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From: <nl...@us...> - 2007-02-01 01:03:15
|
Revision: 338
http://svn.sourceforge.net/obo/?rev=338&view=rev
Author: nlw
Date: 2007-01-31 17:03:15 -0800 (Wed, 31 Jan 2007)
Log Message:
-----------
modifying ssi on index, renaming index page
Added Paths:
-----------
phenote/trunk/doc/phenote-website/index.shtml
Removed Paths:
-------------
phenote/trunk/doc/phenote-website/index_text.shtml
Copied: phenote/trunk/doc/phenote-website/index.shtml (from rev 336, phenote/trunk/doc/phenote-website/index_text.shtml)
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/index.shtml 2007-02-01 01:03:15 UTC (rev 338)
@@ -0,0 +1,50 @@
+<!--#include virtual="//ssi/header.html" -->
+
+<div id="page_body">
+
+<!--#include virtual="/ssi/navi_home.html" -->
+
+<div id="main_content">
+<h1>Phenote: A Phenotype Annotation Tool using Ontologies</h1>
+<p>
+<b><i>Phenote</i></b> is both a complete piece of software and a software toolkit designed to facilitate the annotation of biological phenotypes using ontologies. It provides an interface to record genotype-phenotype pairs, together with the provenance for the annotation.
+</p>
+
+<p>Data annotated with Phenote is based on the <a href="http://http://www.fruitfly.org/~cjm/obd/formats.html">EQ model</a> for representing phenotypes, combining entities from any OBO ontology with qualities (such as <a href="http://http://www.bioontology.org/wiki/index.php/PATO:About">PATO</a>).
+</p>
+
+<p>The software can be used as a complete package, or individual compontents can be downloaded and plugged in to your desired application. Check out our <a href="/phenote/info/">Info</a> page to learn more.</p>
+
+<p>This tool is being developed by the <a href="http://berkeleybop.org/">Bioinformatics Core</a> of the <a href="http://www.bioontology.org">National Center for Biomedical Ontology</a>.
+</p>
+
+There are two groups driving the development of this software project:
+<p><a href="http://flybase.bio.indiana.edu/">
+<img class="portrait" height="50" border="0" src="/phenote/images/fly_logo.png" alt="Flybase" /></a>Flybase: The Drosophila Genome Database.
+<br />
+</p>
+<br />
+<br />
+<p><a href="http://zfin.org/"><img class="portrait" border="0" src="/phenote/images/zfin_logo.gif" height="50" alt="Zfin" /></a>ZFIN: The Zebrafish Genome Database
+<br />
+</p>
+<br />
+<br />
+
+We are also collaborating with several groups:
+<p><a href="http://www.nescent.org/"><img class="portrait" border="0" src="/phenote/images/nescent_logo.gif" height="50" alt="Nescent" /></a>NESCENT: The National Evolutionary Synthesis Center
+<br />
+</p>
+<br />
+<br />
+<p><a href="http://www.pharmgkb.org/"><img class="portrait" border="0" src="/phenote/images/pgkb_logo.png" height="50" alt="PharmGKB" /></a>PharmGKB: The Pharmacogenetics and Pharmacogenomics Knowledge Base
+<br />
+</p>
+<br />
+<br />
+
+</div>
+</div>
+
+<!--#include virtual="/phenote/ssi/footer.shtml" -->
+
Deleted: phenote/trunk/doc/phenote-website/index_text.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index_text.shtml 2007-02-01 01:00:28 UTC (rev 337)
+++ phenote/trunk/doc/phenote-website/index_text.shtml 2007-02-01 01:03:15 UTC (rev 338)
@@ -1,50 +0,0 @@
-<!--#include virtual="/phenote/ssi/header.html" -->
-
-<div id="page_body">
-
-<!--#include virtual="/phenote/ssi/navi_home.html" -->
-
-<div id="main_content">
-<h1>Phenote: A Phenotype Annotation Tool using Ontologies</h1>
-<p>
-<b><i>Phenote</i></b> is both a complete piece of software and a software toolkit designed to facilitate the annotation of biological phenotypes using ontologies. It provides an interface to record genotype-phenotype pairs, together with the provenance for the annotation.
-</p>
-
-<p>Data annotated with Phenote is based on the <a href="http://http://www.fruitfly.org/~cjm/obd/formats.html">EQ model</a> for representing phenotypes, combining entities from any OBO ontology with qualities (such as <a href="http://http://www.bioontology.org/wiki/index.php/PATO:About">PATO</a>).
-</p>
-
-<p>The software can be used as a complete package, or individual compontents can be downloaded and plugged in to your desired application. Check out our <a href="/phenote/info/">Info</a> page to learn more.</p>
-
-<p>This tool is being developed by the <a href="http://berkeleybop.org/">Bioinformatics Core</a> of the <a href="http://www.bioontology.org">National Center for Biomedical Ontology</a>.
-</p>
-
-There are two groups driving the development of this software project:
-<p><a href="http://flybase.bio.indiana.edu/">
-<img class="portrait" height="50" border="0" src="/phenote/images/fly_logo.png" alt="Flybase" /></a>Flybase: The Drosophila Genome Database.
-<br />
-</p>
-<br />
-<br />
-<p><a href="http://zfin.org/"><img class="portrait" border="0" src="/phenote/images/zfin_logo.gif" height="50" alt="Zfin" /></a>ZFIN: The Zebrafish Genome Database
-<br />
-</p>
-<br />
-<br />
-
-We are also collaborating with several groups:
-<p><a href="http://www.nescent.org/"><img class="portrait" border="0" src="/phenote/images/nescent_logo.gif" height="50" alt="Nescent" /></a>NESCENT: The National Evolutionary Synthesis Center
-<br />
-</p>
-<br />
-<br />
-<p><a href="http://www.pharmgkb.org/"><img class="portrait" border="0" src="/phenote/images/pgkb_logo.png" height="50" alt="PharmGKB" /></a>PharmGKB: The Pharmacogenetics and Pharmacogenomics Knowledge Base
-<br />
-</p>
-<br />
-<br />
-
-</div>
-</div>
-
-<!--#include virtual="/phenote/ssi/footer.shtml" -->
-
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-02-01 01:00:28
|
Revision: 337
http://svn.sourceforge.net/obo/?rev=337&view=rev
Author: nlw
Date: 2007-01-31 17:00:28 -0800 (Wed, 31 Jan 2007)
Log Message:
-----------
adding perl script to handle website updates
Added Paths:
-----------
phenote/trunk/doc/phenote-website/update_site
Added: phenote/trunk/doc/phenote-website/update_site
===================================================================
--- phenote/trunk/doc/phenote-website/update_site (rev 0)
+++ phenote/trunk/doc/phenote-website/update_site 2007-02-01 01:00:28 UTC (rev 337)
@@ -0,0 +1,36 @@
+#!/usr/local/bin/perl -w
+
+##
+## Script to update phenote.org based on script from berkeleybop.org
+## WARNING: This script depends on subversion acting a certain way.
+##
+
+use strict;
+
+my @files = ();
+
+## Change everything to a more proper permission.
+system("find ./ -type d -exec chmod 775 {} \\;")
+ and die;
+system("find ./ -type f -exec chmod 664 {} \\;")
+ and die;
+
+## Find all the files that are _currently_ taken care of by subversion.
+foreach $_ (`svn status --verbose`){
+ my @fields = split(/\s+/);
+ # Make sure to throw out uncommited files and directories.
+ if ( $fields[0] eq '' && ! -d $fields[4] ){
+ push @files, $fields[4];
+ }
+}
+
+## Make a string of all the files we'll transfer.
+my $string = "";
+foreach $_ (@files){ $string .= $_ . " "; }
+
+## Debug.
+#foreach $_ (@files){ print "(" . $_ . ")\n"; }
+
+## rsync it over...
+system("rsync -lptgoDvzPR -e ssh " . $string . "lsc.lbl.gov:/local/phenote.org_80/www/htdocs")
+ and die;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-01-31 22:52:49
|
Revision: 336
http://svn.sourceforge.net/obo/?rev=336&view=rev
Author: nlw
Date: 2007-01-31 14:52:47 -0800 (Wed, 31 Jan 2007)
Log Message:
-----------
fixing up header, minor changes
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/content/about/index.shtml
phenote/trunk/doc/phenote-website/index_text.shtml
phenote/trunk/doc/phenote-website/ssi/header.html
Modified: phenote/trunk/doc/phenote-website/content/about/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/about/index.shtml 2007-01-31 22:32:08 UTC (rev 335)
+++ phenote/trunk/doc/phenote-website/content/about/index.shtml 2007-01-31 22:52:47 UTC (rev 336)
@@ -42,7 +42,7 @@
</script></p>
<h3><a name="Groups">Groups</a></h3>
-<p><a href="www.bioontology.org"><img class="protrait" height="50" src="/phenote/images/NCBO_logo.jpg" /></a>NCBO</p>
+<p><a href="www.bioontology.org"><img class="protrait" height="50" src="/phenote/images/NCBO_logo.jpg" border="0" /></a>NCBO</p>
<p><a href="www.berkeleybop.org">Berkeley BOP</a>
<h3><a name="funding">Funding Sources</a></h3>
Modified: phenote/trunk/doc/phenote-website/index_text.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-31 22:32:08 UTC (rev 335)
+++ phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-31 22:52:47 UTC (rev 336)
@@ -5,11 +5,12 @@
<!--#include virtual="/phenote/ssi/navi_home.html" -->
<div id="main_content">
+<h1>Phenote: A Phenotype Annotation Tool using Ontologies</h1>
<p>
<b><i>Phenote</i></b> is both a complete piece of software and a software toolkit designed to facilitate the annotation of biological phenotypes using ontologies. It provides an interface to record genotype-phenotype pairs, together with the provenance for the annotation.
+</p>
-
-Data annotated with Phenote is based on the <a href="http://http://www.fruitfly.org/~cjm/obd/formats.html">EQ model</a> for representing phenotypes, combining entities from any OBO ontology with qualities (such as <a href="http://http://www.bioontology.org/wiki/index.php/PATO:About">PATO</a>).
+<p>Data annotated with Phenote is based on the <a href="http://http://www.fruitfly.org/~cjm/obd/formats.html">EQ model</a> for representing phenotypes, combining entities from any OBO ontology with qualities (such as <a href="http://http://www.bioontology.org/wiki/index.php/PATO:About">PATO</a>).
</p>
<p>The software can be used as a complete package, or individual compontents can be downloaded and plugged in to your desired application. Check out our <a href="/phenote/info/">Info</a> page to learn more.</p>
Modified: phenote/trunk/doc/phenote-website/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/header.html 2007-01-31 22:32:08 UTC (rev 335)
+++ phenote/trunk/doc/phenote-website/ssi/header.html 2007-01-31 22:52:47 UTC (rev 336)
@@ -26,7 +26,7 @@
<div id="page_head">
<div class="ehead">
-<h1>Phenote: A Phenotype Annotation Tool using Ontologies</h1>
+<h1>Phenote</h1>
</div>
<div class="page_logo">
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-01-31 22:35:32
|
Revision: 333
http://svn.sourceforge.net/obo/?rev=333&view=rev
Author: nlw
Date: 2007-01-31 14:18:12 -0800 (Wed, 31 Jan 2007)
Log Message:
-----------
updating info
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/content/info/index.shtml
Modified: phenote/trunk/doc/phenote-website/content/info/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-01-31 20:10:15 UTC (rev 332)
+++ phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-01-31 22:18:12 UTC (rev 333)
@@ -7,7 +7,7 @@
<div id="main_content">
<h2>Software Information</h2>
-
+Phenote is both a standalone java application and a software toolkit.
<h3><a name="features">Features of Standalone software</a></h3>
<p>
</p>
@@ -20,31 +20,31 @@
</li>
<li>Ontology navigation and term information display
</li>
- <li>Bulk copy/edit/delete of phenotype-genotype character entries
+ <li>Bulk copy/edit/delete/sort of phenotype-genotype character entries
</li>
<li>Two output formats: phenosyntax and phenoxml
</li>
<li>configurable input fields to allow custom data entry and user-specified ontologies
</li>
+ <li>Preconfigurations available for different communities
+ </li>
</ul>
-<h3><a name="examples">Example Sites Utilizing Phenote components</a></h3>
-The Dictyostelium Genome Database, <a href="http://dictybase.org">
+<h3><a name="web_users">Websites Utilizing Phenote Software Components</a></h3>
+<p>The Dictyostelium Genome Database, <a href="http://dictybase.org">
DictyBase</a>, has a web-based
-<a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">Phenotype Annotation Tool</a> that is directly linked to their own database backend.
