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[Treebase-guts] SF.net SVN: treebase:[642] trunk/treebase-web/src/main/webapp
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From: <rv...@us...> - 2010-03-21 12:11:13
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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
}
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