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thechiselgroup / biomixer

BioMixer
http://bio-mixer.appspot.com/
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display other relationships (e.g. has_part) in addition to parent and child relationships (i.e. is_a) #173

Closed ghost closed 12 years ago

ghost commented 12 years ago

go to http://bioportal.bioontology.org/ontologies/45890?p=terms&jump_to_nav=true&conceptid=GO%3A0071013#details

There are 2 terms listed as values for the "Has Part" relationship "Prp19 complex" and "U5 snRNP".

However, the "has_part" relationship is not displayed in the visualization (previous versions of BioPortal displayed the has_part relationship) http://bioportal.bioontology.org/ontologies/45890?p=terms&jump_to_nav=true&conceptid=GO%3A0071013#visualization

everbeek commented 12 years ago

Have this in place, and dealt with my plugin crashing (see #4). The arcs aren't showing up, but the nodes are, which I suspected would happen once I could test what I had so far. Adding has-a arcs next.

everbeek commented 12 years ago

Arcs will be a separate type, and have the full set of UI entries seen in the Arcs section (visibility toggle, color, etc). The has_part nodes and attendant arcs should only appear in the term neighbourhood view, and not in the mapping or in the path to root view.

everbeek commented 12 years ago

Bo and me talked it over, and showing the has part arcs and nodes only makes sense in the term neighbourhood view, and not in the path to root view and concept mapping view. That is, we will show it by default whe term neighbourhood is selected. When a user expands to a node's Concepts (clicks the node, selects 'Concepts'), we will expand the has part relations as well, regardless of the current active view.

everbeek commented 12 years ago

That was rather straightforward. I made a mistake before and put the has-part relevant code int he path to root area, but have moved it to term neighborhood only. I added the new arc type and attendant changes.The GUI is in place, the arcs are present.

everbeek commented 12 years ago

When I do a Concept expansion, do has-part relations get expanded too? We want them to. Checking...no, they do not appear to. Adding that next.

everbeek commented 12 years ago

I thought that git commit -a would add untracked files. It doesn't. -A might. Thus the CompositeArcType.java is missing from the previous two commits.

everbeek commented 12 years ago

'Concept' expansion in mapping view doesn't add the has_part nodes. Does that service request not give back said info? Look into it. This is the last step prior to closing this issue. Re-designs will be part of a different issue.

everbeek commented 12 years ago

This is committed to master. Finding out from Bo if this should merge into bioportal-integration and be re-deployed immediately or if it will wait for a package of changes to be uploaded.

everbeek commented 12 years ago

This and #181 will be merged to the biportal-integration branch after testing, and deployed.

everbeek commented 12 years ago

Ray suggests that there needs to be a legend or a mouse over to help show the difference between the has_part/[R]has_part and SubClass/SuperClass arcs.

The previous arcs were solid and dashed, and these ones only differ by color. This idea of a legend or mouse over was valid with two line types, but clearly did not come to mind before.

I think there is a case for tool tips on arcs elsewhere...#69 discusses this. It also deals with self-arcs. I will leave this issue closed, and work with the other one.