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From: <mg...@us...> - 2007-07-18 19:48:07
|
Revision: 737
http://svn.sourceforge.net/obo/?rev=737&view=rev
Author: mgibson
Date: 2007-07-18 12:48:09 -0700 (Wed, 18 Jul 2007)
Log Message:
-----------
up the mbs - what the hell
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-18 19:45:01 UTC (rev 736)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-18 19:48:09 UTC (rev 737)
@@ -24,7 +24,7 @@
(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" />
+ <j2se version="1.5+" initial-heap-size="64m" max-heap-size="600m" />
<jar href="jars/phenote.jar" />
<jar href="jars/oboedit.jar" />
<jar href="jars/org.geneontology.jar" />
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-18 19:45:01 UTC (rev 736)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-18 19:48:09 UTC (rev 737)
@@ -24,7 +24,7 @@
(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" />
+ <j2se version="1.5+" initial-heap-size="64m" max-heap-size="600m" />
<jar href="jars/phenote.jar" />
<jar href="jars/oboedit.jar" />
<jar href="jars/org.geneontology.jar" />
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-07-18 20:10:23
|
Revision: 741
http://svn.sourceforge.net/obo/?rev=741&view=rev
Author: mgibson
Date: 2007-07-18 13:10:26 -0700 (Wed, 18 Jul 2007)
Log Message:
-----------
and jetty util jar
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-18 20:07:43 UTC (rev 740)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-18 20:10:26 UTC (rev 741)
@@ -38,6 +38,7 @@
<jar href="jars/log4j-1.2.13.jar" />
<jar href="jars/jh.jar" />
<jar href="jars/jetty-6.1.4.jar" />
+ <jar href="jars/jetty-util-6.1.4.jar" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-18 20:07:43 UTC (rev 740)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-18 20:10:26 UTC (rev 741)
@@ -38,6 +38,7 @@
<jar href="jars/log4j-1.2.13.jar" />
<jar href="jars/jh.jar" />
<jar href="jars/jetty-6.1.4.jar" />
+ <jar href="jars/jetty-util-6.1.4.jar" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-07-19 14:15:19
|
Revision: 746
http://svn.sourceforge.net/obo/?rev=746&view=rev
Author: mgibson
Date: 2007-07-19 07:15:21 -0700 (Thu, 19 Jul 2007)
Log Message:
-----------
added swixml jar to jnlp for jims new stuff
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-19 00:23:07 UTC (rev 745)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-19 14:15:21 UTC (rev 746)
@@ -39,6 +39,7 @@
<jar href="jars/jh.jar" />
<jar href="jars/jetty-6.1.4.jar" />
<jar href="jars/jetty-util-6.1.4.jar" />
+ <jar href="jars/swixml.jar" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-19 00:23:07 UTC (rev 745)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-19 14:15:21 UTC (rev 746)
@@ -39,6 +39,7 @@
<jar href="jars/jh.jar" />
<jar href="jars/jetty-6.1.4.jar" />
<jar href="jars/jetty-util-6.1.4.jar" />
+ <jar href="jars/swixml.jar" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-07-19 14:20:39
|
Revision: 747
http://svn.sourceforge.net/obo/?rev=747&view=rev
Author: mgibson
Date: 2007-07-19 07:20:42 -0700 (Thu, 19 Jul 2007)
Log Message:
-----------
swixml needs jdom
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-19 14:15:21 UTC (rev 746)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-19 14:20:42 UTC (rev 747)
@@ -40,6 +40,7 @@
<jar href="jars/jetty-6.1.4.jar" />
<jar href="jars/jetty-util-6.1.4.jar" />
<jar href="jars/swixml.jar" />
+ <jar href="jars/jdom.jar" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-19 14:15:21 UTC (rev 746)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-19 14:20:42 UTC (rev 747)
@@ -40,6 +40,7 @@
<jar href="jars/jetty-6.1.4.jar" />
<jar href="jars/jetty-util-6.1.4.jar" />
<jar href="jars/swixml.jar" />
+ <jar href="jars/jdom.jar" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-07-23 18:37:01
|
Revision: 763
http://svn.sourceforge.net/obo/?rev=763&view=rev
Author: nlw
Date: 2007-07-23 11:36:45 -0700 (Mon, 23 Jul 2007)
Log Message:
-----------
updates to the website to indicate newest features, also release notes
--ssssThis line, and those below, will be ignored--
M phenote-website/phenote-release-notes.html
M phenote-website/content/software/index.shtml
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/content/software/index.shtml
phenote/trunk/doc/phenote-website/phenote-release-notes.html
Modified: phenote/trunk/doc/phenote-website/content/software/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/software/index.shtml 2007-07-20 22:30:59 UTC (rev 762)
+++ phenote/trunk/doc/phenote-website/content/software/index.shtml 2007-07-23 18:36:45 UTC (rev 763)
@@ -8,7 +8,29 @@
<h2>Phenote Software</h2>
-<h3><a name="current">Current Release: 1.3</a> [<a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Webstart</a>] </h3>
+<h3><a name="current">Beta Release: 1.4 beta 2</a> [<a href=="http://www.phenote.org/phenote/1.4-beta2/phenote.jnlp">Webstart</a>] </h3>
+Newest features:
+<ul>
+ <li>feature: RESTful data input for BIRN's smart atlas</li>
+ <li>feature: Character Template for NESCent/CToL (Jim Balhoff).</li>
+ <li>feature: Progress on gui for config (in progress)</li>
+ <li>feature: Progress on field groups (genotype maker, pub querying...)</li>
+ <li>feature: right-click editing functions for free-text fields in data input frame. right-click copy in table.</li>
+ <li>feature: incorporation of help documentation into Phenote under menu item Help->PhenoteHelp </li>
+ <li>feature: added plant_grammene.cfg configuration, plus appropriate obo files.</li>
+ <li>feature: navigation bar added to top of term info; buttons to traverse worn paths; term name moved up to top of box [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1685540&group_id=76834&atid=887913">1685540</a>]</li>
+ <li>feature: dbxrefs are listed in term info (no external links yet) [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1739399&group_id=76834&atid=887913">1739399</a>]</li>
+ <li>change: 'use term' button moved and replaced with checkmark button in navigation bar</li>
+ <li>change: ontology files can be read with dangling references</li>
+ <li>bugfix: obsolete terms were not being read in from annotation files as Ontology.getTerm was only looking at non obsoleted terms</li>
+ <li>known bug: ontology files using import statements not properly read</li>
+</ul>
+
+<p>
+See the <a href="http://www.phenote.org/phenote-release-notes.html">Release Notes</a> for more detailed information.
+</p>
+
+<h3><a name="current">Current Release: 1.3</a> [<a href="http://www.phenote.org/phenote/1.3/phenote.jnlp">Webstart</a>] </h3>
Newest Features:
<ul>
<li>Web-based documentation and Help features</li>
@@ -24,9 +46,6 @@
<li>Can check for updates to ontology files independently from any URL </li>
<li>Obsolete replacements or consideration terms are displayed in term info with links</li>
</ul>
-<p>
-See the <a href="http://www.phenote.org/phenote-release-notes.html">Release Notes</a> for more detailed information.
-</p>
<p>
To download this version with subversion, use the command:
Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-07-20 22:30:59 UTC (rev 762)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-07-23 18:36:45 UTC (rev 763)
@@ -1,53 +1,34 @@
<!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 Release Notes</title>
</head>
-
<body>
-
-
<h1>Phenote Release Notes</h1>
-
-
<h2>1.4 </h2>
07.20.2007, version <a href="phenote/1.4-beta2/phenote.jnlp">1.4-beta2</a></br>
<ul>
- <li>feature: RESTful data input for birn's smart atlas</li>
- <li>feature: Character Template for nescent/ctol (Jim Balhoff). This is an additional window which edits a separate list of characters using a subset of the fields in the main window. The fields to include are denoted by a group in the config file. This functionality will be used by the PhenoMap project to create a specimen list. The same EQ statement can be applied to many specimens at once by selecting the relevant specimens and generating characters in the main window with the template fields pre-filled. All the new characters are selected and can then be bulk edited.</li>
+ <li>feature: RESTful data input for BIRN's smart atlas</li>
+ <li>feature: Character Template for NESCent/CToL (Jim Balhoff). This is an additional window which edits a separate list of characters using a subset of the fields in the main window. The fields to include are denoted by a group in the config file. This functionality will be used by the PhenoMap project to create a specimen list. The same EQ statement can be applied to many specimens at once by selecting the relevant specimens and generating characters in the main window with the template fields pre-filled. All the new characters are selected and can then be bulk edited.</li>
<li>feature: Progress on gui for config (in progress)</li>
<li>feature: Progress on field groups (genotype maker, pub querying...)</li>
<li>feature: right-click editing functions for free-text fields in data input frame. right-click copy in table.</li>
-
<li>feature: incorporation of help documentation into Phenote under menu item Help->PhenoteHelp </li>
-
<li>feature: added plant_grammene.cfg configuration, plus appropriate obo files.</li>
-
<li>feature: navigation bar added to top of term info; buttons to traverse worn paths; term name moved up to top of box [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1685540&group_id=76834&atid=887913">1685540</a>]</li>
-
<li>feature: dbxrefs are listed in term info (no external links yet) [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1739399&group_id=76834&atid=887913">1739399</a>]</li>
-
+ <li>change: ontology files can be read with dangling references</li>
<li>change: Command line read & write of .tab</li>
<li>change: 'use term' button moved and replaced with checkmark button in navigation bar</li>
-
<li>change: ncbo.cfg changed to always update from master file at url</li>
-
<li>change: birn2.cfg gene_ontology replaced with gene_ontology_edit.obo reference</li>
-
<li>change: Windows splash screen text edited from 'biomedial' to 'biomedical'</li>
-
<li>bugfix: obsolete terms were not being read in from annotation files as Ontology.getTerm was only looking at non obsoleted terms</li>
+ <li>known bug: ontology files using import statements not properly read</li>
</ul>
<h3>version 1.4-beta1 - oops - skipped!</h3>
@@ -55,56 +36,25 @@
<h2>1.3</h2>
-
05.24.2007, version <a href="phenote/1.3/phenote.jnlp">1.3 release</a><br>
-
-
<ul>
-
-
<li>feature: <a href="http://www.phenote.org/help/">Web-based documentation and Help features.</a></li>
-
-
<li>feature: Metadata fields added to configuration. User can name their configuration, add a description, and author [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1676756&group_id=76834&atid=887913">1676756</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1672080&group_id=76834&atid=887913">1672080</a>]</li>
-
-
<li>feature: Descriptions can be added for fields </li>
-
-
<li>feature: Master-to-local overwrite stuff</li>
-
-
<li>feature: Dialog allows user to back out of exiting from File->Exit</li>
-
-
<li>feature: Autocompletion search default settings configurable <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1677411&group_id=76834&atid=887913">1677411</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1669579&group_id=76834&atid=887913">1669579</a>]
</li>
-
<li>feature: User can save search setting defaults if changed during Phenote session</li>
-
-
<li>change: File->New is disabled until next version</li>
-
-
<li>change: ncbo, zfin-standalone, flybase, demo configurations
modified to include master-overwrite feature; keeping track of revision
history in file comments </li>
-
-
<li>change: can read http, https, ftp, ftps for ontology update URLs, not just http [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1718945&group_id=76834&atid=887913">1718945</a>]</li>
-
-
<li>bugfix: Bulk-editing functions are working again</li>
-
-
<li>bugfix: Undo wasn't working for several functions due to a bug in the Copy function [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721044&group_id=76834&atid=887913"> 1721044</a>]</li>
-
-
<li>bugfix: multi-select deletes free-text content replaces with * [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721032&group_id=76834&atid=887913">1721032</a>]</li>
-
<li>bugfix: pre 1.2 post comp data wasnt able to load<big> </big>[<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721470&group_id=76834&atid=887913">1721470</a>]</li>
-
-
</ul>
@@ -113,33 +63,14 @@
<ul>
-
-
<li>feature: Added sample config for BIRN</li>
-
-
<li>feature: Added SAO.obo ontology for BIRN</li>
-
-
<li>feature: Namespace config writes back</li>
-
-
<li>feature: Can specify more than one website for ontology update</li>
-
-
<li>feature: Empty field shows all terms in ontology rather than none</li>
-
-
<li>feature: Can add more differentia to post comp</li>
-
-
<li>bugfix: Config update/merge bug where fields in wrong order fixed.</li>
-
-
<li>known bug: can't read post-compositions from phenote versions 1.1 and prior</li>
-
-
-
</ul>
@@ -150,61 +81,25 @@
05.02.2007, version <a href="phenote/1.2/phenote.jnlp">1.2</a><br>
-
-
<ul>
-
-
<li>feature: Can post-compose with >2 terms </li>
-
-
<li>feature: Term history display can be toggled on/off (Settings->Term History menu)</li>
-
-
<li>feature: Synonyms delineated by scope in Term Info: Exact,
Narrow, Broad, General, Related. If the synonym category is given, it
is displayed. For example, the term 'water' has the <i>related</i> synonym H2O, which has the category of a chemical <i>formula</i>.</li>
-
-
<li>feature: Obsolete replacements or consideration terms are displayed in term info with links</li>
-
-
<li>feature: Display term comments in Term Info beneath relationships</li>
-
-
<li>feature: Loading splash screen </li>
-
-
<li>feature: Can configure by namespace for ontologies</li>
-
-
<li>feature: Can automatically update ontologies during startup (configurable)</li>
-
-
<li>feature: Timer added to configuration during ontology update check (configurable)</li>
-
-
<li>feature: Can check which version of phenote is running by selecting Help->About.</li>
-
-
<li>feature: Added common configuration for OMIM curation for use by NCBO (ncbo.cfg).</li>
-
-
<li>feature: can forward and reverse sort columns by repeatedly clicking on column header [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574916&group_id=76834&atid=887913">1574916</a>]</li>
-
-
<li>feature: display ontology namespace in term info box [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1598048&group_id=76834&atid=887913">1598048</a>]</li>
-
-
<li>change: Search filters moved into menu </li>
-
-
<li>change: Updates to the zfin-standalone.cfg for the zebrafish community annotation; only includes GO and ZFanatomy ontologies. </li>
-
-
<li>bugfix: Free-text field text not sticking in "new" or blank rows </li>
-
-
</ul>
@@ -215,15 +110,10 @@
04.06.2007, version <a href="phenote/1.1/phenote.jnlp">1.1.3</a><br>
-
<ul>
-
-
<li>feature: User can change the configuration they want to use at
initialization from file menu; change takes effect after restart.
(previously user had to edit the .phenote/conf/my-phenote file).</li>
-
-
</ul>
@@ -231,65 +121,29 @@
<ul>
-
-
<li>feature: Phenote is now a single webstart app; user chooses
their configuration at startup (used to be hard wired to a
configuration)</li>
-
-
<li>feature: Phenote will merge its default configuration with users' configuration,
preserving user changes as well as adding anything new from phenote
upgrade.</li>
-
-
<li>feature: Beginnings of term history to display recently used ontology terms. Will be clickable in future.</li>
-
-
<li>feature: Data entry panel will spill over into multiple tabs if >12 fields included</li>
-
-
<li>feature: Tab delimited data adapter; data in/output format compatible with excel and other spreadsheet software [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661778&group_id=76834&atid=887913">1661778</a>]</li>
-
-
<li>feature: QueryableDataAdapter interface for developers; enables
connection between input fields and a database backend for quering.
