Documentation votes

Links to annotation

An annotation glyph has been introduced in SBGN ER L1 and SBGN AF L1. It is planned to add it to future versions of SBGN PD. This annotation glyph has to be linked to SBGN objects so as to identify precisely what it refers to.

Entity Relationships Level 1 Version 1 says that the edge linking an annotation to the object it annotates must be significantly different from other edges. The precise type of edge is not specified. Part of the community would like to see that clarified. Four other possibilities have been proposed. One is to define another edge, identified by its connection to an annotation node. Three are based on different symbols: continuous lines, dashed lines, callouts. They are described in this file.. You should look at all the slides because the issues are different with PD, AF and ER.

The example of PD used in the Nature Biotechnology paper has been annotated using the three schemes:

• using different thickness
• using dashed lines
• using callouts

Pitfalls have been pointed out for the four schemes:

• Using a regular SBGN edge is very misleading and would actually need a complex definition since this edge could connect to all kinds of nodes, but also to other edges.
• Using thicker continuous lines may also be confusing with other edges. Furthermore, an important recommendation of SBGN is that the thickness of the line should not bear meaning.
• Using dashed lines would infringe the rule of SBGN to avoid discontinued lines because of the lack of scalability and the risk of having misleading connections within the line.
• Using callouts may be difficult to implement, in particular for software that allow dynamic reorganization of the graphs.

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