臺灣博碩士論文加值系統

我們提供了找尋不同代謝路徑資料庫中相同物件的方法，代謝路徑資料庫中主要包含了化合物、酵素反應以及代謝路徑三種物件，我們依據這三種物件的特性，來找出相同在不同資料庫中相同的物件，最後再使用我們已經找出來結果，進一步的使我們實驗出來的結果更加的精確。酵素反應是由化合物組成的，經由實驗我們可以找出來在不同資料庫中相同的化合物以及酵素反應，我們根據這兩個結果，使用相同酵素反應的資訊來更進一步的尋找更多在不同資料庫中相同的化合物。
在實驗中我們使用了兩個代謝路徑資料庫（MetaCyc、KEGG），經由實驗我們可以找相同的物件在這兩個資料庫中，此外我們也可以找出相異物件，而根據這些相異物件，我們可以觀察出這兩個資料庫資料的不同處，也可以提供給這兩個資料庫的管理者評判是否是本身資料錯誤。

We represent an enhancing technique to discover the relations between pathway databases. The pathway database could separate into three level, which are compound level, reaction level and pathway level. The compounds construct reaction, then several reactions construct a pathway. We use attributes of compounds to find the relation of compounds between pathway databases. Using the relations of compounds induce the relation of next level, reaction level. The relations of reactions could enhance relations of compound level, and could induce the relation of pathway level. When we obtain the relations of pathway, we could enhance the relations of reaction level and compound level. The main idea is using relation of lower level to infer relation of upper level, and using relation of upper level to enhance relation of lower level. The experience databases selected are KEGG database set and MetaCyc pathway database. According to result of experience, we find some duplicate errors in each databases. Furthermore, we find some reactions which is not exist in the other pathway database, and could place the reaction to the right pathway.

Contents
1 Introduction 7
1.1 Pathway database . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.2 Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.3 Summary of this thesis . . . . . . . . . . . . . . . . . . . . . . 9
1.4 Organization of this thesis . . . . . . . . . . . . . . . . . . . . 11
2 Pathway Database 12
2.1 Kyoto Encyclopedia of Genes and Genomes databases . . . . . 12
2.2 MetaCyc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3 Instance Relations 19
3.1 Chemical Compound and Relation in Chemical Compound . . 19
3.2 Enzymatic Reaction . . . . . . . . . . . . . . . . . . . . . . . 21
3.2.1 EC system . . . . . . . . . . . . . . . . . . . . . . . . . 24
3.3 Metabolic Pathway . . . . . . . . . . . . . . . . . . . . . . . . 26
3.4 Analyzing Inconsistency of databases . . . . . . . . . . . . . . 29
4 Relation Discovery with Multi-Level Information 32
4.1 Integration in Chemical Compound Level . . . . . . . . . . . . 33
4.2 Integration in Enzymatic Reaction Level . . . . . . . . . . . . 40
4.3 Integration in Metabolic Pathway Level . . . . . . . . . . . . . 45
4.4 Enhancing Chemical Compound Level and Enzymatic Reac-
tion Level . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
4.4.1 Using Enzymatic Reaction Level to Enhance . . . . . . 50
4.4.2 Using Metabolic Pathway Level to Enhance . . . . . . 51
5 Experiment and Application 54
5.1 Data Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
5.2 Processing Chemical Compound Level . . . . . . . . . . . . . 55
5.3 Processing Enzymatic Reaction Level . . . . . . . . . . . . . . 63
5.4 Enhancing Chemical Compound Level with Result of Enzy-
matic Reaction Level . . . . . . . . . . . . . . . . . . . . . . . 69
5.5 Processing Metabolic Pathway . . . . . . . . . . . . . . . . . . 72
5.6 Enhancing the Enzymatic Reaction Level and Chemical Com-
pound Level with the Result of Metabolic Pathway Level . . . 73
5.6.1 Enzymatic Reaction Level . . . . . . . . . . . . . . . . 76
5.6.2 Chemical Compound Level . . . . . . . . . . . . . . . . 77
5.7 Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
6 Conclusion and Future work 81

[1] Aaron Birkland and Golan Yona. BIOZON: a system for uni¯caion, man-
agement and analysis of hetergeneous biological data
[2] Alexander Garcia Castro, Yi-Ping Phoebe and Mark A. Ragan. Informa-
tion Integration in Molecular Bioscience Bioinformatic, Vol4 No.3, Pages
157-173, 2005
[3] John Macauley, Huajun Wang and Nathan Goodman. A Model System
for Studying the Integration of Molecular Biology Databases Bioinfor-
matic, Vol 14 No.7, Pages 575-582, 1998.
[4] L. Krishnamurthy, J. Nadeau, G. Ozsoyoglu, M.Ozsoyoglu, G. Schae®er,
M. Tasan and W. Xu. Pathways database system: an integrated system
for biological pathways Bioinformatic, Vol 19 No.8, Pages 930-937, 2003.
[5] M. L. Green and P. D. Karp. Genome annotation errors in pathways
databases due to semantic ambiguity in partial EC numbers Nucleic Acids
Research, Vol 33 No.13, Pages 4035-4039, 2005.
[6] Yi-Ping Phoebe Chen and Qingfeng Chen. Analyzing Inconsistency To-
ward Enhancing Integration of Biological Molecular Database. APBC
2006, 197-206.
[7] KEGG http://www.genome.jp/kegg/
[8] METACYC http://metacyc.org/
[9] Nomenclature Committee of the International Union
of Biochemistry and Molecular Biology (NC-IUBMB)
http://www.chem.qmul.ac.uk/iubmb/enzyme/