Talk:GPMLChangeProposal

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Alex FEB17: Ah, I didn't notice this page during our last skype call due to the odd login issue. But, now I have access again and will provide feedback on comments. Thanks for putting this information up on the wiki!

Alex FEB17: Good stuff! I am in full support of the proposals for items 1-7. I am not sure about the proposal for item 8: Node/Edge clarification. We will get together and discuss it before our next skype call on Wed. I think proposal 2 for item 9 is a great solution to the notes/comments problem. I am not concerned about them becoming too useful :) And the proposal for item 10 sounds right, but we'll want to discuss that one as well. Again, we should have more complete responses by Wednesday. Thanks!

Alex FEB17: Oh yeah, we should also discuss the division of labor on these proposed changes. I know I haven't contributed as much as I have wanted. I am working on freeing up time specifically for PathVisio and GPML, so now is a good time to for me to committ to tasks. I think Kristina also wants to contribute code.

Thomas APR12: There might be situations where we want to include a group into a group, which is not possible with the current GroupId. E.g. when we have a group of datanodes (in order to organize them dynamically) and a circle that we want to group with these datanodes, just because we want them to move together. We want one group with style "stack" that contains the datanodes and a group without style that contains the stack group and the circle.

A solution for including a group in another group, is to have a Group element. GroupIds now link to the Group element's name and the group itself can have a GroupId too.

Here's an example:

<Pathway ...>
  <DataNode TextLabel="Gene1" ... GroupId="g1">
    <Graphics ... />
    <Xref ... />
  </DataNode>
  <DataNode TextLabel="Gene2" ... GroupId="g1">
    <Graphics .../>
    <Xref .../>
  </DataNode>
  <DataNode TextLabel="Gene3" ... GroupId="g1">
    <Graphics ... />
    <Xref ... />
  </DataNode>
  <Shape Type="Oval" ... GroupId="g2">
    <Graphics ... />
  </Shape>
  <Group name="g1" groupId="g2" style="stacked"/>
  <Group name="g2"/>
</Pathway>

I think having a group element looks more intuitive instead of having two seperate attributes (id and style) to every GPML element (where style should be identical for all elements in a group and is therefore redundant). It also has more perspective too I think, in case we want to expand the possibilities of a group (e.g. linking lines to groups, or even to a specific anchor point of a group). It also makes programming more convenient, since now the group is a real entity and you don't have to deduce the group structure from you data (which is a disadvantage I experienced by using the GraphIds for making multi-segment lines out of seperate two-point lines).

Alex APR12: It would also allow Group properties to be stored at the group-level, such as style and center.