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KEGGtranslator 2.0.1
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@draeger draeger released this 30 Mar 19:31
· 5 commits to 4c411b4577c805608c92742e80276c1ffa4df80e since this release
v2.0.1
9d5a7cb

Bugfixes and improvements

  • Fixed BioPAX and SBGN outputs:
    V2.0 had serious issues, because the required libraries for BioPAX and SBGN were not included in the jar. This Version now includes all required libraries. Please MAIL ME if you encounter any difficulties with this version!

Release notes of KEGGtranslator version 2.0

New features and major changes:

  • New formats:
    • SBGN (KEGG2SBGN, KGML2SBGN)
    • BioPAX Level 2 (KEGG2BioPAX, KGML2BioPAX)
    • BioPAX Level 3
    • SIF (for Cytoscape - KEGG2SIF, KGML2SIF)
    • In addition to Level 2, SBML Level 3 including several extensions (layout, groups, qual) is now supported
    • SBML-qual (KEGG2SBMLqual, KGML2SBMLqual)
    • SBML Level 3 Qualitative Models extension package allows for a proper translation of signaling pathways from KEGG to SBML. Instead of having species and reactions as in SBML-core, SBML-qual uses qualitativeSpecies and transitions between those.
    • GraphML, GML, JPG, etc. are all still supported in this new version.
  • Major enhancements in translations, especially for building initial systems biology models (SBML, BioPAX):
    • Method for proper handling of signaling pathways (SBML-qual)
    • Enhanced model building, avoiding duplicate entries, reactions and completing all missing elements of reactions
    • Unbundling reactions - If multiple reactions are summarized as one, a correct separate reaction is built for each real reaction
    • Revised SBO terms, MIRIAM URNs and further annotations, proper usage of BioPAX classes and attributes
    • Added correct stoichiometry to each reaction and reaction participant
  • Major enhancements in translations, especially for graphical outputs (GraphML, JPG):
    • Support for overview-pathways (such as "Metabolic pathways", "Pathways in cancer", etc.) are now displayed and translated correctly (technically: KEGGtranslator accurately handles the KEGG Graphics-type "line").
    • It is possible to set the original KEGG picture in the background of each translated pathway, therefore maintaining hand-drawn information from the original KEGG pathway visualization (such as compartmentalization or more biological figures).
  • Implemented a novel visualization for SBML, SBML-qual, and SBGN translations
    • Introducing SBGN-style (with reaction-nodes) visualization of KEGG pathways
      KEGG contains mainly visualizations of signaling pathways. Reactions in KGMLs are not visualized, just relations. With this SBGN-style visualization, KEGGtranslator also supports a proper visualization of reactions, contained in a KEGG pathway.
    • Introducing a detail panel that can give more details for each element (species, reaction, etc.) upon selection
    • Using the layout extension for visualization
    • Supporting auto-layout if not predefined layout is available
  • Atom balance check of all reactions
    The atom balance of each reaction can be checked to identify invalid or erroneous reactions.
  • Completely reworked node labeling with a novel option that can be used to change the labeling procedure
  • Layout information from the KGML can now be written using the standardized SBML layout extension

Improvements and bugfixes:

  • Enhanced support for MAC OS X
  • Enhanced speed and caching (application is now much faster)
  • Enhanced stability and robustness
  • Handling of synonymous KEGG identifiers (e.g., if an element is listed in KGML with its KEGG GLYCAN identifier but reactions use the corresponding KEGG COMPOUND identifier, KEGGtranslator now detects automatically that the same element is referenced).
  • Detection of swapped reactions (reversible reactions might be present in another direction in a KGML file than in the KEGG database. Detection of this is crucial for identification of missing reaction participants).

Comments:

The recently released application InCroMAP works jointly with KEGGtranslator and is able to perform pathway enrichments and visualizations of various microarray types in KEGG pathways.

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