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jsaction="click:LUvzV"></div></div></header><div role="main" tabindex="-1" class="UtePc RCETm" dir="ltr"><section id="h.p_ID_3" class="yaqOZd LB7kq gk8rDe" style=""><div class="IFuOkc"></div><div class="mYVXT"><div class="LS81yb VICjCf j5pSsc db35Fc" tabindex="-1"><div class="hJDwNd-AhqUyc-uQSCkd Ft7HRd-AhqUyc-uQSCkd purZT-AhqUyc-II5mzb ZcASvf-AhqUyc-II5mzb pSzOP-AhqUyc-qWD73c Ktthjf-AhqUyc-qWD73c JNdkSc SQVYQc"><div class="JNdkSc-SmKAyb LkDMRd"><div class="" jscontroller="sGwD4d" jsaction="zXBUYb:zTPCnb;zQF9Uc:Qxe3nd;" jsname="F57UId"><div class="oKdM2c ZZyype Kzv0Me"><div id="h.p_ID_5" class="hJDwNd-AhqUyc-uQSCkd Ft7HRd-AhqUyc-uQSCkd jXK9ad D2fZ2 zu5uec OjCsFc dmUFtb wHaque g5GTcb JYTMs"><div class="jXK9ad-SmKAyb"><div class="tyJCtd mGzaTb Depvyb baZpAe lkHyyc"><h2 id="h.p_ID_13" class="CDt4Ke zfr3Q JYVBee" style="text-align: left;">ZAISA</h2></div></div></div></div></div></div></div></div></div></section><section id="h.p_ID_18" class="yaqOZd" style=""><div class="IFuOkc"></div><div class="mYVXT"><div class="LS81yb VICjCf j5pSsc db35Fc" tabindex="-1"><div class="hJDwNd-AhqUyc-uQSCkd Ft7HRd-AhqUyc-uQSCkd purZT-AhqUyc-II5mzb ZcASvf-AhqUyc-II5mzb pSzOP-AhqUyc-qWD73c Ktthjf-AhqUyc-qWD73c JNdkSc SQVYQc"><div class="JNdkSc-SmKAyb LkDMRd"><div class="" jscontroller="sGwD4d" jsaction="zXBUYb:zTPCnb;zQF9Uc:Qxe3nd;" jsname="F57UId"><div class="oKdM2c ZZyype Kzv0Me"><div id="h.p_ID_24" class="hJDwNd-AhqUyc-uQSCkd Ft7HRd-AhqUyc-uQSCkd jXK9ad D2fZ2 zu5uec OjCsFc dmUFtb wHaque g5GTcb JYTMs"><div class="jXK9ad-SmKAyb"><div class="tyJCtd mGzaTb Depvyb baZpAe"><p id="h.p_ID_32" class="CDt4Ke zfr3Q">The Zone Analysis In Scientific Articles (ZAISA) project ran from 2003 to 2006.</p><p id="h.p_ID_34" class="CDt4Ke zfr3Q">About</p><p id="h.p_ID_36" class="CDt4Ke zfr3Q">Text mining in the scientific domains such as molecular biology is now recognized by scientists as an essential technique for enabling access to information contained in archived journal articles and abstract collections such as MEDLINE: Since major domain databases often contain incomplete and contradictory results over generations of experiments, scientists need to return to the source journal articles to confirm and complete templates of factual information. While major progress has been made by the international research community on bio-named entity extraction, i.e. the identification and classification of terminology, further progress aimed at pin-pointing facts related to experimental results has proven to be difficult. Current technology does not suffice to identify the main result of the investigation among the large number of facts mentioned in each article, most of which relate to the work of others. In this project, we propose to create a critically needed knowledge source that will enable future research progress for the purpose just mentioned: a publicly available training collection of journals annotated for rhetorical regions called zones.</p><p id="h.p_ID_38" class="CDt4Ke zfr3Q">Our notion of zone is essentially different from the core notion used in the widely known rhetorical structure theory (RST) (Mann and Thompson, 1987), that is, the hierarchical organization of propositions (or clauses). We emphasize a small set of classes with shallow nesting where the importance of the internal structure of clauses on the logical basis is not definitive. Rather, our approach emphasizes empirically determined class transitions together with weak linguistic clues used as feature information for machine learning. In the second year, we will use the annotated collection to automatically classify zones, using the machine learning methods we are already familiar with such as support vector machines and maximum entropy. For example, where the author mentions his/her specific aim, background publications, his/her experimental design, specific results of the experiments and their implications, discusses the significance of his/her findings in comparison with previous work, etc.