Metabolic network annotation
With this Java software you can (I) browse and annotate existing
biological networks and (II) reconstruct biological networks.
Please cite the paper in Bioinformatics
Annotating existing networks
Using Metannogen to annotate an existing SBML file
With the Java
program Metannogen you can browse and annotate existing
biological networks given in SBML.
It is optimized for compartmentalized metabolic networks.
Metannogen provides advance features to facilitate manual
attachment of annotation texts and cross-references.
Types of annotations added by curators:
- Source of information (Database or literature cross-references)
- Private notes, remarks, to-do's
- Questions to colleagues
- Database searches: Google, Pubmed, Blast
- Predictions: Sub-cellular localizations
Controlled vocabulary. Syntax like string variable declaration in programming language BASIC.
Customizable input masks may be defined.
- Simple XML Attributes
- Rdf Annotations
- Highlighting rules
- Evidence level
Information which is intended for automated processing by
Metannogen is entered by the curator in form of variable
declarations in the computer languages PERL or BASIC.
gives rise to the
following annotation of a reaction inside the SBML document:
The default rules for the text conversion are taken from the file
Further files with rules can be added with the program option "-annotationFormats".
Those annotations that can be generated automatically, are fed into Metannogen
via line oriented tab separated files rather than typed manually.
Metannogen can be used as a plugin for graphical network design
tools, providing advanced capabilities for annotating
reactions. The communication between the App and Metannogen
works simply by network sockets and is language independent.
See Controlling Metannogen through other application
and Controlling other application through Metannogen
for technical details.
Reconstruction of metabolic networks
Reconstruction of a metabolic network by a team of curators.
The datasets are stored on a central password-protected web server.
The information in the dataset as well as optional dictionary files are used
to export an SBML file.
Metannogen can also be used as the primary tool for network reconstruction.
This is particular useful for large metabolic networks.
It had been the basic tool for the reconstruction
a compartmentalized metabolic network of the hepatocyte.
However, smaller networks are easier reconstructed using a graphical network constructor.
In this case Metannogen may serve as an interactive annotation tool.
- Click demo without Kegg
- Or demo including Kegg
(Very long download time at 1st start)
- Find the expandable tree for the network components of Recon1 and Kegg.
- Add annotations for the reactions of KEGG or RECON1 using the context menu (right click).
- Use the export methods in the "File" menu to create SBML files.
For own projects, the program options need to be customized as
described in Starting
Features of Metannogen
Improvements since publication in 2007
- Pubmed based literature management
- Association of full text PDF files
- Automated download of Uniprot and Pubmed documents
- Sharing PDF full text files
- Multi keyword highlighting
- Customizable cross-links
- Customizable shell commands
- Customizable export as , and CSV.
- Interface to libSBML.
- Backup for each session with time stamp. Logging all dataset uploads on the server.
- Tools for topological network analysation
Kegg Pathway maps
- Click-able reactions and metabolites
- Highlighting by
- Visualization of numeric data like mRNA expression levels
- Metannogen can not only be used to reconstruct networks but also to annotate existing networks
- Implementation of the Miriam standard
- Several new editing aids like tab-key word completion, spell check
- Self defined shell scripts and web services for text words and text selections
- In addition to Web services where the parameters are
encoded in the URL, also web services where the parameters are
in the HTTP header (so-called POST
- Find&Replace in many datasets/annotations
- Visualization of numeric data such as gene expression in graphical KEGG maps
- Improved responsiveness and reduced memory consumption
- Ready for inter-operation with other systems biology software
- Fixing problems of browsable trees
GNU-License. Source code included in jar-file. Free of charge.
Tested on Linux, Windows-XP (SP2) and OpenSolaris, MacOSX.
Bug reports and suggestions
- aMAZE LightBench