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From: <rv...@us...> - 2010-03-11 14:02:43
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Revision: 535
http://treebase.svn.sourceforge.net/treebase/?rev=535&view=rev
Author: rvos
Date: 2010-03-11 14:02:36 +0000 (Thu, 11 Mar 2010)
Log Message:
-----------
Changes as per http://docs.google.com/Doc?docid=0AXEQpupFgwYiZGg4bXF6bl82NmZwdm50cmRz&hl=en
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-09 22:27:21 UTC (rev 534)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-11 14:02:36 UTC (rev 535)
@@ -1,27 +1,13 @@
<div class="gutter">
<p>
-<strong>TreeBASE</strong> is a relational database of phylogenetic information hosted by the University at Buffalo.
-In previous years the database has been hosted by Harvard University Herbaria, Leiden University EEW,
-and the University of California, Davis. TreeBASE stores phylogenetic trees and the data matrices
-used to generate them from published research papers. We encourage biologists to submit phylogenetic
-data that are either published or in press, especially if these data were not fully presented
-in the publication due to space limitations. TreeBASE accepts all types of phylogenetic data (e.g.,
-trees of species, trees of populations, trees of genes) representing all biotic taxa. For more information,
-see an introduction to TreeBASE, information on searching, the database schema, and a graphic presentation
-of the web site's internal structure. Also, check out some ideas on why you might want to use TreeBASE.</p>
-<p>
-TreeBASE is now a participant in CIPRES, the NSF-sponsored Cyberinfrastructure for Phylogenetic Research
-project. As such, it is being redesigned from the ground up through collaborative research among Computer
-Scientists, Biologists, and Programmers. Presently TreeBASE is being mirrored at the San Diego Supercomputer
-Center at UCSD. Eventually, the redesigned, new and improved CIPRES version of TreeBASE will take over. In
-the meantime, please send us suggestions of what kinds of features or functions would you like designed
-into the new database? Are there new or unusual data types, queries, and functions that are not already
-offered by the current version of TreeBASE? Please send your suggestions here.</p>
-<p>
-The WWW implementation of TreeBASE requires a forms-capable and frames-capable browser. We would be
-very grateful for any feedback on TreeBASE, including suggestions for improvement. In particular, if
-you encounter any errors please let us know.</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" />
@@ -43,8 +29,5 @@
<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" />
- <img src="images/webin.gif" alt="WebIN" width="80" height="26" />
- <img src="images/scout.gif" alt="Scout Report Selection" width="80" height="26" />
- <img src="images/OSX.gif" alt="OSX" width="80" height="26" />
</p>
</div>
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From: <sfr...@us...> - 2010-03-23 17:45:03
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Revision: 651
http://treebase.svn.sourceforge.net/treebase/?rev=651&view=rev
Author: sfrgpiel
Date: 2010-03-23 17:44:56 +0000 (Tue, 23 Mar 2010)
Log Message:
-----------
Added verbiage to the splash page
Modified Paths:
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trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
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 14:50:54 UTC (rev 650)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-23 17:44:56 UTC (rev 651)
@@ -2,21 +2,19 @@
<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>
- 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>
+ 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>
+ <ul>
+ <li>Richer annotation of metadata (journal DOIs, specimen georeferences, Genbank accession numbers, etc) </li>
+ <li>A mapping between taxon labels and taxonomic names in uBio and NCBI for improved normalization of names</li>
+ <li>The ability to visualize and edit trees using Phylowidget</li>
+ <li>The ability to search on tree topology</li>
+ <li>Persistent and resolvable URIs for data objects in TreeBASE (i.e. studies, trees, matrices) serve as both globally unique identification numbers and resource locators. These can be included in articles and on researcher's websites, making access to TreeBASE data only a click away</li>
+ <li>Data are delivered in several serializations, including <a href="https://www.nescent.org/wg_phyloinformatics/Supporting_NEXUS_Documentation" target="_blank">NEXUS</a> and <a href="http://www.nexml.org" target="_blank">NeXML</a></li>
+ <li> A special URL gives journal editors and reviewers anonymous advanced access to data</li>
+ <li>Programmatic access to the data using the <a href="https://www.nescent.org/wg_evoinfo/PhyloWS" target="_blank">PhyloWS API</a>. Queries are expressed in URLs using PhyloWS syntax and can return results in RDF as RSS 1.0 feeds, which means that users can set their favorite RSS Reader to fetch all new TreeBASE studies that satisfy a particular query (e.g. return all studies published in "Systematic Biology," or return all trees that include "Homo sapiens," etc)</li>
+ </ul>
+ <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
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From: <hl...@us...> - 2010-03-23 22:56:30
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Revision: 653
http://treebase.svn.sourceforge.net/treebase/?rev=653&view=rev
Author: hlapp
Date: 2010-03-23 22:56:16 +0000 (Tue, 23 Mar 2010)
Log Message:
-----------
Canonicalized URLs.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
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 18:15:11 UTC (rev 652)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-23 22:56:16 UTC (rev 653)
@@ -10,11 +10,11 @@
<li>The ability to visualize and edit trees using Phylowidget</li>
<li>The ability to search on tree topology</li>
<li>Persistent and resolvable URIs for data objects in TreeBASE (i.e. studies, trees, matrices) serve as both globally unique identification numbers and resource locators. These can be included in articles and on researcher's websites, making access to TreeBASE data only a click away</li>
- <li>Data are delivered in several serializations, including <a href="https://www.nescent.org/wg_phyloinformatics/Supporting_NEXUS_Documentation" target="_blank">NEXUS</a> and <a href="http://www.nexml.org" target="_blank">NeXML</a></li>
+ <li>Data are delivered in several serializations, including <a href="http:/hackathon.nescent.org/Supporting_NEXUS_Documentation" target="_blank">NEXUS</a> and <a href="http://www.nexml.org" target="_blank">NeXML</a></li>
<li> A special URL gives journal editors and reviewers anonymous advanced access to data</li>
- <li>Programmatic access to the data using the <a href="https://www.nescent.org/wg_evoinfo/PhyloWS" target="_blank">PhyloWS API</a>. Queries are expressed in URLs using PhyloWS syntax and can return results in RDF as RSS 1.0 feeds, which means that users can set their favorite RSS Reader to fetch all new TreeBASE studies that satisfy a particular query (e.g. return all studies published in "Systematic Biology," or return all trees that include "Homo sapiens," etc)</li>
+ <li>Programmatic access to the data using the <a href="http://evoinfo.nescent.org/PhyloWS" target="_blank">PhyloWS API</a>. Queries are expressed in URLs using PhyloWS syntax and can return results in RDF as RSS 1.0 feeds, which means that users can set their favorite RSS Reader to fetch all new TreeBASE studies that satisfy a particular query (e.g. return all studies published in "Systematic Biology," or return all trees that include "Homo sapiens," etc)</li>
</ul>
<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
+</div>
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