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treebase-guts
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From: <yo...@us...> - 2010-03-05 20:09:14
|
Revision: 528
http://treebase.svn.sourceforge.net/treebase/?rev=528&view=rev
Author: youjun
Date: 2010-03-05 20:09:08 +0000 (Fri, 05 Mar 2010)
Log Message:
-----------
add Help link; update content
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/rowSegmentDataTable.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/uploadRowSegmentData.jsp
trunk/treebase-web/src/main/webapp/common/adminMenu.jsp
trunk/treebase-web/src/main/webapp/common/searchMenuRight.jsp
trunk/treebase-web/src/main/webapp/common/searchSummaryMenuRight.jsp
trunk/treebase-web/src/main/webapp/common/submissionMenu.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/rowSegmentDataTable.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/rowSegmentDataTable.jsp 2010-03-05 18:36:12 UTC (rev 527)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/rowSegmentDataTable.jsp 2010-03-05 20:09:08 UTC (rev 528)
@@ -9,8 +9,9 @@
<fieldset>
-<legend>Row segment data</legend>
-
+<legend>Row segment data
+ <a href="#" class="openHelp" onclick="openHelp('rowSegmentDataTable')"><img class="iconButton" src="<fmt:message key="icons.help"/>" /></a>
+</legend>
<b style="font-size:125%"> Check if header is included in the file: </b> <input type="checkbox" name="cbox" value="Butter" checked = true><br>
<div style="overflow:auto; width:100%;">
<table border="1" class="list">
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/uploadRowSegmentData.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/uploadRowSegmentData.jsp 2010-03-05 18:36:12 UTC (rev 527)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/uploadRowSegmentData.jsp 2010-03-05 20:09:08 UTC (rev 528)
@@ -15,7 +15,9 @@
<!-- Since we are not ready for it that is why line is commented -->
<form method="post" enctype="multipart/form-data" >
<fieldset>
- <legend>Upload tab delimited file</legend>
+ <legend>Upload tab delimited file
+ <a href="#" class="openHelp" onclick="openHelp('uploadRowSegmentData')"><img class="iconButton" src="<fmt:message key="icons.help"/>" /></a>
+ </legend>
<table border="0" cellpadding="1">
<tr>
Modified: trunk/treebase-web/src/main/webapp/common/adminMenu.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/adminMenu.jsp 2010-03-05 18:36:12 UTC (rev 527)
+++ trunk/treebase-web/src/main/webapp/common/adminMenu.jsp 2010-03-05 20:09:08 UTC (rev 528)
@@ -4,7 +4,7 @@
<div id="mainMenu">
<div id="gutter">
<div id="menu">
-<a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif;"/>Tool Box</a>
+<a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif;"/> Tool Box</a>
<menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter">
<menu:displayMenu name="StudyManagementMenu"/>
<menu:displayMenu name="UserManagementMenu"/>
Modified: trunk/treebase-web/src/main/webapp/common/searchMenuRight.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/searchMenuRight.jsp 2010-03-05 18:36:12 UTC (rev 527)
+++ trunk/treebase-web/src/main/webapp/common/searchMenuRight.jsp 2010-03-05 20:09:08 UTC (rev 528)
@@ -4,7 +4,7 @@
<div id="mainMenu">
<div id="gutter">
<div id="menu">
-<a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif;"/>Tool Box</a>
+<a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif;"/> Tool Box</a>
<menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter" >
<menu:displayMenu name="Searches" />
</menu:useMenuDisplayer>
Modified: trunk/treebase-web/src/main/webapp/common/searchSummaryMenuRight.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/searchSummaryMenuRight.jsp 2010-03-05 18:36:12 UTC (rev 527)
+++ trunk/treebase-web/src/main/webapp/common/searchSummaryMenuRight.jsp 2010-03-05 20:09:08 UTC (rev 528)
@@ -4,7 +4,7 @@
<div id="mainMenu">
<div id="gutter">
<div id="menu">
-<a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif;"/>Tool Box</a>
+<a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif;"/> Tool Box</a>
<menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter">
<menu:displayMenu name="SubmissionInfo"/>
<menu:displayMenu name="Citation"/>
Modified: trunk/treebase-web/src/main/webapp/common/submissionMenu.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/submissionMenu.jsp 2010-03-05 18:36:12 UTC (rev 527)
+++ trunk/treebase-web/src/main/webapp/common/submissionMenu.jsp 2010-03-05 20:09:08 UTC (rev 528)
@@ -4,7 +4,7 @@
<div id="mainMenu">
<div id="gutter">
<div id="menu">
-<a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif;"/>Tool Box</a>
+<a onclick="switchMenu();" style="cursor: pointer;"><img id="tb" src="../images/minus.gif;"/> Tool Box</a>
<menu:useMenuDisplayer name="ListMenu" permissions="rolesAdapter">
<menu:displayMenu name="SubmissionHome"/>
<menu:displayMenu name="SubmissionNotes"/>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-03-11 16:45:06
|
Revision: 545
http://treebase.svn.sourceforge.net/treebase/?rev=545&view=rev
Author: rvos
Date: 2010-03-11 16:44:59 +0000 (Thu, 11 Mar 2010)
Log Message:
-----------
Adding people page as per http://docs.google.com/Doc?docid=0AXEQpupFgwYiZGg4bXF6bl82NmZwdm50cmRz&hl=en
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml
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/styles/styles.css
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml 2010-03-11 16:44:23 UTC (rev 544)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml 2010-03-11 16:44:59 UTC (rev 545)
@@ -9,6 +9,7 @@
<pattern>/home.html</pattern>
<pattern>/about.html</pattern>
<pattern>/urlAPI.html</pattern>
+ <pattern>/people.html</pattern>
</decorator>
<!-- decoration page for search pages -->
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2010-03-11 16:44:23 UTC (rev 544)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2010-03-11 16:44:59 UTC (rev 545)
@@ -858,6 +858,8 @@
<prop key="/home.html">filenameController</prop>
<prop key="/login.html">filenameController</prop>
<prop key="/urlAPI.html">filenameController</prop>
+ <prop key="/people.html">filenameController</prop>
+
<prop key="/user/viewXML.html">filenameController</prop>
<prop key="/test/phylowidget.html">filenameController</prop>
<prop key="/test/newPhylowidget.html">filenameController</prop>
Modified: trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2010-03-11 16:44:23 UTC (rev 544)
+++ trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2010-03-11 16:44:59 UTC (rev 545)
@@ -9,7 +9,7 @@
<ul id="innerNavlist">
<li><a href="<c:url value="/about.html"/>"><fmt:message key="nav.overview"/></a></li>
<li><a href="#"><fmt:message key="nav.technology"/></a></li>
- <li><a href="#"><fmt:message key="nav.people"/></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>
</ul>
</li>
Modified: trunk/treebase-web/src/main/webapp/styles/styles.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/styles.css 2010-03-11 16:44:23 UTC (rev 544)
+++ trunk/treebase-web/src/main/webapp/styles/styles.css 2010-03-11 16:44:59 UTC (rev 545)
@@ -281,6 +281,22 @@
vertical-align: middle
}
+/* People tables
+*******************************************************************************************/
+table.peopleTable td {
+ width: 130px;
+ text-align: center;
+ vertical-align: top;
+ padding-bottom: 20px;
+ padding-top: 20px;
+}
+
+table.peopleTable img {
+ border: 1px solid silver;
+ padding: 5px;
+ background-color: white;
+}
+
/* Left Sidebar Navigation Menu
*******************************************************************************************/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-03-12 00:02:38
|
Revision: 547
http://treebase.svn.sourceforge.net/treebase/?rev=547&view=rev
Author: rvos
Date: 2010-03-12 00:02:30 +0000 (Fri, 12 Mar 2010)
Log Message:
-----------
BIG COMMIT: THIS CHANGES MUCH OF THE STATIC PAGE STYLES
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml
trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.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/footer.jsp
trunk/treebase-web/src/main/webapp/common/header.jsp
trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
trunk/treebase-web/src/main/webapp/styles/displaytag.css
trunk/treebase-web/src/main/webapp/styles/styles.css
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp
trunk/treebase-web/src/main/webapp/images/TreeBASE.png
trunk/treebase-web/src/main/webapp/images/architecture.jpeg
trunk/treebase-web/src/main/webapp/images/gradient.jpg
trunk/treebase-web/src/main/webapp/images/logo_bg.jpg
trunk/treebase-web/src/main/webapp/images/nescent_logo.png
trunk/treebase-web/src/main/webapp/images/people/
trunk/treebase-web/src/main/webapp/images/people/anon.jpg
trunk/treebase-web/src/main/webapp/images/people/bpiel.gif
trunk/treebase-web/src/main/webapp/images/people/hlapp.jpeg
trunk/treebase-web/src/main/webapp/images/people/krice.gif
trunk/treebase-web/src/main/webapp/images/people/mdonoghue.gif
trunk/treebase-web/src/main/webapp/images/people/mjdominus.jpeg
trunk/treebase-web/src/main/webapp/images/people/msanderson.gif
trunk/treebase-web/src/main/webapp/images/people/rvos.jpg
trunk/treebase-web/src/main/webapp/images/people/teriksson.gif
trunk/treebase-web/src/main/webapp/images/people/vtannen.jpeg
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml 2010-03-12 00:02:30 UTC (rev 547)
@@ -10,6 +10,7 @@
<pattern>/about.html</pattern>
<pattern>/urlAPI.html</pattern>
<pattern>/people.html</pattern>
+ <pattern>/technology.html</pattern>
</decorator>
<!-- decoration page for search pages -->
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp 2010-03-12 00:02:30 UTC (rev 547)
@@ -1,103 +1,105 @@
-<div class="gutter">
- <h1>Overview</h1>
- <p>
- TreeBASE is a relational database designed to manage and explore information on
- phylogenetic relationships (Sanderson et al., 1993, 1994; Piel et al., 1996;
- Morel, 1996; Piel et al., 2000). It includes phylogenetic trees and data
- matrices, together with information about the relevant publication, taxa,
- morphological and sequence-based characters, and published analyses.
- </p>
- <p>
- The database is designed to allow retrieval of trees and data from different
- studies so that existing phylogenetic results may be reassessed, compared,
- combined and reused. Applications include:
- </p>
- <ul>
- <li>
- to locate information on the phylogeny of particular groups of interest.
- </li>
- <li>
- to obtain datasets for studies of character evolution, including general
- patterns across many groups, such as patterns of homoplasy.
- </li>
- <li>
- in studies of biogeography -- to retrieve trees with representatives in
- particular geographical areas.
- </li>
- <li>
- in studies of coevolution -- to retrieve information on host and parasite
- phylogenies.
- </li>
- <li>
- in studies of congruence and combination of data -- to retrieve all molecular
- and morphological phylogenies for particular groups.
- </li>
- <li>
- in studies of phylogenetic methods -- to retrieve all parsimony or maximum
- likelihood reconstructions, for example, or to download datasets of various
- sorts to test methods.
- </li>
- <li>
- to link together trees of particular groups into more inclusive phylogenies.
- </li>
- <li>
- to discover understudied groups -- a resource for students, funding agencies,
- etc.
- </li>
- <li>
- to retrieve phylogenetic information for use in conservation biology and the
- management of natural resources.
- </li>
- </ul>
- <h2>History, Funding, and Governance</h2>
- <p>
- The prototype for TreeBASE was first launched in 1994 (Sanderson et al. 1994,
- Piel et al., 2002) with funding from NSF SGER (NSF DEB 9318325: "A prototype
- database of phylogenetic studies"). The database underwent a complete
- redevelopment and redesign with funding from the <a href="http://www.phylo.org">
- Cyberinfrastructure for Phylogenetic Research project</a> (NSF EF 0331654:
- "Building the Tree of Life -- A National Resource for Phyloinformatics and
- Computational Phylogenetics").
- </p>
- <p>
- TreeBASE was released in March 2010 as one of the main products of The
- Phyloinformatics Research Foundation, Inc., a Connecticut non-profit
- corporation. The Foundation provides direction, governance, and continuity for
- software, data sharing, and communication standards to promote phyloinformatic
- research for the scientific community.
- </p>
- <p>
- The current version of the database is 2.0 (released March 2010), and is hosted
- by the National Evolutionary Synthesis Center (<a href="http://www.nescent.org">
- NESCent</a>). In previous years the database has been hosted by the
- <a href="http://www.peabody.yale.edu/">Yale Peabody Museum</a>, the
- <a href="http://www.sdsc.edu">San Diego Supercomputer Center</a>, the
- <a href="http://www.buffalo.edu">University at Buffalo</a>,
- <a href="http://www.harvard.edu">Harvard University</a>,
- <a href="http://www.leiden.edu">Leiden University</a>, and the
- <a href="http://www.ucdavid.edu">University of California, Davis</a>.
- </p>
- <h2>Related resources</h2>
- <ul>
- <li><a href="http://eol.org">Encyclopedia of Life</a>: A new project to create an
- online reference source and database for every one of the 1.8 million species that
- are named and known on this planet.</li>
- <li><a href="http://tolweb.org">Tree of Life Web Project</a>: A collaborative
- effort of biologists and nature enthusiasts from around the world. On more than
- 10,000 World Wide Web pages, the project provides information about biodiversity,
- the characteristics of different groups of organisms, and their evolutionary history</li>
- <li><a href="http://mesquiteproject.org">Mesquite</a>: Experimental, modular
- software for evolutionary biology, designed to help biologists analyze comparative
- data about organisms in a phylogenetic context.
- </li>
- </ul>
- <h2>Logo</h2>
- <p>
- The logo displayed on the TreeBASE web-application has been adapted to match the
- color style of the website. Please use the logo shown here for linking to or citing
- TreeBASE.
- <center>
- <img src="images/TreeBASE.png" alt="TreeBASE Logo" width="108" height="66" />
- </center>
- </p>
+<div id="contentRight">
+ <div class="gutter">
+ <h1>Overview</h1>
+ <p>
+ TreeBASE is a relational database designed to manage and explore information on
+ phylogenetic relationships (Sanderson et al., 1993, 1994; Piel et al., 1996;
+ Morel, 1996; Piel et al., 2000). It includes phylogenetic trees and data
+ matrices, together with information about the relevant publication, taxa,
+ morphological and sequence-based characters, and published analyses.
+ </p>
+ <p>
+ The database is designed to allow retrieval of trees and data from different
+ studies so that existing phylogenetic results may be reassessed, compared,
+ combined and reused. Applications include:
+ </p>
+ <ul>
+ <li>
+ to locate information on the phylogeny of particular groups of interest.
+ </li>
+ <li>
+ to obtain datasets for studies of character evolution, including general
+ patterns across many groups, such as patterns of homoplasy.
+ </li>
+ <li>
+ in studies of biogeography -- to retrieve trees with representatives in
+ particular geographical areas.
+ </li>
+ <li>
+ in studies of coevolution -- to retrieve information on host and parasite
+ phylogenies.
+ </li>
+ <li>
+ in studies of congruence and combination of data -- to retrieve all molecular
+ and morphological phylogenies for particular groups.
+ </li>
+ <li>
+ in studies of phylogenetic methods -- to retrieve all parsimony or maximum
+ likelihood reconstructions, for example, or to download datasets of various
+ sorts to test methods.
+ </li>
+ <li>
+ to link together trees of particular groups into more inclusive phylogenies.
+ </li>
+ <li>
+ to discover understudied groups -- a resource for students, funding agencies,
+ etc.
+ </li>
+ <li>
+ to retrieve phylogenetic information for use in conservation biology and the
+ management of natural resources.
+ </li>
+ </ul>
+ <h2>History, Funding, and Governance</h2>
+ <p>
+ The prototype for TreeBASE was first launched in 1994 (Sanderson et al. 1994,
+ Piel et al., 2002) with funding from NSF SGER (NSF DEB 9318325: "A prototype
+ database of phylogenetic studies"). The database underwent a complete
+ redevelopment and redesign with funding from the <a href="http://www.phylo.org">
+ Cyberinfrastructure for Phylogenetic Research project</a> (NSF EF 0331654:
+ "Building the Tree of Life -- A National Resource for Phyloinformatics and
+ Computational Phylogenetics").
+ </p>
+ <p>
+ TreeBASE was released in March 2010 as one of the main products of The
+ Phyloinformatics Research Foundation, Inc., a Connecticut non-profit
+ corporation. The Foundation provides direction, governance, and continuity for
+ software, data sharing, and communication standards to promote phyloinformatic
+ research for the scientific community.
+ </p>
+ <p>
+ The current version of the database is 2.0 (released March 2010), and is hosted
+ by the National Evolutionary Synthesis Center (<a href="http://www.nescent.org">
+ NESCent</a>). In previous years the database has been hosted by the
+ <a href="http://www.peabody.yale.edu/">Yale Peabody Museum</a>, the
+ <a href="http://www.sdsc.edu">San Diego Supercomputer Center</a>, the
+ <a href="http://www.buffalo.edu">University at Buffalo</a>,
+ <a href="http://www.harvard.edu">Harvard University</a>,
+ <a href="http://www.leiden.edu">Leiden University</a>, and the
+ <a href="http://www.ucdavid.edu">University of California, Davis</a>.
+ </p>
+ <h2>Related resources</h2>
+ <ul>
+ <li><a href="http://eol.org">Encyclopedia of Life</a>: A new project to create an
+ online reference source and database for every one of the 1.8 million species that
+ are named and known on this planet.</li>
+ <li><a href="http://tolweb.org">Tree of Life Web Project</a>: A collaborative
+ effort of biologists and nature enthusiasts from around the world. On more than
+ 10,000 World Wide Web pages, the project provides information about biodiversity,
+ the characteristics of different groups of organisms, and their evolutionary history</li>
+ <li><a href="http://mesquiteproject.org">Mesquite</a>: Experimental, modular
+ software for evolutionary biology, designed to help biologists analyze comparative
+ data about organisms in a phylogenetic context.
+ </li>
+ </ul>
+ <h2>Logo</h2>
+ <p>
+ The logo displayed on the TreeBASE web-application has been adapted to match the
+ color style of the website. Please use the logo shown here for linking to or citing
+ TreeBASE.
+ <center>
+ <img src="images/TreeBASE.png" alt="TreeBASE Logo" width="108" height="66" />
+ </center>
+ </p>
+ </div>
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-12 00:02:30 UTC (rev 547)
@@ -1,33 +1,36 @@
-<div class="gutter">
-<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>
+<div id="contentRight">
+ <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>
+ </div>
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp 2010-03-12 00:02:30 UTC (rev 547)
@@ -1,115 +1,118 @@
-<div class="gutter">
- <table class="peopleTable">
- <thead><tr><th colspan="6"><h2>Current contributors</h2></th></tr></thead>
- <tr>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Vladimir Gapeyev"/>
- <br/><strong>Vladimir Gapeyev</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Youjun Guo"/>
- <br/><strong>Youjun Guo</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/hlapp.jpeg" width="81" height="108" alt="Hilmar Lapp"/>
- <br/><strong>Hilmar Lapp</strong>
- <br/>Deployment Manager
- </td>
- <td>
- <img src="images/people/bpiel.gif" width="81" height="108" alt="William Piel"/>
- <br/><strong>William Piel</strong>
- <br/>Data Editor
- <br />Prototype Developer
- </td>
- <td>
- <img src="images/people/vtannen.jpeg" width="81" height="108" alt="Val Tannen"/>
- <br/><strong>Val Tannen</strong>
- <br/>Development Leader
- </td>
- <td>
- <img src="images/people/rvos.jpg" width="81" height="108" alt="Rutger Vos"/>
- <br/><strong>Rutger Vos</strong>
- <br/>Developer
- <br/>API Design
- </td>
- </tr>
- </table>
-
- <table class="peopleTable">
- <thead><tr><th colspan="6"><h2>Past contributors</h2></th></tr></thead>
- <tr>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Lucie Chan"/>
- <br/><strong>Lucie Chan</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Shirley Cohen"/>
- <br/><strong>Shirley Cohen</strong>
- <br/>Student Researcher
- </td>
- <td>
- <img src="images/people/mjdominus.jpeg" width="81" height="108" alt="Mark J. Dominus"/>
- <br/><strong>Mark J. Dominus</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/mdonoghue.gif" width="81" height="108" alt="Michael Donoghue"/>
- <br/><strong>Michael Donoghue</strong>
- <br/>Conceptual Issues
- </td>
- <td>
- <img src="images/people/teriksson.gif" width="81" height="108" alt="Torsten Eriksson"/>
- <br/><strong>Torsten Eriksson</strong>
- <br/>Prototype Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Madhusudan Gujral"/>
- <br/><strong>Madhusudan Gujral</strong>
- <br/>Developer
- </td>
- </tr>
- <tr>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Chris Henze"/>
- <br/><strong>Chris Henze</strong>
- <br/>Prototype Developer
- </td>
- <td>
- <img src="images/people/krice.gif" width="81" height="108" alt="Ken Rice"/>
- <br/><strong>Ken Rice</strong>
- <br/>Prototype Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Jin Ruan"/>
- <br/><strong>Jin Ruan</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/msanderson.gif" width="81" height="108" alt="Mike Sanderson"/>
- <br/><strong>Mike Sanderson</strong>
- <br/>Conceptual Issues
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Can van Tran"/>
- <br/><strong>Can van Tran</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Tracy Zhao"/>
- <br/><strong>Tracy Zhao</strong>
- <br/>Developer
- </td>
- </tr>
- </table>
-
- <h2>Phyloinformatics Research Foundation Inc, Board</h2>
- <ul>
- <li>Michael Donoghue</li>
- <li>David Maddison</li>
- <li>William Piel</li>
- <li>Val Tannen</li>
- </ul>
+<div id="contentRight">
+ <div class="gutter">
+ <h1>People</h1>
+ <table class="peopleTable">
+ <thead><tr><th colspan="6"><h2>Current contributors</h2></th></tr></thead>
+ <tr>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Vladimir Gapeyev"/>
+ <br/><strong>Vladimir Gapeyev</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Youjun Guo"/>
+ <br/><strong>Youjun Guo</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/hlapp.jpeg" width="81" height="108" alt="Hilmar Lapp"/>
+ <br/><strong>Hilmar Lapp</strong>
+ <br/>Deployment Manager
+ </td>
+ <td>
+ <img src="images/people/bpiel.gif" width="81" height="108" alt="William Piel"/>
+ <br/><strong>William Piel</strong>
+ <br/>Data Editor
+ <br />Prototype Developer
+ </td>
+ <td>
+ <img src="images/people/vtannen.jpeg" width="81" height="108" alt="Val Tannen"/>
+ <br/><strong>Val Tannen</strong>
+ <br/>Development Leader
+ </td>
+ <td>
+ <img src="images/people/rvos.jpg" width="81" height="108" alt="Rutger Vos"/>
+ <br/><strong>Rutger Vos</strong>
+ <br/>Developer
+ <br/>API Design
+ </td>
+ </tr>
+ </table>
+
+ <table class="peopleTable">
+ <thead><tr><th colspan="6"><h2>Past contributors</h2></th></tr></thead>
+ <tr>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Lucie Chan"/>
+ <br/><strong>Lucie Chan</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Shirley Cohen"/>
+ <br/><strong>Shirley Cohen</strong>
+ <br/>Student Researcher
+ </td>
+ <td>
+ <img src="images/people/mjdominus.jpeg" width="81" height="108" alt="Mark J. Dominus"/>
+ <br/><strong>Mark J. Dominus</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/mdonoghue.gif" width="81" height="108" alt="Michael Donoghue"/>
+ <br/><strong>Michael Donoghue</strong>
+ <br/>Conceptual Issues
+ </td>
+ <td>
+ <img src="images/people/teriksson.gif" width="81" height="108" alt="Torsten Eriksson"/>
+ <br/><strong>Torsten Eriksson</strong>
+ <br/>Prototype Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Madhusudan Gujral"/>
+ <br/><strong>Madhusudan Gujral</strong>
+ <br/>Developer
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Chris Henze"/>
+ <br/><strong>Chris Henze</strong>
+ <br/>Prototype Developer
+ </td>
+ <td>
+ <img src="images/people/krice.gif" width="81" height="108" alt="Ken Rice"/>
+ <br/><strong>Ken Rice</strong>
+ <br/>Prototype Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Jin Ruan"/>
+ <br/><strong>Jin Ruan</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/msanderson.gif" width="81" height="108" alt="Mike Sanderson"/>
+ <br/><strong>Mike Sanderson</strong>
+ <br/>Conceptual Issues
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Can van Tran"/>
+ <br/><strong>Can van Tran</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Tracy Zhao"/>
+ <br/><strong>Tracy Zhao</strong>
+ <br/>Developer
+ </td>
+ </tr>
+ </table>
+
+ <h2>Phyloinformatics Research Foundation Inc, Board</h2>
+ <ul>
+ <li>Michael Donoghue</li>
+ <li>David Maddison</li>
+ <li>William Piel</li>
+ <li>Val Tannen</li>
+ </ul>
+ </div>
</div>
\ No newline at end of file
Added: trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp 2010-03-12 00:02:30 UTC (rev 547)
@@ -0,0 +1,152 @@
+<div id="contentRight">
+ <div class="gutter">
+ <h1>Technology</h1>
+ <h2>Data Content</h2>
+ <p>
+ The primary data objects in TreeBASE are bibliographic references to published
+ phylogenetic studies, taxon by character data matrices, and phylogenetic trees
+ resulting from the analysis of such data matrices. Information is also
+ available that links data matrices and trees, including types of analyses
+ performed, software used, etc. Wherever possible, taxon labels are mapped to
+ uBio's name services and NCBI's taxonomy.
+ </p>
+ <h2>Implementation Technologies</h2>
+ <ul>
+ <li>Database: <a href="http://www.postgresql.org/">PostgreSQL 8.3</a></li>
+ <li>Programming language: Java (web-application), Perl (data migration and
+ maintenance)</li>
+ <li>Database ORM: <a href="http://www.hibernate.org/">Hibernate</a></li>
+ <li>Web-application framework: <a href="http://www.springsource.org/">
+ Spring</a></li>
+ <li>Submission file parsing: <a href="http://mesquiteproject.org/">
+ Mesquite</a></li>
+ <li>Tree Visualization: <a href="http://www.phylowidget.org/">
+ PhyloWidget</a></li>
+ </ul>
+ <h2>Source Code</h2>
+ <p>
+ Development of <a href="https://sourceforge.net/projects/treebase/">TreeBASE
+ is hosted at SourceForge</a>. All source code can be downloaded from the
+ <a href="https://sourceforge.net/projects/treebase/develop">TreeBASE
+ subversion repository</a> at SourceForge under a BSD license.
+ Documentation on installing and running TreeBASE can be
+ found at the <a href="https://sourceforge.net/apps/mediawiki/treebase/index.php?title=Main_Page">
+ TreeBASE wiki</a>.
+ </p>
+ <h2>Architecture</h2>
+ <p>
+ TreeBASE has a tiered Java-based architecture using the Hibernate and Spring
+ frameworks built on a PostgreSQL database. The following schematic illustrates
+ the content and features of this software stack:
+ </p>
+ <img src="images/architecture.jpeg"/>
+ <ol>
+ <li>
+ TreeBASE stores alignments, character matrices, and trees used for research
+ that is published in peer-reviewed journals and books.
+ </li>
+ <li>
+ Each study has one or more analyses; each analysis has one or more steps;
+ each step associates matrices and trees with algorithms and software.
+ </li>
+ <li>
+ Each row of sequence alignments or coded characters has a taxon label that
+ maps to leaf nodes on associated trees. Trees are hashed to allow topological
+ querying.
+ </li>
+ <li>
+ Each row in a character matrix can be subdivided into one or more row segments;
+ each row segment can have associated specimen, tissue, or gene sequence metadata.
