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From: <mg...@us...> - 2006-11-22 19:32:11
|
Revision: 213
http://svn.sourceforge.net/obo/?rev=213&view=rev
Author: mgibson
Date: 2006-11-22 11:32:10 -0800 (Wed, 22 Nov 2006)
Log Message:
-----------
webstart
-This line, and those below, will be ignored--
A phenote-website/phenote-flybase.jnlp
A phenote-website/phenote-zfin.jnlp
Added Paths:
-----------
phenote/trunk/doc/phenote-website/phenote-flybase.jnlp
phenote/trunk/doc/phenote-website/phenote-zfin.jnlp
Added: phenote/trunk/doc/phenote-website/phenote-flybase.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-flybase.jnlp (rev 0)
+++ phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2006-11-22 19:32:10 UTC (rev 213)
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<jnlp
+spec="1.0+"
+codebase="http://toy.lbl.gov:9010/phenote/0.9/"
+href="phenote-flybase.jnlp">
+<information>
+ <title>Phenote 0.9</title>
+ <vendor>BBOP</vendor>
+ <description>Phenote 0.9</description>
+ <!-- Declares that the application can run without
+ access to the server it was downloaded from -->
+ <offline-allowed />
+</information>
+<security>
+ <!-- Request that the application be given full
+ access to the local (executing) machine,
+ as if it were a regular Java application.
+ Requires that all JAR files be signed
+ by a trusted party -->
+ <all-permissions />
+</security>
+<resources>
+ <!-- Specify the versions of the Java Runtime Environment
+ (JRE) that are supported by the application.
+ Multiple entries of this kind are allowed, in which
+ case they are considered to be in order of preference -->
+ <j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
+ <jar href="jars/phenote-signed.jar" />
+ <jar href="jars/oboedit-signed.jar" />
+ <jar href="jars/org.geneontology-signed.jar" />
+ <jar href="jars/BrowserLauncher2-10rc4-signed.jar" />
+ <jar href="jars/jsr173_1.0_api-signed.jar" />
+ <jar href="jars/phenoxmlbeans-signed.jar" />
+ <jar href="jars/phenoteconfigbeans-signed.jar" />
+ <jar href="jars/xbean-signed.jar" />
+ <jar href="jars/tomcat-servlet-signed.jar" />
+ <jar href="jars/te-common-signed.jar" />
+ <jar href="jars/log4j-1.2.13-signed.jar" />
+</resources>
+<application-desc main-class="phenote.main.Phenote">
+ <argument>-c</argument>
+ <argument>/initial-flybase.cfg</argument>
+</application-desc>
+</jnlp>
+
+
+
Added: phenote/trunk/doc/phenote-website/phenote-zfin.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-zfin.jnlp (rev 0)
+++ phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2006-11-22 19:32:10 UTC (rev 213)
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<jnlp
+spec="1.0+"
+codebase="http://toy.lbl.gov:9010/phenote/0.9/"
+href="phenote-zfin.jnlp">
+<information>
+ <title>Phenote 0.9</title>
+ <vendor>BBOP</vendor>
+ <description>Phenote 0.9</description>
+ <!-- Declares that the application can run without
+ access to the server it was downloaded from -->
+ <offline-allowed />
+</information>
+<security>
+ <!-- Request that the application be given full
+ access to the local (executing) machine,
+ as if it were a regular Java application.
+ Requires that all JAR files be signed
+ by a trusted party -->
+ <all-permissions />
+</security>
+<resources>
+ <!-- Specify the versions of the Java Runtime Environment
+ (JRE) that are supported by the application.
+ Multiple entries of this kind are allowed, in which
+ case they are considered to be in order of preference -->
+ <j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
+ <jar href="jars/phenote-signed.jar" />
+ <jar href="jars/oboedit-signed.jar" />
+ <jar href="jars/org.geneontology-signed.jar" />
+ <jar href="jars/BrowserLauncher2-10rc4-signed.jar" />
+ <jar href="jars/jsr173_1.0_api-signed.jar" />
+ <jar href="jars/phenoxmlbeans-signed.jar" />
+ <jar href="jars/phenoteconfigbeans-signed.jar" />
+ <jar href="jars/tomcat-servlet-signed.jar" />
+ <jar href="jars/xbean-signed.jar" />
+ <jar href="jars/te-common-signed.jar" />
+ <jar href="jars/log4j-1.2.13-signed.jar" />
+</resources>
+<application-desc main-class="phenote.main.Phenote">
+ <argument>-c</argument>
+ <argument>/initial-zfin.cfg</argument>
+</application-desc>
+</jnlp>
+
+
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2006-11-22 19:58:53
|
Revision: 218
http://svn.sourceforge.net/obo/?rev=218&view=rev
Author: mgibson
Date: 2006-11-22 11:58:50 -0800 (Wed, 22 Nov 2006)
Log Message:
-----------
1.0
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-flybase.jnlp
phenote/trunk/doc/phenote-website/phenote-human.jnlp
phenote/trunk/doc/phenote-website/phenote-zfin.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-flybase.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2006-11-22 19:43:42 UTC (rev 217)
+++ phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2006-11-22 19:58:50 UTC (rev 218)
@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<jnlp
spec="1.0+"
-codebase="http://toy.lbl.gov:9010/phenote/0.9/"
+codebase="http://toy.lbl.gov:9010/phenote/1.0/"
href="phenote-flybase.jnlp">
<information>
- <title>Phenote 0.9</title>
+ <title>Phenote 1.0</title>
<vendor>BBOP</vendor>
- <description>Phenote 0.9</description>
+ <description>Phenote standalone app via webstart</description>
<!-- Declares that the application can run without
access to the server it was downloaded from -->
<offline-allowed />
@@ -25,17 +25,17 @@
Multiple entries of this kind are allowed, in which
case they are considered to be in order of preference -->
<j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
- <jar href="jars/phenote-signed.jar" />
- <jar href="jars/oboedit-signed.jar" />
- <jar href="jars/org.geneontology-signed.jar" />
- <jar href="jars/BrowserLauncher2-10rc4-signed.jar" />
- <jar href="jars/jsr173_1.0_api-signed.jar" />
- <jar href="jars/phenoxmlbeans-signed.jar" />
- <jar href="jars/phenoteconfigbeans-signed.jar" />
- <jar href="jars/xbean-signed.jar" />
- <jar href="jars/tomcat-servlet-signed.jar" />
- <jar href="jars/te-common-signed.jar" />
- <jar href="jars/log4j-1.2.13-signed.jar" />
+ <jar href="jars/phenote.jar" />
+ <jar href="jars/oboedit.jar" />
+ <jar href="jars/org.geneontology.jar" />
+ <jar href="jars/BrowserLauncher2-10rc4.jar" />
+ <jar href="jars/jsr173_1.0_api.jar" />
+ <jar href="jars/phenoxmlbeans.jar" />
+ <jar href="jars/phenoteconfigbeans.jar" />
+ <jar href="jars/xbean.jar" />
+ <jar href="jars/tomcat-servlet.jar" />
+ <jar href="jars/te-common.jar" />
+ <jar href="jars/log4j-1.2.13.jar" />
</resources>
<application-desc main-class="phenote.main.Phenote">
<argument>-c</argument>
Modified: phenote/trunk/doc/phenote-website/phenote-human.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-human.jnlp 2006-11-22 19:43:42 UTC (rev 217)
+++ phenote/trunk/doc/phenote-website/phenote-human.jnlp 2006-11-22 19:58:50 UTC (rev 218)
@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<jnlp
spec="1.0+"
-codebase="http://toy.lbl.gov:9010/phenote/0.9/"
+codebase="http://toy.lbl.gov:9010/phenote/1.0/"
href="phenote-human.jnlp">
<information>
- <title>Phenote 0.9</title>
+ <title>Phenote 1.0</title>
<vendor>BBOP</vendor>
- <description>Phenote 0.9</description>
+ <description>Phenote standalone app via webstart</description>
<!-- Declares that the application can run without
access to the server it was downloaded from -->
<offline-allowed />
@@ -26,16 +26,16 @@
case they are considered to be in order of preference -->
<j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
<jar href="jars/phenote.jar" />
- <jar href="jars/oboedit-signed.jar" />
- <jar href="jars/org.geneontology-signed.jar" />
- <jar href="jars/BrowserLauncher2-10rc4-signed.jar" />
- <jar href="jars/jsr173_1.0_api-signed.jar" />
- <jar href="jars/phenoxmlbeans-signed.jar" />
- <jar href="jars/phenoteconfigbeans-signed.jar" />
- <jar href="jars/tomcat-servlet-signed.jar" />
- <jar href="jars/xbean-signed.jar" />
- <jar href="jars/te-common-signed.jar" />
- <jar href="jars/log4j-1.2.13-signed.jar" />
+ <jar href="jars/oboedit.jar" />
+ <jar href="jars/org.geneontology.jar" />
+ <jar href="jars/BrowserLauncher2-10rc4.jar" />
+ <jar href="jars/jsr173_1.0_api.jar" />
+ <jar href="jars/phenoxmlbeans.jar" />
+ <jar href="jars/phenoteconfigbeans.jar" />
+ <jar href="jars/tomcat-servlet.jar" />
+ <jar href="jars/xbean.jar" />
+ <jar href="jars/te-common.jar" />
+ <jar href="jars/log4j-1.2.13.jar" />
<</resources>
<application-desc main-class="phenote.gui.Phenote">
<argument>-c</argument>
Modified: phenote/trunk/doc/phenote-website/phenote-zfin.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2006-11-22 19:43:42 UTC (rev 217)
+++ phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2006-11-22 19:58:50 UTC (rev 218)
@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<jnlp
spec="1.0+"
-codebase="http://toy.lbl.gov:9010/phenote/0.9/"
+codebase="http://toy.lbl.gov:9010/phenote/1.0/"
href="phenote-zfin.jnlp">
<information>
- <title>Phenote 0.9</title>
+ <title>Phenote 1.0</title>
<vendor>BBOP</vendor>
- <description>Phenote 0.9</description>
+ <description>Phenote standalone app via webstart</description>
<!-- Declares that the application can run without
access to the server it was downloaded from -->
<offline-allowed />
@@ -25,17 +25,17 @@
Multiple entries of this kind are allowed, in which
case they are considered to be in order of preference -->
<j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
- <jar href="jars/phenote-signed.jar" />
- <jar href="jars/oboedit-signed.jar" />
- <jar href="jars/org.geneontology-signed.jar" />
- <jar href="jars/BrowserLauncher2-10rc4-signed.jar" />
- <jar href="jars/jsr173_1.0_api-signed.jar" />
- <jar href="jars/phenoxmlbeans-signed.jar" />
- <jar href="jars/phenoteconfigbeans-signed.jar" />
- <jar href="jars/tomcat-servlet-signed.jar" />
- <jar href="jars/xbean-signed.jar" />
- <jar href="jars/te-common-signed.jar" />
- <jar href="jars/log4j-1.2.13-signed.jar" />
+ <jar href="jars/phenote.jar" />
+ <jar href="jars/oboedit.jar" />
+ <jar href="jars/org.geneontology.jar" />
+ <jar href="jars/BrowserLauncher2-10rc4.jar" />
+ <jar href="jars/jsr173_1.0_api.jar" />
+ <jar href="jars/phenoxmlbeans.jar" />
+ <jar href="jars/phenoteconfigbeans.jar" />
+ <jar href="jars/tomcat-servlet.jar" />
+ <jar href="jars/xbean.jar" />
+ <jar href="jars/te-common.jar" />
+ <jar href="jars/log4j-1.2.13.jar" />
</resources>
<application-desc main-class="phenote.main.Phenote">
<argument>-c</argument>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-01-11 22:11:19
|
Revision: 283
http://svn.sourceforge.net/obo/?rev=283&view=rev
Author: mgibson
Date: 2007-01-11 14:11:20 -0800 (Thu, 11 Jan 2007)
Log Message:
-----------
config file name change in jnlp
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-flybase.jnlp
phenote/trunk/doc/phenote-website/phenote-zfin.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-flybase.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2007-01-11 21:11:32 UTC (rev 282)
+++ phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2007-01-11 22:11:20 UTC (rev 283)
@@ -39,7 +39,7 @@
</resources>
<application-desc main-class="phenote.main.Phenote">
<argument>-c</argument>
- <argument>/initial-flybase.cfg</argument>
+ <argument>/flybase.cfg</argument>
</application-desc>
</jnlp>
Modified: phenote/trunk/doc/phenote-website/phenote-zfin.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2007-01-11 21:11:32 UTC (rev 282)
+++ phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2007-01-11 22:11:20 UTC (rev 283)
@@ -39,7 +39,7 @@
</resources>
<application-desc main-class="phenote.main.Phenote">
<argument>-c</argument>
- <argument>/initial-zfin.cfg</argument>
+ <argument>/zfin-standalone.cfg</argument>
</application-desc>
</jnlp>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-01-12 17:42:18
|
Revision: 284
http://svn.sourceforge.net/obo/?rev=284&view=rev
Author: mgibson
Date: 2007-01-12 09:42:15 -0800 (Fri, 12 Jan 2007)
Log Message:
-----------
updated phenote page and release notes for 1.0 release
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-release-notes.html
phenote/trunk/doc/phenote-website/phenote.html
Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-01-11 22:11:20 UTC (rev 283)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-01-12 17:42:15 UTC (rev 284)
@@ -1,86 +1,160 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
- <meta content="text/html; charset=ISO-8859-1"
- http-equiv="content-type">
+
+
+ <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
+
+
<title>Phenote Release Notes</title>
</head>
+
+
<body>
+
<h1>Phenote Release Notes</h1>
-1.0
-will probably come out in December.<br>
+
+1.1
+will probably come out in February<br>
+<br>
+<h2><span style="text-decoration: underline;">1.0</span></h2>
+<a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br>
+
+<a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br>
+<a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DichtyBase
+webby phenote</a><br>
+<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby
+Phenote(components used by Zfin)</a><br>
+<br>
+January 12, 2007<br>
+<br>
+The main improvement here is the ability to add any field you like, not
+just E,Q,GC,GT,Pub. In the configured webstarts Stage, Evidence,
+Description, Abnormal, and Absent have been added through this new
+mechanism. This entailed a refactoring of the datamodel.<br>
+<br>
+Webby phenote is now using JSP and Spring.<br>
+<br>
+There has been some recent work with UVictoria for ontology graph
+visualization. This is coming along well and hopefully will be seen in
+the next release.
