计算机辅助医学
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计算机辅助医学 医学知识库. 刘雷 上海生物信息技术研究中心 2013.4.12. 提纲. 基本概念. 1. 关键技术. 2. 应用实例. 3. 基本概念. 医生根据具体病人的症状和体征进行推理的时候,这两种类知识是相互交织的。. 科学知识. 临床诊疗. 经验知识. 医学知识的来源 科学知识 - 认知和推理等 经验知识 - 专家临床经验等. 基本概念. 传统医学以医生的经验为主导. 问题. 误诊. 漏诊. 晚诊. 不合理用药. 基本概念. 医学知识爆炸. 医学知识数量. 医生个体医学知识与临床循证知识的巨大鸿沟. 医生个体医学知识.

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计算机辅助医学 医学知识库

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计算机辅助医学医学知识库

刘雷

上海生物信息技术研究中心

2013.4.12


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提纲

基本概念

1

关键技术

2

应用实例

3


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基本概念

医生根据具体病人的症状和体征进行推理的时候,这两种类知识是相互交织的。

科学知识

临床诊疗

经验知识

  • 医学知识的来源

    • 科学知识-认知和推理等

    • 经验知识-专家临床经验等


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基本概念

  • 传统医学以医生的经验为主导

问题

误诊

漏诊

晚诊

不合理用药


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基本概念

  • 医学知识爆炸

医学知识数量

医生个体医学知识与临床循证知识的巨大鸿沟

医生个体医学知识

2003

2006

2000

2010


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基本概念

A knowledge base is a special kind of database for knowledge management, providing the means for the computerized collection, organization, and retrieval of knowledge.

知识库的定义


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基本概念

知识获取(knowledge acquisition)是指从某个领域或某些知识源(如专家、书本或专家处理的实例)获取专家系统实现问题求解所需要的专门知识,包括共性知识和个性知识。

知识库

抽提、归纳、总结

  • 直接获取

  • 间接获取

知识获取的方式


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基本概念

再构造

确定领域问题

再构造

概念化

再设计

形式化和编码

测试

知识获取的步骤


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知识库构建的关键问题

知识的完整性

知识的安全性

知识获取工具

知识管理


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医学知识库构建的关键技术

本体(ontology)

  • 医学知识模型的构建

    • 适合医学知识表达、存储、检索和共享的医学知识模型

    • 知识模型应涵盖医学知识实体及实体间的关系


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医学知识库构建的关键技术

本体(ontology)

  • An ontology is an explicit description of a domain:

    • concepts

    • properties and attributes of concepts

    • constraints on properties and attributes

    • Individuals (often, but not always)

  • An ontology defines

    • a common vocabulary

    • a shared understanding


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医学知识库构建的关键技术

本体(ontology)

Why Develop an Ontology?

  • To share common understanding of the structure of information

    • among people

    • among software agents

  • To enable reuse of domain knowledge

    • to avoid “re-inventing the wheel”

    • to introduce standards to allow interoperability


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医学知识库构建的关键技术

本体(ontology)

Why Develop an Ontology?

  • To make domain assumptions explicit

    • easier to change domain assumptions (consider a genetics knowledge base)

    • easier to understand and update legacy data

  • To separate domain knowledge from the operational knowledge

    • re-use domain and operational knowledge separately (e.g., configuration based on constraints)


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医学知识库构建的关键技术

本体(ontology)

An Ontology Is Often Just the Beginning

Databases

Declare

structure

Ontologies

Knowledge

bases

Provide

domain

description

Domain-independent

applications

Software agents

Problem-solving methods


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医学知识库构建的关键技术

本体(ontology)

Biomedical ontology in action

  • Knowledge Management

    • Annotating Data and Resources

      • Biomedical ontology serves as a source of vocabulary for the purpose of annotating data or indexing documents.

      • Indexing is principally used in reference to the assignment of entries from a controlled vocabulary to documents

      • The indexing of clinical documents is generally referred to as coding

      • In biology, the functional description of experimental data is usually referred to as annotation

    • Accessing Biomedical Information

    • Mapping across Biomedical Ontologies


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医学知识库构建的关键技术

本体(ontology)

Biomedical ontology in action

  • Knowledge Management

    • Annotating Data and Resources

    • Accessing Biomedical Information

      • The main function of the indexing of large document collections such as MEDLINE is to support accurate retrieval

      • Several biomedical search engines exploit MeSH and the UMLS to provide access to the biomedical literature

      • The automatic classification of biomedical documents is also generally supported by ontologies.

    • Mapping across Biomedical Ontologies


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医学知识库构建的关键技术

本体(ontology)

Biomedical ontology in action

  • Knowledge Management

    • Annotating Data and Resources

    • Accessing Biomedical Information

    • Mapping across Biomedical Ontologies

      • users can choose from a variety of ontologies and select the artifact that best fits their purpose.

      • resources annotated to different ontologies become more difficult to integrate, unless mappings are created among ontologies in order to identify equivalent concepts across ontologies.


