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From: <yo...@us...> - 2010-03-21 13:45:44
|
Revision: 643
http://treebase.svn.sourceforge.net/treebase/?rev=643&view=rev
Author: youjun
Date: 2010-03-21 13:45:31 +0000 (Sun, 21 Mar 2010)
Log Message:
-----------
fix tree open link, open in its own page
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp
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 12:11:02 UTC (rev 642)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp 2010-03-21 13:45:31 UTC (rev 643)
@@ -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}" target="_blank">Tr${tree.id }</a>
+ <a href="${url}">Tr${tree.id }</a>
</display:column>
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: <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: SourceForge.net <no...@so...> - 2010-03-21 00:17:44
|
Bugs item #2973950, was opened at 2010-03-20 20:17 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973950&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: View Tree Keeps Opening New Windows Initial Comment: When a user in the Search side clicks on a tree to view it in PhyloWidget, the result is that a new window opens (this is good). But if the user then returns to the list of trees and clicks on another tree, we get another new window instead of opening up into the existing phylowidget window. Let's change this so that the target of the popup window uses a standard name (eg "PhyloWidget") and then all subsequent clicks on trees point to this same target. Also, please change the hover-over label from "Tree Section" to "View Tree" ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973950&group_id=248804 |
|
From: <vga...@us...> - 2010-03-20 23:05:05
|
Revision: 640
http://treebase.svn.sourceforge.net/treebase/?rev=640&view=rev
Author: vgapeyev
Date: 2010-03-20 23:04:58 +0000 (Sat, 20 Mar 2010)
Log Message:
-----------
Missing resource strings.
(This is already in the build released at treebase.org)
Modified Paths:
--------------
trunk/treebase-web/src/main/resources/ApplicationResources.properties
Modified: trunk/treebase-web/src/main/resources/ApplicationResources.properties
===================================================================
--- trunk/treebase-web/src/main/resources/ApplicationResources.properties 2010-03-20 22:57:40 UTC (rev 639)
+++ trunk/treebase-web/src/main/resources/ApplicationResources.properties 2010-03-20 23:04:58 UTC (rev 640)
@@ -88,6 +88,8 @@
nav.technology=Technology
nav.people=People
nav.partnerships=Partnerships
+nav.references=References
+nav.journals=Journals
#-- top navigation menu --
nav.personalinfo = Personal Information
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: SourceForge.net <no...@so...> - 2010-03-20 22:59:09
|
Bugs item #2973932, was opened at 2010-03-20 18:46 Message generated for change (Settings changed) made by hlapp You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973932&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) >Assigned to: Hilmar Lapp (hlapp) Summary: Broken link in Advanced Search box Initial Comment: Under each tab in the search page there is a link to "TreeBASE help page about searching" which points to http://www.treebase.org/treebase-web/help/urlAPI.jsp. The correct URL is actually "http://www.treebase.org/treebase-web/urlAPI.html" -- but I suggest instead that our text say "visit the description of TreeBASE's PhyloWS implementation." and then provide "http://sourceforge.net/apps/mediawiki/treebase/index.php?title=API" as the hyperlink. ---------------------------------------------------------------------- >Comment By: Hilmar Lapp (hlapp) Date: 2010-03-20 18:59 Message: I fixed this in the source code, svn commit# 639. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973932&group_id=248804 |
|
From: <hl...@us...> - 2010-03-20 22:57:46
|
Revision: 639
http://treebase.svn.sourceforge.net/treebase/?rev=639&view=rev
Author: hlapp
Date: 2010-03-20 22:57:40 +0000 (Sat, 20 Mar 2010)
Log Message:
-----------
Fixed link to stale url API page.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/querySearchBox.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/querySearchBox.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/querySearchBox.jsp 2010-03-20 18:38:46 UTC (rev 638)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/querySearchBox.jsp 2010-03-20 22:57:40 UTC (rev 639)
@@ -17,10 +17,10 @@
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. For
more information on how this is used, visit the
- <a href="/treebase-web/help/urlAPI.jsp">TreeBASE help page about searching</a>.
+ <a href="/treebase-web/urlAPI.html">TreeBASE help page about searching</a>.