Queryable fields get a retrieve button.</li>
-
-
<li>feature: Autocompletion search with ALL ontologies in a field instead of just one [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1575241&group_id=76834&atid=887913">1575241</a>]</li>
-
-
<li>feature: Retrieve ontology files from URL if more up to date or no local found; only from a single repository for all [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1648337&group_id=76834&atid=887913">1648337</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574906&group_id=76834&atid=887913">1574906</a>]</li>
-
-
<li>feature: fixed releases available for checkout via sourceforge [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1670345&group_id=76834&atid=887913">1670345</a>]</li>
-
-
<li>feature: display xtns in load/save menu choices [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1594508&group_id=76834&atid=887913">1594508</a>]</li>
-
-
<li>change: Refactored code for field guis</li>
-
-
<li>change: Layout improved</li>
-
-
<li>change: OBSOLETE is displayed in red next to obsolete term in term info [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1581589&group_id=76834&atid=887913">1581589</a>]</li>
-
-
<li>change: human.cfg configuration to include obo foundary ontologies GO, SO, CL, ChEBI, PATO, OBI, Relations, unit, and spatial [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1633287&group_id=76834&atid=887913">1633287</a>]</li>
-
-
<li>bugfix: Ontology chooser reflects current term</li>
-
-
<li>bugfix: phenosyntax reader broken [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1684591&group_id=76834&atid=887913">1684591</a>]</li>
-
-
<li>bugfix: post-composed terms not loading [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661728&group_id=76834&atid=887913">1661728</a>]</li>
-
-
</ul>
@@ -312,19 +166,11 @@
field desired, not just E,Q,GC,GT,Pub. Stage, Evidence, Description,
Abnormal, and Absent have been added through this new mechanism in the
newest configurations. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574912&group_id=76834&atid=887913">1574912</a>]</li>
-
-
<li>change: Webby phenote is now using JSP and Spring.</li>
-
-
<li>change: 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.</li>
-
-
<li>bugfix: absent fields not displaying in human 1.03 [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661973&group_id=76834&atid=887913">1661973</a>]</li>
-
-
</ul>
@@ -345,45 +191,24 @@
<li>feature: Undo - can step backward through previous actions</li>
-
-
<li>feature: Quartz scheduler used to schedule when to check for new obo files. Added by Christian Pich of Zfin. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1588669&group_id=76834&atid=887913">1588669</a>]</li>
-
-
<li>change: upgraded PhenoteServlet to Spring framework. Added by Christian Pich [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1588670&group_id=76834&atid=887913">1588670</a>]</li>
-
-
<li>feature: Synonyms are displayed from autocomplete with [syn]; when
selected the term name (not the synonym) goes into the field and table (webby & standalone)</li>
-
-
<li>feature: obsoletes are displayed from autocomplete with [obs]</li>
-
-
<li>feature: Bulk update & copy in standalone. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1579885&group_id=76834&atid=887913">1579885</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1579882&group_id=76834&atid=887913">1579882</a>] </li>
-
-
<li>change: search types interface changed from radio buttons to checkboxes (j. balhoff)</li>
-
-
- <li>bugfix: file-save button changed to say "save" not "load"
- </li>
-
+ <li>bugfix: file-save button changed to say "save" not "load"</li>
<li>feature: file-save recognizes and chooses appropriate data
adapter based on file extension (.psx for phenosyntax and .xml for
phenoxml)</li>
-
-
<li>change: Single quotes escaped for javascript fns.</li>
-
-
</ul>
<h2>0.8
<hr></h2>
-
10.02.2006, version <a href="phenote/0.8/phenote-flybase.jnlp">0.8-fly</a>,
<a href="phenote/0.8/phenote-zfin.jnlp">0.8-zfin</a>,
<a href="http://165.124.152.194/web/html/interface.html">DictyBase
@@ -391,27 +216,13 @@
<ul>
-
-
<li>feature: Added post composition to standalone phenote. </li>
-
-
<li>feature: Actions are logged for both webby/servlet & standalone.</li>
-
-
<li>feature: Pheno-xml reader (thanks to Jim Balhoff) and improvements to pheno-xml
writer (does pub & genetic context)</li>
-
-
<li> feature: Command line reading & writing of phenoxml & phenosyntax.</li>
-
-
<li>feature: Application exits on window exit (unless servlet)</li>
-
-
<li>feature: Can filter out stage terms from zfin anatomy</li>
-
-
</ul>
@@ -428,44 +239,20 @@
<li>feature: entity chooser (web)</li>
-
-
<li>feature: 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).</li>
-
-
<li>feature: entity field and term info installed into zfin (web)
phenotype site. Term info & completion are scrollable.</li>
-
-
<li>feature: standalone version can read & write pheno-syntax with ids & term names in comments</li>
-
-
<li>feature: standalone entity chooser</li>
-
-
<li>feature: added pub field</li>
-
-
<li>feature: added 'use term' button in term info</li>
-
-
<li>feature: can sort table by any field in forward order by clicking on headers</li>
-
-
- <li>change: personal config file gets copied out of jar
- </li>
-
+ <li>change: personal config file gets copied out of jar</li>
<li>change: directory for file load/save remembered</li>
-
-
<li>change: layout fixed</li>
-
-
<li>bugfix: paste for mac fixed</li>
-
-
</ul>
@@ -485,12 +272,8 @@
(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! </li>
-
-
<li> feature: writing pheno-xml format, and uses the latest
PATO ontology (as of July 28, 2006).</li>
-
-
</ul>
@@ -522,19 +305,10 @@
04.26.2006, version <a href="phenote/0.4/phenote-flybase.jnlp">0.4-flybase</a>, <a href="phenote/0.4/phenote-zfin.jnlp">0.4-zfin</a><br>
-
<ul>
-
-
<li>feature: Added Genetic Context field.</li>
-
-
<li>feature: Parent & child terms in term info are now clickable/navigable.</li>
-
-
<li>feature: HTML Links in descriptions are clickable (should bring up default browser)</li>
-
-
<li>feature: configuration files 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.
@@ -542,14 +316,8 @@
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.</li>
-
-
<li>bugfix: can't delete to 0 rows</li>
-
-
<li>bugfix: synonym search duplicates removed</li>
-
-
<li>Development: 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
@@ -557,15 +325,8 @@
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.</li>
-
-
<li>Development: Renamed Phenotype to Character. Added Character interface CharacterI.</li>
-
-
<li>Development: Added tests to test suite.</li>
-
-
-
</ul>
@@ -593,60 +354,24 @@
<ul>
-
-
<li>feature: Completion terms now sorted alphabeitcally.</li>
-
-
<li>feature: Obsoletes are now in addition to regular terms, not in lieu of.</li>
-
-
<li>feature: Filtering out attribute values (todo: change to actually filter in
values)</li>
-
-
<li>change: Html formatting of term info (todo: make terms selectable)</li>
-
-
<li>feature: Children relations are in term info</li>
-
-
<li>change: Term info layout greatly improved</li>
-
-
<li>change: Term info in scroller</li>
-
-
<li>change: Border with label around term info</li>
-
-
<li>change: Put definition at end of term info</li>
-
-
<li>bugfix: Backspace in ontology combo box</li>
-
-
<li>bugfix: Selection of item in comp list causing exception, not going in term box</li>
-
-
<li>bugfix: No terms with just 1 char</li>
-
-
<li>bugfix: Popup was staying up after selection</li>
-
-
<li>development: Test suite added! (todo: add more tests)</li>
-
-
<li>development: Migrated to jdk 1.5 (which caused some of the bugs above)</li>
-
-
<li>development: Ant file made build.xml.</li>
-
-
<li>development: CompletionList refactored into Ontology (prompted by sorting)</li>
-
-
</ul>
@@ -659,23 +384,13 @@
<ul>
-
-
<li>feature: term completion on Synonyms, Definitions and Obsoletes</li>
-
-
<li>feature: mouse-over on term in completion list displays info in 'term info' text area</li>
-
-
<li>Todo: layout, scrollbar, border w title, ordering & lumping
parents
& children, formatting. Also perhaps have children & parents be
clickable in some fashion either html-like clickable text or as buttons.</li>
-
-
<li>known bugs: If you hit backspace in term completion fields it gets wacky </li>
-
-
</ul>
@@ -693,7 +408,5 @@
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.</p>
-
-
</body>
</html>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-07-23 19:03:33
|
Revision: 765
http://svn.sourceforge.net/obo/?rev=765&view=rev
Author: nlw
Date: 2007-07-23 12:03:23 -0700 (Mon, 23 Jul 2007)
Log Message:
-----------
slimmed the navi menus, added a screen shot, fixed some links,
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/content/about/index.shtml
phenote/trunk/doc/phenote-website/content/info/index.shtml
phenote/trunk/doc/phenote-website/content/software/index.shtml
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_info.html
Added Paths:
-----------
phenote/trunk/doc/phenote-website/images/phenote_screenshot.png
Modified: phenote/trunk/doc/phenote-website/content/about/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/about/index.shtml 2007-07-23 19:01:29 UTC (rev 764)
+++ phenote/trunk/doc/phenote-website/content/about/index.shtml 2007-07-23 19:03:23 UTC (rev 765)
@@ -11,8 +11,10 @@
<h3><a name="lists">Mailing lists</a></h3>
<p>There are several mailing lists pertaining to Phenote:</p>
<ul>
- <li>Join in on discussions pertaining to Phenote by <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">subscribing to the mailing list</a>
+ <li>Join in on discussions pertaining to Phenote for the users: <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">subscribing to the mailing list</a>
</li>
+<li>If you are interested in the software development issues: <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-dev">subscribing to the dev mailing list</a>
+ </li>
<li>Keep on top of changes to phenote. Join the
<ul>
<li><a href="https://lists.sourceforge.net/lists/listinfo/obo-svn-commit">svn commit mailing list</a>
@@ -27,7 +29,8 @@
<h3><a name="Bugs">Bug Reporting</a></h3>
<p>If you find bugs in Phenote, please <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">submit a bug report</a> on our Bug Tracker located on sourceforge.</p>
-<p>Please use this same tracker to submit your enhancement and feature requests.</p>
+<p>If you are submitting a bug, please note what version you are using.</p>
+<p>If you are submitting a feature request, please select "new feature" from the "group" menu.</p>
<br />
Modified: phenote/trunk/doc/phenote-website/content/info/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-07-23 19:01:29 UTC (rev 764)
+++ phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-07-23 19:03:23 UTC (rev 765)
@@ -38,26 +38,19 @@
Visit our <a href="/content/software/">Downloads</a> page to get the latest version of Phenote.
</p>
-<h3><a name="web_users">Websites Utilizing Phenote Software Components</a></h3>
-<p>The Dictyostelium Genome Database, <a href="http://dictybase.org">
-DictyBase</a>, has a web-based
-<a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">Phenotype Annotation Tool</a> that is directly linked to their own database backend.</p>
+<h3><a name="screenshot">Screenshot</a></h3>
+<img class="portrait" height="50" border="0" src="/images/phenote_screenshot.png" alt="Screenshot" />
<br />
-<p>
-<a href="http://zfin.org">Zfin</a> has an integrated phenotype annotation tool in their internal website. [screenshot or link to be added].
-</p>
-<br />
<h3><a name="documentation">Documentation</a></h3>
-<p>[A <a href="">Phenotype Annotation User Guide</a> is being developed.]</p>
+<p>Browse the <a href="http://www.phenote.org/help">Phenote on-line documentation</a> </p>
<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>
+To keep up-to-date on information about the latest release, please read our <a href="/phenote-release-notes.html">[Release Notes]</a>.
<br />
-
</div>
</div>
Modified: phenote/trunk/doc/phenote-website/content/software/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/software/index.shtml 2007-07-23 19:01:29 UTC (rev 764)
+++ phenote/trunk/doc/phenote-website/content/software/index.shtml 2007-07-23 19:03:23 UTC (rev 765)
@@ -63,7 +63,7 @@
You can also browse the subversion repository at: <br /> https://obo.svn.sourceforge.net/viewvc/obo/phenote/
</p>
<p>
-For instructions on running Phenote, or downloading the sourcecode, visit our <a href="/content/howtos">How-to pages</a> our our new <a href="www.phenote.org/help">HELP</a> pages.
+For instructions on running Phenote, or downloading the sourcecode, visit our <a href="/content/howtos">How-to pages</a> our our new <a href="http://www.phenote.org/help">HELP</a> pages.
</p>
Added: phenote/trunk/doc/phenote-website/images/phenote_screenshot.png
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/phenote_screenshot.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Modified: phenote/trunk/doc/phenote-website/ssi/navi_about.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_about.html 2007-07-23 19:01:29 UTC (rev 764)
+++ phenote/trunk/doc/phenote-website/ssi/navi_about.html 2007-07-23 19:03:23 UTC (rev 765)
@@ -14,15 +14,9 @@
<a href="/content/software/">Downloads</a>
</li>
<li>
- <a href="/content/howtos/">How-tos</a>
+ <a href="http://www.phenote.org/help/">User's Guide</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>
@@ -41,9 +35,6 @@
</li>
</ul>
</li>
- <li>
- <a href="/content/links/">Links</a>
- </li>
<li>
<a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page">Working Group</a>
</li>
Modified: phenote/trunk/doc/phenote-website/ssi/navi_home.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-07-23 19:01:29 UTC (rev 764)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-07-23 19:03:23 UTC (rev 765)
@@ -11,21 +11,12 @@
<a href="/content/software/">Downloads</a>
</li>
<li>
- <a href="/content/howtos/">How-tos</a>
+ <a href="http://www.phenote.org/help/">User's Guide</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>
</li>
<li>
- <a href="/content/under_construction.shtml">Links</a>
- </li>
- <li>
<a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page">Working Group</a>
</li>
<li>
Modified: phenote/trunk/doc/phenote-website/ssi/navi_info.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_info.html 2007-07-23 19:01:29 UTC (rev 764)
+++ phenote/trunk/doc/phenote-website/ssi/navi_info.html 2007-07-23 19:03:23 UTC (rev 765)
@@ -14,15 +14,15 @@
<a href="#features">Features</a>
</li>
<li>
- <a href="#web_users">Web Examples</a>
+ <a href="#screenshot">Screenshot</a>
</li>
<li>
- <a href="#documentation">Documentation</a>
+ <a href="#documentation">User's Guide</a>
<li>
<a href="#roadmap">Roadmap</a>
</li>
<li>
- <a href="/content/info/release_notes.html">Release Notes</a>
+ <a href="/phenote_release_notes.html">Release Notes</a>
</li>
</ul>
</li>
@@ -30,20 +30,11 @@
<a href="/content/software/">Downloads</a>
</li>
<li>
- <a href="/content/howtos/">How-tos</a>
+ <a href="http://www.phenote.org/help/">User's Guide</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>
</li>
- <li>
- <a href="/content/under_construction.shtml">Links</a>
- </li>
<li>
<a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page">Working Group</a>
</li>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-08-30 20:04:23
|
Revision: 858
http://obo.svn.sourceforge.net/obo/?rev=858&view=rev
Author: mgibson
Date: 2007-08-30 13:04:20 -0700 (Thu, 30 Aug 2007)
Log Message:
-----------
added quaqua jar to webstart jnlp
but i think theres gonna be issues with the jnilib for qua qua
dont know how to slip that into webstart
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-08-30 18:17:27 UTC (rev 857)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-08-30 20:04:20 UTC (rev 858)
@@ -41,6 +41,7 @@
<jar href="jars/jetty-util-6.1.4.jar" />
<jar href="jars/swixml.jar" />
<jar href="jars/jdom.jar" />
+ <jar href="jars/quaqua.jar" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-08-30 18:17:27 UTC (rev 857)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-08-30 20:04:20 UTC (rev 858)
@@ -41,6 +41,7 @@
<jar href="jars/jetty-util-6.1.4.jar" />
<jar href="jars/swixml.jar" />
<jar href="jars/jdom.jar" />
+ <jar href="jars/quaqua.jar" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-12 21:11:36
|
Revision: 879
http://obo.svn.sourceforge.net/obo/?rev=879&view=rev
Author: nlw
Date: 2007-09-12 14:11:39 -0700 (Wed, 12 Sep 2007)
Log Message:
-----------
couple of changes
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/images/elephant_icon3.jpg
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/images/elephant_icon3.jpg
===================================================================
(Binary files differ)
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-09-12 21:08:41 UTC (rev 878)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-09-12 21:11:39 UTC (rev 879)
@@ -6,6 +6,7 @@
<information>
<title>Phenote @@phenote.version@@</title>
<vendor>National Center for Biomedical Ontology</vendor>
+ <icon href="images/phenote_logo.jpg" />
<description>Phenote standalone app via webstart</description>
<!-- Declares that the application can run without
access to the server it was downloaded from -->
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-14 00:23:05
|
Revision: 887
http://obo.svn.sourceforge.net/obo/?rev=887&view=rev
Author: nlw
Date: 2007-09-13 17:23:09 -0700 (Thu, 13 Sep 2007)
Log Message:
-----------
added some pages, took some away
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/download.shtml
phenote/trunk/doc/phenote-website/new/download.shtml~
phenote/trunk/doc/phenote-website/new/release-notes.shtml
phenote/trunk/doc/phenote-website/new/team.shtml
Added Paths:
-----------
phenote/trunk/doc/phenote-website/images/BIRN_logo.gif
phenote/trunk/doc/phenote-website/images/xenbase_logo.gif
phenote/trunk/doc/phenote-website/new/screenshots.shtml
phenote/trunk/doc/phenote-website/new/users.shtml
Removed Paths:
-------------
phenote/trunk/doc/phenote-website/new/browse.shtml
phenote/trunk/doc/phenote-website/new/browse.shtml.~1.3.~
phenote/trunk/doc/phenote-website/new/join.shtml
phenote/trunk/doc/phenote-website/new/lit.shtml~
phenote/trunk/doc/phenote-website/new/literature.shtml
phenote/trunk/doc/phenote-website/new/literature.shtml.~1.3.~
phenote/trunk/doc/phenote-website/new/mappings.txt
Added: phenote/trunk/doc/phenote-website/images/BIRN_logo.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/BIRN_logo.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/doc/phenote-website/images/xenbase_logo.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/xenbase_logo.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Deleted: phenote/trunk/doc/phenote-website/new/browse.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/browse.shtml 2007-09-13 23:39:28 UTC (rev 886)
+++ phenote/trunk/doc/phenote-website/new/browse.shtml 2007-09-14 00:23:09 UTC (rev 887)
@@ -1,397 +0,0 @@
-<!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">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Open Biomedical Ontologies Foundry</title>
-
- <script src="js/enhancer.js" type="text/javascript"></script>
- <link href="css/enhancer.css"
- media="all"
- rel="Stylesheet"
- type="text/css" />
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
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- Ontology Browser
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- <p>
- Browse the tree by clicking on the category names; click on
- an ontology name to view more information on it.
