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[Treebase-guts] SF.net SVN: treebase:[631] trunk/treebase-web/src/main/webapp
|
From: <yo...@us...> - 2010-03-20 15:51:48
|
Revision: 631
http://treebase.svn.sourceforge.net/treebase/?rev=631&view=rev
Author: youjun
Date: 2010-03-20 15:51:38 +0000 (Sat, 20 Mar 2010)
Log Message:
-----------
page content update
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml
trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/newPhylowidget.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
trunk/treebase-web/src/main/webapp/login.jsp
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp
trunk/treebase-web/src/main/webapp/images/bugs_mail.jpg
trunk/treebase-web/src/main/webapp/images/help_mail.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/
trunk/treebase-web/src/main/webapp/images/journal_files/image001.gif
trunk/treebase-web/src/main/webapp/images/journal_files/image002.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/image003.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/image004.gif
trunk/treebase-web/src/main/webapp/images/journal_files/image005.gif
trunk/treebase-web/src/main/webapp/images/journal_files/image006.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/image007.gif
trunk/treebase-web/src/main/webapp/images/journal_files/image008.gif
trunk/treebase-web/src/main/webapp/images/journal_files/image009.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/image010.gif
trunk/treebase-web/src/main/webapp/images/journal_files/image011.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/image012.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/image013.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/image014.gif
trunk/treebase-web/src/main/webapp/images/journal_files/image015.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/image016.gif
trunk/treebase-web/src/main/webapp/images/journal_files/image017.gif
trunk/treebase-web/src/main/webapp/images/journal_files/image018.gif
trunk/treebase-web/src/main/webapp/images/journal_files/image019.jpg
trunk/treebase-web/src/main/webapp/images/partnership/
trunk/treebase-web/src/main/webapp/images/partnership/image001.jpg
trunk/treebase-web/src/main/webapp/images/partnership/image002.jpg
trunk/treebase-web/src/main/webapp/images/partnership/image003.jpg
trunk/treebase-web/src/main/webapp/images/partnership/image004.jpg
trunk/treebase-web/src/main/webapp/images/people/bpiel.jpeg
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml 2010-03-19 21:44:13 UTC (rev 630)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml 2010-03-20 15:51:38 UTC (rev 631)
@@ -11,6 +11,10 @@
<pattern>/urlAPI.html</pattern>
<pattern>/people.html</pattern>
<pattern>/technology.html</pattern>
+ <pattern>/partnership.html</pattern>
+ <pattern>/reference.html</pattern>
+ <pattern>/contact.html</pattern>
+ <pattern>/journal.html</pattern>
</decorator>
<!-- decoration page for search pages -->
Added: trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp 2010-03-20 15:51:38 UTC (rev 631)
@@ -0,0 +1,56 @@
+<div class=Section1>
+
+<h1>Contacts</h1>
+
+<h2>Help</h2>
+
+<p>For questions about data submission and data content, please
+contact: </p>
+
+<p><img src="images/help_mail.jpg"> </p>
+
+<h2>Bugs</h2>
+
+<p>To report software bugs, browser conflicts, and ergonomic
+inefficiencies, please contact:</p>
+
+<p><img src="images/bugs_mail.jpg"> </p>
+
+<p>Alternatively, you can enter a bug report directly into our
+sourceforge online bug tracker. For that, please follow these steps:</p>
+
+
+
+<p>I. If you have a SourceForge account, log in to it and
+proceed to (II) below. Otherwise:</p>
+
+<p>1. Visit <a
+href="http://sourceforge.net/account/registration/"
+title="http://sourceforge.net/account/registration/" id=wa5w>http://sourceforge.net/account/registration/</a>
+and fill in the form.<br>
+2. After you confirm the account creation by email, log in at <a
+href="http://sourceforge.net/account/login.php"
+title="http://sourceforge.net/account/login.php" id=uguh>http://sourceforge.net/account/login.php</a></p>
+
+
+<p>II. Visit <a
+href="https://sourceforge.net/tracker2/?group_id=248804&atid=1126676"
+title="https://sourceforge.net/tracker2/?group_id=248804&atid=1126676"
+id="xjq:">https://sourceforge.net/tracker2/?group_id=248804&atid=1126676</a></p>
+
+
+<p>On this page you can browse the bug database.</p>
+
+
+<p>III. Click the "add new" button. Add the
+description of the bug. Long outputs or error messages can be attached as
+separate files if you prefer.</p>
+
+
+
+<p>Click "add artifact" to submit the report.</p>
+
+
+</div>
+
+
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-19 21:44:13 UTC (rev 630)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-20 15:51:38 UTC (rev 631)
@@ -2,35 +2,21 @@
<div class="gutter">
<h1>Welcome to TreeBASE</h1>
<p>
- TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and
- the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species,
- trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the
- public if they are used in a publication that is in press or published in a peer-reviewed scientific
- journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or
- in review can be submitted to TreeBASE but are only available to the publication editors or reviewers using
- a special access code.
- </p>
- <p id="sponsors">
- <img src="images/aem.gif" alt="AEM" width="80" height="26" />
- <img src="images/whs.gif" alt="WHS" width="80" height="26" />
- <img src="images/evo.gif" alt="Evolution" width="80" height="26" />
- <img src="images/fgb.gif" alt="FGB" width="80" height="26" />
- <img src="images/gpprcg.gif" alt="GPPRCG" width="80" height="26" />
- <img src="images/invsys.gif" alt="Invertebrate Systematics" width="80" height="26" />
- <img src="images/psa.gif" alt="PSA" width="80" height="26" />
- <img src="images/tl.gif" alt="Lichenologist" width="80" height="26" />
- <img src="images/mpe.gif" alt="MPE" width="80" height="26" />
- <img src="images/msa.gif" alt="Mycologia" width="80" height="26" />
- <img src="images/mpg.jpg" alt="Mycological Progress" width="80" height="26" />
- <img src="images/myc.gif" alt="Mycological Research" width="80" height="26" />
- <img src="images/mycsci.gif" alt="Myoscience" width="80" height="26" />
- <img src="images/ode.gif" alt="ODE" width="80" height="26" />
- <img src="images/aps.jpg" alt="APS" width="80" height="26" />
- <img src="images/nebs.gif" alt="Rhodora" width="80" height="26" />
- <img src="images/stmyc.gif" alt="Mycology" width="80" height="26" />
- <img src="images/ssb.gif" alt="SSB" width="80" height="26" />
- <img src="images/aspt.gif" alt="Systematic Botany" width="80" height="26" />
- <img src="images/tq.gif" alt="Technical Quarterly" width="80" height="26" />
- </p>
+ TreeBASE is a repository of phylogenetic information, specifically
+ user-submitted phylogenetic trees and the data used to generate them.