<h2><span style="text-decoration: underline;">0.9</span></h2>
+
<a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br>
+
<a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br>
+
<a href="http://165.124.152.194/web/html/interface.html">DichtyBase
webby phenote</a><br>
+
<br>
+
mid November 2006<br>
+
<br>
+
Undo<br>
+
Christian Pich(Zfin) has added a Quartz scheduler to phenote, which
zfin takes advantage of, to schedule when to check for new obo files.<br>
+
Also Christian Pich upgraded the PhenoteServlet to the Spring framework
- much nicer!<br>
+
Synonyms are now returned from auto complete with [syn] and when
selected the term goes in the field (webby & standalone), obsoletes
hits with [obs]<br>
+
Bulk update & copy in standalone.<br>
+
Jim Balhoff(Nescent) changed radio buttons to checkboxes, and file
saver says save not load and recognizes adapter by file extensions,
psx->phenosyntax, .xml -> phenoxml <br>
+
Single quotes escaped for javascript fns.<br>
+
<h2><span style="text-decoration: underline;">0.8</span></h2>
+
<a href="0.8/phenote-flybase.jnlp">Phenote 0.8 for fly.</a><br>
+
<a href="0.8/phenote-zfin.jnlp">Phenote (standalone) 0.8 for zfin</a><br>
+
<a href="http://165.124.152.194/web/html/interface.html">DichtyBase
webby phenote</a><br>
+
<br>
+
10/2/06<br>
+
Added post composition to standalone phenote. Logging for both
webby/servlet & standalone.<br>
+
Pheno-xml reader (thanks to Jim Balhoff) and improvements to pheno-xml
writer (does pub & genetic context)<br>
+
Command line reading & writing of phenoxml & phenosyntax.<br>
+
Application exits on window exit (unless servlet)<br>
+
Can filter out stage terms from zfin anatomy<br>
+
<h2><span style="text-decoration: underline;">0.7</span></h2>
+
<a href="0.7/phenote-flybase.jnlp">Phenote 0.7 for fly.</a><br>
+
<a href="0.7/phenote-zfin.jnlp">Phenote (standalone) 0.7 for zfin</a><br>
+
<a href="http://165.124.152.194/web/html/interface.html">DichtyBase
webby phenote</a><br>
+
<br>
+
Web: entity chooser, can configure to check for new obo files and load
them. (These are installed at zfin, if anyone would like to see them
publicly let me know). Entity field and term info installed into zfin
phenotype site. term info & completion are scrollable.<br>
+
Standalone: can read & write pheno-syntax with ids & term names
in comments, entity chooser, pub field, use button in term info, sort
table by clicking on headers, personal config file gets copied out of
jar, paste mac bug fixed, file load/save remembered,layout fixed<br>
+
<br>
-<h2><span style="font-weight: bold;"><span
- style="text-decoration: underline;">0.6</span></span></h2>
+
+<h2><span style="font-weight: bold;"><span style="text-decoration: underline;">0.6</span></span></h2>
+
<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote
(0.6)</a><br>
+
<a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br>
+
<a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br>
+
<br>
+
The main feature of release 0.6 is a webby phenote. This is in its
extremely early stages (very little functionality and buggy). At this
point it only does Entity and Quality fields and term info and thats
it, and even thats buggy, but more coming soon! <br>
+
<br>
+
Not much new in the stand alone phenote (as Ive been working on the
webby phenote). Mainly it can write pheno-xml, and it uses the latest
pato (as of July 28, 2006).<br>
-<h2><span style="font-weight: bold;"><span
- style="text-decoration: underline;">0.5</span></span></h2>
+
+<h2><span style="font-weight: bold;"><span style="text-decoration: underline;">0.5</span></span></h2>
+
<br>
+
<a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br>
+
<a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br>
+
<br>
+
5/12/06<br>
+
No new additions to the gui here. In preparation for my visit to
Cambridge/FlyBase, I worked on a FlyBase dataadapter. This is phenote
first data adapter so I also laid down the foundations for data
@@ -92,14 +166,23 @@
tested yet with Proforma, but it works in the test suite. Added special
FlyBase character wrappers that do the parsing and creating of Proforma
character strings.<br>
+
<h2><span style="text-decoration: underline;">0.4</span></h2>
+
<a href="0.4/phenote-flybase.jnlp">0.4 flybase webstart</a><br>
+
<a href="0.4/phenote-zfin.jnlp">0.4 zfin webstart</a><br>
+
<br>
+
4/26/06<br>
+
Added Genetic Context field.<br>
+
Parent & child terms in term info are now clickable/navigable.<br>
+
Links in descriptions are clickable (should bring up default browser)<br>
+
Added configuration to configure ontologies & fields. This is
currently at a devloper level (xml file) not a user level(gui - todo).
There is a command line argument for which configuration file to use.
@@ -107,95 +190,162 @@
change the code to do it (like was done for the ctol release). The
configuration for now is for developers (internal xml file), on the
todo is to have a gui configuration for users.<br>
+
Minor bugs: cant delete to 0 rows anymore, synonym search
duplicates taken out<br>
+
<br>
+
Dev stuff:<br>
+
Refactored for configuration & adding field. Made the internal code
much more generic for adding new fields from configuration, got rid of
a lot of hard wiring. Part of this was instituring
model-view-controller in some places where views were improperly
talking to other views. In theory this should also make it easier to
plop a web gui on top of the current phenote model & controller.<br>
+
Renamed Phenotype to Character. Added Character interface CharacterI.<br>
+
Added tests to test suite.<br>
+
<br>
+
<h2><span style="text-decoration: underline;">0.3.1 (CToL)<br>
+
</span></h2>
+
<a href="0.3.1/phenote-webstart.jnlp">0.3.1 phenote webstart (for CToL)</a><br>
+
<br>
+
4/7/06<br>
+
0.3.1 is identical to 0.3 except that it has ontologies for CToL
(fish evolution group). In particular it uses a fish taxonomy<br>
+
ontology for the id (in this taxonomy) choosing. On the todo is the
ability to configure ontologies, but not there yet, so for now need to
hardwire with seaparate jar file. This clearly makes the todo item a
bit more pressing.<br>
+
<h2><span style="text-decoration: underline;">0.3</span></h2>
+
<a href="0.3/phenote-webstart.jnlp">0.3 phenote webstart</a><br>
+
<br>
+
4/7/06<br>
+
Release for NESCent fish eveolution meeting. No major new functionality
here. Cleaned up and fixed a lot of the bugs in 0.2, which was rather
buggy.<br>
+
<br>
+
Completion terms now sorted alphabeitcally.<br>
+
Obsolete is now in addition to regular terms, not in lieu of.<br>
+
Filtering out attribute values (todo: change to actually filter in
values)<br>
+
Html formatting of term info (todo: make terms selectable)<br>
+
Children relations are in term info<br>
+
Term info layout greatly improved<br>
+
Term info in scroller<br>
+
Border with label around term info<br>
+
Put definition at end of term info<br>
+
<br>
+
Fixed bugs:<br>
+
Backspace in ontology combo box<br>
+
Selection of item in comp list causing exception, not going in term box<br>
+
No terms with just 1 char<br>
+
Popup was staying up after selection<br>
+
<br>
+
Dev stuff:<br>
+
Test suite added! (todo: add more tests)<br>
+
Migrated to jdk 1.5 (which caused some of the bugs above)<br>
+
Ant file made build.xml.<br>
+
CompletionList refactored into Ontology (prompted by sorting)<br>
+
<br>
+
<br>
+
<h2><span style="text-decoration: underline;">0.2</span></h2>
+
<a href="0.2/phenote-webstart.jnlp">0.2 phenote webstart</a><br>
+
<br>
+
3/27/06<br>
+
Added the ability to do term completion on Synonyms, Definitions, and
Obsoletes. Also can mouse over a term in a completion list and get
information about it in the term info text area. <br>
+
<br>
+
The term info area needs a lot of work.<br>
+
TODO:<br>
+
layout, scrollbar, border w title, ordering & lumping parents
& children, formatting. <br>
+
Also perhaps have children & parents be clickable in some fashion
either html-like clickable text or as buttons.<br>
+
Theres also bugs in term completion boxes. If you start backspacing it
gets wacky for instance.<br>
+
<br>
+
<a href="0.2/phenote-webstart.jnlp"><br>
+
</a>
<h2><span style="text-decoration: underline;">0.1</span></h2>
+
<a href="0.1/phenote-webstart.jnlp">0.1 phenote webstart</a><br>
+
<br>
+
3/1/06<br>
+
0.1 was the initial phenote release (known briefly as the plumper at
the time). It just had a genotype, anatomy and pato fields, where
anatomy and pato did term completion (just on term names) with there
ontologies in a drop down list. There was also the phenotype table that
tracked phenotype instances being edited in the above fields. This very
limited functionality was demo'd at the cbio meeting 3/3/06 at Stanford.<br>
+
<br>
+
<a href="0.2/phenote-webstart.jnlp"></a><br>
+
<br>
+
<br>
+
<a href="phenote.html">Phenote main page</a><br>
+
</body>
</html>
Modified: phenote/trunk/doc/phenote-website/phenote.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.html 2007-01-11 22:11:20 UTC (rev 283)
+++ phenote/trunk/doc/phenote-website/phenote.html 2007-01-12 17:42:15 UTC (rev 284)
@@ -1,125 +1,194 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
- <meta content="text/html; charset=ISO-8859-1"
- http-equiv="content-type">
+
+
+ <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
+
+
<title>Phenote</title>
</head>
+
+
<body>
+
<h1 style="text-align: left;"><span style="font-weight: bold;"></span>Phenote<br>
+
</h1>
+
<br>
+
Phenote is a tool to annotate phenotypes using the Entity Quality
paradigm. It takes advantage of
ontologies. It uses term completion to allow curators quick access to
the ontology terms they want to use. <br>
+
<br>
-<a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br>
+<a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br>
+
<br>
-<a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br>
+
+<a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br>
<br>
+
+<br>
+
To be clear the above webstart links for zfin & fly were made via
configuration not hard wired code. Thus one could in theory configure
phenote for ones own purposes.<br>
+
<br>
-Recent addditions include the ability to post compose terms, bul
+
+Recent addditions include the ability to add any field you like, post compose terms, bulk
update, undo, spring framework, and
synonyms now are shown in the completion list.<br>
+
<br>
+
Zebrafish requires
components of phenote(to plug into their non-public
website), not a full web app. Here is a proof of concept of some of
those
components:<br>
+
<br>
+
<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby
Phenote(components used by Zfin)</a><br>
+
<br>
+
Webby phenote is a collaboration with Sohel Merchant at dictyBase.