</p>
<div>
<textarea name="query" style="width:100%"></textarea><br/>
<input type="submit" style="width:100%" value="Evaluate query"/>
</div>
-</fieldset>
\ No newline at end of file
+</fieldset>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: SourceForge.net <no...@so...> - 2010-03-20 22:46:45
|
Bugs item #2973932, was opened at 2010-03-20 18:46 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973932&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Broken link in Advanced Search box Initial Comment: Under each tab in the search page there is a link to "TreeBASE help page about searching" which points to http://www.treebase.org/treebase-web/help/urlAPI.jsp. The correct URL is actually "http://www.treebase.org/treebase-web/urlAPI.html" -- but I suggest instead that our text say "visit the description of TreeBASE's PhyloWS implementation." and then provide "http://sourceforge.net/apps/mediawiki/treebase/index.php?title=API" as the hyperlink. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973932&group_id=248804 |
|
From: <hl...@us...> - 2010-03-20 18:38:52
|
Revision: 638
http://treebase.svn.sourceforge.net/treebase/?rev=638&view=rev
Author: hlapp
Date: 2010-03-20 18:38:46 +0000 (Sat, 20 Mar 2010)
Log Message:
-----------
Replace unclickable and copy&paste-resistant email addresses with hyperlinked
text (yes, you can obfuscate email from harvesting). Clean up a little the
excessive whitespace.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp
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 18:28:42 UTC (rev 637)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp 2010-03-20 18:38:46 UTC (rev 638)
@@ -5,22 +5,16 @@
<h2>Help</h2>
<p>For questions about data submission and data content, please
-contact: </p>
+contact the TreeBASE helpdesk: <a href="mailto:help@treebase.org">help@treebase.org</a></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>
+inefficiencies, please email your issue report to the TreeBASE bug queue: <a href="mailto:bugs@treebase.org">bugs@treebase.org</a></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>
+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>
@@ -32,25 +26,14 @@
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>
+id="xjq:">https://sourceforge.net/tracker2/?group_id=248804&atid=1126676</a>. On this page you can browse the bug database.</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>
-
-
+separate files if you prefer. Click "add artifact" to submit the report.</p>
</div>
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|
|
From: <hl...@us...> - 2010-03-20 18:28:48
|
Revision: 637
http://treebase.svn.sourceforge.net/treebase/?rev=637&view=rev
Author: hlapp
Date: 2010-03-20 18:28:42 +0000 (Sat, 20 Mar 2010)
Log Message:
-----------
Remove excessive whitespace and make markup at least a little bit constistent.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp 2010-03-20 18:16:27 UTC (rev 636)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp 2010-03-20 18:28:42 UTC (rev 637)
@@ -1,31 +1,14 @@
<div id="contentRight">
<div class="gutter">
<h1>Data Access</h1>
-
<p><b>Web Browser User Interface</b></p>
-<p> </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><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>
-
+<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
@@ -38,78 +21,61 @@
<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
+<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). </span><br>
-<br>
-<i><u>Links to objects within TreeBASE</u></i><br>
-<br>
-TreeBASE issues persistent and resolvable uniform resource identifiers (URIs)
+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>
-<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>
+ URI to a study:
</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>
+ 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'>
- <p>URI to a matrix:</p>
+ URI to a matrix:
</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>
+ 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'>
- <p>URI to a tree:</p>
+ URI to a tree:
</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>
+ http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2026
</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
+<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. </span></p>
+taxon of interest will alert the user with a new RSS article. </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>
+entire periodic data dumps that comply with a
+standard data model, such as BioSQL.</p>
-<p> </p>
-
-
-
-
-
- </div>
-</div>
\ No newline at end of file
+</div></div>
\ No newline at end of file
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|
|
From: <hl...@us...> - 2010-03-20 18:16:33
|
Revision: 636
http://treebase.svn.sourceforge.net/treebase/?rev=636&view=rev
Author: hlapp
Date: 2010-03-20 18:16:27 +0000 (Sat, 20 Mar 2010)
Log Message:
-----------
Looks like this has been deprecated and is now in WEB-INF/pages.
Removed Paths:
-------------
trunk/treebase-web/src/main/webapp/help/urlAPI.jsp
Deleted: trunk/treebase-web/src/main/webapp/help/urlAPI.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/help/urlAPI.jsp 2010-03-20 18:12:59 UTC (rev 635)
+++ trunk/treebase-web/src/main/webapp/help/urlAPI.jsp 2010-03-20 18:16:27 UTC (rev 636)
@@ -1,110 +0,0 @@
-<%@ include file="/common/taglibs.jsp"%>
-
-<title>URL API</title>
-<content tag="heading">URL API</content>
-<body id="submissions"/>
-<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>
- 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.
\ No newline at end of file
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|
|
From: <vga...@us...> - 2010-03-20 18:13:06
|
Revision: 635
http://treebase.svn.sourceforge.net/treebase/?rev=635&view=rev
Author: vgapeyev
Date: 2010-03-20 18:12:59 +0000 (Sat, 20 Mar 2010)
Log Message:
-----------
Some line breaks.
