometric coefficients.

Stimulation and Necessary Stimulation do not include transporter and channel activities, at least not in the official 2006 or 2010 specs.  I guess they extended it as a matter of convention,  just like we conventionally extended catalysis. Frankly, neither are correct, but I’m fine with adopting the same convention as Augustin, et al. if it helps interoperability, etc.

However, my only argument against this would be that if we’re going to go through the trouble of finding all the “wrong” catalysis interactions to switch them to necessary stimulation, we’d be better off switching them to a new, unique interaction type, i.e. a placeholder for actual transport activity. Otherwise, we’ll be in this same spot later on down the road when we have to find all the “wrong” necessary stimulations and switch them to the eventual correct one (which does not exist in any official standard today).

But other that this point, I’m fine with it. It’s not more wrong than what we’ve got now :)

 - Alex

On May 28, 2020, at 4:51 AM, Egon Willighagen <egon.wil...@gmail.com> wrote:

Hi all,

following up from our discussion on enzymatic reactions, we discussed a membrane transport facilitated by a (membrane) protein. I asked Augustin Luna on the COVID19 Disease Maps Slack channel and he quickly replied. They already answered this question [0]:

<image.png>

So, the answer is "necessary stimulation" :)

If everyone is happy with this, I will continue along that road. I quite like this representation. We already have the glyph in PathVisio (and we did not remove it in the simplification?).

Egon

0.https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005740

--

Hi, do you like citation networks? Already 51% of all citations are available available for innovative new uses. Join me in asking the American Chemical Society to join the Initiative for Open Citations too. SpringerNature, the RSC and many others already did.

-----

E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/u/egonwillighagen

[Egon Willighagen]

Alex,

I agree with your argumentation. 

What I need to check now is got back to that paper from this image, because that is about SBGN and I thought they were, albeit similar, really different things. That is, an SBGN interaction type may have the same name as a MIM interaction type, they still have different namespace (ontology). Or if SBGN inherits from MIM. I'll be back...

Egon

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