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- <ul>
- <li>
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- <a id="anat_page" class="page" href="#anat"><img src="images/minus.gif" title="Close node" alt="-" id="anatImg"> anatomy</a>
- <ul id="anat">
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell"><img src="images/arrow.gif" alt="->"> cell type</a>
- </li>
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- <a id="gross_page" class="page" href="#gross"><img src="images/minus.gif" title="Close node" alt="-" id="grossImg"> gross anatomy</a>
- <ul id="gross">
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- <a id="animanat_page" class="page" href="#animanat"><img src="images/minus.gif" title="Close node" alt="-" id="animanatImg"> animal gross anatomy</a>
- <ul id="animanat">
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=worm_anatomy"><img src="images/arrow.gif" alt="->"> C. elegans gross anatomy</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_anatomy"><img src="images/arrow.gif" alt="->"> Drosophila gross anatomy</a>
- </li>
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- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=evoc"><img src="images/arrow.gif" alt="->"> eVoc (Expressed Sequence Annotation for Humans)</a>
- </li>
- <li>
- <a id="fishanat_page" class="page" href="#fishanat"><img src="images/minus.gif" title="Close node" alt="-" id="fishanatImg"> fish anatomy</a>
- <ul id="fishanat">
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=medaka_anatomy_development"><img src="images/arrow.gif" alt="->"> Medaka fish anatomy and development</a>
- </li>
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=zebrafish_anatomy"><img src="images/arrow.gif" alt="->"> Zebrafish anatomy and development</a>
- </li>
- </ul>
- </li>
- <li>
- <a id="humanat_page" class="page" href="#humanat"><img src="images/minus.gif" title="Close node" alt="-" id="humanatImg"> human developmental anatomy</a>
- <ul id="humanat">
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- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=human-dev-anat-staged"><img src="images/arrow.gif" alt="->"> Human developmental anatomy, timed</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=human-dev-anat-abstract"><img src="images/arrow.gif" alt="->"> Human developmental anatomy, abstract</a>
- </li>
- </ul>
- </li>
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=mosquito_anatomy"><img src="images/arrow.gif" alt="->"> Mosquito gross anatomy</a>
- </li>
- <li>
- <a id="musanat_page" class="page" href="#musanat"><img src="images/minus.gif" title="Close node" alt="-" id="musanatImg"> mouse anatomy</a>
- <ul id="musanat">
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=adult_mouse_anatomy"><img src="images/arrow.gif" alt="->"> Mouse adult anatomy</a>
- </li>
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=emap"><img src="images/arrow.gif" alt="->"> Mouse anatomy and development</a>
- </li>
- </ul>
- </li>
- </ul>
- </li>
- <li>
-
- <a id="microanat_page" class="page" href="#microanat"><img src="images/minus.gif" title="Close node" alt="-" id="microanatImg"> microbial anatomy</a>
- <ul id="microanat">
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=fungal_anatomy"><img src="images/arrow.gif" alt="->"> Fungal anatomy</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=dictyostelium_discoideum_anatomy"><img src="images/arrow.gif" alt="->"> Dictyostelium anatomy</a>
- </li>
-
- </ul>
- </li>
- <li>
- <a id="plantant_page" class="page" href="#plantant"><img src="images/minus.gif" title="Close node" alt="-" id="plantantImg"> plant anatomy</a>
- <ul id="plantant">
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=cereal_anatomy"><img src="images/arrow.gif" alt="->"> Cereal anatomy</a>
- </li>
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=zea_mays_anatomy"><img src="images/arrow.gif" alt="->"> Maize anatomy</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=po_anatomy"><img src="images/arrow.gif" alt="->"> Plant anatomy</a>
- </li>
- </ul>
- </li>
-
- </ul>
- </li>
- <li>
- <img src="images/x.gif" alt="X"> organ
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=brenda"><img src="images/arrow.gif" alt="->"> BRENDA tissue / enzyme source</a>
- </li>
-
- </ul>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=animalhist"><img src="images/arrow.gif" alt="->"> animal natural history and life history</a>
- </li>
- <li>
- <a id="biochem_page" class="page" href="#biochem"><img src="images/minus.gif" title="Close node" alt="-" id="biochemImg"> chemical</a>
- <ul id="biochem">
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=chebi"><img src="images/arrow.gif" alt="->"> chemical entities of biological interest</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=fix"><img src="images/arrow.gif" alt="->"> physico-chemical methods and properties</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=rex"><img src="images/arrow.gif" alt="->"> physico-chemical process</a>
- </li>
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=systems_biology"><img src="images/arrow.gif" alt="->"> systems biology</a>
- </li>
- </ul>
- </li>
- <li>
- <a id="time_page" class="page" href="#time"><img src="images/minus.gif" title="Close node" alt="-" id="timeImg"> development</a>
- <ul id="time">
-
- <li>
- <a id="animatime_page" class="page" href="#animatime"><img src="images/minus.gif" title="Close node" alt="-" id="animatimeImg"> animal development</a>
- <ul id="animatime">
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=worm_development"><img src="images/arrow.gif" alt="->"> C. elegans development</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_development"><img src="images/arrow.gif" alt="->"> Drosophila development</a>
- </li>
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=evoc"><img src="images/arrow.gif" alt="->"> eVOC (Expressed Sequence Annotation for Humans)</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=medaka_anatomy_development"><img src="images/arrow.gif" alt="->"> medaka fish anatomy and development</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=emap"><img src="images/arrow.gif" alt="->"> Mouse anatomy and development</a>
- </li>
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=plasmodium_life_cycle"><img src="images/arrow.gif" alt="->"> Plasmodium life cycle</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=zebrafish_anatomy"><img src="images/arrow.gif" alt="->"> Zebrafish anatomy and development</a>
- </li>
- </ul>
- </li>
-
- <li>
- <a id="planttime_page" class="page" href="#planttime"><img src="images/minus.gif" title="Close node" alt="-" id="planttimeImg"> plant development</a>
- <ul id="planttime">
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=po_temporal"><img src="images/arrow.gif" alt="->"> plant growth and developmental stage</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=temporal_gramene"><img src="images/arrow.gif" alt="->"> cereal plant development</a>
- </li>
-
- </ul>
- </li>
- </ul>
- </li>
- <li>
- <a id="etho_page" class="page" href="#etho"><img src="images/minus.gif" title="Close node" alt="-" id="ethoImg"> ethology</a>
- <ul id="etho">
- <li>
-
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=habronattus_courtship"><img src="images/arrow.gif" alt="->"> Habronattus courtship</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=loggerhead_nesting"><img src="images/arrow.gif" alt="->"> Loggerhead nesting</a>
- </li>
- </ul>
- </li>
- <li>
-
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=evidence_code"><img src="images/arrow.gif" alt="->"> evidence codes</a>
- </li>
- <li>
- <a id="expr_page" class="page" href="#expr"><img src="images/minus.gif" title="Close node" alt="-" id="exprImg"> experimental conditions</a>
- <ul id="expr">
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=image"><img src="images/arrow.gif" alt="->"> biological imaging methods</a>
- </li>
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=mged"><img src="images/arrow.gif" alt="->"> microarray experimental conditions</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=nmr"><img src="images/arrow.gif" alt="->"> nuclear magnetic resonance experiment conditions</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=obi"><img src="images/arrow.gif" alt="->"> ontology for biomedical investigations</a>
- </li>
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=fix"><img src="images/arrow.gif" alt="->"> physico-chemical methods and properties</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=sep"><img src="images/arrow.gif" alt="->"> sample processing and separation techniques</a>
- </li>
- </ul>
-
- </li>
- <li>
- <a id="geno_page" class="page" href="#geno"><img src="images/minus.gif" title="Close node" alt="-" id="genoImg"> genomic and proteomic</a>
- <ul id="geno">
- <li>
- <a id="gp_page" class="page" href="#gp"><img src="images/minus.gif" title="Close node" alt="-" id="gpImg"> gene product</a>
- <ul id="gp">
- <li>
-
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=biological_process"><img src="images/arrow.gif" alt="->"> biological process</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=cellular_component"><img src="images/arrow.gif" alt="->"> cellular component</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=event"><img src="images/arrow.gif" alt="->"> event</a>
- </li>
-
- <li>
- <img src="images/x.gif" alt="X"> gene product name
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=molecular_function"><img src="images/arrow.gif" alt="->"> molecular function</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=molecule_role"><img src="images/arrow.gif" alt="->"> molecule role</a>
- </li>
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=mao"><img src="images/arrow.gif" alt="->"> multiple alignment</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=pathway"><img src="images/arrow.gif" alt="->"> pathway</a>
- </li>
- <li>
- <a id="prot_page" class="page" href="#prot"><img src="images/minus.gif" title="Close node" alt="-" id="protImg"> protein</a>
- <ul id="prot">
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=cob"><img src="images/arrow.gif" alt="->"> protein covalent bond</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=interpro"><img src="images/arrow.gif" alt="->"> protein domain</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=psi-mod"><img src="images/arrow.gif" alt="->"> protein modification</a>
- </li>
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=psi-mi"><img src="images/arrow.gif" alt="->"> protein-protein interaction</a>
- </li>
- </ul>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=provenance"><img src="images/arrow.gif" alt="->"> proteomics data and process provenance</a>
- </li>
-
- </ul>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=sequence"><img src="images/arrow.gif" alt="->"> sequence types and features</a>
- </li>
- </ul>
- </li>
- <li>
-
- <a id="meta_page" class="page" href="#meta"><img src="images/minus.gif" title="Close node" alt="-" id="metaImg"> metabolomics</a>
- <ul id="meta">
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=nmr"><img src="images/arrow.gif" alt="->"> nuclear magnetic resonance experiment conditions</a>
- </li>
- </ul>
- </li>
- <li>
-
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=relationship"><img src="images/arrow.gif" alt="->"> OBO relationship types</a>
- </li>
- <li>
- <a id="pheno_page" class="page" href="#pheno"><img src="images/minus.gif" title="Close node" alt="-" id="phenoImg"> phenotype</a>
- <ul id="pheno">
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=plant_trait"><img src="images/arrow.gif" alt="->"> cereal plant trait</a>
- </li>
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=evoc"><img src="images/arrow.gif" alt="->"> eVOC (Expressed Sequence Annotation for Humans)</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=disease_ontology"><img src="images/arrow.gif" alt="->"> human diseases</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype"><img src="images/arrow.gif" alt="->"> mammalian phenotype</a>
- </li>
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=medaka_anatomy_development"><img src="images/arrow.gif" alt="->"> medaka fish anatomy and development</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=mouse_pathology"><img src="images/arrow.gif" alt="->"> mouse pathology</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=plant_environment"><img src="images/arrow.gif" alt="->"> plant enviromental conditions</a>
- </li>
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=quality"><img src="images/arrow.gif" alt="->"> PATO</a>
- </li>
- </ul>
- </li>
- <li>
- <a id="taxo_page" class="page" href="#taxo"><img src="images/minus.gif" title="Close node" alt="-" id="taxoImg"> taxonomic classification</a>
- <ul id="taxo">
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncbi_taxonomy"><img src="images/arrow.gif" alt="->"> NCBI organismal classification</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=newt"><img src="images/arrow.gif" alt="->"> SwissProt organismal classification</a>
- </li>
- </ul>
- </li>
-
- <li>
- <a id="vocab_page" class="page" href="#vocab"><img src="images/minus.gif" title="Close node" alt="-" id="vocabImg"> vocabularies</a>
- <ul id="vocab">
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=flybase_vocab"><img src="images/arrow.gif" alt="->"> FlyBase controlled vocabulary</a>
- </li>
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=mesh"><img src="images/arrow.gif" alt="->"> MESH</a>
- </li>
-
- <li>
- <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncithesaurus"><img src="images/arrow.gif" alt="->"> NCI Thesaurus</a>
- </li>
- </ul>
- </li>
- </ul>
- </div>
-
-
-
-
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- </div>
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-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
- "http://www.w3.org/TR/html4/strict.dtd">
-<html>
-<head>
- <title>Browse the OBO Ontologies</title>
- <link href="/css/stylesheet.css" rel="stylesheet" type="text/css">
- <meta http-equiv="content-type" content="text/html; charset=iso-8859-1">
- <meta name="description" content="Hierarchical browser of the ontologies available from OBO">
-<script src="enhancer.js" type="text/javascript"></script>
-</head>
-<body>
-
-<div id="header">
- <h1>the obo foundry </h1>
-</div>
-
-<div id="content">
-
-<!--#include virtual="/ssi/navi_bar.html" -->
-
-<div class="main-text">
- <h2>Ontology Browser</h2>
- <p>
- Browse the tree by clicking on the category names; click on an ontology name to view more information on it.
- </p>
- <div class="browser" id="tree">
- <ul>
- <li>
- <a id="anat_page" class="page" href="#anat"><img src="images/minus.gif" title="Close node" alt="-" id="anatImg"> anatomy</a>
- <ul id="anat">
- <li>
- <a href="../cgi-bin/detail.cgi?id=cell"><img src="images/arrow.gif" alt="->"> cell type</a>
- </li>
- <li>
- <a id="gross_page" class="page" href="#gross"><img src="images/minus.gif" title="Close node" alt="-" id="grossImg"> gross anatomy</a>
- <ul id="gross">
- <li>
- <a id="animanat_page" class="page" href="#animanat"><img src="images/minus.gif" title="Close node" alt="-" id="animanatImg"> animal gross anatomy</a>
- <ul id="animanat">
- <li>
- <a href="../cgi-bin/detail.cgi?id=worm_anatomy"><img src="images/arrow.gif" alt="->"> C. elegans gross anatomy</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=fly_anatomy"><img src="images/arrow.gif" alt="->"> Drosophila gross anatomy</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=evoc"><img src="images/arrow.gif" alt="->"> eVoc (Expressed Sequence Annotation for Humans)</a>
- </li>
- <li>
- <a id="fishanat_page" class="page" href="#fishanat"><img src="images/minus.gif" title="Close node" alt="-" id="fishanatImg"> fish anatomy</a>
- <ul id="fishanat">
- <li>
- <a href="../cgi-bin/detail.cgi?id=medaka_anatomy_development"><img src="images/arrow.gif" alt="->"> Medaka fish anatomy and development</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=zebrafish_anatomy"><img src="images/arrow.gif" alt="->"> Zebrafish anatomy and development</a>
- </li>
- </ul>
- </li>
- <li>
- <a id="humanat_page" class="page" href="#humanat"><img src="images/minus.gif" title="Close node" alt="-" id="humanatImg"> human developmental anatomy</a>
- <ul id="humanat">
- <li>
- <a href="../cgi-bin/detail.cgi?id=human-dev-anat-staged"><img src="images/arrow.gif" alt="->"> Human developmental anatomy, timed</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=human-dev-anat-abstract"><img src="images/arrow.gif" alt="->"> Human developmental anatomy, abstract</a>
- </li>
- </ul>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=mosquito_anatomy"><img src="images/arrow.gif" alt="->"> Mosquito gross anatomy</a>
- </li>
- <li>
- <a id="musanat_page" class="page" href="#musanat"><img src="images/minus.gif" title="Close node" alt="-" id="musanatImg"> mouse anatomy</a>
- <ul id="musanat">
- <li>
- <a href="../cgi-bin/detail.cgi?id=adult_mouse_anatomy"><img src="images/arrow.gif" alt="->"> Mouse adult anatomy</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=emap"><img src="images/arrow.gif" alt="->"> Mouse anatomy and development</a>
- </li>
- </ul>
- </li>
- </ul>
- </li>
- <li>
- <a id="microanat_page" class="page" href="#microanat"><img src="images/minus.gif" title="Close node" alt="-" id="microanatImg"> microbial anatomy</a>
- <ul id="microanat">
- <li>
- <a href="../cgi-bin/detail.cgi?id=fungal_anatomy"><img src="images/arrow.gif" alt="->"> Fungal anatomy</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=dictyostelium_discoideum_anatomy"><img src="images/arrow.gif" alt="->"> Dictyostelium anatomy</a>
- </li>
- </ul>
- </li>
- <li>
- <a id="plantant_page" class="page" href="#plantant"><img src="images/minus.gif" title="Close node" alt="-" id="plantantImg"> plant anatomy</a>
- <ul id="plantant">
- <li>
- <a href="../cgi-bin/detail.cgi?id=cereal_anatomy"><img src="images/arrow.gif" alt="->"> Cereal anatomy</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=zea_mays_anatomy"><img src="images/arrow.gif" alt="->"> Maize anatomy</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=po_anatomy"><img src="images/arrow.gif" alt="->"> Plant anatomy</a>
- </li>
- </ul>
- </li>
- </ul>
- </li>
- <li>
- <img src="images/x.gif" alt="X"> organ
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=brenda"><img src="images/arrow.gif" alt="->"> BRENDA tissue / enzyme source</a>
- </li>
- </ul>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=animalhist"><img src="images/arrow.gif" alt="->"> animal natural history and life history</a>
- </li>
- <li>
- <a id="biochem_page" class="page" href="#biochem"><img src="images/minus.gif" title="Close node" alt="-" id="biochemImg"> chemical</a>
- <ul id="biochem">
- <li>
- <a href="../cgi-bin/detail.cgi?id=chebi"><img src="images/arrow.gif" alt="->"> chemical entities of biological interest</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=fix"><img src="images/arrow.gif" alt="->"> physico-chemical methods and properties</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=rex"><img src="images/arrow.gif" alt="->"> physico-chemical process</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=systems_biology"><img src="images/arrow.gif" alt="->"> systems biology</a>
- </li>
- </ul>
- </li>
- <li>
- <a id="time_page" class="page" href="#time"><img src="images/minus.gif" title="Close node" alt="-" id="timeImg"> development</a>
- <ul id="time">
- <li>
- <a id="animatime_page" class="page" href="#animatime"><img src="images/minus.gif" title="Close node" alt="-" id="animatimeImg"> animal development</a>
- <ul id="animatime">
- <li>
- <a href="../cgi-bin/detail.cgi?id=worm_development"><img src="images/arrow.gif" alt="->"> C. elegans development</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=fly_development"><img src="images/arrow.gif" alt="->"> Drosophila development</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=evoc"><img src="images/arrow.gif" alt="->"> eVOC (Expressed Sequence Annotation for Humans)</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=medaka_anatomy_development"><img src="images/arrow.gif" alt="->"> medaka fish anatomy and development</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=emap"><img src="images/arrow.gif" alt="->"> Mouse anatomy and development</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=plasmodium_life_cycle"><img src="images/arrow.gif" alt="->"> Plasmodium life cycle</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=zebrafish_anatomy"><img src="images/arrow.gif" alt="->"> Zebrafish anatomy and development</a>