+ TreeBASE accepts all types of phylogenetic data (e.g., trees of species,
+ trees of populations, trees of genes) representing all biotic taxa.
+ Data in TreeBASE are exposed to the public if they are used in a
+ publication that is in press or published in a peer-reviewed
+ scientific journal, book, conference proceedings, or thesis.
+ Data used in publications that are in preparation or in review can be
+ submitted to TreeBASE but are only available to the publication
+ editors or reviewers using a special access code.
+ </p>
+ <p>
+ As of early 2010, TreeBASE contains 6,500 trees in 2,500 publications
+ written by 4,500 different authors. These trees have 135,000 distinct
+ taxon labels that map to approximately 60,000 distinct taxa.
+ </p>
</div>
</div>
\ No newline at end of file
Added: trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2010-03-20 15:51:38 UTC (rev 631)
@@ -0,0 +1,349 @@
+
+
+<div class=Section1>
+
+<h1><span>Journals</span></h1>
+
+<p>In addition to providing a digital library, TreeBASE serves the scientific community
+by offering journal editors and reviewers special advanced anonymous access to
+submitted data. This access improves the quality of the review process because
+reviewers can inspect and evaluate the data, and in turn that also improves the
+quality of data in TreeBASE. Below is a list of journals that recommend or
+require submission to TreeBASE as an integral part of their publication
+policies. We encourage other journals and scientific societies to do the same
+because archiving and sharing of scientific data is critical for promoting
+subsequent reuse of published data, leveraging the cumulative knowledge of
+science, and maximizing the impact of scientific publications on future
+research. </p>
+
+
+<table class=MsoNormalTable border=0 cellspacing=0 cellpadding=0
+ style='background:white' id="p9:6">
+ <tr>
+ <td valign=top style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><b>Journal Hyperlink</b></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><b>PhyloWS URL to Studies in TreeBASE</b><br>
+ (note: add "&format=rss1" to the end of each URL to use it in
+ your favorite RSS reader)</p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <span style='font-size:10.0pt'><a
+ href="http://www.wiley.com/bw/journal.asp?ref=0014-3820" title=link id=i1y.><img width=121 height=40 src="images/journal_files/image001.gif"
+ alt=Evolution align=bottom border=0></a></span></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><span style='font-size:10.0pt'><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Evolution"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Evolution"
+ id=snnr>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Evolution</a></span></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <span style='font-size:10.0pt'><a
+ href="http://www3.interscience.wiley.com/journal/119423602/home" title=link
+ id=sik5><img border=0 width=121 height=40
+ src="images/journal_files/image002.jpg"></a></span></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><span style='font-size:10.0pt'><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Evolutionary+Applications%22"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Evolutionary+Applications%22"
+ id="n15_">http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Evolutionary+Applications%22</a></span></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <span style='font-size:10.0pt'><a
+ href="http://www.elsevier.com/wps/find/journaldescription.cws_home/720691/description#description"
+ title=link id=ctp6><img border=0 width=121 height=40
+ src="images/journal_files/image003.jpg"></a></span></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><span style='font-size:10.0pt'><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Fungal+Biology%22"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Fungal+Biology%22"
+ id=z97n>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Fungal+Biology%22</a></span></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <span style='font-size:10.0pt'><a
+ href="http://www.publish.csiro.au/nid/120.htm" title=link id=vixi><img border=0 width=121 height=40
+ src="images/journal_files/image004.gif" alt="Invertebrate Systematics" align=bottom></a></span></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><span style='font-size:10.0pt'><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Invertebrate+Systematics%22"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Invertebrate+Systematics%22"
+ id=zv-p>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Invertebrate+Systematics%22</a></span></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <span style='font-size:10.0pt'><a href="http://www.msafungi.org/" title=link
+ id=i138><img border=0 width=121 height=40
+ src="images/journal_files/image005.gif" alt="Join MSA" align=bottom></a></span></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><span style='font-size:10.0pt'><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Mycologia"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Mycologia"
+ id=fgv3>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Mycologia</a></span></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <span style='font-size:10.0pt'><a
+ href="http://www.springer.com/life+sciences/plant+sciences/journal/11557"
+ title=link id=r0.d><img border=0 width=121 height=40
+ src="images/journal_files/image006.jpg" alt="Get MycPro" align=bottom></a></span></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><span style='font-size:10.0pt'><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Mycologial+Progress%22"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Mycologial+Progress%22"
+ id="x_40">http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Mycologial+Progress%22</a></span></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <span style='font-size:10.0pt'><a
+ href="http://www.elsevier.com/wps/find/journaldescription.cws_home/707043/description#description"
+ title=link id=f3oo><img border=0 width=121 height=40
+ src="images/journal_files/image007.gif" alt="Join BMS" align=bottom></a></span></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><span style='font-size:10.0pt'><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Mycologial+Research%22"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Mycologial+Research%22"
+ id=pm9.>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Mycologial+Research%22</a></span></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <a href="http://www.springer.com/life+sciences/microbiology/journal/10267"
+ title=link id="ap:."><img border=0 width=121 height=40
+ src="images/journal_files/image008.gif" alt=Mycoscience align=bottom></a></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><span style='font-size:10.0pt'><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Mycoscience"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Mycoscience"
+ id=dr.h>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Mycoscience</a></span></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <a href="http://www.mycosphere.org/" title=link id=bgaq><img border=0 width=121 height=40
+ src="images/journal_files/image009.jpg"></a></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><span style='font-size:10.0pt'><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Mycosphere"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Mycosphere"
+ id=hbsg>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Mycosphere</a></span></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <a
+ href="http://www.elsevier.com/wps/find/journaldescription.cws_home/701789/description#description"
+ title=link id=cp74><img border=0 width=121 height=40
+ src="images/journal_files/image010.gif" alt="Organisms, Diversity, and Evolution"
+ align=bottom></a></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Organisms+Diversity+&+Evolution%22"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Organisms+Diversity+&+Evolution%22"