Modified Paths:
--------------
trunk/treebase-core/db/cleaning/2010-03-14_fix_taxonlabelset/README.txt
Modified: trunk/treebase-core/db/cleaning/2010-03-14_fix_taxonlabelset/README.txt
===================================================================
--- trunk/treebase-core/db/cleaning/2010-03-14_fix_taxonlabelset/README.txt 2010-03-20 17:55:15 UTC (rev 634)
+++ trunk/treebase-core/db/cleaning/2010-03-14_fix_taxonlabelset/README.txt 2010-03-20 18:12:59 UTC (rev 635)
@@ -1,5 +1,10 @@
-In the March migration, newly imported records were parked under a study_id with study_id 10215. The taxonlabelset table failed to have its study_id remapped to the newly created studies, so instead it retained the original temporary study_id. The update_taxonlabelset.sql query updates the study_id field in the taxonlabelset
+In the March migration, newly imported records were parked under a study_id with study_id 10215. The taxonlabelset table failed
+to have its study_id remapped to the newly created studies, so instead it retained the original temporary study_id.
+The update_taxonlabelset.sql query updates the study_id field in the taxonlabelset
-In the March migration, newly created treeblock records received NULL values for taxonlabelset_id, causing the download of trees to fail and causing a selection of trees under the Trees tab to fail to show the related selection of taxa after clicking on the Taxa tab. The map_treeblock_to_taxonlabelset.sql query addresses the problem by updating the treeblock's taxonlabelset_id using a value from one of the matrices related by way of an analysisstep.
+In the March migration, newly created treeblock records received NULL values for taxonlabelset_id, causing the download of trees to fail and
+causing a selection of trees under the Trees tab to fail to show the related selection of taxa after clicking on the Taxa tab.
+The map_treeblock_to_taxonlabelset.sql query addresses the problem by updating the treeblock's taxonlabelset_id using a value
+from one of the matrices related by way of an analysisstep.
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|
|
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)
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|
|
From: <yo...@us...> - 2010-03-20 16:08:34
|
Revision: 632
http://treebase.svn.sourceforge.net/treebase/?rev=632&view=rev
Author: youjun
Date: 2010-03-20 16:08:26 +0000 (Sat, 20 Mar 2010)
Log Message:
-----------
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/reference.jsp
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 15:51:38 UTC (rev 631)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/contact.jsp 2010-03-20 16:08:26 UTC (rev 632)
@@ -7,14 +7,14 @@
<p>For questions about data submission and data content, please
contact: </p>
-<p><img src="images/help_mail.jpg"> </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> <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>
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 15:51:38 UTC (rev 631)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2010-03-20 16:08:26 UTC (rev 632)
@@ -296,10 +296,6 @@
</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"
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 15:51:38 UTC (rev 631)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/reference.jsp 2010-03-20 16:08:26 UTC (rev 632)
@@ -1,5 +1,5 @@
-<h1>Reference</h1>
+<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.
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|
|
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
===================================================================
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Ad...
[truncated message content] |
|
From: SourceForge.net <no...@so...> - 2010-03-20 04:14:29
|
Bugs item #2973661, was opened at 2010-03-20 00:14 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973661&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Taxa List has labels listed in duplicates, triplicates, etc Initial Comment: When a user is submitting data and clicks on the taxon list page (http://treebase.nescent.org/treebase-web/user/taxaList.html) the taxon labels are duplicated or triplicated, or quadrupled (etc) depending on the study. This bug appears to have cropped up just recently -- I would have noticed it before. Each distinct taxon label should be listed once. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973661&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2010-03-19 22:45:19
|
Bugs item #2973502, was opened at 2010-03-19 18:08 Message generated for change (Settings changed) made by vgapeyev You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973502&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: data Group: None Status: Open >Priority: 8 Private: No Submitted By: Vladimir Gapeyev (vgapeyev) Assigned to: Mark Dominus (mjdominus) Summary: Numbers of studies in TB2 and TB1 are different Initial Comment: [This is based on Bill's email of 2010-03-19: https://sourceforge.net/mailarchive/forum.php?thread_name=F1EC532F-64D4-4F51-9397-2F7F7C6644F8%40yale.edu&forum_name=treebase-devel ] We have a total of 2417 studies in TreeBASE2. That includes two new ones that were never in TreeBASE1. TreeBASE1, however, has 2427 studies -- so that means we have 12 missing studies. Not a show-stopper. After release, we will identify these and re-enter them manually. Note: The 2417 number for TB2 is after duplicates of Study 84 are removed: http://purl.org/phylo/treebase/phylows/study/find?query=tb.identifier.study=66+or+tb.identifier.study=67+or+tb.identifier.study=68+or+tb.identifier.study=69+or+tb.identifier.study=70+or+tb.identifier.study=71+or+tb.identifier.study=72+or+tb.identifier.study=73&recordSchema=study ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973502&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2010-03-19 22:08:37
