チケット #220: orefil_top_en.2.html

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1<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
2<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="utf-8" lang="utf-8">
3<head>
4  <title>OReFiL: an Online Resource Finder for Lifesciences</title>
5  <meta name="keywords" content="search,online resource,tool,database,lifescience,bioinformatics,biomedicine,webpage,webservice,MeSH,MEDLINE,PubMed,peer-reviewed paper" />
6  <meta name="description" content="Search for online resources introduced in peer-reviewed papers in lifescience" />
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10  <script type="text/javascript" src="/javascripts/jquery.highlight-1.js"></script>
11  <script type="text/javascript">//<![CDATA[
12  jQuery.noConflict();
13  //]]></script>
14  <link rel="stylesheet" type="text/css" href="/stylesheets/layout.css"/>
15  <link rel="search" type="application/opensearchdescription+xml" title="OReFiL" href="orefil.xml" />
16  <link href="http://bl05.dbcls.jp:18091/en/search/new.atom" rel="alternate" title="ATOM" type="application/atom+xml" />
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21<body>
22  <div class="header">
23    <div class="sign">
24      <div class="middle">
25                <form action="/en/sessions/create" class="sign-form" method="get" name="sign-in-form">        DBCLS OpenID URL:
26        &nbsp;
27        <input class="openid-input" name="openid_url" size="30" maxlength="256" type="text" value=""/> 
28        <input class="sign-in-submit" type="submit" value="Sign In" />
29        <span>&nbsp;&nbsp;|&nbsp;&nbsp;</span>
30        <a href="https://openid.dbcls.jp/account/signup" class="sign-up">Sign Up</a>
31        <span>&nbsp;&nbsp;|&nbsp;&nbsp;</span>
32                <a href="/ja/">日本語</a>
33                </form>              </div>
34    </div>
35  </div>
36
37 
38  <div class="main">
39    <h1 class="top"><a href="/"><img alt="OreFil Logo" class="link_image" hspace="0" src="/images/OReFiL_Logo.png?1230263519" vspace="0" /></a> OReFiL: an Online Resource Finder for Lifesciences</h1>
40<div class="subtitle">
41  Search for online resources introduced in peer-reviewed papers in lifescience (Bioinformatics, Biomedicine, etc.)
42</div>
43<div class="top-search-form">
44   <form action="/en/search" method="get" name="QueryForm">
45   Query: <input id="query" maxlength="512" name="query" size="100" type="text" />
46   Max. Results:  <input id="count" maxlength="5" name="count" size="7" type="text" value="50" /> <br />
47   Sort by :
48   <input checked="checked" name="sort_by" value="relevance" type="radio" />Relevance&nbsp;
49   <input  name="sort_by" value="date" type="radio" />Updated&nbsp;
50   <input  name="sort_by" value="rating" type="radio" />Rating&nbsp;
51   <br />
52   Search Options :
53   <label><input checked="checked" id="hide_unfetched" name="hide_unfetched" type="checkbox" value="on" />Hide page-not-found entries</label>
54   <label><input id="feedback" name="feedback" type="checkbox" value="on" />Turn on relevance-feedback</label> <br />
55   <input type="submit" value="SUBMIT" />
56   <input type="reset"  name="reset" value="RESET" />
57   <input type="button"  value="CLEAR" onclick="document.QueryForm.query.value=''" /><br />
58   <a href="/en/help" class="hlp">HELP</a> <input type="button"  value="try &quot;genome&quot;" onclick="document.QueryForm.query.value='genome'" /> <br />
59   <span class="with-img">Found a bug? We'd be glad if you'd tell us: <img align="top" alt="yayamamo AT cb DOT k DOT u-tokyo DOT ac DOT jp" border="0" hspace="0" src="/images/yycontact.png?1230263519" vspace="0" /> <br /></span>
60   <span>Thank you. </span>
61   </form>
62</div>
63<div class="tips">
64  <h3><a id="sec_1">What is OReFiL?</a></h3>
65<p>OReFiL stands for <i><b>O</b>nline <b>Re</b>source <b>Fi</b>nder for <b>L</b>ifescience</i>.
66It facilitates a search for online resources that are introduced in peer-reviewed papers.
67You can search by MeSH terms or author names in addition to free words.
68OReFiL extracts all URLs from MEDLINE abstracts and PubMed-indexed BioMed Central full-papers (implementation or availability sections), and indexes them with MeSH terms and author names.</p>
69<h3><a id="sec_2">What is the benefit of using OReFiL?</a></h3>
70<ol>
71
72<li>OReFiL returns up-to-date query-relevant online resources that is introduced in peer-reviewed papers.</li>
73<li>Users can search for online resources not only by free words, but also by MeSH terms or author names.</li>
74<li>Users can easily verify each hit resource by following the links to its corresponding PubMed entry, webpages having a link to that of the hit resource, or papers citing it through the search systems of BioMed Central, Scirus, HighWire Press, or Google Scholar.</li>
75<li>Users can quickly confirm the existence of an online resource webpage.</li>
76</ol>
77
78  <h3>Tips</h3>
79  <ul>
80    <li>
81
82      <span style="font-size:1.5em">Q</span>uery can be any keywords.