+ id=lcqz>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Organisms+Diversity+&+Evolution%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <a href="http://www.persoonia.org/" title=link id=w.mk><img border=0 width=121 height=40
+ src="images/journal_files/image011.jpg"></a></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><span style='font-size:10.0pt'><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Persoonia"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Persoonia"
+ id=fyta>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Persoonia</a></span></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <a href="http://apsjournals.apsnet.org/loi/phyto?cookieSet=1" title=link
+ id=mjqe><img border=0 width=121 height=40
+ src="images/journal_files/image012.jpg" alt="Join APS" align=bottom></a></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><span style='font-size:10.0pt'><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Phytopahology"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Phytopahology"
+ id=g3p3>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Phytopahology</a></span></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <a href="http://www.apsnet.org/pd/" title=link id=c0cs><img border=0 width=121 height=40
+ src="images/journal_files/image013.jpg"></a></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><span style='font-size:10.0pt'><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Plant+Disease%22"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Plant+Disease%22"
+ id=yqwc>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Plant+Disease%22</a></span></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <a href="http://www.rhodora.org/Rhodora.html" title=link id=jdv1><img border=0 width=121 height=40
+ src="images/journal_files/image014.gif" alt=Rhodora align=bottom></a></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><span style='font-size:10.0pt'><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Rhodora"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Rhodora"
+ id=pmzl>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Rhodora</a></span></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <a
+ href="http://www.rbg.vic.gov.au/science/information-and-resources/science-publications/muelleria"
+ title=link id=u9eq><img border=0 width=121 height=40
+ src="images/journal_files/image015.jpg"></a></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><span style='font-size:10.0pt'><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Muelleria"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Muelleria"
+ id="psm:">http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Muelleria</a></span></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <a href="http://www.studiesinmycology.org/" title=link id=s1hf><img border=0 width=121 height=40
+ src="images/journal_files/image016.gif" alt="Studies in Mycology" align=bottom></a></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Studies+in+Mycology%22"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Studies+in+Mycology%22"
+ id=ockh>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Studies+in+Mycology%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <a href="http://systbiol.org/" title=link id=ljmi><img border=0 width=121 height=40
+ src="images/journal_files/image017.gif" alt="Join SSB" align=bottom></a></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Systematic+Biology%22"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Systematic+Biology%22"
+ id=an6v>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Systematic+Biology%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <a href="http://www.sysbot.org/" title=link id=t9z8><img border=0 width=121 height=40
+ src="images/journal_files/image018.gif" alt="Join ASPT" align=bottom></a></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Systematic+Botany%22"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Systematic+Botany%22"
+ id=n5tf>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Systematic+Botany%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal>
+ <a href="http://tropical-bryology.org/" title=link id=n.b1><img border=0 width=121 height=40
+ src="images/journal_files/image019.jpg"></a></p>
+ </td>
+ <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p class=MsoNormal><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Tropical+Bryology%22"
+ title="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Tropical+Bryology%22"
+ id=t8hh>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Tropical+Bryology%22</a></p>
+ </td>
+ </tr>
+</table>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal><b>Other Journals with a Significant Presence in TreeBASE</b>:
+<a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%2American+Journal+of+Botany%22"
+title="American Journal of Botany" id=gyux>American Journal of Botany</a>; <a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Annals+of+the+Missouri+Botanical+Garden%22"
+title="Annals of the Missouri Botanical Garden" id=upm6>Annals of the Missouri
+Botanical Garden</a>; <a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Biological+Journal+of+the+Linnean+Society%22"
+title="Biological Journal of the Linnean Society" id=lhjm>Biological Journal of
+the Linnean Society</a>; <a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22BMC+Evolutionary+Biology%22"
+title="BMC Evolutionary Biology" id=jug2>BMC Evolutionary Biology</a>; <a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Canadian+Journal+of+Botany%22"
+title="Canadian Journal of Botany" id=q0.s>Canadian Journal of Botany</a>; <a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Cladistics"
+title=Cladistics id=vl2m>Cladistics</a>; <a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Fungal+Diversity%22"
+title="Fungal Diversity" id=eosa>Fungal Diversity</a>; <a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22International+Journal+of+Plant+Sciences%22"
+title="International Journal of Plant Sciences" id=ch9v>International Journal
+of Plant Sciences</a>; <a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Journal+of+Phycology%22"
+title="Journal of Phycology" id=sm-n>Journal of Phycology</a>; <a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Molecular+Biology+and+Evolution%22"
+title="Molecular Biology and Evolution" id=i256>Molecular Biology and Evolution</a>;
+<a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Molecular+Ecology%22"
+title="Molecular Ecology" id="pxv_">Molecular Ecology</a>; <a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Molecular+Phylogenetics+and+Evolution%22"
+title="Molecular Phylogenetics and Evolution" id="x2_7">Molecular Phylogenetics
+and Evolution</a>; <a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Plant+Systematics+and+Evolution%22"
+title="Plant Systematics and Evolution" id=ms2.>Plant Systematics and Evolution</a>;
+<a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Proceeding+of+the+National+Academy+of+Sciences+of+the+United+States+of+America%22"
+title="Proceeding of the National Academy of Sciences of the United States of America"
+id=qudx>Proceeding of the National Academy of Sciences of the United States of
+America</a>; <a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=%22Proceedings+of+the+Royal+Society+B%22"
+title="Proceedings of the Royal Society B" id=nphn>Proceedings of the Royal
+Society B</a>; <a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Taxon"
+title=Taxon id=vc5e>Taxon</a>; <a
+href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Zootaxa"
+title=Zootaxa id=b4cg>Zootaxa</a></p>
+
+</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/newPhylowidget.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/newPhylowidget.jsp 2010-03-19 21:44:13 UTC (rev 630)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/newPhylowidget.jsp 2010-03-20 15:51:38 UTC (rev 631)
@@ -172,23 +172,7 @@
<div id="comments" style="margin: 5px">
Make a selection by clicking on the tree list.