- </li>
- </ul>
- </li>
- <li>
- <a id="planttime_page" class="page" href="#planttime"><img src="images/minus.gif" title="Close node" alt="-" id="planttimeImg"> plant development</a>
- <ul id="planttime">
- <li>
- <a href="../cgi-bin/detail.cgi?id=po_temporal"><img src="images/arrow.gif" alt="->"> plant growth and developmental stage</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=temporal_gramene"><img src="images/arrow.gif" alt="->"> cereal plant development</a>
- </li>
- </ul>
- </li>
- </ul>
- </li>
- <li>
- <a id="etho_page" class="page" href="#etho"><img src="images/minus.gif" title="Close node" alt="-" id="ethoImg"> ethology</a>
- <ul id="etho">
- <li>
- <a href="../cgi-bin/detail.cgi?id=habronattus_courtship"><img src="images/arrow.gif" alt="->"> Habronattus courtship</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=loggerhead_nesting"><img src="images/arrow.gif" alt="->"> Loggerhead nesting</a>
- </li>
- </ul>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=evidence_code"><img src="images/arrow.gif" alt="->"> evidence codes</a>
- </li>
- <li>
- <a id="expr_page" class="page" href="#expr"><img src="images/minus.gif" title="Close node" alt="-" id="exprImg"> experimental conditions</a>
- <ul id="expr">
- <li>
- <a href="../cgi-bin/detail.cgi?id=image"><img src="images/arrow.gif" alt="->"> biological imaging methods</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=mged"><img src="images/arrow.gif" alt="->"> microarray experimental conditions</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=nmr"><img src="images/arrow.gif" alt="->"> nuclear magnetic resonance experiment conditions</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=obi"><img src="images/arrow.gif" alt="->"> ontology for biomedical investigations</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=fix"><img src="images/arrow.gif" alt="->"> physico-chemical methods and properties</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=sep"><img src="images/arrow.gif" alt="->"> sample processing and separation techniques</a>
- </li>
- </ul>
- </li>
- <li>
- <a id="geno_page" class="page" href="#geno"><img src="images/minus.gif" title="Close node" alt="-" id="genoImg"> genomic and proteomic</a>
- <ul id="geno">
- <li>
- <a id="gp_page" class="page" href="#gp"><img src="images/minus.gif" title="Close node" alt="-" id="gpImg"> gene product</a>
- <ul id="gp">
- <li>
- <a href="../cgi-bin/detail.cgi?id=biological_process"><img src="images/arrow.gif" alt="->"> biological process</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=cellular_component"><img src="images/arrow.gif" alt="->"> cellular component</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=event"><img src="images/arrow.gif" alt="->"> event</a>
- </li>
- <li>
- <img src="images/x.gif" alt="X"> gene product name
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=molecular_function"><img src="images/arrow.gif" alt="->"> molecular function</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=molecule_role"><img src="images/arrow.gif" alt="->"> molecule role</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=mao"><img src="images/arrow.gif" alt="->"> multiple alignment</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=pathway"><img src="images/arrow.gif" alt="->"> pathway</a>
- </li>
- <li>
- <a id="prot_page" class="page" href="#prot"><img src="images/minus.gif" title="Close node" alt="-" id="protImg"> protein</a>
- <ul id="prot">
- <li>
- <a href="../cgi-bin/detail.cgi?id=cob"><img src="images/arrow.gif" alt="->"> protein covalent bond</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=interpro"><img src="images/arrow.gif" alt="->"> protein domain</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=psi-mod"><img src="images/arrow.gif" alt="->"> protein modification</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=psi-mi"><img src="images/arrow.gif" alt="->"> protein-protein interaction</a>
- </li>
- </ul>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=provenance"><img src="images/arrow.gif" alt="->"> proteomics data and process provenance</a>
- </li>
- </ul>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=sequence"><img src="images/arrow.gif" alt="->"> sequence types and features</a>
- </li>
- </ul>
- </li>
- <li>
- <a id="meta_page" class="page" href="#meta"><img src="images/minus.gif" title="Close node" alt="-" id="metaImg"> metabolomics</a>
- <ul id="meta">
- <li>
- <a href="../cgi-bin/detail.cgi?id=nmr"><img src="images/arrow.gif" alt="->"> nuclear magnetic resonance experiment conditions</a>
- </li>
- </ul>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=relationship"><img src="images/arrow.gif" alt="->"> OBO relationship types</a>
- </li>
- <li>
- <a id="pheno_page" class="page" href="#pheno"><img src="images/minus.gif" title="Close node" alt="-" id="phenoImg"> phenotype</a>
- <ul id="pheno">
- <li>
- <a href="../cgi-bin/detail.cgi?id=plant_trait"><img src="images/arrow.gif" alt="->"> cereal plant trait</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=evoc"><img src="images/arrow.gif" alt="->"> eVOC (Expressed Sequence Annotation for Humans)</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=disease_ontology"><img src="images/arrow.gif" alt="->"> human diseases</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=mammalian_phenotype"><img src="images/arrow.gif" alt="->"> mammalian phenotype</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=medaka_anatomy_development"><img src="images/arrow.gif" alt="->"> medaka fish anatomy and development</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=mouse_pathology"><img src="images/arrow.gif" alt="->"> mouse pathology</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=plant_environment"><img src="images/arrow.gif" alt="->"> plant enviromental conditions</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=quality"><img src="images/arrow.gif" alt="->"> PATO</a>
- </li>
- </ul>
- </li>
- <li>
- <a id="taxo_page" class="page" href="#taxo"><img src="images/minus.gif" title="Close node" alt="-" id="taxoImg"> taxonomic classification</a>
- <ul id="taxo">
- <li>
- <a href="../cgi-bin/detail.cgi?id=ncbi_taxonomy"><img src="images/arrow.gif" alt="->"> NCBI organismal classification</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=newt"><img src="images/arrow.gif" alt="->"> SwissProt organismal classification</a>
- </li>
- </ul>
- </li>
- <li>
- <a id="vocab_page" class="page" href="#vocab"><img src="images/minus.gif" title="Close node" alt="-" id="vocabImg"> vocabularies</a>
- <ul id="vocab">
- <li>
- <a href="../cgi-bin/detail.cgi?id=flybase_vocab"><img src="images/arrow.gif" alt="->"> FlyBase controlled vocabulary</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=mesh"><img src="images/arrow.gif" alt="->"> MESH</a>
- </li>
- <li>
- <a href="../cgi-bin/detail.cgi?id=ncithesaurus"><img src="images/arrow.gif" alt="->"> NCI Thesaurus</a>
- </li>
- </ul>
- </li>
- </ul>
- </div>
-</div>
-</body>
-</html>
Modified: phenote/trunk/doc/phenote-website/new/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-13 23:39:28 UTC (rev 886)
+++ phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-14 00:23:09 UTC (rev 887)
@@ -10,8 +10,8 @@
<!--#include virtual="ssi/header.html" -->
- <div id="main_container_aux">
- <div id="main_content_aux">
+ <div id="main_container">
+ <div id="main_content">
<div class="catch_phrase">
</div>
<h3>Launch Phenote in your browser</h3>
Modified: phenote/trunk/doc/phenote-website/new/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-13 23:39:28 UTC (rev 886)
+++ phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-14 00:23:09 UTC (rev 887)
@@ -82,6 +82,7 @@
</ul>
</div>
</div>
+ </div>
<!--#include virtual="ssi/footer.html" -->
Deleted: phenote/trunk/doc/phenote-website/new/join.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/join.shtml 2007-09-13 23:39:28 UTC (rev 886)
+++ phenote/trunk/doc/phenote-website/new/join.shtml 2007-09-14 00:23:09 UTC (rev 887)
@@ -1,54 +0,0 @@
-<!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">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Open Biomedical Ontologies Foundry</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container_aux">
- <div id="main_content_aux">
- <div class="catch_phrase">
- How to Join the OBO Foundry
- </div>
-
- <h3>Step 1: Survey </h3>
- <p>
- Find out what is already availble in the domain you are interested in. While the perfect solution may not yet exist it is important to contact people who share an interest in that domain and to learn from them (and gain their investment in using this ontology). Assess these ontologies critically and give them your comments, effective groups welcome this interest. If the domain is not yet covered by any existing ontology, then perhaps ask yourself why.
- </p>
-
- <h3>Step 2: If ontology is active and applied, then ask to collaborate </h3>
- <p>
- As the primary goal is interoperability it is crucial that ontologies be shared by different groups. Ontology development is inherently a community exercise, and therefore collaboration is essential. In order to be collaborative however, your partners must be active and responsive. Likewise applying the ontology to key data sets leads to fewer problems in the ontology and more commitment to fixing remaining problems because important research data is involved that scientists depend upon. All of the OBO Foundry contributors have agreed to be active and apply their ontologies.
- </p>
-
- <h3>Step 3: If a relevant, but moribund, ontology is found then learn from it</h3>
- <p>
- It is much more expedient to learn from previous work than to start from scratch. Synthesize whatever is already available whenever possible.
- </p>
-
- <h3>Step 4: Agree to sustained improvements</h3>
- <p>
- The only essential requirement for joining the OBO Foundry is agreement to adopt and refine a set of principles that prove effective for ontology development in serving the biomedical research community.
- </p>
-
- <h3>Step 5: E-mail us</h3>
- <p>
- Let us know who you are and what you're doing--contact us
- <b><script type="text/javascript">
- obfuscate("lists.sourceforge.net","obo-discuss","here");
- </script></b>.
- We look foward to hearing from you.
- </p>
-
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/new/lit.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/new/lit.shtml~ 2007-09-13 23:39:28 UTC (rev 886)
+++ phenote/trunk/doc/phenote-website/new/lit.shtml~ 2007-09-14 00:23:09 UTC (rev 887)
@@ -1,136 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?><!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"><head><meta http-equiv="content-type" content="text/html; charset=utf-8" /><title>REFERENCES WHICH MAY BE INCORPORATED (USES OF OBO FOUNDRY):</title><meta name="generator" content="StarOffice/OpenOffice.org XSLT (http://xml.openoffice.org/sx2ml)" /><meta name="author" content="Barry Smith" /><meta name="created" content="2007-04-29T08:16:00" /><meta name="changedby" content="Frédéric Tremblay" /><meta name="changed" content="2007-04-30T22:08:00" /><base href="." /><style type="text/css">
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- </style></head><body dir="ltr"><p class="P4">REFERENCES WHICH MAY BE INCORPORATED (USES OF OBO FOUNDRY): </p><p class="P2"> </p><p class="P1"><span class="T4">Antezana E, Tsiporkova E, Mironov V, et al. 2006 “A cell-cycle knowledge integration framework”, Lecture Notes in Computer Science 4075: 19-34. </span><a href="http://www.psb.ugent.be/cbd/cco/cellcycleframework.pdf"><span class="Internetlink"><span class="T2">http://www.psb.ugent.be/cbd/cco/cellcycleframework.pdf</span></span></a></p><p class="P1"><span class="T4">Aranguren ME, Bechoffer S, Lord P, Sattler U, Stevens R 2007 “Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL”, BMC Bioinformatics, 8: 57. </span><a href="http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1819394&blobtype=pdf"><span class="Internetlink"><span class="T2">http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1819394&blobtype=pdf</span></span></a></p><p class="P1"><span class="T4">Arnaiz O, Cain S, Cohen J, Sperling L 2006 “ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data”, Nucleic Acids Res Dec 7. </span><a href="http://nar.oxfordjournals.org/cgi/screenpdf/35/suppl_1/D439"><span class="Internetlink"><span class="T2">http://nar.oxfordjournals.org/cgi/screenpdf/35/suppl_1/D439</span></span></a></p><p class="P1"><span class="T4">Baker CJO, Shaban-Nejad A, Su X, Haarslev V, Butler G 2006 “Semantic Web infrastructure for fungal enzyme biotechnologists”, J Web Semantics 4 (3). </span><a href="http://users.encs.concordia.ca/~haarslev/publications/JWS-2006.pdf"><span class="Internetlink"><span class="T2">http://users.encs.concordia.ca/~haarslev/publications/JWS-2006.pdf</span></span></a></p><p class="P1"><span class="T4">Bard JBL 2005 “Anatomics: the intersection of anatomy and bioinformatics”, Journal of Anatomy 206 (1): 1-16 Jan. </span><a href="http://www.blackwell-synergy.com/doi/pdf/10.1111/j.0021-8782.2005.00376.x?cookieSet=1"><span class="Internetlink"><span class="T2">http://www.blackwell-synergy.com/doi/pdf/10.1111/j.0021-8782.2005.00376.x?cookieSet=1</span></span></a></p><p class="P1"><span class="T4">Bittner T, Goldberg LJ 2006 “The Qualitative and Time-Dependent Character of Spatial Relations in Biomedical Ontologies”, O. Bodenreider, ed., Proceedings of KR-MED, 47-55. </span><a href="http://www.acsu.buffalo.edu/~bittner3/BittnerGoldbergKRMed.pdf"><span class="Internetlink"><span class="T2">http://www.acsu.buffalo.edu/~bittner3/BittnerGoldbergKRMed.pdf</span></span></a></p><p class="Standard"><span class="T4">Blake JA, Bult CJ 2006 “Beyond the data deluge: Data integration and bio-ontologies”, Journal of Biomedical Informatics 39 (3): 314-320. </span><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16564748"><span class="Internetlink"><span class="T2">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16564748</span></span></a></p><p class="P1"><span class="T4">Bodenreider O. 2006 “Lexical, terminological and ontological resources for biological text mining”, in Ananiadou S, McNaught J, (eds.) Text mining for biology and biomedicine, Artech House, 43-66. </span><a href="http://lhncbc.nlm.nih.gov/lhc/docs/published/2006/pub2006007.pdf"><span class="Internetlink"><span class="T2">http://lhncbc.nlm.nih.gov/lhc/docs/published/2006/pub2006007.pdf</span></span></a></p><p class="P1"><span class="T4">Bontas EP, Schlangen D, Schrader T 2005 “Creating ontologies for content representation - The OntoSeed suite”, Lecture Notes in Computer Science 3761: 1296-1313. </span><a href="http://userpage.fu-berlin.de/~paslaru/papers/jods2006.pdf"><span class="Internetlink"><span class="T2">http://userpage.fu-berlin.de/~paslaru/papers/jods2006.pdf</span></span></a></p><p class="P1"><span class="T4">Burek P, Hoehndorf R, Loebe F, Visagie J, Herre H Kelso J. 2006 “A top-level ontology of functions and its application in the Open Biomedical Ontologies”, Bioinformatics, Vol. 22 no. 14: e66–e73. </span><a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e66"><span class="Internetlink"><span class="T2">http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e66</span></span></a></p><p class="P1"><span class="T4">Castro AG, Rocca-Serra P, Stevens R, Taylor C, Nashar K, Ragan MA, Sansone SA 2006 “The use of concept maps during knowledge elicitation in ontology development processes–-the nutrigenomics use case”, BMC Bioinformatics 25 (7): 267. </span><a href="http://www.biomedcentral.com/1471-2105/7/267/abstract"><span class="Internetlink"><span class="T2">http://www.biomedcentral.com/1471-2105/7/267/abstract</span></span></a></p><p class="P1"><span class="T4">Ceusters W 2006 “Towards a Realism-Based Metric for Quality Assurance in Ontology Matching”, Formal Ontology in Information Systems - Proceedings of the Fourth International Conference (FOIS 2006), Edited by Brandon Bennett, Christiane Fellbaum, New York: IOS Press, 321-332. </span><a href="http://ontology.buffalo.edu/bfo/Ontology_Matching.pdf"><span class="Internetlink"><span class="T2">http://ontology.buffalo.edu/bfo/Ontology_Matching.pdf</span></span></a></p><p class="P1"><span class="T4">Ceusters W, Smith B 2006 “A Realism-Based Approach to the Evolution of Biomedical Ontologies”, Proceedings of the Annual AMIA Symposium, Washington DC, 121-125. </span><a href="http://ontology.buffalo.edu/bfo/Versioning.pdf"><span class="Internetlink"><span class="T2">http://ontology.buffalo.edu/bfo/Versioning.pdf</span></span></a></p><p class="P1"><span class="T4">Dameron O, Roques É, Rubin DL, Marquet G, and Burgun A 2006 “Grading lung tumors using OWL-DL based reasoning”, In 9th International Protégé Conference. </span><a href="http://www.med.univ-rennes1.fr/~dameron/publis/2006protege-dameron.pdf"><span class="Internetlink"><span class="T2">http://www.med.univ-rennes1.fr/~dameron/publis/2006protege-dameron.pdf</span></span></a></p><p class="P1"><span class="T4">Dolbey A, Ellsworth M, Scheffczykx J 2006 “BioFrameNet: A Domain-Specific FrameNet Extension with Links to Biomedical Ontologies”, O. Bodenreider, ed., Proceedings of KR-MED, 87-94. </span><a href="http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-222/krmed2006-p10.pdf"><span class="Internetlink"><span class="T2">http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-222/krmed2006-p10.pdf</span></span></a></p><p class="P1"><span class="T4">Donnelly M, Bittner T, Rosse C 2006 “A formal theory for spatial representation and reasoning in biomedical ontologies”, Artificial Intelligence in Medicine 36 (1): 1-27. </span><a href="http://www.acsu.buffalo.edu/~md63/DonnellyAIMed05.pdf"><span class="Internetlink"><span class="T2">http://www.acsu.buffalo.edu/~md63/DonnellyAIMed05.pdf</span></span></a></p><p class="P1"><span class="T4">Friedberg I 2006 “Automated protein function prediction - the genomic challenge”, Briefings in Bioinformatics 7 (3): 225-242. </span><a href="http://bib.oxfordjournals.org/cgi/content/abstract/bbl004?ijkey=n3AzMhAJ4nZjzAy&keytype=ref"><span class="Internetlink"><span class="T2">http://bib.oxfordjournals.org/cgi/content/abstract/bbl004?ijkey=n3AzMhAJ4nZjzAy&keytype=ref</span></span></a></p><p class="P1"><span class="T4">Friedman C, Borlawsky T, Shagina L, et al. 2006 “Bio-Ontology and text: bridging the modeling gap”, Bioinformatics 22 (19): 2421-2429. </span><a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/19/2421"><span class="Internetlink"><span class="T2">http://bioinformatics.oxfordjournals.org/cgi/content/abstr...
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From: <nl...@us...> - 2007-09-17 23:16:23
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Revision: 912
http://obo.svn.sourceforge.net/obo/?rev=912&view=rev
Author: nlw
Date: 2007-09-17 16:16:26 -0700 (Mon, 17 Sep 2007)
Log Message:
-----------
moved the new site to the main page
Modified Paths:
--------------
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--- phenote/trunk/doc/phenote-website/about.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/about.shtml 2007-09-17 23:16:26 UTC (rev 912)
@@ -0,0 +1,71 @@
+<!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">
+ <head>
+
+ <!--#include virtual="ssi/head.html" -->
+ <title>Phenote</title>
+
+ </head>
+ <body>
+
+ <!--#include virtual="ssi/header.html" -->
+
+ <div id="main_container_aux">
+ <div id="main_content_aux">
+ <div class="catch_phrase">
+ About Phenote
+ </div>
+
+ <p>
+ Phenote 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. Typical users of Phenote include literature curators, laboratory researchers, and clinicians looking for a method to record data in a user-friendly and computable way.