+ </li>
+ <li>
+ Names in the rows of a matrix and in row segment metadata can independently
+ map to a dictionary of name variants, which maps to a taxonomy. This taxonomy will
+ 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>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp 2010-03-12 00:02:30 UTC (rev 547)
@@ -1,109 +1,122 @@
-<div class="gutter">
-<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:
- <div style="background-color:;padding:10px">
- <strong>taxon/find?query=tb.identifier.ncbi=<em><ncbi taxon id></em></strong>
+<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>
</div>
- or by its name like so:
- <div style="background-color:;padding:10px">
- <strong>taxon/find?query=tb.title.taxon=<em><name></em></strong>
- </div>
- 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:
- <div style="background-color:;padding:10px">
- <strong>study/find?query=dcterms.contributor=Huelsenbeck or dcterms.contributor=Ronquist</strong>
- </div>
- 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.:
- <div style="background-color:;padding:10px">
- <strong>taxon/find?query=dcterms.title=="Homo sapiens"&recordSchema=tree</strong>
- </div>
- 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.:
- <div style="background-color:;padding:10px">
- <strong>taxon/find?query=tb.title.taxon=<em><name></em>&format=rss1</strong>
- </div>
- 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>
</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 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2010-03-12 00:02:30 UTC (rev 547)
@@ -859,6 +859,7 @@
<prop key="/login.html">filenameController</prop>
<prop key="/urlAPI.html">filenameController</prop>
<prop key="/people.html">filenameController</prop>
+ <prop key="/technology.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/footer.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/footer.jsp 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/common/footer.jsp 2010-03-12 00:02:30 UTC (rev 547)
@@ -1,8 +1,30 @@
<%@ include file="/common/taglibs.jsp" %>
-<p style="text-align:center"><!-- Revision <%= org.cipres.treebase.Version.VCSID %> -->
-<br />
- <a href="http://validator.w3.org/check?uri=referer"><img src="<fmt:message key="icons.xhtml" />" alt="XHTML" title="Validate page markup" class="iconButton" style="vertical-align:middle"/></a>
- <a href="http://jigsaw.w3.org/css-validator/check/referer"><img src="<fmt:message key="icons.css"/>" alt="CSS" title="Validate page styles" class="iconButton" style="vertical-align:middle"/></a><br />
- <a href="http://www.nescent.org/"><img src="<c:url value="/images/nescent_logo.gif"/>" alt="NESCent" width="101" height="83" border="0" /></a>
-</p>
\ No newline at end of file
+<p class="footerLogo"><!-- Revision <%= org.cipres.treebase.Version.VCSID %> -->
+ <a href="http://www.nescent.org/">
+ <img
+ src="<c:url value="/images/nescent_logo.png"/>"
+ alt="NESCent"
+ width="83"
+ height="83"
+ border="0" />
+ </a>
+</p>
+<p style="text-align:center">
+ <a href="http://validator.w3.org/check?uri=referer">
+ <img
+ src="<fmt:message key="icons.xhtml" />"
+ alt="XHTML"
+ title="Validate page markup"
+ class="iconButton"
+ style="vertical-align:middle"/>
+ </a>
+ <a href="http://jigsaw.w3.org/css-validator/check/referer">
+ <img
+ src="<fmt:message key="icons.css"/>"
+ alt="CSS"
+ title="Validate page styles"
+ class="iconButton"
+ style="vertical-align:middle"/>
+ </a>
+</p>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/common/header.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/header.jsp 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/common/header.jsp 2010-03-12 00:02:30 UTC (rev 547)
@@ -1,4 +1,8 @@
<%@ include file="/common/taglibs.jsp"%>
-<h1><a href="<c:url value="/home.html"/>"><img src="<c:url value="/images/logo.gif"/>" alt="TreeBase Logo" width="523" height="112" border="0" /></a></h1>
-
+<h1>
+ <a href="<c:url value="/home.html"/>">
+ <img src="<c:url value="/images/logo.gif"/>" alt="TreeBase Logo" width="523" height="112" border="0" />
+ </a>
+</h1>
+<img src="images/gradient.jpg" style="width:100%;height:10px"/>
Modified: trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2010-03-12 00:02:30 UTC (rev 547)
@@ -1,20 +1,22 @@
<%@ include file="/common/taglibs.jsp"%>
-
-<div class="gutter">
- <div id="navcontainer">
- <ul id="navlist">
- <li><a href="<c:url value="/search/studySearch.html"/>"><fmt:message key="nav.search.treebase"/></a></li>
- <li><a href="<c:url value="/user/processUser.html"/>"><fmt:message key="nav.submit"/></a></li>
- <li><span style="font-weight:bold;border-bottom: 1px solid #CCC;padding:3px;display:block"><fmt:message key="nav.about"/></span>
- <ul id="innerNavlist">
- <li><a href="<c:url value="/about.html"/>"><fmt:message key="nav.overview"/></a></li>
- <li><a href="#"><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>
- </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>
- </ul>
+<div>
+ <div class="gutter" id="sidebarLeftGutter">
+ <div id="navcontainer">
+ <ul id="navlist">
+ <li><a href="<c:url value="/search/studySearch.html"/>"><fmt:message key="nav.search.treebase"/></a></li>
+ <li><a href="<c:url value="/user/processUser.html"/>"><fmt:message key="nav.submit"/></a></li>
+ <li><span class="navlistHeading"><fmt:message key="nav.about"/></span>
+ <ul id="innerNavlist">
+ <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>
+ </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>
+ </ul>
+ </div>
</div>
-</div>
+ <img src="<c:url value="images/footer_bg.gif"/>" style="width:100%"/>
+</div>
\ No newline at end of file
Added: trunk/treebase-web/src/main/webapp/images/TreeBASE.png
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/TreeBASE.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/architecture.jpeg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/architecture.jpeg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/gradient.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/gradient.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/logo_bg.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/logo_bg.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/nescent_logo.png
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/nescent_logo.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/anon.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/anon.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/bpiel.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/bpiel.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/hlapp.jpeg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/hlapp.jpeg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/krice.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/krice.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/mdonoghue.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/mdonoghue.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/mjdominus.jpeg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/mjdominus.jpeg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/msanderson.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/msanderson.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/rvos.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/rvos.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/teriksson.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/teriksson.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/vtannen.jpeg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/vtannen.jpeg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: trunk/treebase-web/src/main/webapp/styles/displaytag.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/displaytag.css 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/styles/displaytag.css 2010-03-12 00:02:30 UTC (rev 547)
@@ -15,8 +15,6 @@
width: 80%;
}
-
-
table.list {
border: 1px solid #808080;
border-collapse: collapse;
@@ -24,18 +22,18 @@
width: 100%;
background: white;
}
+
table.list td {
- padding-left: 3px;
+ padding-left: 3px
}
-
table.list th {
background-color: silver;
padding: 2px;
padding-left: 3px;
border-bottom: 1px solid black;
text-align: left;
- color: black;
+ color: black;
white-space: nowrap
}
@@ -162,4 +160,4 @@
table.detail th {
text-align: right;
padding: 0px 3px 0px 0px;
-}
+}
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/styles/styles.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/styles.css 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/styles/styles.css 2010-03-12 00:02:30 UTC (rev 547)
@@ -1,31 +1,32 @@
body {
margin: 0;
padding: 0;
- font-family: Verdana, sans-serif;
- font-size: small;
+ font-family: "Helvetica Neue", GillSans, helvetica, "lucida sans", arial, sans-serif;
+ font-size: 80%;
+ line-height: 1.5em
}
/* Link Styles
*******************************************************************************************/
-#content a:link {
+#content a:link, #contentRight a:link {
color: #003366;
text-decoration: none;
font-weight: bold
}
-#content a:visited {
+#content a:visited, #contentRight a:visited {
color: #3863a4;
text-decoration: none;
font-weight: bold
}
-#content a:hover {
+#content a:hover, #contentRight a:hover {
border-bottom: 2px solid orangered;
font-weight: bold
}
-#content a:active {
+#content a:active, #contentRight a:active {
text-decoration: underline;
font-weight: bold
}
@@ -34,44 +35,59 @@
*******************************************************************************************/
h1, h2, h3 {
- color: #003366;
+ color: #003366
}
#content h2 {
- background: #BED1E5 url(../img/off_bg.gif) repeat-x left top;
+ background: #BED1E5 url("../images/off_bg.gif") repeat-x left top;
padding: 5px !important
}
+#contentRight h1 {
+ margin: 0px;
+ padding: 15px;
+ border-top: 1px solid silver;
+ background-image: url("../images/footer_bg.gif")
+}
+
+#contentRight h2, #contentRight h3, #contentRight p {
+ padding-left: 15px !important;
+ padding-right: 15px !important;
+ padding-top: 15px !important
+}
+
+#contentRight h2 {
+ border-top: 1px solid silver
+}
+
/* Page Structure/Layout
***************************...
[truncated message content] |
|
From: <yo...@us...> - 2010-03-18 02:03:44
|
Revision: 622
http://treebase.svn.sourceforge.net/treebase/?rev=622&view=rev
Author: youjun
Date: 2010-03-18 02:03:37 +0000 (Thu, 18 Mar 2010)
Log Message:
-----------
re-build phylowidget tree.jsp will use new file name
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/tree.jsp
trunk/treebase-web/src/main/webapp/test/phylowidget/PhyloWidget.jar
trunk/treebase-web/src/main/webapp/test/phylowidget/core.jar
trunk/treebase-web/src/main/webapp/test/phylowidget/itext.jar
trunk/treebase-web/src/main/webapp/test/phylowidget/jgrapht-jdk1.5.jar
trunk/treebase-web/src/main/webapp/test/phylowidget/pdf.jar
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/tree.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/tree.jsp 2010-03-17 19:44:13 UTC (rev 621)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/tree.jsp 2010-03-18 02:03:37 UTC (rev 622)
@@ -105,7 +105,7 @@
archive="PhyloWidget.jar,core.jar,itext.jar,jgrapht-jdk1.5.jar,pdf.jar"
mayscript="true"
width="600" height="600">
-
+ <param name="menuFile" value="nondb-menus.xml" />
<param name="image" value="loading.gif" />
<param name="boxmessage" value="Loading Processing software..." />
<param name="boxbgcolor" value="#FFFFFF" />
Modified: trunk/treebase-web/src/main/webapp/test/phylowidget/PhyloWidget.jar
===================================================================
(Binary files differ)
Modified: trunk/treebase-web/src/main/webapp/test/phylowidget/core.jar
===================================================================
(Binary files differ)
Modified: trunk/treebase-web/src/main/webapp/test/phylowidget/itext.jar
===================================================================
(Binary files differ)
Modified: trunk/treebase-web/src/main/webapp/test/phylowidget/jgrapht-jdk1.5.jar
===================================================================
(Binary files differ)
Modified: trunk/treebase-web/src/main/webapp/test/phylowidget/pdf.jar
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
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>
Added: trunk/treebase-web/src/main/webapp/images/bugs_mail.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/bugs_mail.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/help_mail.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/help_mail.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/image001.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/image001.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/image002.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/image002.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/image003.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/image003.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/image004.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/image004.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/image005.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/image005.gif
___________________________________________________________________
Ad...
[truncated message content] |
|
From: <hl...@us...> - 2010-03-20 17:25:22
|
Revision: 633
http://treebase.svn.sourceforge.net/treebase/?rev=633&view=rev
Author: hlapp
Date: 2010-03-20 17:25:13 +0000 (Sat, 20 Mar 2010)
Log Message:
-----------
Remove wrong NESCent logo (don't you ever take that from the website) and
replace with the correct one.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp
Removed Paths:
-------------
trunk/treebase-web/src/main/webapp/images/partnership/image001.jpg
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp 2010-03-20 16:08:26 UTC (rev 632)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp 2010-03-20 17:25:13 UTC (rev 633)
@@ -5,7 +5,7 @@
<p class=MsoNormal> </p>
<p class=MsoNormal><img width=160 height=100
-src="images/partnership/image001.jpg" style='height:100px;width:160px'> The
+src="images/nescent_logo.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
Deleted: trunk/treebase-web/src/main/webapp/images/partnership/image001.jpg
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2012-02-14 22:09:34
|
Revision: 1068
http://treebase.svn.sourceforge.net/treebase/?rev=1068&view=rev
Author: rvos
Date: 2012-02-14 22:09:28 +0000 (Tue, 14 Feb 2012)
Log Message:
-----------
Made buttons smaller, added line break before them
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
trunk/treebase-web/src/main/webapp/images/mendeley-logo.png
trunk/treebase-web/src/main/webapp/images/twitter-logo.png
Modified: trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2012-02-14 21:57:32 UTC (rev 1067)
+++ trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2012-02-14 22:09:28 UTC (rev 1068)
@@ -20,7 +20,8 @@
<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>
+ <br />
<center>
<a href="http://www.mendeley.com/groups/734351/treebase/" title="All publications in TreeBASE on Mendeley">
<img src="<c:url value="images/mendeley-logo.png"/>" alt="All publications in TreeBASE on Mendeley" />
Modified: trunk/treebase-web/src/main/webapp/images/mendeley-logo.png
===================================================================
(Binary files differ)
Modified: trunk/treebase-web/src/main/webapp/images/twitter-logo.png
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-03-21 11:40:33
|
Revision: 641
http://treebase.svn.sourceforge.net/treebase/?rev=641&view=rev
Author: rvos
Date: 2010-03-21 11:40:26 +0000 (Sun, 21 Mar 2010)
Log Message:
-----------
Cleaned ugly HTML.
Modified 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/styles/styles.css
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp 2010-03-20 23:04:58 UTC (rev 640)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp 2010-03-21 11:40:26 UTC (rev 641)
@@ -1,39 +1,46 @@
-<div class=Section1>
+<div id="contentRight">
+ <div class="gutter">
+ <h1>Contacts</h1>
+ <h2>Help</h2>
+ <p>
+ For questions about data submission and data content, please
+ contact the TreeBASE helpdesk:
+ <a href="mailto:help@treebase.org">help@treebase.org</a>
+ </p>
-<h1>Contacts</h1>
+ <h2>Bugs</h2>
+ <p>
+ To report software bugs, browser conflicts, and ergonomic
+ inefficiencies, please email your issue report to the TreeBASE bug queue:
+ <a href="mailto:bugs@treebase.org">bugs@treebase.org</a>
+ </p>
-<h2>Help</h2>
+ <p>
+ Alternatively, you can enter a bug report directly into our
+ SourceForge online bug tracker. For that, please follow these steps:
+ </p>
+ <ol style="list-style-type:upper-roman">
+ <li>If you have a SourceForge account, log in to it and
+ proceed to (II) below. Otherwise:</li>
+
+ <ol>
+ <li>Visit <a
+ href="http://sourceforge.net/account/registration/">http://sourceforge.net/account/registration/</a>
+ and fill in the form.</li>
+
+ <li>After you confirm the account creation by email, log in at <a
+ href="http://sourceforge.net/account/login.php">http://sourceforge.net/account/login.php</a></li>
+ </ol>
+
+ <li> Visit <a
+ href="https://sourceforge.net/tracker2/?group_id=248804&atid=1126676">
+ https://sourceforge.net/tracker2/?group_id=248804&atid=1126676</a>. On this page you can browse the bug database.</li>
-<p>For questions about data submission and data content, please
-contact the TreeBASE helpdesk: <a href="mailto:help@treebase.org">help@treebase.org</a></p>
-
-<h2>Bugs</h2>
-
-<p>To report software bugs, browser conflicts, and ergonomic
-inefficiencies, please email your issue report to the TreeBASE bug queue: <a href="mailto:bugs@treebase.org">bugs@treebase.org</a></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>. 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. Click "add artifact" to submit the report.</p>
+ <li>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. Click "add artifact" to submit the report.</li>
+ </ol>
+ </div>
</div>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2010-03-20 23:04:58 UTC (rev 640)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2010-03-21 11:40:26 UTC (rev 641)
@@ -1,345 +1,326 @@
-
-
-<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 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><b>Journal Hyperlink</b></p>
- </td>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p><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>
- <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><span style='font-size:10.0pt'><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DEvolution"
- title="Find records in TreeBASE for articles published in Evolution"
- id=snnr>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DEvolution</a></span></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><span style='font-size:10.0pt'><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22"
- title="Find records in TreeBASE for articles published in Evolutionary Applications"
- id="n15_">http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22</a></span></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><span style='font-size:10.0pt'><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22"
- title="Find records in TreeBASE for articles published in Fungal Biology"
- id=z97n>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22</a></span></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><span style='font-size:10.0pt'><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22"
- title="Find records in TreeBASE for articles published in Invertebrate Systematics"
- id=zv-p>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22</a></span></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><span style='font-size:10.0pt'><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycologia"
- title="Find records in TreeBASE for articles published in Mycologia"
- id=fgv3>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycologia</a></span></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><span style='font-size:10.0pt'><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22"
- title="Find records in TreeBASE for articles published in Mycologial Progress"
- id="x_40">http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22</a></span></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><span style='font-size:10.0pt'><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22"
- title="Find records in TreeBASE for articles published in Mycologial Research"
- id=pm9.>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22</a></span></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><span style='font-size:10.0pt'><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycoscience"
- title="Find records in TreeBASE for articles published in Mycoscience"
- id=dr.h>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycoscience</a></span></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><span style='font-size:10.0pt'><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycosphere"
- title="Find records in TreeBASE for articles published in Mycosphere"
- id=hbsg>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycosphere</a></span></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22"
- title="Find records in TreeBASE for articles published in Organisms Diversity & Evolution"
- id=lcqz>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22</a></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><span style='font-size:10.0pt'><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPersoonia"
- title="Find records in TreeBASE for articles published in Persoonia"
- id=fyta>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPersoonia</a></span></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><span style='font-size:10.0pt'><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPhytopahology"
- title="Find records in TreeBASE for articles published in Phytopahology"
- id=g3p3>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPhytopahology</a></span></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><span style='font-size:10.0pt'><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22"
- title="Find records in TreeBASE for articles published in Plant Disease"
- id=yqwc>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22</a></span></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><span style='font-size:10.0pt'><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DRhodora"
- title="Find records in TreeBASE for articles published in Rhodora"
- id=pmzl>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DRhodora</a></span></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><span style='font-size:10.0pt'><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMuelleria"
- title="Find records in TreeBASE for articles published in Muelleria"
- id="psm:">http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMuelleria</a></span></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22"
- title="Find records in TreeBASE for articles published in Studies in Mycology"
- id=ockh>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22</a></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22"
- title="Find records in TreeBASE for articles published in Systematic Biology"
- id=an6v>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22</a></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22"
- title="Find records in TreeBASE for articles published in Systematic Botany"
- id=n5tf>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22</a></p>
- </td>
- </tr>
- <tr>
- <td style='padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- <p>
- <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><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22"
- title="Find records in TreeBASE for articles published in Tropical Bryology"
- id=t8hh>http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22</a></p>
- </td>
- </tr>
+<div id="contentRight">
+<div class="gutter">
+<h1>Journals</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>
+ <tr>
+ <td valign="top">
+ <p><b>Journal Hyperlink</b></p>
+ </td>
+ <td>
+ <p><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>
+ <p><a href="http://www.wiley.com/bw/journal.asp?ref=0014-3820"
+ title="Evolution"> <img class="journal"
+ src="images/journal_files/image001.gif" alt="Evolution"/> </a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DEvolution"
+ title="Find records in TreeBASE for articles published in Evolution">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DEvolution
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www3.interscience.wiley.com/journal/119423602/home">
+ <img class="journal"
+ src="images/journal_files/image002.jpg"> </a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22"
+ title="Find records in TreeBASE for articles published in Evolutionary Applications">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www.elsevier.com/wps/find/journaldescription.cws_home/720691/description#description">
+ <img class="journal"
+ src="images/journal_files/image003.jpg" /></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22"
+ title="Find records in TreeBASE for articles published in Fungal Biology">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.publish.csiro.au/nid/120.htm">
+ <img class="journal"
+ src="images/journal_files/image004.gif"
+ alt="Invertebrate Systematics" /> </a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22"
+ title="Find records in TreeBASE for articles published in Invertebrate Systematics">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.msafungi.org/"> <img class="journal" src="images/journal_files/image005.gif"
+ alt="Join MSA" /></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycologia"
+ title="Find records in TreeBASE for articles published in Mycologia">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycologia</a>
+ </p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www.springer.com/life+sciences/plant+sciences/journal/11557">
+ <img class="journal"
+ src="images/journal_files/image006.jpg" alt="Get MycPro"/> </a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22"
+ title="Find records in TreeBASE for articles published in Mycologial Progress">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22</a>
+ </p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www.elsevier.com/wps/find/journaldescription.cws_home/707043/description#description">
+ <img class="journal"
+ src="images/journal_files/image007.gif" alt="Join BMS">
+ </a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22"
+ title="Find records in TreeBASE for articles published in Mycologial Research">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www.springer.com/life+sciences/microbiology/journal/10267">
+ <img class="journal"
+ src="images/journal_files/image008.gif" alt=Mycoscience></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycoscience"
+ title="Find records in TreeBASE for articles published in Mycoscience">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycoscience</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.mycosphere.org/"><img class="journal" src="images/journal_files/image009.jpg"></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycosphere"
+ title="Find records in TreeBASE for articles published in Mycosphere">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycosphere</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www.elsevier.com/wps/find/journaldescription.cws_home/701789/description#description">
+ <img class="journal"
+ src="images/journal_files/image010.gif"
+ alt="Organisms, Diversity, and Evolution"></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22"
+ title="Find records in TreeBASE for articles published in Organisms Diversity & Evolution">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.persoonia.org/"><img class="journal" src="images/journal_files/image011.jpg"></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPersoonia"
+ title="Find records in TreeBASE for articles published in Persoonia">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPersoonia</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://apsjournals.apsnet.org/loi/phyto?cookieSet=1"
+ title=link> <img class="journal"
+ src="images/journal_files/image012.jpg" alt="Join APS"></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPhytopahology"
+ title="Find records in TreeBASE for articles published in Phytopahology">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPhytopahology</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.apsnet.org/pd/"><img class="journal" src="images/journal_files/image013.jpg"></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22"
+ title="Find records in TreeBASE for articles published in Plant Disease">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.rhodora.org/Rhodora.html"><img
+ class="journal"
+ src="images/journal_files/image014.gif" alt="Rhodora"></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DRhodora"
+ title="Find records in TreeBASE for articles published in Rhodora">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DRhodora</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www.rbg.vic.gov.au/science/information-and-resources/science-publications/muelleria">
+ <img class="journal"
+ src="images/journal_files/image015.jpg"></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMuelleria"
+ title="Find records in TreeBASE for articles published in Muelleria">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMuelleria</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.studiesinmycology.org/"><img class="journal" src="images/journal_files/image016.gif"
+ alt="Studies in Mycology"></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22"
+ title="Find records in TreeBASE for articles published in Studies in Mycology">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://systbiol.org/"><img class="journal" src="images/journal_files/image017.gif" alt="Join SSB"/>
+ </a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22"
+ title="Find records in TreeBASE for articles published in Systematic Biology">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.sysbot.org/"><img class="journal" src="images/journal_files/image018.gif"
+ alt="Join ASPT"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22"
+ title="Find records in TreeBASE for articles published in Systematic Botany">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://tropical-bryology.org/"><img class="journal" src="images/journal_files/image019.jpg"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22"
+ title="Find records in TreeBASE for articles published in Tropical Bryology">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22</a></p>
+ </td>
+ </tr>
</table>
-<p><b>Other Journals with a Significant Presence in TreeBASE</b>:
-<a
-href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%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%3D%3D%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%3D%3D%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%3D%3D%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%3D%3D%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%3D%3DCladistics"
-title=Cladistics id=vl2m>Cladistics</a>; <a
-href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Diversity%22"
-title="Fungal Diversity" id=eosa>Fungal Diversity</a>; <a
-href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%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%3D%3D%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%3D%3D%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%3D%3D%22Molecular+Ecology%22"
-title="Molecular Ecology" id="pxv_">Molecular Ecology</a>; <a
-href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%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%3D%3D%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%3D%3D%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
+<p><b>Other Journals with a Significant Presence in TreeBASE</b>: <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%2American+Journal+of+Botany%22"
+ title="American Journal of Botany">American Journal of Botany</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Annals+of+the+Missouri+Botanical+Garden%22"
+ title="Annals of the Missouri Botanical Garden">Annals of the
+Missouri Botanical Garden</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Biological+Journal+of+the+Linnean+Society%22"
+ title="Biological Journal of the Linnean Society">Biological
+Journal of the Linnean Society</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22BMC+Evolutionary+Biology%22"
+ title="BMC Evolutionary Biology">BMC Evolutionary Biology</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Canadian+Journal+of+Botany%22"
+ title="Canadian Journal of Botany">Canadian Journal of Botany</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DCladistics"
+ title="Cladistics">Cladistics</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Diversity%22"
+ title="Fungal Diversity">Fungal Diversity</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22International+Journal+of+Plant+Sciences%22"
+ title="International Journal of Plant Sciences">International
+Journal of Plant Sciences</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Journal+of+Phycology%22"
+ title="Journal of Phycology">Journal of Phycology</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Molecular+Biology+and+Evolution%22"
+ title="Molecular Biology and Evolution">Molecular Biology and
+Evolution</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Molecular+Ecology%22"
+ title="Molecular Ecology">Molecular Ecology</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Molecular+Phylogenetics+and+Evolution%22"
+ title="Molecular Phylogenetics and Evolution">Molecular
+Phylogenetics and Evolution</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Systematics+and+Evolution%22"
+ title="Plant Systematics and Evolution">Plant Systematics and
+Evolution</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%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">
+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%3D%3D%22Proceedings+of+the+Royal+Society+B%22"
-title="Proceedings of the Royal Society B" id=nphn>Proceedings of the Royal
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Proceedings+of+the+Royal+Society+B%22"
+ title="Proceedings of the Royal Society B">Proceedings of the Royal
Society B</a>; <a
-href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DTaxon"
-title=Taxon id=vc5e>Taxon</a>; <a
-href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DZootaxa"
-title=Zootaxa id=b4cg>Zootaxa</a></p>
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DTaxon"
+ title="Taxon">Taxon</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DZootaxa"
+ title="Zootaxa">Zootaxa</a></p>
+</div>
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp 2010-03-20 23:04:58 UTC (rev 640)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp 2010-03-21 11:40:26 UTC (rev 641)
@@ -1,56 +1,59 @@
-<div class=Section1>
-
-<h1>Partnerships</h1>
-
-<p> </p>
-
-<p><img width=160 height=100
-src="images/nescent_logo.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 style='margin-bottom:12.0pt'> </p>
-
-<p><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 style='margin-bottom:12.0pt'> </p>
-
-<p><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 style='margin-bottom:12.0pt'><br>
-<br>
-</p>
-
-<p><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> </p>
-
+<div id="contentRight">
+ <div class="gutter">
+ <h1>Partnerships</h1>
+ <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
+ <img
+ width="160"
+ src="images/nescent_logo.jpg"
+ style="display:inline;float:left;margin-right:15px"/>The
+ <a
+ href="http://www.nescent.org"
+ title="National Evolutionary Synthesis Center (NESCent)">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 style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
+ <img
+ width="160"
+ height="100"
+ src="images/partnership/image002.jpg"
+ style="display:inline;float:left;margin-right:15px"/>
+ <a
+ href="http://www.datadryad.org"
+ title="Dryad">Dryad</a> is an 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."
+ </p>
+ <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
+ <img
+ width="160"
+ height="100"
+ src="images/partnership/image003.jpg"
+ style="display:inline;float:left;margin-right:15px"/>
+ TreeBASE currently makes use of <a
+ href="http://www.ubio.org/index.php?pagename=services_overview"
+ title="uBio's taxonomic name services">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">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.
+ </p>
+ <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
+ <img
+ width="160"
+ height="100"
+ src="images/partnership/image004.jpg"
+ style="display:inline;float:left;margin-right:15px"/>Many thanks to the National Science Foundation
+ for their valuable support.
