Python 医学知识图谱问答系统（一），建立医学知识图谱，基于neo4j知识图谱的医学问答体系_基于noej4医药知识图谱

医学知识问答，知识图谱建设部分，建设过程如下：

一.首先，准备数据，主要为结构化的医学数据，包含实体和关系

原始数据样式（来源于刘焕勇老师整理的医学数据）：

 二.在neo4j数据库中建立空数据库，并且启用数据库，我这里用的是桌面版的neo4j，效果如下：

用户名：neo4j，密码：123456，大家根据自己需求设定，启用数据库：

 三.开始写Python将数据导入数据库

import os
import json
from py2neo import Graph,Node

1.设置文件读取路径：

cur_dir = '/'.join(os.path.abspath(__file__).split('/')[:-1])
data_path = os.path.join(cur_dir, 'data/medical.json')

2.连接数据库设置：

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="neo4j",  # 数据库user name，如果没有更改过，应该是neo4j
    password="123456")

3.读取文件函数，根据实体类型（药品、食物、检查、科室、药品大类、疾病、症状）和关系类型（科室和科室关系、疾病和食物禁忌关系、疾病和宜吃食物关系、疾病和建议食物关系、疾病和通用药品关系、疾病和建议药品关系、疾病和检查的关系、药品和生产厂家的关系、疾病和症状的关系、疾病和并发症的关系、疾病和科室的关系）建立相应的空列表，把他们装起来：

    '''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

4.建立节点函数：

    '''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

5.创建知识图谱中心疾病的节点：

'''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

6.创建知识图谱实体节点类型schema：

'''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

7.创建实体关系边：

    '''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')

8.创建实体关联边

    '''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

9.导出实体文件，应用于问答系统的建设：

    '''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

全部代码：

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="neo4j",  # 数据库user name，如果没有更改过，应该是neo4j
            password="123456")
 
    '''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()
    handler.create_graphnodes()     
    handler.create_graphrels()

代码参考刘焕勇老师的项目，连接如下，Author: lhy<lhy_in_blcu@126.com,https://huangyong.github.io>