Node and Edge States, Comments and Literature Refs Should be Imported in New Columns

wikipathways / cytoscape-wikipathways-app

WikiPathways app for Cytoscape to open and access pathways from WikiPathways

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Node and Edge States, Comments and Literature Refs Should be Imported in New Columns #91

Open AlexanderPico opened 5 years ago

AlexanderPico commented 5 years ago

Can we grab the comments and literature references associated with individual nodes and edges and write those to new columns in CyTables?

Use case 1: Phosphorylation states

These states are associated with parent nodes. The comments for these states should be captures in the Node Table as a new attribute for the parent node.
Example: WP3972

Use case 2: Literature refs

Nodes and Edges can have literature references associated with them. Capturing just the PMID is sufficient. These should be written to a CyTable as a new column.
Example: WP554

Use case 3: Comments

Nodes and Edges can have comments. Write these out to a new column as well.
Example: WP3008

ariutta commented 5 years ago

Literature refs for specific DataNodes and for the entire pathway are being captured and saved at the pathway level. For example, WP554 has pmid:17464936 for the entire pathway and pmid:15134803 specifically for DataNodes "b75c3" (Aldosterone), "e14ac" (CYP11B2) and "ec3b5" (NR3C2). When imported as pathway, 17464936 and 15134803 are in the Network Table, but 15134803 does not show up for any of the specific nodes.

@AlexanderPico, should 15134803 show up at all in the Network Table in this case? Or should it only be for the specific nodes?

AlexanderPico commented 2 years ago

The feature was fine as-is, but it looks like we lost it in 3.3.8. Need to dig it up from other branch...