|
Bugs item #2973502, was opened at 2010-03-19 18:08 Message generated for change (Tracker Item Submitted) made by vgapeyev You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973502&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: data Group: None Status: Open Priority: 5 Private: No Submitted By: Vladimir Gapeyev (vgapeyev) Assigned to: Mark Dominus (mjdominus) Summary: Numbers of studies in TB2 and TB1 are different Initial Comment: [This is based on Bill's email of 2010-03-19: https://sourceforge.net/mailarchive/forum.php?thread_name=F1EC532F-64D4-4F51-9397-2F7F7C6644F8%40yale.edu&forum_name=treebase-devel ] We have a total of 2417 studies in TreeBASE2. That includes two new ones that were never in TreeBASE1. TreeBASE1, however, has 2427 studies -- so that means we have 12 missing studies. Not a show-stopper. After release, we will identify these and re-enter them manually. Note: The 2417 number for TB2 is after duplicates of Study 84 are removed: http://purl.org/phylo/treebase/phylows/study/find?query=tb.identifier.study=66+or+tb.identifier.study=67+or+tb.identifier.study=68+or+tb.identifier.study=69+or+tb.identifier.study=70+or+tb.identifier.study=71+or+tb.identifier.study=72+or+tb.identifier.study=73&recordSchema=study ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2973502&group_id=248804 |
|
From: <vga...@us...> - 2010-03-19 21:44:20
|
Revision: 630
http://treebase.svn.sourceforge.net/treebase/?rev=630&view=rev
Author: vgapeyev
Date: 2010-03-19 21:44:13 +0000 (Fri, 19 Mar 2010)
Log Message:
-----------
Fixes to run on Production before the release
Added Paths:
-----------
trunk/treebase-core/db/cleaning/pre-release_hotfixes/
trunk/treebase-core/db/cleaning/pre-release_hotfixes/README.txt
trunk/treebase-core/db/cleaning/pre-release_hotfixes/fix_taxonlabelset.sql
Added: trunk/treebase-core/db/cleaning/pre-release_hotfixes/README.txt
===================================================================
--- trunk/treebase-core/db/cleaning/pre-release_hotfixes/README.txt (rev 0)
+++ trunk/treebase-core/db/cleaning/pre-release_hotfixes/README.txt 2010-03-19 21:44:13 UTC (rev 630)
@@ -0,0 +1,65 @@
+fix_taxonlabels.sql
+ detects TaxonLabelSets whose study_id still refers to a dummy study used for loading from TB1 dumps
+ and updates it to the proper real study.
+
+
+
+=============================================================
+Some relevant correspondence:
+
+From: vla...@du...
+ Subject: Re: [Treebase-devel] Some results of testing with a user
+ Date: March 19, 2010 4:00:22 PM EDT
+ To: wil...@ya...
+ Cc: Tre...@li...
+
+On Mar 19, 2010, at 3:25 PM, William Piel wrote:
+
+
+On Mar 19, 2010, at 12:07 PM, William Piel wrote:
+
+
+On Mar 19, 2010, at 11:44 AM, Hilmar Lapp wrote:
+
+On Mar 18, 2010, at 8:06 PM, Vladimir Gapeyev wrote:
+
+(1) Unexpected different results on the Taxa tab -- a feature or a bug? E.g., find a single study, e.g. 10051.
+ -- Click the study (which goes to Citation tab), then to Taxa tab ==> "Nothing to display"
+ -- Go to Matrices tab; click on "View Taxa" in the table ==> it goes back to the Taxa tab, showing lots of stuff
+ -- Go back to Citation tab; then Taxa tab ==> "Nothing found to display"
+ -- Go to Trees tab; click on "View Taxa" in the table ==> it goes back to the Taxa tab, showing lots of stuff.
+
+This is for Bill to judge in terms of what kind of problem it may signal, and hence how severe it is.
+
+This may be severe -- let's at least understand why it is happening. It is affecting a lot of studies.
+
+I think I've figured out what's going on here. I took one taxon label that maps nicely and compared it with another taxon label that does not map nicely, and then I ran queries on tables related to these taxon labels. The main difference is that in the good case the taxonlabelset table has the correct study_id, while in the bad case the taxonlabelset has "2264" as study_id instead of "10053", which is what it should be.
+
+Last weekend I had solved this problem using an update query that assumed that study_id 10215 was the only "placeholder" for migrated records. Turns out that there seems to be another one: 2264. Vladimir, can you confirm that study_id 2264 is another placeholder? And if so, can you let me know if there are any other placeholder study_ids that I'm not aware of.
+
+If this is the problem as I think it is, the solution is the following update:
+
+UPDATE taxonlabelset SET study_id = mx.study_id
+FROM matrix mx JOIN taxonlabelset tls USING (taxonlabelset_id)
+WHERE tls.study_id = 2264
+AND mx.study_id <> 2264
+AND taxonlabelset.taxonlabelset_id = tls.taxonlabelset_id
+
+I followed a similar path and was reaching a similar conclusion. Here is a query that shows all TaxonLabelSets whose tls.study_id is not the same as the study reachable from the TLS via a matrix:
+
+select s.study_id, m.matrix_id, tls.*
+from study s, taxonlabelset tls, matrix m
+where s.study_id = m.study_id and tls.taxonlabelset_id = m.taxonlabelset_id
+ and s.study_id <> tls.study_id
+order by s.study_id
+
+The only Study IDs showing up as tls.study_id in the result are 22 and 2264.