</p><p id="h.p_ID_40" class="CDt4Ke zfr3Q">Example</p><p id="h.p_ID_42" class="CDt4Ke zfr3Q">The following is an illustration of our zone analysis of a passage taken from the Result section of a NAR journal article; we have removed the content words to highlight the influence of other phrases (Numbering is added; “ref.” and “Fig.#” indicate respectively a reference and Figure.):</p></div></div></div></div></div></div></div></div></div></section><section id="h.p_ID_43" class="yaqOZd" style=""><div class="IFuOkc"></div><div class="mYVXT"><div class="LS81yb VICjCf j5pSsc db35Fc" tabindex="-1"><div class="hJDwNd-AhqUyc-c5RTEf Ft7HRd-AhqUyc-c5RTEf JNdkSc SQVYQc L6cTce-purZT L6cTce-pSzOP"><div class="JNdkSc-SmKAyb LkDMRd"><div class="" jscontroller="sGwD4d" jsaction="zXBUYb:zTPCnb;zQF9Uc:Qxe3nd;" jsname="F57UId"></div></div></div><div class="hJDwNd-AhqUyc-wNfPc Ft7HRd-AhqUyc-wNfPc purZT-AhqUyc-II5mzb ZcASvf-AhqUyc-II5mzb pSzOP-AhqUyc-qWD73c Ktthjf-AhqUyc-qWD73c JNdkSc SQVYQc"><div class="JNdkSc-SmKAyb LkDMRd"><div class="" jscontroller="sGwD4d" jsaction="zXBUYb:zTPCnb;zQF9Uc:Qxe3nd;" jsname="F57UId"><div class="oKdM2c ZZyype Kzv0Me"><div id="h.p_ID_49" class="hJDwNd-AhqUyc-wNfPc Ft7HRd-AhqUyc-wNfPc pSzOP-AhqUyc-qWD73c Ktthjf-AhqUyc-qWD73c jXK9ad D2fZ2 zu5uec OjCsFc dmUFtb wHaque g5GTcb JYTMs"><div class="jXK9ad-SmKAyb"><div class="tyJCtd mGzaTb Depvyb baZpAe"><p id="h.p_ID_57" class="CDt4Ke zfr3Q">[1] Microarrays have been used to map replication in yeast (ref.). [2] We performed a similar experiment in Salmonella [3] to demonstrate<sup> </sup>that ….... [4] First, …... [5] The resulting plot<sup> </sup>represents the relative increase in gene copy number ……(Fig.#). [6] A similar experiment was performed using<sup> </sup>…… (Fig.#). [7] The position of genes …… are scrambled …... Yet, …... [8] As ……, this observation will be worthy of further research. [9] Deviations from …… are more profound<sup> </sup>in Typhi CT18. [10] We speculate that …… [11] Nevertheless, this experiment shows<sup> </sup>that …… [12] Finally, many genes were induced in ……[13] The results also confirm the recent<sup> </sup>discovery of MntH …… (ref.)</p><p id="h.p_ID_59" class="CDt4Ke zfr3Q"><strong>Fig. 1</strong> - Example of zones in a fragment of a NAR journal article</p></div></div></div></div></div></div></div><div class="hJDwNd-AhqUyc-II5mzb Ft7HRd-AhqUyc-II5mzb JNdkSc SQVYQc L6cTce-purZT L6cTce-pSzOP"><div class="JNdkSc-SmKAyb LkDMRd"><div class="" jscontroller="sGwD4d" jsaction="zXBUYb:zTPCnb;zQF9Uc:Qxe3nd;" jsname="F57UId"></div></div></div></div></div></section><section id="h.p_ID_81" class="yaqOZd" style=""><div class="IFuOkc"></div><div class="mYVXT"><div class="LS81yb VICjCf j5pSsc db35Fc" tabindex="-1"><div class="hJDwNd-AhqUyc-uQSCkd Ft7HRd-AhqUyc-uQSCkd purZT-AhqUyc-II5mzb ZcASvf-AhqUyc-II5mzb pSzOP-AhqUyc-qWD73c Ktthjf-AhqUyc-qWD73c JNdkSc SQVYQc"><div class="JNdkSc-SmKAyb LkDMRd"><div class="" jscontroller="sGwD4d" jsaction="zXBUYb:zTPCnb;zQF9Uc:Qxe3nd;" jsname="F57UId"><div class="oKdM2c ZZyype Kzv0Me"><div id="h.p_ID_87" class="hJDwNd-AhqUyc-uQSCkd Ft7HRd-AhqUyc-uQSCkd jXK9ad D2fZ2 zu5uec OjCsFc dmUFtb wHaque g5GTcb JYTMs"><div class="jXK9ad-SmKAyb"><div class="tyJCtd mGzaTb Depvyb baZpAe"><p id="h.p_ID_95" class="CDt4Ke zfr3Q">In the above, [1] provides background information related to the author’s experiment (BACKGROUND), [3] mentions the aim of the experiment (PROBLEM SETTING), whereas [2], [4], and [6] state the experiments performed (METHOD). [5], [7], and [9] provide the results of the corresponding experiment (RESULT). [8] assesses the observation just mentioned (IMPLICATION). [10] provides the author’s conjecture on the result (IMPLICATION), whereas [11] provides an insight/finding obtained from (the result of) the experiment mentioned in [6] (INSIGHT). [12] provides another result of an experiment. [13] mentions the author’s insight obtained as well as relates the result to that in previous work (INSIGHT and CONNECTION). The annotation of the whole article (with a multi-colored representation) and the set of zone categories used are provided below.</p><p id="h.p_ID_97" class="CDt4Ke zfr3Q">Linkage to Related Work</p><p id="h.p_ID_99" class="CDt4Ke zfr3Q">The work on zone analysis is based partly on earlier work by Dr. Simone Teufel ( Cambridge , UK ) who examined journals in the computational linguistics domain. Molecular Biology domain texts, however, seem to be much more formally structured within the framework of experimental researches than the ones used in Teufel’s study and more focused on results. Our proposed research is unique in being focused on making sense of the myriad of results (and other aspects of the work) in each article as well as its application to text mining and the proposed use of machine learning.</p><p id="h.p_ID_101" class="CDt4Ke zfr3Q">Pre-analysis of EMBO journal articles (published in LREC’2004) by the NII group has shown that unlike content-based classification tasks in text mining such as the named entity task or event extraction which use technical terms as their major features, the identification of zones rests largely on the use of subtle clues such as common vocabulary words and phrases, section titles and the ordering of previous zone assignment. Given our hypothesis based on the pre-analysis that the task is feasible, we work on the ZAISA project in order to prove our ideas and make this a practical reality. In particular, we aim at the annotation of texts for the suggested zone classes and the proof that automatic classification is indeed possible using ‘weak’ linguistic clues.</p><p id="h.p_ID_103" class="CDt4Ke zfr3Q">Publications</p><ul class="n8H08c UVNKR" style="list-style-type: ;"><ul class="n8H08c UVNKR" style="list-style-type: ;"><li id="h.p_ID_105" class="TYR86d Sn3DJc zfr3Q">Mizuta, Y., Korhonen, A., Mullen, T. and Collier, N. (2006), “Zone analysis in biology articles as a basis for information extraction”, <em>International Journal of Medical Informatics</em>, Elsevier, 75(6): 468-487. [<a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpubmed%2F16112609%3Fitool%3DEntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum%26ordinalpos%3D14&sa=D&sntz=1&usg=AOvVaw2A2vrd3gVIqc0dtQqcXxG_" target="_blank">pubmed</a>]</li><li id="h.p_ID_107" class="TYR86d Sn3DJc zfr3Q">Mullen, A., Mizuta, Y. and Collier, N. (2005), "A baseline feature set for learning rhetorical zones using full articles in the biomedical domain", <em>SIGKDD Explorations</em>, 7(1):52-58, ACM. [pdf]</li></ul><li id="h.p_ID_109" class="TYR86d Sn3DJc zfr3Q">Mizuta, Y., Kawamoto, S., Mullen, T., Kawazoe, A., and Collier, N. (2005), “Creation of a dataset for zone analysis in biomedical texts: the design process and preliminary investigations”, Proc. 1<sup>st</sup> International Symposium on Languages in Biology and Medicine, Daejeon, Korea, November 24-26.