royludo/cd2sbgnml

Translation between CellDesigner-flavoured SBML and SBGN-ML

cd2sbgnml's Issues

Info boxes placed incorrectly

We recently noticed in Newt that info boxes are not correctly placed around associated nodes by the converter. We now explicitly tile info boxes when importing from CellDesigner in Newt (iVis-at-Bilkent/sbgnviz.js@1d0b5ae) but other tools will not be doing this and will expect them in correct/valid locations.

Parent - child relation inconsistency

When you import from the CellDesigner sample M_phase.xml, pretty much all nodes except the process nodes go into the single compartment but not the process nodes. If there is no direct way to infer this from CD file, one could check the substrates and products of each process and if they all belong to the same compartment, the process could also be placed there.

Merge edit points too close to the ports

Also infer ports from already places points, if those points are in a good configuration (aligned, placed at approximately the same distance)

TODO list for CD->SBGN

• logic gates

• modifiers pointing to direct links (without process) -> abandoned, not valid SBGN

• anchor points for receptors

• and truncated proteins

• reversible reactions

• keep style information

• keep notes

• residues for NA features

• style consistency for process/logic gates

• clone markers

• entities pointing to UNKNOWN logic gates must point directly to concerned process

• MIRIAM annotations

• label location for complexes

• logic gate reactions

Consecutive conversions result in NullPointerException

By using the compartment_closeup.xml file that is provided under samples folder, I tried converting the file from cd to sbgnml and from sbgnml to cd consecutively.

Cell Designer -> SBGNML conversion was successful.
SBGNML -> Cell Designer conversion was successful.
Cell Designer -> SBGNML conversion resulted in a NullPointerException with the following error message,

Exception in thread "main" java.lang.NullPointerException at fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper.addBasicLists(ModelWrapper.java:105) at fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper.create(ModelWrapper.java:62) at fr.curie.cd2sbgnml.CD2SBGNML.toSbgn(CD2SBGNML.java:53) at fr.curie.cd2sbgnml.CD2SBGNML.convert(CD2SBGNML.java:789) at fr.curie.cd2sbgnml.Cd2SbgnmlScript.convert(Cd2SbgnmlScript.java:48) at fr.curie.cd2sbgnml.Cd2SbgnmlScript.main(Cd2SbgnmlScript.java:33)

Because of this issue, I am not able to import the file that is exported by using cd2sbgnml library.

Improve GUI usability

• Auto generate output and log in same folder if nothing specified.

• highlight direction of translation better

Conversion failure

Could be due to ToDo items in earlier issues

• Open newt
• Files->Samples->Cam-Camk Dependent Signaling to the nucleus
• Export->Cell Designer
• Conversion fails

reaction node labels lost in translation

Hi

I noticed that the reaction node labels, i.e. the reaction names like "PGMT" do not get transferred to the GraphML files produced. It is captured in the SBGN but not the GraphML

Step1_ReconMap_2.01_Original.xml

Step2_ReconMap_SBGN_from_CellDesigner.sbgn, PGMT is node="pr_4e79f0a2-236d-4abd-918e-2a94b664eb90"

Step3_ReconMap_yEd_from_SBGN.graphml

Thank you.

Use libsbgn 0.2

Downgrade from the unstable to last stable version of libsbgn to ensure compatibility with most tools.

Misc issues from 0.4.2

• On windows:
  • double arrow char in app title not recognized
  • button animation always flickers
  • BOM still causes problems
• unnecessary 'remove' appearing in log

TODO list for SBGN -> CD

• logic gates connecting phenotypes

• open/closed states variables and associated ion channel state

• notes and annotations

• annotation glyphs