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研究生:謝昌旌
研究生(外文):Chang-ching Hsieh
論文名稱:生物文件之動力式資訊擷取
論文名稱(外文):Auto Extraction of Kinetic Information from Biochemical Literatures
指導教授:蔡志忠蔡志忠引用關係
學位類別:碩士
校院名稱:國立中正大學
系所名稱:資訊工程所
學門:工程學門
學類:電資工程學類
論文種類:學術論文
論文出版年:2006
畢業學年度:94
語文別:英文
論文頁數:69
中文關鍵詞:資料探勘
外文關鍵詞:Datat Mining
相關次數:
  • 被引用被引用:0
  • 點閱點閱:264
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自從系統生物學開始發展,越來愈多的科學家開始使用數學式去表示一個複
雜的反應過程。系統生物學主要使用大量的參數和數學式去計算模擬生物的反應
過程。去測量並且找出參數的名稱以及數值是非常不容易的,大部分的數據有時
會出現在全文的論文上面,然而要去一篇一篇的找出它們卻是相當煩瑣,因此我
們則建立一個系統可以自動的擷取出每篇論文所有相關於動力式的參數名稱以
及數值。
Since the development of system biology, some scientists use
mathematical modeling to description complex pathway process. Systems
biology aims at the computational simulation of complex systems and
essential part focuses on solving a large number of parameterized
differential equations. Measuring those parameters and finding whose
named entities is very important, however those parameter value
sometime existed on full length paper and finding them in literature is
tedious. So we development an information extraction system to finding
whose value and named entities automatically.
1 Introduction 7
2 Information Extraction of Kinetic Model in Systems Biology 9
2.1 System Biology . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.2 Models of Biochemical . . . . . . . . . . . . . . . . . . . . . . 9
2.2.1 Model: . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.2.2 Mathematical Model: . . . . . . . . . . . . . . . . . . . 10
2.3 Kinetic Model . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.3.1 Thermodynamics: . . . . . . . . . . . . . . . . . . . . . 10
2.3.2 Kinetics: . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.4 Kinetic Model of Biochemical System . . . . . . . . . . . . . . 11
2.4.1 Representation of Biochemical Systems . . . . . . . . . 11
2.4.2 Model of Biochemical Kinetics Reaction . . . . . . . . 12
2.4.3 Kinetics Moel: . . . . . . . . . . . . . . . . . . . . . . . 13
2.5 Association Rule . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.6 SDOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.7 WordNet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.8 Problem Formulation . . . . . . . . . . . . . . . . . . . . . . . 22
2.9 System Architecture of KIND . . . . . . . . . . . . . . . . . . 22
4
3 Extraction of Kinetic Sentences 25
3.1 Data Preprocess . . . . . . . . . . . . . . . . . . . . . . . . . . 25
3.2 Mining Kinetic Parameter Sentence . . . . . . . . . . . . . . 27
3.2.1 Title , Author , Date , Abstract . . . . . . . . . . . . . 27
3.2.2 Sentence Format Filter . . . . . . . . . . . . . . . . . . 27
3.2.3 Kinetic Parameter Sentence Format . . . . . . . . . . . 29
3.2.4 Boundary , Closed interval . . . . . . . . . . . . . . . . 29
3.2.5 Kinetic Parameter . . . . . . . . . . . . . . . . . . . . 31
3.2.6 EC50,IC50,pK value and Activity Unit . . . . . . . . . 32
3.2.7 Constant Parameter . . . . . . . . . . . . . . . . . . . 33
3.2.8 Condition Value . . . . . . . . . . . . . . . . . . . . . . 33
3.3 Experiment result . . . . . . . . . . . . . . . . . . . . . . . . . 37
4 Extraction of Kinetic Parameters 39
4.1 Named Entity features . . . . . . . . . . . . . . . . . . . . . . 39
4.1.1 Orthographic Features . . . . . . . . . . . . . . . . . . 39
4.1.2 Head Noun, Surface Clue and POS Features . . . . . . 40
4.1.3 Morphological Features . . . . . . . . . . . . . . . . . . 41
4.1.4 Dictionary . . . . . . . . . . . . . . . . . . . . . . . . . 42
4.1.5 Kinetic Parameter . . . . . . . . . . . . . . . . . . . . 42
4.1.6 Boundary Extension . . . . . . . . . . . . . . . . . . . 42
4.1.7 Synonym . . . . . . . . . . . . . . . . . . . . . . . . . . 43
4.1.8 Experiment Result . . . . . . . . . . . . . . . . . . . . 44
4.2 Formulate sentence . . . . . . . . . . . . . . . . . . . . . . . . 45
4.2.1 Tagging . . . . . . . . . . . . . . . . . . . . . . . . . . 45
5
4.2.2 Matching Algorithm . . . . . . . . . . . . . . . . . . . 47
4.2.3 Experiment Result . . . . . . . . . . . . . . . . . . . . 50
4.2.4 System Screenshot . . . . . . . . . . . . . . . . . . . . 50
5 Conclusion 55
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