MIM type for translocation?

[Egon Willighagen]

Dear Dr Augustin Luna,

if not mistaken, you have been involved in the development of the Molecular Interaction Maps (MIM) interaction types. Just before christmas we had a WikiPathways curation event about MIM interaction and annotated more interactions... in doing so, we ran into quite a number of translocations (e.g. metabolites that move from outside the cell into the cytoplasm). In an older article about MIM I found it mentioned translocation, but it seems to have disappeared from later versions.

Do you remember why it was lost and/or what we should be using in WikiPathways to type translocations of entities (e.g. metabolites)?

Egon

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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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ORCID: 0000-0001-7542-0286
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[Martina Summer-Kutmon]

Egon, 

The MIM interactions that we have in the PV/WP palette is only a subset of all MIM interactions. I am not sure how and why the types were selected which are now included in the basic palette (was before I joined the project). Anwesha did some work on the interaction types sometime in 2016. I will have a look at her work with Denise and see what are the best next steps in relation to WikiPathways / PathVisio interaction types.

- Tina

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[Egon Willighagen]

Tina, yes, I was aware of that, but I was really thinking about the MIM specs itself: while a paper discusses mim:translocation, later specifications no longer mention it.

On a PV and pvjs side, it's easy to add, as the article shows it's depicted as a regular Arrow, so minimal effort is needed.

Egon

On Fri, Feb 16, 2018 at 10:22 AM, Martina Summer-Kutmon <mku...@gmail.com> wrote:

Egon, 

The MIM interactions that we have in the PV/WP palette is only a subset of all MIM interactions. I am not sure how and why the types were selected which are now included in the basic palette (was before I joined the project). Anwesha did some work on the interaction types sometime in 2016. I will have a look at her work with Denise and see what are the best next steps in relation to WikiPathways / PathVisio interaction types.

- Tina

On Fri, Feb 16, 2018 at 6:09 AM, Egon Willighagen <egon.wil...@gmail.com> wrote:

Dear Dr Augustin Luna,

if not mistaken, you have been involved in the development of the Molecular Interaction Maps (MIM) interaction types. Just before christmas we had a WikiPathways curation event about MIM interaction and annotated more interactions... in doing so, we ran into quite a number of translocations (e.g. metabolites that move from outside the cell into the cytoplasm). In an older article about MIM I found it mentioned translocation, but it seems to have disappeared from later versions.

Do you remember why it was lost and/or what we should be using in WikiPathways to type translocations of entities (e.g. metabolites)?

Egon

--

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

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Martina Summer-Kutmon, PhD
email: mku...@gmail.com
skype: mkutmon

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[Martina Summer-Kutmon]

There is a MIM-plugin (https://www.ncbi.nlm.nih.gov/pubmed/21636591) for PathVisio but I don't think it has been ported to PV3. That plugin has all interaction types included. You might want to start looking there.

Tina

[Martina Summer-Kutmon]

But you are right, the latest spec from 2010 doesn't seem to have a transport or translocation interaction type anymore.

- Tina

[Mark Woon]

We would love to see those added back as well...

-Mark 

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[Augustin Luna]

Thanks for the interest. Translocation never made it into the MIM
notation that we used with Wikipathways because we couldn't get the
semantics as precise as we wanted it. Most of my time at this point
regarding notation is spent on SBGN. I encourage Wikipathways to push
support for that notation; not a judgment on the strengths of the
notations, simply at the moment it has more effort around it.

That said, Wikipathways and PathVisio was always very flexible as a
drawing tool, and you should be able to just draw a stochiometric
conversion across a membrane boundary, as a simple solution.

Augustin Luna

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