Is CE 16:1:0 format supported by LION?

[OlyaVv]

Dear friends,

I am currently trying to use LION for the data analysis, and the format of nomenclature we use in our lab (Shevchenko, MPI-CBG, Dresden) does not seem to be supported by your software (please find the example below).
It is also likely that I am doing something wrong.
Could you please clarify this to me?

All the best,
Olya

input	LION ID	LION name
CE 16:1:0	not found	not found
CE 16:0:0	not found	not found
CE 18:3:0	not found	not found
CE 18:2:0	not found	not found
CE 18:1:0	not found	not found
CE 20:5:0	not found	not found
CE 20:4:0	not found	not found
CE 20:3:0	not found	not found
CE 20:1:0	not found	not found
CE 20:0:0	not found	not found
CE 22:6:0	not found	not found

[martijnmolenaar]

Hey Olya!

Many notation formats exist. I have not seen this format before, can you indicate what represents the number after the second colon? Do you have more examples of this format?

If you use the semicolon in stead of the second colon (usually used to indicate number of hydroxyl groups) it should work (note that the last number is neglected, OH-groups are not yet supported in LION):
CE 16:1;0

KR, Martijn

[OlyaVv]

Dear Martijn,

Thank you so much fro your response, indeed it indicates the OH-group. This nomenclature is the output from the software called LipidXplorer (https://wiki.mpi-cbg.de/lipidx/Main_Page).
Other examples:
Cer 30:1:2
CL 56:4:0
DG 33:1:0
PC 25:0:0
PE 25:0:0
PS 25:0:0
PI 25:0:0
SM 30:1:1
LPC 13:0:0
LPE 13:0:0
PG 25:0:0
PA 33:1:0
LPA 16:0:0
LPI 13:0:0
LPS 13:0:0
LPG 13:0:0

Thank you for your suggestion. I will try it out and will get back to you/

All the best,
Olya

[martijnmolenaar]

Thanks. I will add this notation format to the web-tool's lipid notation standardizer script in the next update. For the time being, please remove the last 2 characters -- for example in excel: '=LEFT(A1,LEN(A1)-2)'.

[OlyaVv]

Awesome!

[OlyaVv]

Dear Martjin,

I have checked - not it's working (omitting OH groups).
Is there a way I could save in a graphic format the LION network view?

All the best,
Olya

[martijnmolenaar]

Hey Olya,

This is currently not really possible. You can save it as a png by right clicking on the network, but the resolution is not so high. Let me know if you need it urgently, I can build a custom script for you.

KR, Martijn

[OlyaVv]

Hi again,

Thank you, that is not urgent. I was just interested.

All the best,
Olya

[martijnmolenaar]

Hey Olya,

I added a button to download the network now in SVG (vector image). It is not exactly the same as shown in the browser, but pretty close. For some reason, the button will download the file only after the second click.

The CE 18:1:0 format is now also supported.

KR, Martijn

[OlyaVv]

Hey Martijn,

I only was able to check it today - somehow this button does not work and closes the progress, so you kind of have to re-do all the work again.

All the best,
Olya

[martijnmolenaar]

Hey Olya,

Indeed, there is a bug (the first time it does not download the figure), but after a second click it works in my hands. Not in your hands?

KR, Martijn

[OlyaVv]

Hi Martijn,

No, it does not work in my hands. As soon as I click the button it just sort of redirects me to the error page and I have to re-load all the data again to try it again.

All the best,
Olya

[martijnmolenaar]

Hey Olya,

I now improved the network-download. Hope it will work now for you :)

[OlyaVv]

Hey Martijn,

Thank you so much!
Indeed, the file is downloadable now.
However:

1. .png file looks not as fancy as on the preview in browser, and the nodes are in different order
2. .svg file is 0kb

But anyways, thanks a lot, it is actually working now!

All the best,
Olya

[martijnmolenaar]

Thanks for the close inspection. Two lines of code were still missing, indeed. Updated that.
The SVG now also works, and the arrows are now in the right direction.

The network doesn't look as pretty as the interactive version, the R-package that we use (visNetwork) does not support image rendering unfortunately (for now?). So I have to convert it to an iGraph object. With the SVG-file, you could do some refinement in Inkscape, for instance, if necessary.

[OlyaVv]

Thank you so so so much!