+
+#2264 was picked up by the migration scripts during my 1st migration -- not something I could have known ahead of time, since the scripts were creating a fresh dummy study in my testing daabase! By the time of the 2nd migration batch I realized it was going on and created the 10215 study.
+
+I see Bill has already run a fix on the 2264 TLSs. Should we do it for 22-TLSs as well?
+
+
+
+
+
\ No newline at end of file
Added: trunk/treebase-core/db/cleaning/pre-release_hotfixes/fix_taxonlabelset.sql
===================================================================
--- trunk/treebase-core/db/cleaning/pre-release_hotfixes/fix_taxonlabelset.sql (rev 0)
+++ trunk/treebase-core/db/cleaning/pre-release_hotfixes/fix_taxonlabelset.sql 2010-03-19 21:44:13 UTC (rev 630)
@@ -0,0 +1,22 @@
+BEGIN TRANSACTION;
+
+\echo These TaxonLabelSet.study_ids will be updated:
+
+select s.study_id, s.tb_studyid, m.matrix_id, tls.*
+from study s, taxonlabelset tls, matrix m
+where s.study_id = m.study_id and tls.taxonlabelset_id = m.taxonlabelset_id
+ and s.study_id <> tls.study_id
+order by s.study_id;
+
+
+\echo =================== Updating ===================
+
+update taxonlabelset tls
+ set study_id = s.study_id
+from study s, matrix m
+where tls.taxonlabelset_id = m.taxonlabelset_id and m.study_id = s.study_id
+ and s.study_id <> tls.study_id
+returning s.study_id, s.tb_studyid, m.matrix_id, tls.*;
+
+
+COMMIT;
\ 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: SourceForge.net <no...@so...> - 2010-03-18 20:05:23
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Bugs item #2970482, was opened at 2010-03-15 00:24 Message generated for change (Comment added) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2970482&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 9 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: youjun guo (youjun) Summary: unauthorized user can edit trees using phylowidget Initial Comment: This is a significant security hole: an unauthorized user (e.g. an anonymous user or a non-admin person) can view a tree using phylowidget (i.e. through the search interface), reroot the tree, and then click the "save back to the database" menu item -- and, unfortunately, the save does work and the data are permanently changed! We need to block this hole. Only if the user is the owner of the tree -- and where the tree belongs to a "in progress" study -- should the user be allowed to modify the tree and save it back to the database. Frankly, to avoid confusion it would be better to have a duplicate set of phylowidget pages: one available through the submission system (and this one contains the "save back to database" menu item) and one available through the search interface (and this one would not have the "save back to database" menu item). Also, note that the "Quick Links" box makes no sense for the phylowidget page deployed in the submission system, as following those links exits the submission pages. ---------------------------------------------------------------------- >Comment By: William Piel (sfrgpiel) Date: 2010-03-18 16:05 Message: Save to database has been disabled for people coming from the search interface. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2970482&group_id=248804 |
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From: <vga...@us...> - 2010-03-18 16:12:37
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Revision: 629
http://treebase.svn.sourceforge.net/treebase/?rev=629&view=rev
Author: vgapeyev
Date: 2010-03-18 16:12:31 +0000 (Thu, 18 Mar 2010)
Log Message:
-----------
More appropriate tooltip message for disabled analysis downloads
Modified Paths:
--------------
trunk/treebase-web/src/main/resources/ApplicationResources.properties
trunk/treebase-web/src/main/webapp/WEB-INF/pages/algorithm.jsp
Modified: trunk/treebase-web/src/main/resources/ApplicationResources.properties
===================================================================
--- trunk/treebase-web/src/main/resources/ApplicationResources.properties 2010-03-18 15:30:48 UTC (rev 628)
+++ trunk/treebase-web/src/main/resources/ApplicationResources.properties 2010-03-18 16:12:31 UTC (rev 629)
@@ -305,6 +305,7 @@
matrix.description = Description
download.original = Download Original File