</div>
- <c:if test="${treeBlockID != null}">
- <fieldset style="margin-left:5px;margin-right:5px;background-color:white">
- <legend>Quick links</legend>
- <p style="text-align:left">
- <a href="/treebase-web/search/study/trees.html?id=${studyID}" target="_new">
- <img class="iconButton" style="vertical-align:middle" src="<fmt:message key="icons.trees"/>" />
- Containing tree set
- </a>
- </p>
- <p style="text-align:left">
- <a href="/treebase-web/search/study/summary.html?id=${studyID}" target="_new">
- <img class="iconButton" style="vertical-align:middle" src="<fmt:message key="icons.citation"/>" />
- Containing study
- </a>
- </p>
- </fieldset>
- </c:if>
+
</td>
</tr>
</table>
Added: trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp 2010-03-20 15:51:38 UTC (rev 631)
@@ -0,0 +1,56 @@
+<div class=Section1>
+
+<h1>Partnerships</h1>
+
+<p class=MsoNormal> </p>
+
+<p class=MsoNormal><img width=160 height=100
+src="images/partnership/image001.jpg" style='height:100px;width:160px'> The
+<a href="http://www.nescent.org"
+title="National Evolutionary Synthesis Center (NESCent)" id=qhvf>National
+Evolutionary Synthesis Center (NESCent)</a> is a national center sponsored by
+NSF with the mission of facilitating synthetic research in evolutionary
+biology. Through a partnership with CIPRES and TreeBASE, NESCent is serving to
+deploy, maintain, and host TreeBASE.</p>
+
+<p class=MsoNormal style='margin-bottom:12.0pt'> </p>
+
+<p class=MsoNormal><br>
+<img border=0 width=160 height=100 src="images/partnership/image002.jpg"
+style='height:100px;width:160px'><span style='font-size:10.0pt'><a
+href="http://www.datadryad.org" title=Dryad id=hqpf>Dryad</a> is a open
+digital repository of author-submitted published data which supports many
+journals in evolutionary biology and ecology. Metadata in TreeBASE is
+being harvested and mirrored by Dryad using the TreeBASE OAI-PMH service.
+Metadata for existing TreeBASE records is being enriched through manual and
+semi-automated mechanisms. Dryad is also forwarding phylogenetic data
+depositions to TreeBASE at the request of the author. These activities are
+funded by NSF DBI 0743720: "A Digital Repository for Preservation and
+Sharing of Data Underlying Published Works in Evolutionary Biology."</span></p>
+
+<p class=MsoNormal style='margin-bottom:12.0pt'> </p>
+
+<p class=MsoNormal><img border=0 width=160 height=100
+src="images/partnership/image003.jpg" style='height:100px;width:160px'><span
+style='font-size:10.0pt'>TreeBASE currently makes use of <a
+href="http://www.ubio.org/index.php?pagename=services_overview"
+title="uBio's taxonomic name services" id=k03k>uBio's taxonomic name services</a>
+to match taxon labels in submitted trees and matrices against uBio's dictionary
+of nomenclature. TreeBASE further uses this mapping to acquire and store <a
+href="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=howlink"
+title="NCBI taxids" id=jh1k>NCBI taxids</a>. In prior years, TreeBASE has
+provided a bulk list of its taxonomy to uBio in order to store links to
+TreeBASE, and there are plans to automate this procedure in the future. </span></p>
+
+<p class=MsoNormal style='margin-bottom:12.0pt'><br>
+<br>
+</p>
+
+<p class=MsoNormal><img border=0 width=160 height=100
+src="images/partnership/image004.jpg" style='height:100px;width:160px'>Many
+thanks to the National Science Foundation for their valuable support.</p>
+
+<p class=MsoNormal> </p>
+
+</div>
+
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp 2010-03-19 21:44:13 UTC (rev 630)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp 2010-03-20 15:51:38 UTC (rev 631)
@@ -20,10 +20,10 @@
<br/>Deployment Manager
</td>
<td>
- <img src="images/people/bpiel.gif" width="81" height="108" alt="William Piel"/>
+ <img src="images/people/bpiel.jpeg" width="81" height="108" alt="William Piel"/>
<br/><strong>William Piel</strong>
- <br/>Data Editor
- <br />Prototype Developer
+ <br/>Content Editor
+ <br />Prototype Dev
</td>
<td>
<img src="images/people/vtannen.jpeg" width="81" height="108" alt="Val Tannen"/>
@@ -60,7 +60,7 @@
<td>
<img src="images/people/mdonoghue.gif" width="81" height="108" alt="Michael Donoghue"/>
<br/><strong>Michael Donoghue</strong>
- <br/>Conceptual Issues
+ <br/>Concept
</td>
<td>
<img src="images/people/teriksson.gif" width="81" height="108" alt="Torsten Eriksson"/>
@@ -92,7 +92,8 @@
<td>
<img src="images/people/msanderson.gif" width="81" height="108" alt="Mike Sanderson"/>
<br/><strong>Mike Sanderson</strong>
- <br/>Conceptual Issues
+ <br/>Concept
+ <br/>Prototype Dev
</td>
<td>
<img src="images/people/anon.jpg" width="81" height="108" alt="Can van Tran"/>
Added: trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp 2010-03-20 15:51:38 UTC (rev 631)
@@ -0,0 +1,85 @@
+
+<h1>Reference</h1>
+ <p>
+ <strong>Blake, J. A., C. J. Bult, M. J. Donoghue, J. Humphries, and C. Fields.</strong>
+ 1994. Interoperability of biological databases: a meeting report.