Here is what they have done:<br>
+
<br>
-<a
- href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DichtyBase
+
+<a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DichtyBase
webby phenote</a><br>
+
<br>
+
<br>
+
I am doing these
-releases to get feedback. Please report any bugs (ideally through the <a
- href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">bug
+releases to get feedback. Please report any bugs (ideally through the <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">bug
tracker</a>) and let me know what you
think (mg...@fr...).<br>
+
<br>
-Currently under development (still buggy):<br>
-<br>
-<a href="1.0/phenote-flybase.jnlp">Phenote dev 1.0 for fly</a><br>
-<br>
-<a href="1.0/phenote-zfin.jnlp">Phenote dev 1.0 for zfin</a><br>
-<br>
-<br>
+
<h4>Phenote links:<br>
+
</h4>
+
<a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Phenote
email list</a><br>
+
<a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">Phenote
bug tracker</a><br>
-<a
- href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-bug-tracker">Bug
+
+<a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-bug-tracker">Bug
tracker email list</a><br>
+
<a href="https://sourceforge.net/svn/?group_id=76834">Phenote source
code (obo sourceforge svn)</a><br>
+
<a href="https://lists.sourceforge.net/lists/listinfo/obo-svn-commit">Phenote
svn commit email list</a><br>
-<a
- href="http://wiki.dictybase.org/dictywiki/index.php/Phenotype_Curation_Tool_Documentation#Usage">Dichty
+
+<a href="http://wiki.dictybase.org/dictywiki/index.php/Phenotype_Curation_Tool_Documentation#Usage">Dichty
webby phenote wiki developer docs</a><br>
-<a
- href="http://www.bioontology.org/wiki-internal/index.php/Phenotype_Annotation_Tool">Phenote
+
+<a href="http://www.bioontology.org/wiki-internal/index.php/Phenotype_Annotation_Tool">Phenote
ncbo internal wiki (ncbo folk only)</a><br>
+
<br>
+
<a href="phenote-release-notes.html">Phenote Release Notes and old
webstart releases</a><br>
+
<br>
+
If the Phenote webstart link fails to do anything, then there are
probably problems
-with webstart and/or java(has to be jdk 1.5). Take a look at my <a
- href="webstart-troubleshooting.html">webstart troubleshooting</a><br>
+with webstart and/or java(has to be jdk 1.5). Take a look at my <a href="webstart-troubleshooting.html">webstart troubleshooting</a><br>
+
page.<br>
+
<br>
+
Click here for <a href="phenote-java-requirements.html">phenote java
requirements</a><br>
+
<br>
+
<br>
+
<br>
+
Old releases: <br>
+
<br>
+
+<a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br>
+
+<a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br>
+<br>
<a href="0.8/phenote-flybase.jnlp">Phenote 0.8 for fly.</a><br>
+
<a href="0.8/phenote-zfin.jnlp">Phenote (standalone) 0.8 for zfin</a><br>
+
<br>
+
<a href="0.7/phenote-flybase.jnlp">Phenote 0.7 for fly.</a><br>
+
<a href="0.7/phenote-zfin.jnlp">Phenote (standalone) 0.7 for zfin</a><br>
+
<br>
+
<a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br>
+
<br>
+
<a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br>
+
<br>
+
<a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br>
+
<br>
+
<a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br>
+
<br>
+
<a href="0.4/phenote-flybase.jnlp">Phenote 0.4 webstart for FlyBase</a><br>
+
<br>
+
<a href="0.4/phenote-zfin.jnlp">Phenote 0.4 webstart for ZFIN</a><br>
+
<br>
+
<a href="0.3.1/phenote-webstart.jnlp">Phenote for CToL group (0.3.1)</a>
(a special release for the CToL group that uses fish
taxonomy)<br>
+
<br>
+
<a href="0.3/phenote-webstart.jnlp">Phenote 0.3</a><br>
+
<br>
+
<a href="0.2/phenote-webstart.jnlp">Phenote 0.2</a><br>
+
<br>
+
<a href="0.1/phenote-webstart.jnlp">Phenote 0.1</a><br>
+
<br>
+
<br>
+
</body>
</html>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-01-18 16:15:14
|
Revision: 295
http://svn.sourceforge.net/obo/?rev=295&view=rev
Author: mgibson
Date: 2007-01-18 08:15:13 -0800 (Thu, 18 Jan 2007)
Log Message:
-----------
added the rest of the html files from the website -
should phenote-website be taken out of doc dir and given its own dir?
Added Paths:
-----------
phenote/trunk/doc/phenote-website/phenote-java-requirements.html
phenote/trunk/doc/phenote-website/webstart-troubleshooting.html
Added: phenote/trunk/doc/phenote-website/phenote-java-requirements.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-java-requirements.html (rev 0)
+++ phenote/trunk/doc/phenote-website/phenote-java-requirements.html 2007-01-18 16:15:13 UTC (rev 295)
@@ -0,0 +1,32 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+ <meta content="text/html; charset=ISO-8859-1"
+ http-equiv="content-type">
+ <title>Java version for Phenote</title>
+</head>
+<body>
+<h1>Java requirements for Phenote</h1>
+<br>
+Phenote requires Java 1.5. I hope this is OK with everybody. If there
+are issues please let me know(mg...@fr...). 1.5 has been out
+for around 2 years, and has a lot of nice features. The big issue is
+Macs. Mac Tiger supports 1.5 where earlier version (Panther &
+earlier) do not as far as I know. So upgrading to Tiger would then be a
+requirement for using Phenote. Tiger has been out for over a year now
+and is now pretty stable, so I hope this isn't a cumbersome
+requirement. I have emailed with zfin and it seems the Mac users there
+are actually already all upgraded to Tiger.<br>
+<br>
+As for windows, linux and solaris, if you do not already have jdk 1.5
+it can be downloaded from sun:<br>
+<br>
+<a href="http://java.sun.com/j2se/1.5.0/download.jsp">http://java.sun.com/j2se/1.5.0/download.jsp</a><br>
+<br>
+<br>
+<br>
+<a href="phenote.html">Phenote main page</a><br>
+<br>
+<br>
+</body>
+</html>
Added: phenote/trunk/doc/phenote-website/webstart-troubleshooting.html
===================================================================
--- phenote/trunk/doc/phenote-website/webstart-troubleshooting.html (rev 0)
+++ phenote/trunk/doc/phenote-website/webstart-troubleshooting.html 2007-01-18 16:15:13 UTC (rev 295)
@@ -0,0 +1,103 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+ <meta content="text/html; charset=ISO-8859-1"
+ http-equiv="content-type">
+ <title>Phenote webstart trouble shooting</title>
+</head>
+<body>
+<h2>Phenote Webstart Troubleshooting<br>
+</h2>
+<br>
+Webstart is a way of launching java applications from the web. Just
+click
+on a link and the application will download to your computer, and come
+up. Webstart is somewhat difficult, but I've got it working in some
+situations for Phenote.
+Future clicks on the link should recognize that you've already
+downloaded
+it, and will just bring up the downloaded application. If the
+application
+changes/upgrades on the server, this will be recognized and a click on
+the
+link will download the new upgraded application. So its more or less a
+web
+installer. On the <a href="phenote.html">main phenote page</a>
+there are links to the latest phenote webstart links to try.<br>
+<p>The indication that a link works is that you get a popup
+that says "Java Loading", or something like that and then a bunch of
+files get downloaded and eventually the application actually comes up.
+For this to work with a browser, the browser has to recognize java
+webstart links, which have a jnlp suffix. Macs tend to have
+webstart pre-installed on their browsers. Windows seems to as
+well. Linux does not and I don't know about Solaris. If its not
+working what you basically have to do is set up an association in the
+browser between whats called a mime type, which is
+"application/x-java-jnlp-file" in this case, and the webstart
+application, which you need to find on your computer(more on this
+below).<br>
+<br>
+These are the steps I had to go through to get webstart installed on my
+Mozilla browser on Linux, which does not come with webstart
+pre-installed. <br>
+<br>
+First you need to see if you have webstart already installed on your
+computer. If you have java on your computer then usually webstart comes
+with java so you should have it. So if you have java you first need to
+find out where it is installed. In linux you type "which java" at the
+command line. For me this comes back with<br>
+<br>
+/usr/lib/java/bin/java</p>
+<p>You then need to make sure you are using java 1.5, phenote requires
+1.4. Do a "java-version" at the command line. If you have anything less
+than 1.5, you need to install java 1.5, or if you have 1.5 installed
+somewhere (but its not the default) you need to find it and grab its
+javaws. If you try to webstart phenote with a java less than 1.5
+nothing will happen and it won't even indicate that its the wrong java,
+you just have to know.<br>
+<br>
+So what I found is in java 1.5 javaws is in both the bin and jre
+directory. So cd to
+/usr/lib/java and do a "ls jre" and "ls bin" (on windows "dir jre"
+& "dir bin") and look for a file called "javaws", which is the
+webstart application. The full path plus javaws is what you will need
+below. So for me its "/usr/lib/java/jre/javaws"<br>
+<br>
+If webstart is not on your computer (or network) you can download it
+from(make sure its from java 1.5):<br>
+<br>
+<a href="http://java.sun.com/products/javawebstart/download.jsp">http://java.sun.com/products/javawebstart/download.jsp</a><br>
+<br>
+<br>
+Now that we've found the webstart application we are ready to associate
+it with a mime type in the browser. Here is how it is done in Mozilla
+on linux, I hope other browsers are somewhat similar.<br>
+<br>
+Hit the "Edit" menu, and its "Preferences" sub menu to get the
+Preferences dialog. Expand the "Navigator" category, and under
+that click on "Helper Application", which is where mime types get
+associated with applications. Click the "New Type" button, which brings
+up a New Type dialog box. In the "MIME Type" field enter
+"application/x-java-jnlp-file". Under "Description" you can just
+put "Java Webstart". Under "Extension" put "jnlp". Click on "Open it
+with:" and in the associated field either entor or browse for the
+location of webstart on your computer. This is what you were digging
+for above. For my computer I enter "/usr/lib/java/jre/javaws", the
+location of my webstart app. then deselect "Always ask me before
+handling files of this type", as who wants to keep being asked, and hit
+"OK" and hit "OK" as well in the Helper Applications dialog.<br>
+<br>
+You now need to restart your browser for it to pick up the new mime
+type association for webstart and hopefully the above link should now
+work. <br>
+<br>
+One thing thats also handy if there are problems bringing up webstart
