Commit 047d1351 authored by ina's avatar ina
Browse files

adding files

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bond id label_mutagenic
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<uri id="Automatically generated entry, Timestamp=1585753668055" name="duplicate:https://gitlab.cern.ch/bgkotse/genappi/owao" uri="owao1.owl"/>
<uri id="Automatically generated entry, Timestamp=1585753668055" name="duplicate:https://gitlab.cern.ch/bgkotse/genappi/owao" uri="owao2.owl"/>
</group>
</catalog>
This diff is collapsed.
This diff is collapsed.
style,ID,label
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_blueBackground_white_large_right,90,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_redBackground_white_medium_right,135,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_big_right,13,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_redBackground_white_medium_left,133,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_large_right,73,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_greenBackground_white_large_left,104,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_tiny_center,22,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_large_left,33,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_tiny_center,64,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_greenBackground_white_small_right,100,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_medium_left,28,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_huge_center,60,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_huge_center,78,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_purpleBackground_white_small_right,116,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_large_left,7,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_massive_left,79,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_tiny_left,21,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_orangeBackground_white_large_left,145,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_small_left,47,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_medium_center,69,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_greenBackground_white_large_right,106,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_massive_left,17,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_small_center,48,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_purpleBackground_white_medium_center,118,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_big_left,11,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_redBackground_white_huge_left,142,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_big_left,56,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_tiny_left,63,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_massive_center,43,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_large_center,54,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_purpleBackground_white_medium_left,117,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_redBackground_white_big_center,140,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_large_center,72,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_huge_left,77,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_redBackground_white_big_left,139,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_small_right,67,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_purpleBackground_white_large_center,121,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_greenBackground_white_tiny_center,97,1
style,ID,label
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_purpleBackground_white_big_center,124,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_tiny_right,4,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_greenBackground_white_large_center,105,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_redBackground_white_small_left,130,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_big_center,12,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_small_left,24,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_huge_center,40,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_medium_right,6,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_blueBackground_white_small_center,83,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_greenBackground_white_big_left,107,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_big_center,57,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_small_center,66,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_medium_left,50,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_small_left,5,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_purpleBackground_white_huge_left,126,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_big_center,37,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_big_center,75,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_blueBackground_white_big_right,93,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_redBackground_white_large_center,137,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_mini_left,19,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_small_right,49,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_tiny_center,2,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_purpleBackground_white_large_right,122,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_large_center,34,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_huge_right,16,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_small_right,30,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_greenBackground_white_small_left,98,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_greenBackground_white_medium_right,103,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_blueBackground_white_small_left,82,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_large_right,9,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_blueBackground_white_medium_left,85,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_small_center,26,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_big_right,38,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_massive_center,18,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_redBackground_white_tiny_left,128,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_small_center,25,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_redBackground_white_huge_center,143,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_greenBackground_white_medium_center,102,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_blueBackground_white_big_center,92,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_orangeBackground_white_medium_left,144,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_big_left,74,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_big_right,58,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_blueBackground_white_tiny_center,81,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_mini_center,20,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_small_right,27,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_purpleBackground_white_large_left,120,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_tiny_right,23,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_medium_left,31,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_huge_right,41,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_purpleBackground_white_tiny_left,112,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_mini_left,62,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_greenBackground_white_huge_center,111,