+<a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">Phenotype Annotation Tool</a> that is directly linked to their own database backend.</p>
<br />
-<a href="http://zfin.org">Zfin</a> has an integrated phenotype annotation tool in their internal website. Here's a screenshot of their interface [to be added].
-<br />
-
-<h3><a name="webstart">Running Phenote Webstart Version(s)</a></h3>
-<h3><a name="install">Downloading and Installing Phenote</a></h3>
<p>
+<a href="http://zfin.org">Zfin</a> has an integrated phenotype annotation tool in their internal website. [screenshot or link to be added].
</p>
-<h3><a name="config">Custom Configuration</a></h3>
-<p>
-Phenote can be customized for data entry fields, and the ontologies that are desired to be included.
-</p>
+<br />
+<h3><a name="documentation">Documentation</a></h3>
+<p><a href="">Phenotype Annotation User Guide</a></p>
+
+<h3><a name="roadmap">Roadmap</a></h3>
+
<h3><a name="rel_notes">Release Notes</a></h3>
<a href="http://toy.lbl.gov:9010/phenote/phenote-release-notes.html">[Release Notes]</a>
<br />
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-01-31 22:32:53
|
Revision: 335
http://svn.sourceforge.net/obo/?rev=335&view=rev
Author: nlw
Date: 2007-01-31 14:32:08 -0800 (Wed, 31 Jan 2007)
Log Message:
-----------
add howto navi
Added Paths:
-----------
phenote/trunk/doc/phenote-website/ssi/navi_howtos.html
Added: phenote/trunk/doc/phenote-website/ssi/navi_howtos.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_howtos.html (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/navi_howtos.html 2007-01-31 22:32:08 UTC (rev 335)
@@ -0,0 +1,44 @@
+<div id="navi">
+<div class="navi_head"></div>
+<ul>
+<!-- <li>
+ Home
+--> </li>
+ <li>
+ <a href="/phenote/">Home</a>
+ </li>
+ <li>
+ <a href="/phenote/content/info/">Software Info</a>
+ </li>
+ <li>
+ <a href="/phenote/content/software/">Downloads</a>
+ </li>
+ <li>
+ <a href="/phenote/content/howtos/">How-tos</a>
+ <ul>
+ <li>
+ <a href="#software">Software</a>
+ </li>
+ <li>
+ <a href="#annotation">Annotation</a>
+ </li>
+ </ul>
+ </li>
+ <li>
+ <a href="/phenote/content/refs/">References</a>
+ </li>
+ <li>
+ <a href="/phenote/content/faq/">FAQ</a>
+ </li>
+ <li>
+ <a href="/phenote/content/about/">About us</a>
+ </li>
+ <li>
+ <a href="/phenote/content/links/">Links</a>
+ </li>
+ <li>
+ <a href="http://www.bioontology.org/wiki-internal/index.php/Phenote_-_A_Phenotype_Annotation_Tool">Internal Wiki</a>
+ </li>
+</ul>
+</div>
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-01-31 22:19:11
|
Revision: 334
http://svn.sourceforge.net/obo/?rev=334&view=rev
Author: nlw
Date: 2007-01-31 14:18:33 -0800 (Wed, 31 Jan 2007)
Log Message:
-----------
updating navi
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/ssi/navi_info.html
Modified: phenote/trunk/doc/phenote-website/ssi/navi_info.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_info.html 2007-01-31 22:18:12 UTC (rev 333)
+++ phenote/trunk/doc/phenote-website/ssi/navi_info.html 2007-01-31 22:18:33 UTC (rev 334)
@@ -13,8 +13,13 @@
<li>
<a href="#features">Features</a>
</li>
+ <li>
+ <a href="#web_users">Web Examples</a>
+ </li>
+ <li>
+ <a href="#documentation">Documentation</a>
<li>
- <a href="#soft_req">Software requirements</a>
+ <a href="#roadmap">Roadmap</a>
</li>
<li>
<a href="/phenote/content/info/release_notes.html">Release Notes</a>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-01-31 20:10:18
|
Revision: 332
http://svn.sourceforge.net/obo/?rev=332&view=rev
Author: nlw
Date: 2007-01-31 12:10:15 -0800 (Wed, 31 Jan 2007)
Log Message:
-----------
added info on "features"
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/content/info/index.shtml
Modified: phenote/trunk/doc/phenote-website/content/info/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-01-31 18:57:13 UTC (rev 331)
+++ phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-01-31 20:10:15 UTC (rev 332)
@@ -8,8 +8,34 @@
<h2>Software Information</h2>
-<h3><a name="features">Features</a></h3>
+<h3><a name="features">Features of Standalone software</a></h3>
<p>
+</p>
+<ul>
+ <li>Friendly spreadsheet-like interface
+ </li>
+ <li>Type-ahead-suggest (autocompletion) for terms within ontologies
+ </li>
+ <li>Use of any OBO-format ontology
+ </li>
+ <li>Ontology navigation and term information display
+ </li>
+ <li>Bulk copy/edit/delete of phenotype-genotype character entries
+ </li>
+ <li>Two output formats: phenosyntax and phenoxml
+ </li>
+ <li>configurable input fields to allow custom data entry and user-specified ontologies
+ </li>
+</ul>
+
+<h3><a name="examples">Example Sites Utilizing Phenote components</a></h3>
+The Dictyostelium Genome Database, <a href="http://dictybase.org">
+DictyBase</a>, has a web-based
+<a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">Phenotype Annotation Tool</a> that is directly linked to their own database backend.
+<br />
+<a href="http://zfin.org">Zfin</a> has an integrated phenotype annotation tool in their internal website. Here's a screenshot of their interface [to be added].
+<br />
+
<h3><a name="webstart">Running Phenote Webstart Version(s)</a></h3>
<h3><a name="install">Downloading and Installing Phenote</a></h3>
<p>
@@ -19,9 +45,11 @@
Phenote can be customized for data entry fields, and the ontologies that are desired to be included.
</p>
+<h3><a name="rel_notes">Release Notes</a></h3>
+<a href="http://toy.lbl.gov:9010/phenote/phenote-release-notes.html">[Release Notes]</a>
+<br />
-<br />
-</p>
+
</div>
</div>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-01-31 18:57:16
|
Revision: 331
http://svn.sourceforge.net/obo/?rev=331&view=rev
Author: nlw
Date: 2007-01-31 10:57:13 -0800 (Wed, 31 Jan 2007)
Log Message:
-----------
about content
Added Paths:
-----------
phenote/trunk/doc/phenote-website/content/about/index.shtml
Added: phenote/trunk/doc/phenote-website/content/about/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/about/index.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/content/about/index.shtml 2007-01-31 18:57:13 UTC (rev 331)
@@ -0,0 +1,56 @@
+<!--#include virtual="/phenote/ssi/header.html" -->
+
+<div id="page_body">
+
+<!--#include virtual="/phenote/ssi/navi_home.html" -->
+
+<div id="main_content">
+
+<h2>About Phenote</h2>
+
+<h3><a name="lists">Mailing lists</a></h3>
+<p>There are several mailing lists pertaining to Phenote:</p>
+<ul>
+ <li>Join in on discussions pertaining to Phenote by <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">subscribing to the mailing list</a>
+ </li>
+ <li>Keep on top of changes to phenote. Join the
+ <ul>
+ <li><a href="https://lists.sourceforge.net/lists/listinfo/obo-svn-commit">svn commit mailing list</a>
+ </li>
+ <li><a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-bug-tracker">phenote bug tracker list</a>
+ </li>
+ </ul>
+ </li>
+</ul>
+
+<br />
+
+<h3><a name="Bugs">Bug Reporting</a></h3>
+<p>If you find bugs in Phenote, please <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">submit a bug report on our Bug Tracker</a> located on sourceforge.</p>
+<p>Please use this same tracker to submit your enhancement and feature requests.</p>
+
+<br />
+
+<h3><a name="contact">Contact Us</a></h3>
+<p>Software Development:
+<script type="text/javascript">
+obfuscate("fruitfly.org", "mgibson", "Mark Gibson");
+</script></p>
+<p>Requirements, Analysis, Documentation:
+<script type="text/javascript">
+obfuscate("lbl.gov", "nlwashington", "Nicole Washington");
+</script></p>
+
+<h3><a name="Groups">Groups</a></h3>
+<p><a href="www.bioontology.org"><img class="protrait" height="50" src="/phenote/images/NCBO_logo.jpg" /></a>NCBO</p>
+<p><a href="www.berkeleybop.org">Berkeley BOP</a>
+
+<h3><a name="funding">Funding Sources</a></h3>
+The funding for Phenote development is provided from the National Center for Biomedical Ontologies, which is part of the
+<a href="http://www.bisti.nih.gov/ncbc/index.cfm">National Centers for Biomedical Computing</a> network,
+supported by the <a href="http://nihroadmap.nih.gov/">NIH Roadmap</a>.
+
+</div>
+</div>
+
+<!--#include virtual="/phenote/ssi/footer.shtml" -->
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-01-31 18:54:50
|
Revision: 330
http://svn.sourceforge.net/obo/?rev=330&view=rev
Author: nlw
Date: 2007-01-31 10:54:01 -0800 (Wed, 31 Jan 2007)
Log Message:
-----------
edit navis, added about/contact info
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/index_text.shtml
Added Paths:
-----------
phenote/trunk/doc/phenote-website/content/about/
phenote/trunk/doc/phenote-website/content/documentation/index.shtml
phenote/trunk/doc/phenote-website/content/howtos/index.shtml
phenote/trunk/doc/phenote-website/content/info/index.shtml
Removed Paths:
-------------
phenote/trunk/doc/phenote-website/content/documentation/index.html
phenote/trunk/doc/phenote-website/content/howtos/index.html
phenote/trunk/doc/phenote-website/content/info/index.html
Deleted: phenote/trunk/doc/phenote-website/content/documentation/index.html
===================================================================
--- phenote/trunk/doc/phenote-website/content/documentation/index.html 2007-01-31 17:36:42 UTC (rev 329)
+++ phenote/trunk/doc/phenote-website/content/documentation/index.html 2007-01-31 18:54:01 UTC (rev 330)
@@ -1,18 +0,0 @@
-<!--#include virtual="/phenote/ssi/header.html" -->
-
-<div id="page_body">
-
-<!--#include virtual="/phenote/ssi/navi_home.html" -->
-
-<div id="main_content">
-
-<h2>Documentation</h2>
-
-<h3><a name="general">Using Phenote for literature curration</a></h3>
-
-<br />
-</p>
-</div>
-</div>
-
-<!--#include virtual="/phenote/ssi/footer.shtml" -->
Copied: phenote/trunk/doc/phenote-website/content/documentation/index.shtml (from rev 329, phenote/trunk/doc/phenote-website/content/documentation/index.html)
===================================================================
--- phenote/trunk/doc/phenote-website/content/documentation/index.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/content/documentation/index.shtml 2007-01-31 18:54:01 UTC (rev 330)
@@ -0,0 +1,18 @@
+<!--#include virtual="/phenote/ssi/header.html" -->
+
+<div id="page_body">
+
+<!--#include virtual="/phenote/ssi/navi_home.html" -->
+
+<div id="main_content">
+
+<h2>Documentation</h2>
+
+<h3><a name="general">Using Phenote for literature curration</a></h3>
+
+<br />
+</p>
+</div>
+</div>
+
+<!--#include virtual="/phenote/ssi/footer.shtml" -->
Deleted: phenote/trunk/doc/phenote-website/content/howtos/index.html
===================================================================
--- phenote/trunk/doc/phenote-website/content/howtos/index.html 2007-01-31 17:36:42 UTC (rev 329)
+++ phenote/trunk/doc/phenote-website/content/howtos/index.html 2007-01-31 18:54:01 UTC (rev 330)
@@ -1,60 +0,0 @@
-<!--#include virtual="/phenote/ssi/header.html" -->
-
-<div id="page_body">
-
-<!--#include virtual="/phenote/ssi/navi_howtos.html" -->
-
-<div id="main_content">
-
-<h2>How-Tos</h2>
-<h3><a name="software">Software</a></h3>
-<h4><a name="webstart">Running Phenote Webstart Version(s)</a></h4>
-<p>
-By clicking any of links below, Phenote will use Webstart to launch the java application from the web. Simply clicking on a link below will download the application to your computer and run. Future clicks on the link should recognize that you've already downloaded the application, and it will simply start the software. If a newer version of the software is detected on the server, the newest version will replace your old version and then run.</p>
-<p>
-Three configurations of Phenote have been created to include the ontologies most appropriate for use by those communities:
-<ul>
-<li><a href="/phenote/phenote-flybase.jnlp">Fly</a></li>
-<li><a href="/phenote/phenote-zfin.jnlp">Zebrafish</a></li>
-<li><a href="/phenote/phenote-human.jnlp">Human</a></li>
-</ul>
-</p>
-<h4>Configuring your browser for Webstart</h4>
-<p>
-You must have Java 1.5 or later installed on your computer.