download.reconstructedfile = Download Reconstructed File
+download.unavailable = File download currently not available
download.nexml = Download NeXML File
download.json = Download JSON File
download.rdf = Download RDF file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/algorithm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/algorithm.jsp 2010-03-18 15:30:48 UTC (rev 628)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/algorithm.jsp 2010-03-18 16:12:31 UTC (rev 629)
@@ -49,8 +49,13 @@
<img
class="iconButton"
src="<fmt:message key="icons.download.reconstructed"/>"
+<%--
title="<fmt:message key="download.reconstructedfile"/>"
- alt="<fmt:message key="download.reconstructedfile"/>"/>
+ alt="<fmt:message key="download.reconstructedfile"/>"
+--%>
+ title="<fmt:message key="download.unavailable"/>"
+ alt="<fmt:message key="download.unavailable"/>"
+ />
<!-- </a> -->
<c:if test="${not empty analysisStepCommand.displayName}">
<c:out value="${analysisStepCommand.displayName}"/>
@@ -58,7 +63,7 @@
<c:if test="${empty analysisStepCommand.displayName}">
<em>Untitled</em>
</c:if>
- </h2>
+ --</h2>
<div <c:if test="${!editable}">style="display:none"</c:if> id="analysisStepCommand<c:out value="${analysisStepCommand.id}"/>">
<c:if test="${editable || ( not empty analysisStepCommand.displayName || not empty analysisStepCommand.notes )}">
<fieldset>
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From: <vga...@us...> - 2010-03-18 15:30:54
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Revision: 628
http://treebase.svn.sourceforge.net/treebase/?rev=628&view=rev
Author: vgapeyev
Date: 2010-03-18 15:30:48 +0000 (Thu, 18 Mar 2010)
Log Message:
-----------
Disabled analysis download as requested in #2972107, to mitigate #2970700 and #2970457
(this one was missed in an earlier commit)
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/algorithm.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/algorithm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/algorithm.jsp 2010-03-18 14:37:11 UTC (rev 627)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/algorithm.jsp 2010-03-18 15:30:48 UTC (rev 628)
@@ -44,13 +44,14 @@
title="<fmt:message key="analysis.notvalidated"/>"
alt="<fmt:message key="analysis.notvalidated"/>"/>
</span>
- <a href="/treebase-web/search/downloadAnAnalysisStep.html?analysisid=${analysisStepCommand.id}&id=${analysisStepCommand.analysis.study.id}">
+<!-- VG 2010-03-17 Disabled analysis download as requested in #2972107, to mitigate #2970700 and #2970457 -->
+<!-- <a href="/treebase-web/search/downloadAnAnalysisStep.html?analysisid=${analysisStepCommand.id}&id=${analysisStepCommand.analysis.study.id}"> -->
<img
class="iconButton"
src="<fmt:message key="icons.download.reconstructed"/>"
title="<fmt:message key="download.reconstructedfile"/>"
alt="<fmt:message key="download.reconstructedfile"/>"/>
- </a>
+<!-- </a> -->
<c:if test="${not empty analysisStepCommand.displayName}">
<c:out value="${analysisStepCommand.displayName}"/>
</c:if>
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From: <vga...@us...> - 2010-03-18 14:37:18
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Revision: 627
http://treebase.svn.sourceforge.net/treebase/?rev=627&view=rev
Author: vgapeyev
Date: 2010-03-18 14:37:11 +0000 (Thu, 18 Mar 2010)
Log Message:
-----------
Catch-up to commit #626.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-03-18 14:31:28 UTC (rev 626)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp 2010-03-18 14:37:11 UTC (rev 627)
@@ -81,9 +81,100 @@
</a>
<!-- save to connotea -->
- <!-- commented out temporarily because this uses the absolute path, which won't work due to proxying -->
- <!-- Insert nav-HIDE-connotea.txt here -->
- <!-- end of commenting out connotea -->
+ <!-- commented out temporarily because this uses the absolute path, which won't work due to proxying - SF Bug 2972133 -->
+ <%--
+ <form method="post" id="connotea" action="http://www.connotea.org/add" enctype="application/x-www-form-urlencoded" name="edit">
+
+ <input
+ name="uri"
+ value="<%= request.getScheme() %>://<%= request.getLocalName() %>:<%= request.getLocalPort() %>/treebase-web/search/study/summary.html?id=<c:out value="${study.id}"/>"
+ type="hidden"/>
+
+ <input
+ name="uri"