+ </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 ontology with qualities (such as PATO).
+ </p>
+
+ <h3>
+ <a href="contact.shtml">
+ Contact us
+ </a>
+ </h3>
+ <p>
+ Who to ask for assistance (and to complain to).
+ </p>
+
+ <h3>
+ <a href="related.shtml">
+ Related Projects
+ </a>
+ </h3>
+ <p>
+ Brief descriptions and links to projects who are relevant
+ to Phenote, ontologies, and annotation.
+ </p>
+
+ <h3>
+ <a href="faq.shtml">
+ Frequently Asked Questions (FAQs)
+ </a>
+ </h3>
+ <p>
+ Common questions about Phenote, ontologies, and annotation,
+ along with their answers.
+ </p>
+
+ <h3>
+ <a href="events.shtml">
+ Upcoming and Past Events
+ </a>
+ </h3>
+ <p>
+ A listing of upcoming and past events related to Phenote and
+ phenotype annotation, including presentations at meetings,
+ online workshops, user group meetings, etc.
+ </p>
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
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Added: phenote/trunk/doc/phenote-website/about.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/about.shtml~ (rev 0)
+++ phenote/trunk/doc/phenote-website/about.shtml~ 2007-09-17 23:16:26 UTC (rev 912)
@@ -0,0 +1,60 @@
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+ <head>
+
+ <!--#include virtual="ssi/head.html" -->
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+
+ </head>
+ <body>
+
+ <!--#include virtual="ssi/header.html" -->
+
+ <div id="main_container_aux">
+ <div id="main_content_aux">
+ <div class="catch_phrase">
+ About Phenote
+ </div>
+
+ <p>
+ Phenote 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. Typical users of Phenote include literature curators, laboratory researchers, and clinicians looking for a method to record data in a user-friendly and computable way.
+ </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 ontology with qualities (such as PATO).
+ </p>
+
+ <h3>
+ <a href="contact.shtml">
+ Contact us
+ </a>
+ </h3>
+ <p>
+ Who to ask for assistance (and to complain to).
+ </p>
+
+ <h3>
+ <a href="related.shtml">
+ Related Projects
+ </a>
+ </h3>
+ <p>
+ Brief descriptions and links to projects who are relevant
+ to Phenote, ontologies, and annotation.
+ </p>
+
+ <h3>
+ <a href="faq.shtml">
+ Frequently Asked Questions (FAQs)
+ </a>
+ </h3>
+ <p>
+ Common questions about Phenote, ontologies, and annotation,
+ along with their answers.
+ </p>
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
+
+ </body>
+</html>
Added: phenote/trunk/doc/phenote-website/contact.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/contact.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/contact.shtml 2007-09-17 23:16:26 UTC (rev 912)
@@ -0,0 +1,75 @@
+<!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">
+ <head>
+
+ <!--#include virtual="ssi/head.html" -->
+ <title>Phenote</title>
+
+ </head>
+ <body>
+
+ <!--#include virtual="ssi/header.html" -->
+
+ <div id="main_container_aux">
+ <div id="main_content_aux">
+
+ <div class="catch_phrase">
+ Contact Us
+ </div>
+ <h1>Email us</h1>
+ <p>Software Development:
+ <script type="text/javascript">
+ obfuscate("berkeleybop.org", "mgibson", "Mark Gibson");
+ </script></p>
+ <p>Requirements, Analysis, Documentation:
+ <script type="text/javascript">
+ obfuscate("lbl.gov", "nlwashington", "Nicole Washington");
+ </script></p>
+ <p>Phenotype EQ model and XML data formats:
+ <script type="text/javascript">
+ obfuscate("berkeleybop.org", "cjm", "Chris Mungall");
+ </script></p>
+ <p>General Questions:
+ <script type="text/javascript">
+ obfuscate("lists.sourceforge.org", "obo-phenote", "Phenote Mailing List");
+ </script></p>
+ <h1>Mailing lists</h1>
+ <p> There are several relevant mailing lists user's and/or developers
+ might be interested in joining:</p>
+ <p>General phenote discussion and announcements
+ [ <script type="text/javascript">
+ obfuscate("lists.sourceforge.org", "obo-phenote", "Email");
+ </script> ]
+ [ <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Join</a> ]</p>
+ <p>Phenote software development
+ [ <script type="text/javascript">
+ obfuscate("lists.sourceforge.org", "obo-phenote-dev", "Email");
+ </script> ]
+ [ <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-dev">Join</a> ]</p>
+ <p>Phenotype annotation discussion list
+ [ <script type="text/javascript">
+ obfuscate("lists.sourceforge.org", "obo-phenotype", "Email");
+ </script> ]
+ [ <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenotype">Join</a> ]</p>
+ <p>General OBO ontology discussion
+ [ <script type="text/javascript">
+ obfuscate("lists.sourceforge.org", "obo-discuss", "Email");
+ </script> ]
+ [ <a href="https://lists.sourceforge.net/lists/listinfo/obo-discuss">Join</a> ]</p>
+ <p>General NCBO discussion
+ [ <script type="text/javascript">
+ obfuscate("lists.stanford.edu", "cbio-everyone", "Email");
+ </script> ]</p>
+ <h1>Reporting Bugs / Requesting Features</h1>
+ <p>If you come across problems during your use of Phenote software,
+ or there's a new feature you are dying to have, please use our
+ tracker on sourceforge to log your request:
+ <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">Request Tracker</a></p>
+
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
+
+ </body>
+</html>
Added: phenote/trunk/doc/phenote-website/contact.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/contact.shtml~ (rev 0)
+++ phenote/trunk/doc/phenote-website/contact.shtml~ 2007-09-17 23:16:26 UTC (rev 912)
@@ -0,0 +1,75 @@
+<!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">
+ <head>
+
+ <!--#include virtual="ssi/head.html" -->
+ <title>Phenote</title>
+
+ </head>
+ <body>
+
+ <!--#include virtual="ssi/header.html" -->
+
+ <div id="main_container_aux">
+ <div id="main_content_aux">
+
+ <div class="catch_phrase">
+ Contact Us
+ </div>
+ <h1>Email us</h1>
+ <p>Software Development:
+ <script type="text/javascript">
+ obfuscate("berkeleybop.org", "mgibson", "Mark Gibson");
+ </script></p>
+ <p>Requirements, Analysis, Documentation:
+ <script type="text/javascript">
+ obfuscate("lbl.gov", "nlwashington", "Nicole Washington");
+ </script></p>
+ <p>Phenotype EQ model and XML data formats:
+ <script type="text/javascript">
+ obfuscate("berkeleybop.org", "cjm", "Chris Mungall");
+ </script></p>
+ <p>General Questions:
+ <script type="text/javascript">
+ obfuscate("lists.sourceforge.org", "obo-phenote", "Phenote Mailing List");
+ </script></p>
+ <h1>Mailing lists</h1>
+ <p> There are several relevant mailing lists user's and/or developers
+ might be interested in joining:</p>
+ <p>General phenote discussion and announcements
+ [ <script type="text/javascript">
+ obfuscate("lists.sourceforge.org", "obo-phenote", "Email");
+ </script> ]
+ [ <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Join</a> ]</p>
+ <p>Phenote software development
+ [ <script type="text/javascript">
+ obfuscate("lists.sourceforge.org", "obo-phenote-dev", "Email");
+ </script> ]
+ [ <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-dev">Join</a> ]</p>
+ <p>Phenotype annotation discussion list
+ [ <script type="text/javascript">
+ obfuscate("lists.sourceforge.org", "obo-phenotype", "Email");
+ </script> ]
+ [ <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenotype">Join</a> ]</p>
+ <p>General OBO ontology discussion
+ [ <script type="text/javascript">
+ obfuscate("lists.sourceforge.org", "obo-discuss", "Email");
+ </script> ]
+ [ <a href="https://lists.sourceforge.net/lists/listinfo/obo-discuss">Join</a> ]</p>
+ <p>General NCBO discussion
+ [ <script type="text/javascript">
+ obfuscate("lists.stanford.edu", "cbio-everyone", "Email");
+ </script> ]</p>
+ <h1>Reporting Bugs / Requesting Features</h1>
+ <p>If you come across problems during your use of Phenote software,
+ or there's a new feature you are dying to have, please use our
+ tracker on sourceforge to log your request:
+ <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">Request Tracker</a></p>
+
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
+
+ </body>
+</html>
Added: phenote/trunk/doc/phenote-website/coordination.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/coordination.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/coordination.shtml 2007-09-17 23:16:26 UTC (rev 912)
@@ -0,0 +1,122 @@
+<!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">
+ <head>
+
+ <!--#include virtual="ssi/head.html" -->
+ <title>Open Biomedical Ontologies Foundry</title>
+
+ </head>
+ <body>
+
+ <!--#include virtual="ssi/header.html" -->
+
+ <div id="main_container_aux">
+ <div id="main_content_aux">
+
+ <div class="catch_phrase">
+ Coordination of the OBO Foundry
+ </div>
+
+ <p>
+ The coordinators of the OBO Foundry are
+ <a href="http://www.gen.cam.ac.uk/Research/ashburner.htm">
+ Michael Ashburner
+ </a>
+ (NCBO, GO),
+ <a href="http://www.berkeleybop.org/content/people/cjm/">
+ Chris Mungall
+ </a>
+ (NCBO, GO, BBOP),
+ Suzanna Lewis
+ (NCBO, GO, BBOP), and
+ <a href="http://ontology.buffalo.edu/smith/">
+ Barry Smith
+ </a>
+ (NCBO, ORG).
+ </p>
+
+ <p>
+ The intention is to provide light-weight management,
+ although the growth of OBO may, in the future, necessitate a
+ more formal structure. It is appropriate to view these
+ people as facilitators who assist independent ontology
+ developers: by organizing meetings, making introductions
+ between different groups, offering comments when requested,
+ engaging in e-mail discussions, making resources available,
+ and other means. They work to ensure that the ontologies
+ being developed are mutually compatible, expandable, and
+ correctable in line with advances in biomedical
+ science. Ontologies are tools of communication, and their
+ utility rests on the network effects that come with wide
+ acceptance. Experience thus far confirms that adherence to
+ OBO principles is largely self-policing because of the
+ positive benefits that accrue to individual members. The
+ task of the OBO coordinators is to help to build this
+ community.
+ </p>
+
+ <h1>Affiliations</h1>
+
+ <h3>
+ <a href="http://bioontology.org/">
+ National Center for Biomedical Ontology (NCBO)
+ </a>
+ </h3>
+ <p>
+ The NCBO is a consortium of leading biologists, clinicians,
+ informaticians, and ontologists who develop innovative
+ technology and methods that allow scientists to create,
+ disseminate, and manage biomedical information and knowledge
+ in machine-processable form.
+ </p>
+
+ <h3>
+ <a href="http://org.buffalo.edu/">
+ Ontology Research Group (ORG)
+ </a>
+ </h3>
+ <p>
+ The ORG is located in the New York State Center of
+ Excellence in Bioinformatics and Life Sciences
+ http://bioinformatics.buffalo.edu/ in Buffalo. It is engaged
+ in foundational ontology research and in biomedical ontology
+ development in the domain of biology and clinical
+ medicine. A special focus of research is electronic health
+ records.
+ </p>
+
+ <h3>
+ <a href="http://www.geneontology.org">
+ Gene Ontology (GO)
+ </a>
+ </h3>
+ <p>
+ The GO project provides a controlled voc abulary to describe
+ gene and gene product attributes in any organism. Members of
+ the GO Consortium supply annotations of gene products using
+ this vocabulary which can be viewed and downloaded via the
+ GO website.
+ </p>
+ <h3>
+ <a href="http://www.berkeleybop.org/">
+ Berkeley Bioinformatics and Ontologies Project (BBOP)
+ </a>
+ </h3>
+ <p>
+ The BBOP is 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 The Gene Ontology, The National Center
+ for Biomedical Ontology, and the Generic Model Organism
+ Database Project.
+ </p>
+
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
+
+ </body>
+</html>
Added: phenote/trunk/doc/phenote-website/css/detail.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/detail.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/detail.css 2007-09-17 23:16:26 UTC (rev 912)
@@ -0,0 +1,17 @@
+
+.detail td {
+ padding: 5px 10px 5px 10px;
+ font-size: 1em;
+ text-align: right;
+}
+
+.detail td.data{
+ width: 85%;
+ text-align: left;
+ background-color: #ccddcc;
+}
+
+.detail td.data a:hover {
+ color: #ffffff;
+ background: #1b5c92
+}
Added: phenote/trunk/doc/phenote-website/css/enhancer.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/enhancer.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/enhancer.css 2007-09-17 23:16:26 UTC (rev 912)
@@ -0,0 +1,42 @@
+/* */
+
+.browser a:hover, a:active {
+ color: #ffffff;
+ background-color: #444444;
+}
+
+.browser a:link {
+ color: #660000;
+ text-decoration: none;
+}
+
+.browser a:visited {
+ color: #888888;
+ text-decoration: none;
+}
+
+.browser img {
+ border: 0;
+}
+
+.browser a.page {
+ font-weight: bold;
+ color: #444444;
+}
+
+.browser a:hover {
+ color: #ffffff;
+ background-color: #444444;
+}
+
+
+.browser ul {
+ padding: 0;
+ list-style-type: none;
+ margin: 2px 0 2px 15px;
+ font-size: 1.0em;
+}
+
+.browser li {
+ margin: 0.2em 2px 0.2em 2px;
+}
Added: phenote/trunk/doc/phenote-website/css/list.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/list.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/list.css 2007-09-17 23:16:26 UTC (rev 912)
@@ -0,0 +1,12 @@
+
+.anEvenRow {
+ font-size: 110%;
+ padding: .33em;
+ background: #ccddcc;
+}
+
+.anOddRow {
+ font-size: 110%;
+ padding: .33em;
+ background: #ffffff;
+}
Added: phenote/trunk/doc/phenote-website/css/main.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/main.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/main.css 2007-09-17 23:16:26 UTC (rev 912)
@@ -0,0 +1,626 @@
+body {
+ margin: 0px 10px auto;
+ padding: 0px;
+ font-family: arial, "Lucida Grande", verdana, helvetica, sans-serif;
+ font-size: 12px;
+ color: #000;
+/* background-color: #CEDEDA; */
+/* background-color: #EEEEDD; */
+/* background-color: #F9F8ED; */
+ background-color: #FFF;
+ text-align: left;
+/* width: 800px; */
+}
+
+/* Make sure the table cells show the right font */
+td { font-family: verdana, arial, helvetica, sans-serif; }
+
+a {
+ text-decoration: underline;
+ padding: 1px;
+}
+a:link {
+ color: #002699;
+}
+a:visited {
+ color: #002699;
+}
+a:hover {
+ text-decoration: none;
+}
+
+a.image:link, a.image:visited, a.image:hover {
+ background: none;
+ padding: 0px;
+ border: none;
+}
+
+a.image img {
+ border: none;
+}
+
+p {
+ font-size: 12px;
+ line-height: 16px;
+}
+
+small {
+ font-size: 10px;
+ line-height: 13px;
+}
+
+x-small {
+ font-size: 9px;
+ line-height: 11px;
+}
+
+blockquote {
+ font-size: 11px;
+ color: #666;
+ margin: 20px;
+}
+
+ul li {
+/* list-style-type: none; */
+}
+
+li {
+ font-size: 12px;
+ line-height: 13px;
+ padding: 3px 0px;
+}
+
+li img {
+ padding-right: 3px;
+}
+
+ul.events {
+ list-style-type: none;
+ padding: 0px;
+ margin: 0px;
+}
+
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+ font-size: 12px;
+}
+
+h1 {
+ padding: 0px;
+ border-bottom: 1px solid #CEDEDA;
+ margin: 0px;
+ color: #033C63;
+ font-size: 16px;
+ font-weight: bold;
+ text-decoration: none;
+}
+
+h1 a, h1 a:link, h1 a:visited {
+ color: #033C63;
+ text-decoration: none;
+}
+
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+ text-decoration: underline;
+}
+
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+ margin: 20px 0px 5px 0px;
+ color: #033C63;
+ font-size: 14px;
+ padding: 0px;
+}
+
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+ border-bottom: 1px solid #CEDEDA;
+ margin-bottom: 15px;
+}
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+ color: #033C63;
+ text-decoration: none;
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+
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+ text-decoration: underline;
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+
+h2.highlight {
+ margin: 0px 0px 0px 0px;
+ margin-bottom: 10px;
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+
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+ color: #033C63;
+ font-size: 12px;
+ padding: 0px;
+}
+
+h3.bio {
+ color: #426D8A;
+ margin: 20px 0px 0px 0px;
+ border-bottom: 1px solid #CEDEDA;
+ margin-bottom: 10px;
+}
+
+h3.highlight {
+ margin: 0px 0px 0px 0px;
+ margin-bottom: 10px;
+}
+
+.smallnote {
+ font-size: 10px;
+ color: #999;
+ font-weight: normal;
+}
+
+#container {
+ background: #fff;
+/* border-right: 1px solid #666; */
+/* border-left: 1px solid #666; */
+ width: 100%;
+}
+
+#content {
+ padding: 10px;
+}
+
+#header{
+/* background: #fff url(../images/cbio_logo.gif) no-repeat 5px 5px; */
+ padding: 5px;
+ margin: 0px;
+ text-align: left;
+ height: 60px;
+/* position: relative; */
+}
+
+#header span#floatright {
+ padding: 35px 5px 0px 0px;
+ font-size: 11px;
+ font-weight: normal;
+ text-align: right;
+/* width: 200px; */
+ position: relative;
+ float: right;
+}
+
+#header.image a:link, #header.image a:visited, #header.image a:hover {
+ background: none;
+ padding: 0px;
+}
+
+#header.image img {
+ border: none;
+}
+
+#nav ul
+{
+ padding: 0;
+ margin: 0;
+ background: #033C63 url(../images/nav_bg.gif) repeat-x 0px 0px;
+ color: #fff;
+ float: left;
+ width: 100%;
+}
+
+#nav ul li {