-Your browser must be configured to recognize webstart appications with the 'jnlp' extension. Most Mac and Windows browsers tend to have webstart pre-installed on their browsers. Linux does not <a href="/phenote/webstart-troubleshooting.html">[more on running Phenote on linux...]</a>. You must set up an association between the MIME type, which is an "application/x-java-jnlp-file".
-</p>
-
-<h4><a name="install">Downloading and Installing Phenote</a></h4>
-<p>The most up-to-date version of phenote can be checked out with subversion using: <br />
-svn co https://phenote.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote
-<br />
-</p>
-<p>
-You can also browse the subversion repository at:
-<a href="http://obo.svn.sourceforge.net/viewvc/obo/phenote/trunk/">
-https://obo.svn.sourceforge.net/viewvc/obo/phenote/trunk/</a>
-<br />
-
-Note that if you use this version, it might be buggy.
-</p>
-
-
-<h4><a name="config">Customizing Input</a></h4>
-<p>
-Phenote can be customized for data entry fields, and the ontologies that are desired to be included.
-</p>
-
-
-<h3><a name="annotation">Making Annotations</a></h3>
-<p>
-</p>
-
-
-
-<br />
-</p>
-</div>
-</div>
-
-<!--#include virtual="/phenote/ssi/footer.shtml" -->
Copied: phenote/trunk/doc/phenote-website/content/howtos/index.shtml (from rev 329, phenote/trunk/doc/phenote-website/content/howtos/index.html)
===================================================================
--- phenote/trunk/doc/phenote-website/content/howtos/index.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-01-31 18:54:01 UTC (rev 330)
@@ -0,0 +1,60 @@
+<!--#include virtual="/phenote/ssi/header.html" -->
+
+<div id="page_body">
+
+<!--#include virtual="/phenote/ssi/navi_howtos.html" -->
+
+<div id="main_content">
+
+<h2>How-Tos</h2>
+<h3><a name="software">Software</a></h3>
+<h4><a name="webstart">Running Phenote Webstart Version(s)</a></h4>
+<p>
+By clicking any of links below, Phenote will use Webstart to launch the java application from the web. Simply clicking on a link below will download the application to your computer and run. Future clicks on the link should recognize that you've already downloaded the application, and it will simply start the software. If a newer version of the software is detected on the server, the newest version will replace your old version and then run.</p>
+<p>
+Three configurations of Phenote have been created to include the ontologies most appropriate for use by those communities:
+<ul>
+<li><a href="/phenote/1.0/phenote-flybase.jnlp">Fly</a></li>
+<li><a href="/phenote/1.0/phenote-zfin.jnlp">Zebrafish</a></li>
+<li><a href="/phenote/1.0/phenote-human.jnlp">Human</a></li>
+</ul>
+</p>
+<h4>Configuring your browser for Webstart</h4>
+<p>
+You must have Java 1.5 or later installed on your computer.
+Your browser must be configured to recognize webstart appications with the 'jnlp' extension. Most Mac and Windows browsers tend to have webstart pre-installed on their browsers. Linux does not <a href="/phenote/webstart-troubleshooting.html">[more on running Phenote on linux...]</a>. You must set up an association between the MIME type, which is an "application/x-java-jnlp-file".
+</p>
+
+<h4><a name="install">Downloading and Installing Phenote</a></h4>
+<p>The most up-to-date version of phenote can be checked out with subversion using: <br />
+svn co https://phenote.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote
+<br />
+</p>
+<p>
+You can also browse the subversion repository at:
+<a href="http://obo.svn.sourceforge.net/viewvc/obo/phenote/trunk/">
+https://obo.svn.sourceforge.net/viewvc/obo/phenote/trunk/</a>
+<br />
+
+Note that if you use this version, it might be buggy.
+</p>
+
+
+<h4><a name="config">Customizing Input</a></h4>
+<p>
+Phenote can be customized for data entry fields, and the ontologies that are desired to be included.
+</p>
+
+
+<h3><a name="annotation">Making Annotations</a></h3>
+<p>
+</p>
+
+
+
+<br />
+</p>
+</div>
+</div>
+
+<!--#include virtual="/phenote/ssi/footer.shtml" -->
Deleted: phenote/trunk/doc/phenote-website/content/info/index.html
===================================================================
--- phenote/trunk/doc/phenote-website/content/info/index.html 2007-01-31 17:36:42 UTC (rev 329)
+++ phenote/trunk/doc/phenote-website/content/info/index.html 2007-01-31 18:54:01 UTC (rev 330)
@@ -1,28 +0,0 @@
-<!--#include virtual="/phenote/ssi/header.html" -->
-
-<div id="page_body">
-
-<!--#include virtual="/phenote/ssi/navi_info.html" -->
-
-<div id="main_content">
-
-<h2>Software Information</h2>
-
-<h3><a name="features">Features</a></h3>
-<p>
-<h3><a name="webstart">Running Phenote Webstart Version(s)</a></h3>
-<h3><a name="install">Downloading and Installing Phenote</a></h3>
-<p>
-</p>
-<h3><a name="config">Custom Configuration</a></h3>
-<p>
-Phenote can be customized for data entry fields, and the ontologies that are desired to be included.
-</p>
-
-
-<br />
-</p>
-</div>
-</div>
-
-<!--#include virtual="/phenote/ssi/footer.shtml" -->
Copied: phenote/trunk/doc/phenote-website/content/info/index.shtml (from rev 329, phenote/trunk/doc/phenote-website/content/info/index.html)
===================================================================
--- phenote/trunk/doc/phenote-website/content/info/index.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-01-31 18:54:01 UTC (rev 330)
@@ -0,0 +1,28 @@
+<!--#include virtual="/phenote/ssi/header.html" -->
+
+<div id="page_body">
+
+<!--#include virtual="/phenote/ssi/navi_info.html" -->
+
+<div id="main_content">
+
+<h2>Software Information</h2>
+
+<h3><a name="features">Features</a></h3>
+<p>
+<h3><a name="webstart">Running Phenote Webstart Version(s)</a></h3>
+<h3><a name="install">Downloading and Installing Phenote</a></h3>
+<p>
+</p>
+<h3><a name="config">Custom Configuration</a></h3>
+<p>
+Phenote can be customized for data entry fields, and the ontologies that are desired to be included.
+</p>
+
+
+<br />
+</p>
+</div>
+</div>
+
+<!--#include virtual="/phenote/ssi/footer.shtml" -->
Modified: phenote/trunk/doc/phenote-website/index_text.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-31 17:36:42 UTC (rev 329)
+++ phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-31 18:54:01 UTC (rev 330)
@@ -16,26 +16,31 @@
<p>This tool is being developed by the <a href="http://berkeleybop.org/">Bioinformatics Core</a> of the <a href="http://www.bioontology.org">National Center for Biomedical Ontology</a>.
</p>
-<p>
+
There are two groups driving the development of this software project:
<p><a href="http://flybase.bio.indiana.edu/">
<img class="portrait" height="50" border="0" src="/phenote/images/fly_logo.png" alt="Flybase" /></a>Flybase: The Drosophila Genome Database.
<br />
</p>
<br />
+<br />
<p><a href="http://zfin.org/"><img class="portrait" border="0" src="/phenote/images/zfin_logo.gif" height="50" alt="Zfin" /></a>ZFIN: The Zebrafish Genome Database
<br />
</p>
-</p>
-<p>
+<br />
+<br />
+
We are also collaborating with several groups:
<p><a href="http://www.nescent.org/"><img class="portrait" border="0" src="/phenote/images/nescent_logo.gif" height="50" alt="Nescent" /></a>NESCENT: The National Evolutionary Synthesis Center
<br />
</p>
+<br />
+<br />
<p><a href="http://www.pharmgkb.org/"><img class="portrait" border="0" src="/phenote/images/pgkb_logo.png" height="50" alt="PharmGKB" /></a>PharmGKB: The Pharmacogenetics and Pharmacogenomics Knowledge Base
<br />
</p>
-</p>
+<br />
+<br />
</div>
</div>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-01-31 17:38:13
|
Revision: 329
http://svn.sourceforge.net/obo/?rev=329&view=rev
Author: nlw
Date: 2007-01-31 09:36:42 -0800 (Wed, 31 Jan 2007)
Log Message:
-----------
changed filenames, edits to navis
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/ssi/navi_info.html
Added Paths:
-----------
phenote/trunk/doc/phenote-website/content/documentation/index.html
phenote/trunk/doc/phenote-website/content/howtos/index.html
phenote/trunk/doc/phenote-website/content/info/index.html
Removed Paths:
-------------
phenote/trunk/doc/phenote-website/content/documentation/index.shtml
phenote/trunk/doc/phenote-website/content/howtos/index.shtml
phenote/trunk/doc/phenote-website/content/info/index.shtml
Copied: phenote/trunk/doc/phenote-website/content/documentation/index.html (from rev 328, phenote/trunk/doc/phenote-website/content/documentation/index.shtml)
===================================================================
--- phenote/trunk/doc/phenote-website/content/documentation/index.html (rev 0)
+++ phenote/trunk/doc/phenote-website/content/documentation/index.html 2007-01-31 17:36:42 UTC (rev 329)
@@ -0,0 +1,18 @@
+<!--#include virtual="/phenote/ssi/header.html" -->
+
+<div id="page_body">
+
+<!--#include virtual="/phenote/ssi/navi_home.html" -->
+
+<div id="main_content">
+
+<h2>Documentation</h2>
+
+<h3><a name="general">Using Phenote for literature curration</a></h3>
+
+<br />
+</p>
+</div>
+</div>
+
+<!--#include virtual="/phenote/ssi/footer.shtml" -->
Deleted: phenote/trunk/doc/phenote-website/content/documentation/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/documentation/index.shtml 2007-01-31 06:56:35 UTC (rev 328)
+++ phenote/trunk/doc/phenote-website/content/documentation/index.shtml 2007-01-31 17:36:42 UTC (rev 329)
@@ -1,18 +0,0 @@
-<!--#include virtual="/phenote/ssi/header.html" -->
-
-<div id="page_body">
-
-<!--#include virtual="/phenote/ssi/navi_home.html" -->
-
-<div id="main_content">
-
-<h2>Documentation</h2>
-
-<h3><a name="general">Using Phenote for literature curration</a></h3>
-
-<br />
-</p>
-</div>
-</div>
-
-<!--#include virtual="/phenote/ssi/footer.shtml" -->
Copied: phenote/trunk/doc/phenote-website/content/howtos/index.html (from rev 328, phenote/trunk/doc/phenote-website/content/howtos/index.shtml)
===================================================================
--- phenote/trunk/doc/phenote-website/content/howtos/index.html (rev 0)
+++ phenote/trunk/doc/phenote-website/content/howtos/index.html 2007-01-31 17:36:42 UTC (rev 329)
@@ -0,0 +1,60 @@
+<!--#include virtual="/phenote/ssi/header.html" -->
+
+<div id="page_body">
+
+<!--#include virtual="/phenote/ssi/navi_howtos.html" -->
+
+<div id="main_content">
+
+<h2>How-Tos</h2>
+<h3><a name="software">Software</a></h3>
+<h4><a name="webstart">Running Phenote Webstart Version(s)</a></h4>
+<p>
+By clicking any of links below, Phenote will use Webstart to launch the java application from the web. Simply clicking on a link below will download the application to your computer and run. Future clicks on the link should recognize that you've already downloaded the application, and it will simply start the software. If a newer version of the software is detected on the server, the newest version will replace your old version and then run.</p>
+<p>
+Three configurations of Phenote have been created to include the ontologies most appropriate for use by those communities:
+<ul>
+<li><a href="/phenote/phenote-flybase.jnlp">Fly</a></li>
+<li><a href="/phenote/phenote-zfin.jnlp">Zebrafish</a></li>
+<li><a href="/phenote/phenote-human.jnlp">Human</a></li>
+</ul>
+</p>
+<h4>Configuring your browser for Webstart</h4>
+<p>
+You must have Java 1.5 or later installed on your computer.