+ </p>
+ </div>
</div>
-
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp 2010-03-20 23:04:58 UTC (rev 640)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp 2010-03-21 11:40:26 UTC (rev 641)
@@ -1,5 +1,6 @@
-
-<h1>References</h1>
+<div id="contentRight">
+ <div class="gutter">
+ <h1>References</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.
@@ -82,4 +83,6 @@
<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
+ </p>
+ </div>
+</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/styles/styles.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/styles.css 2010-03-20 23:04:58 UTC (rev 640)
+++ trunk/treebase-web/src/main/webapp/styles/styles.css 2010-03-21 11:40:26 UTC (rev 641)
@@ -300,6 +300,16 @@
padding-bottom: 20px
}
+/* Journal page
+*******************************************************************************************/
+
+img.journal {
+ width: 121px;
+ height: 40px;
+ border: 0;
+ align: bottom
+}
+
/* Left Sidebar Navigation Menu
*******************************************************************************************/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-03-21 12:11:13
|
Revision: 642
http://treebase.svn.sourceforge.net/treebase/?rev=642&view=rev
Author: rvos
Date: 2010-03-21 12:11:02 +0000 (Sun, 21 Mar 2010)
Log Message:
-----------
Cleaned ugly HTML.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp
trunk/treebase-web/src/main/webapp/styles/styles.css
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp 2010-03-21 11:40:26 UTC (rev 641)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp 2010-03-21 12:11:02 UTC (rev 642)
@@ -1,81 +1,67 @@
<div id="contentRight">
<div class="gutter">
<h1>Data Access</h1>
-
-<p><b>Web Browser User Interface</b></p>
-
-<p>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.</p>
-
-<p><b>Programmatic Data Access</b></p>
-
-<p>In addition to the web interface, TreeBASE can be accessed programmatically through a stateless web service interface and URL architecture. This interface can deliver data in several different formats, including NEWICK, NEXUS, JSON, NeXML.</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><i><u>Links to external objects</u></i></p>
-
-<p>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). </p>
-
-<p><i><u>Links to objects within TreeBASE</u></i></p>
-
-<p>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>
-
-<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'>
- URI to a study:
- </td>
- <td width="50%" style='width:50.0%;padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- http://purl.org/phylo/treebase/phylows/study/TB2:S1925
- </td>
- </tr>
- <tr>
- <td width=100 style='width:60.0pt;padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- URI to a matrix:
- </td>
- <td width="50%" style='width:50.0%;padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- http://purl.org/phylo/treebase/phylows/matrix/TB2:M2610
- </td>
- </tr>
- <tr>
- <td width=100 style='width:60.0pt;padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- URI to a tree:
- </td>
- <td width="50%" style='width:50.0%;padding:1.8pt 1.8pt 1.8pt 1.8pt'>
- http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2026
- </td>
- </tr>
-</table>
-
-<p><b>RSS Feeds</b></p>
-
-<p>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. </p>
-
-<p><b>Data Dumps</b></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 with a
-standard data model, such as BioSQL.</p>
-
-</div></div>
\ No newline at end of file
+ <h2>Web Browser User Interface</h2>
+ <p>
+ 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.
+ </p>
+ <h2>Programmatic Data Access</h2>
+ <p>
+ In addition to the web interface, TreeBASE can be accessed programmatically
+ through a stateless web service interface and URL architecture. This
+ interface can deliver data in several different formats, including NEWICK,
+ NEXUS, JSON, NeXML.
+ </p>
+ <ul>
+ <li>
+ a <a href="http://evoinfo.nescent.org/PhyloWS"
+ title="PhyloWS">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">TreeBASE's PhyloWS
+ implementation</a> is at the TreeBASE wiki.
+ </li>
+ <li>
+ <a href="http://www.openarchives.org/pmh/" title="OAI-PMH">OAI-PMH</a>
+ harvesting interface, coming soon.
+ </li>
+ <li>SQL data dumps, coming soon.</li>
+ </ul>
+ <h2>Links to external objects</h2>
+ <p>
+ 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).
+ </p>
+ <h2>Links to objects within TreeBASE</h2>
+ <p>
+ 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>
+ <dl>
+ <dt>URI to a study</dt>
+ <dd>http://purl.org/phylo/treebase/phylows/study/TB2:S1925</dd>
+ <dt>URI to a matrix</dt>
+ <dd>http://purl.org/phylo/treebase/phylows/matrix/TB2:M2610</dd>
+ <dt>URI to a tree</dt>
+ <dd>http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2026</dd>
+ </dl>
+ <h2>RSS Feeds</h2>
+ <p>
+ When TreeBASE's API delivers a list of results in RDF/XML, it 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.
+ </p>
+ <h2>Data Dumps</h2>
+ <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 with a standard data model, such as BioSQL.
+ </p>
+ </div>
+</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/styles/styles.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/styles.css 2010-03-21 11:40:26 UTC (rev 641)
+++ trunk/treebase-web/src/main/webapp/styles/styles.css 2010-03-21 12:11:02 UTC (rev 642)
@@ -52,12 +52,14 @@
background-image: url("../images/footer_bg.gif")
}
-#contentRight h2, #contentRight h3, #contentRight p, #content p, #content h3 {
+#contentRight h2, #contentRight h3, #contentRight p, #content p, #content h3, #contentRight dl {
padding-left: 15px !important;
padding-right: 15px !important;
padding-top: 15px !important
}
+dt { font-weight: bold }
+
#contentRight h2 {
border-top: 1px solid #3d649f
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2010-03-22 16:17:59
|
Revision: 644
http://treebase.svn.sourceforge.net/treebase/?rev=644&view=rev
Author: youjun
Date: 2010-03-22 16:17:53 +0000 (Mon, 22 Mar 2010)
Log Message:
-----------
re-sign the phylowidget.jar
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/limitedPhylowidget.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp
trunk/treebase-web/src/main/webapp/test/phylowidget/PhyloWidget.jar
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/limitedPhylowidget.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/limitedPhylowidget.jsp 2010-03-21 13:45:31 UTC (rev 643)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/limitedPhylowidget.jsp 2010-03-22 16:17:53 UTC (rev 644)
@@ -119,7 +119,7 @@
<param name="showBranchLengths" value="true"/>
<param name="useBranchLengths" value="true"/>
-->
- <param name="menuFile" value="nondb-menus.xml" />
+ <param name="menuFile" value="limited-menus.xml" />
<param name="image" value="loading.gif" />
<param name="boxmessage" value="Loading PhyloWidget software..." />
<param name="boxbgcolor" value="#FFFFFF" />
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 2010-03-21 13:45:31 UTC (rev 643)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp 2010-03-22 16:17:53 UTC (rev 644)
@@ -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="myplwidget">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}" target="_blank">
+ <a href="${url}" target="myplwidget">
<img
class="iconButton"
src="<fmt:message key="icons.list"/>"
Modified: trunk/treebase-web/src/main/webapp/test/phylowidget/PhyloWidget.jar
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-03-22 23:05:06
|
Revision: 646
http://treebase.svn.sourceforge.net/treebase/?rev=646&view=rev
Author: rvos
Date: 2010-03-22 23:04:55 +0000 (Mon, 22 Mar 2010)
Log Message:
-----------
Made more xhtml compliant
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp
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/people.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.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/common/header.jsp
trunk/treebase-web/src/main/webapp/common/search-nav.jsp
trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp 2010-03-22 19:30:21 UTC (rev 645)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp 2010-03-22 23:04:55 UTC (rev 646)
@@ -1,105 +1,103 @@
-<div id="contentRight">
- <div class="gutter">
- <h1>Overview</h1>
- <p>
- TreeBASE is a relational database designed to manage and explore information on
- phylogenetic relationships (Sanderson et al., 1993, 1994; Piel et al., 1996;
- Morel, 1996; Piel et al., 2000). It includes phylogenetic trees and data
- matrices, together with information about the relevant publication, taxa,
- morphological and sequence-based characters, and published analyses.
- </p>
- <p>
- The database is designed to allow retrieval of trees and data from different
- studies so that existing phylogenetic results may be reassessed, compared,
- combined and reused. Applications include:
- </p>
- <ul>
- <li>
- to locate information on the phylogeny of particular groups of interest.
- </li>
- <li>
- to obtain datasets for studies of character evolution, including general
- patterns across many groups, such as patterns of homoplasy.
- </li>
- <li>
- in studies of biogeography -- to retrieve trees with representatives in
- particular geographical areas.
- </li>
- <li>
- in studies of coevolution -- to retrieve information on host and parasite
- phylogenies.
- </li>
- <li>
- in studies of congruence and combination of data -- to retrieve all molecular
- and morphological phylogenies for particular groups.
- </li>
- <li>
- in studies of phylogenetic methods -- to retrieve all parsimony or maximum
- likelihood reconstructions, for example, or to download datasets of various
- sorts to test methods.
- </li>
- <li>
- to link together trees of particular groups into more inclusive phylogenies.
- </li>
- <li>
- to discover understudied groups -- a resource for students, funding agencies,
- etc.
- </li>
- <li>
- to retrieve phylogenetic information for use in conservation biology and the
- management of natural resources.
- </li>
- </ul>
- <h2>History, Funding, and Governance</h2>
- <p>
- The prototype for TreeBASE was first launched in 1994 (Sanderson et al. 1994,
- Piel et al., 2002) with funding from NSF SGER (NSF DEB 9318325: "A prototype
- database of phylogenetic studies"). The database underwent a complete
- redevelopment and redesign with funding from the <a href="http://www.phylo.org">
- Cyberinfrastructure for Phylogenetic Research project</a> (NSF EF 0331654:
- "Building the Tree of Life -- A National Resource for Phyloinformatics and
- Computational Phylogenetics").
- </p>
- <p>
- TreeBASE was released in March 2010 as one of the main products of The
- Phyloinformatics Research Foundation, Inc., a Connecticut non-profit
- corporation. The Foundation provides direction, governance, and continuity for
- software, data sharing, and communication standards to promote phyloinformatic
- research for the scientific community.
- </p>
- <p>
- The current version of the database is 2.0 (released March 2010), and is hosted
- by the National Evolutionary Synthesis Center (<a href="http://www.nescent.org">
- NESCent</a>). In previous years the database has been hosted by the
- <a href="http://www.peabody.yale.edu/">Yale Peabody Museum</a>, the
- <a href="http://www.sdsc.edu">San Diego Supercomputer Center</a>, the
- <a href="http://www.buffalo.edu">University at Buffalo</a>,
- <a href="http://www.harvard.edu">Harvard University</a>,
- <a href="http://www.leiden.edu">Leiden University</a>, and the
- <a href="http://www.ucdavid.edu">University of California, Davis</a>.
- </p>
- <h2>Related resources</h2>
- <ul>
- <li><a href="http://eol.org">Encyclopedia of Life</a>: A new project to create an
- online reference source and database for every one of the 1.8 million species that
- are named and known on this planet.</li>
- <li><a href="http://tolweb.org">Tree of Life Web Project</a>: A collaborative
- effort of biologists and nature enthusiasts from around the world. On more than
- 10,000 World Wide Web pages, the project provides information about biodiversity,
- the characteristics of different groups of organisms, and their evolutionary history</li>
- <li><a href="http://mesquiteproject.org">Mesquite</a>: Experimental, modular
- software for evolutionary biology, designed to help biologists analyze comparative
- data about organisms in a phylogenetic context.
- </li>
- </ul>
- <h2>Logo</h2>
- <p>
- The logo displayed on the TreeBASE web-application has been adapted to match the
- color style of the website. Please use the logo shown here for linking to or citing
- TreeBASE.
- <center>
- <img src="images/TreeBASE.png" alt="TreeBASE Logo" width="108" height="66" />
- </center>
- </p>
- </div>
+<div class="gutter">
+ <h1>Overview</h1>
+ <p>
+ TreeBASE is a relational database designed to manage and explore information on
+ phylogenetic relationships (Sanderson et al., 1993, 1994; Piel et al., 1996;
+ Morel, 1996; Piel et al., 2000). It includes phylogenetic trees and data
+ matrices, together with information about the relevant publication, taxa,
+ morphological and sequence-based characters, and published analyses.
+ </p>
+ <p>
+ The database is designed to allow retrieval of trees and data from different
+ studies so that existing phylogenetic results may be reassessed, compared,
+ combined and reused. Applications include:
+ </p>
+ <ul>
+ <li>
+ to locate information on the phylogeny of particular groups of interest.
+ </li>
+ <li>
+ to obtain datasets for studies of character evolution, including general
+ patterns across many groups, such as patterns of homoplasy.
+ </li>
+ <li>
+ in studies of biogeography -- to retrieve trees with representatives in
+ particular geographical areas.
+ </li>
+ <li>
+ in studies of coevolution -- to retrieve information on host and parasite
+ phylogenies.
+ </li>
+ <li>
+ in studies of congruence and combination of data -- to retrieve all molecular
+ and morphological phylogenies for particular groups.
+ </li>
+ <li>
+ in studies of phylogenetic methods -- to retrieve all parsimony or maximum
+ likelihood reconstructions, for example, or to download datasets of various
+ sorts to test methods.
+ </li>
+ <li>
+ to link together trees of particular groups into more inclusive phylogenies.
+ </li>
+ <li>
+ to discover understudied groups -- a resource for students, funding agencies,
+ etc.
+ </li>
+ <li>
+ to retrieve phylogenetic information for use in conservation biology and the
+ management of natural resources.
+ </li>
+ </ul>
+ <h2>History, Funding, and Governance</h2>
+ <p>
+ The prototype for TreeBASE was first launched in 1994 (Sanderson et al. 1994,
+ Piel et al., 2002) with funding from NSF SGER (NSF DEB 9318325: "A prototype
+ database of phylogenetic studies"). The database underwent a complete
+ redevelopment and redesign with funding from the <a href="http://www.phylo.org">
+ Cyberinfrastructure for Phylogenetic Research project</a> (NSF EF 0331654:
+ "Building the Tree of Life -- A National Resource for Phyloinformatics and
+ Computational Phylogenetics").
+ </p>
+ <p>
+ TreeBASE was released in March 2010 as one of the main products of The
+ Phyloinformatics Research Foundation, Inc., a Connecticut non-profit
+ corporation. The Foundation provides direction, governance, and continuity for
+ software, data sharing, and communication standards to promote phyloinformatic
+ research for the scientific community.
+ </p>
+ <p>
+ The current version of the database is 2.0 (released March 2010), and is hosted
+ by the National Evolutionary Synthesis Center (<a href="http://www.nescent.org">
+ NESCent</a>). In previous years the database has been hosted by the
+ <a href="http://www.peabody.yale.edu/">Yale Peabody Museum</a>, the
+ <a href="http://www.sdsc.edu">San Diego Supercomputer Center</a>, the
+ <a href="http://www.buffalo.edu">University at Buffalo</a>,
+ <a href="http://www.harvard.edu">Harvard University</a>,
+ <a href="http://www.leiden.edu">Leiden University</a>, and the
+ <a href="http://www.ucdavid.edu">University of California, Davis</a>.
+ </p>
+ <h2>Related resources</h2>
+ <ul>
+ <li><a href="http://eol.org">Encyclopedia of Life</a>: A new project to create an
+ online reference source and database for every one of the 1.8 million species that
+ are named and known on this planet.</li>
+ <li><a href="http://tolweb.org">Tree of Life Web Project</a>: A collaborative
+ effort of biologists and nature enthusiasts from around the world. On more than
+ 10,000 World Wide Web pages, the project provides information about biodiversity,
+ the characteristics of different groups of organisms, and their evolutionary history</li>
+ <li><a href="http://mesquiteproject.org">Mesquite</a>: Experimental, modular
+ software for evolutionary biology, designed to help biologists analyze comparative
+ data about organisms in a phylogenetic context.
+ </li>
+ </ul>
+ <h2>Logo</h2>
+ <p>
+ The logo displayed on the TreeBASE web-application has been adapted to match the
+ color style of the website. Please use the logo shown here for linking to or citing
+ TreeBASE.
+ </p>
+ <div style="width:100%;text-align:center">
+ <img src="images/TreeBASE.png" alt="TreeBASE Logo" width="108" height="66" />
+ </div>
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp 2010-03-22 19:30:21 UTC (rev 645)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp 2010-03-22 23:04:55 UTC (rev 646)
@@ -1,46 +1,40 @@
-<div id="contentRight">
- <div class="gutter">
- <h1>Contacts</h1>
- <h2>Help</h2>
- <p>
- For questions about data submission and data content, please
- contact the TreeBASE helpdesk:
- <a href="mailto:help@treebase.org">help@treebase.org</a>
- </p>
+<div class="gutter">
+ <h1>Contacts</h1>
+ <h2>Help</h2>
+ <p>
+ For questions about data submission and data content, please
+ contact the TreeBASE helpdesk:
+ <a href="mailto:help@treebase.org">help@treebase.org</a>
+ </p>
- <h2>Bugs</h2>
- <p>
- To report software bugs, browser conflicts, and ergonomic
- inefficiencies, please email your issue report to the TreeBASE bug queue:
- <a href="mailto:bugs@treebase.org">bugs@treebase.org</a>
- </p>
+ <h2>Bugs</h2>
+ <p>
+ To report software bugs, browser conflicts, and ergonomic
+ inefficiencies, please email your issue report to the TreeBASE bug queue:
+ <a href="mailto:bugs@treebase.org">bugs@treebase.org</a>
+ </p>
- <p>
- Alternatively, you can enter a bug report directly into our
- SourceForge online bug tracker. For that, please follow these steps:
- </p>
- <ol style="list-style-type:upper-roman">
- <li>If you have a SourceForge account, log in to it and
- proceed to (II) below. Otherwise:</li>
-
- <ol>
- <li>Visit <a
- href="http://sourceforge.net/account/registration/">http://sourceforge.net/account/registration/</a>
- and fill in the form.</li>
-
- <li>After you confirm the account creation by email, log in at <a
- href="http://sourceforge.net/account/login.php">http://sourceforge.net/account/login.php</a></li>
- </ol>
-
- <li> Visit <a
- href="https://sourceforge.net/tracker2/?group_id=248804&atid=1126676">
- https://sourceforge.net/tracker2/?group_id=248804&atid=1126676</a>. On this page you can browse the bug database.</li>
+ <p>
+ Alternatively, you can enter a bug report directly into our
+ SourceForge online bug tracker. For that, please follow these steps:
+ </p>
+ <ol style="list-style-type:upper-roman">
+ <li>If you have a SourceForge account, log in to it and
+ proceed to (II) below. Otherwise visit <a
+ href="http://sourceforge.net/account/registration/">
+ http://sourceforge.net/account/registration/</a>
+ and fill in the form. After you confirm the account creation by email, log in at <a
+ href="http://sourceforge.net/account/login.php">http://sourceforge.net/account/login.php
+ </a></li>
+
+ <li> Visit <a
+ href="https://sourceforge.net/tracker2/?group_id=248804&atid=1126676">
+ https://sourceforge.net/tracker2/?group_id=248804&atid=1126676</a>. On this page you can browse the bug database.</li>
- <li>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. Click "add artifact" to submit the report.</li>
- </ol>
- </div>
+ <li>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. Click "add artifact" to submit the report.</li>
+ </ol>
</div>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2010-03-22 19:30:21 UTC (rev 645)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2010-03-22 23:04:55 UTC (rev 646)
@@ -1,326 +1,350 @@
-<div id="contentRight">
<div class="gutter">
-<h1>Journals</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>
- <tr>
- <td valign="top">
- <p><b>Journal Hyperlink</b></p>
- </td>
- <td>
- <p><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>
- <p><a href="http://www.wiley.com/bw/journal.asp?ref=0014-3820"
- title="Evolution"> <img class="journal"
- src="images/journal_files/image001.gif" alt="Evolution"/> </a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DEvolution"
- title="Find records in TreeBASE for articles published in Evolution">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DEvolution
- </a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a
- href="http://www3.interscience.wiley.com/journal/119423602/home">
- <img class="journal"
- src="images/journal_files/image002.jpg"> </a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22"
- title="Find records in TreeBASE for articles published in Evolutionary Applications">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22
- </a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a
- href="http://www.elsevier.com/wps/find/journaldescription.cws_home/720691/description#description">
+ <h1>Journals</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>
+ <tr>
+ <td valign="top">
+ <p><b>Journal Hyperlink</b></p>
+ </td>
+ <td>
+ <p><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>
+ <p><a href="http://www.wiley.com/bw/journal.asp?ref=0014-3820"
+ title="Evolution">
+ <img class="journal"
+ src="images/journal_files/image001.gif" alt="Evolution"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DEvolution"
+ title="Find records in TreeBASE for articles published in Evolution">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DEvolution
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p>
+ <a
+ href="http://www3.interscience.wiley.com/journal/119423602/home">
+ <img class="journal"
+ src="images/journal_files/image002.jpg" alt="Evolutionary Applications"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22"
+ title="Find records in TreeBASE for articles published in Evolutionary Applications">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p>
+ <a
+ href="http://www.elsevier.com/wps/find/journaldescription.cws_home/720691/description#description">
+ <img class="journal"
+ src="images/journal_files/image003.jpg" alt="Fungal Biology"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22"
+ title="Find records in TreeBASE for articles published in Fungal Biology">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p>
+ <a href="http://www.publish.csiro.au/nid/120.htm">
+ <img class="journal"
+ src="images/journal_files/image004.gif"
+ alt="Invertebrate Systematics" />
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22"
+ title="Find records in TreeBASE for articles published in Invertebrate Systematics">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.msafungi.org/">
+ <img class="journal" src="images/journal_files/image005.gif" alt="Mycologia" /></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycologia"
+ title="Find records in TreeBASE for articles published in Mycologia">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycologia</a>
+ </p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www.springer.com/life+sciences/plant+sciences/journal/11557">
<img class="journal"
- src="images/journal_files/image003.jpg" /></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22"
- title="Find records in TreeBASE for articles published in Fungal Biology">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22
- </a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.publish.csiro.au/nid/120.htm">
- <img class="journal"
- src="images/journal_files/image004.gif"
- alt="Invertebrate Systematics" /> </a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22"
- title="Find records in TreeBASE for articles published in Invertebrate Systematics">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22
- </a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.msafungi.org/"> <img class="journal" src="images/journal_files/image005.gif"
- alt="Join MSA" /></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycologia"
- title="Find records in TreeBASE for articles published in Mycologia">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycologia</a>
- </p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a
- href="http://www.springer.com/life+sciences/plant+sciences/journal/11557">
- <img class="journal"
- src="images/journal_files/image006.jpg" alt="Get MycPro"/> </a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22"
- title="Find records in TreeBASE for articles published in Mycologial Progress">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22</a>
- </p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a
- href="http://www.elsevier.com/wps/find/journaldescription.cws_home/707043/description#description">
- <img class="journal"
- src="images/journal_files/image007.gif" alt="Join BMS">
- </a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22"
- title="Find records in TreeBASE for articles published in Mycologial Research">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a
- href="http://www.springer.com/life+sciences/microbiology/journal/10267">
- <img class="journal"
- src="images/journal_files/image008.gif" alt=Mycoscience></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycoscience"
- title="Find records in TreeBASE for articles published in Mycoscience">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycoscience</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.mycosphere.org/"><img class="journal" src="images/journal_files/image009.jpg"></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycosphere"
- title="Find records in TreeBASE for articles published in Mycosphere">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycosphere</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a
- href="http://www.elsevier.com/wps/find/journaldescription.cws_home/701789/description#description">
- <img class="journal"
- src="images/journal_files/image010.gif"
- alt="Organisms, Diversity, and Evolution"></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22"
- title="Find records in TreeBASE for articles published in Organisms Diversity & Evolution">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.persoonia.org/"><img class="journal" src="images/journal_files/image011.jpg"></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPersoonia"
- title="Find records in TreeBASE for articles published in Persoonia">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPersoonia</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://apsjournals.apsnet.org/loi/phyto?cookieSet=1"
- title=link> <img class="journal"
- src="images/journal_files/image012.jpg" alt="Join APS"></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPhytopahology"
- title="Find records in TreeBASE for articles published in Phytopahology">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPhytopahology</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.apsnet.org/pd/"><img class="journal" src="images/journal_files/image013.jpg"></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22"
- title="Find records in TreeBASE for articles published in Plant Disease">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.rhodora.org/Rhodora.html"><img
- class="journal"
- src="images/journal_files/image014.gif" alt="Rhodora"></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DRhodora"
- title="Find records in TreeBASE for articles published in Rhodora">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DRhodora</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a
- href="http://www.rbg.vic.gov.au/science/information-and-resources/science-publications/muelleria">
- <img class="journal"
- src="images/journal_files/image015.jpg"></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMuelleria"
- title="Find records in TreeBASE for articles published in Muelleria">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMuelleria</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.studiesinmycology.org/"><img class="journal" src="images/journal_files/image016.gif"
- alt="Studies in Mycology"></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22"
- title="Find records in TreeBASE for articles published in Studies in Mycology">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://systbiol.org/"><img class="journal" src="images/journal_files/image017.gif" alt="Join SSB"/>
- </a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22"
- title="Find records in TreeBASE for articles published in Systematic Biology">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://www.sysbot.org/"><img class="journal" src="images/journal_files/image018.gif"
- alt="Join ASPT"/></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22"
- title="Find records in TreeBASE for articles published in Systematic Botany">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22</a></p>
- </td>
- </tr>
- <tr>
- <td>
- <p><a href="http://tropical-bryology.org/"><img class="journal" src="images/journal_files/image019.jpg"/></a></p>
- </td>
- <td>
- <p><a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22"
- title="Find records in TreeBASE for articles published in Tropical Bryology">
- http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22</a></p>
- </td>
- </tr>
-</table>
+ src="images/journal_files/image006.jpg" alt="Mycologial Progress"/> </a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22"
+ title="Find records in TreeBASE for articles published in Mycologial Progress">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22</a>
+ </p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www.elsevier.com/wps/find/journaldescription.cws_home/707043/description#description">
+ <img class="journal"
+ src="images/journal_files/image007.gif" alt="Mycologial Research"/>
+ </a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22"
+ title="Find records in TreeBASE for articles published in Mycologial Research">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www.springer.com/life+sciences/microbiology/journal/10267">
+ <img class="journal"
+ src="images/journal_files/image008.gif" alt="Mycoscience"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycoscience"
+ title="Find records in TreeBASE for articles published in Mycoscience">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycoscience</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.mycosphere.org/">
+ <img class="journal" src="images/journal_files/image009.jpg" alt="Mycosphere"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycosphere"
+ title="Find records in TreeBASE for articles published in Mycosphere">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMycosphere</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www.elsevier.com/wps/find/journaldescription.cws_home/701789/description#description">
+ <img class="journal"
+ src="images/journal_files/image010.gif"
+ alt="Organisms, Diversity, and Evolution"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22"
+ title="Find records in TreeBASE for articles published in Organisms Diversity & Evolution">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.persoonia.org/">
+ <img class="journal" src="images/journal_files/image011.jpg" alt="Persoonia"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPersoonia"
+ title="Find records in TreeBASE for articles published in Persoonia">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPersoonia</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p>
+ <a href="http://apsjournals.apsnet.org/loi/phyto?cookieSet=1">
+ <img
+ class="journal"
+ src="images/journal_files/image012.jpg"
+ alt="Phytopahology"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPhytopahology"
+ title="Find records in TreeBASE for articles published in Phytopahology">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DPhytopahology</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.apsnet.org/pd/">
+ <img class="journal" src="images/journal_files/image013.jpg" alt="Plant Disease"/>
+ </a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22"
+ title="Find records in TreeBASE for articles published in Plant Disease">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.rhodora.org/Rhodora.html"><img
+ class="journal"
+ src="images/journal_files/image014.gif" alt="Rhodora"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DRhodora"
+ title="Find records in TreeBASE for articles published in Rhodora">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DRhodora</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
+ href="http://www.rbg.vic.gov.au/science/information-and-resources/science-publications/muelleria">
+ <img class="journal"
+ src="images/journal_files/image015.jpg" alt="Muelleria"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMuelleria"
+ title="Find records in TreeBASE for articles published in Muelleria">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DMuelleria</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.studiesinmycology.org/">
+ <img class="journal" src="images/journal_files/image016.gif"
+ alt="Studies in Mycology"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22"
+ title="Find records in TreeBASE for articles published in Studies in Mycology">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://systbiol.org/">
+ <img class="journal" src="images/journal_files/image017.gif" alt="Systematic Biology"/>
+ </a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22"
+ title="Find records in TreeBASE for articles published in Systematic Biology">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://www.sysbot.org/">
+ <img class="journal" src="images/journal_files/image018.gif"
+ alt="Systematic Botany"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22"
+ title="Find records in TreeBASE for articles published in Systematic Botany">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a href="http://tropical-bryology.org/">
+ <img class="journal" src="images/journal_files/image019.jpg" alt="Tropical Bryology"/>
+ </a></p>
+ </td>
+ <td>
+ <p><a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22"
+ title="Find records in TreeBASE for articles published in Tropical Bryology">
+ http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22</a></p>
+ </td>
+ </tr>
+ </table>
+
+ <p><b>Other Journals with a Significant Presence in TreeBASE</b>: <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%2American+Journal+of+Botany%22"
+ title="American Journal of Botany">American Journal of Botany</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Annals+of+the+Missouri+Botanical+Garden%22"
+ title="Annals of the Missouri Botanical Garden">Annals of the
+ Missouri Botanical Garden</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Biological+Journal+of+the+Linnean+Society%22"
+ title="Biological Journal of the Linnean Society">Biological
+ Journal of the Linnean Society</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22BMC+Evolutionary+Biology%22"
+ title="BMC Evolutionary Biology">BMC Evolutionary Biology</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Canadian+Journal+of+Botany%22"
+ title="Canadian Journal of Botany">Canadian Journal of Botany</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DCladistics"
+ title="Cladistics">Cladistics</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Diversity%22"
+ title="Fungal Diversity">Fungal Diversity</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22International+Journal+of+Plant+Sciences%22"
+ title="International Journal of Plant Sciences">International
+ Journal of Plant Sciences</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Journal+of+Phycology%22"
+ title="Journal of Phycology">Journal of Phycology</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Molecular+Biology+and+Evolution%22"
+ title="Molecular Biology and Evolution">Molecular Biology and
+ Evolution</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Molecular+Ecology%22"
+ title="Molecular Ecology">Molecular Ecology</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Molecular+Phylogenetics+and+Evolution%22"
+ title="Molecular Phylogenetics and Evolution">Molecular
+ Phylogenetics and Evolution</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Systematics+and+Evolution%22"
+ title="Plant Systematics and Evolution">Plant Systematics and
+ Evolution</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%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">
+ 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%3D%3D%22Proceedings+of+the+Royal+Society+B%22"
+ title="Proceedings of the Royal Society B">Proceedings of the Royal
+ Society B</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DTaxon"
+ title="Taxon">Taxon</a>; <a
+ href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DZootaxa"
+ title="Zootaxa">Zootaxa</a></p>
-<p><b>Other Journals with a Significant Presence in TreeBASE</b>: <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%2American+Journal+of+Botany%22"
- title="American Journal of Botany">American Journal of Botany</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Annals+of+the+Missouri+Botanical+Garden%22"
- title="Annals of the Missouri Botanical Garden">Annals of the
-Missouri Botanical Garden</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Biological+Journal+of+the+Linnean+Society%22"
- title="Biological Journal of the Linnean Society">Biological
-Journal of the Linnean Society</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22BMC+Evolutionary+Biology%22"
- title="BMC Evolutionary Biology">BMC Evolutionary Biology</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Canadian+Journal+of+Botany%22"
- title="Canadian Journal of Botany">Canadian Journal of Botany</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DCladistics"
- title="Cladistics">Cladistics</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Fungal+Diversity%22"
- title="Fungal Diversity">Fungal Diversity</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22International+Journal+of+Plant+Sciences%22"
- title="International Journal of Plant Sciences">International
-Journal of Plant Sciences</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Journal+of+Phycology%22"
- title="Journal of Phycology">Journal of Phycology</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Molecular+Biology+and+Evolution%22"
- title="Molecular Biology and Evolution">Molecular Biology and
-Evolution</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Molecular+Ecology%22"
- title="Molecular Ecology">Molecular Ecology</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Molecular+Phylogenetics+and+Evolution%22"
- title="Molecular Phylogenetics and Evolution">Molecular
-Phylogenetics and Evolution</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%22Plant+Systematics+and+Evolution%22"
- title="Plant Systematics and Evolution">Plant Systematics and
-Evolution</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3D%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">
-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%3D%3D%22Proceedings+of+the+Royal+Society+B%22"
- title="Proceedings of the Royal Society B">Proceedings of the Royal
-Society B</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DTaxon"
- title="Taxon">Taxon</a>; <a
- href="http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName%3D%3DZootaxa"
- title="Zootaxa">Zootaxa</a></p>
-
-</div>
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp 2010-03-22 19:30:21 UTC (rev 645)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/partnership.jsp 2010-03-22 23:04:55 UTC (rev 646)
@@ -1,59 +1,62 @@
-<div id="contentRight">
- <div class="gutter">
- <h1>Partnerships</h1>
- <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
- <img
- width="160"
- src="images/nescent_logo.jpg"
- style="display:inline;float:left;margin-right:15px"/>The
- <a
- href="http://www.nescent.org"
- title="National Evolutionary Synthesis Center (NESCent)">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 style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
- <img
- width="160"
- height="100"
- src="images/partnership/image002.jpg"
- style="display:inline;float:left;margin-right:15px"/>
- <a
- href="http://www.datadryad.org"
- title="Dryad">Dryad</a> is an 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."
