每年發表並收錄在可自由存取資料庫中的生物文獻越來越多，此優點是讓研究人員可以輕易地直接藉由網路進行文獻搜索也因此有更多機會可以找到有興趣的研究主題或內容。但相反的，因為越來越多的公開文獻開放為自由存取導致多數的使用者發現目前似乎越來越難讓資訊可以有效地在短時間內被發現並使用。
本研究針對生醫文獻內的蛋白親和力和蛋白質相互作用資訊開發自動化提取演算法，並將所找出的資訊存放於公開資料庫提供全球的研究人員自由存取。我們先藉由觀察蛋白親和力相關的全文文章開發了四個模組句型，並設計一個記分功能排列的函數來找出正確的蛋白親和力描述句子。經實驗證明我們的開發的句型偵測結合記分功能函數能有效識別紀錄於生醫文獻全文內的蛋白親和力，藉此省下過去須依賴人工閱讀才能找出重要資訊所需要花費的時間及相關成本。
我們也提出整合機器學習和樣板模式的偵測方法來擷取文獻內的生物路徑證據，幫助研究人員可以藉由瀏覽器直接進行生物路徑的延伸探索，藉此找出新的生物關聯路徑。此外我們也提出了一個有效率的文章排名系統，幫助文獻標記人員快速找出描述特定化學物與疾病的相關文章，藉此增加標記生物事件的效率。
本論文的主要目標是幫助研究人員快速並有效的識別出在生物醫學文章中的重要資料，讓各研究人員可以在很短的時間內有效地發掘出文獻內的重要內容和資訊。

With the increasing availability of full-text literature, researchers easily and effectively keep track of interesting research topics by searching literature online. In contrast, due to the sheer volume of available biological literature, researchers are finding it difficult to locate needed information. In this study, we focused mainly on two major topics: the extraction of data deposition statement and the ability of literature triage from large scale of biomedical articles.
For the extraction of deposition data, we focused on protein-binding affinities and extraction of protein-protein interactions. We developed four sentence patterns that were used to scan full-text articles as well as a scoring function to rank the sentences that match our patterns. The proposed sentence patterns can effectively identify the protein-binding affinities in full-text articles. Furthermore, we also proposed an integrated machine-learning and rule-based algorithm to extract the biological evidence of protein interactions occurring in MEDLINE full-text articles. In addition, an interactive web-based platform has also been constructed for researchers to visualize and manipulate existing KEGG pathways using Cytoscape web API. Lastly, a flexible ranking system was developed to assist curators for chemical-gene-disease relevant articles triage.
The major goal of this study is to assist researchers in identifying useful messages in biomedical articles that matter most and effectively keep up-to-date on progress and discoveries in a short time.

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