+is to bring up the browsers java console (this may not be supported by
+all browsers). This should give some feedback on things happening
+behind the scenes of the webstart application, so its good for trouble
+shooting. In mozilla this can be brought up with menu <br>
+Tools->Web Development->Java Console.<br>
+<br>
+</p>
+</body>
+</html>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-01-30 18:51:46
|
Revision: 312
http://svn.sourceforge.net/obo/?rev=312&view=rev
Author: nlw
Date: 2007-01-30 10:35:57 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
adding website dirs and files, largeley undeveloped
Added Paths:
-----------
phenote/trunk/doc/phenote-website/content/
phenote/trunk/doc/phenote-website/css/
phenote/trunk/doc/phenote-website/css/bbop.css
phenote/trunk/doc/phenote-website/css/style-alpha.css
phenote/trunk/doc/phenote-website/css/style-light.css
phenote/trunk/doc/phenote-website/css/style-square.css
phenote/trunk/doc/phenote-website/css/style-stark.css
phenote/trunk/doc/phenote-website/css/style-tile.css
phenote/trunk/doc/phenote-website/css/style.css
phenote/trunk/doc/phenote-website/images/
phenote/trunk/doc/phenote-website/images/NCBO_logo.jpg
phenote/trunk/doc/phenote-website/images/lbl_logo.gif
phenote/trunk/doc/phenote-website/images/oboedit_logo.gif
phenote/trunk/doc/phenote-website/index_text.shtml
phenote/trunk/doc/phenote-website/javascript/
phenote/trunk/doc/phenote-website/javascript/obfuscate.js
phenote/trunk/doc/phenote-website/ssi/
phenote/trunk/doc/phenote-website/ssi/footer.html
phenote/trunk/doc/phenote-website/ssi/footer.shtml
phenote/trunk/doc/phenote-website/ssi/header.html
phenote/trunk/doc/phenote-website/ssi/navi_about.html
phenote/trunk/doc/phenote-website/ssi/navi_home.html
phenote/trunk/doc/phenote-website/ssi/navi_home.html~
phenote/trunk/doc/phenote-website/ssi/navi_publications.html
Added: phenote/trunk/doc/phenote-website/css/bbop.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/bbop.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/bbop.css 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,657 @@
+body
+{ background: #fff;
+ margin: 5px 0;
+ font: 1em Verdana, Arial, Helvetica, sans-serif;
+ color: #000;
+}
+
+h1, h2, h3, h4
+{ font-family: "trebuchet ms", "lucida grande", arial, sans-serif;
+}
+
+h1 { font-size: 2em;
+ text-align: center; }
+h2 { font-size: 1.6em; }
+h3 { font-size: 1.4em; }
+h4 { font-size: 1.2em; }
+
+a
+{ color: #006;
+ text-decoration: none;
+ border-bottom : 1px dotted #006;
+ padding: 0.1em 2px;
+ background: #e9effa;
+}
+
+a:hover, a:active
+{ color: #fff;
+ background: #3875D7;
+ border: none;
+}
+
+a.img
+{ background: #fff;
+ border: none;
+}
+
+a.img img
+{ border: 1px solid #fff;
+ padding: 2px;
+}
+
+a.img:hover img, a.img:active img
+{ border: 1px solid #3875D7;
+}
+
+a.anchor
+{ visibility: hidden;
+}
+
+div.header, div.footer
+{ width: 100%;
+ background: #e9effa;
+ border-width: 3px 0 3px 0;
+ border-color: #3875D7;
+ border-style: solid;
+}
+
+.footer p
+{ margin: 0;
+ padding: 5px;
+ font-size: 0.7em;
+ text-align: right;
+ line-height: 1.4em;
+}
+
+.footer a
+{ border: none;
+}
+
+.footer img
+{ border: 0;
+ float: left;
+ margin: 5px 10px;
+}
+
+div.header
+{ background: url(../images/GO-head.gif) #e9effa 0 -10px no-repeat;
+}
+
+.header h1
+{ font: italic 2em "trebuchet ms", "lucida grande", arial, sans-serif;
+ margin: 0;
+ padding: 15px 5px 5px 125px;
+ color: #3875D7;
+ text-align: left;
+}
+
+.header form, .header p
+{ margin: 0;
+ padding: 3px;
+ font-size: 0.9em;
+}
+
+div.content
+{ background: url(../images/bg.gif) #fff left top repeat-y;
+}
+
+/* page layout */
+#navBox
+{ width: 180px;
+ padding: 0;
+ margin: 0;
+ float: left;
+}
+
+/* nav bar on left */
+#navLeft
+{ font-size: 0.8em;
+ line-height: 130%;
+ padding-top: 10px;
+}
+
+#navLeft ul
+{ list-style: none;
+ margin: 0;
+ padding: 0;
+}
+
+#navLeft a
+{ display: block;
+ color: #000;
+ margin: 0;
+ background: #cddcf3;
+ border-bottom: 1px solid #fff;
+ padding: 2px 15px 2px 5px;
+}
+
+#navLeft li.head a
+{ font-weight: bold;
+}
+
+#navLeft li.sub a
+{ background: #EBF1FC;
+ padding: 2px 5px 2px 15px;
+}
+
+#navLeft li a:hover
+{ color: #fff;
+ background: #3875D7;
+}
+
+#navLeft li.sub
+{ display: none;
+}
+
+#navLeft.all li
+{ display: block;
+}
+
+#navLeft li.dl
+{ display: block;
+}
+
+#navLeft.docs li.docs
+{ display: block;
+}
+
+#navLeft.abt li.abt
+{ display: block;
+}
+
+#navLeft.tools li.tools
+{ display: block;
+}
+
+#navLeft.cur li.cur
+{ display: block;
+}
+
+#navLeft li.top
+{ display: inline;
+}
+
+/* page contents */
+div.main
+{ margin-left: 180px;
+ padding: 10px;
+}
+
+/* pages without left hand navigation menu */
+div.photo
+{ padding: 10px;
+ margin: 0;
+}
+
+p.intro, div.main p
+{ padding: 10px;
+}
+
+div.main p, div.main div.block, .photo p
+{ line-height: 1.6em;
+}
+
+/* table of contents */
+div.navPage
+{ border: 2px solid #ccc;
+ background: #EBF1FC;
+ padding: 5px 5%;
+ font-size: 0.9em;
+ line-height: 1.5em;
+}
+
+div.navPage p
+{ margin: 3px 0;
+ padding: 0;
+}
+
+div.navPage ul
+{ list-style: none;
+ margin: 0;
+ padding: 0;
+}
+
+div.navPage li
+{ margin: 3px 0;
+ padding: 0;
+}
+
+div.navPage a
+{ padding: 0 2px;
+ border: solid 1px #ebf1fc;
+}
+
+div.navPage a:hover
+{ border: solid 1px #3875D7;
+ background: #fff;
+ color: #006;
+}
+
+div.navPage li.h2
+{ font-weight: bold;
+}
+
+div.navPage li.h3
+{ font-weight: normal;
+ padding-left: 20px;
+}
+/* end page navigation */
+
+/* extra class for the site map */
+div.navPage li.h1
+{ font-weight: bold;
+ margin-left: -20px;
+ padding-top: 5px;
+ font-size: 1.2em;
+}
+
+/* classes for the navBar on the 2006 annotation camp pages */
+div.navBarDiv
+{ padding: 3px 0;
+ margin: 10px -10px;
+ border-width: 3px 0 3px 0;
+ border-color: #3875D7;
+ border-style: solid;
+ background: #e9effa;
+ font-size: 1.2em;
+}
+
+ul.navBar
+{ margin: 0;
+ padding: 1px;
+ list-style: none;
+ background: #e9effa;
+ text-align: center;
+}
+
+ul.navBar li
+{ display: inline;
+ margin: 0;
+ padding: 0;
+}
+
+ul.navBar li a
+{ border: 1px solid #e9effa;
+ padding: 3px 5px;
+ margin: 0;
+}
+
+ul.navBar li a:hover, ul.navBar li a:active
+{ border: 1px solid #fff;
+ color: #fff;
+ background: #3875D7;
+}
+
+ul.navBar li a.here
+{ color: #000;
+ border: 1px solid #000;
+ background: #fff;
+}
+
+/* bibliography specific */
+h4#setViewOptions
+{ margin-bottom: 1px;
+}
+
+p#viewOptions
+{ color: #006;
+ border: solid 1px #3875D7;
+ background: #fff;
+ padding: 10px;
+ margin-top: 0;
+}
+
+div.biblio ul
+{ font-size: 0.7em;
+ margin: 0 0 0 20px;
+ padding: 0;
+}
+
+div.biblio p
+{ font-size: 0.8em;
+ margin: 15px 0 0 0;
+ padding: 0;
+}
+
+div.biblio p b
+{ font-size: 1.2em;
+}
+
+div.biblio p a
+{ font-size: 1.1em;
+}
+
+/* page contents proper */
+div.block
+{ border: 1px solid #3875D7;
+ margin: 10px 0;
+ font-size: 0.9em;
+ padding: 0 10px;
+}
+
+div.block p, div.block h4
+{ padding: 0;
+ margin: 0.5em 0;
+}
+
+div.block ul
+{ padding: 5px 0;
+ margin: 0 0 0 20px;
+}
+
+div.block li
+{ padding: 0.2em 0;
+ margin: 0;
+}
+
+div.block ul.small
+{ padding: 0 0 5px 0;
+}
+
+div.block ul.small li
+{ padding: 0;
+ margin: 0;
+}
+
+div.block h2
+{ border-bottom: 1px solid #3875D7;
+ background: #e9effa;
+ margin: 0 -10px;
+ padding: 5px 10px;
+}
+
+div.block h3, div.tool h4
+{ border-top: 1px solid #3875D7;
+ margin: 0 -10px;
+ padding: 10px 10px 5px 10px;
+ color: #006;
+ text-align: left;
+}
+
+div.block h2 + h3, div.block h2 + div.tool h4
+{ border-top: 0;
+}
+
+div.block dl
+{ margin: 0;
+ padding: 0;
+}
+
+div.block p.terminal
+{ font: 0.9em monaco, courier, monospace;
+ background: #009;
+ color: #fff;
+ border: 2px solid #ccc;
+ padding: 5px 10px;
+ margin: 0;
+}
+
+/* links at bottom of each block section */
+div.block p.toTop
+{ font-size: 0.8em;
+ line-height: 1.4em;
+ text-align: right;
+ background: #e9effa;
+ margin: 0 -10px;
+ padding: 0.3em;
+}
+
+div.block p.toTop a
+{ background: #cddcf3;
+ color: #000;
+ text-decoration: none;
+ padding: 0.3em;
+ margin: 0;
+ border: none;
+}
+
+div.block p.toTop a:hover, p.toTop a:active
+{ background: #3875D7;
+ color: #fff;
+}
+
+div.diag
+{ width: 80%;
+ margin: 10px 0 20px 10%;
+ background: #e9effa;
+ border: 3px solid #ccc;
+ padding: 5px 10px;
+}
+
+div.contents p
+{ padding: 10px 0 0 0;
+}
+
+table
+{ border: 2px solid #ccc;
+ margin: 10px 0;
+ padding: 0;
+ width: 100%;
+}
+
+div.photo table
+{ background: #ccc;
+ margin: 0;
+}
+
+th
+{ padding: 5px;
+ background: #cddcf3;
+ font-weight: bold;
+ text-align: center;
+ vertical-align: top;
+}
+
+td
+{ padding: 5px;
+ background: #e9effa;
+ vertical-align: top;
+}
+
+td.stdL
+{ background: #cddcf3;
+ font-weight: bold;
+ width: 25%;
+}
+
+.tt
+{ font-family: monaco, courier, monospace;
+}
+
+.wh
+{ background: #fff;
+}
+
+.red
+{ color: #f00;
+}
+
+.blue
+{ color: #00f;
+}
+
+.green
+{ color: #060;
+}
+
+.purple
+{ color: #909;
+}
+
+.C
+{ text-align: center;
+}
+
+.L
+{ text-align: left;
+}
+
+.R
+{ text-align: right;
+}
+
+.term
+{ color: #090;
+ font-weight: 700;
+}
+
+.small
+{ font-size: 0.8em;
+}
+
+ul.noDot
+{ list-style: none;
+}
+
+.w10
+{ width: 10%;
+}
+
+.w20
+{ width: 20%;
+}
+
+.w25
+{ width: 25%;
+}
+
+.w40
+{ width: 40%;
+}
+
+.w75
+{ width: 75%;
+}
+
+.b
+{ font-weight: bold;
+}
+
+.i
+{ font-style: italic;
+}
+
+table.annot td.sep
+{ padding: 0;
+}
+
+ul.inline
+{ margin: 0;
+ padding: 0;
+}
+
+ul.inline li
+{ display: inline;
+ list-style: none;
+ margin: 0 5px;
+ padding: 0;
+}
+
+.floatR
+{ float: right;
+ margin: 0;
+ padding-right: 10px;
+}
+
+div.floatR a
+{ background: #fff;
+ border: none;
+ padding: 3px;
+ margin: 0;
+}
+
+.clearboth
+{ clear: both;
+ height: 1px;
+ visibility: hidden;
+}
+
+.clearR
+{ clear: right;
+ height: 1px;
+ margin: 5px 0;
+ visibility: hidden;
+}
+
+dl.evidence
+{ padding: 0;
+}
+
+.evidence dt
+{ width: 15%;
+ float: left;
+ margin: 0;
+ padding: .5em;
+ border-top: 1px solid #999;
+ font-weight: bold;
+}
+
+/* commented backslash hack for mac-ie5 \*/
+dt { clear: both; }
+/* end hack */
+
+.evidence dd
+{ margin: 0 0 0 15%;
+ padding: .5em;
+ border-top: 1px solid #999;
+}
+
+div.tool div.floatR
+{ margin-top: 5px;
+ padding: 0;
+}
+
+div.tool div.floatR img
+{ margin: 0;
+ padding: 2px;
+}
+
+.block li.dir, .block li.doc, .block li.html, .block li.jpg, .block li.link, .block li.pdf, .block li.ppt, .block li.psd, .block li.sxi, .block li.txt, .block li.zip
+{ background-repeat: no-repeat;
+ background-position: 0% 50%;
+ padding-left: 18px;
+}
+
+.block li.jpg