+Your browser must be configured to recognize webstart appications with the 'jnlp' extension. Most Mac and Windows browsers tend to have webstart pre-installed on their browsers. Linux does not <a href="/phenote/webstart-troubleshooting.html">[more on running Phenote on linux...]</a>. You must set up an association between the MIME type, which is an "application/x-java-jnlp-file".
+</p>
+
+<h4><a name="install">Downloading and Installing Phenote</a></h4>
+<p>The most up-to-date version of phenote can be checked out with subversion using: <br />
+svn co https://phenote.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote
+<br />
+</p>
+<p>
+You can also browse the subversion repository at:
+<a href="http://obo.svn.sourceforge.net/viewvc/obo/phenote/trunk/">
+https://obo.svn.sourceforge.net/viewvc/obo/phenote/trunk/</a>
+<br />
+
+Note that if you use this version, it might be buggy.
+</p>
+
+
+<h4><a name="config">Customizing Input</a></h4>
+<p>
+Phenote can be customized for data entry fields, and the ontologies that are desired to be included.
+</p>
+
+
+<h3><a name="annotation">Making Annotations</a></h3>
+<p>
+</p>
+
+
+
+<br />
+</p>
+</div>
+</div>
+
+<!--#include virtual="/phenote/ssi/footer.shtml" -->
Deleted: phenote/trunk/doc/phenote-website/content/howtos/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-01-31 06:56:35 UTC (rev 328)
+++ phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-01-31 17:36:42 UTC (rev 329)
@@ -1,60 +0,0 @@
-<!--#include virtual="/phenote/ssi/header.html" -->
-
-<div id="page_body">
-
-<!--#include virtual="/phenote/ssi/navi_howtos.html" -->
-
-<div id="main_content">
-
-<h2>How-Tos</h2>
-<h3><a name="software">Software</a></h3>
-<h4><a name="webstart">Running Phenote Webstart Version(s)</a></h4>
-<p>
-By clicking any of links below, Phenote will use Webstart to launch the java application from the web. Simply clicking on a link below will download the application to your computer and run. Future clicks on the link should recognize that you've already downloaded the application, and it will simply start the software. If a newer version of the software is detected on the server, the newest version will replace your old version and then run.</p>
-<p>
-Three configurations of Phenote have been created to include the ontologies most appropriate for use by those communities:
-<ul>
-<li><a href="/phenote/phenote-flybase.jnlp">Fly</a></li>
-<li><a href="/phenote/phenote-zfin.jnlp">Zebrafish</a></li>
-<li><a href="/phenote/phenote-human.jnlp">Human</a></li>
-</ul>
-</p>
-<h4>Configuring your browser for Webstart</h4>
-<p>
-You must have Java 1.5 or later installed on your computer.
-Your browser must be configured to recognize webstart appications with the 'jnlp' extension. Most Mac and Windows browsers tend to have webstart pre-installed on their browsers. Linux does not <a href="/phenote/webstart-troubleshooting.html">[more on running Phenote on linux...]</a>. You must set up an association between the MIME type, which is an "application/x-java-jnlp-file".
-</p>
-
-<h4><a name="install">Downloading and Installing Phenote</a></h4>
-<p>The most up-to-date version of phenote can be checked out with subversion using: <br />
-svn co https://phenote.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote
-<br />
-</p>
-<p>
-You can also browse the subversion repository at:
-<a href="http://obo.svn.sourceforge.net/viewvc/obo/phenote/trunk/">
-https://obo.svn.sourceforge.net/viewvc/obo/phenote/trunk/</a>
-<br />
-
-Note that if you use this version, it might be buggy.
-</p>
-
-
-<h4><a name="config">Customizing Input</a></h4>
-<p>
-Phenote can be customized for data entry fields, and the ontologies that are desired to be included.
-</p>
-
-
-<h3><a name="annotation">Making Annotations</a></h3>
-<p>
-</p>
-
-
-
-<br />
-</p>
-</div>
-</div>
-
-<!--#include virtual="/phenote/ssi/footer.shtml" -->
Copied: phenote/trunk/doc/phenote-website/content/info/index.html (from rev 328, phenote/trunk/doc/phenote-website/content/info/index.shtml)
===================================================================
--- phenote/trunk/doc/phenote-website/content/info/index.html (rev 0)
+++ phenote/trunk/doc/phenote-website/content/info/index.html 2007-01-31 17:36:42 UTC (rev 329)
@@ -0,0 +1,28 @@
+<!--#include virtual="/phenote/ssi/header.html" -->
+
+<div id="page_body">
+
+<!--#include virtual="/phenote/ssi/navi_info.html" -->
+
+<div id="main_content">
+
+<h2>Software Information</h2>
+
+<h3><a name="features">Features</a></h3>
+<p>
+<h3><a name="webstart">Running Phenote Webstart Version(s)</a></h3>
+<h3><a name="install">Downloading and Installing Phenote</a></h3>
+<p>
+</p>
+<h3><a name="config">Custom Configuration</a></h3>
+<p>
+Phenote can be customized for data entry fields, and the ontologies that are desired to be included.
+</p>
+
+
+<br />
+</p>
+</div>
+</div>
+
+<!--#include virtual="/phenote/ssi/footer.shtml" -->
Deleted: phenote/trunk/doc/phenote-website/content/info/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-01-31 06:56:35 UTC (rev 328)
+++ phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-01-31 17:36:42 UTC (rev 329)
@@ -1,28 +0,0 @@
-<!--#include virtual="/phenote/ssi/header.html" -->
-
-<div id="page_body">
-
-<!--#include virtual="/phenote/ssi/navi_info.html" -->
-
-<div id="main_content">
-
-<h2>Software Information</h2>
-
-<h3><a name="features">Features</a></h3>
-<p>
-<h3><a name="webstart">Running Phenote Webstart Version(s)</a></h3>
-<h3><a name="install">Downloading and Installing Phenote</a></h3>
-<p>
-</p>
-<h3><a name="config">Custom Configuration</a></h3>
-<p>
-Phenote can be customized for data entry fields, and the ontologies that are desired to be included.
-</p>
-
-
-<br />
-</p>
-</div>
-</div>
-
-<!--#include virtual="/phenote/ssi/footer.shtml" -->
Modified: phenote/trunk/doc/phenote-website/ssi/navi_info.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_info.html 2007-01-31 06:56:35 UTC (rev 328)
+++ phenote/trunk/doc/phenote-website/ssi/navi_info.html 2007-01-31 17:36:42 UTC (rev 329)
@@ -11,10 +11,10 @@
<a href="/phenote/content/info/">Software Info</a>
<ul>
<li>
- <a href="/phenote/content/info/features.html">Features</a>
+ <a href="#features">Features</a>
</li>
<li>
- <a href="/phenote/content/info/java_req.html">Software requirements</a>
+ <a href="#soft_req">Software requirements</a>
</li>
<li>
<a href="/phenote/content/info/release_notes.html">Release Notes</a>
@@ -25,7 +25,7 @@
<a href="/phenote/content/software/">Downloads</a>
</li>
<li>
- <a href="/phenote/content/documentation/">How-tos</a>
+ <a href="/phenote/content/howtos/">How-tos</a>
</li>
<li>
<a href="/phenote/content/refs/">References</a>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-01-31 06:56:34
|
Revision: 328
http://svn.sourceforge.net/obo/?rev=328&view=rev
Author: nlw
Date: 2007-01-30 22:56:35 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
fixing navi bar
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/ssi/navi_home.html
phenote/trunk/doc/phenote-website/ssi/navi_home.html~
Modified: phenote/trunk/doc/phenote-website/ssi/navi_home.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-01-31 06:45:20 UTC (rev 327)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-01-31 06:56:35 UTC (rev 328)
@@ -14,7 +14,7 @@
<a href="/phenote/content/software/">Downloads</a>
</li>
<li>
- <a href="/phenote/content/documentation/">How-tos</a>
+ <a href="/phenote/content/howtos/">How-tos</a>
</li>
<li>
<a href="/phenote/content/refs/">References</a>
Modified: phenote/trunk/doc/phenote-website/ssi/navi_home.html~
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html~ 2007-01-31 06:45:20 UTC (rev 327)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html~ 2007-01-31 06:56:35 UTC (rev 328)
@@ -8,7 +8,7 @@
<a href="/">Home</a>
</li>
<li>
- <a href="/phenote/content/background/">Background</a>
+ <a href="/phenote/content/info/">Software Info</a>
</li>
<li>
<a href="/phenote/content/software/">Downloads</a>
@@ -23,7 +23,7 @@
<a href="/phenote/content/faq/">FAQ</a>
</li>
<li>
- <a href="/phenote/content/about/">About</a>
+ <a href="/phenote/content/about/">About us</a>
</li>
<li>
<a href="/phenote/content/links/">Links</a>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-01-31 06:45:26
|
Revision: 327
http://svn.sourceforge.net/obo/?rev=327&view=rev
Author: nlw
Date: 2007-01-30 22:45:20 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
more content
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/content/howtos/index.shtml
Modified: phenote/trunk/doc/phenote-website/content/howtos/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-01-31 06:40:09 UTC (rev 326)
+++ phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-01-31 06:45:20 UTC (rev 327)
@@ -11,6 +11,7 @@
<h4><a name="webstart">Running Phenote Webstart Version(s)</a></h4>
<p>
By clicking any of links below, Phenote will use Webstart to launch the java application from the web. Simply clicking on a link below will download the application to your computer and run. Future clicks on the link should recognize that you've already downloaded the application, and it will simply start the software. If a newer version of the software is detected on the server, the newest version will replace your old version and then run.</p>
+<p>
Three configurations of Phenote have been created to include the ontologies most appropriate for use by those communities:
<ul>
<li><a href="/phenote/phenote-flybase.jnlp">Fly</a></li>
@@ -25,10 +26,11 @@
</p>
<h4><a name="install">Downloading and Installing Phenote</a></h4>
-The most up-to-date version of phenote can be checked out with subversion using: <br />
+<p>The most up-to-date version of phenote can be checked out with subversion using: <br />
svn co https://phenote.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote
<br />
-
+</p>
+<p>
You can also browse the subversion repository at:
<a href="http://obo.svn.sourceforge.net/viewvc/obo/phenote/trunk/">
https://obo.svn.sourceforge.net/viewvc/obo/phenote/trunk/</a>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-01-31 06:40:29
|
Revision: 326
http://svn.sourceforge.net/obo/?rev=326&view=rev
Author: nlw
Date: 2007-01-30 22:40:09 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
fixing size of fly icon
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/index_text.shtml
Modified: phenote/trunk/doc/phenote-website/index_text.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-31 01:56:38 UTC (rev 325)
+++ phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-31 06:40:09 UTC (rev 326)
@@ -18,9 +18,11 @@
</p>
<p>
There are two groups driving the development of this software project:
-<p><a href="http://flybase.bio.indiana.edu/"><img class="portrait" height="75" border="0" src="/phenote/images/fly_logo.png" alt="Flybase" /></a>Flybase: The Drosophila Genome Database.
+<p><a href="http://flybase.bio.indiana.edu/">
+<img class="portrait" height="50" border="0" src="/phenote/images/fly_logo.png" alt="Flybase" /></a>Flybase: The Drosophila Genome Database.
<br />
</p>
+<br />
<p><a href="http://zfin.org/"><img class="portrait" border="0" src="/phenote/images/zfin_logo.gif" height="50" alt="Zfin" /></a>ZFIN: The Zebrafish Genome Database
<br />
</p>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-01-31 01:56:39
|
Revision: 325
http://svn.sourceforge.net/obo/?rev=325&view=rev
Author: nlw
Date: 2007-01-30 17:56:38 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
edits to howtos
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/content/documentation/index.shtml
phenote/trunk/doc/phenote-website/content/info/index.shtml
Added Paths:
-----------
phenote/trunk/doc/phenote-website/content/howtos/
phenote/trunk/doc/phenote-website/content/howtos/index.shtml
Modified: phenote/trunk/doc/phenote-website/content/documentation/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/documentation/index.shtml 2007-01-31 00:21:14 UTC (rev 324)
+++ phenote/trunk/doc/phenote-website/content/documentation/index.shtml 2007-01-31 01:56:38 UTC (rev 325)
@@ -8,17 +8,8 @@
<h2>Documentation</h2>
-<h3><a name="general">Making Annotations with Phenote</a></h3>
-<h3><a name="webstart">Running Phenote Webstart Version(s)</a></h3>
-<h3><a name="install">Downloading and Installing Phenote</a></h3>
-<p>
-</p>
-<h3><a name="config">Custom Configuration</a></h3>
-<p>
-Phenote can be customized for data entry fields, and the ontologies that are desired to be included.
