forked from liuhuanyong/QASystemOnMedicalKG
-
Notifications
You must be signed in to change notification settings - Fork 0
/
build_medicalgraph.py
270 lines (230 loc) · 11.2 KB
/
build_medicalgraph.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
#!/usr/bin/env python3
# coding: utf-8
# File: MedicalGraph.py
# Author: lhy<[email protected],https://huangyong.github.io>
# Date: 18-10-3
import os
import json
from py2neo import Graph,Node
class MedicalGraph:
def __init__(self):
cur_dir = '/'.join(os.path.abspath(__file__).split('/')[:-1])
self.data_path = os.path.join(cur_dir, 'data/medical.json')
self.g = Graph(
host="127.0.0.1", # neo4j 搭载服务器的ip地址，ifconfig可获取到
http_port=7474, # neo4j 服务器监听的端口号
user="lhy", # 数据库user name，如果没有更改过，应该是neo4j
password="lhy123")
'''读取文件'''
def read_nodes(self):
# 共７类节点
drugs = [] # 药品
foods = [] # 食物
checks = [] # 检查
departments = [] #科室
producers = [] #药品大类
diseases = [] #疾病
symptoms = []#症状
disease_infos = []#疾病信息
# 构建节点实体关系
rels_department = [] # 科室－科室关系
rels_noteat = [] # 疾病－忌吃食物关系
rels_doeat = [] # 疾病－宜吃食物关系
rels_recommandeat = [] # 疾病－推荐吃食物关系
rels_commonddrug = [] # 疾病－通用药品关系
rels_recommanddrug = [] # 疾病－热门药品关系
rels_check = [] # 疾病－检查关系
rels_drug_producer = [] # 厂商－药物关系
rels_symptom = [] #疾病症状关系
rels_acompany = [] # 疾病并发关系
rels_category = [] # 疾病与科室之间的关系
count = 0
for data in open(self.data_path):
disease_dict = {}
count += 1
print(count)
data_json = json.loads(data)
disease = data_json['name']
disease_dict['name'] = disease
diseases.append(disease)
disease_dict['desc'] = ''
disease_dict['prevent'] = ''
disease_dict['cause'] = ''
disease_dict['easy_get'] = ''
disease_dict['cure_department'] = ''
disease_dict['cure_way'] = ''
disease_dict['cure_lasttime'] = ''
disease_dict['symptom'] = ''
disease_dict['cured_prob'] = ''
if 'symptom' in data_json:
symptoms += data_json['symptom']
for symptom in data_json['symptom']:
rels_symptom.append([disease, symptom])
if 'acompany' in data_json:
for acompany in data_json['acompany']:
rels_acompany.append([disease, acompany])
if 'desc' in data_json:
disease_dict['desc'] = data_json['desc']
if 'prevent' in data_json:
disease_dict['prevent'] = data_json['prevent']
if 'cause' in data_json:
disease_dict['cause'] = data_json['cause']
if 'get_prob' in data_json:
disease_dict['get_prob'] = data_json['get_prob']
if 'easy_get' in data_json:
disease_dict['easy_get'] = data_json['easy_get']
if 'cure_department' in data_json:
cure_department = data_json['cure_department']
if len(cure_department) == 1:
rels_category.append([disease, cure_department[0]])
if len(cure_department) == 2:
big = cure_department[0]
small = cure_department[1]
rels_department.append([small, big])
rels_category.append([disease, small])
disease_dict['cure_department'] = cure_department
departments += cure_department
if 'cure_way' in data_json:
disease_dict['cure_way'] = data_json['cure_way']
if 'cure_lasttime' in data_json:
disease_dict['cure_lasttime'] = data_json['cure_lasttime']
if 'cured_prob' in data_json:
disease_dict['cured_prob'] = data_json['cured_prob']
if 'common_drug' in data_json:
common_drug = data_json['common_drug']
for drug in common_drug:
rels_commonddrug.append([disease, drug])
drugs += common_drug
if 'recommand_drug' in data_json:
recommand_drug = data_json['recommand_drug']
drugs += recommand_drug
for drug in recommand_drug:
rels_recommanddrug.append([disease, drug])
if 'not_eat' in data_json:
not_eat = data_json['not_eat']
for _not in not_eat:
rels_noteat.append([disease, _not])
foods += not_eat
do_eat = data_json['do_eat']
for _do in do_eat:
rels_doeat.append([disease, _do])
foods += do_eat
recommand_eat = data_json['recommand_eat']
for _recommand in recommand_eat:
rels_recommandeat.append([disease, _recommand])
foods += recommand_eat
if 'check' in data_json:
check = data_json['check']
for _check in check:
rels_check.append([disease, _check])
checks += check
if 'drug_detail' in data_json:
drug_detail = data_json['drug_detail']
producer = [i.split('(')[0] for i in drug_detail]
rels_drug_producer += [[i.split('(')[0], i.split('(')[-1].replace(')', '')] for i in drug_detail]
producers += producer
disease_infos.append(disease_dict)
return set(drugs), set(foods), set(checks), set(departments), set(producers), set(symptoms), set(diseases), disease_infos,\
