Documentation
This page provides the tutorial, user guide and FAQ of the MetNetDB program.
Overview
The MetNetDB use a graph based data model. The pathway is a collection of interactions, which contains reactants and products. All biological processes are mapped to interactions. Besides the interactions, relations are introduced to describe the composition of protein complexes and their components. The components can be polypeptides, other protein complexes or molecular.
Entity
Entities are basic components in pathways. They can be genes, RNAs, polypeptides, protein complexes. Also entities can be environment conditions, constraints which are used to describe the dynamic processes. Entities are edited in entity window.
Interaction
Interactions are biochemical reactions. Currently, they can be enzymatic reactions and its catalysis, transport, translation, transcription, protein modification, positive and negative regulations, and other biological processes. Interactions are edited in interaction window.
Relation
Relation is a concept parallel to interaction. We use relation to describe the composition of protein complexes. Composition-AND is used to describe the multi-gene enzymes. The enzyme activity depends on all products of the genes. On the other hand, if any of the gene's product can perform the enzyme activity, the protein complex and the genes have Composition-OR relation. Relations are edited in interaction windows.
Pathway
Pathways are collections of interactions. Pathway are edited in pathway window and pathway preview window.
Synonym and abbreviation
Biologists tend to use synonyms and abbreviations in the literature. This causes ambiguity in the database. Before user input a new entity, they should check if the entity is already in the database. Synonym window let users input new synonyms and abbreviations for entities. Entity window support the search and browse synonyms and abbreviations. Synonym candidate window can let user create new synonym generation rules and curate the generated synonyms.
Reference and comment
Users can add references and comments for entities and interactions in the reference window.
Import and export
One goal of MetNetDB is to support third party software tools. Currently, it can export the propriety XML file for FCModeler through MapBuilder window and SBML file through SBML export menu.