KEGGtranslator 2.5

Improvements in version 2.5

New features:

• Support for SBML Level 2 Version 5
• Use of identifiers.org URIs (uniform resource identifiers) instead of URNs (uniform resource names)
• Support for the flux balance constraints (FBC) package version 2 for SBML: KEGGtranslator now writes the chemical formula into species when converting to Level 3 Version 1.
• Improved user interface with support for more SBML package elements and their attributes
• Update to the latest repository version 1.1 of JSBML, revision 2358
• Produced SBML files have now a correct indentation.

Bug fixes:

• Correct use of the SBML groups extension:
  • In some cases, KEGGtranslator created duplicate identifiers that could not be added to the model.
  • Elements were not correctly linked to group members
• In situations when a link to KEGG containes special characters, such as colons, JSBML refuses writing those in the notes element and throws an exception. As a result, KEGGtranslator crashed. Special characters are now masked in these links.
• Additional code has been added to catch potential excaptions and to hence make the program more stable.

KEGGtranslator 2.4

Improvements in version 2.4.0

With this version, KEGGtranslator has become fully Garuda-compliant. It can now be used as a Garuda gadget, a stand-alone program with full command-line and graphical user interface, and as a Java™ Web Start tool. When used within Garuda, the results of KEGGtranslator can be directly sent to other software tools for furhter processing. KEGGtranslator can also receive KGML files from other gadgets in Garuda.

In particular, the following has been changed:

• Improved support for Mac OS X Mavericks (10.9) and Yosemite (10.10)
• A new version of yFiles has been incorporated
• Update to JSBML version 1.0
• Garuda-compliance.
• Improved support for BioPAX
• A large number of smaller improvements and bug-fixes under the hood, most of which are not directly visible to the user, but that improve quality and stability of the program.

KEGGtranslator 2.3.0

• IMPORTANT: Fixed access to the KEGG API. Updated KEGG adapter to the new REST interface.
• Some minor fixes to SBML-quall translations.
• A generated SBML-layout now always has an ID.

Note:
Since 2013-01-01, KEGG terminated the SOAP interface to retrieve data and started a REST interface. The amount of identifiers that can be resolved simultaneously has been reduced from 100 to 10. This means that KEGGtranslator now requires more time to fetch additional information from KEGG. We're very sorry, however, we cannot change KEGG's restrictions. To overcome this issue, caching of information has been improved such that every information only needs to be downloaded once.

KEGGtranslator 2.2.0

Translations to SBML or BioPAX

• Added separate format options for SBML_L2V4 and SBML_L3V1
• Updated SBML groups extension support to proposal Version 3
• Default compartment now gets an appropriate SBO term
• Added PSI-MI and PSI-MOD ontologies to SBML and BioPAX translations
• Improved the translation of KGML-relations to BioPAX
• Fixed a rare bug that potentially caused spaces in BioPAX IDs

Pathway visualizations and translations to GraphML, GML and similar

• Pathway-visualizations now optionally use reaction nodes to visualize KGML-reactions
  ... therefore, the 'grey arrow' option from the preferences has been renamed to 'include nodes for metabolic reactions'
• Added a novel option and the functionality to convert the KEGG background image to greyscale
• Compound/metabolite/small molecule-nodes now wrap their caption to a maximum of two lines with a maximum width of 66px each
• Captions of groups are now wrapped inside the group node
• Removed the '+' symbol from group nodes

Other bugfixes and improvements

• Improved command-line usability
• Various further improvements related to the visualization of pathways and models

KEGGtranslator 2.0.1

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.

KEGGtranslator 2.0.0

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.

KEGGtranslator 1.2.0

Major:

Compatibility with KEGG PATHWAY after 2011-07-01 (the FTP server must now be avoided, because it is no more publicly available).

New Features:

• Added pictures for chemical formula of compounds in notes
• Added pictures for referenced pathways in notes
• Crosslinked pathways (double-click in graphML visualization on a referenced pathway to open it)
• Added ToolTipText for nodes in GraphML visualization
• Added a status bar

Improvements and bugfixes:

• Improved assignment of node names
• Improved the command-line help text
• Bugfixed some issues with command-line usage
• Fixed heap-space crashes by limiting the cache size
• Fixed notification dialog for new releases

KEGGtranslator 1.1.0

Bugfixes and Improvements

This version of KEGGtranslator contains bugfixes and improvements in nearly every part of KEGGtranslator. The assignment of names for nodes has been improved, the documentation has been enhanced, some crashes and smaller bugfixes have been included and, by default, KEGGtranslator should now automatically take the systems proxy for making connections to the internet.

KEGGtranslator 1.0.0

This is the first version of KEGGtranslator.