ER development
Contents |
Domains, sites and motives
SBGN ER Level 1 Version 1 does not provide structures to represent physical or functional subdivisions of entities. Nevertheless, it is clear that domains are important, and that people want, and need, to represent them.
Different approaches have been proposed so far, in particular the nesting and the subdivision. Both have advantages and disadvantages. Nesting is closer to the underlying, or conceptual, representation, and will probably be favored by computer scientists. Subdivision is closer to the physical structure of the entities and to what we draw in the back on an envelop and in a power-point presentation. It will likely be preferred by biologists. Designing a consistent and robust system will require a significant amount of work and discussion and this page provide materials to base the discussion.
Proposal by Kurt Kohn
Kurt Kohn proposed a comprehensive proposal to encode structures using subdivisions.
- detailed proposal to represent internal structures of entities.
- map of p53
- explanation of the map
Proposal by Michael Blinov
A proposal for hierarchical nesting of entities. It provides a description of domains, sites and individual atoms of biomolecules. The proposal is designed to cover all the requirements and capabilities of subdivision proposal of MIM group. The proposal is consistent with rule-based description used in BioNetGen software and it is expected to be consistent with SBML level 3 extension describing multi-state multi-component species.
- Proposal (pdf) to represent internal structures of entities usinh hierarchical nesting.
- MS Word file.
- Inkscape file with all pictures used in the proposal.