+ <em>Syst. Biol.</em> <strong>43</strong>:585-589.
+ </p>
+ <p>
+ <strong>Donoghue, M. J.</strong>
+ 1994. Progress and prospects in reconstructing plant phylogeny.
+ <em>Ann. Missouri Bot. Gard.</em> <strong>81</strong>:405-418.
+ </p>
+ <p>
+ <strong>Donoghue, M. J. and D. D. Ackerly.</strong>
+ 1996. Phylogenetic uncertainties and sensitivity analyses in comparative biology.
+ <em>Phil. Trans. R. Soc. London B, 351: 1241-1249.</em>
+ </p>
+ <p>
+ <strong>Maddison, W. P. and D. R. Maddison.</strong>
+ 1992.
+ <em>MacClade: Interactive Analysis of Phylogeny and Character Evolution, Vers. 3.0.</em>
+ Sunderland, MA: Sinauer Assoc.
+ </p>
+ <p>
+ <strong>Morell, V.</strong>
+ 1996. TreeBASE: the roots of phylogeny.
+ <em>Science</em> <strong>273</strong>: 569.
+ </p>
+ <p>
+ <strong>Piel, W. H.</strong>
+ 2003. "Phyloinformatics and Tree Networks." In:
+ <strong>Wu, C. H., P. Wang, and J. T. L. Wang,</strong> eds.
+ <em>Computational Biology and Genome Informatics</em>. World Scientific Press.
+ </p>
+ <p>
+ <strong>Piel, W. H., M. J. Donoghue, and M. J. Sanderson.</strong>
+ 2002. "TreeBASE: a database of phylogenetic knowledge." Pp. 41-47. In:
+ <strong>Shimura, J., K. L. Wilson, and D. Gordon,</strong> eds.
+ <em>To the interoperable "Catalog of Life" with partners Species 2000 Asia Oceanea.</em>
+ Research Report from the National Institute for Environmental Studies No. 171, Tsukuba, Japan.
+ </p>
+ <p>
+ <strong>Piel, W. H., M. J. Sanderson, and M. J. Donoghue.</strong>
+ 2003. The Small-World Dynamics of Tree Networks and Data Mining in Phyloinformatics.
+ <em>Bioinformatics</em>, <strong>19</strong>(9): 1162-1168.
+ </p>
+ <p>
+ <strong>Sanderson, M. J., B. G. Baldwin, G. Bharathan, C. S. Campbell, D. Ferguson,
+ J. M. Porter, C. Von Dohlen, M. F. Wojciechowski & M. J. Donoghue.
+ </strong> 1993. The growth of phylogenetic information and the need for a phylogenetic database.
+ <em>Syst. Biol.</em> <strong>42</strong>:562-568.
+ </p>
+ <p>
+ <strong>Sanderson, M. J. and M. J. Donoghue.</strong>
+ 1996. The relationship between homoplasy and confidence in a phylogenetic tree. In:
+ <em>Homoplasy and the Evolutionary Process</em> (<strong>M. Sanderson and L. Hufford</strong>, eds.).
+ San Diego: Academic Press.
+ </p>
+ <p>
+ <strong>Sanderson, M. J., M. J. Donoghue, W. Piel, and T. Eriksson.</strong>
+ 1994. TreeBASE: a prototype database of phylogenetic analyses and an interactive
+ tool for browsing the phylogeny of life.
+ <em>American Journal of Botany</em>, <strong>81</strong>(6): 183.
+ </p>
+ <p>
+ <strong>Shan, H., K. G. Herbert, W. H. Piel, D. Shasha and J. T. L. Wang.</strong>
+ 2002. A Structure-Based Search Engine for Phylogenetic Databases.
+ <em>Proceedings of the 14th International Conference on Scientific and Statistical
+ Database Management (SSDBM 2002),</em> Edinburgh, Scotland, pp. 7-10.
+ </p>
+ <p>
+ <strong>Swofford, D. L.</strong>
+ 1993.
+ <em>PAUP: Phylogenetic Analysis Using Parsimony, Vers. 3.1.1.</em> Washington, DC: Smithsonian Institution.
+ </p>
+ <p>
+ <strong>Wang, J. T. L., H. Shan, D. Shasha, and W. H. Piel.</strong>
+ 2003. TreeRank: A Similarity Measure for Nearest Neighbor Searching in Phylogenetic Databases.
+ <em>Proceedings of the 15th International Conference on Scientific and Statistical Database Management (SSDBM 2003),</em> Cambridge, MA, pp. 171-180.
+ </p>
+ <p>
+ <strong>Wang, J. T. L., H. Shan, D. Shasha and W. H. Piel.</strong>
+ 2005. Fast Structural Search in Phylogenetic Databases
+ <em>. Evolutionary Bioinformatics Online</em>, <strong>1</strong>: 37-46.
+ </p>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp 2010-03-19 21:44:13 UTC (rev 630)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp 2010-03-20 15:51:38 UTC (rev 631)
@@ -19,7 +19,7 @@
<c:param name="id" value="${tree.study.id}" />
</c:url>
<input type="checkbox" id="s-${tree.id }" name="selection" value="${tree.id }" />
- <a href="${url}">Tr${tree.id }</a>
+ <a href="${url}" target="_blank">Tr${tree.id }</a>
</display:column>
@@ -85,7 +85,7 @@
<c:param name="treeid" value="${tree.id}" />
<c:param name="id" value="${tree.study.id}" />
</c:url>
- <a href="${url}">
+ <a href="${url}" target="_blank">
<img
class="iconButton"
src="<fmt:message key="icons.list"/>"
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp 2010-03-19 21:44:13 UTC (rev 630)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp 2010-03-20 15:51:38 UTC (rev 631)
@@ -64,89 +64,5 @@
be mapped to a classification tree in the next release.
