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我需要从前列腺切除术最终诊断报告的平面文件中提取 Gleason 分数。这些分数总是有 Gleason 这个词和两个数字相加成另一个数字。人类在二十多年内输入了这些。包括各种空格和修饰符的约定。以下是迄今为止我的 Backus-Naur 表格，以及两个示例记录。仅针对前列腺切除术，我们正在研究超过一千个病例。

我使用 pyparsing 是因为我正在学习 python，并且对我对正则表达式写作的有限接触没有美好的回忆。

我的问题：如何在不解析可能出现在这些最终诊断中或可能不在这些最终诊断中的所有其他可选数据的情况下提取这些 Gleason 等级？

num = Word(nums)
record ::= accessionDate + accessionNumber + patMedicalRecordNum + finalDxText
accessionDate ::= num + "/" + num + "/" num
accessionNumber ::= "S" + num + "-" + num
patMedicalRecordNum ::= num + "/" + num + "-" + num + "-" + num
finalDxText ::= listOfParts + optionalComment + optionalpTNMStage
listOfParts ::= OneOrMore(part)
part ::= <multiline idiosyncratic freetext which may contain a Gleason score I want> + optionalpTNMStage
optionalComment ::= <multiline idiosyncratic freetext which may contain a Gleason score I don't want>
optionalpTNMStage ::= <multiline idiosyncratic freetext which may contain a Gleason score I don't want>


01/01/11  S11-55555 20/444-55-6666 A.  PROSTATE AND SEMINAL VESICLES, PROSTATECTOMY:                           
                                   -  ADENOCARCINOMA.                                                      

                                   TOTAL GLEASON SCORE:  GLEASON 5+4=9                                     
                                   TUMOR LOCATION:  BILATERAL                                              
                                   TUMOR QUANTITATION:  15% OF PROSTATE INVOLVED BY TUMOR                  
                                   EXTRAPROSTATIC EXTENSION:  PRESENT AT RIGHT POSTERIOR                   
                                   SEMINAL VESICLE INVASION:  PRESENT                                      
                                   MARGINS:  UNINVOLVED                                                    
                                   LYMPHOVASCULAR INVASION:  PRESENT                                       
                                   PERINEURAL INVASION:  PRESENT                                           
                                   LYMPH NODES (SPECIMENS B AND C):                                        
                                      NUMBER EXAMINED:  25                                                 
                                      NUMBER INVOLVED:  1                                                  
                                      DIAMETER OF LARGEST METASTASIS:  1.7 mm                              
                                   ADDITIONAL FINDINGS:  HIGH-GRADE PROSTATIC INTRAEPITHELIAL NEOPLASIA,   
                                      ACUTE AND CHRONIC INFLAMMATION, INTRADUCTAL EXTENSION OF INVASIVE    
                                      CARCINOMA                                                            

                                   PATHOLOGIC STAGE:  pT3b N1 MX                                           

                               B.  LYMPH NODES, RIGHT PELVIC, EXCISION:                                    
                                   -  ONE OF SEVENTEEN LYMPH NODES POSITIVE FOR METASTASIS (1/17).         

                               C.  LYMPH NODES, LEFT PELVIC, EXCISION:                                     
                                   -  EIGHT LYMPH NODES NEGATIVE FOR METASTASIS (0/8).                     
01/02/11  S11-4444 20/111-22-3333 PROSTATE AND SEMINAL VESICLES, PROSTATECTOMY:                               
                                  - ADENOCARCINOMA.                                                        
                                    GLEASON SCORE:  3 + 3 = 6 WITH TERTIARY PATTERN OF 5.                                             
                                    TUMOR QUANTITATION:  APPROXIMATELY 10% BY VOLUME.                      
                                    TUMOR LOCATION:  BILATERAL.                                            
                                    EXTRAPROSTATIC EXTENSION:  NOT IDENTIFIED.                             
                                    MARGINS:  NEGATIVE.                                                    
                                    PERINEURAL INVASION:  IDENTIFIED.                                      
                                    LYMPH-VASCULAR INVASION:  NOT IDENTIFIED.                              
                                    SEMINAL VESICLE/VASA DEFERENTIA INVASION: NOT IDENTIFIED.              
                                    LYMPH NODES:  NONE SUBMITTED.                                          
                                    OTHER:  HIGH GRADE PROSTATIC INTRAEPITHELIAL NEOPLASIA.                
                               PATHOLOGIC STAGE (pTNM):  pT2c NX.

全面披露：我是一名从事研究的医生；这是我第一次真正使用 python 工作。我读过 Lutz 的 Learning Python，Shaw 的 Learning Python the Hard Way，并解决了各种问题集。我在这个论坛 pyparsing wiki 上查看了许多与 pyparsing 相关的问题，我购买并阅读了 McGuire 先生的 Pyparsing 入门。也许我在问一个问题，当我真的应该被告知我正站在“当你必须编写解析器时，这种沮丧的死亡螺旋很常见”（McGuire，17）？我不知道。到目前为止，我很高兴能够从事可能实际上是一个真正的项目。

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3 回答 3

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看一下 pyparsing 中的 SkipTo 解析元素。如果你为 num+num=num 部分定义了一个 pyparsing 结构，你应该能够使用 SkipTo 跳过“Gleason”和那个之间的任何内容。大致像这样（未经测试的伪pyparsing）：

score = num + "+" + num + "=" num
Gleason = "Gleason" + SkipTo(score) + score

PyParsing 默认会跳过空格，使用 SkipTo 你可以跳过任何与你想要的格式不匹配的东西。

于 2012-06-01T19:18:16.537 回答
2

这是一个提取患者数据和任何匹配的 Gleason 数据的示例。

from pyparsing import *
num = Word(nums)
accessionDate = Combine(num + "/" + num + "/" + num)("accDate")
accessionNumber = Combine("S" + num + "-" + num)("accNum")
patMedicalRecordNum = Combine(num + "/" + num + "-" + num + "-" + num)("patientNum")
gleason = Group("GLEASON" + Optional("SCORE:") + num("left") + "+" + num("right") + "=" + num("total"))
assert 'GLEASON 5+4=9' == gleason
assert 'GLEASON SCORE:  3 + 3 = 6' == gleason

patientData = Group(accessionDate + accessionNumber + patMedicalRecordNum)
assert '01/02/11  S11-4444 20/111-22-3333' == patientData

partMatch = patientData("patientData") | gleason("gleason")

lastPatientData = None
for match in partMatch.searchString(data):
    if match.patientData:
        lastPatientData = match
    elif match.gleason:
        if lastPatientData is None:
            print "bad!"
            continue
        print "{0.accDate}: {0.accNum} {0.patientNum} Gleason({1.left}+{1.right}={1.total})".format(
                        lastPatientData.patientData, match.gleason
                        )

印刷：

01/01/11: S11-55555 20/444-55-6666 Gleason(5+4=9)
01/02/11: S11-4444 20/111-22-3333 Gleason(3+3=6)
于 2012-06-01T21:03:42.310 回答
1 
gleason = re.compile("gleason\d+\d=\d")
scores = set()
for record in records:
    for line in record.lower().split("\n"):
        if "gleason" in line:
            scores.add(gleason.match(line.replace(" ", "")).group(0)[7:])

或者其他的东西

于 2012-06-01T19:45:31.670 回答