基因序列比對與微陣列都是常常被用來做基因比較的方法，透過這樣的測試可以將功能相近或表現相似的基因找出，提供用者資訊以進一步分析，然而有許多基因具有相似的結構或在微陣列表現相近是因為其具有類似的功能，而基因經過研究後的功能許多都被使用基因本體論中所定義的專有名詞註解，而在基因本體論當中提供了這些專有名詞的階層式架構，在本論文中，以生物分類的角度來使用這個階層式架構，提出ㄧ相似度量測的方法來計算不同專有名詞間的關係，並且用來對基因進行分析聚類。

　　論文中還對醫生醫文件探勘系統進行修改，以解決網路醫學文件格式變更，與使用過程中所發現之問題，使其能繼續正常使用，並且減少錯誤資訊出現之機率，自動的將文件中重要的資訊擷取出來呈現給使用者。

　　Sequence alignment and micro-array are the two methods often used to identify genes with either similar in function or in expression for further analysis. Studies have shown that genes with resembling functions have similar structure or micro-array expression profiles. And many of these functions are annotated by the vocabulary (so-called GO term) defined in Gene Ontology, in which terms are arranged in polyhierarchical manner. In this thesis, we propose a strategy to measure the similarities among different GO terms by employing the notion of phylogenetics to GO structure. Such similarity measure of GO terms is then applied in gene clustering.

　Meanwhile, the existing text mining system for biomedical documents serves to automatically retrieve important information from biomedical literature and display it to users. We have revised the system to cope with the changes in document format as well as resolve the problems identified during its usage such that the probability of presenting erroneous information is reduced.

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[16] 中央研究院計算中心：http://www.ascc.net

[17] 國家高速網路與計算中心：http://bioinfo.nchc.org.tw

[18] 臺大醫院微陣列核心實驗室：http://microarray.mc.ntu.edu.tw

[19] Biocarta生物路徑網站：http://www.biocarta.com/index.asp

[20] BioRag (Bioresource for array genes) at www.biorag.org

[21] 基因本體論網站：http://www.geneontology.org

[22] KEGG生物路徑網站：http://www.genome.ad.jp/kegg

[23] NCBI網站：http://www.ncbi.nlm.nih.gov

[24] 酵母菌資料庫網站：http://yeast.cellzome.com