+{ background-image: url(../images/icon-jpg.gif);
+}
+
+.block li.html
+{ background-image: url(../images/icon-html.gif);
+}
+
+.block li.ppt
+{ background-image: url(../images/icon-ppt.gif);
+}
+
+.block li.zip
+{ background-image: url(../images/icon-zip.gif);
+}
+
+.block li.psd
+{ background-image: url(../images/icon-psd.gif);
+}
+
+.block li.sxi
+{ background-image: url(../images/icon-unknown.gif);
+}
+
+.block li.txt
+{ background-image: url(../images/icon-txt.gif);
+}
+
+.block li.doc
+{ background-image: url(../images/icon-doc.gif);
+}
+
+.block li.dir
+{ background-image: url(../images/icon-dir.gif);
+}
+
+.block li.pdf
+{ background-image: url(../images/icon-pdf.gif);
+}
+
+.form textarea, .form input
+{ margin: 10px 0;
+}
Added: phenote/trunk/doc/phenote-website/css/style-alpha.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style-alpha.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/style-alpha.css 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,178 @@
+/* Style sheet made to go with the UCSC Japanese Program. */
+
+/* ---------- Default properties. ---------- */
+body {
+ font-family: arial, helvetica, sans-serif;
+ font-size: 100%;
+ background: white url(bg-music5.jpg) repeat top right;
+ color: black;
+ margin: 0;
+ padding: 0;
+ /*border: 3px solid #f4ecd9;*/
+}
+
+/* ---------- "page_head" area. ---------- */
+
+/**/
+#page_head{
+ background-image: url(top_image.jpg);
+ background-repeat: repeat-x;
+ top: 0px;
+ height: 110px;
+ /*border: 5px solid yellow;*/
+}
+
+.ehead{
+ white-space: nowrap;
+ left: 1em;
+ font-size: 1.25em;
+ font-weight: bold;
+ color: yellow;
+ /*color: #121212;*/
+ position: absolute;
+ /*border: 5px solid red;*/
+ z-index: 2;
+}
+
+.jhead{
+ white-space: nowrap;
+ position: absolute;
+ left: 5em;
+ top: 1em;
+ font-size: 1.5em;
+ color: #dddddd;
+ /*border: 5px solid blue;*/
+ z-index: 1;
+}
+
+.language2j{
+ padding: .5em;
+ float: right;
+ color: #888888;
+ /*border: 5px solid #black;*/
+}
+
+/* ---------- "page_body" class. ---------- */
+
+/**/
+#page_body{
+ padding: 1.5em;
+/* border: 5px solid purple;*/
+}
+
+/* ---------- "page_foot" class. ---------- */
+
+/**/
+#page_foot{
+ padding: .5em;
+/* border: 5px solid grey;*/
+}
+
+/* ---------- "main_content" class. ---------- */
+
+/**/
+#main_content{
+height: auto;
+ background: #f4ecd9;
+ padding-left: 1em;
+ padding-right: 1em;
+ padding-bottom: 1em;
+ margin-left: 12em;
+ border: 2px solid black;
+}
+
+#main_content img{
+ /*float: left;*/
+ padding: 1em;
+}
+
+.portrait {
+ float: left;
+}
+
+/**/
+.contact{
+ /*float: left;*/
+ /*border: 5px solid yellow;*/
+}
+
+/* ---------- "copyright" class. ---------- */
+
+/**/
+.copyright{
+ /*float: right;*/
+ /*border: 5px solid orange;*/
+}
+
+/* ---------- "navi" id. ---------- */
+
+/* Tell us what/where a "navi" is... */
+#navi {
+ background: #f4ecd9;
+ float: left;
+ width:8em;
+ padding-top: .5em;
+ padding-bottom: 1em;
+ padding-left: 1em;
+ padding-right: 1em;
+ border: 2px solid blue;
+}
+
+/* How to display "h2"s in a "navi". */
+.navi_head {
+ font-size: 1.1em;
+ color: #36c;
+ font-weight: bold;
+ margin-bottom: .15em;
+ /*border: 1px solid red;*/
+}
+
+/* Give non-anchors a little breathing space. */
+#navi ul {
+ list-style: none;
+ margin: 0 0 0 0;
+ padding: 0;
+ /*border: 1px solid yellow;*/
+}
+
+#navi li {
+ margin: .25em;
+}
+
+#navi li a {
+ text-decoration: none;
+ display: block;
+ color: #0000c0;
+ background: #f4ecd9;
+ /*border: 1px solid grey;*/
+}
+
+/* Highlight "li"'s "a"s on hover. */
+#navi li a:hover {
+ background: #e0e0e0;
+ /*border-color: #0c0c0c;*/
+}
+
+/* */
+#navi ul li {
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid green;*/
+}
+
+/* */
+#navi ul li ul{
+ text-decoration: none;
+ display: block;
+ margin-left: 1em;
+ /*border: 1px solid orange;*/
+}
+
+/* */
+#navi ul li ul li{
+ font-size: .85em;
+ text-decoration: none;
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid purple;*/
+}
Added: phenote/trunk/doc/phenote-website/css/style-light.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style-light.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/style-light.css 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,178 @@
+/* Style sheet made to go with the UCSC Japanese Program. */
+
+/* ---------- Default properties. ---------- */
+body {
+ font-family: arial, helvetica, sans-serif;
+ font-size: 100%;
+ background: white url(bg-music5.jpg) repeat top right;
+ color: black;
+ margin: 0;
+ padding: 0;
+ /*border: 3px solid #f4ecd9;*/
+}
+
+/* ---------- "page_head" area. ---------- */
+
+/**/
+#page_head{
+ background-image: url(top_image.jpg);
+ background-repeat: repeat-x;
+ top: 0px;
+ height: 110px;
+ /*border: 5px solid yellow;*/
+}
+
+.ehead{
+ white-space: nowrap;
+ left: 1em;
+ font-size: 1.25em;
+ font-weight: bold;
+ color: yellow;
+ /*color: #121212;*/
+ position: absolute;
+ /*border: 5px solid red;*/
+ z-index: 2;
+}
+
+.jhead{
+ white-space: nowrap;
+ position: absolute;
+ left: 5em;
+ top: 1em;
+ font-size: 1.5em;
+ color: #dddddd;
+ /*border: 5px solid blue;*/
+ z-index: 1;
+}
+
+.language2j{
+ padding: .5em;
+ float: right;
+ color: #888888;
+ /*border: 5px solid #black;*/
+}
+
+/* ---------- "page_body" class. ---------- */
+
+/**/
+#page_body{
+ padding: 1.5em;
+/* border: 5px solid purple;*/
+}
+
+/* ---------- "page_foot" class. ---------- */
+
+/**/
+#page_foot{
+ padding: .5em;
+/* border: 5px solid grey;*/
+}
+
+/* ---------- "main_content" class. ---------- */
+
+/**/
+#main_content{
+height: auto;
+ background: #f4ecd9;
+ padding-left: 1em;
+ padding-right: 1em;
+ padding-bottom: 1em;
+ margin-left: 12em;
+ border: 2px solid black;
+}
+
+#main_content img{
+ /*float: left;*/
+ padding: 1em;
+}
+
+.portrait {
+ float: left;
+}
+
+/**/
+.contact{
+ /*float: left;*/
+ /*border: 5px solid yellow;*/
+}
+
+/* ---------- "copyright" class. ---------- */
+
+/**/
+.copyright{
+ /*float: right;*/
+ /*border: 5px solid orange;*/
+}
+
+/* ---------- "navi" id. ---------- */
+
+/* Tell us what/where a "navi" is... */
+#navi {
+ background: #f4ecd9;
+ float: left;
+ width:8em;
+ padding-top: .5em;
+ padding-bottom: 1em;
+ padding-left: 1em;
+ padding-right: 1em;
+ border: 2px solid blue;
+}
+
+/* How to display "h2"s in a "navi". */
+.navi_head {
+ font-size: 1.1em;
+ color: #36c;
+ font-weight: bold;
+ margin-bottom: .15em;
+ /*border: 1px solid red;*/
+}
+
+/* Give non-anchors a little breathing space. */
+#navi ul {
+ list-style: none;
+ margin: 0 0 0 0;
+ padding: 0;
+ /*border: 1px solid yellow;*/
+}
+
+#navi li {
+ margin: .25em;
+}
+
+#navi li a {
+ text-decoration: none;
+ display: block;
+ color: #0000c0;
+ background: #f4ecd9;
+ /*border: 1px solid grey;*/
+}
+
+/* Highlight "li"'s "a"s on hover. */
+#navi li a:hover {
+ background: #e0e0e0;
+ /*border-color: #0c0c0c;*/
+}
+
+/* */
+#navi ul li {
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid green;*/
+}
+
+/* */
+#navi ul li ul{
+ text-decoration: none;
+ display: block;
+ margin-left: 1em;
+ /*border: 1px solid orange;*/
+}
+
+/* */
+#navi ul li ul li{
+ font-size: .85em;
+ text-decoration: none;
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid purple;*/
+}
Added: phenote/trunk/doc/phenote-website/css/style-square.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style-square.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/style-square.css 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,178 @@
+/* Style sheet made to go with the UCSC Japanese Program. */
+
+/* ---------- Default properties. ---------- */
+body {
+ font-family: arial, helvetica, sans-serif;
+ font-size: 100%;
+ background: white url(bg-music.jpg) repeat top right;
+ color: black;
+ margin: 0;
+ padding: 0;
+ /*border: 3px solid #f4ecd9;*/
+}
+
+/* ---------- "page_head" area. ---------- */
+
+/**/
+#page_head{
+ background-image: url(top_image.jpg);
+ background-repeat: repeat-x;
+ top: 0px;
+ height: 110px;
+ /*border: 5px solid yellow;*/
+}
+
+.ehead{
+ white-space: nowrap;
+ left: 1em;
+ font-size: 1.25em;
+ font-weight: bold;
+ color: yellow;
+ /*color: #121212;*/
+ position: absolute;
+ /*border: 5px solid red;*/
+ z-index: 2;
+}
+
+.jhead{
+ white-space: nowrap;
+ position: absolute;
+ left: 5em;
+ top: 1em;
+ font-size: 1.5em;
+ color: #dddddd;
+ /*border: 5px solid blue;*/
+ z-index: 1;
+}
+
+.language2j{
+ padding: .5em;
+ float: right;
+ color: #888888;
+ /*border: 5px solid #black;*/
+}
+
+/* ---------- "page_body" class. ---------- */
+
+/**/
+#page_body{
+ padding: 1.5em;
+/* border: 5px solid purple;*/
+}
+
+/* ---------- "page_foot" class. ---------- */
+
+/**/
+#page_foot{
+ padding: .5em;
+/* border: 5px solid grey;*/
+}
+
+/* ---------- "main_content" class. ---------- */
+
+/**/
+#main_content{
+height: auto;
+ background: #f4ecd9;
+ padding-left: 1em;
+ padding-right: 1em;
+ padding-bottom: 1em;
+ margin-left: 12em;
+ border: 2px solid black;
+}
+
+#main_content img{
+ /*float: left;*/
+ padding: 1em;
+}
+
+.portrait {
+ float: left;
+}
+
+/**/
+.contact{
+ /*float: left;*/
+ /*border: 5px solid yellow;*/
+}
+
+/* ---------- "copyright" class. ---------- */
+
+/**/
+.copyright{
+ /*float: right;*/
+ /*border: 5px solid orange;*/
+}
+
+/* ---------- "navi" id. ---------- */
+
+/* Tell us what/where a "navi" is... */
+#navi {
+ background: #f4ecd9;
+ float: left;
+ width:8em;
+ padding-top: .5em;
+ padding-bottom: 1em;
+ padding-left: 1em;
+ padding-right: 1em;
+ border: 2px solid blue;
+}
+
+/* How to display "h2"s in a "navi". */
+.navi_head {
+ font-size: 1.1em;
+ color: #36c;
+ font-weight: bold;
+ margin-bottom: .15em;
+ /*border: 1px solid red;*/
+}
+
+/* Give non-anchors a little breathing space. */
+#navi ul {
+ list-style: none;
+ margin: 0 0 0 0;
+ padding: 0;
+ /*border: 1px solid yellow;*/
+}
+
+#navi li {
+ margin: .25em;
+}
+
+#navi li a {
+ text-decoration: none;
+ display: block;
+ color: #0000c0;
+ background: #f4ecd9;
+ /*border: 1px solid grey;*/
+}
+
+/* Highlight "li"'s "a"s on hover. */
+#navi li a:hover {
+ background: #e0e0e0;
+ /*border-color: #0c0c0c;*/
+}
+
+/* */
+#navi ul li {
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid green;*/
+}
+
+/* */
+#navi ul li ul{
+ text-decoration: none;
+ display: block;
+ margin-left: 1em;
+ /*border: 1px solid orange;*/
+}
+
+/* */
+#navi ul li ul li{
+ font-size: .85em;
+ text-decoration: none;
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid purple;*/
+}