</li>
</ol>
- <h2>Reference</h2>
- <p>
- <strong>Blake, J. A., C. J. Bult, M. J. Donoghue, J. Humphries, and C. Fields.</strong>
- 1994. Interoperability of biological databases: a meeting report.
- <em>Syst. Biol.</em> <strong>43</strong>:585-589.
- </p>
- <p>
- <strong>Donoghue, M. J.</strong>
- 1994. Progress and prospects in reconstructing plant phylogeny.
- <em>Ann. Missouri Bot. Gard.</em> <strong>81</strong>:405-418.
- </p>
- <p>
- <strong>Donoghue, M. J. and D. D. Ackerly.</strong>
- 1996. Phylogenetic uncertainties and sensitivity analyses in comparative biology.
- <em>Phil. Trans. R. Soc. London B (in press).</em>
- </p>
- <p>
- <strong>Maddison, W. P. and D. R. Maddison.</strong>
- 1992.
- <em>MacClade: Interactive Analysis of Phylogeny and Character Evolution, Vers. 3.0.</em>
- Sunderland, MA: Sinauer Assoc.
- </p>
- <p>
- <strong>Morell, V.</strong>
- 1996. TreeBASE: the roots of phylogeny.
- <em>Science</em> <strong>273</strong>: 569.
- </p>
- <p>
- <strong>Piel, W. H.</strong>
- 2003. "Phyloinformatics and Tree Networks." In:
- <strong>Wu, C. H., P. Wang, and J. T. L. Wang,</strong> eds.
- <em>Computational Biology and Genome Informatics</em>. World Scientific Press.
- </p>
- <p>
- <strong>Piel, W. H., M. J. Donoghue, and M. J. Sanderson.</strong>
- 2002. "TreeBASE: a database of phylogenetic knowledge." Pp. 41-47. In:
- <strong>Shimura, J., K. L. Wilson, and D. Gordon,</strong> eds.
- <em>To the interoperable "Catalog of Life" with partners Species 2000 Asia Oceanea.</em>
- Research Report from the National Institute for Environmental Studies No. 171, Tsukuba, Japan.
- </p>
- <p>
- <strong>Piel, W. H., M. J. Sanderson, and M. J. Donoghue.</strong>
- 2003. The Small-World Dynamics of Tree Networks and Data Mining in Phyloinformatics.
- <em>Bioinformatics</em>, <strong>19</strong>(9): 1162-1168.
- </p>
- <p>
- <strong>Sanderson, M. J., B. G. Baldwin, G. Bharathan, C. S. Campbell, D. Ferguson,
- J. M. Porter, C. Von Dohlen, M. F. Wojciechowski & M. J. Donoghue.
- </strong> 1993. The growth of phylogenetic information and the need for a phylogenetic database.
- <em>Syst. Biol.</em> <strong>42</strong>:562-568.
- </p>
- <p>
- <strong>Sanderson, M. J. and M. J. Donoghue.</strong>
- 1996. The relationship between homoplasy and confidence in a phylogenetic tree. In:
- <em>Homoplasy and the Evolutionary Process</em> (<strong>M. Sanderson and L. Hufford</strong>, eds.).
- San Diego: Academic Press.
- </p>
- <p>
- <strong>Sanderson, M. J., M. J. Donoghue, W. Piel, and T. Eriksson.</strong>
- 1994. TreeBASE: a prototype database of phylogenetic analyses and an interactive
- tool for browsing the phylogeny of life.
- <em>American Journal of Botany</em>, <strong>81</strong>(6): 183.
- </p>
- <p>
- <strong>Shan, H., K. G. Herbert, W. H. Piel, D. Shasha and J. T. L. Wang.</strong>
- 2002. A Structure-Based Search Engine for Phylogenetic Databases.
- <em>Proceedings of the 14th International Conference on Scientific and Statistical
- Database Management (SSDBM 2002),</em> Edinburgh, Scotland, pp. 7-10.
- </p>
- <p>
- <strong>Swofford, D. L.</strong>
- 1993.
- <em>PAUP: Phylogenetic Analysis Using Parsimony, Vers. 3.1.1.</em> Washington, DC: Smithsonian Institution.
- </p>
- <p>
- <strong>Wang, J. T. L., H. Shan, D. Shasha, and W. H. Piel.</strong>
- 2003. TreeRank: A Similarity Measure for Nearest Neighbor Searching in Phylogenetic Databases.
- <em>Proceedings of the 15th International Conference on Scientific and Statistical Database Management (SSDBM 2003),</em> Cambridge, MA, pp. 171-180.
- </p>
- <p>
- <strong>Wang, J. T. L., H. Shan, D. Shasha and W. H. Piel.</strong>
- 2005. Fast Structural Search in Phylogenetic Databases.
- <em>Evolutionary Bioinformatics Online</em>, <strong>1</strong>: 37-46.
- </p>
</div>
</div>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp 2010-03-19 21:44:13 UTC (rev 630)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp 2010-03-20 15:51:38 UTC (rev 631)
@@ -1,122 +1,115 @@
<div id="contentRight">
<div class="gutter">
<h1>Data Access</h1>
- <h2>URL API</h2>
- <p>
- The TreeBASE2 website provides users with simple ways to navigate the underlying data
- programmatically. This page describes the stateless web service interface and URL architecture
- that can be used to search the web site and obtain data in a variety of formats with rich semantics.
- </p>
- <h3>PhyloWS support</h3>
- <p>
- The site structure described here is designed to be compliant with the emerging
- <a href="http://evoinfo.nescent.org/PhyloWS">PhyloWS</a> standard. One of the tenets of the
- standard is that URLs contain a <strong>/phylows/</strong> delimiter below which the standard
- recommends a <a href="https://www.nescent.org/wg_evoinfo/PhyloWS/REST">simple API</a> to derefence
- phylogenetic data by their accession numbers. In the examples below, the url fragments come
- immediately below the <strong>/phylows/</strong> delimiter (everything between the
- <strong>http://</strong> and <strong>phylows</strong> is considered
- subject to change, likely to be stabilized using <a href="http://purl.org">purl</a> addresses).
