Getting more out of biomedical documents with GATE's full lifecycle open source text analytics.
Getting more out of biomedical documents with GATE's full lifecycle open source text analytics.
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DOI：
10.1371/journal.pcbi.1002854
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发表时间：
2013
影响因子：
4.3
通讯作者：
Bontcheva K
中科院分区：
文献类型：
--
作者：
Cunningham H;Tablan V;Roberts A;Bontcheva K
本文介绍了GATE系列开源文本分析工具和流程。GATE是其类型中使用最广泛的系统之一，每年的下载率为数万，在学术和工业环境中有许多活跃用户。在本文中，我们报告了三个例子，基于GATE的系统在生命科学和医学。首先，在全基因组关联研究中，有助于发现头颈癌突变关联。第二，医疗记录分析，显着增加了统计权力的治疗/结果模型在英国最大的精神病患者队列。第三，更丰富的药物相关搜索结构。我们还探讨了GATE系列支持示例中所示生命周期各个阶段的方式。我们的结论是，部署文本挖掘的文档抽象或丰富的搜索和导航是最好的思想作为一个过程，并与正确的计算工具和数据收集策略，这个过程可以定义和可重复的。GATE研究计划已经有20年的历史，从最初的文本处理专业开发工具发展成为一个相当全面的生态系统，汇集了来自不同领域的软件开发人员，语言工程师和研究人员。GATE现在有一个强有力的声明，涵盖了文本分析系统生命周期的独特范围。它形成了一个焦点，用于集成和重用许多人（大多数在作者自己的小组之外）在生物医学和其他领域的文本处理中所取得的进步。GATE可以<1>在GNU开放源码许可证下在线获得，并在所有主要操作系统上运行。支持可从活跃的用户和开发人员社区，也在商业基础上。
This software article describes the GATE family of open source text analysis tools and processes. GATE is one of the most widely used systems of its type with yearly download rates of tens of thousands and many active users in both academic and industrial contexts. In this paper we report three examples of GATE-based systems operating in the life sciences and in medicine. First, in genome-wide association studies which have contributed to discovery of a head and neck cancer mutation association. Second, medical records analysis which has significantly increased the statistical power of treatment/outcome models in the UK's largest psychiatric patient cohort. Third, richer constructs in drug-related searching. We also explore the ways in which the GATE family supports the various stages of the lifecycle present in our examples. We conclude that the deployment of text mining for document abstraction or rich search and navigation is best thought of as a process, and that with the right computational tools and data collection strategies this process can be made defined and repeatable. The GATE research programme is now 20 years old and has grown from its roots as a specialist development tool for text processing to become a rather comprehensive ecosystem, bringing together software developers, language engineers and research staff from diverse fields. GATE now has a strong claim to cover a uniquely wide range of the lifecycle of text analysis systems. It forms a focal point for the integration and reuse of advances that have been made by many people (the majority outside of the authors' own group) who work in text processing for biomedicine and other areas. GATE is available online <1> under GNU open source licences and runs on all major operating systems. Support is available from an active user and developer community and also on a commercial basis.
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影响因子：
4.3
作者：
Cohen KB;Hunter L
通讯作者：
Hunter L
DOI：
10.4018/jswis.2009081901
发表时间：
2009-01-01
影响因子：
3.2
作者：
Bizer, Christian;Heath, Tom;Berners-Lee, Tim
通讯作者：
Berners-Lee, Tim
影响因子：
5.8
作者：
Caporaso, J. Gregory;Baumgartner, William A., Jr.;Hunter, Lawrence
通讯作者：
Hunter, Lawrence
影响因子：
64.8
作者：