Added: phenote/trunk/doc/phenote-website/css/style-stark.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style-stark.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/style-stark.css 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,176 @@
+/* Style sheet made to go with the UCSC Japanese Program. */
+
+/* ---------- Default properties. ---------- */
+body {
+ font-family: arial, helvetica, sans-serif;
+ font-size: 100%;
+ background: white url(bg-music.jpg) repeat top right;
+ color: black;
+ margin: 0;
+ padding: 0;
+ /*border: 3px solid #f4ecd9;*/
+}
+
+/* ---------- "page_head" area. ---------- */
+
+/**/
+#page_head{
+ top: 0px;
+ height: 110px;
+ /*border: 5px solid yellow;*/
+}
+
+.ehead{
+ white-space: nowrap;
+ left: 1em;
+ font-size: 1.25em;
+ font-weight: bold;
+ color: red;
+ /*color: #121212;*/
+ position: absolute;
+ /*border: 5px solid red;*/
+ z-index: 2;
+}
+
+.jhead{
+ white-space: nowrap;
+ position: absolute;
+ left: 5em;
+ top: 1em;
+ font-size: 1.5em;
+ color: yellow;
+ /*border: 5px solid blue;*/
+ z-index: 1;
+}
+
+.language2j{
+ padding: .5em;
+ float: right;
+ color: #888888;
+ /*border: 5px solid #black;*/
+}
+
+/* ---------- "page_body" class. ---------- */
+
+/**/
+#page_body{
+ padding: 1.5em;
+/* border: 5px solid purple;*/
+}
+
+/* ---------- "page_foot" class. ---------- */
+
+/**/
+#page_foot{
+ padding: .5em;
+/* border: 5px solid grey;*/
+}
+
+/* ---------- "main_content" class. ---------- */
+
+/**/
+#main_content{
+height: auto;
+ background: #f4ecd9;
+ padding-left: 1em;
+ padding-right: 1em;
+ padding-bottom: 1em;
+ margin-left: 12em;
+ border: 2px solid black;
+}
+
+#main_content img{
+ /*float: left;*/
+ padding: 1em;
+}
+
+.portrait {
+ float: left;
+}
+
+/**/
+.contact{
+ /*float: left;*/
+ /*border: 5px solid yellow;*/
+}
+
+/* ---------- "copyright" class. ---------- */
+
+/**/
+.copyright{
+ /*float: right;*/
+ /*border: 5px solid orange;*/
+}
+
+/* ---------- "navi" id. ---------- */
+
+/* Tell us what/where a "navi" is... */
+#navi {
+ background: #f4ecd9;
+ float: left;
+ width:8em;
+ padding-top: .5em;
+ padding-bottom: 1em;
+ padding-left: 1em;
+ padding-right: 1em;
+ border: 2px solid blue;
+}
+
+/* How to display "h2"s in a "navi". */
+.navi_head {
+ font-size: 1.1em;
+ color: #36c;
+ font-weight: bold;
+ margin-bottom: .15em;
+ /*border: 1px solid red;*/
+}
+
+/* Give non-anchors a little breathing space. */
+#navi ul {
+ list-style: none;
+ margin: 0 0 0 0;
+ padding: 0;
+ /*border: 1px solid yellow;*/
+}
+
+#navi li {
+ margin: .25em;
+}
+
+#navi li a {
+ text-decoration: none;
+ display: block;
+ color: #0000c0;
+ background: #f4ecd9;
+ /*border: 1px solid grey;*/
+}
+
+/* Highlight "li"'s "a"s on hover. */
+#navi li a:hover {
+ background: #e0e0e0;
+ /*border-color: #0c0c0c;*/
+}
+
+/* */
+#navi ul li {
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid green;*/
+}
+
+/* */
+#navi ul li ul{
+ text-decoration: none;
+ display: block;
+ margin-left: 1em;
+ /*border: 1px solid orange;*/
+}
+
+/* */
+#navi ul li ul li{
+ font-size: .85em;
+ text-decoration: none;
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid purple;*/
+}
Added: phenote/trunk/doc/phenote-website/css/style-tile.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style-tile.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/style-tile.css 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,176 @@
+/* Style sheet made to go with the UCSC Japanese Program. */
+
+/* ---------- Default properties. ---------- */
+body {
+ font-family: arial, helvetica, sans-serif;
+ font-size: 100%;
+ background: white url(top_image.jpg) repeat top right;
+ color: black;
+ margin: 0;
+ padding: 0;
+ /*border: 3px solid #f4ecd9;*/
+}
+
+/* ---------- "page_head" area. ---------- */
+
+/**/
+#page_head{
+ top: 0px;
+ height: 110px;
+ /*border: 5px solid yellow;*/
+}
+
+.ehead{
+ white-space: nowrap;
+ left: 1em;
+ font-size: 1.25em;
+ font-weight: bold;
+ color: yellow;
+ /*color: #121212;*/
+ position: absolute;
+ /*border: 5px solid red;*/
+ z-index: 2;
+}
+
+.jhead{
+ white-space: nowrap;
+ position: absolute;
+ left: 5em;
+ top: 1em;
+ font-size: 1.5em;
+ color: #dddddd;
+ /*border: 5px solid blue;*/
+ z-index: 1;
+}
+
+.language2j{
+ padding: .5em;
+ float: right;
+ color: #888888;
+ /*border: 5px solid #black;*/
+}
+
+/* ---------- "page_body" class. ---------- */
+
+/**/
+#page_body{
+ padding: 1.5em;
+/* border: 5px solid purple;*/
+}
+
+/* ---------- "page_foot" class. ---------- */
+
+/**/
+#page_foot{
+ padding: .5em;
+/* border: 5px solid grey;*/
+}
+
+/* ---------- "main_content" class. ---------- */
+
+/**/
+#main_content{
+height: auto;
+ background: #f4ecd9;
+ padding-left: 1em;
+ padding-right: 1em;
+ padding-bottom: 1em;
+ margin-left: 12em;
+ border: 2px solid black;
+}
+
+#main_content img{
+ /*float: left;*/
+ padding: 1em;
+}
+
+.portrait {
+ float: left;
+}
+
+/**/
+.contact{
+ /*float: left;*/
+ /*border: 5px solid yellow;*/
+}
+
+/* ---------- "copyright" class. ---------- */
+
+/**/
+.copyright{
+ /*float: right;*/
+ /*border: 5px solid orange;*/
+}
+
+/* ---------- "navi" id. ---------- */
+
+/* Tell us what/where a "navi" is... */
+#navi {
+ background: #f4ecd9;
+ float: left;
+ width:8em;
+ padding-top: .5em;
+ padding-bottom: 1em;
+ padding-left: 1em;
+ padding-right: 1em;
+ border: 2px solid blue;
+}
+
+/* How to display "h2"s in a "navi". */
+.navi_head {
+ font-size: 1.1em;
+ color: #36c;
+ font-weight: bold;
+ margin-bottom: .15em;
+ /*border: 1px solid red;*/
+}
+
+/* Give non-anchors a little breathing space. */
+#navi ul {
+ list-style: none;
+ margin: 0 0 0 0;
+ padding: 0;
+ /*border: 1px solid yellow;*/
+}
+
+#navi li {
+ margin: .25em;
+}
+
+#navi li a {
+ text-decoration: none;
+ display: block;
+ color: #0000c0;
+ background: #f4ecd9;
+ /*border: 1px solid grey;*/
+}
+
+/* Highlight "li"'s "a"s on hover. */
+#navi li a:hover {
+ background: #e0e0e0;
+ /*border-color: #0c0c0c;*/
+}
+
+/* */
+#navi ul li {
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid green;*/
+}
+
+/* */
+#navi ul li ul{
+ text-decoration: none;
+ display: block;
+ margin-left: 1em;
+ /*border: 1px solid orange;*/
+}
+
+/* */
+#navi ul li ul li{
+ font-size: .85em;
+ text-decoration: none;
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid purple;*/
+}
Added: phenote/trunk/doc/phenote-website/css/style.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/style.css 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,195 @@
+/* Style sheet made to go with snugglebunnies. */
+
+/* ---------- Default properties. ---------- */
+body {
+ font-family: arial, helvetica, sans-serif;
+ font-size: 100%;
+ background: white url(/images/bg_image25.jpg) repeat top right;
+ color: black;
+ margin: 0;
+}
+
+/* ---------- "page_head" area. ---------- */
+
+/**/
+#page_head{
+ /*background-image: url(top_image.jpg);*/
+ /*background-repeat: repeat-x;*/
+ /*background: #ebf1fc;*/
+ top: 0px;
+ height: 110px;
+}
+
+.ehead{
+ white-space: nowrap;
+ left: 1em;
+ font-size: 1.25em;
+ font-weight: bold;
+ color: 999999;
+ position: absolute;
+ z-index: 2;
+}
+
+.jhead{
+ white-space: nowrap;
+ position: absolute;
+ left: 5em;
+ top: 1em;
+ font-size: 1.5em;
+ color: #aabbdd;
+ z-index: 1;
+}
+
+.page_logo{
+ left: .1em;
+ top: .1em;
+ position: absolute;
+ /* padding: .25em; */
+}
+
+
+/* ---------- Effects classes. ---------- */
+
+/**/
+.small{
+ font-size: 80%;
+}
+
+.smaller{
+ font-size: 75%;
+}
+
+.smallest{
+ font-size: 50%;
+}
+
+/* ---------- "page_body" class. ---------- */
+
+/**/
+#page_body{
+ padding: 1.5em;
+}
+
+/* ---------- "page_foot" class. ---------- */
+
+/**/
+#page_foot{
+ /*color: #dddddd;*/
+ font-size: .25em;
+ /*float: right;*/
+}
+
+/* ---------- "main_content" class. ---------- */
+
+/**/
+#main_content{
+height: auto;
+ /*background: #f4ecd9;*/
+ background: #f9f9f9;
+ padding-left: 1em;
+ padding-right: 1em;
+ padding-bottom: 1em;
+ margin-left: 12em;
+ -khtml-border-radius: 1em;
+ -moz-border-radius: 1em;
+ -o-border-radius: 1em;
+ border-radius: 4px;
+ border: 2px solid black;
+}
+
+#main_content img{
+ padding-right: 1em;
+ padding-bottom: 1em;
+}
+
+#main_content .portrait {
+ float: left;
+ /*border: 1px solid brown;*/
+}
+
+#main_content .contact{
+ clear: right;
+ /*border: 1px solid brown;*/
+}
+
+/* ---------- "copyright" class. ---------- */
+
+/**/
+.copyright{
+ /*float: right;*/
+ /*border: 5px solid orange;*/
+}
+
+/* ---------- "navi" id. ---------- */
+
+/* Tell us what/where a "navi" is... */
+#navi {
+ /*background: #f4ecd9;*/
+ background: #f9f9f9;
+ float: left;
+ width:8em;
+ padding-top: .5em;
+ padding-bottom: 1em;
+ padding-left: 1em;
+ padding-right: 1em;
+ border: 2px solid blue;
+ padding: 1em;
+ -khtml-border-radius: 1em;
+ -moz-border-radius: 1em;
+ -o-border-radius: 1em;
+ border-radius: 4px;
+ border: 2px solid blue;
+}
+
+/* How to display "h2"s in a "navi". */
+.navi_head {
+ font-size: 1.1em;
+ color: #36c;
+ font-weight: bold;
+ margin-bottom: .15em;
+}
+
+/* Give non-anchors a little breathing space. */
+#navi ul {
+ list-style: none;
+ margin: 0 0 0 0;
+ padding: 0;
+}
+
+#navi li {
+ margin: .25em;
+}
+
+#navi li a {
+ text-decoration: none;
+ display: inline;
+ color: #0000c0;
+ background: #f9f9f9;
+}
+
+/* Highlight "li"'s "a"s on hover. */
+#navi li a:hover {
+ background: #aabbdd;
+ /*background: #e0e0e0;*/
+}
+
+/* */
+#navi ul li {
+ display: block;
+ background: #f9f9f9;
+}
+
+/* */
+#navi ul li ul{
+ text-decoration: none;
+ display: block;
+ margin-left: 1em;
+}
+
+/* */
+#navi ul li ul li{
+ font-size: .85em;
+ text-decoration: none;
+ display: block;
+ background: #f9f9f9;
+}
Added: phenote/trunk/doc/phenote-website/images/NCBO_logo.jpg
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/NCBO_logo.jpg
___________________________________________________________________
Name: svn:executable
+ *
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/doc/phenote-website/images/lbl_logo.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/lbl_logo.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/doc/phenote-website/images/oboedit_logo.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/oboedit_logo.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/doc/phenote-website/index_text.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index_text.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,43 @@
+<!--#include virtual="/ssi/header.html" -->
+
+<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="/ssi/navi_home.html" -->
+
+<div id="main_content">
+<h2>Welcome...</h2>
+<p>
+</p>
+
+<p>
+...to the Berkeley Bioinformatics and Ontologies Project.