- </p>
- <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
- <img
- width="160"
- height="100"
- src="images/partnership/image003.jpg"
- style="display:inline;float:left;margin-right:15px"/>
- TreeBASE currently makes use of <a
- href="http://www.ubio.org/index.php?pagename=services_overview"
- title="uBio's taxonomic name services">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">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.
- </p>
- <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
- <img
- width="160"
- height="100"
- src="images/partnership/image004.jpg"
- style="display:inline;float:left;margin-right:15px"/>Many thanks to the National Science Foundation
- for their valuable support.
- </p>
- </div>
+<div class="gutter">
+ <h1>Partnerships</h1>
+ <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
+ <img
+ width="160"
+ src="images/nescent_logo.jpg"
+ style="display:inline;float:left;margin-right:15px"
+ alt="NESCent"/>The
+ <a
+ href="http://www.nescent.org"
+ title="National Evolutionary Synthesis Center (NESCent)">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 style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
+ <img
+ width="160"
+ height="100"
+ src="images/partnership/image002.jpg"
+ style="display:inline;float:left;margin-right:15px"
+ alt="Dryad"/>
+ <a
+ href="http://www.datadryad.org"
+ title="Dryad">Dryad</a> is an 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."
+ </p>
+ <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
+ <img
+ width="160"
+ height="100"
+ src="images/partnership/image003.jpg"
+ style="display:inline;float:left;margin-right:15px"
+ alt="uBio"/>
+ TreeBASE currently makes use of <a
+ href="http://www.ubio.org/index.php?pagename=services_overview"
+ title="uBio's taxonomic name services">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">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.
+ </p>
+ <p style="clear:both;border-top: 1px solid #3d649f;padding-top:15px">
+ <img
+ width="160"
+ height="100"
+ src="images/partnership/image004.jpg"
+ style="display:inline;float:left;margin-right:15px"
+ alt="NSF"/>
+ Many thanks to the National Science
+ Foundation for their valuable support.
+ </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 2010-03-22 19:30:21 UTC (rev 645)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp 2010-03-22 23:04:55 UTC (rev 646)
@@ -1,119 +1,117 @@
-<div id="contentRight">
- <div class="gutter">
- <h1>People</h1>
- <table class="peopleTable">
- <thead><tr><th colspan="6"><h2>Current contributors</h2></th></tr></thead>
- <tr>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Vladimir Gapeyev"/>
- <br/><strong>Vladimir Gapeyev</strong>
- <br/>Deployment Maintainer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Youjun Guo"/>
- <br/><strong>Youjun Guo</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/hlapp.jpeg" width="81" height="108" alt="Hilmar Lapp"/>
- <br/><strong>Hilmar Lapp</strong>
- <br/>Deployment Manager
- </td>
- <td>
- <img src="images/people/bpiel.jpeg" width="81" height="108" alt="William Piel"/>
- <br/><strong>William Piel</strong>
- <br/>Content Editor
- <br />Prototype Dev
- </td>
- <td>
- <img src="images/people/vtannen.jpeg" width="81" height="108" alt="Val Tannen"/>
- <br/><strong>Val Tannen</strong>
- <br/>Development Leader
- </td>
- <td>
- <img src="images/people/rvos.jpg" width="81" height="108" alt="Rutger Vos"/>
- <br/><strong>Rutger Vos</strong>
- <br/>Developer
- <br/>API Design
- </td>
- </tr>
- </table>
-
- <table class="peopleTable">
- <thead><tr><th colspan="6"><h2>Past contributors</h2></th></tr></thead>
- <tr>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Lucie Chan"/>
- <br/><strong>Lucie Chan</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Shirley Cohen"/>
- <br/><strong>Shirley Cohen</strong>
- <br/>Student Researcher
- </td>
- <td>
- <img src="images/people/mjdominus.jpeg" width="81" height="108" alt="Mark J. Dominus"/>
- <br/><strong>Mark J. Dominus</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/mdonoghue.gif" width="81" height="108" alt="Michael Donoghue"/>
- <br/><strong>Michael Donoghue</strong>
- <br/>Concept
- </td>
- <td>
- <img src="images/people/teriksson.gif" width="81" height="108" alt="Torsten Eriksson"/>
- <br/><strong>Torsten Eriksson</strong>
- <br/>Prototype Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Madhusudan Gujral"/>
- <br/><strong>Madhusudan Gujral</strong>
- <br/>Developer
- </td>
- </tr>
- <tr>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Chris Henze"/>
- <br/><strong>Chris Henze</strong>
- <br/>Prototype Developer
- </td>
- <td>
- <img src="images/people/krice.gif" width="81" height="108" alt="Ken Rice"/>
- <br/><strong>Ken Rice</strong>
- <br/>Prototype Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Jin Ruan"/>
- <br/><strong>Jin Ruan</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/msanderson.gif" width="81" height="108" alt="Mike Sanderson"/>
- <br/><strong>Mike Sanderson</strong>
- <br/>Concept
- <br/>Prototype Dev
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Can van Tran"/>
- <br/><strong>Can van Tran</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Tracy Zhao"/>
- <br/><strong>Tracy Zhao</strong>
- <br/>Developer
- </td>
- </tr>
- </table>
-
- <h2>Phyloinformatics Research Foundation Inc, Board</h2>
- <ul>
- <li>Michael Donoghue</li>
- <li>David Maddison</li>
- <li>William Piel</li>
- <li>Val Tannen</li>
- </ul>
- </div>
+<div class="gutter">
+ <h1>People</h1>
+ <table class="peopleTable">
+ <thead><tr><th colspan="6"><h2>Current contributors</h2></th></tr></thead>
+ <tr>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Vladimir Gapeyev"/>
+ <br/><strong>Vladimir Gapeyev</strong>
+ <br/>Deployment Maintainer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Youjun Guo"/>
+ <br/><strong>Youjun Guo</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/hlapp.jpeg" width="81" height="108" alt="Hilmar Lapp"/>
+ <br/><strong>Hilmar Lapp</strong>
+ <br/>Deployment Manager
+ </td>
+ <td>
+ <img src="images/people/bpiel.jpeg" width="81" height="108" alt="William Piel"/>
+ <br/><strong>William Piel</strong>
+ <br/>Content Editor
+ <br />Prototype Dev
+ </td>
+ <td>
+ <img src="images/people/vtannen.jpeg" width="81" height="108" alt="Val Tannen"/>
+ <br/><strong>Val Tannen</strong>
+ <br/>Development Leader
+ </td>
+ <td>
+ <img src="images/people/rvos.jpg" width="81" height="108" alt="Rutger Vos"/>
+ <br/><strong>Rutger Vos</strong>
+ <br/>Developer
+ <br/>API Design
+ </td>
+ </tr>
+ </table>
+
+ <table class="peopleTable">
+ <thead><tr><th colspan="6"><h2>Past contributors</h2></th></tr></thead>
+ <tr>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Lucie Chan"/>
+ <br/><strong>Lucie Chan</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Shirley Cohen"/>
+ <br/><strong>Shirley Cohen</strong>
+ <br/>Student Researcher
+ </td>
+ <td>
+ <img src="images/people/mjdominus.jpeg" width="81" height="108" alt="Mark J. Dominus"/>
+ <br/><strong>Mark J. Dominus</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/mdonoghue.gif" width="81" height="108" alt="Michael Donoghue"/>
+ <br/><strong>Michael Donoghue</strong>
+ <br/>Concept
+ </td>
+ <td>
+ <img src="images/people/teriksson.gif" width="81" height="108" alt="Torsten Eriksson"/>
+ <br/><strong>Torsten Eriksson</strong>
+ <br/>Prototype Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Madhusudan Gujral"/>
+ <br/><strong>Madhusudan Gujral</strong>
+ <br/>Developer
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Chris Henze"/>
+ <br/><strong>Chris Henze</strong>
+ <br/>Prototype Developer
+ </td>
+ <td>
+ <img src="images/people/krice.gif" width="81" height="108" alt="Ken Rice"/>
+ <br/><strong>Ken Rice</strong>
+ <br/>Prototype Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Jin Ruan"/>
+ <br/><strong>Jin Ruan</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/msanderson.gif" width="81" height="108" alt="Mike Sanderson"/>
+ <br/><strong>Mike Sanderson</strong>
+ <br/>Concept
+ <br/>Prototype Dev
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Can van Tran"/>
+ <br/><strong>Can van Tran</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Tracy Zhao"/>
+ <br/><strong>Tracy Zhao</strong>
+ <br/>Developer
+ </td>
+ </tr>
+ </table>
+
+ <h2>Phyloinformatics Research Foundation Inc, Board</h2>
+ <ul>
+ <li>Michael Donoghue</li>
+ <li>David Maddison</li>
+ <li>William Piel</li>
+ <li>Val Tannen</li>
+ </ul>
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp 2010-03-22 19:30:21 UTC (rev 645)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp 2010-03-22 23:04:55 UTC (rev 646)
@@ -1,88 +1,86 @@
-<div id="contentRight">
- <div class="gutter">
- <h1>References</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. "Tree...
[truncated message content] |
|
From: <rv...@us...> - 2010-03-22 23:06:36
|
Revision: 647
http://treebase.svn.sourceforge.net/treebase/?rev=647&view=rev
Author: rvos
Date: 2010-03-22 23:06:27 +0000 (Mon, 22 Mar 2010)
Log Message:
-----------
Made more compatible with IE8, added facility where all but last analysis is collapsed, to reduce scrolling
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/analysisList.jsp
trunk/treebase-web/src/main/webapp/styles/styles.css
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/analysisList.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/analysisList.jsp 2010-03-22 23:04:55 UTC (rev 646)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/analysisList.jsp 2010-03-22 23:06:27 UTC (rev 647)
@@ -9,6 +9,9 @@
<jsp:include page="analysisList.jsp"/>
--%>
<script type="text/javascript" src="/treebase-web/scripts/user/analysisEditor.js"></script>
+<script type="text/javascript">
+ var myAnalysisIDs = new Array();
+</script>
<c:set var="analysisStepCounter" value="0" scope="request"/>
<c:set var="redirect" value="redirect:/user/analyses.html" scope="request"/>
<c:forEach var="analysisCommand" items="${studyCommand.analysisCommandList}" varStatus="status_analysis">
@@ -18,6 +21,7 @@
<h2>
<a onclick="TreeBASE.collapseExpand('analysis<c:out value="${analysisCommand.id}"/>','block',this)"
style="border:none"
+ id="analysisCollapser<c:out value="${analysisCommand.id}"/>"
title="collapse">
<img
class="iconButton"
@@ -131,7 +135,10 @@
<fieldset
style="padding-left:20px;padding-right:20px;background-color:#E5E5E5;border:none"
- id="analysis<c:out value="${analysisCommand.id}"/>">
+ id="analysis<c:out value="${analysisCommand.id}"/>">
+ <script type="text/javascript">
+ myAnalysisIDs.push('<c:out value="${analysisCommand.id}"/>');
+ </script>
<!-- EDITABLE -->
<c:if test="${editable}">
@@ -330,3 +337,15 @@
</form>
</div>
</c:if>
+
+<c:if test="${editable}">
+ <script type="text/javascript">
+ for ( var i = 0; i < ( myAnalysisIDs.length - 1 ); i++ ) {
+ TreeBASE.collapseExpand(
+ 'analysis'+myAnalysisIDs[i],
+ 'block',
+ $('analysisCollapser'+myAnalysisIDs[i])
+ );
+ }
+ </script>
+</c:if>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/styles/styles.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/styles.css 2010-03-22 23:04:55 UTC (rev 646)
+++ trunk/treebase-web/src/main/webapp/styles/styles.css 2010-03-22 23:06:27 UTC (rev 647)
@@ -22,7 +22,7 @@
}
#content a:hover, #contentRight a:hover {
- border-bottom: 2px solid orangered;
+ border-bottom: 2px solid #FF4500;
font-weight: bold
}
@@ -308,8 +308,9 @@
img.journal {
width: 121px;
height: 40px;
- border: 0;
- align: bottom
+ border: 1px solid silver;
+ margin: 5px;
+ padding: 5px
}
@@ -572,20 +573,10 @@
border: 1px solid silver
}
input.software {
- width: 100%;
- overflow: scroll
}
select.software {
width: 100%
}
.analysisStep {
background-color:white
-}
-
-/* Home page styles
-*******************************************************************************************/
-#sponsors > img {
- border: 1px solid silver;
- margin: 5px;
- padding: 5px
}
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-03-23 18:15:18
|
Revision: 652
http://treebase.svn.sourceforge.net/treebase/?rev=652&view=rev
Author: rvos
Date: 2010-03-23 18:15:11 +0000 (Tue, 23 Mar 2010)
Log Message:
-----------
IE fixes
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSimpleSearchForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsListControls.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSimpleSearchForm.jsp
trunk/treebase-web/src/main/webapp/common/header.jsp
trunk/treebase-web/src/main/webapp/common/meta.jsp
trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp
trunk/treebase-web/src/main/webapp/scripts/common.js
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/scripts/prototype/prototype-1.6.1.js
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-23 18:15:11 UTC (rev 652)
@@ -1,6 +1,6 @@
<div id="contentRight">
<div class="gutter">
- <h1>Welcome to TreeBASE</h1>
+ <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>The current release includes a host of new features and improvements over the previous TreeBASE prototype. New features include:</p>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSimpleSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSimpleSearchForm.jsp 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSimpleSearchForm.jsp 2010-03-23 18:15:11 UTC (rev 652)
@@ -2,11 +2,6 @@
<form id="searchSimple" method="post">
<fieldset>
Search: <input type="hidden" name="formName" value="matrixSimple"/>
- <script type="text/javascript">
- //<![CDATA[
- TreeBASE.register( function() { $('keyword').focus(); } );
- //]]>
- </script>
<input type=text class="textCell" style="width:150px" name="searchTerm" id="keyword" value="${searchTerm}"/>
<button type="submit" name="searchButton" value="matrixID">Matrix ID</button>
<button type="submit" name="searchButton" value="matrixTitle">Title</button>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsListControls.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsListControls.jsp 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsListControls.jsp 2010-03-23 18:15:11 UTC (rev 652)
@@ -1,5 +1,5 @@
<%@ include file="/common/taglibs.jsp"%>
-<script type="text/javascript" src="/treebase-web/scripts/prototype/prototype-1.6.0.3.js"></script>
+<%-- script type="text/javascript" src="/treebase-web/scripts/prototype/prototype-1.6.0.3.js"></script --%>
<c:if test="${! isEmpty }">
<script type="text/javascript">
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp 2010-03-23 18:15:11 UTC (rev 652)
@@ -2,11 +2,6 @@
<form id="searchSimple" method="post">
<fieldset>
Search: <input type="hidden" name="formName" value="searchKeyword"/>
- <script type="text/javascript">
- //<![CDATA[
- TreeBASE.register( function() { $('keyword').focus(); } );
- //]]>
- </script>
<input type="text" class="textCell" style="width:150px" name="searchTerm" id="keyword" value="${searchTerm}"/>
<button type="submit" name="searchButton" value="studyID">Study ID</button>
<button type="submit" name="searchButton" value="legacyStudyID">Legacy Study ID</button>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSimpleSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSimpleSearchForm.jsp 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSimpleSearchForm.jsp 2010-03-23 18:15:11 UTC (rev 652)
@@ -1,12 +1,7 @@
<%@ include file="/common/taglibs.jsp"%>
<form id="searchSimple" method="post">
<fieldset>
- Search: <input type="hidden" name="formName" value="treeSimple"/>
- <script type="text/javascript">
- //<![CDATA[
- TreeBASE.register( function() { $('keyword').focus(); } );
- //]]>
- </script>
+ Search: <input type="hidden" name="formName" value="treeSimple"/>
<input type="text" class="textCell" style="width:150px" name="searchTerm" id="keyword" value="${searchTerm}"/>
<button type="submit" name="searchButton" value="treeID">Tree ID</button>
<button type="submit" name="searchButton" value="treeTitle">Title</button>
Modified: trunk/treebase-web/src/main/webapp/common/header.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/header.jsp 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/common/header.jsp 2010-03-23 18:15:11 UTC (rev 652)
@@ -1,8 +1,17 @@
<%@ include file="/common/taglibs.jsp"%>
-<h1>
+<h1 style="padding-bottom:0px !important;margin-bottom:0px !important">
<a href="<c:url value="/home.html"/>">
- <img src="<c:url value="/images/logo.gif"/>" alt="TreeBase Logo" width="523" height="112" border="0" />
+ <img
+ src="<c:url value="/images/logo.gif"/>"
+ alt="TreeBase Logo"
+ width="523"
+ height="112"
+ border="0" />
</a>
+ <img
+ src="<c:url value="/images/gradient.jpg"/>"
+ style="width:100%;height:10px;padding:0px !important;margin:0px !important"
+ height="10"
+ alt="" />
</h1>
-<img src="images/gradient.jpg" style="width:100%;height:10px" alt="" />
Modified: trunk/treebase-web/src/main/webapp/common/meta.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/meta.jsp 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/common/meta.jsp 2010-03-23 18:15:11 UTC (rev 652)
@@ -7,3 +7,22 @@
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"/>
<meta name="author" content="Rutger A. Vos (rut...@gm...)"/>
<link rel="icon" href="<c:url value="/images/favicon.ico"/>"/>
+<%
+ String ua = request.getHeader( "User-Agent" );
+ boolean isMSIE = ( ua != null && ua.indexOf( "MSIE" ) != -1 );
+ boolean isOldMSIE = false;
+ if ( isMSIE ) {
+ isOldMSIE = ua.indexOf("MSIE 8.0") == -1;
+
+ }
+%>
+<!-- <%= ua %> -->
+<% if( isOldMSIE ){ %>
+ <script type="text/javascript">
+ alert("Please upgrade your browser!\n\n"+
+ "The TreeBASE team simply do not have the resources to support\n"+
+ "old versions of Internet Explorer. There are many good, free\n"+
+ "browsers available (IE8, FireFox, Safari, Chrome, Opera, etc.),\n"+
+ "please use one of those instead.");
+ </script>
+<% } %>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp 2010-03-23 18:15:11 UTC (rev 652)
@@ -29,8 +29,9 @@
<script type="text/javascript" src="<c:url value='/dwr/engine.js'/>"> </script>
<script type="text/javascript" src="<c:url value='/dwr/util.js'/>"></script>
-<script type="text/javascript" src="<c:url value='/scripts/prototype/prototype.js'/>"></script>
+<!-- script type="text/javascript" src="<c:url value='/scripts/prototype/prototype.js'/>"></script-->
<script type="text/javascript" src="<c:url value='/scripts/prototype/prototype-1.6.0.3.js'/>"></script>
+<!-- script type="text/javascript" src="<c:url value='/scripts/prototype/prototype-1.6.1.js'/>"></script-->
<script type="text/javascript" src="<c:url value='/scripts/script.aculo.us/effects.js'/>"></script>
<script type="text/javascript" src="<c:url value='/scripts/script.aculo.us/controls.js'/>"></script>
Modified: trunk/treebase-web/src/main/webapp/scripts/common.js
===================================================================
--- trunk/treebase-web/src/main/webapp/scripts/common.js 2010-03-23 17:44:56 UTC (rev 651)
+++ trunk/treebase-web/src/main/webapp/scripts/common.js 2010-03-23 18:15:11 UTC (rev 652)
@@ -1,223 +1,224 @@
-var newwindow
-
-function popup_new_window(url)
-{
- newwindow=window.open(url,'help','width=800,height=400,scrollbars=yes,menubar=no,resizable=yes,toolbar=no,status=no');
-}
-function popup(url) {
- if (newwindow)
- newwindow.close();
-
- newwindow=window.open(url,'help','width=600,height=400,scrollbars=yes,menubar=no,resizable=yes,toolbar=no,status=no');
- newwindow.moveTo(220, 100)
-}
-function popupWithSizes(url, width, height) {
- if (newwindow) newwindow.close();
- newwindow=window.open(url,'help','width=' + width + ',height=' + height + ',scrollbars=yes,menubar=no,resizable=yes,toolbar=no,status=no');
-}
-function openHelp(tag) {
- var url = '/treebase-web/help.html?helpTag=' + tag;
- var req = new Ajax.Request(url, {
- 'method':'get',
- 'onSuccess':function(response){
- top.consoleRef=window.open('','help',
- 'width=400,height=350'
- +',menubar=no'
- +',toolbar=no'
- +',location=no'
- +',status=no'
- +',top=100'
- +',left=100'
- +',scrollbars=yes'
- +',resizable=yes');
- if ( top.consoleRef == null || top.consoleRef.closed ) {
- alert("Couldn't open window! The help system requires that popups are allowed for the TreeBASE site.");
- }
- top.consoleRef.document.writeln(response.responseText);
- top.consoleRef.document.close();
- }
- });
-}
-
-/*
- The TreeBASE object has three functions:
- 1. it provides for a way to scope our javascript code within the TreeBASE
- namespace so it doesn't clash with all the other libraries we're using
- 2. it allows you to register callbacks with it
- 3. it implements a TreeBASE.initialize() method that executes those
- registered callbacks. Typically we would call this from within the
- body tag, i.e. <body onload="TreeBASE.initialize()"/>, as is done in the
- main template. This allows us to write more unobtrusive javascript.
-*/
-var TreeBASE = {
- 'init' : [],
- 'initialize' : function () {
- for ( var i = 0; i < TreeBASE.init.length; i++ ) {
- TreeBASE.init[i]();
- }
- },
- 'register' : function(func) {
- TreeBASE.init.push(func);
- }
-};
-
-/*
- Here we register a function that fetches all table headers for columns that
- contain icon buttons (i.e. of class "iconColumn"). It sets the background of
- those header cells to pink, and places a link to the icon legend in the first
- of these header cells.