-</p>
+<h3><a name="general">Using Phenote for literature curration</a></h3>
-
<br />
</p>
</div>
Added: phenote/trunk/doc/phenote-website/content/howtos/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/howtos/index.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-01-31 01:56:38 UTC (rev 325)
@@ -0,0 +1,58 @@
+<!--#include virtual="/phenote/ssi/header.html" -->
+
+<div id="page_body">
+
+<!--#include virtual="/phenote/ssi/navi_howtos.html" -->
+
+<div id="main_content">
+
+<h2>How-Tos</h2>
+<h3><a name="software">Software</a></h3>
+<h4><a name="webstart">Running Phenote Webstart Version(s)</a></h4>
+<p>
+By clicking any of links below, Phenote will use Webstart to launch the java application from the web. Simply clicking on a link below will download the application to your computer and run. Future clicks on the link should recognize that you've already downloaded the application, and it will simply start the software. If a newer version of the software is detected on the server, the newest version will replace your old version and then run.</p>
+Three configurations of Phenote have been created to include the ontologies most appropriate for use by those communities:
+<ul>
+<li><a href="/phenote/phenote-flybase.jnlp">Fly</a></li>
+<li><a href="/phenote/phenote-zfin.jnlp">Zebrafish</a></li>
+<li><a href="/phenote/phenote-human.jnlp">Human</a></li>
+</ul>
+</p>
+<h4>Configuring your browser for Webstart</h4>
+<p>
+You must have Java 1.5 or later installed on your computer.
+Your browser must be configured to recognize webstart appications with the 'jnlp' extension. Most Mac and Windows browsers tend to have webstart pre-installed on their browsers. Linux does not <a href="/phenote/webstart-troubleshooting.html">[more on running Phenote on linux...]</a>. You must set up an association between the MIME type, which is an "application/x-java-jnlp-file".
+</p>
+
+<h4><a name="install">Downloading and Installing Phenote</a></h4>
+The most up-to-date version of phenote can be checked out with subversion using: <br />
+svn co https://phenote.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote
+<br />
+
+You can also browse the subversion repository at:
+<a href="http://obo.svn.sourceforge.net/viewvc/obo/phenote/trunk/">
+https://obo.svn.sourceforge.net/viewvc/obo/phenote/trunk/</a>
+<br />
+
+Note that if you use this version, it might be buggy.
+</p>
+
+
+<h4><a name="config">Customizing Input</a></h4>
+<p>
+Phenote can be customized for data entry fields, and the ontologies that are desired to be included.
+</p>
+
+
+<h3><a name="annotation">Making Annotations</a></h3>
+<p>
+</p>
+
+
+
+<br />
+</p>
+</div>
+</div>
+
+<!--#include virtual="/phenote/ssi/footer.shtml" -->
Modified: phenote/trunk/doc/phenote-website/content/info/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-01-31 00:21:14 UTC (rev 324)
+++ phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-01-31 01:56:38 UTC (rev 325)
@@ -6,9 +6,10 @@
<div id="main_content">
-<h2>Documentation</h2>
+<h2>Software Information</h2>
-<h3><a name="general">Making Annotations with Phenote</a></h3>
+<h3><a name="features">Features</a></h3>
+<p>
<h3><a name="webstart">Running Phenote Webstart Version(s)</a></h3>
<h3><a name="install">Downloading and Installing Phenote</a></h3>
<p>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-01-31 00:19:22
|
Revision: 323
http://svn.sourceforge.net/obo/?rev=323&view=rev
Author: nlw
Date: 2007-01-30 16:19:20 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
more content
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/index_text.shtml
phenote/trunk/doc/phenote-website/ssi/navi_home.html
phenote/trunk/doc/phenote-website/ssi/navi_home.html~
Added Paths:
-----------
phenote/trunk/doc/phenote-website/content/info/
phenote/trunk/doc/phenote-website/content/info/index.shtml
phenote/trunk/doc/phenote-website/ssi/navi_info.html
Added: phenote/trunk/doc/phenote-website/content/info/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/info/index.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-01-31 00:19:20 UTC (rev 323)
@@ -0,0 +1,27 @@
+<!--#include virtual="/phenote/ssi/header.html" -->
+
+<div id="page_body">
+
+<!--#include virtual="/phenote/ssi/navi_info.html" -->
+
+<div id="main_content">
+
+<h2>Documentation</h2>
+
+<h3><a name="general">Making Annotations with Phenote</a></h3>
+<h3><a name="webstart">Running Phenote Webstart Version(s)</a></h3>
+<h3><a name="install">Downloading and Installing Phenote</a></h3>
+<p>
+</p>
+<h3><a name="config">Custom Configuration</a></h3>
+<p>
+Phenote can be customized for data entry fields, and the ontologies that are desired to be included.
+</p>
+
+
+<br />
+</p>
+</div>
+</div>
+
+<!--#include virtual="/phenote/ssi/footer.shtml" -->
Modified: phenote/trunk/doc/phenote-website/index_text.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-31 00:01:34 UTC (rev 322)
+++ phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-31 00:19:20 UTC (rev 323)
@@ -12,23 +12,28 @@
Data annotated with Phenote is based on the <a href="http://http://www.fruitfly.org/~cjm/obd/formats.html">EQ model</a> for representing phenotypes, combining entities from any OBO ontology with qualities (such as <a href="http://http://www.bioontology.org/wiki/index.php/PATO:About">PATO</a>).
</p>
-<p>The software can be used as a complete package, or individual compontents can be downloaded and plugged in to your desired application. [Learn More]</p>
+<p>The software can be used as a complete package, or individual compontents can be downloaded and plugged in to your desired application. Check out our <a href="/phenote/info/">Info</a> page to learn more.</p>
<p>This tool is being developed by the <a href="http://berkeleybop.org/">Bioinformatics Core</a> of the <a href="http://www.bioontology.org">National Center for Biomedical Ontology</a>.
</p>
<p>
There are two groups driving the development of this software project:
-<ul>
- <li><p><a href="http://flybase.bio.indiana.edu/"><img class="portrait" border="0" src="/phenote/images/fly_logo.png" alt="Flybase" /></a><h3>Flybase: The Drosophila Genome Database.</h3></li></p>
- <li><p><a href="http://zfin.org/"><img class="portrait" border="0" src="/phenote/images/zfin_logo.gif" alt="Zfin" /></a>ZFIN: The Zebrafish Genome Database</li></p>
-</ul>
+<p><a href="http://flybase.bio.indiana.edu/"><img class="portrait" height="75" border="0" src="/phenote/images/fly_logo.png" alt="Flybase" /></a>Flybase: The Drosophila Genome Database.
+<br />
</p>
+<p><a href="http://zfin.org/"><img class="portrait" border="0" src="/phenote/images/zfin_logo.gif" height="50" alt="Zfin" /></a>ZFIN: The Zebrafish Genome Database
+<br />
+</p>
+</p>
<p>
We are also collaborating with several groups:
-<p><a href="http://www.nescent.org/"><img class="portrait" border="0" src="/phenote/images/nescent_logo.gif" alt="Nescent" /></a>NESCENT: The National Evolutionary Synthesis Center</p>
-<p><a href="http://www.pharmgkb.org/"><img class="portrait" border="0" src="/phenote/images/pgkb_logo.png" alt="PharmGKB" /></a>PharmGKB: The Pharmacogenetics and Pharmacogenomics Knowledge Base
+<p><a href="http://www.nescent.org/"><img class="portrait" border="0" src="/phenote/images/nescent_logo.gif" height="50" alt="Nescent" /></a>NESCENT: The National Evolutionary Synthesis Center
+<br />
</p>
+<p><a href="http://www.pharmgkb.org/"><img class="portrait" border="0" src="/phenote/images/pgkb_logo.png" height="50" alt="PharmGKB" /></a>PharmGKB: The Pharmacogenetics and Pharmacogenomics Knowledge Base
+<br />
</p>
+</p>
</div>
</div>
Modified: phenote/trunk/doc/phenote-website/ssi/navi_home.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-01-31 00:01:34 UTC (rev 322)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-01-31 00:19:20 UTC (rev 323)
@@ -8,13 +8,13 @@
<a href="/">Home</a>
</li>
<li>
- <a href="/phenote/content/background/">Background</a>
+ <a href="/phenote/content/info/">Software Info</a>
</li>
<li>
<a href="/phenote/content/software/">Downloads</a>
</li>
<li>
- <a href="/phenote/content/documentation/">Documentation</a>
+ <a href="/phenote/content/documentation/">How-tos</a>
</li>
<li>
<a href="/phenote/content/refs/">References</a>
@@ -23,7 +23,7 @@
<a href="/phenote/content/faq/">FAQ</a>
</li>
<li>
- <a href="/phenote/content/about/">About</a>
+ <a href="/phenote/content/about/">About us</a>
</li>
<li>
<a href="/phenote/content/links/">Links</a>
Modified: phenote/trunk/doc/phenote-website/ssi/navi_home.html~
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html~ 2007-01-31 00:01:34 UTC (rev 322)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html~ 2007-01-31 00:19:20 UTC (rev 323)
@@ -14,7 +14,7 @@
<a href="/phenote/content/software/">Downloads</a>
</li>
<li>
- <a href="/phenote/content/documentation/">Documentation</a>
+ <a href="/phenote/content/documentation/">How-tos</a>
</li>
<li>
<a href="/phenote/content/refs/">References</a>
@@ -33,4 +33,4 @@
</li>
</ul>
</div>
-</div>
+
Added: phenote/trunk/doc/phenote-website/ssi/navi_info.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_info.html (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/navi_info.html 2007-01-31 00:19:20 UTC (rev 323)
@@ -0,0 +1,47 @@
+<div id="navi">
+<div class="navi_head"></div>
+<ul>
+<!-- <li>
+ Home
+--> </li>
+ <li>
+ <a href="/">Home</a>
+ </li>
+ <li>
+ <a href="/phenote/content/info/">Software Info</a>
+ <ul>
+ <li>
+ <a href="/phenote/content/info/features.html">Features</a>
+ </li>
+ <li>
+ <a href="/phenote/content/info/java_req.html">Software requirements</a>
+ </li>
+ <li>
+ <a href="/phenote/content/info/release_notes.html">Release Notes</a>
+ </li>
+ </ul>
+ </li>
+ <li>
+ <a href="/phenote/content/software/">Downloads</a>
+ </li>
+ <li>
+ <a href="/phenote/content/documentation/">How-tos</a>
+ </li>
+ <li>
+ <a href="/phenote/content/refs/">References</a>
+ </li>
+ <li>
+ <a href="/phenote/content/faq/">FAQ</a>
+ </li>
+ <li>
+ <a href="/phenote/content/about/">About us</a>
+ </li>
+ <li>
+ <a href="/phenote/content/links/">Links</a>
+ </li>
+ <li>
+ <a href="http://www.bioontology.org/wiki-internal/index.php/Phenote_-_A_Phenotype_Annotation_Tool">Internal Wiki</a>
+ </li>
+</ul>
+</div>
+
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|
|
From: <nl...@us...> - 2007-01-31 00:01:35
|
Revision: 322
http://svn.sourceforge.net/obo/?rev=322&view=rev
Author: nlw
Date: 2007-01-30 16:01:34 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
adding content
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/index_text.shtml
phenote/trunk/doc/phenote-website/ssi/header.html
Modified: phenote/trunk/doc/phenote-website/index_text.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-30 23:11:42 UTC (rev 321)
+++ phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-31 00:01:34 UTC (rev 322)
@@ -5,16 +5,30 @@
<!--#include virtual="/phenote/ssi/navi_home.html" -->
<div id="main_content">
-<h2>Phenotype Annotation Tools</h2>
<p>
-Phenote is a software tool currently being developed by the National Center for Biomedical Ontology to facilitate the annotation of biological phenotypes. Its development is being driven by several groups, including:
+<b><i>Phenote</i></b> is both a complete piece of software and a software toolkit designed to facilitate the annotation of biological phenotypes using ontologies. It provides an interface to record genotype-phenotype pairs, together with the provenance for the annotation.
+
+
+Data annotated with Phenote is based on the <a href="http://http://www.fruitfly.org/~cjm/obd/formats.html">EQ model</a> for representing phenotypes, combining entities from any OBO ontology with qualities (such as <a href="http://http://www.bioontology.org/wiki/index.php/PATO:About">PATO</a>).