+</p>
+
+<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" -->
+
Added: phenote/trunk/doc/phenote-website/javascript/obfuscate.js
===================================================================
--- phenote/trunk/doc/phenote-website/javascript/obfuscate.js (rev 0)
+++ phenote/trunk/doc/phenote-website/javascript/obfuscate.js 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,9 @@
+function obfuscate( domain, name, optionalText )
+{
+ document.write('<a href="mai' + 'lto:' + name + '@' + domain + '">');
+ if (optionalText == "")
+ document.write(name + '@' + domain);
+ else
+ document.write(optionalText);
+ document.write('<\/a>');
+}
Added: phenote/trunk/doc/phenote-website/ssi/footer.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/footer.html (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/footer.html 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1 @@
+
\ No newline at end of file
Added: phenote/trunk/doc/phenote-website/ssi/footer.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/footer.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/footer.shtml 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,23 @@
+<div id="page_foot">
+<div class="contact">
+<!-- TODO add obfuscate.js webmaster stuff here. -->
+</div>
+
+<div class="copyright">
+<!--
+©2006
+-->
+</div>
+
+<div class="last_modified">
+<!--
+<!--#config timefmt="%A %B %d, %Y" -->
+Last modified:
+<!--#echo var="LAST_MODIFIED" -->
+-->
+</div>
+</div>
+
+</body>
+
+</html>
Added: phenote/trunk/doc/phenote-website/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/header.html (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/header.html 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,45 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
+
+<head>
+
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+
+<!-- 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" />
+
+<script type="text/javascript" src="/javascript/obfuscate.js"></script>
+
+<title>Phenote: A Phenotype Annotation Tool</title>
+
+<!-- My comments! -->
+
+</head>
+
+<body>
+
+<div id="page_head">
+
+<div class="ehead">
+<h1>Phenote</h1>
+</div>
+
+<div class="jhead">
+<h1>BBOP</h1>
+</div>
+
+<div class="page_logo">
+<img src="/images/stolen-logo.gif" alt="logo" />
+</div>
+
+</div>
+
Added: phenote/trunk/doc/phenote-website/ssi/navi_about.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_about.html (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/navi_about.html 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,47 @@
+<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>
+
Added: phenote/trunk/doc/phenote-website/ssi/navi_home.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,36 @@
+<div id="navi">
+<div class="navi_head"></div>
+<ul>
+<!-- <li>
+ Home
+--> </li>
+ <li>
+ <a href="/">Home</a>
+ </li>
+ <li>
+ <a href="/content/projects/">Background</a>
+ </li>
+ <li>
+ <a href="/content/software/">Downloads</a>
+ </li>
+ <li>
+ <a href="/content/software/">Documentation</a>
+ </li>
+ <li>
+ <a href="/content/publications/">References</a>
+ </li>
+ <li>
+ <a href="/content/faq/">FAQ</a>
+ </li>
+ <li>
+ <a href="/content/about/">About</a>
+ </li>
+ <li>
+ <a href="/content/links/">Links</a>
+ </li>
+ <li>
+ <a href="/mediawiki">Wiki</a>
+ </li>
+</ul>
+</div>
+
Added: phenote/trunk/doc/phenote-website/ssi/navi_home.html~
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html~ (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html~ 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,36 @@
+<div id="navi">
+<div class="navi_head"></div>
+<ul>
+<!-- <li>
+ Home
+--> </li>
+ <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>
+ </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>
+
Added: phenote/trunk/doc/phenote-website/ssi/navi_publications.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_publications.html (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/navi_publications.html 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,30 @@
+<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: <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: <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: <mg...@us...> - 2007-12-05 20:44:55
|
Revision: 1265
http://obo.svn.sourceforge.net/obo/?rev=1265&view=rev
Author: mgibson
Date: 2007-12-05 12:44:54 -0800 (Wed, 05 Dec 2007)
Log Message:
-----------
webstart for 1.5 release
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote.html
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.html 2007-12-05 20:39:03 UTC (rev 1264)
+++ phenote/trunk/doc/phenote-website/phenote.html 2007-12-05 20:44:54 UTC (rev 1265)
@@ -1,13 +1,11 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
+<html><head>
<meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
- <title>Phenote</title>
-</head>
+ <title>Phenote</title></head>
<body>
@@ -22,15 +20,10 @@
ontologies. It uses term completion to allow curators quick access to
the ontology terms they want to use. <br>
+<br><a href="1.5/phenote.jnlp">Phenote 1.5</a><br>
<br>
-<a href="1.5-beta1/phenote.jnlp">Phenote 1.5-beta1</a><br>
-
-<a href="1.4/phenote.jnlp">Phenote 1.4</a><br>
-
<br>
-<br>
-
After phenote downloads the java jar files (takes a while) it will ask
you what configuration you would like to use, fly, zfin, human,worm,birn....<br>
@@ -299,6 +292,10 @@
+<a href="1.5-beta1/phenote.jnlp">Phenote 1.5-beta1</a><br>
+
+<a href="1.4/phenote.jnlp">Phenote 1.4</a><br>
+
<a href="1.4-beta3/phenote.jnlp">Phenote 1.4-beta3</a><br>
<a href="1.4-beta2/phenote.jnlp">Phenote 1.4-beta2</a><br>
@@ -841,5 +838,4 @@
-</body>
-</html>
+</body></html>
\ No newline at end of file
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-12-05 20:39:03 UTC (rev 1264)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-12-05 20:44:54 UTC (rev 1265)
@@ -30,7 +30,6 @@
<jar href="jars/oboedit.jar" />
<jar href="jars/obo.jar" />
<jar href="jars/bbop.jar" />
- <!-- jar href="jars/org.geneontology.jar" / -->
<jar href="jars/BrowserLauncher2-10rc4.jar" />
<jar href="jars/jsr173_1.0_api.jar" />
<jar href="jars/phenoxmlbeans.jar" />
@@ -51,7 +50,13 @@
<jar href="jars/swingx-2007_10_14.jar"/>
<nativelib href="jars/phenote-nativelibs.jar"/>
+ <!-- jars not needed for webstart(?) axis, commons-beanutils-1.6, commons-discovery,
+ commons-lang, eutils,jaxrpc, jdom, jebl, jhindexer, jlfgr, jnlp, jsp, jsr
+ jst, junit, jwf, layouts, libquaqua, macify? -->
+ <!-- jars needed for phenote2 but not phenote1? idw-gpl, commons*? -->
+
+
<property name="phenote.version" value="@@phenote.version@@"/>
<property name="phenote.build" value="@@phenote.build@@"/>
</resources>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
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>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
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>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
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>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-01-31 00:01:35
|
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>
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>
+
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 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 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...> - 2007-02-01 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 01:12:05
|
Revision: 339
http://svn.sourceforge.net/obo/?rev=339&view=rev
Author: nlw
Date: 2007-01-31 17:11:31 -0800 (Wed, 31 Jan 2007)
Log Message:
-----------
edits to add NCBO logo
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/css/style.css
phenote/trunk/doc/phenote-website/index.shtml
phenote/trunk/doc/phenote-website/ssi/header.html
Modified: phenote/trunk/doc/phenote-website/css/style.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style.css 2007-02-01 01:03:15 UTC (rev 338)
+++ phenote/trunk/doc/phenote-website/css/style.css 2007-02-01 01:11:31 UTC (rev 339)
@@ -22,7 +22,7 @@
.ehead{
white-space: nowrap;
- left: 1em;
+ left: 10em;
font-size: 1.25em;
font-weight: bold;
color: 999999;
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2007-02-01 01:03:15 UTC (rev 338)
+++ phenote/trunk/doc/phenote-website/index.shtml 2007-02-01 01:11:31 UTC (rev 339)
@@ -1,4 +1,4 @@
-<!--#include virtual="//ssi/header.html" -->
+<!--#include virtual="/ssi/header.html" -->
<div id="page_body">
@@ -10,7 +10,7 @@
<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>Data annotated with Phenote is based on the <a href="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 2007-02-01 01:03:15 UTC (rev 338)
+++ phenote/trunk/doc/phenote-website/ssi/header.html 2007-02-01 01:11:31 UTC (rev 339)
@@ -30,7 +30,7 @@
</div>
<div class="page_logo">
-<img src="/phenote/images/" />
+<img src="/phenote/images/NCBO_logo.jpg" />
</div>
</div>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-02-01 01:15:26
|
Revision: 340
http://svn.sourceforge.net/obo/?rev=340&view=rev
Author: nlw
Date: 2007-01-31 17:15:20 -0800 (Wed, 31 Jan 2007)
Log Message:
-----------
added link to ncbo, moving image
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/css/style.css
phenote/trunk/doc/phenote-website/ssi/header.html
Modified: phenote/trunk/doc/phenote-website/css/style.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style.css 2007-02-01 01:11:31 UTC (rev 339)
+++ phenote/trunk/doc/phenote-website/css/style.css 2007-02-01 01:15:20 UTC (rev 340)
@@ -22,7 +22,7 @@
.ehead{
white-space: nowrap;
- left: 10em;
+ left: 1em;
font-size: 1.25em;
font-weight: bold;
color: 999999;
Modified: phenote/trunk/doc/phenote-website/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/header.html 2007-02-01 01:11:31 UTC (rev 339)
+++ phenote/trunk/doc/phenote-website/ssi/header.html 2007-02-01 01:15:20 UTC (rev 340)
@@ -26,11 +26,13 @@
<div id="page_head">
<div class="ehead">
+<br />
+<br />
<h1>Phenote</h1>
</div>
<div class="page_logo">
-<img src="/phenote/images/NCBO_logo.jpg" />
+<a href="http://www.bioontology.org"><img class="portrait" border="0" src="/phenote/images/NCBO_logo.jpg" align="right" /></a>
</div>
</div>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-02-01 01:42:32
|
Revision: 344
http://svn.sourceforge.net/obo/?rev=344&view=rev
Author: nlw
Date: 2007-01-31 17:41:33 -0800 (Wed, 31 Jan 2007)
Log Message:
-----------
adding under construction page, editing the navi home page
Modified Paths:
--------------
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/under_construction.shtml
Added: phenote/trunk/doc/phenote-website/content/under_construction.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/under_construction.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/content/under_construction.shtml 2007-02-01 01:41:33 UTC (rev 344)
@@ -0,0 +1,14 @@
+<!--#include virtual="/ssi/header.html" -->
+
+<div id="page_body">
+
+<!--#include virtual="/ssi/navi_home.html" -->
+
+<div id="main_content">
+
+<h2>This page is under construction</h2>
+
+</div>
+</div>
+
+<!--#include virtual="/ssi/footer.shtml" -->
Modified: phenote/trunk/doc/phenote-website/ssi/navi_home.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-02-01 01:33:58 UTC (rev 343)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-02-01 01:41:33 UTC (rev 344)
@@ -8,25 +8,25 @@
<a href="/">Home</a>
</li>
<li>
- <a href="/phenote/content/info/">Software Info</a>
+ <a href="/content/info/">Software Info</a>
</li>
<li>
- <a href="/phenote/content/software/">Downloads</a>
+ <a href="/content/under_construction.shtml">Downloads</a>
</li>
<li>
- <a href="/phenote/content/howtos/">How-tos</a>
+ <a href="/content/howtos/">How-tos</a>
</li>
<li>
- <a href="/phenote/content/refs/">References</a>
+ <a href="/content/under_construction.shtml">References</a>
</li>
<li>
- <a href="/phenote/content/faq/">FAQ</a>
+ <a href="/content/under_construction.shtml">FAQ</a>
</li>
<li>
- <a href="/phenote/content/about/">About us</a>
+ <a href="/content/about/">About us</a>
</li>
<li>
- <a href="/phenote/content/links/">Links</a>
+ <a href="/content/under_construction.shtml">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~ 2007-02-01 01:33:58 UTC (rev 343)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html~ 2007-02-01 01:41:33 UTC (rev 344)
@@ -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>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-02-01 01:50:45
|
Revision: 345
http://svn.sourceforge.net/obo/?rev=345&view=rev
Author: nlw
Date: 2007-01-31 17:50:44 -0800 (Wed, 31 Jan 2007)
Log Message:
-----------
changing ssis
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/content/about/index.shtml
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
phenote/trunk/doc/phenote-website/index.shtml
phenote/trunk/doc/phenote-website/ssi/navi_howtos.html
phenote/trunk/doc/phenote-website/ssi/navi_info.html
Modified: phenote/trunk/doc/phenote-website/content/about/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/about/index.shtml 2007-02-01 01:41:33 UTC (rev 344)
+++ phenote/trunk/doc/phenote-website/content/about/index.shtml 2007-02-01 01:50:44 UTC (rev 345)
@@ -1,8 +1,8 @@