-*/
-TreeBASE.register(
- function () {
- var headers = document.getElementsByTagName('th');
- var iconColumnHeaders = new Array();
- for ( var i = 0; i < headers.length; i++ ) {
- if ( headers[i].className == 'iconColumn' ) {
- iconColumnHeaders.push(headers[i]);
- }
- }
- if ( iconColumnHeaders.length > 0 ) {
- iconColumnHeaders[0].innerHTML = '<a href="/treebase-web/help/iconLegend.jsp"><img src="/treebase-web/images/icons/help.png" class="iconButton" alt="Icon Legend" title="Icon Legend"/></a>';
- for ( var i = 0; i < iconColumnHeaders.length; i++ ) {
- iconColumnHeaders[i].style.backgroundColor = 'pink';
- }
- }
- }
-);
-
-/*
- Here we register a function that fetches all input elements for text of class
- "textCell", to which we add the following behaviours:
- 1. onfocus (i.e. we click in the input) it selects the text it contains
- 2. onfocus we change the border to soft blue
- 3. onblur (i.e. we leave the input) we go back to the previous border
-*/
-TreeBASE.register(
- function() {
- var inputs = $(document).getElementsByClassName('textCell');
- for ( var i = 0; i < inputs.length; i++ ) {
- if ( inputs[i] ) {
- var currentColor = inputs[i].style.borderColor;
- inputs[i].onfocus = function () {
- this.style.borderColor = '#3863A4';
- this.select();
- }
- inputs[i].onblur = function () {
- this.style.borderColor = currentColor;
- }
- }
- }
- }
-);
-
-TreeBASE.register(
- function () {
- if ( document.getElementsByClassName ) {
- var checkBoxCells = document.getElementsByClassName('checkBoxColumn');
- var buttonContainer = $('buttonContainer');
- if ( checkBoxCells.length > 0 && buttonContainer ) {
- var checkButton = new Element('input',{'type':'button','value':'Check all'});
- checkButton.observe('click',function () {
- for ( var i = 0; i < checkBoxCells.length; i++ ) {
- if ( checkBoxCells[i] ) {
- var checkBoxes = $(checkBoxCells[i]).select('input');
- for ( var j = 0; j < checkBoxes.length; j++ ) {
- if ( checkBoxes[j] && checkBoxes[j].type == 'checkbox' || checkBoxes[j].type == 'radio' ) {
- if ( ! checkBoxes[j].disabled ) {
- checkBoxes[j].checked = 'checked';
- }
- }
- }
- }
- }
- });
- var uncheckButton = new Element('input',{'type':'button','value':'Uncheck all'});
- uncheckButton.observe('click',function () {
- for ( var i = 0; i < checkBoxCells.length; i++ ) {
- if ( checkBoxCells[i] ) {
- var checkBoxes = $(checkBoxCells[i]).select('input');
- for ( var j = 0; j < checkBoxes.length; j++ ) {
- if ( checkBoxes[j] && checkBoxes[j].type == 'checkbox' || checkBoxes[j].type == 'radio' ) {
- if ( ! checkBoxes[j].disabled ) {
- checkBoxes[j].checked = null;
- }
- }
- }
- }
- }
- });
- var invertButton = new Element('input',{'type':'button','value':'Invert'});
- invertButton.observe('click',function () {
- for ( var i = 0; i < checkBoxCells.length; i++ ) {
- if ( checkBoxCells[i] ) {
- var checkBoxes = $(checkBoxCells[i]).select('input');
- for ( var j = 0; j < checkBoxes.length; j++ ) {
- if ( checkBoxes[j] && checkBoxes[j].type == 'checkbox' || checkBoxes[j].type == 'radio' ) {
- if ( ! checkBoxes[j].disabled ) {
- if ( checkBoxes[j].checked ) {
- checkBoxes[j].checked = null;
- }
- else {
- checkBoxes[j].checked = 'checked';
- }
- }
- }
- }
- }
- }
- });
- buttonContainer.insertBefore(invertButton,buttonContainer.firstChild);
- buttonContainer.insertBefore(uncheckButton,buttonContainer.firstChild);
- buttonContainer.insertBefore(checkButton,buttonContainer.firstChild);
- }
- }
- }
-);
-
-/* add a tooltip for the help buttons */
-TreeBASE.register(
- function() {
- var links = document.getElementsByTagName('a');
- for ( var i = 0; i < links.length; i++ ) {
- var link = $(links[i]);
- if ( link.hasClassName('openHelp') ) {
- if ( link.title == null || link.title == '' ) {
- link.title = 'Open help popup';
- }
- }
- }
- }
-);
-
-/*
- Collapse/expands elements (identified by id), where
- the expanded version is shown as 'displayAs' (i.e.
- 'block' or 'inline'). This behaviour is added to
- 'link', such that:
- <a onclick="TreeBASE.collapseExpand('foo','block',this)">
- <img src="/treebase-web/images/plus.gif"/>
- </a>
- <div id="foo">
- <!-- this will be collapsed/expanded -->
- </div>
-*/
-TreeBASE.collapseExpand = function(id,displayAs,link) {
- var objToExpand = $(id);
- var img = $(link).firstDescendant();
- if ( img == null ) {
- img = document.createElement(img);
- link.appendChild(img);
- }
- if ( objToExpand.style.display == 'none' ) {
- objToExpand.style.display = displayAs;
- img.src='/treebase-web/images/minus.gif';
- img.alt='collapse'
- link.title='collapse';
- }
- else {
- objToExpand.style.display = 'none';
- img.src='/treebase-web/images/plus.gif';
- img.alt='expand';
- link.title='expand';
- }
-}
+var newwindow
+
+function popup_new_window(url)
+{
+ newwindow=window.open(url,'help','width=800,height=400,scrollbars=yes,menubar=no,resizable=yes,toolbar=no,status=no');
+}
+function popup(url) {
+ if (newwindow)
+ newwindow.close();
+
+ newwindow=window.open(url,'help','width=600,height=400,scrollbars=yes,menubar=no,resizable=yes,toolbar=no,status=no');
+ newwindow.moveTo(220, 100)
+}
+function popupWithSizes(url, width, height) {
+ if (newwindow) newwindow.close();
+ newwindow=window.open(url,'help','width=' + width + ',height=' + height + ',scrollbars=yes,menubar=no,resizable=yes,toolbar=no,status=no');
+}
+function openHelp(tag) {
+ var url = '/treebase-web/help.html?helpTag=' + tag;
+ var req = new Ajax.Request(url, {
+ 'method':'get',
+ 'onSuccess':function(response){
+ top.consoleRef=window.open('','help',
+ 'width=400,height=350'
+ +',menubar=no'
+ +',toolbar=no'
+ +',location=no'
+ +',status=no'
+ +',top=100'
+ +',left=100'
+ +',scrollbars=yes'
+ +',resizable=yes');
+ if ( top.consoleRef == null || top.consoleRef.closed ) {
+ alert("Couldn't open window! The help system requires that popups are allowed for the TreeBASE site.");
+ }
+ top.consoleRef.document.writeln(response.responseText);
+ top.consoleRef.document.close();
+ }
+ });
+}
+
+/*
+ The TreeBASE object has three functions:
+ 1. it provides for a way to scope our javascript code within the TreeBASE
+ namespace so it doesn't clash with all the other libraries we're using
+ 2. it allows you to register callbacks with it
+ 3. it implements a TreeBASE.initialize() method that executes those
+ registered callbacks. Typically we would call this from within the
+ body tag, i.e. <body onload="TreeBASE.initialize()"/>, as is done in the
+ main template. This allows us to write more unobtrusive javascript.
+*/
+var TreeBASE = {
+ 'init' : [],
+ 'initialize' : function () {
+ for ( var i = 0; i < TreeBASE.init.length; i++ ) {
+ TreeBASE.init[i]();
+ }
+ },
+ 'register' : function(func) {
+ TreeBASE.init.push(func);
+ }
+};
+
+/*
+ Here we register a function that fetches all table headers for columns that
+ contain icon buttons (i.e. of class "iconColumn"). It sets the background of
+ those header cells to pink, and places a link to the icon legend in the first
+ of these header cells.
+*/
+TreeBASE.register(
+ function () {
+ var headers = document.getElementsByTagName('th');
+ var iconColumnHeaders = new Array();
+ for ( var i = 0; i < headers.length; i++ ) {
+ if ( headers[i].className == 'iconColumn' ) {
+ iconColumnHeaders.push(headers[i]);
+ }
+ }
+ if ( iconColumnHeaders.length > 0 ) {
+ iconColumnHeaders[0].innerHTML = '<a href="/treebase-web/help/iconLegend.jsp"><img src="/treebase-web/images/icons/help.png" class="iconButton" alt="Icon Legend" title="Icon Legend"/></a>';
+ for ( var i = 0; i < iconColumnHeaders.length; i++ ) {
+ iconColumnHeaders[i].style.backgroundColor = 'pink';
+ }
+ }
+ }
+);
+
+/*
+ Here we register a function that fetches all input elements for text of class
+ "textCell", to which we add the following behaviours:
+ 1. onfocus (i.e. we click in the input) it selects the text it contains
+ 2. onfocus we change the border to soft blue
+ 3. onblur (i.e. we leave the input) we go back to the previous border
+*/
+
+TreeBASE.register(
+ function() {
+ var inputs = $$('.textCell');
+ for ( var i = 0; i < inputs.length; i++ ) {
+ if ( inputs[i] ) {
+ var currentColor = inputs[i].style.borderColor;
+ inputs[i].onfocus = function () {
+ this.style.borderColor = '#3863A4';
+ this.select();
+ }
+ inputs[i].onblur = function () {
+ this.style.borderColor = currentColor;
+ }
+ }
+ }
+ }
+);
+
+TreeBASE.register(
+ function () {
+ if ( document.getElementsByClassName ) {
+ var checkBoxCells = $$('.checkBoxColumn');
+ var buttonContainer = $('buttonContainer');
+ if ( checkBoxCells.length > 0 && buttonContainer ) {
+ var checkButton = new Element('input',{'type':'button','value':'Check all'});
+ checkButton.observe('click',function () {
+ for ( var i = 0; i < checkBoxCells.length; i++ ) {
+ if ( checkBoxCells[i] ) {
+ var checkBoxes = $(checkBoxCells[i]).select('input');
+ for ( var j = 0; j < checkBoxes.length; j++ ) {
+ if ( checkBoxes[j] && checkBoxes[j].type == 'checkbox' || checkBoxes[j].type == 'radio' ) {
+ if ( ! checkBoxes[j].disabled ) {
+ checkBoxes[j].checked = 'checked';
+ }
+ }
+ }
+ }
+ }
+ });
+ var uncheckButton = new Element('input',{'type':'button','value':'Uncheck all'});
+ uncheckButton.observe('click',function () {
+ for ( var i = 0; i < checkBoxCells.length; i++ ) {
+ if ( checkBoxCells[i] ) {
+ var checkBoxes = $(checkBoxCells[i]).select('input');
+ for ( var j = 0; j < checkBoxes.length; j++ ) {
+ if ( checkBoxes[j] && checkBoxes[j].type == 'checkbox' || checkBoxes[j].type == 'radio' ) {
+ if ( ! checkBoxes[j].disabled ) {
+ checkBoxes[j].checked = null;
+ }
+ }
+ }
+ }
+ }
+ });
+ var invertButton = new Element('input',{'type':'button','value':'Invert'});
+ invertButton.observe('click',function () {
+ for ( var i = 0; i < checkBoxCells.length; i++ ) {
+ if ( checkBoxCells[i] ) {
+ var checkBoxes = $(checkBoxCells[i]).select('input');
+ for ( var j = 0; j < checkBoxes.length; j++ ) {
+ if ( checkBoxes[j] && checkBoxes[j].type == 'checkbox' || checkBoxes[j].type == 'radio' ) {
+ if ( ! checkBoxes[j].disabled ) {
+ if ( checkBoxes[j].checked ) {
+ checkBoxes[j].checked = null;
+ }
+ else {
+ checkBoxes[j].checked = 'checked';
+ }
+ }
+ }
+ }
+ }
+ }
+ });
+ buttonContainer.insertBefore(invertButton,buttonContainer.firstChild);
+ buttonContainer.insertBefore(uncheckButton,buttonContainer.firstChild);
+ buttonContainer.insertBefore(checkButton,buttonContainer.firstChild);
+ }
+ }
+ }
+);
+
+/* add a tooltip for the help buttons */
+TreeBASE.register(
+ function() {
+ var links = document.getElementsByTagName('a');
+ for ( var i = 0; i < links.length; i++ ) {
+ var link = $(links[i]);
+ if ( link.hasClassName('openHelp') ) {
+ if ( link.title == null || link.title == '' ) {
+ link.title = 'Open help popup';
+ }
+ }
+ }
+ }
+);
+
+/*
+ Collapse/expands elements (identified by id), where
+ the expanded version is shown as 'displayAs' (i.e.
+ 'block' or 'inline'). This behaviour is added to
+ 'link', such that:
+ <a onclick="TreeBASE.collapseExpand('foo','block',this)">
+ <img src="/treebase-web/images/plus.gif"/>
+ </a>
+ <div id="foo">
+ <!-- this will be collapsed/expanded -->
+ </div>
+*/
+TreeBASE.collapseExpand = function(id,displayAs,link) {
+ var objToExpand = $(id);
+ var img = $(link).firstDescendant();
+ if ( img == null ) {
+ img = document.createElement(img);
+ link.appendChild(img);
+ }
+ if ( objToExpand.style.display == 'none' ) {
+ objToExpand.style.display = displayAs;
+ img.src='/treebase-web/images/minus.gif';
+ img.alt='collapse'
+ link.title='collapse';
+ }
+ else {
+ objToExpand.style.display = 'none';
+ img.src='/treebase-web/images/plus.gif';
+ img.alt='expand';
+ link.title='expand';
+ }
+}
Added: trunk/treebase-web/src/main/webapp/scripts/prototype/prototype-1.6.1.js
===================================================================
--- trunk/treebase-web/src/main/webapp/scripts/prototype/prototype-1.6.1.js (rev 0)
+++ trunk/treebase-web/src/main/webapp/scripts/prototype/prototype-1.6.1.js 2010-03-23 18:15:11 UTC (rev 652)
@@ -0,0 +1,4874 @@
+/* Prototype JavaScript framework, version 1.6.1
+ * (c) 2005-2009 Sam Stephenson
+ *
+ * Prototype is freely distributable under the terms of an MIT-style license.
+ * For details, see the Prototype web site: http://www.prototypejs.org/
+ *
+ *--------------------------------------------------------------------------*/
+
+var Prototype = {
+ Version: '1.6.1',
+
+ Browser: (function(){
+ var ua = navigator.userAgent;
+ var isOpera = Object.prototype.toString.call(window.opera) == '[object Opera]';
+ return {
+ IE: !!window.attachEvent && !isOpera,
+ Opera: isOpera,
+ WebKit: ua.indexOf('AppleWebKit/') > -1,
+ Gecko: ua.indexOf('Gecko') > -1 && ua.indexOf('KHTML') === -1,
+ MobileSafari: /Apple.*Mobile.*Safari/.test(ua)
+ }
+ })(),
+
+ BrowserFeatures: {
+ XPath: !!document.evaluate,
+ SelectorsAPI: !!document.querySelector,
+ ElementExtensions: (function() {
+ var constructor = window.Element || window.HTMLElement;
+ return !!(constructor && constructor.prototype);
+ })(),
+ SpecificElementExtensions: (function() {
+ if (typeof window.HTMLDivElement !== 'undefined')
+ return true;
+
+ var div = document.createElement('div');
+ var form = document.createElement('form');
+ var isSupported = false;
+
+ if (div['__proto__'] && (div['__proto__'] !== form['__proto__'])) {
+ isSupported = true;
+ }
+
+ div = form = null;
+
+ return isSupported;
+ })()
+ },
+
+ ScriptFragment: '<script[^>]*>([\\S\\s]*?)<\/script>',
+ JSONFilter: /^\/\*-secure-([\s\S]*)\*\/\s*$/,
+
+ emptyFunction: function() { },
+ K: function(x) { return x }
+};
+
+if (Prototype.Browser.MobileSafari)
+ Prototype.BrowserFeatures.SpecificElementExtensions = false;
+
+
+var Abstract = { };
+
+
+var Try = {
+ these: function() {
+ var returnValue;
+
+ for (var i = 0, length = arguments.length; i < length; i++) {
+ var lambda = arguments[i];
+ try {
+ returnValue = lambda();
+ break;
+ } catch (e) { }
+ }
+
+ return returnValue;
+ }
+};
+
+/* Based on Alex Arnell's inheritance implementation. */
+
+var Class = (function() {
+ function subclass() {};
+ function create() {
+ var parent = null, properties = $A(arguments);
+ if (Object.isFunction(properties[0]))
+ parent = properties.shift();
+
+ function klass() {
+ this.initialize.apply(this, arguments);
+ }
+
+ Object.extend(klass, Class.Methods);
+ klass.superclass = parent;
+ klass.subclasses = [];
+
+ if (parent) {
+ subclass.prototype = parent.prototype;
+ klass.prototype = new subclass;
+ parent.subclasses.push(klass);
+ }
+
+ for (var i = 0; i < properties.length; i++)
+ klass.addMethods(properties[i]);
+
+ if (!klass.prototype.initialize)
+ klass.prototype.initialize = Prototype.emptyFunction;
+
+ klass.prototype.constructor = klass;
+ return klass;
+ }
+
+ function addMethods(source) {
+ var ancestor = this.superclass && this.superclass.prototype;
+ var properties = Object.keys(source);
+
+ if (!Object.keys({ toString: true }).length) {
+ if (source.toString != Object.prototype.toString)
+ properties.push("toString");
+ if (source.valueOf != Object.prototype.valueOf)
+ properties.push("valueOf");
+ }
+
+ for (var i = 0, length = properties.length; i < length; i++) {
+ var property = properties[i], value = source[property];
+ if (ancestor && Object.isFunction(value) &&
+ value.argumentNames().first() == "$super") {
+ var method = value;
+ value = (function(m) {
+ return function() { return ancestor[m].apply(this, arguments); };
+ })(property).wrap(method);
+
+ value.valueOf = method.valueOf.bind(method);
+ value.toString = method.toString.bind(method);
+ }
+ this.prototype[property] = value;
+ }
+
+ return this;
+ }
+
+ return {
+ create: create,
+ Methods: {
+ addMethods: addMethods
+ }
+ };
+})();
+(function() {
+
+ var _toString = Object.prototype.toString;
+
+ function extend(destination, source) {
+ for (var property in source)
+ destination[property] = source[property];
+ return destination;
+ }
+
+ function inspect(object) {
+ try {
+ if (isUndefined(object)) return 'undefined';
+ if (object === null) return 'null';
+ return object.inspect ? object.inspect() : String(object);
+ } catch (e) {
+ if (e instanceof RangeError) return '...';
+ throw e;
+ }
+ }
+
+ function toJSON(object) {
+ var type = typeof object;
+ switch (type) {
+ case 'undefined':
+ case 'function':
+ case 'unknown': return;
+ case 'boolean': return object.toString();
+ }
+
+ if (object === null) return 'null';
+ if (object.toJSON) return object.toJSON();
+ if (isElement(object)) return;
+
+ var results = [];
+ for (var property in object) {
+ var value = toJSON(object[property]);
+ if (!isUndefined(value))
+ results.push(property.toJSON() + ': ' + value);
+ }
+
+ return '{' + results.join(', ') + '}';
+ }
+
+ function toQueryString(object) {
+ return $H(object).toQueryString();
+ }
+
+ function toHTML(object) {
+ return object && object.toHTML ? object.toHTML() : String.interpret(object);
+ }
+
+ function keys(object) {
+ var results = [];
+ for (var property in object)
+ results.push(property);
+ return results;
+ }
+
+ function values(object) {
+ var results = [];
+ for (var property in object)
+ results.push(object[property]);
+ return results;
+ }
+
+ function clone(object) {
+ return extend({ }, object);
+ }
+
+ function isElement(object) {
+ return !!(object && object.nodeType == 1);
+ }
+
+ function isArray(object) {
+ return _toString.call(object) == "[object Array]";
+ }
+
+
+ function isHash(object) {
+ return object instanceof Hash;
+ }
+
+ function isFunction(object) {
+ return typeof object === "function";
+ }
+
+ function isString(object) {
+ return _toString.call(object) == "[object String]";
+ }
+
+ function isNumber(object) {
+ return _toString.call(object) == "[object Number]";
+ }
+
+ function isUndefined(object) {
+ return typeof object === "undefined";
+ }
+
+ extend(Object, {
+ extend: extend,
+ inspect: inspect,
+ toJSON: toJSON,
+ toQueryString: toQueryString,
+ toHTML: toHTML,
+ keys: keys,
+ values: values,
+ clone: clone,
+ isElement: isElement,
+ isArray: isArray,
+ isHash: isHash,
+ isFunction: isFunction,
+ isString: isString,
+ isNumber: isNumber,
+ isUndefined: isUndefined
+ });
+})();
+Object.extend(Function.prototype, (function() {
+ var slice = Array.prototype.slice;
+
+ function update(array, args) {
+ var arrayLength = array.length, length = args.length;
+ while (length--) array[arrayLength + length] = args[length];
+ return array;
+ }
+
+ function merge(array, args) {
+ array = slice.call(array, 0);
+ return update(array, args);
+ }
+
+ function argumentNames() {
+ var names = this.toString().match(/^[\s\(]*function[^(]*\(([^)]*)\)/)[1]
+ .replace(/\/\/.*?[\r\n]|\/\*(?:.|[\r\n])*?\*\//g, '')
+ .replace(/\s+/g, '').split(',');
+ return names.length == 1 && !names[0] ? [] : names;
+ }
+
+ function bind(context) {
+ if (arguments.length < 2 && Object.isUndefined(arguments[0])) return this;
+ var __method = this, args = slice.call(arguments, 1);
+ return function() {
+ var a = merge(args, arguments);
+ return __method.apply(context, a);
+ }
+ }
+
+ function bindAsEventListener(context) {
+ var __method = this, args = slice.call(arguments, 1);
+ return function(event) {
+ var a = update([event || window.event], args);
+ return __method.apply(context, a);
+ }
+ }
+
+ function curry() {
+ if (!arguments.length) return this;
+ var __method = this, args = slice.call(arguments, 0);
+ return function() {
+ var a = merge(args, arguments);
+ return __method.apply(this, a);
+ }
+ }
+
+ function delay(timeout) {
+ var __method = this, args = slice.call(arguments, 1);
+ timeout = timeout * 1000
+ return window.setTimeout(function() {
+ return __method.apply(__method, args);
+ }, timeout);
+ }
+
+ function defer() {
+ var args = update([0.01], arguments);
+ return this.delay.apply(this, args);
+ }
+
+ function wrap(wrapper) {
+ var __method = this;
+ return function() {
+ var a = update([__method.bind(this)], arguments);
+ return wrapper.apply(this, a);
+ }
+ }
+
+ function methodize() {
+ if (this._methodized) return this._methodized;
+ var __method = this;
+ return this._methodized = function() {
+ var a = update([this], arguments);
+ return __method.apply(null, a);
+ };
+ }
+
+ return {
+ argumentNames: argumentNames,
+ bind: bind,
+ bindAsEventListener: bindAsEventListener,
+ curry: curry,
+ delay: delay,
+ defer: defer,
+ wrap: wrap,
+ methodize: methodize
+ }
+})());
+
+
+Date.prototype.toJSON = function() {
+ return '"' + this.getUTCFullYear() + '-' +
+ (this.getUTCMonth() + 1).toPaddedString(2) + '-' +
+ this.getUTCDate().toPaddedString(2) + 'T' +
+ this.getUTCHours().toPaddedString(2) + ':' +
+ this.getUTCMinutes().toPaddedString(2) + ':' +
+ this.getUTCSeconds().toPaddedString(2) + 'Z"';
+};
+
+
+RegExp.prototype.match = RegExp.prototype.test;
+
+RegExp.escape = function(str) {
+ return String(str).replace(/([.*+?^=!:${}()|[\]\/\\])/g, '\\$1');
+};
+var PeriodicalExecuter = Class.create({
+ initialize: function(callback, frequency) {
+ this.callback = callback;
+ this.frequency = frequency;
+ this.currentlyExecuting = false;
+
+ this.registerCallback();
+ },
+
+ registerCallback: function() {
+ this.timer = setInterval(this.onTimerEvent.bind(this), this.frequency * 1000);
+ },
+
+ execute: function() {
+ this.callback(this);
+ },
+
+ stop: function() {
+ if (!this.timer) return;
+ clearInterval(this.timer);
+ this.timer = null;
+ },
+
+ onTimerEvent: function() {
+ if (!this.currentlyExecuting) {
+ try {
+ this.currentlyExecuting = true;
+ this.execute();
+ this.currentlyExecuting = false;
+ } catch(e) {
+ this.currentlyExecuting = false;
+ throw e;
+ }
+ }
+ }
+});
+Object.extend(String, {
+ interpret: function(value) {
+ return value == null ? '' : String(value);
+ },
+ specialChar: {
+ '\b': '\\b',
+ '\t': '\\t',
+ '\n': '\\n',
+ '\f': '\\f',
+ '\r': '\\r',
+ '\\': '\\\\'
+ }
+});
+
+Object.extend(String.prototype, (function() {
+
+ function prepareReplacement(replacement) {
+ if (Object.isFunction(replacement)) return replacement;
+ var template = new Template(replacement);
+ return function(match) { return template.evaluate(match) };
+ }
+
+ function gsub(pattern, replacement) {
+ var result = '', source = this, match;
+ replacement = prepareReplacement(replacement);
+
+ if (Object.isString(pattern))
+ pattern = RegExp.escape(pattern);
+
+ if (!(pattern.length || pattern.source)) {
+ replacement = replacement('');
+ return replacement + source.split('').join(replacement) + replacement;
+ }
+
+ while (source.length > 0) {
+ if (match = source.match(pattern)) {
+ result += source.slice(0, match.index);
+ result += String.interpret(replacement(match));
+ source = source.slice(match.index + match[0].length);
+ } else {
+ result += source, source = '';
+ }
+ }
+ return result;
+ }
+
+ function sub(pattern, replacement, count) {
+ replacement = prepareReplacement(replacement);
+ count = Object.isUndefined(count) ? 1 : count;
+
+ return this.gsub(pattern, function(match) {
+ if (--count < 0) return match[0];
+ return replacement(match);
+ });
+ }
+
+ function scan(pattern, iterator) {
+ this.gsub(pattern, iterator);
+ return String(this);
+ }
+
+ function truncate(length, truncation) {
+ length = length || 30;
+ truncation = Object.isUndefined(truncation) ? '...' : truncation;
+ return this.length > length ?
