WikiPathways Questions & Comments

Questions and requests for using WikiPathways (for Alex Pico's visit on Feb 24, 2014)

Questions can also be sent to wikipathways-discuss@googlegroups.com

Questions

1. How are edits resolved when multiple people are working on a single pathway simultaneously?

2. What does the "Hypothetical pathway" tag signify?

3. Unconnected lines? Any way to resolve in entirety these edges?

4. Can we include chemicals as nodes in the pathway? Are these supposed to be represented by the "Metabolite" node?

5. How to add more information to the nodes and edges?

6. Expression  data overview- how flexible is the data that can be visualized?

7.overlay of conditions, can we extend this to add phenotypic outcomes or pathway outcomes?

8. What tools use BioPax formats?

9. Ortholog templates- transverses?

Requests

1. googlesque "who else is logged in and or editing" notification or google-type real-time collaborative editing view. 
Edits are being lost

2. Reference/Citation numbers are oriented according to the edge/interation such that some numbers are displayed upside-down. These should always be right-side up

3. The current viewport for a pathway (in standard viewing/browsing mode, as opposed to editing mode) has a 
fixed height and is quite small. Can we make the viewing window resizable?

4. Annotations to nodes and edges (such as comments and references) are only available from the network diagram
 in editing mode. Can we make it so that annotations to nodes and edges are available by (for example) 
right-clicking on a node or edge in the viewing/browsing mode?

5. Can we connect pathways to each other?

6. Model interaction templates to maintain consistencies.

notes

NCBO- mapping wbbt to wikipathways cell ontology