rels_check, rels_recommandeat, rels_noteat, rels_doeat, rels_department, rels_commonddrug, rels_drug_producer, rels_recommanddrug,\
rels_symptom, rels_acompany, rels_category
'''建立节点'''
def create_node(self, label, nodes):
count = 0
for node_name in nodes:
node = Node(label, name=node_name)
self.g.create(node)
count += 1
print(count, len(nodes))
return
'''创建知识图谱中心疾病的节点'''
def create_diseases_nodes(self, disease_infos):
count = 0
for disease_dict in disease_infos:
node = Node("Disease", name=disease_dict['name'], desc=disease_dict['desc'],
prevent=disease_dict['prevent'] ,cause=disease_dict['cause'],
easy_get=disease_dict['easy_get'],cure_lasttime=disease_dict['cure_lasttime'],
cure_department=disease_dict['cure_department']
,cure_way=disease_dict['cure_way'] , cured_prob=disease_dict['cured_prob'])
self.g.create(node)
count += 1
print(count)
return
'''创建知识图谱实体节点类型schema'''
def create_graphnodes(self):
Drugs, Foods, Checks, Departments, Producers, Symptoms, Diseases, disease_infos,rels_check, rels_recommandeat, rels_noteat, rels_doeat, rels_department, rels_commonddrug, rels_drug_producer, rels_recommanddrug,rels_symptom, rels_acompany, rels_category = self.read_nodes()
self.create_diseases_nodes(disease_infos)
self.create_node('Drug', Drugs)
print(len(Drugs))
self.create_node('Food', Foods)
print(len(Foods))
self.create_node('Check', Checks)
print(len(Checks))
self.create_node('Department', Departments)
print(len(Departments))
self.create_node('Producer', Producers)
print(len(Producers))
self.create_node('Symptom', Symptoms)
return
'''创建实体关系边'''
def create_graphrels(self):
Drugs, Foods, Checks, Departments, Producers, Symptoms, Diseases, disease_infos, rels_check, rels_recommandeat, rels_noteat, rels_doeat, rels_department, rels_commonddrug, rels_drug_producer, rels_recommanddrug,rels_symptom, rels_acompany, rels_category = self.read_nodes()
self.create_relationship('Disease', 'Food', rels_recommandeat, 'recommand_eat', '推荐食谱')
self.create_relationship('Disease', 'Food', rels_noteat, 'no_eat', '忌吃')
self.create_relationship('Disease', 'Food', rels_doeat, 'do_eat', '宜吃')
self.create_relationship('Department', 'Department', rels_department, 'belongs_to', '属于')
self.create_relationship('Disease', 'Drug', rels_commonddrug, 'common_drug', '常用药品')
self.create_relationship('Producer', 'Drug', rels_drug_producer, 'drugs_of', '生产药品')
self.create_relationship('Disease', 'Drug', rels_recommanddrug, 'recommand_drug', '好评药品')
self.create_relationship('Disease', 'Check', rels_check, 'need_check', '诊断检查')
self.create_relationship('Disease', 'Symptom', rels_symptom, 'has_symptom', '症状')
self.create_relationship('Disease', 'Disease', rels_acompany, 'acompany_with', '并发症')
self.create_relationship('Disease', 'Department', rels_category, 'belongs_to', '所属科室')
'''创建实体关联边'''
def create_relationship(self, start_node, end_node, edges, rel_type, rel_name):
count = 0
# 去重处理
set_edges = []
for edge in edges:
set_edges.append('###'.join(edge))
all = len(set(set_edges))
for edge in set(set_edges):
edge = edge.split('###')
p = edge[0]
q = edge[1]
query = "match(p:%s),(q:%s) where p.name='%s'and q.name='%s' create (p)-[rel:%s{name:'%s'}]->(q)" % (
start_node, end_node, p, q, rel_type, rel_name)
try:
self.g.run(query)
count += 1
print(rel_type, count, all)
except Exception as e:
print(e)
return
'''导出数据'''
def export_data(self):
Drugs, Foods, Checks, Departments, Producers, Symptoms, Diseases, disease_infos, rels_check, rels_recommandeat, rels_noteat, rels_doeat, rels_department, rels_commonddrug, rels_drug_producer, rels_recommanddrug, rels_symptom, rels_acompany, rels_category = self.read_nodes()
f_drug = open('drug.txt', 'w+')
f_food = open('food.txt', 'w+')
f_check = open('check.txt', 'w+')
f_department = open('department.txt', 'w+')
f_producer = open('producer.txt', 'w+')
f_symptom = open('symptoms.txt', 'w+')
f_disease = open('disease.txt', 'w+')
f_drug.write('\n'.join(list(Drugs)))
f_food.write('\n'.join(list(Foods)))
f_check.write('\n'.join(list(Checks)))
f_department.write('\n'.join(list(Departments)))
f_producer.write('\n'.join(list(Producers)))
f_symptom.write('\n'.join(list(Symptoms)))
f_disease.write('\n'.join(list(Diseases)))
f_drug.close()
f_food.close()
f_check.close()
f_department.close()
f_producer.close()
f_symptom.close()
f_disease.close()
return
if __name__ == '__main__':
handler = MedicalGraph()
# handler.export_data()