+</p>
+
+<p>The software can be used as a complete package, or individual compontents can be downloaded and plugged in to your desired application. [Learn More]</p>
+
+<p>This tool is being developed by the <a href="http://berkeleybop.org/">Bioinformatics Core</a> of the <a href="http://www.bioontology.org">National Center for Biomedical Ontology</a>.
+</p>
+<p>
+There are two groups driving the development of this software project:
<ul>
- <li><a href="http://flybase.bio.indiana.edu/"><img class="portrait" border="0" src="/phenote/images/fly_logo.png" alt="Flybase" /></a><h3>Flybase: The Drosophila Genome Database.</h3></li>
- <li><a href="http://zfin.org/"><img class="portrait" border="0" src="/phenote/images/zfin_logo.gif" alt="Zfin" /></a>ZFIN: The Zebrafish Genome Database</li>
- <li><a href="http://www.nescent.org/"><img class="portrait" border="0" src="/phenote/images/nescent_logo.gif" alt="NESCENT" /></a>NESCENT: The National Evolultionary Synthesis Center</li>
+ <li><p><a href="http://flybase.bio.indiana.edu/"><img class="portrait" border="0" src="/phenote/images/fly_logo.png" alt="Flybase" /></a><h3>Flybase: The Drosophila Genome Database.</h3></li></p>
+ <li><p><a href="http://zfin.org/"><img class="portrait" border="0" src="/phenote/images/zfin_logo.gif" alt="Zfin" /></a>ZFIN: The Zebrafish Genome Database</li></p>
</ul>
-
</p>
+<p>
+We are also collaborating with several groups:
+<p><a href="http://www.nescent.org/"><img class="portrait" border="0" src="/phenote/images/nescent_logo.gif" alt="Nescent" /></a>NESCENT: The National Evolutionary Synthesis Center</p>
+<p><a href="http://www.pharmgkb.org/"><img class="portrait" border="0" src="/phenote/images/pgkb_logo.png" alt="PharmGKB" /></a>PharmGKB: The Pharmacogenetics and Pharmacogenomics Knowledge Base
+</p>
+</p>
</div>
</div>
Modified: phenote/trunk/doc/phenote-website/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/header.html 2007-01-30 23:11:42 UTC (rev 321)
+++ phenote/trunk/doc/phenote-website/ssi/header.html 2007-01-31 00:01:34 UTC (rev 322)
@@ -30,7 +30,7 @@
</div>
<div class="page_logo">
-<img src="/phenote/images/NCBO_logo.jpg" alt="logo" />
+<img src="/phenote/images/" />
</div>
</div>
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|
|
From: <mg...@us...> - 2007-01-30 23:11:44
|
Revision: 321
http://svn.sourceforge.net/obo/?rev=321&view=rev
Author: mgibson
Date: 2007-01-30 15:11:42 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
broke out webstart jars target in ant
Modified Paths:
--------------
phenote/trunk/build.xml
Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml 2007-01-30 23:07:27 UTC (rev 320)
+++ phenote/trunk/build.xml 2007-01-30 23:11:42 UTC (rev 321)
@@ -386,7 +386,7 @@
<!-- todo do all jars not just phenote - take out -signed -->
<!-- depends on sym link phenote-webstart and env var PHENOTE_VERSION -->
<!-- target name="build-webstart" depends="build-sign-jars,webstart"/ -->
- <target name="build-webstart" depends="build-all,jar,webstart,sign-webstart-jars"/>
+ <target name="build-webstart" depends="build-all,jar"/>
<!-- target name="build-sign-jars" depends="build-all,jar,sign-jars"/ -->
@@ -404,13 +404,7 @@
<!-- need to test if PHENOTE_VERSION is defined - possible?? -->
- <target name="webstart" depends="webstart-webpages,copy-jnlps">
- <echo message="Env Var PHENOTE VERSION is set to ${env.PHENOTE_VERSION}" />
- <mkdir dir="phenote-webstart/${env.PHENOTE_VERSION}"/>
- <copy todir="phenote-webstart/${env.PHENOTE_VERSION}/jars">
- <fileset file="${lib}/*.jar"/>
- </copy>
- </target>
+ <target name="webstart" depends="webstart-jars,webstart-webpages,copy-jnlps"/>
<target name="webstart-webpages">
<copy todir="phenote-webstart">
@@ -431,6 +425,16 @@
</target>
+ <target name="webstart-jars" depends="copy-webstart-jars,sign-webstart-jars"/>
+
+ <target name="copy-webstart-jars">
+ <echo message="Env Var PHENOTE VERSION is set to ${env.PHENOTE_VERSION}" />
+ <mkdir dir="phenote-webstart/${env.PHENOTE_VERSION}"/>
+ <copy todir="phenote-webstart/${env.PHENOTE_VERSION}/jars">
+ <fileset file="${lib}/*.jar"/>
+ </copy>
+ </target>
+
<target name="sign-webstart-jars">
<signjar keystore="plumpkey" alias="signFiles"
storepass="plumper" keypass="plumper">
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|
|
From: <nl...@us...> - 2007-01-30 23:07:29
|
Revision: 320
http://svn.sourceforge.net/obo/?rev=320&view=rev
Author: nlw
Date: 2007-01-30 15:07:27 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
trying to find the bug
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/index_text.shtml
phenote/trunk/doc/phenote-website/ssi/header.html
phenote/trunk/doc/phenote-website/ssi/navi_home.html~
Modified: phenote/trunk/doc/phenote-website/index_text.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-30 22:35:50 UTC (rev 319)
+++ phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-30 23:07:27 UTC (rev 320)
@@ -9,9 +9,9 @@
<p>
Phenote is a software tool currently being developed by the National Center for Biomedical Ontology to facilitate the annotation of biological phenotypes. Its development is being driven by several groups, including:
<ul>
- <li><a href="http://flybase.bio.indiana.edu/"><img class="portrait" border="0" src="/phenote/images/fly_logo.png"></a><h3>Flybase: The Drosophila Genome Database.</h3></li>
- <li><a href="http://zfin.org/"><img class="portrait" border="0" src="/phenote/images/zfin_logo.gif"></a>ZFIN: The Zebrafish Genome Database</li>
- <li><a href="http://www.nescent.org/"><img class="portrait" border="0" src="/phenote/images/nescent_logo.gif" alt="NESCENT"></a></a>NESCENT: The National Evolultionary Synthesis Center</li>
+ <li><a href="http://flybase.bio.indiana.edu/"><img class="portrait" border="0" src="/phenote/images/fly_logo.png" alt="Flybase" /></a><h3>Flybase: The Drosophila Genome Database.</h3></li>
+ <li><a href="http://zfin.org/"><img class="portrait" border="0" src="/phenote/images/zfin_logo.gif" alt="Zfin" /></a>ZFIN: The Zebrafish Genome Database</li>
+ <li><a href="http://www.nescent.org/"><img class="portrait" border="0" src="/phenote/images/nescent_logo.gif" alt="NESCENT" /></a>NESCENT: The National Evolultionary Synthesis Center</li>
</ul>
</p>
Modified: phenote/trunk/doc/phenote-website/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/header.html 2007-01-30 22:35:50 UTC (rev 319)
+++ phenote/trunk/doc/phenote-website/ssi/header.html 2007-01-30 23:07:27 UTC (rev 320)
@@ -9,9 +9,9 @@
<meta name="keywords" content="Phenotype, Annotation, Phenote, NCBO, National Center for Biomedical Ontology, Ontology, Berkeley Bioinformatics and Ontology Project, BBOP, Curation, EQ model, entities and qualities, phenotype annotation, PATO, phenotype and trait ontology, OBO, Open Biomedical Ontologies" />
<!-- TODO: need an icon -->
-<link rel="icon" href="" type="images/png" />
-<link rel="shortcut icon" href="" type="images/png" />
-<link rel="stylesheet" type="text/css" href="/phenote/css/bbop.css" title="standard" />
+<link rel="icon" href="" type="image/png" />
+<link rel="shortcut icon" href="" type="image/png" />
+<link rel="stylesheet" type="text/css" href="/phenote/css/style.css" title="standard" />
<script type="text/javascript" src="/phenote/javascript/obfuscate.js"></script>
@@ -30,7 +30,7 @@
</div>
<div class="page_logo">
-<img src="/phenote/images/NCBO.jpg" alt="logo" />
+<img src="/phenote/images/NCBO_logo.jpg" alt="logo" />
</div>
</div>
Modified: phenote/trunk/doc/phenote-website/ssi/navi_home.html~
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html~ 2007-01-30 22:35:50 UTC (rev 319)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html~ 2007-01-30 23:07:27 UTC (rev 320)
@@ -14,7 +14,7 @@
<a href="/phenote/content/software/">Downloads</a>
</li>
<li>
- <a href="/phenote/content/docs/">Documentation</a>
+ <a href="/phenote/content/documentation/">Documentation</a>
</li>
<li>
<a href="/phenote/content/refs/">References</a>
@@ -33,4 +33,4 @@
</li>
</ul>
</div>
-
+</div>
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|
|
From: <nl...@us...> - 2007-01-30 22:35:50
|
Revision: 319
http://svn.sourceforge.net/obo/?rev=319&view=rev
Author: nlw
Date: 2007-01-30 14:35:50 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
trying to get the page formating to work
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/ssi/header.html
Modified: phenote/trunk/doc/phenote-website/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/header.html 2007-01-30 22:18:56 UTC (rev 318)
+++ phenote/trunk/doc/phenote-website/ssi/header.html 2007-01-30 22:35:50 UTC (rev 319)
@@ -5,13 +5,13 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
-<meta name="description" content="Phenote Home Page">
+<meta name="description" content="Phenote Home Page" />
<meta name="keywords" content="Phenotype, Annotation, Phenote, NCBO, National Center for Biomedical Ontology, Ontology, Berkeley Bioinformatics and Ontology Project, BBOP, Curation, EQ model, entities and qualities, phenotype annotation, PATO, phenotype and trait ontology, OBO, Open Biomedical Ontologies" />
<!-- TODO: need an icon -->
<link rel="icon" href="" type="images/png" />
<link rel="shortcut icon" href="" type="images/png" />
-<link rel="stylesheet" type="/text/css" href="/phenote/css/bbop.css" title="standard" />
+<link rel="stylesheet" type="text/css" href="/phenote/css/bbop.css" title="standard" />
<script type="text/javascript" src="/phenote/javascript/obfuscate.js"></script>
@@ -29,12 +29,8 @@
<h1>Phenote: A Phenotype Annotation Tool using Ontologies</h1>
</div>
-<div class="jhead">
-<h1>BBOP</h1>
-</div>
-
<div class="page_logo">
-<img src="/phenote/images/NCBO.gif" alt="logo" />
+<img src="/phenote/images/NCBO.jpg" alt="logo" />
</div>
</div>
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|
|
From: <nl...@us...> - 2007-01-30 22:19:03
|
Revision: 318
http://svn.sourceforge.net/obo/?rev=318&view=rev
Author: nlw
Date: 2007-01-30 14:18:56 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
trying to fix the look and feel
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/index_text.shtml
phenote/trunk/doc/phenote-website/ssi/header.html
Modified: phenote/trunk/doc/phenote-website/index_text.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-30 22:08:43 UTC (rev 317)
+++ phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-30 22:18:56 UTC (rev 318)
@@ -2,38 +2,20 @@
<div id="page_body">
-<!-- A short and funny little quote. -->
-<!--
-<div id="quote">
-<div class="quote_body">
-Here is a quote.