+ value="<%= request.getScheme() %>://<%= request.getLocalName() %>:<%= request.getLocalPort() %>/treebase-web/search/study/summary.html?id=<c:out value="${study.id}"/>"
+ type="hidden"/>
+
+ <input name="ctitle" value="<c:out value="${cit.title}"/>" type="hidden"/>
+ <input name="ctitle2" value="<c:out value="${cit.title}"/>" type="hidden"/>
+
+ <c:choose>
+ <c:when test="${cit.citationType == 'Article'}">
+ <input name="cjournal" value="<c:out value="${cit.journal}"/>" type="hidden"/>
+ <input name="cjournal2" value="<c:out value="${cit.journal}"/>" type="hidden"/>
+
+ <input name="cvolume" value="<c:out value="${cit.volume}"/>" type="hidden"/>
+ <input name="cvolume2" value="<c:out value="${cit.volume}"/>" type="hidden"/>
+
+ <input name="cissue" value="<c:out value="${cit.issue}"/>" type="hidden"/>
+ <input name="cissue2" value="<c:out value="${cit.issue}"/>" type="hidden"/>
+ </c:when>
+ <c:otherwise>
+ <input name="cjournal" value="" type="hidden"/>
+ <input name="cjournal2" value="" type="hidden"/>
+
+ <input name="cvolume" value="" type="hidden"/>
+ <input name="cvolume2" value="" type="hidden"/>
+
+ <input name="cissue" value="" type="hidden"/>
+ <input name="cissue2" value="" type="hidden"/>
+ </c:otherwise>
+ </c:choose>
+
+ <input name="cpages" value="<c:out value="${cit.pages}"/>" type="hidden"/>
+ <input name="cpages2" value="<c:out value="${cit.pages}"/>" type="hidden"/>
+
+ <input name="cdate" value="<c:out value="${cit.publishYear}"/>" type="hidden"/>
+ <input name="cdate2" value="<c:out value="${cit.publishYear}"/>" type="hidden"/>
+
+ <input name="cauthors" value="<c:out value="${cit.authorsAsBibtex}"/>" type="hidden"/>
+ <input name="cauthors2" value="<c:out value="${cit.authorsAsBibtex}"/>" type="hidden"/>
+
+ <!-- JOUR, BOOK or CHAP --><!-- XXX check if article!! -->
+ <input name="cristype" value="JOUR" type="hidden"/>
+ <input name="cristype2" value="JOUR" type="hidden"/>
+
+ <input name="cdoi" value="<c:out value="${cit.doi}"/>" type="hidden"/>
+ <input name="cdoi2" value="<c:out value="${cit.doi}"/>" type="hidden"/>
+
+ <input name="cpubmed" value="<c:out value="${cit.PMID}"/>" type="hidden"/>
+ <input name="cpubmed2" value="<c:out value="${cit.PMID}"/>" type="hidden"/>
+
+ <!-- isbn -->
+ <input name="casin" value="" type="hidden"/> <!-- XXX check if book/in book -->
+ <input name="casin2" value="" type="hidden"/>
+
+ <input name="usertitle" value="<c:out value="${cit.title}"/>" type="hidden"/>
+
+ <input name="tags" value="uploaded, <c:out value="${cit.keywords}"/>" type="hidden"/>
+ <input name="button" value="Save" type="hidden"/>
+
+ <input name="description" value="<c:out value="${study.notes}"/>" type="hidden"/>
+ <input name="mywork" value="0" type="hidden"/>
+ <input name="private" value="0" type="hidden"/>
+ <input name="embargo" value="" type="hidden"/>
+
+ <c:choose>
+ <c:when test="${not empty study.TB1StudyID}">
+ <input name="comment" value="This study was previously identified under the legacy study ID ${study.TB1StudyID} (Status: <c:out value="${study.studyStatus.description}"/>)." type="hidden"/>
+ </c:when>
+ <c:otherwise>
+ <input name="comment" value="This study is part of submission <c:out value="${study.submission.id}"/> (Status: <c:out value="${study.studyStatus.description}"/>)." type="hidden"/>
+ </c:otherwise>
+ </c:choose>
+
+ <input name="button" value="Save" type="hidden"/>
+ <input name="continue" value="0" type="hidden"/>
+ <input name="title" value="<c:out value="${cit.title}"/>" type="hidden"/>
+ <input name=".cgifields" value="private" type="hidden"/>
+ <input name=".cgifields" value="mywork" type="hidden"/>
+ <input name="prefilled" value="1" type="hidden"/>
+ </form>
+ <a href="#" onclick="connotea()">
+ <img src="/treebase-web/images/connotea.gif" alt="Connotea" class="iconButton"/>
+ Connotea
+ </a>
+ --%> <!-- end of commenting out connotea -->
<div id="notice"></div>
</fieldset>
</div>
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From: <vga...@us...> - 2010-03-18 14:31:34
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Revision: 626
http://treebase.svn.sourceforge.net/treebase/?rev=626&view=rev
Author: vgapeyev
Date: 2010-03-18 14:31:28 +0000 (Thu, 18 Mar 2010)
Log Message:
-----------
Improving my previous correction: just use <%-- --> instead of <!-- --> for the outer comment.
