Meeting Notes, October 7, 2010, During COMBINE in Edinburgh
Present: Emek Demir, Stuart Moodie, Anatoly , Gary Bader, Martijn van Iersel, Alice Vileger, Tobias Czauderna, Falk Schreiber, Huaiyu Mi, Augustin Luna
- Several proposals have been discussed on the mailing list, and the
feeling is that we're getting close to a final resolution.
- With regards to specifying segment type (straight, quadratic or
cubic), alice proposes to leave it out altogether, because this information can be derived from the number of control points (0, 1 or 2)
- "controlPoint" will be renamed to "point" for brevity.
Clone marker labels / State val@var
- Currently, clone marker labels are implemented with a second label
element, whereas state labels are done using a specialized "state" tag with attributes variable and value. This is inconsistent because the former is "graphical", the latter is "semantical".
- Resolution: we go for semantical. The "label" for clone marker labels
is replaced with a "clone" element, with an optional text attribute
- The "clone" attribute on glyphs is then redundant and will be removed.
- The "role" attribute on labels will be removed.
- The current implementation for state is left untouched.
Label bounds proposal
- The latest proposal made by Frank was accepted by everybody, the
corresponding bug will be closed.
- Currently there is no way to create stoichiometry labels.
- It was decided to allow subglyphs on arcs for stoichiometry (just like
we allow subglyphs on glyphs for "state" and "unit of information")
- Position of stoichiometry markers is specified using absolute
coordinates (and not e.g. relative positions on the arc)
- There was a whole discussion on what a stoichiometry marker on a
curved line should look like, but a decision on this will have to be taken by the SBGN editors.
- We did not have time to discuss the issue of Compartments & Complex
- We also did not have time to talk about a release plan
Next meeting will be an online meeting (EU-USA time) in November.