-</div>
-<div class="quote_ref">
--Me
-</div>
-</div>
--->
-
<!--#include virtual="/phenote/ssi/navi_home.html" -->
<div id="main_content">
<h2>Phenotype Annotation Tools</h2>
<p>
-</p>
-
-<p>
Phenote is a software tool currently being developed by the National Center for Biomedical Ontology to facilitate the annotation of biological phenotypes. Its development is being driven by several groups, including:
<ul>
-<li><a href="http://flybase.bio.indiana.edu/"><img class="portrait" border="0" src="/phenote/images/fly_logo.png"></a><h3>Flybase: The Drosophila Genome Database.</h3></li>
-<li><a href="http://zfin.org/"><img class="portrait" border="0" src="/phenote/images/zfin_logo.gif"></a>ZFIN: The Zebrafish Genome Database</li>
-<li><a href="http://www.nescent.org/"><img class="portrait" border="0" src="/phenote/images/nescent_logo.gif" alt="NESCENT"></a></a>NESCENT: The National Evolultionary Synthesis Center</li>
+ <li><a href="http://flybase.bio.indiana.edu/"><img class="portrait" border="0" src="/phenote/images/fly_logo.png"></a><h3>Flybase: The Drosophila Genome Database.</h3></li>
+ <li><a href="http://zfin.org/"><img class="portrait" border="0" src="/phenote/images/zfin_logo.gif"></a>ZFIN: The Zebrafish Genome Database</li>
+ <li><a href="http://www.nescent.org/"><img class="portrait" border="0" src="/phenote/images/nescent_logo.gif" alt="NESCENT"></a></a>NESCENT: The National Evolultionary Synthesis Center</li>
+</ul>
-
</p>
-<p>
-
-</p>
</div>
</div>
Modified: phenote/trunk/doc/phenote-website/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/header.html 2007-01-30 22:08:43 UTC (rev 317)
+++ phenote/trunk/doc/phenote-website/ssi/header.html 2007-01-30 22:18:56 UTC (rev 318)
@@ -9,11 +9,11 @@
<meta name="keywords" content="Phenotype, Annotation, Phenote, NCBO, National Center for Biomedical Ontology, Ontology, Berkeley Bioinformatics and Ontology Project, BBOP, Curation, EQ model, entities and qualities, phenotype annotation, PATO, phenotype and trait ontology, OBO, Open Biomedical Ontologies" />
<!-- TODO: need an icon -->
-<link rel="icon" href="" type="/images/png" />
-<link rel="shortcut icon" href="" type="/images/png" />
-<link rel="stylesheet" type="/text/css" href="/phenote/css/style.css" title="standard" />
+<link rel="icon" href="" type="images/png" />
+<link rel="shortcut icon" href="" type="images/png" />
+<link rel="stylesheet" type="/text/css" href="/phenote/css/bbop.css" title="standard" />
-<script type="text/javascript" src="phenote/javascript/obfuscate.js"></script>
+<script type="text/javascript" src="/phenote/javascript/obfuscate.js"></script>
<title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
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|
|
From: <nl...@us...> - 2007-01-30 22:08:44
|
Revision: 317
http://svn.sourceforge.net/obo/?rev=317&view=rev
Author: nlw
Date: 2007-01-30 14:08:43 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
fixed a typo in header include
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/index_text.shtml
Modified: phenote/trunk/doc/phenote-website/index_text.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-30 22:05:46 UTC (rev 316)
+++ phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-30 22:08:43 UTC (rev 317)
@@ -1,4 +1,4 @@
-<!--#include virtual="/phentoe/ssi/header.html" -->
+<!--#include virtual="/phenote/ssi/header.html" -->
<div id="page_body">
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|
|
From: <nl...@us...> - 2007-01-30 22:05:46
|
Revision: 316
http://svn.sourceforge.net/obo/?rev=316&view=rev
Author: nlw
Date: 2007-01-30 14:05:46 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
more edits
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/content/documentation/index.shtml
phenote/trunk/doc/phenote-website/css/style.css
phenote/trunk/doc/phenote-website/ssi/navi_home.html
phenote/trunk/doc/phenote-website/ssi/navi_home.html~
Modified: phenote/trunk/doc/phenote-website/content/documentation/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/documentation/index.shtml 2007-01-30 21:56:49 UTC (rev 315)
+++ phenote/trunk/doc/phenote-website/content/documentation/index.shtml 2007-01-30 22:05:46 UTC (rev 316)
@@ -1,8 +1,8 @@
-<!--#include virtual="/ssi/header.html" -->
+<!--#include virtual="/phenote/ssi/header.html" -->
<div id="page_body">
-<!--#include virtual="/ssi/navi_home.html" -->
+<!--#include virtual="/phenote/ssi/navi_home.html" -->
<div id="main_content">
@@ -24,4 +24,4 @@
</div>
</div>
-<!--#include virtual="/ssi/footer.shtml" -->
+<!--#include virtual="/phenote/ssi/footer.shtml" -->
Modified: phenote/trunk/doc/phenote-website/css/style.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style.css 2007-01-30 21:56:49 UTC (rev 315)
+++ phenote/trunk/doc/phenote-website/css/style.css 2007-01-30 22:05:46 UTC (rev 316)
@@ -4,8 +4,8 @@
body {
font-family: arial, helvetica, sans-serif;
font-size: 100%;
- background: white url(/images/bg_image25.jpg) repeat top right;
- color: black;
+ /*background: white url(/phenote/images/) repeat top right;*/
+ color: grey;
margin: 0;
}
Modified: phenote/trunk/doc/phenote-website/ssi/navi_home.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-01-30 21:56:49 UTC (rev 315)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-01-30 22:05:46 UTC (rev 316)
@@ -14,7 +14,7 @@
<a href="/phenote/content/software/">Downloads</a>
</li>
<li>
- <a href="/phenote/content/docs/">Documentation</a>
+ <a href="/phenote/content/documentation/">Documentation</a>
</li>
<li>
<a href="/phenote/content/refs/">References</a>
Modified: phenote/trunk/doc/phenote-website/ssi/navi_home.html~
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html~ 2007-01-30 21:56:49 UTC (rev 315)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html~ 2007-01-30 22:05:46 UTC (rev 316)
@@ -8,25 +8,25 @@
<a href="/">Home</a>
</li>
<li>
- <a href="/content/background/">Background</a>
+ <a href="/phenote/content/background/">Background</a>
</li>
<li>
- <a href="/content/software/">Downloads</a>
+ <a href="/phenote/content/software/">Downloads</a>
</li>
<li>
- <a href="/content/docs/">Documentation</a>
+ <a href="/phenote/content/docs/">Documentation</a>
</li>
<li>
- <a href="/content/refs/">References</a>
+ <a href="/phenote/content/refs/">References</a>
</li>
<li>
- <a href="/content/faq/">FAQ</a>
+ <a href="/phenote/content/faq/">FAQ</a>
</li>
<li>
- <a href="/content/about/">About</a>
+ <a href="/phenote/content/about/">About</a>
</li>
<li>
- <a href="/content/links/">Links</a>
+ <a href="/phenote/content/links/">Links</a>
</li>
<li>
<a href="http://www.bioontology.org/wiki-internal/index.php/Phenote_-_A_Phenotype_Annotation_Tool">Internal Wiki</a>
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|
|
From: <nl...@us...> - 2007-01-30 21:59:58
|
Revision: 315
http://svn.sourceforge.net/obo/?rev=315&view=rev
Author: nlw
Date: 2007-01-30 13:56:49 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
changed paths, added text
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/index_text.shtml
phenote/trunk/doc/phenote-website/ssi/header.html
phenote/trunk/doc/phenote-website/ssi/navi_home.html
phenote/trunk/doc/phenote-website/ssi/navi_home.html~
Modified: phenote/trunk/doc/phenote-website/index_text.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-30 21:34:51 UTC (rev 314)
+++ phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-30 21:56:49 UTC (rev 315)
@@ -24,8 +24,8 @@
<p>
Phenote is a software tool currently being developed by the National Center for Biomedical Ontology to facilitate the annotation of biological phenotypes. Its development is being driven by several groups, including:
<ul>
-<li><a href="http://flybase.bio.indiana.edu/"><a img="/phenote/images/fly_logo.png"></a><h3>Flybase: The Drosophila Genome Database.</h3></li>
-<li><a href="http://zfin.org/"><a img="/phenote/images/zfin_logo.gif"></a>ZFIN: The Zebrafish Genome Database</li>
+<li><a href="http://flybase.bio.indiana.edu/"><img class="portrait" border="0" src="/phenote/images/fly_logo.png"></a><h3>Flybase: The Drosophila Genome Database.</h3></li>
+<li><a href="http://zfin.org/"><img class="portrait" border="0" src="/phenote/images/zfin_logo.gif"></a>ZFIN: The Zebrafish Genome Database</li>
<li><a href="http://www.nescent.org/"><img class="portrait" border="0" src="/phenote/images/nescent_logo.gif" alt="NESCENT"></a></a>NESCENT: The National Evolultionary Synthesis Center</li>
Modified: phenote/trunk/doc/phenote-website/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/header.html 2007-01-30 21:34:51 UTC (rev 314)
+++ phenote/trunk/doc/phenote-website/ssi/header.html 2007-01-30 21:56:49 UTC (rev 315)
@@ -9,17 +9,11 @@
<meta name="keywords" content="Phenotype, Annotation, Phenote, NCBO, National Center for Biomedical Ontology, Ontology, Berkeley Bioinformatics and Ontology Project, BBOP, Curation, EQ model, entities and qualities, phenotype annotation, PATO, phenotype and trait ontology, OBO, Open Biomedical Ontologies" />
<!-- TODO: need an icon -->
-<link rel="icon" href="" type="image/png" />
-<link rel="shortcut icon" href="" type="image/png" />
-<link rel="stylesheet" type="text/css" href="/css/style.css" title="standard" />
-<link rel="alternate stylesheet" type="text/css" href="/css/style-square.css" title="square" />
-<link rel="alternate stylesheet" type="text/css" href="/css/style-light.css" title="light" />
-<link rel="alternate stylesheet" type="text/css" href="/css/style-stark.css" title="stark" />
-<link rel="alternate stylesheet" type="text/css" href="/css/style-tile.css" title="tile" />
-<link rel="alternate stylesheet" type="text/css" href="/css/style-curve.css" title="curve" />
-<link rel="alternate stylesheet" type="text/css" href="/css/style-alpha.css" title="alpha" />
+<link rel="icon" href="" type="/images/png" />
+<link rel="shortcut icon" href="" type="/images/png" />
+<link rel="stylesheet" type="/text/css" href="/phenote/css/style.css" title="standard" />
-<script type="text/javascript" src="/javascript/obfuscate.js"></script>
+<script type="text/javascript" src="phenote/javascript/obfuscate.js"></script>
<title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
@@ -40,7 +34,7 @@
</div>
<div class="page_logo">
-<img src="/images/stolen-logo.gif" alt="logo" />
+<img src="/phenote/images/NCBO.gif" alt="logo" />
</div>
</div>
Modified: phenote/trunk/doc/phenote-website/ssi/navi_home.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-01-30 21:34:51 UTC (rev 314)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-01-30 21:56:49 UTC (rev 315)
@@ -8,25 +8,25 @@
<a href="/">Home</a>
</li>
<li>
- <a href="/content/background/">Background</a>
+ <a href="/phenote/content/background/">Background</a>
</li>
<li>
- <a href="/content/software/">Downloads</a>
+ <a href="/phenote/content/software/">Downloads</a>
</li>
<li>
- <a href="/content/docs/">Documentation</a>
+ <a href="/phenote/content/docs/">Documentation</a>
</li>
<li>
- <a href="/content/refs/">References</a>
+ <a href="/phenote/content/refs/">References</a>
</li>
<li>
- <a href="/content/faq/">FAQ</a>
+ <a href="/phenote/content/faq/">FAQ</a>
</li>
<li>
- <a href="/content/about/">About</a>
+ <a href="/phenote/content/about/">About</a>
</li>
<li>
- <a href="/content/links/">Links</a>
+ <a href="/phenote/content/links/">Links</a>
</li>
<li>
<a href="http://www.bioontology.org/wiki-internal/index.php/Phenote_-_A_Phenotype_Annotation_Tool">Internal Wiki</a>
Modified: phenote/trunk/doc/phenote-website/ssi/navi_home.html~
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html~ 2007-01-30 21:34:51 UTC (rev 314)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html~ 2007-01-30 21:56:49 UTC (rev 315)
@@ -8,28 +8,28 @@
<a href="/">Home</a>
</li>
<li>
- <a href="/content/projects/">Projects</a>
+ <a href="/content/background/">Background</a>
</li>
<li>
- <a href="/content/software/">Software</a>
+ <a href="/content/software/">Downloads</a>
</li>
<li>
- <a href="/content/publications/">Publications</a>
+ <a href="/content/docs/">Documentation</a>
</li>
<li>
- <a href="/content/jobs/">Jobs</a>
+ <a href="/content/refs/">References</a>
</li>
<li>
- <a href="/content/about/">About</a>
+ <a href="/content/faq/">FAQ</a>
</li>
<li>
- <a href="/mediawiki">Wiki</a>
+ <a href="/content/about/">About</a>
</li>
<li>
<a href="/content/links/">Links</a>
</li>
<li>
- <a href="/content/faq/">FAQ</a>
+ <a href="http://www.bioontology.org/wiki-internal/index.php/Phenote_-_A_Phenotype_Annotation_Tool">Internal Wiki</a>
</li>
</ul>
</div>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-01-30 21:37:34
|
Revision: 314
http://svn.sourceforge.net/obo/?rev=314&view=rev
Author: nlw
Date: 2007-01-30 13:34:51 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
edits to the index, adding logos
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/index_text.shtml
phenote/trunk/doc/phenote-website/ssi/header.html
phenote/trunk/doc/phenote-website/ssi/navi_home.html
Added Paths:
-----------
phenote/trunk/doc/phenote-website/content/documentation/
phenote/trunk/doc/phenote-website/content/documentation/index.shtml
phenote/trunk/doc/phenote-website/images/fly_logo.png
phenote/trunk/doc/phenote-website/images/nescent_logo.gif
phenote/trunk/doc/phenote-website/images/pgkb_logo.png
phenote/trunk/doc/phenote-website/images/zfin_logo.gif
Removed Paths:
-------------
phenote/trunk/doc/phenote-website/ssi/navi_about.html
phenote/trunk/doc/phenote-website/ssi/navi_publications.html
Added: phenote/trunk/doc/phenote-website/content/documentation/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/documentation/index.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/content/documentation/index.shtml 2007-01-30 21:34:51 UTC (rev 314)
@@ -0,0 +1,27 @@
+<!--#include virtual="/ssi/header.html" -->
+
+<div id="page_body">
+
+<!--#include virtual="/ssi/navi_home.html" -->
+
+<div id="main_content">
+
+<h2>Documentation</h2>
+
+<h3><a name="general">Making Annotations with Phenote</a></h3>
+<h3><a name="webstart">Running Phenote Webstart Version(s)</a></h3>
+<h3><a name="install">Downloading and Installing Phenote</a></h3>
+<p>
+</p>
+<h3><a name="config">Custom Configuration</a></h3>
+<p>
+Phenote can be customized for data entry fields, and the ontologies that are desired to be included.