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_blueBackground_white_large_left,88,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_large_left,53,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_medium_right,32,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_mini_center,1,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_massive_left,42,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_small_left,65,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_blueBackground_white_tiny_left,80,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_purpleBackground_white_big_left,123,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_redBackground_white_large_right,138,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_big_right,76,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_medium_center,29,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_large_right,35,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_blueBackground_white_medium_right,87,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_redBackground_white_big_right,141,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_huge_center,15,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_big_left,36,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_purpleBackground_white_big_right,125,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_medium_right,70,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_purpleBackground_white_huge_center,127,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_blueBackground_white_large_center,89,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_greenBackground_white_big_right,109,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_redBackground_white_medium_center,134,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_greenBackground_white_huge_left,110,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_medium_center,3,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_redBackground_white_small_right,132,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_redBackground_white_tiny_center,129,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_blueBackground_white_medium_center,86,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_large_right,55,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_tiny_center,46,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_greenBackground_white_small_center,99,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_medium_left,68,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_medium_center,51,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_mini_left,0,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_tiny_left,10,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_huge_left,59,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_blueBackground_white_big_left,91,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_massive_left,61,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_purpleBackground_white_tiny_center,113,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_dark_grey_white_large_left,71,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_redBackground_white_large_left,136,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_light_grey_black_huge_left,39,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_greenBackground_white_tiny_left,96,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_greenBackground_white_big_center,108,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_redBackground_white_small_center,131,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_blueBackground_white_small_right,84,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_blueBackground_white_huge_left,94,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_greenBackground_white_medium_left,101,3
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_purpleBackground_white_medium_right,119,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_blueBackground_white_huge_center,95,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_huge_left,14,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_medium_right,52,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_tiny_left,45,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_black_white_mini_left,44,1
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_purpleBackground_white_small_left,114,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_purpleBackground_white_small_center,115,2
https://gitlab.cern.ch/bgkotse/genappi/owao#ui_style_white_black_large_center,8,3
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import numpy as np
from collections import defaultdict
class Vertex(object):
vertex_counter = 0
def __init__(self, name, predicate=False, _from=None, _to=None):
self.name = name
self.predicate = predicate
self._from = _from
self._to = _to
self.id = Vertex.vertex_counter
Vertex.vertex_counter += 1
def __eq__(self, other):
if other is None:
return False
return self.__hash__() == other.__hash__()
def __hash__(self):
if self.predicate:
return hash((self.id, self._from, self._to, self.name))
else:
return hash(self.name)
def __lt__(self, other):
return self.name < other.name
class KnowledgeGraph(object):
def __init__(self):
self._vertices = set()
self._transition_matrix = defaultdict(set)
self._label_map = {}
self._inv_label_map = {}
def add_vertex(self, vertex):
"""Add a vertex to the Knowledge Graph."""
if vertex.predicate:
self._vertices.add(vertex)
else:
self._vertices.add(vertex)
def add_edge(self, v1, v2):
"""Add a uni-directional edge."""
self._transition_matrix[v1].add(v2)
def remove_edge(self, v1, v2):
"""Remove the edge v1 -> v2 if present."""
if v2 in self._transition_matrix[v1]:
self._transition_matrix[v1].remove(v2)
def get_neighbors(self, vertex):
"""Get all the neighbors of vertex (vertex -> neighbor)."""
return self._transition_matrix[vertex]
def visualise(self):
"""Visualise the graph using networkx & matplotlib."""
import matplotlib.pyplot as plt
import networkx as nx
nx_graph = nx.DiGraph()
for v in self._vertices:
if not v.predicate:
name = v.name.split('/')[-1]
nx_graph.add_node(name, name=name, pred=v.predicate)
for v in self._vertices:
if not v.predicate:
v_name = v.name.split('/')[-1]
# Neighbors are predicates
for pred in self.get_neighbors(v):
pred_name = pred.name.split('/')[-1]
for obj in self.get_neighbors(pred):
obj_name = obj.name.split('/')[-1]
nx_graph.add_edge(v_name, obj_name, name=pred_name)
plt.figure(figsize=(10,10))
_pos = nx.circular_layout(nx_graph)
nx.draw_networkx_nodes(nx_graph, pos=_pos)
nx.draw_networkx_edges(nx_graph, pos=_pos)
nx.draw_networkx_labels(nx_graph, pos=_pos)
names = nx.get_edge_attributes(nx_graph, 'name')
nx.draw_networkx_edge_labels(nx_graph, pos=_pos, edge_labels=names)
plt.show()
def _create_label(self, vertex, n):
"""Take labels of neighbors, sort them lexicographically and join."""
neighbor_names = [self._label_map[x][n - 1]
for x in self.get_neighbors(vertex)]
suffix = '-'.join(sorted(set(map(str, neighbor_names))))
return self._label_map[vertex][n - 1] + '-' + suffix
def weisfeiler_lehman(self, iterations=3):
"""Perform Weisfeiler-Lehman relabeling of the nodes."""
# The idea of using a hashing function is taken from:
# https://github.com/benedekrozemberczki/graph2vec
from hashlib import md5
# Store the WL labels in a dictionary with a two-level key:
# First level is the vertex identifier
# Second level is the WL iteration
self._label_map = defaultdict(dict)
self._inv_label_map = defaultdict(dict)
for v in self._vertices:
self._label_map[v][0] = v.name
self._inv_label_map[v.name][0] = v