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Example: CellDesigner Reference Sheet

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Ludovic Roy edited this page Dec 7, 2017 · 10 revisions

Translation direction: CellDesigner -> SBGN-ML

This example file is one of the samples distributed with CellDesigner. It is called components44.xml and is also provided in this repository's samples folder.

Full results

The original file exported from CellDesigner The translated SBGN exported from Newt
The translated SBGN exported from the SBGN rendering webservice The translated SBGN exported from Vanted

Highlights

Proteins

  • CellDesigner has representations for 2 things that can't be properly translated to SBGN:
    • active/inactive state: active entities have a dashed line on the outside of their shape.
    • hypothetical entities: have a dashed border.
  • Those 2 variables are lost during the translation.
  • Anything that isn't a unit of information or a state variable is also not translated (like the binding region box).
  • The number of multimer unit can be over 2 in CellDesigner and is graphically shown. It is kept in SBGN in the form of a unit of information containing N:unit count, as SBGN doesn't graphically represent more than 2 units.
CellDesigner Newt
SBGN rendering webservice Vanted

Other glyphs and state variables

CellDesigner Newt
SBGN rendering webservice Vanted

Reactions

CellDesigner Newt SBGN rendering webservice Vanted

Unknown logic gate

Unknown logic gates have no counterpart in SBGN and cannot be translated properly. To avoid losing too much information, the decision was made to directly link the concerned input entities to the output process.

CellDesigner Newt

Direct links to other links

Links pointing to other links are only valid for SBGN ER, which is not supported by the translator. Such links will be discarded by the translator.

CellDesigner
Newt

Ports

  • Automatic port generation (here for the AND logic gate) can lead to some change for the links orientation, and some ugly discrepancies depending on how the SBGN is rendered. This is especially true for compact networks. This is due to the ports length being fixed. A more beautiful network can be obtained if enough space is left between every node.
  • Note that unspecified entities (the And in the example below) are sometimes used as a label in some network. They are valid CellDesigner and SBGN entities, and are translated as is, even when wrongly placed. Be careful how you use them.
CellDesigner Newt
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