These are chat archives for jdrudolph/goenrich

20th
Sep 2017
Jan Rudolph
@jdrudolph
Sep 20 2017 08:05
leafs should be easy to get. First construct the GO ontology graph with goenrich. Then calculate node out-degrees with https://networkx.github.io/documentation/networkx-1.10/reference/generated/networkx.DiGraph.out_degree.html.
All nodes with out-degree 0 are leafs.
wouldn't know how to plot the entire ontology in any meaningful way though... you could export the networkx graph to .dot https://networkx.github.io/documentation/networkx-1.10/reference/generated/networkx.drawing.nx_agraph.write_dot.html
then use graphviz to generate the layout/picture
let me know if you manage to get some nice visualization
Alexander Lenail
@zfrenchee
Sep 20 2017 14:23
it was in_degree because the ontology is "backwards"