Specifications

There are three orthogonal and complementary visual languages defined in SBGN: Process Description (PD), Entity Relationship (ER), and Activity Flow (AF). They can be seen as three alternative projections of the underlying, more complex biological information.

Process Description language

The SBGN Process Description (PD) language 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.

Current Specification:

The SBGN PD language Level 1 Version 2.0 – Available at Journal of Integrative Bioinformatics, 2019 Jun 13. doi: 10.1515/jib-2019-0022.

Former Specification:

The SBGN PD language Level 1 Version 1.3 – Available at Journal of Integrative Bioinformatics, 2015 Sep 4;12(2):263. doi: 10.2390/biecoll-jib-2015-263.

For end-users more than software developers SBGN PD Level 1 User Manual is also available.

Entity Relationship language

The SBGN Entity Relationship (ER) language allows you to see all the relationships in which a given entity participates, regardless of the temporal aspects. Relationships can be seen as rules describing the influences of entities nodes on other relationships.

Current Specification:

The SBGN ER language Level 1 Version 2.0 – Available at Journal of Integrative Bioinformatics, 2015 Sep 4;12(2):264. doi: 10.2390/biecoll-jib-2015-264.

Activity Flow language

The SBGN Activity Flow (AF) language 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.

Current Specification:

The SBGN AF language Level 1 Version 1.2 – Available at Journal of Integrative Bioinformatics, 2015 Sep 4;12(2):265. doi: 10.2390/biecoll-jib-2015-265.