从自由文本病理报告中提取结构化信息。
Extracting structured information from free text pathology reports.
作者信息
Schadow Gunther, McDonald Clement J
机构信息
Regenstrief Intstitute and Indiana University School of Medicine, Indianapolis, IN, USA.
出版信息
AMIA Annu Symp Proc. 2003;2003:584-8.
Abstract
We have developed a method that extracts structured information about specimens and their related findings in free-text surgical pathology reports. Our method uses regular expressions that drive a state-automaton on top of XSLT and Java. Text fragments identified are coded against the UMLS. This paper describes the technical approach and reports on a preliminary evaluation study, designed to guide further development. We found that of 275 reviewed reports, 91% were coded at least so that all specimens and their critical pathologic findings were represented in codes.
摘要
我们开发了一种方法，可从手术病理报告的自由文本中提取有关标本及其相关发现的结构化信息。我们的方法使用正则表达式，在XSLT和Java之上驱动状态自动机。识别出的文本片段依据统一医学语言系统（UMLS）进行编码。本文描述了该技术方法，并报告了一项初步评估研究，旨在指导进一步的开发。我们发现，在275份审阅报告中，91%至少进行了编码，以便所有标本及其关键病理发现都能以编码形式呈现。
相似文献
1
Extracting structured information from free text pathology reports.从自由文本病理报告中提取结构化信息。
AMIA Annu Symp Proc. 2003;2003:584-8.
2
Augmenting Oracle Text with the UMLS for enhanced searching of free-text medical reports.使用统一医学语言系统增强原始文本，以改进对自由文本医学报告的搜索。
AMIA Annu Symp Proc. 2007 Oct 11:940.
3
Implementation and evaluation of a negation tagger in a pipeline-based system for information extract from pathology reports.基于管道系统的病理学报告信息提取中否定标记器的实现与评估。
Stud Health Technol Inform. 2004;107(Pt 1):663-7.
4
A normalized lexical lookup approach to identifying UMLS concepts in free text.一种用于在自由文本中识别统一医学语言系统（UMLS）概念的规范化词汇查找方法。
Stud Health Technol Inform. 2007;129(Pt 1):545-9.
5
A universal exchange language for healthcare.一种用于医疗保健的通用交换语言。
Stud Health Technol Inform. 2013;192:949.
6
Automating tissue bank annotation from pathology reports - comparison to a gold standard expert annotation set.通过病理报告实现组织库注释自动化——与黄金标准专家注释集的比较。
AMIA Annu Symp Proc. 2005;2005:460-4.
7
Standard Generalized Markup Language for self-defining structured reports.
Int J Med Inform. 1999 Feb-Mar;53(2-3):203-11. doi: 10.1016/s1386-5056(98)00160-9.
8
9
An indexing scheme for medical free text searches: a prototype.一种用于医学自由文本搜索的索引方案：一个原型。
AMIA Annu Symp Proc. 2006;2006:918.
10
A generalized language for platform-independent structured reporting.一种用于与平台无关的结构化报告的通用语言。
Methods Inf Med. 1997 Aug;36(3):163-71.
引用本文的文献
1
Using Large Language Models to Automate Data Extraction From Surgical Pathology Reports: Retrospective Cohort Study.使用大语言模型自动从外科病理报告中提取数据：回顾性队列研究。
JMIR Form Res. 2025 Apr 7;9:e64544. doi: 10.2196/64544.
2
Leveraging natural language processing for efficient information extraction from breast cancer pathology reports: Single-institution study.利用自然语言处理技术从乳腺癌病理报告中高效提取信息：单机构研究。
PLoS One. 2025 Feb 18;20(2):e0318726. doi: 10.1371/journal.pone.0318726. eCollection 2025.
3
Applications of Large Language Models in Pathology.大语言模型在病理学中的应用。
Bioengineering (Basel). 2024 Mar 31;11(4):342. doi: 10.3390/bioengineering11040342.
4
Automated medical chart review for breast cancer outcomes research: a novel natural language processing extraction system.自动化医疗图表审查在乳腺癌结局研究中的应用：一种新颖的自然语言处理提取系统。
BMC Med Res Methodol. 2022 May 12;22(1):136. doi: 10.1186/s12874-022-01583-z.
5
Rule-Based Information Extraction from Free-Text Pathology Reports Reveals Trends in South African Female Breast Cancer Molecular Subtypes and Ki67 Expression.基于规则的自由文本病理学报告信息提取揭示了南非女性乳腺癌分子亚型和 Ki67 表达的趋势。
Biomed Res Int. 2022 Jan 20;2022:6157861. doi: 10.1155/2022/6157861. eCollection 2022.
6
A Question-and-Answer System to Extract Data From Free-Text Oncological Pathology Reports (CancerBERT Network): Development Study.从自由文本肿瘤病理学报告（CancerBERT 网络）中提取数据的问答系统：开发研究。
J Med Internet Res. 2022 Mar 23;24(3):e27210. doi: 10.2196/27210.
7
Current approaches to identify sections within clinical narratives from electronic health records: a systematic review.当前从电子健康记录中识别临床叙述部分的方法：系统评价。
BMC Med Res Methodol. 2019 Jul 18;19(1):155. doi: 10.1186/s12874-019-0792-y.
8
Automating the Capture of Structured Pathology Data for Prostate Cancer Clinical Care and Research.为前列腺癌临床护理与研究自动采集结构化病理数据
JCO Clin Cancer Inform. 2019 Jul;3:1-8. doi: 10.1200/CCI.18.00084.
9
Text Mining and Automation for Processing of Patient Referrals.文本挖掘和自动化在患者转介处理中的应用。
Appl Clin Inform. 2018 Jan;9(1):232-237. doi: 10.1055/s-0038-1639482. Epub 2018 Mar 28.
10
Application of Text Information Extraction System for Real-Time Cancer Case Identification in an Integrated Healthcare Organization.文本信息提取系统在综合医疗保健机构中用于实时癌症病例识别的应用。
J Pathol Inform. 2017 Dec 14;8:48. doi: 10.4103/jpi.jpi_55_17. eCollection 2017.
本文引用的文献
1
2
3
Use of general-purpose negation detection to augment concept indexing of medical documents: a quantitative study using the UMLS.使用通用否定检测增强医学文档的概念索引：一项使用统一医学语言系统的定量研究
J Am Med Inform Assoc. 2001 Nov-Dec;8(6):598-609. doi: 10.1136/jamia.2001.0080598.
4
Quality assurance in anatomic pathology: automated SNOMED coding.解剖病理学中的质量保证：自动SNOMED编码
J Am Med Inform Assoc. 1996 Jul-Aug;3(4):270-2. doi: 10.1136/jamia.1996.96413134.
5
Experience with a mixed semantic/syntactic parser.使用混合语义/句法解析器的经验。
Proc Annu Symp Comput Appl Med Care. 1995:284-8.
6
Natural language processing and the representation of clinical data.自然语言处理与临床数据的表示
J Am Med Inform Assoc. 1994 Mar-Apr;1(2):142-60. doi: 10.1136/jamia.1994.95236145.
7
Unlocking clinical data from narrative reports: a study of natural language processing.从叙述性报告中解锁临床数据：一项自然语言处理研究
Ann Intern Med. 1995 May 1;122(9):681-8. doi: 10.7326/0003-4819-122-9-199505010-00007.
Zotero 插件