Specifications

This page provides a summary of the state of the current working drafts of SBGN languages. We will try to keep this page up to date as documents are revised and released. All documents and source files are available in the Subversion repository for SBGN on Sourceforge.net, so this page is in fact simply a way to access relevant files more directly and quickly.

Process Diagram

The SBGN Process Diagram (PD) notation shows the temporal courses of biochemical interactions in a network. It can be used to show all the molecular interactions taking place in a network of biochemical entities, with the same entity appearing multiple times in the same diagram.

SBGN Process Diagram Level 1 specification: Public Release (PDF)

Some errors have been spotted in the specification since its release, and will be corrected in a further version. Meanwhile, the corrections can be found here

Entity Relationship Diagram

The SBGN Entity Relationship Diagram (ERD) notation allows you to see all the relationships in which a given entity participates, regardless of the temporal aspects. Entities only once in the diagram, making the ERD insensitive to the combinatorial explosion that can result in the PD.

SBGN Entity Relationship Diagram Level 1 specification: Not yet ready

Activity Flow Diagram

The SBGN Activity Flow Diagram (AFD) notation depicts the flow of information between biochemical entities in a network. It omits information about the state transitions of entities and is particularly convenient for representing the effects of perturbations, whether genetic or environmental in nature.

SBGN Activity Flow Diagram Level 1 specification: Not yet ready