Metabolic network annotation
Metannogen

With this Java software you can (I) browse and annotate existing biological networks and (II) reconstruct biological networks.
Please cite the paper in Bioinformatics Abstract PDF

Annotating existing networks

**Figure:** 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:

Free text
- 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. For example

        $IS_DESCRIBED_BY="PUBMED:12345 UNIPROT:P0A7B8"

gives rise to the following annotation of a reaction inside the SBML document:

         <annotation>
          <rdf:RDF 
           xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" 
           xmlns:bqmodel="http://biomodels.net/model-qualifiers/">             
           <rdf:Description rdf:is="#metaid_test1"> 
            <bqbiol:isDescribedBy>> 
             <rdf:Bag>
              <rdf:li rdf:resource="urn:miriam:pubmed:12345"/> 
              <rdf:li rdf:resource="urn:miriam:uniprot:P0A7B8"/> 
              </rdf:Bag> 
             </bqbiol:is>
           </rdf:Description>           
          </rdf:RDF> 
         </annotation>

The default rules for the text conversion are taken from the file http//:.../annotationFormats.txt. 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

**Figure:** 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 of , 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.

Start demo

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 Metannogen (See Overview program options).

Features of Metannogen

Text views

Pubmed based literature management
- Association of full text PDF files
- Automated download of Uniprot and Pubmed documents
- Sharing PDF full text files
Spell-check
Multi keyword highlighting
Customizable
Auto
.
- Customizable cross-links
- Customizable shell commands

Data Management/Export

Search&Replace
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

Improvements since publication in 2007

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

Availability:

GNU-License. Source code included in jar-file. Free of charge. Tested on Linux, Windows-XP (SP2) and OpenSolaris, MacOSX.

Related projects

MetaCyc
aMAZE LightBench
Meta-All
PaVESy
MetNetMaker

Reactome
CellDesigner
Cytoscape
JUICE:

Sycamore:
semanticSBML
PINT
Utilities for viewing Large text files

Bug reports and suggestions to

christophgil

googlemail

com

Metabolic network annotationMetannogen