- </p>
- <h3>Site sections</h3>
- <p>The data on the TreeBASE2 website are organized in four subsections:</p>
- <ul>
- <li><strong>taxon/</strong> <em>operational taxonomic units, taxonomic mappings and outlinks</em></li>
- <li><strong>matrix/</strong> <em>character state matrices, morphological character definitions</em></li>
- <li><strong>tree/</strong> <em>contains trees and tree nodes</em></li>
- <li><strong>study/</strong> <em>full submission records, including citation and analysis records</em></li>
- </ul>
- <p>
- Within those four sections, every item in the TreeBASE2 database can be de-referenced by appending
- the item's full identifier to the right section name. For example, <strong>tree/TB2:Tr2227</strong>
- represents a tree (and returns a simple RDF file to describe the tree). For some classes of objects,
- these short addresses can be passed a <strong>format</strong>
- parameter to specify in which data format to represent the object:
- <a href="/treebase-web/phylows/study/TB2:S1787?format=html">study/TB2:S1787?format=html</a>.
- Identifiers that match any of the following expressions can be represented as <strong>nexml</strong>,
- <strong>nexus</strong>, <strong>rdf</strong> or <strong>html</strong> (i.e. in a web page):
- </p>
- <ul>
- <li><strong>matrix/TB2:M[0-9]+</strong> <em>character state matrix</em></li>
- <li><strong>tree/TB2:Tr[0-9]+</strong> <em>phylogenetic tree</em></li>
- <li><strong>study/TB2:S[0-9]+</strong> <em>study record</em></li>
- </ul>
- <h3>NeXML support</h3>
- <p>
- The <strong>nexml</strong> and the <strong>rdf</strong> download options both use output
- generated by the java support libraries available from the
- <a href="http://nexml.org/nexml/java">nexml website</a>. The website uses the nexml annotation
- feature extensively to transmit all the metadata stored by the database. Nexml annotations
- are <a href="http://www.w3.org/TR/xhtml-rdfa-primer/">RDFa</a> compliant element structures
- that use <a href="http://www.w3.org/TR/curie/">CURIE</a> strings to identify metadata properties,
- and @content attributes to store the property value. For example, this (simplified) annotation:
- <strong>
- <meta content="uBio:2538170" property="tb:identifier.ubio"/>
- </strong>
- means that the element that encloses it has a special kind of identifier attached to it, namely
- one that TreeBASE recognizes as originating in <a href="/treebase-web/phylows/taxon/uBio:2538170">uBio</a>.
- </p>
- <p>
- The salient part is
- the CURIE string predicate <strong>tb:identifier.ubio</strong>, which is one of a
- <a href="http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw">long list</a> of
- proposed predicates that are written in TreeBASE's NeXML output and can be used as
- <a href="http://www.loc.gov/standards/sru/specs/cql.html">CQL</a> search predicates. The predicates
- proposed (and now experimentally transmitted) are intended to be subclasses of predicates
- from commonly used vocabularies. For example, <strong>tb:identifier.ubio</strong> inherits from
- <a href="http://dublincore.org/documents/dcmi-terms/#terms-identifier">dcterms:identifier</a> and
- so any of the latter's semantics apply to the former, which is refined to indicate that the
- value is a uBio namebank ID.
- </p>
- <h3>Searching</h3>
- <p>
- The TreeBASE website can be searched using a subset of constructs from the
- <a href="http://www.loc.gov/standards/sru/specs/cql.html">CQL</a> specification. Specifically,
- the predicates
- <a href="http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw">listed here with
- an asterisk</a> can be used in statements in the site section they apply to, such that, for example
- a taxon can be retrieved by its ncbi ID like so:
- </p>
- <div style="background-color:;padding:10px">
- <strong>taxon/find?query=tb.identifier.ncbi=<em><ncbi taxon id></em></strong>
- </div>
- <p>
- or by its name like so:
- </p>
- <div style="background-color:;padding:10px">
- <strong>taxon/find?query=tb.title.taxon=<em><name></em></strong>
- </div>
- <p>
- or using an exact match
- (<strong>==</strong>) or a case-insensitive one (<strong>=/ignoreCase</strong>). These statements
- can be combined with boolean <strong>and</strong>, <strong>or</strong> and <strong>not</strong>.
- For example:
- </p>
- <div style="background-color:;padding:10px">
- <strong>study/find?query=dcterms.contributor=Huelsenbeck or dcterms.contributor=Ronquist</strong>
- </div>
- <p>
- Finally, searching can be modified to project the results from one section info those of another. The
- effect is roughly the same as switching between tabs in the search section: if the results are a
- list of tree and you click on the matrix search tab, the trees are converted to the set of matrices
- on which the trees are based. This behaviour can be used by specifying the
- <strong>recordSchema=<section></strong> argument, i.e.:
- </p>
- <div style="background-color:;padding:10px">
- <strong>taxon/find?query=dcterms.title=="Homo sapiens"&recordSchema=tree</strong>
- </div>
- <p>
- returns all the trees that have <em>Homo sapiens</em> in them.
- By default, all these queries return a web page, but with a <strong>format=rss1</strong> argument
- the search results are listed in an RDF compatible RSS1.0 file, i.e.:
- </p>
- <div style="background-color:;padding:10px">
- <strong>taxon/find?query=tb.title.taxon=<em><name></em>&format=rss1</strong>
- </div>
- <p>
- The returned results in RSS1.0 use the short urls of the form <strong><section>/<id></strong>, whose
- returned resource descriptions (like <a href="/treebase-web/phylows/tree/TB2:Tr2227">
- this</a> one) need to be scanned to discover suitable serialization formats.