Burton, Paul R.;Clayton, David G.;Cardon, Lon R.;Craddock, Nick;Deloukas, Panos;Duncanson, Audrey;Kwiatkowski, Dominic P.;McCarthy, Mark I.;Ouwehand, Willem H.;Samani, Nilesh J.;Todd, John A.;Donnelly, Peter;Barrett, Jeffrey C.;Davison, Dan;Easton, Doug;Evans, David;Leung, Hin-Tak;Marchini, Jonathan L.;Morris, Andrew P.;Spencer, Chris C. A.;Tobin, Martin D.;Attwood, Antony P.;Boorman, James P.;Cant, Barbara;Everson, Ursula;Hussey, Judith M.;Jolley, Jennifer D.;Knight, Alexandra S.;Koch, Kerstin;Meech, Elizabeth;Nutland, Sarah;Prowse, Christopher V.;Stevens, Helen E.;Taylor, Niall C.;Walters, Graham R.;Walker, Neil M.;Watkins, Nicholas A.;Winzer, Thilo;Jones, Richard W.;McArdle, Wendy L.;Ring, Susan M.;Strachan, David P.;Pembrey, Marcus;Breen, Gerome;St Clair, David;Caesar, Sian;Gordon-Smith, Katherine;Jones, Lisa;Fraser, Christine;Green, Elain K.;Grozeva, Detelina;Hamshere, Marian L.;Holmans, Peter A.;Jones, Ian R.;Kirov, George;Moskvina, Valentina;Nikolov, Ivan;O'Donovan, Michael C.;Owen, Michael J.;Collier, David A.;Elkin, Amanda;Farmer, Anne;Williamson, Richard;McGuffin, Peter;Young, Allan H.;Ferrier, I. Nicol;Ball, Stephen G.;Balmforth, Anthony J.;Barrett, Jennifer H.;Bishop, D. Timothy;Iles, Mark M.;Maqbool, Azhar;Yudasheve, Nadira;Hall, Alistair S.;Braund, Peter S.;Dixon, Richard J.;Mangino, Massimo;Stevens, Suzanne;Thompson, John R.;Bredin, Francesca;Tremelling, Mark;Parkes, Miles;Drummond, Hazel;Lees, Charles W.;Nimmo, Elaine R.;Satsangi, Jack;Fisher, Sheila A.;Forbes, Alistair;Lewis, Cathryn M.;Onnie, Clive M.;Prescott, Natalie J.;Sanderson, Jeremy;Mathew, Christopher G.;Barbour, Jamie;Mohiuddin, M. Khalid;Todhunter, Catherine E.;Mansfield, John C.;Ahmad, Tariq;Cummings, Fraser R.;Jewell, Derek P.;Webster, John;Brown, Morris J.;Lathrop, G. Mark;Connell, John;Dominiczak, Anna;Marcano, Carolina A. Braga;Burke, Beverley;Dobson, Richard;Gungadoo, Johannie;Lee, Kate L.;Munroe, Patricia B.;Newhouse, Stephen J.;Onipinla, Abiodun;Wallace, Chris;Xue, Mingzhan;Caulfield, Mark;Farrall, Martin;Barton, Anne;Bruce, Ian N.;Donovan, Hannah;Eyre, Steve;Gilbert, Paul D.;Hider, Samantha L.;Hinks, Anne M.;John, Sally L.;Potter, Catherine;Silman, Alan J.;Symmons, Deborah P. M.;Thomson, Wendy;Worthington, Jane;Dunger, David B.;Widmer, Barry;Frayling, Timothy M.;Freathy, Rachel M.;Lango, Hana;Perry, John R. B.;Shields, Beverley M.;Weedon, Michael N.;Hattersley, Andrew T.;Hitman, Graham A.;Walker, Mark;Elliott, Kate S.;Groves, Christopher J.;Lindgren, Cecilia M.;Rayner, Nigel W.;Timpson, Nicholas J.;Zeggini, Eleftheria;Newport, Melanie;Sirugo, Giorgio;Lynons, Emily;Vannberg, Fredrik;Brown, Matthew A.;Franklyn, Jayne A.;Heward, Joanne M.;Simmonds, Matthew J.;Hill, Adrian V. S.;Bradbury, Linda A.;Farrar, Claire;Pointon, Jennifer J.;Wordsmith, Paul;Gough, Stephen C. L.;Seal, Sheila;Stratton, Michael R.;Rahman, Nazneen;Ban, Maria;Goris, An;Sawcer, Stephen J.;Compston, Alistair;Conway, David;Jallow, Muminatou;Bumpstead, Suzannah J.;Chaney, Amy;Downes, Kate;Ghori, Mohammed J. R.;Gwilliam, Rhian;Inouye, Michael;Keniry, Andrew;King, Emma;McGinnis, Ralph;Potter, Simon;Ravindrarajah, Rathi;Whittaker, Pamela;Withers, David;Easton, Doug;Pereira-Gale, Joanne;Hallgrimsdottir, Ingilef B.;Howie, Bryan N.;Su, Zhan;Teo, Yik Ying;Vukcevic, Damjan;Bentley, David;Caulfield, Mark;Mathew, Christopher G.;Worthington, Jane
通讯作者：
Worthington, Jane
DOI：
10.1197/jamia.m1757
发表时间：
2005-09-01
影响因子：
6.4
作者：
Ao, H;Takagi, TI
通讯作者：
Takagi, TI