+ display: inline;
+ list-style-type: none;
+ }
+
+#nav ul li a
+{
+ font-size: 12px;
+ padding: 0.6em 1em;
+/* background-color: #000; */
+ color: #fff;
+ text-decoration: none;
+ float: left;
+/* border-right: 1px solid #fff; */
+}
+
+#nav ul li a:hover
+{
+ background-color: #1B5C92;
+ color: #fff;
+}
+
+#nav .selected a, #nav .selected a:hover {
+/* background-color: #1B5C92; */
+ background-color: #1B5C92;
+ color: #fff;
+ font-weight: bold;
+ text-decoration: none;
+}
+
+div.nav_empty
+{
+ padding: 0px;
+ margin: 0px;
+ border: none;
+ color: #1c2b48;
+ background-color: #033C63;
+ height: 5px;
+ font-size: 1px;
+ line-height: 0;
+ width: 100%;
+}
+
+#subnav ul
+{
+ padding: 0;
+ margin: 0;
+/* background-color: #69A263; */
+/* background-color: #73AFB7; */
+ background-color: #CCDDCC;
+ color: #033C63;
+ float: left;
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+}
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+}
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+}
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+ color: #033C63;
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+ text-decoration: none;
+}
+
+
+div.subnav_empty
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+ margin: 0px;
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+}
+
+.clearall {
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+ clear: both;
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+}
+
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+}
+
+#footer {
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+ padding: 10px;
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+}
+
+#breadcrumbs {
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+}
+
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+ border-top: 1px solid #ccc;
+}
+
+#main_container {
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+ width: 65%;
+ text-align: left;
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+}
+
+#main_content {
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+}
+
+#main_container_aux {
+ float: left;
+ width: 80%;
+ text-align: left;
+ margin-left: 10%;
+}
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+}
+
+#main_container_aux p, #main_container_aux h3 {
+ font-size: 120%;
+}
+
+#sidebar_container {
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+ float: left;
+ width: 33%;
+ text-align: left;
+}
+
+#sidebar_content {
+ padding: 10px;
+}
+
+#sidebar_content h2 {
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+}
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+ width: 49%;
+ text-align: left;
+ margin: 0 0 12px 0;
+}
+
+#content .full_bio {
+ float: left;
+ text-align: center;
+ margin: 0 0 12px 0;
+}
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+#content .half_bio {
+ float: left;
+ width: 49%;
+ text-align: center;
+ margin: 0 0 12px 0;
+}
+
+#content .third_bio {
+ float: left;
+ width: 33%;
+ text-align: center;
+ margin: 0 0 12px 0;
+}
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+#content .fourth_bio {
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+ width: 24%;
+ text-align: center;
+ margin: 0 0 12px 0;
+}
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+#content .full_bio p, #content .half_bio p, #content .third_bio p, #content .fourth_bio p {
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+ padding: 0 10px;
+}
+
+#content .full_bio img, #content .half_bio img, #content .third_bio img, #content .fourth_bio img {
+ border: 1px solid #999;
+ margin: 2px;
+ padding: 5px;
+}
+
+.content_box_head_green {
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+ font-weight: bold;
+ font-size: 12px;
+ color: #033C63;
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+}
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+ border-right: 1px solid #1B5C92;
+ border-left: 1px solid #1B5C92;
+ background-color: #1B5C92;
+ font-weight: bold;
+ font-size: 12px;
+ color: #FFF;
+ line-height: 16px;
+ padding: 6px;
+}
+
+.content_box_blue {
+ border: 1px solid #1B5C92;
+ border-top: 0px;
+ border-color: #1B5C92;
+ margin-bottom: 10px;
+ padding: 6px;
+}
+
+.content_box_green {
+ border: 1px solid #A9C6A9;
+ border-top: 0px;
+ border-color: #A9C6A9;
+ margin-bottom: 10px;
+ padding: 6px;
+}
+
+
+.catch_phrase {
+ color: #1B5C92;
+ font-weight: bold;
+ font-size: 18px;
+ font-style: italic;
+ text-align: center;
+}
+
+.centered_phrase {
+ text-align: center;
+ margin-top: 1em;
+ margin-bottom: .5em;
+}
+
+.collage {
+ margin-top: 30px;
+ margin-bottom: 30px;
+ margin-right: auto;
+ margin-left: auto;
+ width: 400px;
+ text-align:center;
+ background-color: #CEDEDA;
+ border: 5px solid #A9C6A9;
+}
+
+.featured_tools {
+ margin-top: 30px;
+}
+
+.more {
+ text-align: right;
+ font-size: 11px;
+}
+
+table.events {
+/* width: 100%; */
+/* border-top: 1px solid #A9C6A9; */
+/* border-right: 1px solid #A9C6A9; */
+ border-left: 1px solid #A9C6A9;
+/* border-bottom: 1px solid #A9C6A9; */
+ margin-top: 10px;
+}
+
+th.events {
+ color: #033C63;
+ border-right: 1px solid #A9C6A9;
+ border-bottom: 1px solid #A9C6A9;
+ border-left: 1px solid #A9C6A9;
+ border-top: 1px solid #A9C6A9;
+ text-align: left;
+ background: #A9C6A9;
+}
+
+td.events {
+ border-right: 1px solid #A9C6A9;
+ border-bottom: 1px solid #A9C6A9;
+ background: #FFF;
+}
+
+td.events_alt {
+ border-right: 1px solid #A9C6A9;
+ border-bottom: 1px solid #A9C6A9;
+ background: #F5FAFA;
+}
+
+img.section_head {
+ float: left;
+}
+
+div.evts {
+ overflow: auto;
+}
+
+.icon_green {
+ background-color: #A9C6A9;
+ background-image: url(../images/bg_rounded.gif);
+ background-repeat: no-repeat;
+ vertical-align:text-bottom;
+}
+
+.icon_blue {
+ background-color: #1B5C92;
+ background-image: url(../images/bg_rounded.gif);
+ background-repeat: no-repeat;
+ vertical-align:text-bottom;
+}
+
+.quick_link {
+ margin: 5px;
+}
+
+.content_box_highlight {
+ border: 2px solid #A9C6A9;
+/* border-color: #A9C6A9; */
+ background-color: #EDF3F1;
+ margin-top: 10px;
+ margin-bottom: 10px;
+ padding: 6px;
+}
+
+.screen_shot {
+ border: 3px solid #666;
+}
+
+.search {
+ margin-bottom: 10px;
+/* margin-top: 10px; */
+/* padding-top: 5px; */
+ padding-bottom: 5px;
+ border-bottom: 1px dotted #1B5C92;
+/* border-top: 1px dotted #1B5C92; */
+ font-size: 11px;
+}
+
+.search h1 {
+ font-size: 12px;
+ color: #1B5C92;
+ text-decoration: none;
+ border:none;
+ padding:0px;
+ margin:0px;
+}
+
+a.highlight_text_yellow, a:hover.highlight_text_yellow, a:visited.highlight_text_yellow, a:active.highlight_text_yellow {
+ font-size: 24px;
+ color: #E9BA56;
+ text-decoration:none;
+ font-weight: bold;
+}
+
+a.highlight_text_blue, a:hover.highlight_text_blue, a:visited.highlight_text_blue, a:active.highlight_text_blue {
+ font-size: 24px;
+ font-weight: bold;
+ color: #1B5C92;
+ text-decoration:none;
+}
+
+a.highlight_normal, a:hover.highlight_normal, a:visited.highlight_normal, a:active.highlight_normal {
+ font-size: 24px;
+ font-weight: normal;
+ color: #000000;
+ text-decoration:none;
+}
+
+h1.introduction {
+ padding: 0px;
+ margin: 0px;
+ border-bottom: 1px solid #CEDEDA;
+ font-size: 24px;
+ font-weight: bold;
+ color: #1B5C92;
+ text-decoration: none;
+}
+
+.blue_divider hr {
+display:none;
+}
+
+.blue_divider {
+border-bottom:1px solid #033C63;
+height:1px;
+}
+
+
+.crit em{
+ color: #009922;
+}
\ No newline at end of file
Added: phenote/trunk/doc/phenote-website/css/main.css~
===================================================================
--- phenote/trunk/doc/phenote-website/css/main.css~ (rev 0)
+++ phenote/trunk/doc/phenote-website/css/main.css~ 2007-09-17 23:16:26 UTC (rev 912)
@@ -0,0 +1,626 @@
+body {
+ margin: 0px 10px auto;
+ padding: 0px;
+ font-family: arial, "Lucida Grande", verdana, helvetica, sans-serif;
+ font-size: 12px;
+ color: #000;
+/* background-color: #CEDEDA; */
+/* background-color: #EEEEDD; */
+/* background-color: #F9F8ED; */
+ background-color: #FFF;
+ text-align: left;
+/* width: 800px; */
+}
+
+/* Make sure the table cells show the right font */
+td { font-family: verdana, arial, helvetica, sans-serif; }
+
+a {
+ text-decoration: underline;
+ padding: 1px;
+}
+a:link {
+ color: #002699;
+}
+a:visited {
+ color: #002699;
+}
+a:hover {
+ text-decoration: none;
+}
+
+a.image:link, a.image:visited, a.image:hover {
+ background: none;
+ padding: 0px;
+ color: #000000;
+}
+
+a.image img {
+ border: none;
+}
+
+p {
+ font-size: 12px;
+ line-height: 16px;
+}
+
+small {
+ font-size: 10px;
+ line-height: 13px;
+}
+
+x-small {
+ font-size: 9px;
+ line-height: 11px;
+}
+
+blockquote {
+ font-size: 11px;
+ color: #666;
+ margin: 20px;
+}
+
+ul li {
+/* list-style-type: none; */
+}
+
+li {
+ font-size: 12px;
+ line-height: 13px;
+ padding: 3px 0px;
+}
+
+li img {
+ padding-right: 3px;
+}
+
+ul.events {
+ list-style-type: none;
+ padding: 0px;
+ margin: 0px;
+}
+
+li.events {
+ font-size: 12px;
+}
+
+h1 {
+ padding: 0px;
+ border-bottom: 1px solid #CEDEDA;
+ margin: 0px;
+ color: #033C63;
+ font-size: 16px;
+ font-weight: bold;
+ text-decoration: none;
+}
+
+h1 a, h1 a:link, h1 a:visited {
+ color: #033C63;
+ text-decoration: none;
+}
+
+h1 a:hover {
+ text-decoration: underline;
+}
+
+h2, h2.bio {
+ margin: 20px 0px 5px 0px;
+ color: #033C63;
+ font-size: 14px;
+ padding: 0px;
+}
+
+h2.bio {
+ border-bottom: 1px solid #CEDEDA;
+ margin-bottom: 15px;
+}
+
+h2 a, h2 a:link, h2 a:visited {
+ color: #033C63;
+ text-decoration: none;
+}
+
+h2 a:hover {
+ text-decoration: underline;
+}
+
+h2.highlight {
+ margin: 0px 0px 0px 0px;
+ margin-bottom: 10px;
+}
+
+h3, h3.bio {
+ color: #033C63;
+ font-size: 12px;
+ padding: 0px;
+}
+
+h3.bio {
+ color: #426D8A;
+ margin: 20px 0px 0px 0px;
+ border-bottom: 1px solid #CEDEDA;
+ margin-bottom: 10px;
+}
+
+h3.highlight {
+ margin: 0px 0px 0px 0px;
+ margin-bottom: 10px;
+}
+
+.smallnote {
+ font-size: 10px;
+ color: #999;
+ font-weight: normal;
+}
+
+#container {
+ background: #fff;
+/* border-right: 1px solid #666; */
+/* border-left: 1px solid #666; */
+ width: 100%;
+}
+
+#content {
+ padding: 10px;
+}
+
+#header{
+/* background: #fff url(../images/cbio_logo.gif) no-repeat 5px 5px; */
+ padding: 5px;
+ margin: 0px;
+ text-align: left;
+ height: 60px;
+/* position: relative; */
+}
+
+#header span#floatright {
+ padding: 35px 5px 0px 0px;
+ font-size: 11px;
+ font-weight: normal;
+ text-align: right;
+/* width: 200px; */
+ position: relative;
+ float: right;
+}
+
+#header.image a:link, #header.image a:visited, #header.image a:hover {
+ background: none;
+ padding: 0px;
+}
+
+#header.image img {
+ border: none;
+}
+
+#nav ul
+{
+ padding: 0;
+ margin: 0;
+ background: #033C63 url(../images/nav_bg.gif) repeat-x 0px 0px;
+ color: #fff;
+ float: left;
+ width: 100%;
+}
+
+#nav ul li {
+ display: inline;
+ list-style-type: none;
+ }
+
+#nav ul li a
+{
+ font-size: 12px;
+ padding: 0.6em 1em;
+/* background-color: #000; */
+ color: #fff;
+ text-decoration: none;
+ float: left;
+/* border-right: 1px solid #fff; */
+}
+
+#nav ul li a:hover
+{
+ background-color: #1B5C92;
+ color: #fff;
+}
+
+#nav .selected a, #nav .selected a:hover {
+/* background-color: #1B5C92; */
+ background-color: #1B5C92;
+ color: #fff;
+ font-weight: bold;
+ text-decoration: none;
+}
+
+div.nav_empty
+{
+ padding: 0px;
+ margin: 0px;
+ border: none;
+ color: #1c2b48;
+ background-color: #033C63;
+ height: 5px;
+ font-size: 1px;
+ line-height: 0;
+ width: 100%;
+}
+
+#subnav ul
+{
+ padding: 0;
+ margin: 0;
+/* background-color: #69A263; */
+/* background-color: #73AFB7; */
+ background-color: #CCDDCC;
+ color: #033C63;
+ float: left;
+ width: 100%;
+}
+
+#subnav ul li {
+ display: inline;
+ list-style-type: none;
+}
+
+#subnav ul li a
+{
+ font-size: 11px;
+ padding: 0.4em 1.2em;
+/* background-color: #5F9F04; */
+ background-color: #CCDDCC;
+ color: #033C63;
+ text-decoration: none;
+ float: left;
+}
+
+#subnav ul li a:hover
+{
+ background-color: #CCDDCC;
+ text-decoration: underline;
+ color: #033C63;
+}
+
+#subnav .selected a, #subnav .selected a:hover {
+ background-color: #CCDDCC;
+ color: #033C63;
+ font-weight: bold;
+ text-decoration: none;
+}
+
+
+div.subnav_empty
+{
+ padding: 0px;
+ margin: 0px;
+ border: none;
+ color: #1c2b48;
+ background-color: #CCDDCC;
+ height: 5px;
+ font-size: 1px;
+ line-height: 0;
+ width: 100%;
+}
+
+.clearall {
+ padding: 0px;
+ clear: both;
+ font-size: 0px;
+}
+
+.clear {
+ clear: both;
+}
+
+#footer {
+ border-top: 1px #ccc solid;
+ padding: 10px;
+/* margin-top: 10px; */
+ font-size: 90%;
+ text-align: center;
+}
+
+#breadcrumbs {
+ padding-bottom: 10px;
+ font-size: 90%;
+}
+
+.separator {
+ border-top: 1px solid #ccc;
+}
+
+#main_container {
+ float: left;
+ width: 65%;
+ text-align: left;
+ border-right: 1px solid #ccc;
+}
+
+#main_content {
+ padding: 10px;
+}
+
+#main_container_aux {
+ float: left;
+ width: 80%;
+ text-align: left;
+ margin-left: 10%;
+}
+
+#main_content_aux {
+ padding: 10px;
+}
+
+#main_container_aux p, #main_container_aux h3 {
+ font-size: 120%;
+}
+
+#sidebar_container {
+/* border-left: 1px solid #ccc; */
+ float: left;
+ width: 33%;
+ text-align: left;
+}
+
+#sidebar_content {
+ padding: 10px;
+}
+
+#sidebar_content h2 {
+ margin: 0px 0px 5px 0px;
+}
+
+#content .half {
+ float: left;
+ width: 49%;
+ text-align: left;
+ margin: 0 0 12px 0;
+}
+
+#content .full_bio {
+ float: left;
+ text-align: center;
+ margin: 0 0 12px 0;
+}
+
+#content .half_bio {
+ float: left;
+ width: 49%;
+ text-align: center;
+ margin: 0 0 12px 0;
+}
+
+#content .third_bio {
+ float: left;
+ width: 33%;
+ text-align: center;
+ margin: 0 0 12px 0;
+}
+
+#content .fourth_bio {
+ float: left;
+ width: 24%;
+ text-align: center;
+ margin: 0 0 12px 0;
+}
+
+#content .full_bio p, #content .half_bio p, #content .third_bio p, #content .fourth_bio p {
+ margin: 0;
+ padding: 0 10px;
+}
+
+#content .full_bio img, #content .half_bio img, #content .third_bio img, #content .fourth_bio img {
+ border: 1px solid #999;
+ margin: 2px;
+ padding: 5px;
+}
+
+.content_box_head_green {
+/* border-top: 1px solid #AABBAA; */
+ border-top: 1px solid #A9C6A9;
+ border-right: 1px solid #A9C6A9;
+ border-left: 1px solid #A9C6A9;
+/* background: #CCDDA5; */
+ background-color: #A9C6A9;
+ font-weight: bold;
+ font-size: 12px;
+ color: #033C63;
+ line-height: 16px;
+ padding: 6px;
+}
+
+.content_box_head_blue {
+ border-top: 1px solid #1B5C92;
+ border-right: 1px solid #1B5C92;
+ border-left: 1px solid #1B5C92;
+ background-color: #1B5C92;
+ font-weight: bold;
+ font-size: 12px;
+ color: #FFF;
+ line-height: 16px;
+ padding: 6px;
+}
+
+.content_box_blue {
+ border: 1px solid #1B5C92;
+ border-top: 0px;
+ border-color: #1B5C92;
+ margin-bottom: 10px;
+ padding: 6px;
+}
+
+.content_box_green {
+ border: 1px solid #A9C6A9;
+ border-top: 0px;
+ border-color: #A9C6A9;
+ margin-bottom: 10px;
+ padding: 6px;
+}
+
+
+.catch_phrase {
+ color: #1B5C92;
+ font-weight: bold;
+ font-size: 18px;
+ font-style: italic;
+ text-align: center;
+}
+
+.centered_phrase {
+ text-align: center;
+ margin-top: 1em;
+ margin-bottom: .5em;
+}
+
+.collage {
+ margin-top: 30px;
+ margin-bottom: 30px;
+ margin-right: auto;
+ margin-left: auto;
+ width: 400px;
+ text-align:center;
+ background-color: #CEDEDA;
+ border: 5px solid #A9C6A9;
+}
+
+.featured_tools {
+ margin-top: 30px;
+}
+
+.more {
+ text-align: right;
+ font-size: 11px;
+}
+
+table.events {
+/* width: 100%; */
+/* border-top: 1px solid #A9C6A9; */
+/* border-right: 1px solid #A9C6A9; */
+ border-left: 1px solid #A9C6A9;
+/* border-bottom: 1px solid #A9C6A9; */
+ margin-top: 10px;
+}
+
+th.events {
+ color: #033C63;
+ border-right: 1px solid #A9C6A9;
+ border-bottom: 1px solid #A9C6A9;
+ border-left: 1px solid #A9C6A9;
+ border-top: 1px solid #A9C6A9;
+ text-align: left;
+ background: #A9C6A9;
+}
+
+td.events {
+ border-right: 1px solid #A9C6A9;
+ border-bottom: 1px solid #A9C6A9;
+ background: #FFF;
+}
+
+td.events_alt {
+ border-right: 1px solid #A9C6A9;
+ border-bottom: 1px solid #A9C6A9;
+ background: #F5FAFA;
+}
+
+img.section_head {
+ float: left;
+}
+
+div.evts {
+ overflow: auto;
+}
+
+.icon_green {
+ background-color: #A9C6A9;
+ background-image: url(../images/bg_rounded.gif);
+ background-repeat: no-repeat;
+ vertical-align:text-bottom;
+}
+
+.icon_blue {
+ background-color: #1B5C92;
+ background-image: url(../images/bg_rounded.gif);
+ background-repeat: no-repeat;
+ vertical-align:text-bottom;
+}
+
+.quick_link {
+ margin: 5px;
+}
+
+.content_box_highlight {
+ border: 2px solid #A9C6A9;
+/* border-color: #A9C6A9; */
+ background-color: #EDF3F1;
+ margin-top: 10px;
+ margin-bottom: 10px;
+ padding: 6px;
+}
+
+.screen_shot {
+ border: 3px solid #666;
+}
+
+.search {
+ margin-bottom: 10px;
+/* margin-top: 10px; */
+/* padding-top: 5px; */
+ padding-bottom: 5px;
+ border-bottom: 1px dotted #1B5C92;
+/* border-top: 1px dotted #1B5C92; */
+ font-size: 11px;
+}
+
+.search h1 {
+ font-size: 12px;
+ color: #1B5C92;
+ text-decoration: none;