+ this.slice(0, length - truncation.length) + truncation : String(this);
+ }
+
+ function strip() {
+ return this.replace(/^\s+/, '').replace(/\s+$/, '');
+ }
+
+ function stripTags() {
+ return this.replace(/<\w+(\s+("[^"]*"|'[^']*'|[^>])+)?>|<\/\w+>/gi, '');
+ }
+
+ function stripScripts() {
+ return this.replace(new RegExp(Prototype.ScriptFragment, 'img'), '');
+ }
+
+ function extractScripts() {
+ var matchAll = new RegExp(Prototype.ScriptFragment, 'img');
+ var matchOne = new RegExp(Prototype.ScriptFragment, 'im');
+ return (this.match(matchAll) || []).map(function(scriptTag) {
+ return (scriptTag.match(matchOne) || ['', ''])[1];
+ });
+ }
+
+ function evalScripts() {
+ return this.extractScripts().map(function(script) { return eval(script) });
+ }
+
+ function escapeHTML() {
+ return this.replace(/&/g,'&').replace(/</g,'<').replace(/>/g,'>');
+ }
+
+ function unescapeHTML() {
+ return this.stripTags().replace(/</g,'<').replace(/>/g,'>').replace(/&/g,'&');
+ }
+
+
+ function toQueryParams(separator) {
+ var match = this.strip().match(/([^?#]*)(#.*)?$/);
+ if (!match) return { };
+
+ return match[1].split(separator || '&').inject({ }, function(hash, pair) {
+ if ((pair = pair.split('='))[0]) {
+ var key = decodeURIComponent(pair.shift());
+ var value = pair.length > 1 ? pair.join('=') : pair[0];
+ if (value != undefined) value = decodeURIComponent(value);
+
+ if (key in hash) {
+ if (!Object.isArray(hash[key])) hash[key] = [hash[key]];
+ hash[key].push(value);
+ }
+ else hash[key] = value;
+ }
+ return hash;
+ });
+ }
+
+ function toArray() {
+ return this.split('');
+ }
+
+ function succ() {
+ return this.slice(0, this.length - 1) +
+ String.fromCharCode(this.charCodeAt(this.length - 1) + 1);
+ }
+
+ function times(count) {
+ return count < 1 ? '' : new Array(count + 1).join(this);
+ }
+
+ function camelize() {
+ var parts = this.split('-'), len = parts.length;
+ if (len == 1) return parts[0];
+
+ var camelized = this.charAt(0) == '-'
+ ? parts[0].charAt(0).toUpperCase() + parts[0].substring(1)
+ : parts[0];
+
+ for (var i = 1; i < len; i++)
+ camelized += parts[i].charAt(0).toUpperCase() + parts[i].substring(1);
+
+ return camelized;
+ }
+
+ function capitalize() {
+ return this.charAt(0).toUpperCase() + this.substring(1).toLowerCase();
+ }
+
+ function underscore() {
+ return this.replace(/::/g, '/')
+ .replace(/([A-Z]+)([A-Z][a-z])/g, '$1_$2')
+ .replace(/([a-z\d])([A-Z])/g, '$1_$2')
+ .replace(/-/g, '_')
+ .toLowerCase();
+ }
+
+ function dasherize() {
+ return this.replace(/_/g, '-');
+ }
+
+ function inspect(useDoubleQuotes) {
+ var escapedString = this.replace(/[\x00-\x1f\\]/g, function(character) {
+ if (character in String.specialChar) {
+ return String.specialChar[character];
+ }
+ return '\\u00' + character.charCodeAt().toPaddedString(2, 16);
+ });
+ if (useDoubleQuotes) return '"' + escapedString.replace(/"/g, '\\"') + '"';
+ return "'" + escapedString.replace(/'/g, '\\\'') + "'";
+ }
+
+ function toJSON() {
+ return this.inspect(true);
+ }
+
+ function unfilterJSON(filter) {
+ return this.replace(filter || Prototype.JSONFilter, '$1');
+ }
+
+ function isJSON() {
+ var str = this;
+ if (str.blank()) return false;
+ str = this.replace(/\\./g, '@').replace(/"[^"\\\n\r]*"/g, '');
+ return (/^[,:{}\[\]0-9.\-+Eaeflnr-u \n\r\t]*$/).test(str);
+ }
+
+ function evalJSON(sanitize) {
+ var json = this.unfilterJSON();
+ try {
+ if (!sanitize || json.isJSON()) return eval('(' + json + ')');
+ } catch (e) { }
+ throw new SyntaxError('Badly formed JSON string: ' + this.inspect());
+ }
+
+ function include(pattern) {
+ return this.indexOf(pattern) > -1;
+ }
+
+ function startsWith(pattern) {
+ return this.indexOf(pattern) === 0;
+ }
+
+ function endsWith(pattern) {
+ var d = this.length - pattern.length;
+ return d >= 0 && this.lastIndexOf(pattern) === d;
+ }
+
+ function empty() {
+ return this == '';
+ }
+
+ function blank() {
+ return /^\s*$/.test(this);
+ }
+
+ function interpolate(object, pattern) {
+ return new Template(this, pattern).evaluate(object);
+ }
+
+ return {
+ gsub: gsub,
+ sub: sub,
+ scan: scan,
+ truncate: truncate,
+ strip: String.prototype.trim ? String.prototype.trim : strip,
+ stripTags: stripTags,
+ stripScripts: stripScripts,
+ extractScripts: extractScripts,
+ evalScripts: evalScripts,
+ escapeHTML: escapeHTML,
+ unescapeHTML: unescapeHTML,
+ toQueryParams: toQueryParams,
+ parseQuery: toQueryParams,
+ toArray: toArray,
+ succ: succ,
+ times: times,
+ camelize: camelize,
+ capitalize: capitalize,
+ underscore: underscore,
+ dasherize: dasherize,
+ inspect: inspect,
+ toJSON: toJSON,
+ unfilterJSON: unfilterJSON,
+ isJSON: isJSON,
+ evalJSON: evalJSON,
+ include: include,
+ startsWith: startsWith,
+ endsWith: endsWith,
+ empty: empty,
+ blank: blank,
+ interpolate: interpolate
+ };
+})());
+
+var Template = Class.create({
+ initialize: function(template, pattern) {
+ this.template = template.toString();
+ this.pattern = pattern || Template.Pattern;
+ },
+
+ evaluate: function(object) {
+ if (object && Object.isFunction(object.toTemplateReplacements))
+ object = object.toTemplateReplacements();
+
+ return this.template.gsub(this.pattern, function(match) {
+ if (object == null) return (match[1] + '');
+
+ var before = match[1] || '';
+ if (before == '\\') return match[2];
+
+ var ctx = object, expr = match[3];
+ var pattern = /^([^.[]+|\[((?:.*?[^\\])?)\])(\.|\[|$)/;
+ match = pattern.exec(expr);
+ if (match == null) return before;
+
+ while (match != null) {
+ var comp = match[1].startsWith('[') ? match[2].replace(/\\\\]/g, ']') : match[1];
+ ctx = ctx[comp];
+ if (null == ctx || '' == match[3]) break;
+ expr = expr.substring('[' == match[3] ? match[1].length : match[0].length);
+ match = pattern.exec(expr);
+ }
+
+ return before + String.interpret(ctx);
+ });
+ }
+});
+Template.Pattern = /(^|.|\r|\n)(#\{(.*?)\})/;
+
+var $break = { };
+
+var Enumerable = (function() {
+ function each(iterator, context) {
+ var index = 0;
+ try {
+ this._each(function(value) {
+ iterator.call(context, value, index++);
+ });
+ } catch (e) {
+ if (e != $break) throw e;
+ }
+ return this;
+ }
+
+ function eachSlice(number, iterator, context) {
+ var index = -number, slices = [], array = this.toArray();
+ if (number < 1) return array;
+ while ((index += number) < array.length)
+ slices.push(array.slice(index, index+number));
+ return slices.collect(iterator, context);
+ }
+
+ function all(iterator, context) {
+ iterator = iterator || Prototype.K;
+ var result = true;
+ this.each(function(value, index) {
+ result = result && !!iterator.call(context, value, index);
+ if (!result) throw $break;
+ });
+ return result;
+ }
+
+ function any(iterator, context) {
+ iterator = iterator || Prototype.K;
+ var result = false;
+ this.each(function(value, index) {
+ if (result = !!iterator.call(context, value, index))
+ throw $break;
+ });
+ return result;
+ }
+
+ function collect(iterator, context) {
+ iterator = iterator || Prototype.K;
+ var results = [];
+ this.each(function(value, index) {
+ results.push(iterator.call(context, value, index));
+ });
+ return results;
+ }
+
+ function detect(iterator, context) {
+ var result;
+ this.each(function(value, index) {
+ if (iterator.call(context, value, index)) {
+ result = value;
+ throw $break;
+ }
+ });
+ return result;
+ }
+
+ function findAll(iterator, context) {
+ var results = [];
+ this.each(function(value, index) {
+ if (iterator.call(context, value, index))
+ results.push(value);
+ });
+ return results;
+ }
+
+ function grep(filter, iterator, context) {
+ iterator = iterator || Prototype.K;
+ var results = [];
+
+ if (Object.isString(filter))
+ filter = new RegExp(RegExp.escape(filter));
+
+ this.each(function(value, index) {
+ if (filter.match(value))
+ results.push(iterator.call(context, value, index));
+ });
+ return results;
+ }
+
+ function include(object) {
+ if (Object.isFunction(this.indexOf))
+ if (this.indexOf(object) != -1) return true;
+
+ var found = false;
+ this.each(function(value) {
+ if (value == object) {
+ found = true;
+ throw $break;
+ }
+ });
+ return found;
+ }
+
+ function inGroupsOf(number, fillWith) {
+ fillWith = Object.isUndefined(fillWith) ? null : fillWith;
+ return this.eachSlice(number, function(slice) {
+ while(slice.length < number) slice.push(fillWith);
+ return slice;
+ });
+ }
+
+ function inject(memo, iterator, context) {
+ this.each(function(value, index) {
+ memo = iterator.call(context, memo, value, index);
+ });
+ return memo;
+ }
+
+ function invoke(method) {
+ var args = $A(arguments).slice(1);
+ return this.map(function(value) {
+ return value[method].apply(value, args);
+ });
+ }
+
+ function max(iterator, context) {
+ iterator = iterator || Prototype.K;
+ var result;
+ this.each(function(value, index) {
+ value = iterator.call(context, value, index);
+ if (result == null || value >= result)
+ result = value;
+ });
+ return result;
+ }
+
+ function min(iterator, context) {
+ iterator = iterator || Prototype.K;
+ var result;
+ this.each(function(value, index) {
+ value = iterator.call(context, value, index);
+ if (result == null || value < result)
+ result = value;
+ });
+ return result;
+ }
+
+ function partition(iterator, context) {
+ iterator = iterator || Prototype.K;
+ var trues = [], falses = [];
+ this.each(function(value, index) {
+ (iterator.call(context, value, index) ?
+ trues : falses).push(value);
+ });
+ return [trues, falses];
+ }
+
+ function pluck(property) {
+ var results = [];
+ this.each(function(value) {
+ results.push(value[property]);
+ });
+ return results;
+ }
+
+ function reject(iterator, context) {
+ var results = [];
+ this.each(function(value, index) {
+ if (!iterator.call(context, value, index))
+ results.push(value);
+ });
+ return results;
+ }
+
+ function sortBy(iterator, context) {
+ return this.map(function(value, index) {
+ return {
+ value: value,
+ criteria: iterator.call(context, value, index)
+ };
+ }).sort(function(left, right) {
+ var a = left.criteria, b = right.criteria;
+ return a < b ? -1 : a > b ? 1 : 0;
+ }).pluck('value');
+ }
+
+ function toArray() {
+ return this.map();
+ }
+
+ function zip() {
+ var iterator = Prototype.K, args = $A(arguments);
+ if (Object.isFunction(args.last()))
+ iterator = args.pop();
+
+ var collections = [this].concat(args).map($A);
+ return this.map(function(value, index) {
+ return iterator(collections.pluck(index));
+ });
+ }
+
+ function size() {
+ return this.toArray().length;
+ }
+
+ function inspect() {
+ return '#<Enumerable:' + this.toArray().inspect() + '>';
+ }
+
+
+
+
+
+
+
+
+
+ return {
+ each: each,
+ eachSlice: eachSlice,
+ all: all,
+ every: all,
+ any: any,
+ some: any,
+ collect: collect,
+ map: collect,
+ detect: detect,
+ findAll: findAll,
+ select: findAll,
+ filter: findAll,
+ grep: grep,
+ include: include,
+ member: include,
+ inGroupsOf: inGroupsOf,
+ inject: inject,
+ invoke: invoke,
+ max: max,
+ min: min,
+ partition: partition,
+ pluck: pluck,
+ reject: reject,
+ sortBy: sortBy,
+ toArray: toArray,
+ entries: toArray,
+ zip: zip,
+ size: size,
+ inspect: inspect,
+ find: detect
+ };
+})();
+function $A(iterable) {
+ if (!iterable) return [];
+ if ('toArray' in Object(iterable)) return iterable.toArray();
+ var length = iterable.length || 0, results = new Array(length);
+ while (length--) results[length] = iterable[length];
+ return results;
+}
+
+function $w(string) {
+ if (!Object.isString(string)) return [];
+ string = string.strip();
+ return string ? string.split(/\s+/) : [];
+}
+
+Array.from = $A;
+
+
+(function() {
+ var arrayProto = Array.prototype,
+ slice = arrayProto.slice,
+ _each = arrayProto.forEach; // use native browser JS 1.6 implementation if available
+
+ function each(iterator) {
+ for (var i = 0, length = this.length; i < length; i++)
+ iterator(this[i]);
+ }
+ if (!_each) _each = each;
+
+ function clear() {
+ this.length = 0;
+ return this;
+ }
+
+ function first() {
+ return this[0];
+ }
+
+ function last() {
+ return this[this.length - 1];
+ }
+
+ function compact() {
+ return this.select(function(value) {
+ return value != null;
+ });
+ }
+
+ function flatten() {
+ return this.inject([], function(array, value) {
+ if (Object.isArray(value))
+ return array.concat(value.flatten());
+ array.push(value);
+ return array;
+ });
+ }
+
+ function without() {
+ var values = slice.call(arguments, 0);
+ return this.select(function(value) {
+ return !values.include(value);
+ });
+ }
+
+ function reverse(inline) {
+ return (inline !== false ? this : this.toArray())._reverse();
+ }
+
+ function uniq(sorted) {
+ return this.inject([], function(array, value, index) {
+ if (0 == index || (sorted ? array.last() != value : !array.include(value)))
+ array.push(value);
+ return array;
+ });
+ }
+
+ function intersect(array) {
+ return this.uniq().findAll(function(item) {
+ return array.detect(function(value) { return item === value });
+ });
+ }
+
+
+ function clone() {
+ return slice.call(this, 0);
+ }
+
+ function size() {
+ return this.length;
+ }
+
+ function inspect() {
+ return '[' + this.map(Object.inspect).join(', ') + ']';
+ }
+
+ function toJSON() {
+ var results = [];
+ this.each(function(object) {
+ var value = Object.toJSON(object);
+ if (!Object.isUndefined(value)) results.push(value);
+ });
+ return '[' + results.join(', ') + ']';
+ }
+
+ function indexOf(item, i) {
+ i || (i = 0);
+ var length = this.length;
+ if (i < 0) i = length + i;
+ for (; i < length; i++)
+ if (this[i] === item) return i;
+ return -1;
+ }
+
+ function lastIndexOf(item, i) {
+ i = isNaN(i) ? this.length : (i < 0 ? this.length + i : i) + 1;
+ var n = this.slice(0, i).reverse().indexOf(item);
+ return (n < 0) ? n : i - n - 1;
+ }
+
+ function concat() {
+ var array = slice.call(this, 0), item;
+ for (var i = 0, length = arguments.length; i < length; i++) {
+ item = arguments[i];
+ if (Object.isArray(item) && !('callee' in item)) {
+ for (var j = 0, arrayLength = item.length; j < arrayLength; j++)
+ array.push(item[j]);
+ } else {
+ array.push(item);
+ }
+ }
+ return array;
+ }
+
+ Object.extend(arrayProto, Enumerable);
+
+ if (!arrayProto._reverse)
+ arrayProto._reverse = arrayProto.reverse;
+
+ Object.extend(arrayProto, {
+ _each: _each,
+ clear: clear,
+ first: first,
+ last: last,
+ compact: compact,
+ flatten: flatten,
+ without: without,
+ reverse: reverse,
+ uniq: uniq,
+ intersect: intersect,
+ clone: clone,
+ toArray: clone,
+ size: size,
+ inspect: inspect,
+ toJSON: toJSON
+ });
+
+ var CONCAT_ARGUMENTS_BUGGY = (function() {
+ return [].concat(arguments)[0][0] !== 1;
+ })(1,2)
+
+ if (CONCAT_ARGUMENTS_BUGGY) arrayProto.concat = concat;
+
+ if (!arrayProto.indexOf) arrayProto.indexOf = indexOf;
+ if (!arrayProto.lastIndexOf) arrayProto.lastIndexOf = lastIndexOf;
+})();
+function $H(object) {
+ return new Hash(object);
+};
+
+var Hash = Class.create(Enumerable, (function() {
+ function initialize(object) {
+ this._object = Object.isHash(object) ? object.toObject() : Object.clone(object);
+ }
+
+ function _each(iterator) {
+ for (var key in this._object) {
+ var value = this._object[key], pair = [key, value];
+ pair.key = key;
+ pair.value = value;
+ iterator(pair);
+ }
+ }
+
+ function set(key, value) {
+ return this._object[key] = value;
+ }
+
+ function get(key) {
+ if (this._object[key] !== Object.prototype[key])
+ return this._object[key];
+ }
+
+ function unset(key) {
+ var value = this._object[key];
+ delete this._object[key];
+ return value;
+ }
+
+ function toObject() {
+ return Object.clone(this._object);
+ }
+
+ function keys() {
+ return this.pluck('key');
+ }
+
+ function values() {
+ return this.pluck('value');
+ }
+
+ function index(value) {
+ var match = this.detect(function(pair) {
+ return pair.value === value;
+ });
+ return match && match.key;
+ }
+
+ function merge(object) {
+ return this.clone().update(object);
+ }
+
+ function update(object) {
+ return new Hash(object).inject(this, function(result, pair) {
+ result.set(pair.key, pair.value);
+ return result;
+ });
+ }
+
+ function toQueryPair(key, value) {
+ if (Object.isUndefined(value)) return key;
+ return key + '=' + encodeURIComponent(String.interpret(value));
+ }
+
+ function toQueryString() {
+ return this.inject([], function(results, pair) {
+ var key = encodeURIComponent(pair.key), values = pair.value;
+
+ if (values && typeof values == 'object') {
+ if (Object.isArray(values))
+ return results.concat(values.map(toQueryPair.curry(key)));
+ } else results.push(toQueryPair(key, values));
+ return results;
+ }).join('&');
+ }
+
+ function inspect() {
+ return '#<Hash:{' + this.map(function(pair) {
+ return pair.map(Object.inspect).join(': ');
+ }).join(', ') + '}>';
+ }
+
+ function toJSON() {
+ return Object.toJSON(this.toObject());
+ }
+
+ function clone() {
+ return new Hash(this);
+ }
+
+ return {
+ initialize: initialize,
+ _each: _each,
+ set: set,
+ get: get,
+ unset: unset,
+ toObject: toObject,
+ toTemplateReplacements: toObject,
+ keys: keys,
+ values: values,
+ index: index,
+ merge: merge,
+ update: update,
+ toQueryString: toQueryString,
+ inspect: inspect,
+ toJSON: toJSON,
+ clone: clone
+ };
+})());
+
+Hash.from = $H;
+Object.extend(Number.prototype, (function() {
+ function toColorPart() {
+ return this.toPaddedString(2, 16);
+ }
+
+ function succ() {
+ return this + 1;
+ }
+
+ function times(iterator, context) {
+ $R(0, this, true).each(iterator, context);
+ return this;
+ }
+
+ function toPaddedString(length, radix) {
+ var string = this.toString(radix || 10);
+ return '0'.times(length - string.length) + string;
+ }
+
+ function toJSON() {
+ return isFinite(this) ? this.toString() : 'null';
+ }
+
+ function abs() {
+ return Math.abs(this);
+ }
+
+ function round() {
+ return Math.round(this);
+ }
+
+ function ceil() {
+ return Math.ceil(this);
+ }
+
+ function floor() {
+ return Math.floor(this);
+ }
+
+ return {
+ toColorPart: toColorPart,
+ succ: succ,
+ times: times,
+ toPaddedString: toPaddedString,
+ toJSON: toJSON,
+ abs: abs,
+ round: round,
+ ceil: ceil,
+ floor: floor
+ };
+})());
+
+function $R(start, end, exclusive) {
+ return new ObjectRange(start, end, exclusive);
+}
+
+var O...
[truncated message content] |
|
From: <sfr...@us...> - 2011-03-16 20:18:24
|
Revision: 775
http://treebase.svn.sourceforge.net/treebase/?rev=775&view=rev
Author: sfrgpiel
Date: 2011-03-16 20:18:18 +0000 (Wed, 16 Mar 2011)
Log Message:
-----------
Added blurb and icon for AJB
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/images/journal_files/image022.gif
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2011-03-16 16:21:59 UTC (rev 774)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2011-03-16 20:18:18 UTC (rev 775)
@@ -28,6 +28,23 @@
</tr>
<tr>
<td>
+ <p><a href="http://www.amjbot.org/"
+ title="American Journal of Botany">
+ <img class="journal"
+ src="images/journal_files/image022.gif" alt="AJB"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22American%20Journal%20of%20Botany%22"
+ title="Find records in TreeBASE for articles published in the American Journal of Botany">
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22American%20Journal%20of%20Botany%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
<p><a href="http://www.wiley.com/bw/journal.asp?ref=0014-3820"
title="Evolution">
<img class="journal"
@@ -332,8 +349,6 @@
</table>
<p><b>Other Journals with a Significant Presence in TreeBASE</b>: <a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%2American+Journal+of+Botany%22"
- title="American Journal of Botany">American Journal of Botany</a>; <a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Annals+of+the+Missouri+Botanical+Garden%22"
title="Annals of the Missouri Botanical Garden">Annals of the
Missouri Botanical Garden</a>; <a
Added: trunk/treebase-web/src/main/webapp/images/journal_files/image022.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/image022.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sfr...@us...> - 2011-05-01 00:57:51
|
Revision: 825
http://treebase.svn.sourceforge.net/treebase/?rev=825&view=rev
Author: sfrgpiel
Date: 2011-05-01 00:57:43 +0000 (Sun, 01 May 2011)
Log Message:
-----------
Additional modifications to the data management plan text
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp
trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp 2011-04-30 22:03:40 UTC (rev 824)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp 2011-05-01 00:57:43 UTC (rev 825)
@@ -4,26 +4,33 @@
<div class="gutter">
<h1>NSF Data Management Plan</h1>
-<p>To foster the sharing and dissemination of data produced by sponsored research, the National Science Foundation requires a data management plan for all proposals. At a minimum, these data consist of whatever is necessary to validate research findings by the scientific community, which includes (1) analyzed data, and metadata that (2) provide provenance and (3) define how the data were generated. </p>
-<h2>Data Ingest and Storage</h2>
-<p>The three kinds of data required by NSF are accepted by TreeBASE, whether submitted directly to TreeBASE or indirectly by way of <a href="http://datadryad.org/" target="_blank">Dryad</a>. For (1), we accept NEXUS character block data with datatypes standard, continuous, DNA, RNA, and protein, and non-reticulating phylogenetic trees with branch lengths and clade support values. For (2) we parse and store character labels and state labels in submitted NEXUS files and we map taxon labels to NCBI and uBio external taxonomies. Additionally, we accept the following metadata: museum specimen numbers in accordance with the Registry of Biological Repositories (<a href="http://www.biorepositories.org" target="_blank">RBR</a>), Genbank accession numbers, other accession numbers, and Darwin Core compatible specimen metadata: collecting date, collector, latitude/longitude, elevation, country, state, and locality. For (3), we store and share the original uploaded NEXUS files (including any program-specific command blocks that can define substitution models and search parameters) as well as offer metadata files in analysis description records for annotating software, algorithm, and commands used. TreeBASE only shares data that are linked to a manuscript that is accepted by a peer reviewed publication (e.g. journal article, reviewed book or book section, academic thesis accepted by a thesis committee, etc). </p>
+<p>To foster the sharing and dissemination of data produced by sponsored research, the National Science Foundation requires a data management plan for all proposals. The kinds of data that must be shared generally include whatever the scientific community needs to validate research findings. In particular, researchers must present a plan to share (1) analyzed data, (2) metadata that provide provenance information, and (3) metadata that describe how the data were generated. </p>
+<h2>Data Submission and Storage</h2>
+<p>For phylogenetics, the three kinds of data mentioned above and required by NSF are all accepted by TreeBASE, whether submitted directly to TreeBASE or indirectly by way of <a href="http://datadryad.org/" target="_blank">Dryad</a>. For data type (1), we accept NEXUS formatted data with characters of datatype standard, continuous, DNA, RNA, and protein, and non-reticulating phylogenetic trees with branch lengths and clade support values. For metadata type (2) we parse and store morphological character labels and state labels in submitted NEXUS files and we map taxon labels to NCBI and uBio external taxonomies. Additionally, we accept the following metadata: museum specimen numbers in accordance with the Registry of Biological Repositories (<a href="http://www.biorepositories.org" target="_blank">RBR</a>), Genbank accession numbers, other accession numbers, and Darwin Core compatible specimen metadata: collecting date, collector, latitude/longitude, elevation, country, state, and locality. For metadata type (3), we store and share the original uploaded NEXUS files (including any program-specific command blocks that can define substitution models and search parameters) as well as provide data entry fields to describe software, algorithm, and commands used. TreeBASE only shares data that are linked to a manuscript that is accepted by a peer reviewed publication (e.g. journal article, reviewed book or book section, or academic thesis approved by a thesis committee). </p>
<h2>Data Integrity and Verification</h2>
-<p>TreeBASE helps to certify data integrity by: (A) only accepting NEXUS data that are successfully parsed by a server-side headless version of <a href="http://mesquiteproject.org/" target="_blank">Mesquite</a>, (B) verifying that taxon labels in matrices and relevant trees are consistent, (C) verifying that data objects are not 'orphaned' (i.e. unlinked to an analysis), and (D) verifying that taxon labels are recognizable by biologists, spelled correctly, and mapped to external taxonomies whenever possible. TreeBASE provides a special advanced access URL for anonymous reviewers and referees to provide additional quality control. Although additional NSF requirements relating to provenance and how data were generated are not normally required or scrutinized by TreeBASE, submitters who flag their submission as NSF-sponsored data will receive special attention by our staff. In these cases, TreeBASE staff will check to make sure that provenance and analysis metadata are adequately provided, and, as needed, communicate with the submitter and assist in properly formatting and ingesting these data. </p>
+<p>TreeBASE helps to certify data integrity by: </p>
+<ul>
+ <li>Validating submitted NEXUS files by parsing them with <a href="http://mesquiteproject.org/" target="_blank">Mesquite</a> on the TreeBASE server</li>
+ <li>Verifying that taxon labels in matrices and relevant trees are consistent</li>
+ <li>Verifying that data objects are not 'orphaned' (i.e. unlinked to an analysis)</li>
+ <li>Verifying that taxon labels are recognizable by biologists, spelled correctly, and mapped to external taxonomies whenever possible</li>
+</ul>
+<p>TreeBASE provides an advanced access URL for anonymous reviewers and referees to provide additional quality control before the data are made public. Although additional NSF requirements relating to provenance and how data were generated are not normally required or scrutinized by TreeBASE staff, submitters who flag their submission (in the submission notes section) as NSF-sponsored data will receive special attention by our staff. In these cases, TreeBASE staff will check to make sure that provenance and analysis metadata are adequately provided, and, as needed, communicate with the submitter and assist in properly formatting and ingesting these data. </p>
<h2>Data Standards and Dissemination</h2>
-<p>TreeBASE plans to remain in compliance with the emerging, but still evolving, standard of Minimal Information for a Phylogenetic Analysis (<a href="http://www.nescent.org/sites/evoio/MIAPA" target="_blank">MIAPA</a>). In addition, TreeBASE publishes persistant and resolvable globally unique identifiers for all major data objects and disseminates data and metadata using commonly accepted standards. A Restful <a href="http://www.nescent.org/wg/evoinfo/index.php?title=PhyloWS" target="_blank">PhyloWS</a> API exposes metadata using RSS feeds in RDF; a <a href="http://www.nexml.org/" target="_blank">NeXML</a> serialization exposes data marked up with metadata using published vocabularies and fully qualified URIs in compliance with <a href="http://linkeddata.org/" target="_blank">Linked Data</a> standards. Basic record metadata are published through an OIA-PMH service and records are mirrored by Dryad, which provides a secondary Dryad <a href="http://www.datacite.org" target="_blank">DataCite DOI</a>. However, for most people in the scientific community, data will be retrieved using the web user interface and downloaded in the NEXUS format, and metadata will be downloaded in tab-separated text format. </p>
