Ontologies for Bioinformatics (Hardcover)
暫譯: 生物資訊學的本體論 (精裝版)

Kenneth Baclawski, Tianhua Niu

  • 出版商: MIT
  • 出版日期: 2005-09-23
  • 售價: $1,390
  • 貴賓價: 9.8$1,362
  • 語言: 英文
  • 頁數: 440
  • 裝訂: Hardcover
  • ISBN: 0262025914
  • ISBN-13: 9780262025911
  • 相關分類: 生物資訊 Bioinformatics
  • 立即出貨 (庫存 < 3)

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商品描述

Description:

Recent advances in biotechnology, spurred by the Human Genome Project, have resulted in the accumulation of vast amounts of new data. Ontologies -- computer-readable, precise formulations of concepts (and the relationship among them) in a given field -- are a critical framework for coping with the exponential growth of valuable biological data generated by high-output technologies. This book introduces the key concepts and applications of ontologies and ontology languages in bioinformatics and will be an essential guide for bioinformaticists, computer scientists, and life science researchers.

The three parts of Ontologies for Bioinformatics ask, and answer, three pivotal questions: what ontologies are; how ontologies are used; and what ontologies could be (which focuses on how ontologies could be used for reasoning with uncertainty). The authors first introduce the notion of an ontology, from hierarchically organized ontologies to more general network organizations, and survey the best-known ontologies in biology and medicine. They show how to construct and use ontologies, classifying uses into three categories: querying, viewing, and transforming data to serve diverse purposes. Contrasting deductive, or Boolean, logic with inductive reasoning, they describe the goal of a synthesis that supports both styles of reasoning. They discuss Bayesian networks as a way of expressing uncertainty, describe data fusion, and propose that the World Wide Web can be extended to support reasoning with uncertainty. They call this inductive reasoning web the Bayesian web.

Kenneth Baclawski is Associate Professor of Computer Science at Northeastern University.

Tianhua Niu is Assistant Professor of Medicine at Harvard Medical School and Director of Bioinformatics, Division of Preventive Medicine, at Brigham and Women's Hospital, Boston.

 

 

Table of Contents:

Preface xi
I Introduction to Ontologies 1
1 Hierarchies and Relationships 3
2 XML Semantics 35
3 Rules and Inference 51
4 The Semantic Web and Bioinformatics Applications 61
5 Survey of Ontologies in Bioinformatics 89
II Building and Using Ontologies 127
6 Information Retrieval 129
7 Sequence Similarity Searching Tools 155
8 Query Languages 175
9 The Transformation Process 187
10 Transforming with Traditional Programming Languages 203
11 The XML Transformation Language 261
12 Building Bioinformatics Ontologies 281
III Reasoning with Uncertainty 319
13 Inductive vs. Deductive Reasoning 321
14 Bayesian Networks 331
15 Combining Information 355
16 The Bayesian Web 369
17 Answers to Selected Exercises 379
References 393
Index 413

商品描述(中文翻譯)

描述:
最近在生物技術方面的進展,受到人類基因組計畫的推動,導致大量新數據的累積。本體論(ontologies)——在特定領域中可被計算機讀取的精確概念表述(及其之間的關係)——是應對由高產出技術生成的有價值生物數據指數增長的關鍵框架。本書介紹了本體論及本體語言在生物信息學中的關鍵概念和應用,將成為生物信息學家、計算機科學家和生命科學研究人員的重要指南。

《生物信息學的本體論》分為三個部分,提出並回答三個關鍵問題:本體論是什麼;本體論如何被使用;本體論可以是什麼(重點在於本體論如何用於不確定性推理)。作者首先介紹本體論的概念,從層次組織的本體論到更一般的網絡組織,並調查生物學和醫學中最知名的本體論。他們展示了如何構建和使用本體論,將用途分類為三類:查詢、查看和轉換數據以服務於不同的目的。通過對比演繹邏輯(或布爾邏輯)與歸納推理,他們描述了支持這兩種推理風格的綜合目標。他們討論了貝葉斯網絡作為表達不確定性的一種方式,描述了數據融合,並提出可以擴展萬維網以支持不確定性推理。他們稱這種歸納推理網為貝葉斯網。

Kenneth Baclawski是東北大學計算機科學的副教授。

Tianhua Niu是哈佛醫學院的醫學助理教授,並擔任波士頓布萊根婦女醫院預防醫學部生物信息學主任。

目錄:
前言
I 本體論介紹
1 層次結構與關係
2 XML 語義
3 規則與推理
4 語義網與生物信息學應用
5 生物信息學中的本體論調查
II 構建與使用本體論
6 信息檢索
7 序列相似性搜索工具
8 查詢語言
9 轉換過程
10 使用傳統編程語言進行轉換
11 XML 轉換語言
12 構建生物信息學本體論
III 不確定性推理
13 歸納推理與演繹推理
14 貝葉斯網絡
15 信息結合
16 貝葉斯網
17 選擇練習的答案
參考文獻
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