+ border:none;
+ padding:0px;
+ margin:0px;
+}
+
+a.highlight_text_yellow, a:hover.highlight_text_yellow, a:visited.highlight_text_yellow, a:active.highlight_text_yellow {
+ font-size: 24px;
+ color: #E9BA56;
+ text-decoration:none;
+ font-weight: bold;
+}
+
+a.highlight_text_blue, a:hover.highlight_text_blue, a:visited.highlight_text_blue, a:active.highlight_text_blue {
+ font-size: 24px;
+ font-weight: bold;
+ color: #1B5C92;
+ text-decoration:none;
+}
+
+a.highlight_normal, a:hover.highlight_normal, a:visited.highlight_normal, a:active.highlight_normal {
+ font-size: 24px;
+ font-weight: normal;
+ color: #000000;
+ text-decoration:none;
+}
+
+h1.introduction {
+ padding: 0px;
+ margin: 0px;
+ border-bottom: 1px solid #CEDEDA;
+ font-size: 24px;
+ font-weight: bold;
+ color: #1B5C92;
+ text-decoration: none;
+}
+
+.blue_divider hr {
+display:none;
+}
+
+.blue_divider {
+border-bottom:1px solid #033C63;
+height:1px;
+}
+
+
+.crit em{
+ color: #009922;
+}
\ No newline at end of file
Added: phenote/trunk/doc/phenote-website/css/menu.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/menu.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/menu.css 2007-09-17 23:16:26 UTC (rev 912)
@@ -0,0 +1,68 @@
+/*
+ * Menu based on the incredible suckerfish:
+ * http://www.htmldog.com/articles/suckerfish/
+ */
+
+#menu ul {
+ width: 100%;
+ background: #033c63 url(../images/nav_bg.gif) repeat-x 0px 0px;
+ color: #ffffff;
+ float: left;
+ list-style: none;
+ padding: 0; /* Remove any previous setting */
+ padding-top: .33em;
+ padding-bottom: .33em;
+ margin: 0 0 0 0; /* Remove any previous setting */
+ /*border-width: 1px 0;*/
+ /*line-height: 1;*/
+ /*font-weight: bold;*/
+ /*border: solid #eda;*/
+ /*margin: 0 0 1em 0;*/
+}
+
+#menu a {
+ display: block;
+ width: 10em;
+ w\idth: 6em; /* IE 6 box hack */
+ color: #ffffff;
+ text-decoration: none;
+ padding: 0.25em 2em;
+}
+
+#menu li {
+ float: left;
+ padding: 0;
+ width: 10em;
+}
+
+#menu li ul {
+ background: #033c63; /* Remove the background image from sub-menu */
+ position: absolute;
+ left: -999em;
+ height: auto;
+ width: 14.4em;
+ w\idth: 13.9em; /* IE 6 box hack */
+ /*font-weight: normal;*/
+ /*border-width: 0.25em;*/
+ margin: 0;
+}
+
+#menu li li {
+ padding-right: .9em;
+ width: 13em
+}
+
+#menu li ul a {
+ width: 13em;
+ w\idth: 9em; /* IE 6 box hack */
+}
+
+#menu li:hover ul,
+#menu li.pseudohover ul {
+ left: auto;
+}
+
+#menu li:hover,
+#menu li.pseudohover {
+ background: #1b5c92;
+}
Added: phenote/trunk/doc/phenote-website/css/table.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/table.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/table.css 2007-09-17 23:16:26 UTC (rev 912)
@@ -0,0 +1,49 @@
+
+
+.themeTable td {
+ font-size: .9em;
+ text-align: left;
+ padding: 2px;
+}
+
+.themeTable th {
+ font-size: 1em;
+ text-align: center;
+ background: #ffffff;
+ border-width: 2px 0 2px 0;
+ border-style: solid;
+ border-color: #1b5c92;
+}
+
+.themeTable th a {
+ display: block;
+ padding: 3px;
+}
+
+.themeTable th a:hover {
+ color: #ffffff;
+ background: #444444;
+}
+
+.themeTable TH a:link,
+th a:visited {
+ color: #444444;
+}
+
+.themeTable td.evenRow {
+ background-color: #ccddcc;
+}
+
+.themeTable td.oddRow {
+ background-color: #ffffff;
+}
+
+.themeTable a:hover {
+ color: #ffffff;
+ background-color: #1b5c92;
+}
+
+.themeTable th a:hover {
+ color: #ffffff;
+ background-color: #1b5c92;
+}
Added: phenote/trunk/doc/phenote-website/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/download.shtml 2007-09-17 23:16:26 UTC (rev 912)
@@ -0,0 +1,92 @@
+<!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">
+ <head>
+
+ <!--#include virtual="ssi/head.html" -->
+ <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
+
+ </head>
+ <body>
+
+ <!--#include virtual="ssi/header.html" -->
+
+ <div id="main_container">
+ <div id="main_content">
+ <div class="catch_phrase">
+ </div>
+ <h2><a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Launch Phenote in your browser</a></h2>
+ <p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
+ <ul><li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></strong></li>
+ <li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.3/phenote.jnlp">1.3</a> </strong></li>
+ <li><a href="http://www.phenote.org/phenote/phenote.html">Older releases</a></li>
+ </ul>
+ <p> You may be prompted to sign a certificate and allow the download. This will take a few minutes the first time you do this.
+ </p>
+ <h2>Run Phenote at the command line</h2>
+ <p> To run phenote on the command line, linux or MacOSX users will need to checkout Phenote from the subversion repository. This can be done with the following command:</p>
+ <ul>
+ <li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.4-beta3/ phenote</b>
+ </li>
+ <li>Stable release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.3/ phenote</b>
+ </li>
+ <li>Latest: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote </b>
+ </li>
+ </ul>
+ <p>Once you've got it, you can run Phenote with ant with the command: <b>ant run</b>
+ </p>
+ <h2>Hardware requirements</h2>
+ <ul>
+ <li> 400 Mhz processor or faster.</li>
+ <li> 500+ MB RAM </li>
+ <li> 200 MB free disk space on your computer </li>
+ <li> Internet connection (broadband is best). Required for automatic updates of ontologies and some functions. </li>
+ </ul>
+ <h2>Software requirements</h2>
+ <ul>
+ <li> PC running Windows XP; Mac OSX; Linux </li>
+ <li> Webstart: Internet browser with webstart installed </li>
+ <li> Command line: Java 1.5 or later; Ant </li>
+ </ul>
+
+ </div>
+ </div>
+
+ <div id="sidebar_container">
+
+ <div id="sidebar_content">
+
+ <div class="content_box_head_blue">
+ Recently added features, version 1.4-beta3
+ </div>
+
+ <div class="content_box_blue">
+ <b>feature</b>: Native look-and-feel enabled for interface. Users should now see Mac or Windows style depending on their system.<br />
+ <b>feature</b>: read-only field (needs work)<br />
+ <b>feature</b>: config disabpng of copy of field (for db ids)<br />
+ <b>feature</b>: display property values of terms in term info<br />
+ <b>feature</b>: Phylogeny Chooser for NESCent/PhenoMap project. A user can import a phylogenetic tree in Newick format. The user can use the tree
+ viewer to select rows within the character template - typically taxonomic groups.<br />
+ <b>feature</b>: term fields can be nullified<br />
+ <b>feature</b>: separate queries to backend for different groups, implemented in worm<br />
+ <b>feature</b>: ID field type, requires ":"<br />
+ <b>feature</b>: can get unique list of deleted annots<br />
+ <b>feature</b>: added group adapter framework<br />
+ <b>feature</b>: fly genotype group adapter makes fly genotype strings from tab/group<br />
+ <b>feature</b>: worm group adapter makes reference terms from ref query<br />
+ <b>change</b>: on term completion if adding a letter use previous completion list<br />
+ <b>change</b>: worm adapter query tab working properly<br />
+ <b>change</b>: build file takes param for webstart version deployment, and puts in jnlp<br />
+ <b>change</b>: group adapters can psten for CharList changes<br />
+ <b>change</b>: added/corrected BIRN ontologies<br />
+ <b>bugfix</b>: load of file doesnt crash on post comp parsing bug<br />
+ <b>bugfix</b>: doesnt load obo files specified twice twice<br />
+ <b>bugfix</b>: view menu show up at initialization<br />
+ <b>bugfix</b>: layout of term history with split pane proper<br />
+ </div>
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
+
+ </body>
+</html>
Added: phenote/trunk/doc/phenote-website/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml~ (rev 0)
+++ phenote/trunk/doc/phenote-website/download.shtml~ 2007-09-17 23:16:26 UTC (rev 912)
@@ -0,0 +1,88 @@
+<!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">
+ <head>
+
+ <!--#include virtual="ssi/head.html" -->
+ <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
+
+ </head>
+ <body>
+
+ <!--#include virtual="ssi/header.html" -->
+
+ <div id="main_container">
+ <div id="main_content">
+ <div class="catch_phrase">
+ </div>
+ <h2><a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Launch Phenote in your browser</a></h2>
+ <p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
+ <ul><li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></strong></li>
+ <li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.3/phenote.jnlp">1.3</a> </strong></li>
+ <li><a href="http://www.phenote.org/phenote/phenote.html">Older releases</a></li>
+ </ul>
+ <p> You may be prompted to sign a certificate and allow the download. This will take a few minutes the first time you do this.
+ </p>
+ <h2>Run Phenote at the command line</h2>
+ <p> To run phenote on the command line, linux or MacOSX users will need to checkout Phenote from the subversion repository. This can be done with the following command:</p>
+ <ul><li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.4-beta3/ phenote</b> </li>
+ <li>Stable release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.3/ phenote</b>
+ <li>Latest: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote </b></li>
+ </ul>
+ <p>Once you've got it, you can run Phenote with ant with the command: <b>ant run</b>
+ </p>
+ <h2>Hardware requirements</h2>
+ <ul>
+ <li> 400 Mhz processor or faster.</li>
+ <li> 500+ MB RAM </li>
+ <li> 200 MB free disk space on your computer </li>
+ <li> Internet connection (broadband is best). Required for automatic updates of ontologies and some functions. </li>
+ </ul>
+ <h2>Software requirements</h2>
+ <ul>
+ <li> PC running Windows XP; Mac OSX; Linux </li>
+ <li> Webstart: Internet browser with webstart installed </li>
+ <li> Command line: Java 1.5 or later; Ant </li>
+ </ul>
+
+ </div>
+ </div>
+
+ <div id="sidebar_container">
+
+ <div id="sidebar_content">
+
+ <div class="content_box_head_blue">
+ Recently added features, version 1.4-beta3
+ </div>
+
+ <div class="content_box_blue">
+ <b>feature</b>: Native look-and-feel enabled for interface. Users should now see Mac or Windows style depending on their system.<br />
+ <b>feature</b>: read-only field (needs work)<br />
+ <b>feature</b>: config disabpng of copy of field (for db ids)<br />
+ <b>feature</b>: display property values of terms in term info<br />
+ <b>feature</b>: Phylogeny Chooser for NESCent/PhenoMap project. A user can import a phylogenetic tree in Newick format. The user can use the tree
+ viewer to select rows within the character template - typically taxonomic groups.<br />
+ <b>feature</b>: term fields can be nullified<br />
+ <b>feature</b>: separate queries to backend for different groups, implemented in worm<br />
+ <b>feature</b>: ID field type, requires ":"<br />
+ <b>feature</b>: can get unique list of deleted annots<br />
+ <b>feature</b>: added group adapter framework<br />
+ <b>feature</b>: fly genotype group adapter makes fly genotype strings from tab/group<br />
+ <b>feature</b>: worm group adapter makes reference terms from ref query<br />
+ <b>change</b>: on term completion if adding a letter use previous completion list<br />
+ <b>change</b>: worm adapter query tab working properly<br />
+ <b>change</b>: build file takes param for webstart version deployment, and puts in jnlp<br />
+ <b>change</b>: group adapters can psten for CharList changes<br />
+ <b>change</b>: added/corrected BIRN ontologies<br />
+ <b>bugfix</b>: load of file doesnt crash on post comp parsing bug<br />
+ <b>bugfix</b>: doesnt load obo files specified twice twice<br />
+ <b>bugfix</b>: view menu show up at initialization<br />
+ <b>bugfix</b>: layout of term history with split pane proper<br />
+ </div>
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
+
+ </body>
+</html>
Added: phenote/trunk/doc/phenote-website/events.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/events.shtml 2007-09-17 23:16:26 UTC (rev 912)
@@ -0,0 +1,107 @@
+<!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">
+ <head>
+
+ <!--#include virtual="ssi/head.html" -->
+ <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
+
+ </head>
+ <body>
+
+ <!--#include virtual="ssi/header.html" -->
+
+ <div id="main_container_aux">
+ <div id="main_content_aux">
+ <div class="catch_phrase">
+ News and Events
+ </div>
+
+ <h1>Upcoming Events, 2007</h1>
+ <h2>September</h2>
+ <ul>
+ <li>
+ </li>
+ </ul>
+
+ <h2>October</h2>
+ <ul>
+ <li>Oct 2, Phenote Users Group, Online
+ </li>
+ <li>Oct 23-25, Ontology Best Practices Workshop, <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">Biocurator Meeting</a>, Hayes Mansion, San Jose, CA
+ </li>
+ </ul>
+
+ <h2>November</h2>
+ <ul>
+ <li>Nov 6, Phenote Users Group, Online
+ </li>
+ <li>Nov 27, <a href="http://www.bioontology.org/">NCBO</a> Scientific Advisory Board meeting</li>
+ </ul>
+
+ <h2>December</h2>
+ <ul>
+ <li>Dec 4, Phenote Users Group, Online
+ </li>
+ </ul>
+
+ <h1>Past News and Events, 2007</h1>
+ <h2>September</h2>
+ <ul>
+ <li>Sept 17, New website released
+ </li>
+ <li>Sept 4, Phenote Users Group, Online
+ </li>
+ </ul>
+ <h2>August</h2>
+ <ul>
+ <li>Aug 29, Phenote Demo, <a href="http://darwin.nerc-oxford.ac.uk/gc_wiki/index.php/EnvO_Workshop">Environment Ontology Workshop</a>, Oxford, UK</li>
+ <li>Aug 28, new 1.4 beta 3 released [<a href="http://www.phenote.org/downloads.shtml">Release notes</a>...]</li>
+ <li>Aug 22-24, Phenote Demo, <a href="http://wiki.modencode.org/index.php/White">K. White group, ModENCODE</a>, Chicago, IL
+ </li>
+ <li>Apr 16, site visit, <a href="http://www.wormbase.org">Wormbase</a>, Pasadena, CA
+ </li>
+ <li>Aug 13-15, site visit, <a href="http://www.nbirn.net/research/mouse/index.shtm">BIRN</a>, San Diego, CA
+ </li>
+ <li>Aug 7, <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote:Agendas_.26_Transcripts">Phenote Users Group</a>, Online
+ </li>
+ </ul>
+ <h2>July</h2>
+ <ul>
+ <li>July 3, <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote:Agendas_.26_Transcripts">Phenote Users Group</a>, Online
+ </li>
+ </ul>
+ <h2>June</h2>
+ <ul>
+ <li>June 6, "Representing Phenotypes in OWL", <a href="http://owled2007.iut-velizy.uvsq.fr">OWL: Experiences and Directions Conference</a> Presentation, Innsbruck, Austria. [<a href="http://owled2007.iut-velizy.uvsq.fr/PapersPDF/paper_40.pdf">PDF</a>]
+ </li>
+ <li>June 5, <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote:Agendas_.26_Transcripts">Phenote Users Group</a>, Online
+ </li>
+ </ul>
+ <h2>May</h2>
+ <ul>
+ <li>May 1, <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote:Agendas_.26_Transcripts">Phenote Users Group</a>, Online
+ </li>
+ </ul>
+ <h2>April</h2>
+ <ul>
+ <li>Apr 12-13, site visit, <a href="http://www.nbirn.net/research/mouse/index.shtm">BIRN</a>, San Diego, CA
+ </li>
+ <li>Apr 11-12, site visit, <a href="http://www.wormbase.org">Wormbase</a>, Pasadena, CA
+ </li>
+ <li>Apr 10, <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote:Agendas_.26_Transcripts">Phenote Users Group</a>, Online
+ </li>
+ <li>Apr 5, <a href="http://www.bioontology.org/">NCBO</a> Scientific Advisory Board meeting</li>
+ </ul>
+ <h2>March</h2>
+ <ul>
+ <li>Mar 28-29, site visit, <a href="http://zfin.org">ZFin</a>, Eugene, OR
+ </li>
+ </ul>
+
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
+
+</body>
+</html>
Added: phenote/trunk/doc/phenote-website/events.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml~ (rev 0)
+++ phenote/trunk/doc/phenote-website/events.shtml~ 2007-09-17 23:16:26 UTC (rev 912)
@@ -0,0 +1,107 @@
+<!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">
+ <head>
+
+ <!--#include virtual="ssi/head.html" -->
+ <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
+
+ </head>
+ <body>
+
+ <!--#include virtual="ssi/header.html" -->
+
+ <div id="main_container_aux">
+ <div id="main_content_aux">
+ <div class="catch_phrase">
+ News and Events
+ </div>
+
+ <h1>Upcoming Events, 2007</h1>
+ <h2>September</h2>
+ <ul>
+ <li>
+ </li>
+ </ul>
+
+ <h2>October</h2>
+ <ul>
+ <li>Oct 2, Phenote Users Group, Online
+ </li>
+ <li>Oct 23-25, Ontology Best Practices Workshop, <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">Biocurator Meeting</a>, Hayes Mansion, San Jose, CA
+ </li>
+ </ul>
+
+ <h2>November</h2>
+ <ul>
+ <li>Nov 6, Phenote Users Group, Online
+ </li>
+ <li>Nov 27, <a href="http://www.bioontology.org/">NCBO</a> Scientific Advisory Board meeting</li>
+ </ul>
+
+ <h2>December</h2>
+ <ul>
+ <li>Dec 4, Phenote Users Group, Online
+ </li>
+ </ul>
+
+ <h1>Past Events, 2007</h1>
+ <h2>September</h2>
+ <ul>
+ <li>Sept 17, New website released
+ </li>
+ <li>Sept 4, Phenote Users Group, Online
+ </li>
+ </ul>
+ <h2>August</h2>
+ <ul>
+ <li>Aug 29, Phenote Demo, <a href="http://darwin.nerc-oxford.ac.uk/gc_wiki/index.php/EnvO_Workshop">Environment Ontology Workshop</a>, Oxford, UK</li>
+ <li>Aug 28, new 1.4 beta 3 released [<a href="http://www.phenote.org/downloads.shtml">Release notes</a>...]</li>
+ <li>Aug 22-24, Phenote Demo, <a href=...