83      Each keyword can be modified to specify a context by adding the following modifiers after it:
84      <ul>
85        <li><b>.tiab</b> for titles and abstracts (<i>e.g.</i>,<span class="quote"><a href="http://orefil.dbcls.jp/search?query=apoptosis.tiab&amp;count=50&amp;sort_by=relevance&amp;hide_unfetched=on">apoptosis.tiab</a></span>),</li>
86        <li><b>.auth</b> for author names, and</li>
87        <li><b>.mesh</b> / <b>.majr</b> / <b>.noexp</b> for MeSH terms.</li>
88      </ul>
89
90      An example is  <span class="quote"><a href="http://orefil.dbcls.jp/search?query=Proteins.mesh&amp;count=50&amp;sort_by=relevance&amp;hide_unfetched=on">Proteins.mesh</a></span>
91      (a mesh term followed by ".mesh" is for all kinds of MeSH headers,
92      by ".majr" for those of MeSH headers of major topics with semantic expansion,
93      or ".noexp" for those without semantic expansion).
94    </li>
95    <li>
96      <span style="font-size:1.5em">A</span> multiword keyword can be expressed using the <b>#1</b> operator with parentheses such as <span class="quote"><a href="http://orefil.dbcls.jp/search?query=%231%28text+mining%29&amp;count=50&amp;sort_by=relevance&amp;hide_unfetched=on">#1(text mining)</a></span> or <span class="quote"><a href="http://orefil.dbcls.jp/search?query=%231%28Sequence+Analysis%29&amp;count=50&amp;sort_by=relevance&amp;hide_unfetched=on">#1(Sequence Analysis)</a></span>.
97    </li>
98    <li>
99      <span style="font-size:1.5em">B</span>oolean <b>"AND"</b> operator can be used using the <b>#band</b> operator with parentheses such as  <span class="quote"><a href="http://orefil.dbcls.jp/search?query=%23band%28pathway+apoptosis%29&amp;count=50&amp;sort_by=relevance&amp;hide_unfetched=on">#band(pathway apoptosis)</a></span>.
100    </li>
101    <li>
102      <span style="font-size:1.5em">B</span>oolean-AND-like language-model-based search can be done using the <b>#filreq</b> operator with parentheses such as  <span class="quote"><a href="http://orefil.dbcls.jp/search?query=%23filreq%28Software.noexp+%231%28sequence+analysis%29%29&amp;count=50&amp;sort_by=relevance&amp;hide_unfetched=on">#filreq(Software.noexp #1(sequence analysis))</a></span>.
103      In this example, OReFiL only considers those resources whose MEDLINE entries have the MeSH term "Software" and rank them according to the query #1(sequence analysis).
104    </li>
105    <li>
106
107      <span style="font-size:1.5em">P</span>unctuations are ignored. So, "Databases, Protein" and "Databases Protein" are identical.
108    </li>
109    <li>
110      <span style="font-size:1.5em">N</span>on-alpha-numericals except for query operations are ignored. For example, "Variation (Genetics)" and "Variation Genetics" are identical.
111    </li>
112    <li>
113      <span style="font-size:1.5em">T</span>his system uses Lemur Toolkit (Indri), and the query language can be learned  <a href="http://www.lemurproject.org/lemur/IndriQueryLanguage.php">here</a>.
114    </li>
115    <li>
116      <span style="font-size:1.5em">D</span>etailed information of this system can be found at
117      <a href="http://www.biomedcentral.com/1471-2105/8/287/abstract">BMC Bioinformatics 2007, 8:287</a>.<br/>
118
119      <a href="http://www.biomedcentral.com/1471-2105/8/287">
120        <img alt="www.biomedcentral.com" src="http://www.biomedcentral.com/images/articles/link.gif" border="0" />
121      </a>
122    </li>
123    </ul>
124    <p>
125      <u>Last index update: Dec 8, 2008</u>
126    </p>
127
128</div>
129
130  </div>
131  <hr/>
132  <div class="footer">
133    <center>
134      Comments &amp; suggestions are welcome.
135      Please contact to: yayamamo AT cb DOT k DOT u-tokyo DOT ac DOT jp
136      <p>
137        &copy; Copyright 2007-2008 University of Tokyo / DBCLS
138      </p>
139      <p>
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