-<!--#include virtual="/phenote/ssi/header.html" -->
+<!--#include virtual="/ssi/header.html" -->
<div id="page_body">
-<!--#include virtual="/phenote/ssi/navi_home.html" -->
+<!--#include virtual="/ssi/navi_home.html" -->
<div id="main_content">
@@ -53,4 +53,4 @@
</div>
</div>
-<!--#include virtual="/phenote/ssi/footer.shtml" -->
+<!--#include virtual="/ssi/footer.shtml" -->
Modified: phenote/trunk/doc/phenote-website/content/documentation/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/documentation/index.shtml 2007-02-01 01:41:33 UTC (rev 344)
+++ phenote/trunk/doc/phenote-website/content/documentation/index.shtml 2007-02-01 01:50:44 UTC (rev 345)
@@ -1,8 +1,8 @@
-<!--#include virtual="/phenote/ssi/header.html" -->
+<!--#include virtual="/ssi/header.html" -->
<div id="page_body">
-<!--#include virtual="/phenote/ssi/navi_home.html" -->
+<!--#include virtual="/ssi/navi_home.html" -->
<div id="main_content">
@@ -15,4 +15,4 @@
</div>
</div>
-<!--#include virtual="/phenote/ssi/footer.shtml" -->
+<!--#include virtual="/ssi/footer.shtml" -->
Modified: phenote/trunk/doc/phenote-website/content/howtos/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-02-01 01:41:33 UTC (rev 344)
+++ phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-02-01 01:50:44 UTC (rev 345)
@@ -1,8 +1,8 @@
-<!--#include virtual="/phenote/ssi/header.html" -->
+<!--#include virtual="/ssi/header.html" -->
<div id="page_body">
-<!--#include virtual="/phenote/ssi/navi_howtos.html" -->
+<!--#include virtual="/ssi/navi_howtos.html" -->
<div id="main_content">
@@ -57,4 +57,4 @@
</div>
</div>
-<!--#include virtual="/phenote/ssi/footer.shtml" -->
+<!--#include virtual="/ssi/footer.shtml" -->
Modified: phenote/trunk/doc/phenote-website/content/info/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-02-01 01:41:33 UTC (rev 344)
+++ phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-02-01 01:50:44 UTC (rev 345)
@@ -1,8 +1,8 @@
-<!--#include virtual="/phenote/ssi/header.html" -->
+<!--#include virtual="/ssi/header.html" -->
<div id="page_body">
-<!--#include virtual="/phenote/ssi/navi_info.html" -->
+<!--#include virtual="/ssi/navi_info.html" -->
<div id="main_content">
@@ -41,16 +41,16 @@
<br />
<h3><a name="documentation">Documentation</a></h3>
-<p><a href="">Phenotype Annotation User Guide</a></p>
+<p>[A <a href="">Phenotype Annotation User Guide</a> is being developed.]</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>
+<a href="phenote-release-notes.html">[Release Notes]</a>
<br />
</div>
</div>
-<!--#include virtual="/phenote/ssi/footer.shtml" -->
+<!--#include virtual="/ssi/footer.shtml" -->
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2007-02-01 01:41:33 UTC (rev 344)
+++ phenote/trunk/doc/phenote-website/index.shtml 2007-02-01 01:50:44 UTC (rev 345)
@@ -46,5 +46,5 @@
</div>
</div>
-<!--#include virtual="/phenote/ssi/footer.shtml" -->
+<!--#include virtual="/ssi/footer.shtml" -->
Modified: phenote/trunk/doc/phenote-website/ssi/navi_howtos.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_howtos.html 2007-02-01 01:41:33 UTC (rev 344)
+++ phenote/trunk/doc/phenote-website/ssi/navi_howtos.html 2007-02-01 01:50:44 UTC (rev 345)
@@ -5,13 +5,13 @@
Home
--> </li>
<li>
- <a href="/phenote/">Home</a>
+ <a href="/">Home</a>
</li>
<li>
- <a href="/phenote/content/info/">Software Info</a>
+ <a href="/content/info/">Software Info</a>
</li>
<li>
- <a href="/phenote/content/software/">Downloads</a>
+ <a href="/content/under_construction.shtml">Downloads</a>
</li>
<li>
<a href="/phenote/content/howtos/">How-tos</a>
@@ -25,16 +25,16 @@
</ul>
</li>
<li>
- <a href="/phenote/content/refs/">References</a>
+ <a href="/content/under_construction.shtml">References</a>
</li>
<li>
- <a href="/phenote/content/faq/">FAQ</a>
+ <a href="/content/under_construction">FAQ</a>
</li>
<li>
- <a href="/phenote/content/about/">About us</a>
+ <a href="/content/about/">About us</a>
</li>
<li>
- <a href="/phenote/content/links/">Links</a>
+ <a href="/content/under_construction.shtml">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_info.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_info.html 2007-02-01 01:41:33 UTC (rev 344)
+++ phenote/trunk/doc/phenote-website/ssi/navi_info.html 2007-02-01 01:50:44 UTC (rev 345)
@@ -8,7 +8,7 @@
<a href="/">Home</a>
</li>
<li>
- <a href="/phenote/content/info/">Software Info</a>
+ <a href="/content/info/">Software Info</a>
<ul>
<li>
<a href="#features">Features</a>
@@ -22,24 +22,24 @@
<a href="#roadmap">Roadmap</a>
</li>
<li>
- <a href="/phenote/content/info/release_notes.html">Release Notes</a>
+ <a href="/content/info/release_notes.html">Release Notes</a>
</li>
</ul>
</li>
<li>
- <a href="/phenote/content/software/">Downloads</a>
+ <a href="/content/under_construction.shtml">Downloads</a>
</li>
<li>
- <a href="/phenote/content/howtos/">How-tos</a>
+ <a href="/content/howtos/">How-tos</a>
</li>
<li>
- <a href="/phenote/content/refs/">References</a>
+ <a href="/content/under_construction.shtml">References</a>
</li>
<li>
- <a href="/phenote/content/faq/">FAQ</a>
+ <a href="/content/under_construction.shtml">FAQ</a>
</li>
<li>
- <a href="/phenote/content/about/">About us</a>
+ <a href="/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...> - 2007-02-01 17:20:40
|
Revision: 346
http://svn.sourceforge.net/obo/?rev=346&view=rev
Author: nlw
Date: 2007-02-01 09:20:12 -0800 (Thu, 01 Feb 2007)
Log Message:
-----------
adding dicty logo, moving collaboration info from front page
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/content/about/index.shtml
phenote/trunk/doc/phenote-website/index.shtml
Added Paths:
-----------
phenote/trunk/doc/phenote-website/images/go_logo.gif
Modified: phenote/trunk/doc/phenote-website/content/about/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/about/index.shtml 2007-02-01 01:50:44 UTC (rev 345)
+++ phenote/trunk/doc/phenote-website/content/about/index.shtml 2007-02-01 17:20:12 UTC (rev 346)
@@ -41,10 +41,45 @@
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" border="0" /></a>NCBO</p>
-<p><a href="www.berkeleybop.org">Berkeley BOP</a>
+<p>
+Learn more about our supporting organizations by visiting their websites:
+<a href="http://www.bioontology.org">NCBO</a> <br />
+<a href="www.berkeleybop.org">Berkeley BOP</a> <br />
+</p>
+<h3><a name="collaborations">Collaborations</a></h3>
+This software is being developed in collaboration with several organizations:
+<p><a href="http://flybase.bio.indiana.edu/">
+<img class="portrait" height="50" border="0" src="/images/fly_logo.png"\
+ alt="Flybase" /></a>Flybase: The Drosophila Genome Database.
+</p>
+<p><a href="http://www.zfin.org/"><img class="portrait" border="0" src="/im\
+ages/zfin_logo.gif" height="50" alt="Zfin" /></a>ZFIN: The Zebrafish Genome Dat\
+abase
+</p>
+We are also collaborating with several groups:
+<p><a href="http://www.geneontology.org/"><img class="portrait" border="0" src="/images/go_logo.gif" height="50" alt="GO" /></a>The Gene Ontology
+<br />
+<br />
+</p>
+<p><a href="http://www.nescent.org/">
+<img class="portrait" border="0" src="/images/nescent_logo.gif" height="50" alt="Nescent" /></a>NESCENT: The Nati\
+onal Evolutionary Synthesis Center
+<br />
+</p>
+<br />
+<br />
+<p><a href="http://www.pharmgkb.org/"><img class="portrait" border="0" src="/images/pgkb_logo.png" height="50" alt="PharmGKB" /></a>PharmGKB: The Phar\
+macogenetics and Pharmacogenomics Knowledge Base
+<br />
+<br />
+</p>
+<p><a href="http://www.dictybase.org/"><img class="portrait" border="0" src="/images/dicty_logo.png" height="50" alt="Dictybase" /></a>Dictybase
+<br />
+<br />
+</p>
+
+
<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,
Added: phenote/trunk/doc/phenote-website/images/go_logo.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/go_logo.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2007-02-01 01:50:44 UTC (rev 345)
+++ phenote/trunk/doc/phenote-website/index.shtml 2007-02-01 17:20:12 UTC (rev 346)
@@ -5,44 +5,32 @@
<!--#include virtual="/ssi/navi_home.html" -->
<div id="main_content">
-<h1>Phenote: A Phenotype Annotation Tool using Ontologies</h1>
+<h2>Phenote: A Phenotype Annotation Tool using Ontologies</h2>
<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://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://www.fruitfly.org/~cjm/obd/formats.html">EQ model</a> for representing phenotypes, combining entities from any OBO ontology with qualities (such as from <a href="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>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="/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:
+There are two groups driving the development of this software project through the NCBO:
<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.
+<img class="portrait" height="50" border="0" src="/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
+<p><a href="http://www.zfin.org/"><img class="portrait" border="0" src="/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>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-02-01 17:27:39
|
Revision: 347
http://svn.sourceforge.net/obo/?rev=347&view=rev
Author: nlw
Date: 2007-02-01 09:27:29 -0800 (Thu, 01 Feb 2007)
Log Message:
-----------
editing more stuff
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/content/info/index.shtml
phenote/trunk/doc/phenote-website/ssi/navi_info.html
Added Paths:
-----------
phenote/trunk/doc/phenote-website/ssi/navi_about.html
Modified: phenote/trunk/doc/phenote-website/content/info/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-02-01 17:20:12 UTC (rev 346)
+++ phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-02-01 17:27:29 UTC (rev 347)
@@ -46,7 +46,7 @@
<h3><a name="roadmap">Roadmap</a></h3>
<h3><a name="rel_notes">Release Notes</a></h3>
-<a href="phenote-release-notes.html">[Release Notes]</a>
+<a href="/phenote-release-notes.html">[Release Notes]</a>
<br />
Added: phenote/trunk/doc/phenote-website/ssi/navi_about.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_about.html (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/navi_about.html 2007-02-01 17:27:29 UTC (rev 347)
@@ -0,0 +1,52 @@
+<div id="navi">
+<div class="navi_head"></div>
+<ul>
+<!-- <li>
+ Home
+--> </li>
+ <li>
+ <a href="/">Home</a>
+ </li>
+ <li>
+ <a href="/content/info/">Software Info</a>
+ </li>
+ <li>
+ <a href="/content/under_construction.shtml">Downloads</a>
+ </li>
+ <li>
+ <a href="/content/howtos/">How-tos</a>
+ </li>
+ <li>
+ <a href="/content/under_construction.shtml">References</a>
+ </li>
+ <li>
+ <a href="/content/under_construction.shtml">FAQ</a>
+ </li>
+ <li>
+ <a href="/content/about/">About us</a>
+ <ul>
+ <li>
+ <a href="#lists">Mailing Lists</a>
+ </li>
+ <li>
+ <a href="#bugs">Bug Reporting</a>
+ </li>
+ <li>
+ <a href="#contact">Contact us</a>
+ <li>
+ <a href="#collaborations">Collaborations</a>
+ </li>
+ <li>
+ <a href="#funding">Funding Sources</a>
+ </li>
+ </ul>
+ </li>
+ <li>
+ <a href="/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>
+
Modified: phenote/trunk/doc/phenote-website/ssi/navi_info.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_info.html 2007-02-01 17:20:12 UTC (rev 346)
+++ phenote/trunk/doc/phenote-website/ssi/navi_info.html 2007-02-01 17:27:29 UTC (rev 347)
@@ -42,7 +42,7 @@
<a href="/content/about/">About us</a>
</li>
<li>
- <a href="/phenote/content/links/">Links</a>
+ <a href="/content/under_construction.shtml">Links</a>
</li>
<li>
<a href="http://www.bioontology.org/wiki-internal/index.php/Phenote_-_A_Phenotype_Annotation_Tool">Internal Wiki</a>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-02-01 18:12:56
|
Revision: 349
http://svn.sourceforge.net/obo/?rev=349&view=rev
Author: nlw
Date: 2007-02-01 10:12:49 -0800 (Thu, 01 Feb 2007)
Log Message:
-----------
trying out this stylesheet thing
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/content/about/index.shtml
phenote/trunk/doc/phenote-website/css/style.css
Modified: phenote/trunk/doc/phenote-website/content/about/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/about/index.shtml 2007-02-01 17:48:05 UTC (rev 348)
+++ phenote/trunk/doc/phenote-website/content/about/index.shtml 2007-02-01 18:12:49 UTC (rev 349)
@@ -55,7 +55,7 @@
<h3><a name="collaborations">Collaborations</a></h3>
This software is being developed in collaboration with several organizations:
-<table border="0">
+<table border="0" class="collab_table">
<tr>
<td><a href="http://flybase.bio.indiana.edu/">
<img class="portrait" height="50" border="0" src="/images/fly_logo.png"alt="Flybase" /></a>
Modified: phenote/trunk/doc/phenote-website/css/style.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style.css 2007-02-01 17:48:05 UTC (rev 348)
+++ phenote/trunk/doc/phenote-website/css/style.css 2007-02-01 18:12:49 UTC (rev 349)
@@ -110,6 +110,11 @@
#main_content .contact{
clear: right;
/*border: 1px solid brown;*/
+
+#main_content .collab_table{
+align: center;
+col {width: 100;}
+td {align: center; }
}
/* ---------- "copyright" class. ---------- */
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
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