</li><li id="h.p_ID_111" class="TYR86d Sn3DJc zfr3Q">Mizuta, Y. and Collier, N. (2004), "An annotation scheme for rhetorical analysis of biology articles", Proc. 4<sup>th</sup> International Conference on Language Resources and Evaluation (LREC'2004), Lisbon, Portugal, May 26-28. [pdf]</li></ul><p id="h.p_ID_113" class="CDt4Ke zfr3Q">Members</p><ul class="n8H08c UVNKR" style="list-style-type: ;"><li id="h.p_ID_115" class="TYR86d Sn3DJc zfr3Q">Yoko Mizuta</li><li id="h.p_ID_117" class="TYR86d Sn3DJc zfr3Q">Tony Mullen</li><li id="h.p_ID_119" class="TYR86d Sn3DJc zfr3Q">Anna Korhonen</li><li id="h.p_ID_121" class="TYR86d Sn3DJc zfr3Q">Nigel Collier</li></ul><p id="h.p_ID_123" class="CDt4Ke zfr3Q">Appendix 1</p><p id="h.p_ID_125" class="CDt4Ke zfr3Q">Sample illustration of zone analysis of a full-text NAR journal article</p><p id="h.p_ID_127" class="CDt4Ke zfr3Q">Zone categories used in the NAR journal example are given below:</p></div></div></div></div></div></div></div></div></div></section><section id="h.p_ID_143" class="yaqOZd" style=""><div class="IFuOkc"></div><div class="mYVXT"><div class="LS81yb VICjCf j5pSsc db35Fc" tabindex="-1"><div class="hJDwNd-AhqUyc-c5RTEf Ft7HRd-AhqUyc-c5RTEf JNdkSc SQVYQc L6cTce-purZT L6cTce-pSzOP"><div class="JNdkSc-SmKAyb LkDMRd"><div class="" jscontroller="sGwD4d" jsaction="zXBUYb:zTPCnb;zQF9Uc:Qxe3nd;" jsname="F57UId"></div></div></div><div class="hJDwNd-AhqUyc-OiUrBf Ft7HRd-AhqUyc-OiUrBf purZT-AhqUyc-II5mzb ZcASvf-AhqUyc-II5mzb pSzOP-AhqUyc-qWD73c Ktthjf-AhqUyc-qWD73c JNdkSc SQVYQc"><div class="JNdkSc-SmKAyb LkDMRd"><div class="" jscontroller="sGwD4d" jsaction="zXBUYb:zTPCnb;zQF9Uc:Qxe3nd;" jsname="F57UId"><div class="oKdM2c ZZyype Kzv0Me"><div id="h.p_ID_149" class="hJDwNd-AhqUyc-OiUrBf Ft7HRd-AhqUyc-OiUrBf jXK9ad D2fZ2 zu5uec OjCsFc dmUFtb wHaque g5GTcb"><div class="jXK9ad-SmKAyb"><div class="tyJCtd OWlOyc baZpAe"><div jscontroller="VYKRW" jsaction="rcuQ6b:rcuQ6b;"><div class="WIdY2d M1aSXe"><div jsname="WXxXjd" style="padding-top: 95.6493506494%"></div><div class="YMEQtf"><div jsname="jkaScf" jscontroller="szRU7e" class="w536ob" data-enable-interaction="true" data-url="https://1081503520-atari-embeds.googleusercontent.com/embeds/16cb204cf3a9d4d223a0a3fd8b0eec5d/inner-frame-minified.html" data-code="<table xmlns="http://www.w3.org/1999/xhtml" border="0" width="581" data-table-local-id="table-3"> <tbody> <tr> <td width="114"> <font size="2"> <span lang="EN-US">Zone</span> </font> </td> <td width="167"> <font size="2">Color/font used</font> </td> <td width="280"> <font size="2">Role</font> </td> </tr> <tr> <td width="114"> <font size="2"> <span lang="EN-US">BACKGROUND</span> </font> </td> <td width="167"> <font size="2">yellow</font> </td> <td width="280"> <font size="2"> <span lang="EN-US">to provide an assumption (e.g. generally accepted fact, previous work)</span> </font> </td> </tr> <tr> <td width="114"> <font size="2">PROBLEM SETTING</font> </td> <td width="167"> <font size="2">green</font> </td> <td width="280"> <font size="2"> <span lang="EN-US">to identify a problem to solve; goal of the research</span> </font> </td> </tr> <tr> <td width="114"> <font size="2">OUTLINE</font> </td> <td width="167"> <font size="2">red</font> </td> <td width="280"> <font size="2"> <span lang="EN-US">to characterize one’s work (i.e. meta-description of the work)</span> </font> </td> </tr> <tr> <td width="114"> <font size="2">TEXTUAL</font> </td> <td width="167"> <font size="2">pink</font> </td> <td width="280"> <font size="2"> <span lang="EN-US">to provide the organization of the paper</span> </font> </td> </tr> <tr> <td width="114"> <font size="2">OWN</font> </td> <td width="167"> <font size="2"> <br /> </font> </td> <td width="280"> <font size="2"> <span lang="EN-US">to present the author’s own work (consisting of 5 sub categories given below)</span> </font> </td> </tr> <tr> <td width="114"> <font size="2"> <span lang="EN-US">METHOD</span> </font> </td> <td width="167"> <font size="2">orange</font> </td> <td width="280"> <font size="2"> <span lang="EN-US">to