臺灣博碩士論文加值系統

研究背景：
近年來生物醫學文獻發表量日益增加，從2014年起每年發表文章已突破100萬篇，研究者想要透過傳統閱讀方式整理這些文獻越來越困難，因此有必要借助電腦自動化整理大量文獻並提供有用的資訊。目前自動化整理生物資訊之著名相關網站如Coremine、 STRING、 DisGeNet等，都只能看到查詢的字詞直接相關字詞，然而卻看不到間接相關性。
研究目的：
本研究欲探討PubMed收錄之非結構化摘要中，醫學主題詞 (MeSH)與基因名稱間不同年代使用次數的高低情形與各詞彙間的相關強度。
材料與方法：
本篇研究所採取的研究設計為text-mining design，研究樣本為PubMed文獻所刊登之摘要，於2016年7月8日檢索並下載Abstract(text)文字檔案，共26,295,751篇。將檔案分割為各篇文章，收集各篇摘要及年代。利用美國國立醫學圖書館編製的醫學主題詞至MeSHBrowser進行27,883個字的同義字的檢索後建立醫學主題詞字庫，利用國際人類基因組組織命名委員會對基因命名的正式名稱至NCBI Gene進行別稱檢索後建立39,903個人類基因字庫；利用文字比對擷取各摘要中所包含的67,786個醫學主題詞與基因名稱，以年為單位計算各醫學主題詞及基因名稱於摘要中出現次數，並使用word2vec分析醫學主題詞及基因名稱間的相關強度。
結果：
本研究建立互動式網站，提供查詢醫學主題詞與基因名稱在各年代摘要中出現次數與頻率，以及最常一起出現在摘要中的相關字詞 ( https://yihsin.shinyapps.io/meshgeneterm_relation/ )。本研究發現在2012年開始有很多文章在摘要中提到China，次數排名第10名，更於2016年向前擠進前八名，象徵中國在學術界的崛起。另外Health從排行7到排行第3名，也許是表示近幾年更多文章重視健康的議題。最常一起出現在摘要中的相關字詞舉退化性關節炎為例，與退化性關節炎最常一起出現在摘要中有截肢手術、指甲、髕骨、膝關節、單倍體、體檢與癱瘓，其中看的到截肢手術也與癱瘓、膝關節以及髕骨有相關(相關性大於0.6)。
結論：
利用本研究建立的網站，可以知道各醫學主題詞與基因名稱在摘要中不同年代使用次數與頻率，以及最常與哪些字一起出現的相關強度，表示這些字常常在做研究時一起被提及與討論，同時也可以看到間接相關，讓研究者在探索新領域時能快速有概括性的了解，取得建議研究的方向，以利往後跨領域之科學研究。

Background:
In recent years, biomedical literature published by leaps and bounds, especially papers had exceeded 1 million in 2014. Based upon studies available on the databases, it is difficult for the users to sort out from the massive literature and organize sets of qualitative. At present, there have the well-known websites such as Coremine, STRING, DisGeNet, ect. However, it can only inquire the words directly related to the words without any indirect relevance suggestions. Thus, there is huge justification for addressing the issue.

Purpose:
In this study, we investigated that the number of use in each years and the relationship between medical subject headings (MeSH) and gene names in the non-structured abstracts of PubMed.

Materials and Methods:
The study used text-mining design. The study samples are published articles in the PubMed from 1809 to 2016. We divide the files into articles, collect the abstracts and the publication of years. Using the MeSH from the American National Library of Medicine to the MeSHBrowser, 27,883 word synonyms were used to establish the MeSH dictionary. The official name of 39,903 human genes was named by the Human Genome Organization Nomenclature Committee. After searched from NCBI Gene build the gene dictionary, the 67,786 medical subject headings and gene names were included in the abstracts were extracted from the abstracts. The number of MeSH and gene names in the abstract were calculated by each years. We used word2vec to analyze the relevance between the MeSH and gene name.

Result:
We build an interactive website which provides the information on the number of use in different years and the relevant words that most often appear together between MeSH and gene names in the abstract ( https://yihsin.shinyapps.io/meshgeneterm_relation/ ). For example, most often appearance together with Osteoarthritis in the summary are Osteotomy, Nails, Patella, Knee Joint, Monosomy, Physical Examination and Paralysis. Also, Osteotomy is related with paralysis, knee Joints and patella (correlation greater than 0.6).

Conclusion:
Base on the website developed of this study, it provides the number of use in different years between the MeSH and gene names, and what words were most associated with them, which indicating that these words were often mentioned and discussed together in medical publications. Also we can know the indirect correlation between them. So that researchers in the exploration of new areas can quickly have a general understanding.

目錄 i
表目錄 iii
圖目錄 iv
摘要 v
Abstract viii
第一章 前言 1
第一節 研究背景 1
第二節 研究動機與重要性 3
第三節 研究目的 5
第二章 文獻探討 6
第一節 大數據與非結構化資料 6
第二節 文字探勘技術 11
第三節 探討疾病與基因間的關係 16
第四節 PubMed 生物醫學資料庫 18
第五節 MeSH 醫學主題詞 20
第六節 Gene Term基因名稱 28
第三章 研究方法 30
第一節 研究設計與流程 30
第二節 資料收集 32
第三節 統計方法 35
第四節 資料視覺化 36
第四章 研究結果 37
第一節 各醫學主題詞與基因名稱不同年代使用次數與頻率 37
第二節 醫學主題詞與基因名稱次數排名 39
第三節 各醫學主題詞與基因名稱間的相關強度 48
第四節 各醫學主題詞與基因名稱間的間接相關強度-資料視覺化 53
第五章 討論 56
第一節 NCBI封鎖使用PubMed的權限 56
第二節 各醫學主題詞與基因名稱次數校正 60
第三節 結果摘要 64
第四節 研究結果與其他網站比較 67
第五節 本研究之優勢 79
第六節 本研究之限制 80
第六章 結論 81
第七章 未來展望 82
第八章 參考文獻 83
第九章 附錄 88

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