python - 使用Python提取医疗信息

Question

我是一名护士，我知道 python 但我不是专家，只是用它来处理 DNA 序列
我们得到了用人类语言编写的医院记录，我应该将这些数据插入数据库或 csv 文件，但它们超过 5000 行，这可能很难。所有数据都以一致的格式编写让我给你举个例子

11/11/2010 - 09:00am : He got nausea, vomiting and died 4 hours later

我应该得到以下数据

Sex: Male
Symptoms: Nausea
    Vomiting
Death: True
Death Time: 11/11/2010 - 01:00pm

另一个例子

11/11/2010 - 09:00am : She got heart burn, vomiting of blood and died 1 hours later in the operation room

我明白了

Sex: Female
Symptoms: Heart burn
    Vomiting of blood
Death: True
Death Time: 11/11/2010 - 10:00am

当我说 in 时顺序不一致......所以 in 是一个关键字，之后的所有文本都是一个地方，直到我找到另一个关键字
在开始时，他或她确定性别，得到 ........ 接下来是一组症状，我应该根据分隔符拆分，分隔符可以是逗号、连字符或其他任何东西，但它对于同一行是一致的< br/>died ..... hours later also should get how to get however, sometimes the patient still alive and discharge ....etc
这就是说我们有很多约定，我认为如果我可以用关键字和模式标记文本，我就可以完成工作。因此，如果您知道一个有用的函数/模块/教程/工具，最好在 python 中执行此操作(如果不是 python，那么 gui 工具会很好)

一些信息:

there are a lot of rules to express various medical data but here are few examples
- Start with the same date/time format followed by a space followd by a colon followed by a space followed by He/She followed space followed by rules separated by and
- Rules:
    * got <symptoms>,<symptoms>,....
    * investigations were done <investigation>,<investigation>,<investigation>,......
    * received <drug or procedure>,<drug or procedure>,.....
    * discharged <digit> (hour|hours) later
    * kept under observation
    * died <digit> (hour|hours) later
    * died <digit> (hour|hours) later in <place>
other rules do exist but they follow the same idea

Answer 1

这使用 dateutil解析日期(例如“11/11/2010 - 09:00am”)和 parsedatetime解析相对时间(例如“4 小时后”):

import dateutil.parser as dparser
import parsedatetime.parsedatetime as pdt
import parsedatetime.parsedatetime_consts as pdc
import time
import datetime
import re
import pprint
pdt_parser = pdt.Calendar(pdc.Constants())   
record_time_pat=re.compile(r'^(.+)\s+:')
sex_pat=re.compile(r'\b(he|she)\b',re.IGNORECASE)
death_time_pat=re.compile(r'died\s+(.+hours later).*$',re.IGNORECASE)
symptom_pat=re.compile(r'[,-]')

def parse_record(astr):    
    match=record_time_pat.match(astr)
    if match:
        record_time=dparser.parse(match.group(1))
        astr,_=record_time_pat.subn('',astr,1)
    else: sys.exit('Can not find record time')
    match=sex_pat.search(astr)    
    if match:
        sex=match.group(1)
        sex='Female' if sex.lower().startswith('s') else 'Male'
        astr,_=sex_pat.subn('',astr,1)
    else: sys.exit('Can not find sex')
    match=death_time_pat.search(astr)
    if match:
        death_time,date_type=pdt_parser.parse(match.group(1),record_time)
        if date_type==2:
            death_time=datetime.datetime.fromtimestamp(
                time.mktime(death_time))
        astr,_=death_time_pat.subn('',astr,1)
        is_dead=True
    else:
        death_time=None
        is_dead=False
    astr=astr.replace('and','')    
    symptoms=[s.strip() for s in symptom_pat.split(astr)]
    return {'Record Time': record_time,
            'Sex': sex,
            'Death Time':death_time,
            'Symptoms': symptoms,
            'Death':is_dead}


if __name__=='__main__':
    tests=[('11/11/2010 - 09:00am : He got nausea, vomiting and died 4 hours later',
            {'Sex':'Male',
             'Symptoms':['got nausea', 'vomiting'],
             'Death':True,
             'Death Time':datetime.datetime(2010, 11, 11, 13, 0),
             'Record Time':datetime.datetime(2010, 11, 11, 9, 0)}),
           ('11/11/2010 - 09:00am : She got heart burn, vomiting of blood and died 1 hours later in the operation room',
           {'Sex':'Female',
             'Symptoms':['got heart burn', 'vomiting of blood'],
             'Death':True,
             'Death Time':datetime.datetime(2010, 11, 11, 10, 0),
             'Record Time':datetime.datetime(2010, 11, 11, 9, 0)})
           ]

    for record,answer in tests:
        result=parse_record(record)
        pprint.pprint(result)
        assert result==answer
        print

产量:

{'Death': True,
 'Death Time': datetime.datetime(2010, 11, 11, 13, 0),
 'Record Time': datetime.datetime(2010, 11, 11, 9, 0),
 'Sex': 'Male',
 'Symptoms': ['got nausea', 'vomiting']}

{'Death': True,
 'Death Time': datetime.datetime(2010, 11, 11, 10, 0),
 'Record Time': datetime.datetime(2010, 11, 11, 9, 0),
 'Sex': 'Female',
 'Symptoms': ['got heart burn', 'vomiting of blood']}

注意:小心解析日期。 “8/9/2010”是指 8 月 9 日还是 9 月 8 日？所有的记录员都使用相同的约定吗？如果您选择使用 dateutil(如果日期字符串的结构不严格，我真的认为这是最好的选择)请务必阅读 dateutil documentation 中关于“格式优先级”的部分。所以你可以(希望)正确解决'8/9/2010'。如果您不能保证所有记录管理员都使用相同的约定来指定日期，那么将手动检查此脚本的结果。无论如何，这可能是明智的。