import/export authors from SBGN-ML

added SBGN label

mentioned in merge request !1518 (merged)

closed

No additional comments here. I assume this is about the information in the map description. In Newt it is possible to add that, not sure about other tools. I was able to upload a file from Newt to MINERVA. Not sure where I can see this map information in MINERVA. It does not show in the info tab. Then after exporting from MINERVA, I can not open it in Newt: “Incorrect file format”.

@alexander.mazein Newt still does not support the SBGN export from MINERVA, I guess this is a v0.2 vs v0.3 incompatibility

It works, as long as authors data is contained in "Notes" in the beginning of the original CD XML file with the following structure:

<notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>Author:
<br />

Marcio Acencio, Luxembourg Centre for Systens Biomedicine, University of Luxembourg
<br />

<br />

Alexander Mazein, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg
<br />

<br />

Description:
Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, entry, translation, transcription, replication, assembly and release.</body></html></notes><annotation>
<celldesigner:extension>

When using vCard in the original CD XML file as shown below, the final SBGN-ML does not show any author data:

<vCard:N rdf:parseType="Resource">
<vCard:Family>Garapati</vCard:Family>
<vCard:Given>Phani Vijay</vCard:Given>
</vCard:N>

reopened

Thank you Marcio. I just checked in Vanted (SBGN-ED), there I do not see a way to add author information. In other words, it is good to have support in MINERVA for that but for now I do not know any other tool/editor that supports that. In Newt there are notes but that does not seem to work with MINERVA. SBGN-ED might not have it as soon as I see. I'll check with Tobias on that to be sure

Hi Alexander! By using CellDesigner, we can go to "Component" and "Model Notes" to add author information.

@piotr.gawron this does not work, I've uploaded the attached CellDesigner file with author info filled out.

SBGN cnoverted from it does not have author info.

aaa.xml

aaa.sbgn

Plus, CellDesigner does not produce a proper SBGN, at least that was the case when I tried SBGN export some years ago. That is why I checked if Newt or SBGN-ED have this option to add author information or some map notes. Newt has it but it does not show in MINERVA. Wight Newt we can discuss with Ugur, maybe it could be adjusted to how it is implemented for MINERVA

It seems authors information will be ok only in a SBGN-ML that was converted from a CD XML containing author data in "Notes". But this seems not ok in SBGN-ML files produced in pure SBGN-native editors. I have not tried to add "Notes" manually into a "pure" SBGN-ML. Has someone tried to do do?

Tobias confirmed that there is no such functionality in SBGN-ED. Potentially it could be added but should be together with other tools, would not make sense to have it only in SBGN-ED

changed milestone to %16.3.0~beta.1

mentioned in merge request !1616 (merged)

closed

Looks okay. As Marcio described, it is visible in the SBGN-ML file. Though, this can not be confirmed via other tools since no other tool supports it for now

import/export authors from SBGN-ML

Designs

Child items 0

Activity