Removed Paths:
-------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav-HIDE-connotea.txt
Deleted: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav-HIDE-connotea.txt
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav-HIDE-connotea.txt 2010-03-18 14:18:10 UTC (rev 625)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav-HIDE-connotea.txt 2010-03-18 14:31:28 UTC (rev 626)
@@ -1,94 +0,0 @@
-<--! VG 2010-03-22 This is supposed to be a part of nav.jsp -- search for "save to connotea" -->
-<--! Since there are many small comments in this fragment, commenting it out in nav.jsp did not work out well. -->
-
- <form method="post" id="connotea" action="http://www.connotea.org/add" enctype="application/x-www-form-urlencoded" name="edit">
-
- <input
- name="uri"
- value="<%= request.getScheme() %>://<%= request.getLocalName() %>:<%= request.getLocalPort() %>/treebase-web/search/study/summary.html?id=<c:out value="${study.id}"/>"
- type="hidden"/>
-
- <input
- name="uri"
- value="<%= request.getScheme() %>://<%= request.getLocalName() %>:<%= request.getLocalPort() %>/treebase-web/search/study/summary.html?id=<c:out value="${study.id}"/>"
- type="hidden"/>
-
- <input name="ctitle" value="<c:out value="${cit.title}"/>" type="hidden"/>
- <input name="ctitle2" value="<c:out value="${cit.title}"/>" type="hidden"/>
-
- <c:choose>
- <c:when test="${cit.citationType == 'Article'}">
- <input name="cjournal" value="<c:out value="${cit.journal}"/>" type="hidden"/>
- <input name="cjournal2" value="<c:out value="${cit.journal}"/>" type="hidden"/>
-
- <input name="cvolume" value="<c:out value="${cit.volume}"/>" type="hidden"/>
- <input name="cvolume2" value="<c:out value="${cit.volume}"/>" type="hidden"/>
-
- <input name="cissue" value="<c:out value="${cit.issue}"/>" type="hidden"/>
- <input name="cissue2" value="<c:out value="${cit.issue}"/>" type="hidden"/>
- </c:when>
- <c:otherwise>
- <input name="cjournal" value="" type="hidden"/>
- <input name="cjournal2" value="" type="hidden"/>
-
- <input name="cvolume" value="" type="hidden"/>
- <input name="cvolume2" value="" type="hidden"/>
-
- <input name="cissue" value="" type="hidden"/>
- <input name="cissue2" value="" type="hidden"/>
- </c:otherwise>
- </c:choose>
-
- <input name="cpages" value="<c:out value="${cit.pages}"/>" type="hidden"/>
- <input name="cpages2" value="<c:out value="${cit.pages}"/>" type="hidden"/>
-
- <input name="cdate" value="<c:out value="${cit.publishYear}"/>" type="hidden"/>
- <input name="cdate2" value="<c:out value="${cit.publishYear}"/>" type="hidden"/>
-
- <input name="cauthors" value="<c:out value="${cit.authorsAsBibtex}"/>" type="hidden"/>
- <input name="cauthors2" value="<c:out value="${cit.authorsAsBibtex}"/>" type="hidden"/>
-
- <!-- JOUR, BOOK or CHAP --><!-- XXX check if article!! -->
- <input name="cristype" value="JOUR" type="hidden"/>
- <input name="cristype2" value="JOUR" type="hidden"/>
-
- <input name="cdoi" value="<c:out value="${cit.doi}"/>" type="hidden"/>
- <input name="cdoi2" value="<c:out value="${cit.doi}"/>" type="hidden"/>
-
- <input name="cpubmed" value="<c:out value="${cit.PMID}"/>" type="hidden"/>
- <input name="cpubmed2" value="<c:out value="${cit.PMID}"/>" type="hidden"/>
-
- <!-- isbn -->
- <input name="casin" value="" type="hidden"/> <!-- XXX check if book/in book -->
- <input name="casin2" value="" type="hidden"/>
-
- <input name="usertitle" value="<c:out value="${cit.title}"/>" type="hidden"/>
-
- <input name="tags" value="uploaded, <c:out value="${cit.keywords}"/>" type="hidden"/>
- <input name="button" value="Save" type="hidden"/>
-
- <input name="description" value="<c:out value="${study.notes}"/>" type="hidden"/>
- <input name="mywork" value="0" type="hidden"/>
- <input name="private" value="0" type="hidden"/>
- <input name="embargo" value="" type="hidden"/>
-
- <c:choose>
- <c:when test="${not empty study.TB1StudyID}">
- <input name="comment" value="This study was previously identified under the legacy study ID ${study.TB1StudyID} (Status: <c:out value="${study.studyStatus.description}"/>)." type="hidden"/>
- </c:when>
- <c:otherwise>
- <input name="comment" value="This study is part of submission <c:out value="${study.submission.id}"/> (Status: <c:out value="${study.studyStatus.description}"/>)." type="hidden"/>
- </c:otherwise>
- </c:choose>
-
- <input name="button" value="Save" type="hidden"/>
- <input name="continue" value="0" type="hidden"/>
- <input name="title" value="<c:out value="${cit.title}"/>" type="hidden"/>
- <input name=".cgifields" value="private" type="hidden"/>
- <input name=".cgifields" value="mywork" type="hidden"/>
- <input name="prefilled" value="1" type="hidden"/>
- </form>
- <a href="#" onclick="connotea()">
- <img src="/treebase-web/images/connotea.gif" alt="Connotea" class="iconButton"/>
- Connotea
- </a>
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