present the experimental procedure taken and materials used</span> </font> </td> </tr> <tr> <td width="114"> <font size="2"> <span lang="EN-US">RESULT</span> </font> </td> <td width="167"> <font size="2"> f <span lang="EN-US">uchsia</span> </font> </td> <td width="280"> <font size="2"> <span lang="EN-US">to provide the result of the experiment performed</span> </font> </td> </tr> <tr> <td width="114"> <font size="2">INSIGHT</font> </td> <td width="167"> <font size="2">blue</font> </td> <td width="280"> <font size="2">to provide insights/findings obtained (e.g. the author's interpretation of the result, conclusion)</font> </td> </tr> <tr> <td width="114"> <font size="2">IMPLICATION</font> </td> <td width="167"> <font size="2">sky blue</font> </td> <td width="280"> <font size="2"> <span lang="EN-US">to provide the implications of the result, weaker insights (e.g. conjecture, assessment of the work, applications, future work)</span> </font> </td> </tr> <tr> <td width="114"> <font size="2">ELSE</font> </td> <td width="167"> <font size="2"> <br /> </font> </td> <td width="280"> <font size="2">to provide anything else</font> </td> </tr> <tr> <td width="114"> <font size="2">DIFFERENCE</font> </td> <td width="167"> <font size="2">boldface</font> </td> <td width="280"> <font size="2"> <span lang="EN-US"> to contrast the author’s work <span> </span> with other work (theory, data) </span> </font> </td> </tr> <tr> <td width="114"> <font size="2">CONNECTION</font> </td> <td width="167"> <font size="2">boldface</font> </td> <td width="280"> <font size="2"> <span lang="EN-US">to relate the author’s work to other work (theory, data)</span> </font> </td> </tr> </tbody> </table>" jsaction="rcuQ6b:WYd;"><div class="EmVfjc qs41qe UzswCe" data-loadingmessage=" " jscontroller="qAKInc" jsaction="animationend:kWijWc;dyRcpb:dyRcpb" data-active="true" jsname="Hy6Uif"><div class="Cg7hO" aria-live="assertive" jsname="vyyg5"> </div><div jsname="Hxlbvc" class="xu46lf"><div class="ir3uv uWlRce co39ub"><div class="xq3j6 ERcjC"><div class="X6jHbb GOJTSe"></div></div><div class="HBnAAc"><div class="X6jHbb GOJTSe"></div></div><div class="xq3j6 dj3yTd"><div class="X6jHbb GOJTSe"></div></div></div><div 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DIFFERENCE and CONNECTION overlap with some of the other categories.</p></div></div></div></div></div></div></div></div></div></section></div><div class="Xpil1b xgQ6eb"></div><div jscontroller="j1RDQb" jsaction="rcuQ6b:rcuQ6b;MxH79b:JdcaS;FaOgy:XuHpsb;" class="dZA9kd ynRLnc" data-last-updated-at-time="1594658449507" data-is-preview="false"><div role="button" class="U26fgb JRtysb WzwrXb I12f0b K2mXPb zXBiaf ynRLnc" jscontroller="iSvg6e" jsaction="click:cOuCgd; mousedown:UX7yZ; mouseup:lbsD7e; mouseenter:tfO1Yc; mouseleave:JywGue; focus:AHmuwe; blur:O22p3e; contextmenu:mg9Pef;touchstart:p6p2H; touchmove:FwuNnf; touchend:yfqBxc(preventDefault=true); touchcancel:JMtRjd;;keydown:I481le;" jsshadow jsname="Bg3gkf" aria-label="Site actions" aria-disabled="false" tabindex="0" aria-haspopup="true" aria-expanded="false" data-menu-corner="bottom-start" data-anchor-corner="top-start"><div class="NWlf3e MbhUzd" jsname="ksKsZd"></div><span jsslot class="MhXXcc oJeWuf"><span class="Lw7GHd snByac"><svg width="24" height="24" viewBox="0 0 24 24" focusable="false" class=" NMm5M"><path d="M11 17h2v-6h-2v6zm1-15C6.48 2 2 6.48 2 12s4.48 10 10 10 10-4.48 10-10S17.52 2 12 2zm0 18c-4.41 0-8-3.59-8-8s3.59-8 8-8 8 3.59 8 8-3.59 8-8 8zM11 9h2V7h-2v2z"/></svg></span></span><div jsname="xl07Ob" style="display:none" aria-hidden="true"><div class="JPdR6b hVNH5c" jscontroller="uY3Nvd" jsaction="IpSVtb:TvD9Pc;fEN2Ze:xzS4ub;frq95c:LNeFm;cFpp9e:J9oOtd; 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