- </p>
+
+
+<p><b>Web Browser User Interface</b></p>
+
+<p> </p>
+
+<p><span>Primary access to the
+database is through its web interface, where users most commonly search on
+authors, citations, and taxa. Datasets are downloadable in NEXUS and NeXML
+formats for further analysis.</span></p>
+
+<p> </p>
+
+<p><span>TreeBASE can be
+accessed programmatically through a stateless web service interface and URL
+architecture.</span> This interface can deliver data in several different
+formats, including NEWICK, NEXUS, JSON, NeXML.</p>
+
+<p> </p>
+
+<p><b>Programmatic Data Access</b></p>
+
+<p>In addition to the web interface, there are several forms of
+programmatic access to the contents:</p>
+
+<ul type=disc>
+ <li>a <a href="http://evoinfo.nescent.org/PhyloWS"
+ title=PhyloWS id=fp8u>PhyloWS</a> RESTful API. A detailed description
+ of <a
+ href="https://sourceforge.net/apps/mediawiki/treebase/index.php?title=API"
+ title="TreeBASE's PhyloWS implementation" id=sb5r>TreeBASE's PhyloWS
+ implementation</a> is at the TreeBASE wiki. </li>
+ <li><a href="http://www.openarchives.org/pmh/" title=OAI-PMH
+ id=basz>OAI-PMH</a> harvesting interface, coming soon.</li>
+ <li>SQL data dumps, coming soon.</li>
+</ul>
+
+<p> </p>
+
+<p><i><u>Links to external objects</u></i></p>
+
+<p><br>
+<span>TreeBASE stores references to and provides
+outlinks to external objects including DOIs (for publications), NameBankIDs and
+NCBI taxids (for taxa), and Genbank accession numbers (for sequences). </span><br>
+<br>
+<i><u>Links to objects within TreeBASE</u></i><br>
+<br>
+TreeBASE issues persistent and resolvable uniform resource identifiers (URIs)
+to studies, matrices, trees, and nodes in trees. These allow external
+data services to link directly into TreeBASE resources. For example: </p>
+
+<p> </p>
+
+<table border=0 cellspacing=0 cellpadding=0 width=600
+ style='width:5.0in' id=ua52>
+ <tr>
+ <td width=100 style='width:60.0pt;padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p>URI to a study:</p>
+ </td>
+ <td width="50%" style='width:50.0%;padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p>http://purl.org/phylo/treebase/phylows/study/TB2:S1925</p>
+ </td>
+ </tr>
+ <tr>
+ <td width=100 style='width:60.0pt;padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p>URI to a matrix:</p>
+ </td>
+ <td width="50%" style='width:50.0%;padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p>http://purl.org/phylo/treebase/phylows/matrix/TB2:M2610</p>
+ </td>
+ </tr>
+ <tr>
+ <td width=100 style='width:60.0pt;padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p>URI to a tree:</p>
+ </td>
+ <td width="50%" style='width:50.0%;padding:1.8pt 1.8pt 1.8pt 1.8pt'>
+ <p>http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2026</p>
+ </td>
+ </tr>
+</table>
+
+<p> </p>
+
+<p><b>RSS Feeds</b></p>
+
+<p style='margin-bottom:12.0pt'><br>
+<span>When TreeBASE's API delivers a list of results
+in RDF/XML, it typically expresses this in RSS 1.0. This delivery allows
+programmatic capture of these results as well as human perusal using a RSS
+client reader or browser. For example, a user interested in a certain taxon
+could express a query as a PhyloWS URL and enter it into his or her favorite
+RSS reader. As a result, any new submissions to TreeBASE that includes this
+taxon of interest will alert the user with a new RSS article. </span></p>
+
+<p><b>Data Dumps</b></p>
+
+<p> </p>
+
+<p>In the future, users who wish to perform queries and
+analyses beyond the scope and performance of TreeBASE will be able to acquire
+entire periodic data dumps that comply<span style='background:white'> with a
+standard data model, such as BioSQL.</span></p>
+
+<p> </p>
+
+
+
+
+
</div>
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2010-03-19 21:44:13 UTC (rev 630)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2010-03-20 15:51:38 UTC (rev 631)
@@ -862,6 +862,10 @@
<prop key="/urlAPI.html">filenameController</prop>
<prop key="/people.html">filenameController</prop>
<prop key="/technology.html">filenameController</prop>
+ <prop key="/partnership.html">filenameController</prop>
+ <prop key="/reference.html">filenameController</prop>
+ <prop key="/journal.html">filenameController</prop>
+ <prop key="/contact.html">filenameController</prop>
<prop key="/user/viewXML.html">filenameController</prop>
<prop key="/test/phylowidget.html">filenameController</prop>
Modified: trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2010-03-19 21:44:13 UTC (rev 630)
+++ trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2010-03-20 15:51:38 UTC (rev 631)
@@ -10,11 +10,13 @@
<li><a href="<c:url value="/about.html"/>"><fmt:message key="nav.overview"/></a></li>
<li><a href="<c:url value="/technology.html"/>"><fmt:message key="nav.technology"/></a></li>
<li><a href="<c:url value="/people.html"/>"><fmt:message key="nav.people"/></a></li>
- <li><a href="#"><fmt:message key="nav.partnerships"/></a></li>
+ <li><a href="<c:url value="/partnership.html"/>"><fmt:message key="nav.partnerships"/></a></li>
+ <li><a href="<c:url value="/reference.html"/>"><fmt:message key="nav.references"/></a></li>
</ul>
</li>
<li><a href="<c:url value="/urlAPI.html"/>"><fmt:message key="nav.dataaccess"/></a></li>
- <li><a href="#"><fmt:message key="nav.contact"/></a></li>
+ <li><a href="<c:url value="/journal.html"/>"><fmt:message key="nav.journals"/></a></li>
+ <li><a href="<c:url value="/contact.html"/>"><fmt:message key="nav.contact"/></a></li>
</ul>
</div>
</div>
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