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医学知识库构建的关键技术

本体(ontology)

Biomedical ontology in action

  • Data Integration, Exchange and Semantic Interoperability

    • Information Exchange and Semantic Interoperability

      • RxNorm, UMLS, SNOMED CT clinical information systems

      • LONIC exchange of laboratory data

      • The HL7 Clinical Document Architecture, Release 2 (CDA R2) model is "richly expressive, enabling the formal representation of clinical statements"

    • Information and Data Integration


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医学知识库构建的关键技术

本体(ontology)

Biomedical ontology in action

  • Data Integration, Exchange and Semantic Interoperability

    • Information Exchange and Semantic Interoperability

    • Information and Data Integration

      • ontology support the standardization required from warehousing approaches to data integration

      • mediation-based approaches use ontologies for defining a global schema and mapping between the global schema and local schemas

      • ontologies facilitate the integration of datasets, often by providing a common reference for biomedical entities in several datasets.


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医学知识库构建的关键技术

本体(ontology)

Biomedical ontology in action

  • Decision Support and Reasoning

    • Data Selection

      • By providing an abstraction of some domain, ontologies can help define groups from a high level value for the independent variable, instead of listing all possible values

    • Data Aggregation

    • Decision Support

    • Natural Language Processing Applications

    • Knowledge Discovery

cancer of upper-inner quadrant of breast

cancer of lower-outer quadrant of breast

breast cancer


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医学知识库构建的关键技术

本体(ontology)

Biomedical ontology in action

  • Decision Support and Reasoning

    • Data Selection

    • Data Aggregation

      • ontologies are used for identifying the characteristics of groups obtained through various methods

      • ICD 10

    • Decision Support

    • Natural Language Processing Applications

    • Knowledge Discovery


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医学知识库构建的关键技术

本体(ontology)

Biomedical ontology in action

  • Decision Support and Reasoning

    • Data Selection

    • Data Aggregation

    • Decision Support

      • ontologies provide a standard vocabulary for biomedical entities, helping standardize and integrate data sources

      • ontologies are a source of computable domain knowledge that can be exploited for decision support purposes, often in combination with business rules

    • Natural Language Processing Applications

    • Knowledge Discovery


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医学知识库构建的关键技术

本体(ontology)

Biomedical ontology in action

  • Decision Support and Reasoning

    • Data Selection

    • Data Aggregation

    • Decision Support

    • Natural Language Processing Applications

    • Knowledge Discovery

term recognition

NLP

ontology

domain knowledge


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医学知识库构建的关键技术

本体(ontology)

Biomedical ontology in action

  • Decision Support and Reasoning

    • Data Selection

    • Data Aggregation

    • Decision Support

    • Natural Language Processing Applications

    • Knowledge Discovery

      • ontologies are a component of the data-driven approach to biomedical research

      • ontologies have been used for identifying relations between genotype and phenotype,

Data mining


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医学知识库构建的关键技术

文本挖掘

文本知识发现(Knowledge Discovery in Texts)就是从文本集中发现和挖掘归纳性的知识,如有用的模式、模型、趋势、规则等知识

生物医学文本

NLP

Machine Learning

电子病历

健康档案

医学文献

……

知识库

知识


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医学知识库构建的关键技术

文本挖掘

A

B

A

C

B

C

镁缺乏

偏头疼

生物医学文献挖掘这个概念最早在1986年由芝加哥大学教授Don R.Swanson提出


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医学知识库构建的关键技术

文本挖掘

  • 评测标准

  • 召回率

  • 准确率

  • F-测度

  • 一般流程

  • 信息检索

  • (Information Retrieval,IR)

  • 实体识别

  • (Entity Recognition,ER)

  • 信息抽提

  • (Information Extraction,IE)


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医学知识库构建的关键技术

知识库构建

知识的存储

知识的查询

知识的展示

知识的更新


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医学知识库

MD Consult-Medical Doctor Consult

该数据库被称为“临床医学知识库”、“内科医师的在线临床工具”,是临床卫生科技人员的循证医学资源参考数据库。

MD Consult由世界最大的三家英文医学出版商Mosby、Lippincott Williams&Wilkins、

W.B.Saunders联合创建,由世界上五大出版社之一的Elsevier Science出版发行,于1997年开始正式投入使用。


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医学知识库

  • MD Consult是一个集成医学文献、图书、临床指南、药物等的综合性医学知识库

六、药物库(Drugs)

七、诊疗指南(Guidelines)

八、医学图片(Images)

九、医学新闻(News)

十、继续医学教育(CME)

一、First Consult

二、参考书籍(Books)

三、医学期刊(Journals)

四、北美临床杂志(The Clinics)

五、病人教育(Patient Education)


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医学知识库

常见症状列表


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医学知识库

  • MD Consult是一个集成医学文献、图书、临床指南、药物等的综合性医学知识库

Keywords:colorectal cancer


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医学知识库

  • 问答系统


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医学知识库

NLP

Vocabulary

  • 问答系统


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医学知识库

  • 基于知识库的临床决策支持系统

  • 规则库

  • 条件库

  • 动态规则库


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医学知识库

  • Disease and condition

  • Symptoms

  • Drugs and supplements

  • Tests and procedures

  • Healthy lifestyle

Mayo Clinic-Health information


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医学知识库


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医学知识库


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医学知识库


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医学知识库


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医学知识库

Symptom checker


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医学知识库

Drugs and supplements


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医学知识库

Drugs


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医学知识库

Tests


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参考资料

蒋立辉 ,王 伟.医学 知 识 库 与 医学知识的获取.

O. Bodenreider. Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support.

Daniel L. Rubin, Nigam H. Shah and Natalya F. Noy. Biomedical ontologies: a functional perspective.


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谢谢!

2013.4.12


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