+<p>TreeBASE plans to remain in compliance with the emerging, but still evolving, standard of Minimal Information for a Phylogenetic Analysis (<a href="http://www.nescent.org/sites/evoio/MIAPA" target="_blank">MIAPA</a>). In addition, TreeBASE publishes persistant and resolvable globally unique identifiers (GUIDs) for all major data objects and disseminates data and metadata using commonly accepted standards. A Restful <a href="http://www.nescent.org/wg/evoinfo/index.php?title=PhyloWS" target="_blank">PhyloWS</a> API exposes metadata using RSS feeds in RDF; a <a href="http://www.nexml.org/" target="_blank">NeXML</a> serialization exposes data marked up with metadata using published vocabularies and fully qualified URIs in compliance with <a href="http://linkeddata.org/" target="_blank">Linked Data</a> standards. Basic record metadata are published through an OIA-PMH service, and TreeBASE records are mirrored by Dryad, which provides a secondary Dryad <a href="http://www.datacite.org" target="_blank">DataCite DOI</a>. However, for most people in the scientific community, data will be retrieved using the web user interface and downloaded in the NEXUS format, while metadata can be downloaded separately in a tab-separated text format. </p>
<h2>Data Persistance</h2>
-<p>Although no data service can guarantee indefinite persistance, TreeBASE will make every effort to preserve it services as long as possible. Additionally, the Articles of Incorporation of the <a href="http://www.phylofoundation.org" target="_blank">Phyloinformatics Research Foundation</a>, which oversees TreeBASE activities, specifies that if dissolution is ever required the assets will be transferred to a similar entity with a comparable mission. </p>
+<p>Although no data service can guarantee indefinite persistance, TreeBASE will make every effort to preserve its services as long as possible. Additionally, the Articles of Incorporation of the <a href="http://www.phylofoundation.org" target="_blank">Phyloinformatics Research Foundation</a>, which oversees TreeBASE activities, specify that if dissolution is ever required the assets will be transferred to a similar entity with a comparable mission. </p>
<h2>Preparing a Data Management Plan for NSF</h2>
-<p>Scientists are welcome to designate TreeBASE as their selected repository and dissemination service for phylogenetic data generated by sponsored research. In this document, the following should be mentioned:</p>
+<p>Scientists are welcome to designate TreeBASE as their selected repository and dissemination service for phylogenetic data generated by sponsored research. In their Data Management Plan, we suggest that the following be mentioned:</p>
<ul>
- <li>Specify the name(s) of the person(s) responsible for preparing the data matrices, trees, and metadata for submission to TreeBASE.</li>
- <li>Identify the kinds of data that will be submitted, including provenance and analysis metadata as outlined above. For metadata not accepted by TreeBASE (e.g. digital images of specimens), identify other repositories where these will be stored (e.g. <a href="http://www.morphbank.net/" target="_blank">Morphbank</a> or <a href="http://www.morphobank.org/" target="_blank">Morphobank</a>), and indicate how these data objects will be linked between TreeBASE data and the other repository (e.g. using shared specimen catalog numbers). </li>
- <li>For your phylogenetic data, you can report that your data will be serialized using TreeBASE's data formats: NEXUS, for character and tree data alone, and NeXML for these data plus marked up with supplied metadata (e.g. basic Dublin Core publication data, basic Darwin Core specimen information, RBR collection codes and catalog numbers, uBio and NCBI taxon identification numbers, and Genbank accession numbers).</li>
- <li>Provide an overview of access and sharing. For your TreeBASE-submitted data, you can state that TreeBASE makes all data and metadata freely available to the public once the manuscript under review has been accepted by a peer-reviewed publisher. TreeBASE will allow for data embargo periods according to the policies of the journal, but once data are public they are assumed to be released to the public domain without any restrictions on reuse. We recommend that you state that you will provide TreeBASE's resolvable GUIDs for your deposited data in future progress reports to NSF, in relevant publications, and in your lab's web page. </li>
- <li>State that you will flag your submissions to TreeBASE as data subject to your data management plan so as to receive special attention by TreeBASE staff to help ensure that the data are richly annotated and fully compliant for maximum reuse in accordance with community standards in phylogenetics. </li>
+ <li>Specify the name(s) of person(s) responsible for preparing the data matrices, trees, and metadata for submission to TreeBASE.</li>
+ <li>Identify the kinds of data that will be submitted, including provenance and analysis metadata as outlined above. For metadata not accepted by TreeBASE (e.g. digital images of specimens), identify other repositories where these will be stored (e.g. <a href="http://www.morphbank.net/" target="_blank">Morphbank</a> or <a href="http://www.morphobank.org/" target="_blank">Morphobank</a>), and indicate how entities in TreeBASE and in the other repository will be linked (e.g. using shared specimen catalog numbers). </li>
+ <li>For data standards, you can state that your data will be serialized using TreeBASE's data formats: NEXUS, for character and tree data alone, and NeXML for character and tree data with additional metadata (e.g. basic Dublin Core publication data, Darwin Core specimen information, RBR collection codes and catalog numbers, uBio and NCBI taxon identification numbers, and Genbank accession numbers).</li>
+ <li>Provide an overview of access and sharing. For your TreeBASE-submitted data, you can state that TreeBASE makes all data and metadata freely available to the public once the manuscript under review has been accepted by a peer-review publication. TreeBASE will allow data embargo periods according to the policies of the journal, but once data are public they are assumed to be released to the public domain without any restrictions on reuse. We recommend that you state that you will provide TreeBASE's resolvable globally unique identifiers (GUIDs) for your deposited data in future progress reports to NSF, in relevant publications, and in your lab's web page. </li>
+ <li>State that you will flag your submissions to TreeBASE as data subject to your data management plan so as to receive special attention by TreeBASE staff to help ensure that the data are richly annotated and fully compliant for reuse in accordance with community standards in phylogenetics. </li>
</ul>
-<p>TreeBASE suggests that for each submission of data from sponsored research you contribute at least $50 towards defraying the costs of storage and dissemination, as well as in support of the additional scrutiny by TreeBASE staff for NSF data management compliance. This fee is collected by the Phyloinformatics Research Foundation, which overseas TreeBASE activities. Anticipated cost can be budgeted under publication expenses on your grant proposal's budget. </p>
-<p><hr /></p>
+<p>TreeBASE suggests that for each submission of data from sponsored research you contribute at least $100 towards defraying the costs of storage and dissemination, as well as in support of the additional scrutiny by TreeBASE staff for NSF data management compliance. This fee is collected by the Phyloinformatics Research Foundation, which overseas TreeBASE activities. Anticipated costs can be budgeted under publication expenses in your grant proposal's budget. </p>
+<hr /></p>
<table width="100%" border="0">
<tr>
<td width="50%" valign="top">Data storage contribution for sponsored research:</td>
@@ -48,4 +55,5 @@
</tr>
</table>
+
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2011-04-30 22:03:40 UTC (rev 824)
+++ trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2011-05-01 00:57:43 UTC (rev 825)
@@ -14,6 +14,7 @@
<li><a href="<c:url value="/reference.html"/>"><fmt:message key="nav.references"/></a></li>
</ul>
</li>
+ <li><a href="<c:url value="/dataMan.html"/>"><fmt:message key="nav.dataman"/></a></li>
<li><a href="<c:url value="/urlAPI.html"/>"><fmt:message key="nav.dataaccess"/></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>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <hs...@us...> - 2011-05-17 20:17:32
|
Revision: 870
http://treebase.svn.sourceforge.net/treebase/?rev=870&view=rev
Author: hshyket
Date: 2011-05-17 20:17:26 +0000 (Tue, 17 May 2011)
Log Message:
-----------
Adding in Google Analytics tracking functionality
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/decorators/adminTemplate.jsp
trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp
trunk/treebase-web/src/main/webapp/decorators/defaultTemplate.jsp
trunk/treebase-web/src/main/webapp/decorators/mainTemplate.jsp
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/common/googleAnalytics.jsp
trunk/treebase-web/src/main/webapp/scripts/googleAnalytics.js
Added: trunk/treebase-web/src/main/webapp/common/googleAnalytics.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/googleAnalytics.jsp (rev 0)
+++ trunk/treebase-web/src/main/webapp/common/googleAnalytics.jsp 2011-05-17 20:17:26 UTC (rev 870)
@@ -0,0 +1,15 @@
+<%@include file="/common/taglibs.jsp" %>
+<script type="text/javascript" src="<c:url value='/scripts/googleAnalytics.js'/>"></script>
+<script type="text/javascript">
+
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-23411098-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+
+</script>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/decorators/adminTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/adminTemplate.jsp 2011-05-17 19:19:58 UTC (rev 869)
+++ trunk/treebase-web/src/main/webapp/decorators/adminTemplate.jsp 2011-05-17 20:17:26 UTC (rev 870)
@@ -61,6 +61,6 @@
<!-- BEING FOOTER -->
<div id="footer"><c:import url="/common/footer.jsp" /></div>
</div> <!-- END WRAP -->
-
+<jsp:include page="/common/googleAnalytics.jsp"/>
</body>
</html>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp 2011-05-17 19:19:58 UTC (rev 869)
+++ trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp 2011-05-17 20:17:26 UTC (rev 870)
@@ -158,6 +158,6 @@
<!-- BEGIN FOOTER -->
<div id="footer"><c:import url="/common/footer.jsp" /></div>
</div> <!-- END WRAP -->
-
+<jsp:include page="/common/googleAnalytics.jsp"/>
</body>
</html>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/decorators/defaultTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/defaultTemplate.jsp 2011-05-17 19:19:58 UTC (rev 869)
+++ trunk/treebase-web/src/main/webapp/decorators/defaultTemplate.jsp 2011-05-17 20:17:26 UTC (rev 870)
@@ -104,6 +104,6 @@
<!-- BEING FOOTER -->
<div id="footer"><c:import url="/common/footer.jsp" /></div>
</div> <!-- END WRAP -->
-
+<jsp:include page="/common/googleAnalytics.jsp"/>
</body>
</html>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/decorators/mainTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/mainTemplate.jsp 2011-05-17 19:19:58 UTC (rev 869)
+++ trunk/treebase-web/src/main/webapp/decorators/mainTemplate.jsp 2011-05-17 20:17:26 UTC (rev 870)
@@ -28,6 +28,6 @@
<!-- BEING FOOTER -->
<div id="footer"><jsp:include page="/common/footer.jsp"/></div>
</div> <!-- END WRAP -->
-
+<jsp:include page="/common/googleAnalytics.jsp"/>
</body>
</html>
\ No newline at end of file
Added: trunk/treebase-web/src/main/webapp/scripts/googleAnalytics.js
===================================================================
--- trunk/treebase-web/src/main/webapp/scripts/googleAnalytics.js (rev 0)
+++ trunk/treebase-web/src/main/webapp/scripts/googleAnalytics.js 2011-05-17 20:17:26 UTC (rev 870)
@@ -0,0 +1,61 @@
+// This javascript tags file downloads and external links in Google Analytics.
+// You need to be using the Google Analytics New Tracking Code (ga.js)
+// for this script to work.
+// To use, place this file on all pages just above the Google Analytics tracking code.
+// All outbound links and links to non-html files should now be automatically tracked.
+//
+// This script has been provided by Goodwebpractices.com
+// Thanks to ShoreTel, MerryMan and Colm McBarron
+//
+// www.goodwebpractices.com
+// VKI has made changes as indicated below.
+
+if (document.getElementsByTagName) {
+ // Initialize external link handlers
+ var hrefs = document.getElementsByTagName("a");
+ for (var l = 0; l < hrefs.length; l++) {
+ // try {} catch{} block added by erikvold VKI
+ try{
+ //protocol, host, hostname, port, pathname, search, hash
+ if (hrefs[l].protocol == "mailto:") {
+ startListening(hrefs[l],"click",trackMailto);
+ } else if (hrefs[l].hostname == location.host) {
+ var path = hrefs[l].pathname + hrefs[l].search;
+ var isDoc = path.match(/\.(?:doc|eps|jpg|png|svg|xls|ppt|pdf|xls|zip|txt|vsd|vxd|js|css|rar|exe|wma|mov|avi|wmv|mp3|nex)($|\&|\?)/);
+ if (isDoc) {
+ startListening(hrefs[l],"click",trackExternalLinks);
+ }
+ } else if (!hrefs[l].href.match(/^javascript:/)) {
+ startListening(hrefs[l],"click",trackExternalLinks);
+ }
+ }
+ catch(e){
+ continue;
+ }
+ }
+}
+
+function startListening (obj,evnt,func) {
+ if (obj.addEventListener) {
+ obj.addEventListener(evnt,func,false);
+ } else if (obj.attachEvent) {
+ obj.attachEvent("on" + evnt,func);
+ }
+}
+
+function trackMailto (evnt) {
+ var href = (evnt.srcElement) ? evnt.srcElement.href : this.href;
+ var mailto = "/mailto/" + href.substring(7);
+ if (typeof(pageTracker) == "object") pageTracker._trackPageview(mailto);
+}
+
+function trackExternalLinks (evnt) {
+ var e = (evnt.srcElement) ? evnt.srcElement : this;
+ while (e.tagName != "A") {
+ e = e.parentNode;
+ }
+ var lnk = (e.pathname.charAt(0) == "/") ? e.pathname : "/" + e.pathname;
+ if (e.search && e.pathname.indexOf(e.search) == -1) lnk += e.search;
+ if (e.hostname != location.host) lnk = "/external/" + e.hostname + lnk;
+ if (typeof(pageTracker) == "object") pageTracker._trackPageview(lnk);
+}
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sfr...@us...> - 2011-06-04 03:36:33
|
Revision: 899
http://treebase.svn.sourceforge.net/treebase/?rev=899&view=rev
Author: sfrgpiel
Date: 2011-06-04 03:36:27 +0000 (Sat, 04 Jun 2011)
Log Message:
-----------
Updating the list of journals that require TreeBASE
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/images/journal_files/aliso.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/bry.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/ima.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/jfwm.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/myc.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/naf.gif
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2011-06-03 18:53:51 UTC (rev 898)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2011-06-04 03:36:27 UTC (rev 899)
@@ -28,6 +28,23 @@
</tr>
<tr>
<td>
+ <p><a href="http://www.rsabg.org/research-department/scientific-publications"
+ title="Aliso">
+ <img class="journal"
+ src="images/journal_files/aliso.jpg" alt="Aliso"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Aliso%22"
+ title="Find records in TreeBASE for articles published in Aliso">
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Aliso%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
<p><a href="http://www.amjbot.org/"
title="American Journal of Botany">
<img class="journal"
@@ -45,6 +62,23 @@
</tr>
<tr>
<td>
+ <p><a href="http://192.104.39.110/bryologist.html"
+ title="The Bryologist">
+ <img class="journal"
+ src="images/journal_files/bry.jpg" alt="Bryologist"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22The%20Bryologist%22"
+ title="Find records in TreeBASE for articles published in The Bryologist">
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22The%20Bryologist%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
<p><a href="http://www.wiley.com/bw/journal.asp?ref=0014-3820"
title="Evolution">
<img class="journal"
@@ -99,6 +133,24 @@
<tr>
<td>
<p>
+ <a
+ href="http://www.imafungus.org/">
+ <img class="journal"
+ src="images/journal_files/ima.jpg" alt="IMA Fungus"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22IMA+Fungus%22"
+ title="Find records in TreeBASE for articles published in IMA Fungus">
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22IMA+Fungus%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p>
<a href="http://www.publish.csiro.au/nid/120.htm">
<img class="journal"
src="images/journal_files/image004.gif"
@@ -116,6 +168,24 @@
</tr>
<tr>
<td>
+ <p>
+ <a href="http://www.fws.gov/science/jfwm.html">
+ <img class="journal"
+ src="images/journal_files/jfwm.jpg"
+ alt="Journal of Fish and Wildlife Management" />
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Journal+of+Fish+and+Wildlife+Management%22"
+ title="Find records in TreeBASE for articles published in Journal of Fish and Wildlife Management">
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Journal+of+Fish+and+Wildlife+Management%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
<p><a href="http://www.blackwellpublishing.com/journal.asp?ref=0962-1083">
<img class="journal" src="images/journal_files/image021.jpg" alt="Molecular Ecology" /></a></p>
</td>
@@ -173,6 +243,21 @@
<tr>
<td>
<p><a
+ href="http://www.tandf.co.uk/journals/journal.asp?issn=2150-1203">
+ <img class="journal"
+ src="images/journal_files/myc.jpg" alt="Mycology"/>
+ </a></p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycology%22"
+ title="Find records in TreeBASE for articles published in Mycology">
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycology%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
href="http://www.springer.com/life+sciences/microbiology/journal/10267">
<img class="journal"
src="images/journal_files/image008.gif" alt="Mycoscience"/></a></p>
@@ -199,6 +284,21 @@
<tr>
<td>
<p><a
+ href="http://www.fws.gov/science/naf.html">
+ <img class="journal"
+ src="images/journal_files/naf.gif"
+ alt="North American Fauna"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22North+American+Fauna%22"
+ title="Find records in TreeBASE for articles published in North American Fauna">
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22North+American+Fauna%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
href="http://www.elsevier.com/wps/find/journaldescription.cws_home/701789/description#description">
<img class="journal"
src="images/journal_files/image010.gif"
Added: trunk/treebase-web/src/main/webapp/images/journal_files/aliso.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/aliso.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/bry.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/bry.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/ima.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/ima.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/jfwm.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/jfwm.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/myc.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/myc.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/naf.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/naf.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sfr...@us...> - 2011-09-15 15:46:11
|
Revision: 955
http://treebase.svn.sourceforge.net/treebase/?rev=955&view=rev
Author: sfrgpiel
Date: 2011-09-15 15:46:00 +0000 (Thu, 15 Sep 2011)
Log Message:
-----------
updating journal links
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/images/journal_files/amnat.gif
trunk/treebase-web/src/main/webapp/images/journal_files/ejpp.gif
trunk/treebase-web/src/main/webapp/images/journal_files/fd_algo.gif
trunk/treebase-web/src/main/webapp/images/journal_files/fd_bryo.gif
trunk/treebase-web/src/main/webapp/images/journal_files/fd_myco.gif
trunk/treebase-web/src/main/webapp/images/journal_files/jh.gif
trunk/treebase-web/src/main/webapp/images/journal_files/mer.gif
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2011-09-15 14:28:32 UTC (rev 954)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2011-09-15 15:46:00 UTC (rev 955)
@@ -26,6 +26,7 @@
it in your favorite RSS reader)</p>
</td>
</tr>
+<!-- aliso -->
<tr>
<td>
<p><a href="http://www.rsabg.org/research-department/scientific-publications"
@@ -39,10 +40,11 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Aliso%22"
title="Find records in TreeBASE for articles published in Aliso">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Aliso%22
+ <%=purlBase%>study/find?query=prism.publicationName=="Aliso"
</a></p>
</td>
</tr>
+<!-- american journal of botany -->
<tr>
<td>
<p><a href="http://www.amjbot.org/"
@@ -56,12 +58,31 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22American%20Journal%20of%20Botany%22"
title="Find records in TreeBASE for articles published in the American Journal of Botany">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22American%20Journal%20of%20Botany%22
+ <%=purlBase%>study/find?query=prism.publicationName=="American+Journal+of+Botany"
</a></p>
</td>
</tr>
+<!-- american naturalist -->
<tr>
<td>
+ <p><a href="http://www.asnamnat.org/"
+ title="American Naturalist">
+ <img class="journal"
+ src="images/journal_files/amnat.gif" alt="American Naturalist"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22American%20Naturalist%22"
+ title="Find records in TreeBASE for articles published in the American Naturalist">
+ <%=purlBase%>study/find?query=prism.publicationName=="American+Naturalist"
+ </a></p>
+ </td>
+ </tr>
+<!-- the bryologist -->
+ <tr>
+ <td>
<p><a href="http://192.104.39.110/bryologist.html"
title="The Bryologist">
<img class="journal"
@@ -73,12 +94,85 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22The%20Bryologist%22"
title="Find records in TreeBASE for articles published in The Bryologist">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22The%20Bryologist%22
+ <%=purlBase%>study/find?query=prism.publicationName=="The+Bryologist"
</a></p>
</td>
</tr>
+<!-- cryptogamie algologie -->
<tr>
<td>
+ <p><a href="http://www.cryptogamie.com/pagint_en/editeur/revues.php"
+ title="Cryptogamie Algologie">
+ <img class="journal"
+ src="images/journal_files/fd_algo.gif" alt="Cryptogamie Algologie"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Cryptogamie%20Algologie%22"
+ title="Find records in TreeBASE for articles published in the Cryptogamie Algologie">
+ <%=purlBase%>study/find?query=prism.publicationName=="Cryptogamie+Algologie"
+ </a></p>
+ </td>
+ </tr>
+<!-- cryptogamie bryologie -->
+ <tr>
+ <td>
+ <p><a href="http://www.cryptogamie.com/pagint_en/editeur/revue_bryo.php"
+ title="Cryptogamie Bryologie">
+ <img class="journal"
+ src="images/journal_files/fd_algo.gif" alt="Cryptogamie Bryologie"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Cryptogamie%20Bryologie%22"
+ title="Find records in TreeBASE for articles published in the Cryptogamie Bryologie">
+ <%=purlBase%>study/find?query=prism.publicationName=="Cryptogamie+Bryologie"
+ </a></p>
+ </td>
+ </tr>
+<!-- cryptogamie mycologie -->
+ <tr>
+ <td>
+ <p><a href="http://www.cryptogamie.com/pagint_en/editeur/revue_bryo.php"
+ title="Cryptogamie Mycologie">
+ <img class="journal"
+ src="images/journal_files/fd_algo.gif" alt="Cryptogamie Mycologie"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Cryptogamie%20Mycologie%22"
+ title="Find records in TreeBASE for articles published in the Cryptogamie Mycologie">
+ <%=purlBase%>study/find?query=prism.publicationName=="Cryptogamie+Mycologie"
+ </a></p>
+ </td>
+ </tr>
+<!-- european journal of plant pathology" -->
+ <tr>
+ <td>
+ <p><a href="http://www.springer.com/life+sciences/plant+sciences/journal/10658"
+ title=""European Journal of Plant Pathology">
+ <img class="journal"
+ src="images/journal_files/ejpp.gif" alt="European Journal of Plant Pathology"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22European%20Journal%20of%20Plant%20Pathology%22"
+ title="Find records in TreeBASE for articles published in the European Journal of Plant Pathology">
+ <%=purlBase%>study/find?query=prism.publicationName=="European+Journal+of+Plant+Pathology"
+ </a></p>
+ </td>
+ </tr>
+<!-- evolution -->
+ <tr>
+ <td>
<p><a href="http://www.wiley.com/bw/journal.asp?ref=0014-3820"
title="Evolution">
<img class="journal"
@@ -90,10 +184,11 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DEvolution"
title="Find records in TreeBASE for articles published in Evolution">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3DEvolution
+ <%=purlBase%>study/find?query=prism.publicationName==Evolution
</a></p>
</td>
</tr>
+<!-- evolutionary applications -->
<tr>
<td>
<p>
@@ -108,10 +203,11 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22"
title="Find records in TreeBASE for articles published in Evolutionary Applications">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22
+ <%=purlBase%>study/find?query=prism.publicationName=="Evolutionary+Applications"
</a></p>
</td>
</tr>
+<!-- fungal biology -->
<tr>
<td>
<p>
@@ -126,10 +222,11 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22"
title="Find records in TreeBASE for articles published in Fungal Biology">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22
+ <%=purlBase%>study/find?query=prism.publicationName=="Fungal+Biology"
</a></p>
</td>
</tr>
+<!-- ima fungus -->
<tr>
<td>
<p>
@@ -144,10 +241,11 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22IMA+Fungus%22"
title="Find records in TreeBASE for articles published in IMA Fungus">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22IMA+Fungus%22
+ <%=purlBase%>study/find?query=prism.publicationName=="IMA+Fungus"
</a></p>
</td>
</tr>
+<!-- invertebrate systmatics -->
<tr>
<td>
<p>
@@ -162,10 +260,11 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22"
title="Find records in TreeBASE for articles published in Invertebrate Systematics">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22
+ <%=purlBase%>study/find?query=prism.publicationName=="Invertebrate+Systematics"
</a></p>
</td>
</tr>
+<!-- journal of fish and wildlife management -->
<tr>
<td>
<p>
@@ -180,12 +279,31 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Journal+of+Fish+and+Wildlife+Management%22"
title="Find records in TreeBASE for articles published in Journal of Fish and Wildlife Management">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Journal+of+Fish+and+Wildlife+Management%22
+ <%=purlBase%>study/find?query=prism.publicationName=="Journal+of+Fish+and+Wildlife+Management"
</a></p>
</td>
</tr>
+<!-- journal of heredity -->
<tr>
<td>
+ <p><a href="http://jhered.oxfordjournals.org/"
+ title="Journal of Heredity">
+ <img class="journal"
+ src="images/journal_files/jh.gif" alt="Journal of Heredity"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Journal%20of%20Heredity%22"
+ title="Find records in TreeBASE for articles published in the Journal of Heredity">
+ <%=purlBase%>study/find?query=prism.publicationName=="Journal+of+Heredity"
+ </a></p>
+ </td>
+ </tr>
+<!-- molecular ecology -->
+ <tr>
+ <td>
<p><a href="http://www.blackwellpublishing.com/journal.asp?ref=0962-1083">
<img class="journal" src="images/journal_files/image021.jpg" alt="Molecular Ecology" /></a></p>
</td>
@@ -193,12 +311,31 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Molecular+Ecology%22"
title="Find records in TreeBASE for articles published in Molecular Ecology">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Molecular+Ecology%22</a>
+ <%=purlBase%>study/find?query=prism.publicationName=="Molecular+Ecology"</a>
</p>
</td>
</tr>
+<!-- molecular ecology resources -->
<tr>
<td>
+ <p><a href="http://www.wiley.com/bw/journal.asp?ref=1755-098X"
+ title="Molecular Ecology Resources">
+ <img class="journal"
+ src="images/journal_files/mer.gif" alt="Molecular Ecology Resources"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Molecular%20Ecology%20Resources%22"
+ title="Find records in TreeBASE for articles published in the Molecular Ecology Resources">
+ <%=purlBase%>study/find?query=prism.publicationName==Molecular+"Ecology+Resources"
+ </a></p>
+ </td>
+ </tr>
+<!-- mycologia -->
+ <tr>
+ <td>
<p><a href="http://www.msafungi.org/">
<img class="journal" src="images/journal_files/image005.gif" alt="Mycologia" /></a></p>
</td>
@@ -206,10 +343,11 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DMycologia"
title="Find records in TreeBASE for articles published in Mycologia">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3DMycologia</a>
+ <%=purlBase%>study/find?query=prism.publicationName==Mycologia</a>
</p>
</td>
</tr>
+<!-- mycological progress -->
<tr>
<td>
<p><a
@@ -219,12 +357,13 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycologial%20Progress%22"
title="Find records in TreeBASE for articles published in Mycologial Progress">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22</a>
+ <%=purlBase%>study/find?query=prism.publicationName=="Mycologial+Progress"</a>
</p>
</td>
</tr>
+<!-- mycological research -->
<tr>
<td>
<p><a
