Logo


ABOUT
SPECIFICATIONS
SOFTWARE SUPPORT
PUBLICATIONS
EVENTS
FAQ
CONTACT

Learning SBGN
Examples
Reference Cards
Published Maps
Symbol Highlights
Figure to SBGN
Competition
Development Wiki

Software support

This page summarizes what we know about software support for SBGN languages. This knowledge comes from a variety of sources, and is not necessarily complete. If your software or database is not listed below, or if you know of another effort, please post a message to sbgn-discuss.

Software

The following is a list of software packages known to provide support for SBGN. The links to the software packages were correct at the time of recording.

Software Package V / E PD ER AF SBGN-ML
Arcadia V + - - -
Athena E + - - -
Beacon Pathway Editor E - - + -
BIOCHAM E + - - -
Biographer E + + + +
BioUML V + - - -
CellDesigner E + - - +
ChiBE E + - - -
COPASI V + - - -
CySBGN V + + + +
Edinburgh Pathway Editor E + + + -
EscherConverter V + - - +
geneXplain platform E + - - -
iPathways V + - - -
JWS Online V + - - -
KEGGtranslator V + - - +
Krayon for SBGN E + - - +
Mayday MGV V + - - -
Mimoza V + - - -
Netbuilder’ E + - - -
Newt Editor E + - + +
Omix E - - - +
PathVisio E + + + +
SBGN-ED/VANTED E + + + +
SBGNTikZ E + + + -
SBGNViz V + - - +
SBML Layout Viewer V + + + +
SBMM assistant V + - - -
VISIBIOweb V + - - +
yEd Graph Editor E + - + -

V / E - Viewer or Editor
PD – Process Description, ER – Entity Relationship, AF – Activity Flow
SBGN-ML - Load SBGN maps from SBGN-ML format and/or save SBGN maps to SBGN-ML format (see also File Formats)
“+” supported, “-“ not supported

Databases

The following is a list of databases known to provide SBGN maps. The links to the databases were correct at the time of recording.

Database PD ER AF SBGN-ML
Atlas of Cancer Signalling Networks + - - -
AlzPathway + - - -
BioModels Database + - - -
iPAVS + - - -
MetaCrop + - - +
NaviCell + - - -
PANTHER Pathway + - - +
Parkinson’s disease map + - - -
Path2Models* + - + +
Reactome + - - +
RIMAS + - - -
SubtiPathways + - - -

*Path2Models is part of the BioModels Database
PD – Process Description, ER – Entity Relationship, AF – Activity Flow
SBGN-ML - Download of SBGN maps in SBGN-ML format (see also File Formats)
“+” supported, “-“ not supported

File Formats

SBGN-ML

The implementation of SBGN support in software packages may be facilitated by the use of the XML-based file format SBGN-ML. SBGN-ML can be processed and generated by the standard library LibSBGN. LibSBGN is a community project and everyone is welcome to participate.

Discussions around SBGN-ML and LibSBGN take place on sbgn-libsbgn-discuss.

One can compare the rendering of SBGN-ML by different software packages on the LibSBGN Render Comparison site.

BioPAX-SBGN Mapping

Biological Pathways Exchange (BioPAX) is a standard that aims to provide integration, exchange, visualization and analysis of biological pathway data. A substantial amount of BioPAX Level 3 concepts can be represented in SBGN PD via BioPAX-SBGN Mapping. More information regarding BioPAX-SBGN Mapping software can be found here.

Biological Connection Markup Language (BCML)

The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML can be automatically converted into a SBGN-compliant graphical representation. More information regarding BCML software can be found here.