+</p>
+
+
+<br />
+</p>
+</div>
+</div>
+
+<!--#include virtual="/ssi/footer.shtml" -->
Added: phenote/trunk/doc/phenote-website/images/fly_logo.png
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/fly_logo.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/doc/phenote-website/images/nescent_logo.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/nescent_logo.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/doc/phenote-website/images/pgkb_logo.png
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/pgkb_logo.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/doc/phenote-website/images/zfin_logo.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/zfin_logo.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Modified: phenote/trunk/doc/phenote-website/index_text.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-30 19:34:39 UTC (rev 313)
+++ phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-30 21:34:51 UTC (rev 314)
@@ -1,4 +1,4 @@
-<!--#include virtual="/ssi/header.html" -->
+<!--#include virtual="/phentoe/ssi/header.html" -->
<div id="page_body">
@@ -14,30 +14,28 @@
</div>
-->
-<!--#include virtual="/ssi/navi_home.html" -->
+<!--#include virtual="/phenote/ssi/navi_home.html" -->
<div id="main_content">
-<h2>Welcome...</h2>
+<h2>Phenotype Annotation Tools</h2>
<p>
</p>
<p>
-...to the Berkeley Bioinformatics and Ontologies Project.
-</p>
+Phenote is a software tool currently being developed by the National Center for Biomedical Ontology to facilitate the annotation of biological phenotypes. Its development is being driven by several groups, including:
+<ul>
+<li><a href="http://flybase.bio.indiana.edu/"><a img="/phenote/images/fly_logo.png"></a><h3>Flybase: The Drosophila Genome Database.</h3></li>
+<li><a href="http://zfin.org/"><a img="/phenote/images/zfin_logo.gif"></a>ZFIN: The Zebrafish Genome Database</li>
+<li><a href="http://www.nescent.org/"><img class="portrait" border="0" src="/phenote/images/nescent_logo.gif" alt="NESCENT"></a></a>NESCENT: The National Evolultionary Synthesis Center</li>
-<p>
-<a href="/content/jobs/">We're hiring!</a>
+
</p>
<p>
-The BBOP, located at the Lawrence Berkeley National Labs, is a diverse group of scientific researchers and software engineers dedicated to developing tools and applying computational technologies to solve biological problems. Members of the group contribute to a number of projects, including <a href="http://geneontology.org/">The Gene Ontology</a>, <a href="http://bioontology.org">The National Center for Biomedical Ontology</a>, and the <a href="http://gmod.org">Generic Model Organism Database Project</a>. Learn more about our projects <a href="/content/projects/">[here ...]</a>
-</p>
-<p>
-Since our group is focused on the development, use, and integration of ontolgies into biological data analysis, we've set up a <a href="content/faq/">FAQ</a> with answers to some common questions about ontologies.
</p>
</div>
</div>
-<!--#include virtual="/ssi/footer.shtml" -->
+<!--#include virtual="/phenote/ssi/footer.shtml" -->
Modified: phenote/trunk/doc/phenote-website/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/header.html 2007-01-30 19:34:39 UTC (rev 313)
+++ phenote/trunk/doc/phenote-website/ssi/header.html 2007-01-30 21:34:51 UTC (rev 314)
@@ -5,6 +5,8 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+<meta name="description" content="Phenote Home Page">
+<meta name="keywords" content="Phenotype, Annotation, Phenote, NCBO, National Center for Biomedical Ontology, Ontology, Berkeley Bioinformatics and Ontology Project, BBOP, Curation, EQ model, entities and qualities, phenotype annotation, PATO, phenotype and trait ontology, OBO, Open Biomedical Ontologies" />
<!-- TODO: need an icon -->
<link rel="icon" href="" type="image/png" />
@@ -19,7 +21,7 @@
<script type="text/javascript" src="/javascript/obfuscate.js"></script>
-<title>Phenote: A Phenotype Annotation Tool</title>
+<title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
<!-- My comments! -->
@@ -30,7 +32,7 @@
<div id="page_head">
<div class="ehead">
-<h1>Phenote</h1>
+<h1>Phenote: A Phenotype Annotation Tool using Ontologies</h1>
</div>
<div class="jhead">
Deleted: phenote/trunk/doc/phenote-website/ssi/navi_about.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_about.html 2007-01-30 19:34:39 UTC (rev 313)
+++ phenote/trunk/doc/phenote-website/ssi/navi_about.html 2007-01-30 21:34:51 UTC (rev 314)
@@ -1,47 +0,0 @@
-<div id="navi">
-<div class="navi_head"></div>
-<ul>
- <li>
- <a href="/">Home</a>
- </li>
- <li>
- <a href="/content/projects/">Projects</a>
- </li>
- <li>
- <a href="/content/software/">Software</a>
- </li>
- <li>
- <a href="/content/publications/">Publications</a>
- </li>
- <li>
- <a href="/content/jobs/">Jobs</a>
- </li>
- <li>
- <a href="/content/about/">About</a>
- <ul>
- <li>
- <a href="/content/people/">BBOP people</a>
- </li>
- <li>
- <a href="/content/about/contact.shtml">Contact us</a>
- </li>
- <li>
- <a href="/content/about/directions.shtml">Directions</a>
- </li>
- <li>
- <a href="/content/about/area.shtml">Area Info</a>
- </li>
- </ul>
- </li>
- <li>
- <a href="/mediawiki">Wiki</a>
- </li>
- <li>
- <a href="/content/links/">Links</a>
- </li>
- <li>
- <a href="/content/faq/">FAQ</a>
- </li>
-</ul>
-</div>
-
Modified: phenote/trunk/doc/phenote-website/ssi/navi_home.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-01-30 19:34:39 UTC (rev 313)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-01-30 21:34:51 UTC (rev 314)
@@ -8,16 +8,16 @@
<a href="/">Home</a>
</li>
<li>
- <a href="/content/projects/">Background</a>
+ <a href="/content/background/">Background</a>
</li>
<li>
<a href="/content/software/">Downloads</a>
</li>
<li>
- <a href="/content/software/">Documentation</a>
+ <a href="/content/docs/">Documentation</a>
</li>
<li>
- <a href="/content/publications/">References</a>
+ <a href="/content/refs/">References</a>
</li>
<li>
<a href="/content/faq/">FAQ</a>
@@ -29,7 +29,7 @@
<a href="/content/links/">Links</a>
</li>
<li>
- <a href="/mediawiki">Wiki</a>
+ <a href="http://www.bioontology.org/wiki-internal/index.php/Phenote_-_A_Phenotype_Annotation_Tool">Internal Wiki</a>
</li>
</ul>
</div>
Deleted: phenote/trunk/doc/phenote-website/ssi/navi_publications.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_publications.html 2007-01-30 19:34:39 UTC (rev 313)
+++ phenote/trunk/doc/phenote-website/ssi/navi_publications.html 2007-01-30 21:34:51 UTC (rev 314)
@@ -1,30 +0,0 @@
-<div id="navi">
-<div class="navi_head"></div>
-<ul>
- <li>
- <a href="/">Home</a>
- </li>
- <li>
- <a href="/content/projects/">Projects</a>
- </li>
- <li>
- <a href="/content/people/">People</a>
- </li>
- <li>
- <a href="/content/publications/">Publications</a>
- </li>
- <li>
- <a href="/content/jobs/">Jobs</a>
- </li>
- <li>
- <a href="/content/about/">Contact</a>
- </li>
- <li>
- <a href="/mediawiki">Wiki</a>
- </li>
- <li>
- <a href="/content/faq/">FAQ</a>
- </li>
-</ul>
-</div>
-
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-01-30 19:35:38
|
Revision: 313
http://svn.sourceforge.net/obo/?rev=313&view=rev
Author: mgibson
Date: 2007-01-30 11:34:39 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
changed webstart-html target in ant to webstart-webpages and it now copies
over all the stuff nicole just put in not just html - css, js,... (sans jnlp)
Modified Paths:
--------------
phenote/trunk/build.xml
phenote/trunk/src/java/phenote/util/FileUtil.java
Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml 2007-01-30 18:35:57 UTC (rev 312)
+++ phenote/trunk/build.xml 2007-01-30 19:34:39 UTC (rev 313)
@@ -188,8 +188,6 @@
</javac>
</target>
- <!-- JAR The jar target compiles everything, and produces a phenote.jar in
- phenote/jars/phenote.jar. -->
<target name="jar-pase" depends="compile">
<jar destfile="${jarfile}">
<fileset dir="${classfiles}"/>
@@ -198,6 +196,8 @@
</jar>
</target>
+ <!-- JAR The jar target compiles everything, and produces a phenote.jar in
+ phenote/jars/phenote.jar. -->
<target name="jar" depends="compile">
<jar destfile="${jarfile}">
<fileset dir="${classfiles}"/>
@@ -404,7 +404,7 @@
<!-- need to test if PHENOTE_VERSION is defined - possible?? -->
- <target name="webstart" depends="webstart-html,copy-jnlps">
+ <target name="webstart" depends="webstart-webpages,copy-jnlps">
<echo message="Env Var PHENOTE VERSION is set to ${env.PHENOTE_VERSION}" />
<mkdir dir="phenote-webstart/${env.PHENOTE_VERSION}"/>
<copy todir="phenote-webstart/${env.PHENOTE_VERSION}/jars">
@@ -412,10 +412,10 @@
</copy>
</target>
- <target name="webstart-html">
- <echo message="Env Var PHENOTE VERSION is set to ${env.PHENOTE_VERSION}" />
+ <target name="webstart-webpages">
<copy todir="phenote-webstart">
- <fileset file="doc/phenote-website/*.html"/>
+ <!-- fileset file="doc/phenote-website/*.html"/ -->
+ <fileset dir="doc/phenote-website" excludes="*.jnlp"/>
</copy>
</target>
Modified: phenote/trunk/src/java/phenote/util/FileUtil.java
===================================================================
--- phenote/trunk/src/java/phenote/util/FileUtil.java 2007-01-30 18:35:57 UTC (rev 312)
+++ phenote/trunk/src/java/phenote/util/FileUtil.java 2007-01-30 19:34:39 UTC (rev 313)
@@ -71,6 +71,8 @@
// suffix - or who cares?
private static List<URL> getPossibleUrls(String filename) {
List<URL> urls = new ArrayList(5);
+ // hmmm - should full path go last? can be problem with running from
+ // jar as config files are in root(fix), obo files finally given dir
addFile(filename,urls); // full path or relative to pwd
addFile("conf/"+filename,urls);
// ~/.phenote/obo-files cache for obo files - overrides phenote obo-files
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