@@ -235,11 +374,12 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycologial%20Research%22"
title="Find records in TreeBASE for articles published in Mycologial Research">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="Mycologial+Research"</a></p>
</td>
</tr>
+<!-- mycology -->
<tr>
<td>
<p><a
@@ -252,9 +392,10 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycology%22"
title="Find records in TreeBASE for articles published in Mycology">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycology%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="Mycology"</a></p>
</td>
</tr>
+<!-- mycoscience -->
<tr>
<td>
<p><a
@@ -266,9 +407,10 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DMycoscience"
title="Find records in TreeBASE for articles published in Mycoscience">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3DMycoscience</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName==Mycoscience</a></p>
</td>
</tr>
+<!-- mycosphere -->
<tr>
<td>
<p><a href="http://www.mycosphere.org/">
@@ -278,9 +420,10 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DMycosphere"
title="Find records in TreeBASE for articles published in Mycosphere">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3DMycosphere</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName==Mycosphere</a></p>
</td>
</tr>
+<!-- north american fauna -->
<tr>
<td>
<p><a
@@ -291,11 +434,12 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22North+American+Fauna%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22North%20American%20Fauna%22"
title="Find records in TreeBASE for articles published in North American Fauna">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22North+American+Fauna%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="North+American+Fauna"</a></p>
</td>
</tr>
+<!-- organisms, diversity, and evolution -->
<tr>
<td>
<p><a
@@ -306,11 +450,12 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Organisms%20Diversity%20&%20Evolution%22"
title="Find records in TreeBASE for articles published in Organisms Diversity & Evolution">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="Organisms+Diversity+&+Evolution"</a></p>
</td>
</tr>
+<!-- persoonia -->
<tr>
<td>
<p><a href="http://www.persoonia.org/">
@@ -320,9 +465,10 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DPersoonia"
title="Find records in TreeBASE for articles published in Persoonia">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3DPersoonia</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName==Persoonia</a></p>
</td>
</tr>
+<!-- phytopathology -->
<tr>
<td>
<p>
@@ -330,17 +476,18 @@
<img
class="journal"
src="images/journal_files/image012.jpg"
- alt="Phytopahology"/>
+ alt="Phytopathology"/>
</a>
</p>
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DPhytopahology"
- title="Find records in TreeBASE for articles published in Phytopahology">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3DPhytopahology</a></p>
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DPhytopathology"
+ title="Find records in TreeBASE for articles published in Phytopathology">
+ <%=purlBase%>study/find?query=prism.publicationName==Phytopathology</a></p>
</td>
</tr>
+<!-- plant disease -->
<tr>
<td>
<p><a href="http://www.apsnet.org/pd/">
@@ -349,11 +496,12 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Plant%20Disease%22"
title="Find records in TreeBASE for articles published in Plant Disease">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="Plant+Disease"</a></p>
</td>
</tr>
+<!-- plos currents tol -->
<tr>
<td>
<p><a href="http://currents.plos.org/treeoflife"><img
@@ -362,11 +510,12 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22PLoS+Currents:+Tree+of+Life%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22PLoS%20Currents:%20Tree%20of%20Life%22"
title="Find records in TreeBASE for articles published in PLoS Currents: Tree of Life">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22PLoS+Currents:+Tree+of+Life%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="PLoS+Currents:+Tree+of+Life"</a></p>
</td>
</tr>
+<!-- rhodora -->
<tr>
<td>
<p><a href="http://www.rhodora.org/Rhodora.html"><img
@@ -377,9 +526,10 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DRhodora"
title="Find records in TreeBASE for articles published in Rhodora">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3DRhodora</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName==Rhodora</a></p>
</td>
</tr>
+<!-- muelleria -->
<tr>
<td>
<p><a
@@ -391,9 +541,10 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DMuelleria"
title="Find records in TreeBASE for articles published in Muelleria">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3DMuelleria</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName==Muelleria</a></p>
</td>
</tr>
+<!-- studies in mycology -->
<tr>
<td>
<p><a href="http://www.studiesinmycology.org/">
@@ -402,11 +553,12 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Studies%20in%20Mycology%22"
title="Find records in TreeBASE for articles published in Studies in Mycology">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="Studies+in+Mycology"</a></p>
</td>
</tr>
+<!-- systematic biology -->
<tr>
<td>
<p><a href="http://systbiol.org/">
@@ -415,11 +567,12 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Systematic%20Biology%22"
title="Find records in TreeBASE for articles published in Systematic Biology">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="Systematic+Biology"</a></p>
</td>
</tr>
+<!-- systematic botany -->
<tr>
<td>
<p><a href="http://www.sysbot.org/">
@@ -428,11 +581,12 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Systematic%20Botany%22"
title="Find records in TreeBASE for articles published in Systematic Botany">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="Systematic+Botany"</a></p>
</td>
</tr>
+<!-- tropical bryology -->
<tr>
<td>
<p><a href="http://tropical-bryology.org/">
@@ -441,15 +595,15 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Tropical%20Bryology%22"
title="Find records in TreeBASE for articles published in Tropical Bryology">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="Tropical+Bryology"</a></p>
</td>
</tr>
</table>
<p><b>Other Journals with a Significant Presence in TreeBASE</b>: <a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Annals+of+the+Missouri+Botanical+Garden%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Annals%20of%20the%20Missouri%20Botanical%20Garden%22"
title="Annals of the Missouri Botanical Garden">Annals of the
Missouri Botanical Garden</a>; <a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Biological+Journal+of+the+Linnean+Society%22"
Added: trunk/treebase-web/src/main/webapp/images/journal_files/amnat.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/amnat.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/ejpp.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/ejpp.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/fd_algo.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/fd_algo.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/fd_bryo.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/fd_bryo.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/fd_myco.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/fd_myco.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/jh.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/jh.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/mer.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/mer.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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|
|
From: <sfr...@us...> - 2011-09-15 17:46:46
|
Revision: 958
http://treebase.svn.sourceforge.net/treebase/?rev=958&view=rev
Author: sfrgpiel
Date: 2011-09-15 17:46:38 +0000 (Thu, 15 Sep 2011)
Log Message:
-----------
Moving the RSS button to a more logical location
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
trunk/treebase-web/src/main/webapp/common/search-nav.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp 2011-09-15 17:30:52 UTC (rev 957)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp 2011-09-15 17:46:38 UTC (rev 958)
@@ -12,8 +12,6 @@
pageContext.setAttribute("searchOptions", searchOptions);
%>
-<%@page import="org.cipres.treebase.TreebaseUtil"%>
-<% String purlBase = TreebaseUtil.getPurlBase(); %>
<form id="searchSimple" method="post">
<fieldset>
For study IDs with values less than 3000, please search using the "Legacy Study ID" button.<br>
@@ -30,13 +28,6 @@
<a href="#" class="openHelp" onclick="openHelp('studyKeywordSearchForm')">
<img class="iconButton" src="<fmt:message key="icons.help"/>" />
</a>
- <a href="<%=purlBase%>study/find?query=prism.modificationDate%3E%221996-01-01T05:00:00Z%22&format=rss1">
- <img
- class="iconButton"
- src="<fmt:message key="icons.rss"/>"
- title="<fmt:message key="download.rss"/>"
- alt="<fmt:message key="download.rss"/>"/>
- </a>
</fieldset>
<jsp:include page="querySearchBox.jsp"/>
</form>
Modified: trunk/treebase-web/src/main/webapp/common/search-nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/search-nav.jsp 2011-09-15 17:30:52 UTC (rev 957)
+++ trunk/treebase-web/src/main/webapp/common/search-nav.jsp 2011-09-15 17:46:38 UTC (rev 958)
@@ -1,4 +1,6 @@
<%@ include file="/common/taglibs.jsp"%>
+<%@page import="org.cipres.treebase.TreebaseUtil"%>
+<% String purlBase = TreebaseUtil.getPurlBase(); %>
<ul id="s-nav">
<li id="s-navlabel">Search</li>
@@ -49,6 +51,15 @@
src="<fmt:message key="icons.help"/>" alt="?"/>
</a>
</li>
+ <li style="background-color:transparent">
+ <a href="<%=purlBase%>study/find?query=prism.modificationDate%3E%221996-01-01T05:00:00Z%22&format=rss1" style="background-color:transparent; border:none">
+ <img
+ class="iconButton"
+ src="<fmt:message key="icons.rss"/>"
+ title="<fmt:message key="download.rss"/>"
+ alt="<fmt:message key="download.rss"/>"/>
+ </a>
+ </li>
<!--
<li id="st-taxonView"><a href="<c:url value="/search/taxonView.html"/>"><fmt:message key="search.nav.taxonViewTab"/></a></li>
-->
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|
|
From: <hs...@us...> - 2011-09-15 19:37:34
|
Revision: 961
http://treebase.svn.sourceforge.net/treebase/?rev=961&view=rev
Author: hshyket
Date: 2011-09-15 19:37:28 +0000 (Thu, 15 Sep 2011)
Log Message:
-----------
Updating RSS feed date so that it goes 6 months back and changing the RSS icon to add transparency
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/common/search-nav.jsp
trunk/treebase-web/src/main/webapp/images/icons/rss.gif
Modified: trunk/treebase-web/src/main/webapp/common/search-nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/search-nav.jsp 2011-09-15 18:31:04 UTC (rev 960)
+++ trunk/treebase-web/src/main/webapp/common/search-nav.jsp 2011-09-15 19:37:28 UTC (rev 961)
@@ -1,7 +1,17 @@
<%@ include file="/common/taglibs.jsp"%>
<%@page import="org.cipres.treebase.TreebaseUtil"%>
+<%@page import="java.util.Date" %>
+<%@page import="java.util.Calendar" %>
+<%@page import="java.text.SimpleDateFormat;" %>
+
<% String purlBase = TreebaseUtil.getPurlBase(); %>
+<%
+ Calendar cal = Calendar.getInstance();
+ cal.add(Calendar.MONTH, -6);
+ SimpleDateFormat isoFormat = new SimpleDateFormat("yyyy-MM-dd");
+%>
+
<ul id="s-nav">
<li id="s-navlabel">Search</li>
<li id="st-study">
@@ -52,7 +62,7 @@
</a>
</li>
<li style="background-color:transparent">
- <a href="<%=purlBase%>study/find?query=prism.modificationDate%3E%221996-01-01T05:00:00Z%22&format=rss1" style="background-color:transparent; border:none">
+ <a href="<%=purlBase%>study/find?query=prism.modificationDate%3E%22<%=isoFormat.format(cal.getTime())%>T05:00:00Z%22&format=rss1" style="background-color:transparent; border:none" target="_blank">
<img
class="iconButton"
src="<fmt:message key="icons.rss"/>"
Modified: trunk/treebase-web/src/main/webapp/images/icons/rss.gif
===================================================================
(Binary files differ)
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|
|
From: <hs...@us...> - 2011-09-30 16:40:06
|
Revision: 966
http://treebase.svn.sourceforge.net/treebase/?rev=966&view=rev
Author: hshyket
Date: 2011-09-30 16:40:00 +0000 (Fri, 30 Sep 2011)
Log Message:
-----------
Changing size of search content area to fill the user's browser
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp
trunk/treebase-web/src/main/webapp/styles/styles.css
Modified: trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp 2011-09-26 14:47:20 UTC (rev 965)
+++ trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp 2011-09-30 16:40:00 UTC (rev 966)
@@ -141,7 +141,7 @@
<!-- BEGIN RIGHT COLUMN -->
- <div id="content">
+ <div id="content" class="contentsearch">
<div class="gutter">
<c:if test="${not empty page.heading}">
<h2><decorator:getProperty property="page.heading"/></h2>
Modified: trunk/treebase-web/src/main/webapp/styles/styles.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/styles.css 2011-09-26 14:47:20 UTC (rev 965)
+++ trunk/treebase-web/src/main/webapp/styles/styles.css 2011-09-30 16:40:00 UTC (rev 966)
@@ -94,6 +94,11 @@
width: 67%
}
+.contentsearch {
+ float: left;
+ width: 100% !important;
+}
+
/* This sidebar ID is also used for the 3column right sidebar */
#sidebar {
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|
|
From: <hs...@us...> - 2011-11-16 17:08:11
|
Revision: 981
http://treebase.svn.sourceforge.net/treebase/?rev=981&view=rev
Author: hshyket
Date: 2011-11-16 17:08:00 +0000 (Wed, 16 Nov 2011)
Log Message:
-----------
Fixing the way old browser error message was displayed (no longer a popup). Also modified so that future versions of IE are not given an incompatibility message (above IE7).
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/common/meta.jsp
trunk/treebase-web/src/main/webapp/decorators/adminTemplate.jsp
trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp
trunk/treebase-web/src/main/webapp/decorators/defaultTemplate.jsp
trunk/treebase-web/src/main/webapp/decorators/mainTemplate.jsp
trunk/treebase-web/src/main/webapp/decorators/testTemplate.jsp
trunk/treebase-web/src/main/webapp/styles/styles.css
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/common/updateBrowser.jsp
Modified: trunk/treebase-web/src/main/webapp/common/meta.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/meta.jsp 2011-11-02 17:48:18 UTC (rev 980)
+++ trunk/treebase-web/src/main/webapp/common/meta.jsp 2011-11-16 17:08:00 UTC (rev 981)
@@ -11,21 +11,23 @@
<meta name="msvalidate.01" content="D931446190993D0D2D719F2978AC44EB" />
<link rel="icon" href="<c:url value="/images/favicon.ico"/>"/>
<%
+ String browsername = "";
+ String browserversion = "";
String ua = request.getHeader( "User-Agent" );
boolean isMSIE = ( ua != null && ua.indexOf( "MSIE" ) != -1 );
boolean isOldMSIE = false;
if ( isMSIE ) {
- isOldMSIE = ua.indexOf("MSIE 8.0") == -1;
+ //isOldMSIE = ua.indexOf("MSIE 8.0") == -1;
+ String subsString = ua.substring( ua.indexOf("MSIE"));
+ String Info[] = (subsString.split(";")[0]).split(" ");
+ browsername = Info[0];
+ browserversion = Info[1];
+ float version = Float.parseFloat(browserversion);
+ if (version < 8) {
+ isOldMSIE = true;
+
+ }
}
%>
-<!-- <%= ua %> -->
-<% if( isOldMSIE ){ %>
- <script type="text/javascript">
- alert("Please upgrade your browser!\n\n"+
- "The TreeBASE team simply do not have the resources to support\n"+
- "old versions of Internet Explorer. There are many good, free\n"+
- "browsers available (IE8, FireFox, Safari, Chrome, Opera, etc.),\n"+
- "please use one of those instead.");
- </script>
-<% } %>
\ No newline at end of file
+<!-- <%= ua %> -->
\ No newline at end of file
Added: trunk/treebase-web/src/main/webapp/common/updateBrowser.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/updateBrowser.jsp (rev 0)
+++ trunk/treebase-web/src/main/webapp/common/updateBrowser.jsp 2011-11-16 17:08:00 UTC (rev 981)
@@ -0,0 +1,10 @@
+<div id="browserupdate">
+<p>Your browser is not supported by TreeBASE. Please download one of the browsers listed below:</p>
+<p><a href="http://windows.microsoft.com/en-US/internet-explorer/downloads/ie" target="_blank">Internet Explorer</a>
+<a href="http://www.mozilla.org/en-US/firefox/new/" target="_blank">Firefox</a>
+<a href="http://www.google.com/chrome" target="_blank">Chrome</a>
+<a href="http://www.apple.com/safari/download/" target="_blank">Safari</a>
+<a href="http://www.opera.com/download/" target="_blank">Opera</a>
+</p>
+<br />
+</div>
Modified: trunk/treebase-web/src/main/webapp/decorators/adminTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/adminTemplate.jsp 2011-11-02 17:48:18 UTC (rev 980)
+++ trunk/treebase-web/src/main/webapp/decorators/adminTemplate.jsp 2011-11-16 17:08:00 UTC (rev 981)
@@ -26,7 +26,9 @@
</head>
<body <decorator:getProperty property="body.id" writeEntireProperty="true"/>>
-
+<% if( isOldMSIE ){ %>
+<c:import url="/common/updateBrowser.jsp"/>
+<% } %>
<!-- BEGIN WRAP -->
<div id="wrap">
<!-- BEGIN HEADER -->
Modified: trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp 2011-11-02 17:48:18 UTC (rev 980)
+++ trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp 2011-11-16 17:08:00 UTC (rev 981)
@@ -117,7 +117,9 @@
</head>
<body <decorator:getProperty property="body.id" writeEntireProperty="true"/> onload="TreeBASE.initialize()">
-
+<% if( isOldMSIE ){ %>
+<c:import url="/common/updateBrowser.jsp"/>
+<% } %>
<!-- BEGIN WRAP -->
<div id="wrap">
<!-- BEGIN HEADER -->
Modified: trunk/treebase-web/src/main/webapp/decorators/defaultTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/defaultTemplate.jsp 2011-11-02 17:48:18 UTC (rev 980)
+++ trunk/treebase-web/src/main/webapp/decorators/defaultTemplate.jsp 2011-11-16 17:08:00 UTC (rev 981)
@@ -65,7 +65,9 @@
</head>
<body <decorator:getProperty property="body.id" writeEntireProperty="true"/> onload="TreeBASE.initialize()">
-
+<% if( isOldMSIE ){ %>
+<c:import url="/common/updateBrowser.jsp"/>
+<% } %>
<!-- BEGIN WRAP -->
<div id="wrap">
<!-- BEGIN HEADER -->
Modified: trunk/treebase-web/src/main/webapp/decorators/mainTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/mainTemplate.jsp 2011-11-02 17:48:18 UTC (rev 980)
+++ trunk/treebase-web/src/main/webapp/decorators/mainTemplate.jsp 2011-11-16 17:08:00 UTC (rev 981)
@@ -16,7 +16,9 @@
</head>
<body id="info" onload="TreeBASE.initialize()">
-
+<% if( isOldMSIE ){ %>
+<c:import url="/common/updateBrowser.jsp"/>
+<% } %>
<!-- BEGIN WRAP -->
<div id="wrap">
<!-- BEGIN HEADER -->
Modified: trunk/treebase-web/src/main/webapp/decorators/testTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/testTemplate.jsp 2011-11-02 17:48:18 UTC (rev 980)
+++ trunk/treebase-web/src/main/webapp/decorators/testTemplate.jsp 2011-11-16 17:08:00 UTC (rev 981)
@@ -16,7 +16,9 @@
</head>
<body id="info" onload="TreeBASE.initialize()">
-
+<% if( isOldMSIE ){ %>
+<c:import url="/common/updateBrowser.jsp"/>
+<% } %>
<!-- BEGIN WRAP -->
<div id="wrap">
<!-- BEGIN HEADER -->
Modified: trunk/treebase-web/src/main/webapp/styles/styles.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/styles.css 2011-11-02 17:48:18 UTC (rev 980)
+++ trunk/treebase-web/src/main/webapp/styles/styles.css 2011-11-16 17:08:00 UTC (rev 981)
@@ -64,6 +64,19 @@
border-top: 1px solid #3d649f
}
+#browserupdate {
+ background-color: #FFFFC1;
+ text-align: center;
+ margin-bottom: -18px;
+}
+
+#browserupdate a:link, #browserupdate a:visited, #browserupdate a:hover, #browserupdate a:active {
+ color: #003366;
+ text-decoration: none;
+ font-weight: bold;
+ margin-right: 20px;
+}
+
/* Page Structure/Layout
*******************************************************************************************/
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|
|
From: <sfr...@us...> - 2012-01-26 16:56:27
|
Revision: 1021
http://treebase.svn.sourceforge.net/treebase/?rev=1021&view=rev
Author: sfrgpiel
Date: 2012-01-26 16:56:16 +0000 (Thu, 26 Jan 2012)
Log Message:
-----------
BibTeX and RIS clutter the summary page, so this hides them by default with toggle function to display.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp
trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp 2012-01-25 19:22:51 UTC (rev 1020)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp 2012-01-26 16:56:16 UTC (rev 1021)
@@ -116,17 +116,20 @@
RDF
</a> */ %>
</li>
+
+ <li><a onclick="toggle_visibility('bibtexfoo');">Show BibTeX reference</a>
+ <pre id="bibtexfoo" style="display:none;width:100%;overflow:scroll">
+ <c:out value="${cit.bibtexReference}"/>
+ </pre>
+ </li>
+
+ <li><a onclick="toggle_visibility('risfoo');">Show RIS reference</a>
+ <pre id="risfoo" style="display:none;width:100%;overflow:scroll">
+ <c:out value="${cit.risReference}"/>
+ </pre>
+ </li>
</ul>
-<h3>BibTeX reference</h3>
-<pre style="width:100%;overflow:scroll">
-<c:out value="${cit.bibtexReference}"/>
-</pre>
-<h3>RIS reference</h3>
-<pre style="width:100%;overflow:scroll">
-<c:out value="${cit.risReference}"/>
-</pre>
-
</body>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp 2012-01-25 19:22:51 UTC (rev 1020)
+++ trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp 2012-01-26 16:56:16 UTC (rev 1021)
@@ -109,6 +109,14 @@
RemoteUniqueOtherAlgorithmService.findAllUniqueOtherAlgorithmDescriptions(token, function(data) { autocompleter.setChoices(data) });
}
+ function toggle_visibility(id) {
+ var e = document.getElementById(id);
+ if(e.style.display == 'block')
+ e.style.display = 'none';
+ else
+ e.style.display = 'block';
+ }
+
//]]>
</script>
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|
|
From: <rv...@us...> - 2012-02-14 21:23:56
|
Revision: 1062
http://treebase.svn.sourceforge.net/treebase/?rev=1062&view=rev
Author: rvos
Date: 2012-02-14 21:23:50 +0000 (Tue, 14 Feb 2012)
Log Message:
-----------
Adding links to @TreeBASE and @rdmpage's Mendeley group.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/images/mendeley-logo.png
trunk/treebase-web/src/main/webapp/images/twitter-logo.png
Modified: trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2012-02-14 20:40:34 UTC (rev 1061)
+++ trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2012-02-14 21:23:50 UTC (rev 1062)
@@ -20,6 +20,14 @@
<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>
+ <center>
+ <a href="http://twitter.com/treebase" title="Follow @TreeBASE on Twitter">
+ <img src="<c:url value="images/twitter-logo.png" alt="Follow @TreeBASE on twitter"/>
+ </a>
+ <a href="http://www.mendeley.com/groups/734351/treebase/" title="All publications in TreeBASE on Mendeley">
+ <img src="<c:url value="images/mendeley-logo.png" alt="All publications in TreeBASE on Mendeley">
+ </a>
+ </center>
</div>
</div>
<img src="<c:url value="images/footer_bg.gif"/>" style="width:100%" alt="" />
Added: trunk/treebase-web/src/main/webapp/images/mendeley-logo.png
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/mendeley-logo.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/twitter-logo.png
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/twitter-logo.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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From: <rv...@us...> - 2012-02-20 20:32:46
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Revision: 1076
http://treebase.svn.sourceforge.net/treebase/?rev=1076&view=rev
Author: rvos
Date: 2012-02-20 20:32:40 +0000 (Mon, 20 Feb 2012)
Log Message:
-----------
Adding javascript page variables for simplified search box
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSearch.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studySearch.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/taxonSearch.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSearch.jsp
trunk/treebase-web/src/main/webapp/common/search-nav.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSearch.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSearch.jsp 2012-02-20 19:35:10 UTC (rev 1075)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSearch.jsp 2012-02-20 20:32:40 UTC (rev 1076)
@@ -8,13 +8,25 @@
<div id="s-clear"></div>
+<script type="text/javascript">
+ //<![CDATA[
+ // These are the mappings from inferred search term types to search predicates for this scope
+ var predicates = {
+ 'integer' : [ 'tb.identifier.matrix', 'tb.identifier.matrix.tb1', 'tb.ntax.matrix', 'tb.nchar.matrix' ],
+ 'id' : [ 'tb.identifier.matrix', 'tb.identifier.matrix.tb1' ],
+ 'word' : [ 'tb.title.matrix', 'tb.type.matrix' ],
+ 'doi' : [ 'prism.doi' ] // this doesn't work yet, we have no search on doi
+ };
+
+ // purlBase is assigned in /common/search-nav.jsp
+ var phyloWSURI = purlBase + 'matrix/find?query=';
+ //]]>
+</script>
<jsp:include page="matrixSimpleSearchForm.jsp"/>
<c:set var="searchType" value="matrix" scope="request"/>
-<%-- <jsp:include page="studyTaxonLabelSearchForm.jsp"/> --%>
-
<div id="s-clear"></div>
<jsp:include page="searchMessages.jsp"/>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studySearch.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studySearch.jsp 2012-02-20 19:35:10 UTC (rev 1075)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studySearch.jsp 2012-02-20 20:32:40 UTC (rev 1076)
@@ -10,10 +10,24 @@
<div id="s-clear"></div>
+<script type="text/javascript">
+ //<![CDATA[
+ // These are the mappings from inferred search term types to search predicates for this scope
+ var predicates = {
+ 'integer' : [ 'tb.identifier.study', 'tb.identifier.study.tb1' ],
+ 'id' : [ 'tb.identifier.study', 'tb.identifier.study.tb1' ],
+ 'word' : [ 'tb.title.study', 'dcterms.contributor', 'dcterms.abstract', 'dcterms.bibliographicCitation', 'dcterms.subject' ],
+ 'doi' : [ 'prism.doi' ]
+ };
+
+ // purlBase is assigned in /common/search-nav.jsp
+ var phyloWSURI = purlBase + 'study/find?query=';
+ //]]>
+</script>
+
<c:set var="searchType" value="study" scope="request"/>
<jsp:include page="studyKeywordSearchForm.jsp"/>
-<%-- <jsp:include page="studyTaxonLabelSearchForm.jsp"/> --%>
<div id="s-clear"></div>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/taxonSearch.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/taxonSearch.jsp 2012-02-20 19:35:10 UTC (rev 1075)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/taxonSearch.jsp 2012-02-20 20:32:40 UTC (rev 1076)
@@ -8,6 +8,21 @@
<div id="s-clear"></div>
+<script type="text/javascript">
+ //<![CDATA[
+ // These are the mappings from inferred search term types to search predicates for this scope
+ var predicates = {
+ 'integer' : [ 'tb.identifier.ncbi', 'tb.identifier.ubio', 'tb.identifier.taxon', 'tb.identifier.taxon.tb1' ],
+ 'id' : [ 'tb.identifier.ncbi', 'tb.identifier.ubio', 'tb.identifier.taxon', 'tb.identifier.taxon.tb1' ],
+ 'word' : [ 'tb.title.taxon', 'tb.title.taxonLabel', 'tb.title.taxonVariant' ],
+ 'doi' : [ 'prism.doi' ] // this doesn't work yet, we have no search on doi
+ };
+
+ // purlBase is assigned in /common/search-nav.jsp
+ var phyloWSURI = purlBase + 'taxon/find?query=';
+ //]]>
+</script>
+
<c:set var="searchType" value="taxon" scope="request"/>
<jsp:include page="taxonSearchForm.jsp"/>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSearch.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSearch.jsp 2012-02-20 19:35:10 UTC (rev 1075)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSearch.jsp 2012-02-20 20:32:40 UTC (rev 1076)
@@ -10,13 +10,24 @@
<div id="s-clear"></div>
+<script type="text/javascript">
+ //<![CDATA[
+ // These are the mappings from inferred search term types to search predicates for this scope
+ var predicates = {
+ 'integer' : [ 'tb.identifier.tree', 'tb.ntax.tree' ],
+ 'id' : [ 'tb.identifier.tree' ],
+ 'word' : [ 'tb.title.tree', 'tb.type.tree', 'tb.kind.tree', 'tb.quality.tree' ],
+ };
+
+ // purlBase is assigned in /common/search-nav.jsp
+ var phyloWSURI = purlBase + 'tree/find?query=';
+ //]]>
+</script>
+
<jsp:include page="treeSimpleSearchForm.jsp"/>
<c:set var="searchType" value="tree" scope="request"/>
-
-<%-- <jsp:include page="studyTaxonLabelSearchForm.jsp"/> --%>
-
<div id="s-clear"></div>
<jsp:include page="searchMessages.jsp"/>
Modified: trunk/treebase-web/src/main/webapp/common/search-nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/search-nav.jsp 2012-02-20 19:35:10 UTC (rev 1075)
+++ trunk/treebase-web/src/main/webapp/common/search-nav.jsp 2012-02-20 20:32:40 UTC (rev 1076)
@@ -6,6 +6,10 @@
<% String purlBase = TreebaseUtil.getPurlBase(); %>
+<script type="text/javascript">
+ var purlBase = '<%= purlBase %>';
+</script>
+
<%
Calendar cal = Calendar.getInstance();
cal.add(Calendar.MONTH, -6);
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