[truncated message content] |
|
From: <nl...@us...> - 2007-09-17 23:43:24
|
Revision: 914
http://obo.svn.sourceforge.net/obo/?rev=914&view=rev
Author: nlw
Date: 2007-09-17 16:43:28 -0700 (Mon, 17 Sep 2007)
Log Message:
-----------
a few last changes to the website now that its deployed
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/faq.shtml
phenote/trunk/doc/phenote-website/irc_chat/index.shtml
phenote/trunk/doc/phenote-website/ssi/header.html
Added Paths:
-----------
phenote/trunk/doc/phenote-website/phenote-release-notes.shtml
phenote/trunk/doc/phenote-website/ssi/side.html
Removed Paths:
-------------
phenote/trunk/doc/phenote-website/LiteTemplate
phenote/trunk/doc/phenote-website/coordination.shtml
phenote/trunk/doc/phenote-website/index.shtml.~1.4.~
phenote/trunk/doc/phenote-website/ontologies.shtml
phenote/trunk/doc/phenote-website/ontologies.txt
phenote/trunk/doc/phenote-website/participate.shtml
phenote/trunk/doc/phenote-website/phenote-release-notes.html
phenote/trunk/doc/phenote-website/relatedprojects.shtml
phenote/trunk/doc/phenote-website/release-notes.shtml
Deleted: phenote/trunk/doc/phenote-website/LiteTemplate
===================================================================
Deleted: phenote/trunk/doc/phenote-website/coordination.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/coordination.shtml 2007-09-17 23:29:46 UTC (rev 913)
+++ phenote/trunk/doc/phenote-website/coordination.shtml 2007-09-17 23:43:28 UTC (rev 914)
@@ -1,122 +0,0 @@
-<!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">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Open Biomedical Ontologies Foundry</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container_aux">
- <div id="main_content_aux">
-
- <div class="catch_phrase">
- Coordination of the OBO Foundry
- </div>
-
- <p>
- The coordinators of the OBO Foundry are
- <a href="http://www.gen.cam.ac.uk/Research/ashburner.htm">
- Michael Ashburner
- </a>
- (NCBO, GO),
- <a href="http://www.berkeleybop.org/content/people/cjm/">
- Chris Mungall
- </a>
- (NCBO, GO, BBOP),
- Suzanna Lewis
- (NCBO, GO, BBOP), and
- <a href="http://ontology.buffalo.edu/smith/">
- Barry Smith
- </a>
- (NCBO, ORG).
- </p>
-
- <p>
- The intention is to provide light-weight management,
- although the growth of OBO may, in the future, necessitate a
- more formal structure. It is appropriate to view these
- people as facilitators who assist independent ontology
- developers: by organizing meetings, making introductions
- between different groups, offering comments when requested,
- engaging in e-mail discussions, making resources available,
- and other means. They work to ensure that the ontologies
- being developed are mutually compatible, expandable, and
- correctable in line with advances in biomedical
- science. Ontologies are tools of communication, and their
- utility rests on the network effects that come with wide
- acceptance. Experience thus far confirms that adherence to
- OBO principles is largely self-policing because of the
- positive benefits that accrue to individual members. The
- task of the OBO coordinators is to help to build this
- community.
- </p>
-
- <h1>Affiliations</h1>
-
- <h3>
- <a href="http://bioontology.org/">
- National Center for Biomedical Ontology (NCBO)
- </a>
- </h3>
- <p>
- The NCBO is a consortium of leading biologists, clinicians,
- informaticians, and ontologists who develop innovative
- technology and methods that allow scientists to create,
- disseminate, and manage biomedical information and knowledge
- in machine-processable form.
- </p>
-
- <h3>
- <a href="http://org.buffalo.edu/">
- Ontology Research Group (ORG)
- </a>
- </h3>
- <p>
- The ORG is located in the New York State Center of
- Excellence in Bioinformatics and Life Sciences
- http://bioinformatics.buffalo.edu/ in Buffalo. It is engaged
- in foundational ontology research and in biomedical ontology
- development in the domain of biology and clinical
- medicine. A special focus of research is electronic health
- records.
- </p>
-
- <h3>
- <a href="http://www.geneontology.org">
- Gene Ontology (GO)
- </a>
- </h3>
- <p>
- The GO project provides a controlled voc abulary to describe
- gene and gene product attributes in any organism. Members of
- the GO Consortium supply annotations of gene products using
- this vocabulary which can be viewed and downloaded via the
- GO website.
- </p>
- <h3>
- <a href="http://www.berkeleybop.org/">
- Berkeley Bioinformatics and Ontologies Project (BBOP)
- </a>
- </h3>
- <p>
- The BBOP is 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 The Gene Ontology, The National Center
- for Biomedical Ontology, and the Generic Model Organism
- Database Project.
- </p>
-
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
Modified: phenote/trunk/doc/phenote-website/faq.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/faq.shtml 2007-09-17 23:29:46 UTC (rev 913)
+++ phenote/trunk/doc/phenote-website/faq.shtml 2007-09-17 23:43:28 UTC (rev 914)
@@ -19,7 +19,7 @@
<h1>General</h1>
<h3>How do I get started?</h3>
<p>
- You can lauch Phenote directly from your browser. Simply click on the Launch Phenote 'quick link' from the <a href="http://www.phenote.org/">main page</a> or the <a href="http://www.phenote.org/downloads.shtml">Downloads</a> page, and it will launch directly from your browser. It will take a couple of minutes to download all the components, but that's it.
+ You can lauch Phenote directly from your browser. Simply click on the Launch Phenote 'quick link' from the <a href="http://www.phenote.org/">main page</a> or the <a href="http://www.phenote.org/software.shtml">Software</a> page, and it will launch directly from your browser. It will take a couple of minutes to download all the components, but that's it.
</p>
<h3>What's the best forum to ask my burning questions?</h3>
<p>
Deleted: phenote/trunk/doc/phenote-website/index.shtml.~1.4.~
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml.~1.4.~ 2007-09-17 23:29:46 UTC (rev 913)
+++ phenote/trunk/doc/phenote-website/index.shtml.~1.4.~ 2007-09-17 23:43:28 UTC (rev 914)
@@ -1,114 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
- "http://www.w3.org/TR/html4/strict.dtd">
-<html lang="en">
-<head>
- <title>OBO Main</title>
- <link href="/css/stylesheet.css" rel="stylesheet" type="text/css" media="screen" />
- <meta http-equiv="content-type" content="text/html; charset=iso-8859-1" />
- <meta name="description" content="Open Biomedical Ontologies, a collection of freely available well-structured controlled vocabularies." />
-<script src="obfuscate.js" type="text/javascript"></script>
-</head>
-<body>
-
-<div id="header">
- <h1>the obo foundry </h1>
-</div>
-
-<div id="content">
-
-<div class="main-text">
- <div id="about">
-<p>The Open Biomedical Ontologies (OBO) Foundry is a collaborative experiment: to produce well-structured vocabularies for shared use across different biological and medical domains.
- The OBO Foundry introduces a new paradigm for biomedical ontology development by the establishment of gold standard reference ontologies for individual domains of inquiry.
-</p>
-
-<p>
-Those involved comprise a group of biological researchers and ontology developers who agree in advance to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies within the broader OBO framework, and also to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain.
-</p>
-<p>
-By joining the OBO Foundry, the authors of an ontology commit to its maintenance in light of scientific advance, and to soliciting community feedback for its improvement. They also give an assurance that they will work with other Foundry members to ensure that, for any particular domain, there is community convergence on a single reference ontology. Application ontologies developed for specific purposes can then be referred back to this common reference, which will be updated in light of scientific advance. In this way application ontologies, too, for example the application ontologies developed for purposes of managing clinical trial data, can take advantage of the Foundry methodology.
-</p>
-<p>
-This site contains ontologies and points to some other efforts within the community. Ideally we see a range of ontologies being designed for biomedical domains. Some of these will be generic and apply across all organisms and others will be more restricted in scope, for example to specific taxonomic groups.
-</p>
- <ul>
- <li>
- <a href="../cgi-bin/table.cgi" class="site">View the OBO Foundry ontologies in table form</a>
- </li>
- <li>
- <a href="browse.shtml" class="site">Browse the index of the OBO Foundry ontologies</a>
- </li>
- </ul>
- </div>
- <div>
- <h2>coordinators</h2>
- <p><br>
-
-The coordinators of the OBO Foundry are <a
-href="http://www.gen.cam.ac.uk/Research/ashburner.htm">Michael Ashburner</a>
-(NCBO, GO), <a href="http://www.berkeleybop.org/content/people/cjm/">Chris
-Mungall</a> (NCBO, GO, BBOP), Suzanna Lewis (NCBO, GO, BBOP), and <a
-href="http://ontology.buffalo.edu/smith/">Barry Smith</a> (NCBO, ORG).
-
- </p>
- <h3><a href="http://bioontology.org/">National Center for Biomedical Ontology (NCBO)</a></h3>
- <p class="description">
- The NCBO is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods that allow scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form.
- </p>
- <h3> <a href="http://org.buffalo.edu/">Ontology Research Group (ORG)</a></h3>
- <p class="description">
- The ORG is located in the New York State Center of Excellence in Bioinformatics and Life Sciences http://bioinformatics.buffalo.edu/ in Buffalo. It is engaged in foundational ontology research and in biomedical ontology development in the domain of biology and clinical medicine. A special focus of research is electronic health records.
- </p>
- <h3><a href="http://www.geneontology.org">Gene Ontology (GO)</a></h3>
- <p class="description">
- The GO project provides a controlled voc abulary to describe gene and gene product attributes in any organism. Members of the GO Consortium supply annotations of gene products using this vocabulary which can be viewed and downloaded via the GO website.
- </p>
- <h3><a href="http://www.berkeleybop.org/">Berkeley Bioinformatics and Ontologies Project (BBOP)</a></h3>
- <p class="description">
- The BBOP is 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 The Gene Ontology, The National Center for Biomedical Ontology, and the Generic Model Organism Database Project.
- </p>
- </div>
- <div>
- <h2>related projects</h2>
- <h3> <a href="http://www.gmod.org/">Generic Model Organism Databases</a></h3>
- <p class="description">
- The Generic Model Organism Project (GMOD) is a joint effort by the model organism system databases WormBase, FlyBase, MGI, SGD, Gramene, Rat Genome Database, EcoCyc, and TAIR to develop reusable components suitable for creating new community databases of biology.
- </p>
- <h3><a href="http://ifomis.org">Institute for Formal Ontology and Medical Information Science
-(IFOMIS)</a></h3>
- <p class="description">
-The Institute for Formal Ontology and Medical Information Science
-(IFOMIS) comprehends an interdisciplinary research group with members
-from Philosophy, Computer and Information Science, Logic, Medicine,
-and Medical Informatics, focusing on theoretically grounded research
-in both formal and applied ontology.
- </p>
- <h3><a href="http://mged.sf.net/">MGED</a></h3>
- <p class="description">
- The Microarray Gene Expression Data (MGED) Society is an international organisation of biologists, computer scientists, and data analysts that aims to facilitate the sharing of microarray data generated by functional genomics and proteomics experiments.
- </p>
- <h3><a href="http://www.ebi.ac.uk/ontology-lookup/">Ontology Lookup Service</a></h3>
- <p class="description">
- The Ontology Lookup Service is a spin-off of the PRIDE project, which required a centralized query interface for ontology and controlled vocabulary lookup. While many of the ontologies queriable by the OLS are available online, each has its own query interface and output format. The OLS provides a web service interface to query multiple ontologies from a single location with a unified output format.
- </p>
- <h3><a href="http://www.plantontology.org/">Plant Ontology Consortium</a></h3>
- <p class="description">
- The Plant Ontology Consortium (POC) aims to develop, curate and share structured controlled vocabularies (ontologies) that describe plant structures and growth/developmental stages. Through this effort, the project aims to facilitate cross database querying by fostering consistent use of these vocabularies in the annotation of tissue and/or growth stage specific expression of genes, proteins and phenotypes.
- </p>
- <h3><a href="http://www.psidev.info/index.php?q=node/258">Proteomics Standards Initiative</a></h3>
- <p class="description">
- Is also interested in guidelines for the development of Controlled Vocabularies.
- </p>
- <h3><a href="http://www.sofg.org/">Standards and Ontologies for Functional Genomics</a></h3>
- <p class="description">
- SOFG is both a meeting and a website; it aims to bring together biologists, bioinformaticians, and computer scientists who are developing and using standards and ontologies with an emphasis on describing high-throughput functional genomics experiments.
- </p>
- </div>
-</div>
-
-<!--#include virtual="/ssi/navi_bar.html" -->
-
-</div>
-
-</body>
-</html>
Modified: phenote/trunk/doc/phenote-website/irc_chat/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/index.shtml 2007-09-17 23:29:46 UTC (rev 913)
+++ phenote/trunk/doc/phenote-website/irc_chat/index.shtml 2007-09-17 23:43:28 UTC (rev 914)
@@ -1,11 +1,21 @@
-<!--#include virtual="/ssi/header.html" -->
-<div id="page_body">
+<!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">
+ <head>
-<!--#include virtual="/ssi/navi_home.html" -->
+ <!--#include virtual="ssi/head.html" -->
+ <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
-<div id="main_content">
-<h2>Phenote Working Group IRC Chat</h2>
+ </head>
+ <body>
+ <!--#include virtual="ssi/header.html" -->
+
+ <div id="main_container_aux">
+ <div id="main_content_aux">
+ <div class="catch_phrase">
+ Phenote Working Group IRC Chat
+ </div>
+
When: First Tuesday of every month; 8:30am <br/>
<p>You will need an IRC client to visit our chats. You can download any number of <a href="/irc_chat/irc_clients.shtml">free clients</a> to do this. You'll need to connect to the <b>irc.sf.net</b> and join the <b>#phenote</b> channel. </p>
@@ -34,3 +44,5 @@
<!--#include virtual="/ssi/footer.shtml" -->
+ </body>
+</html>
\ No newline at end of file
Deleted: phenote/trunk/doc/phenote-website/ontologies.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/ontologies.shtml 2007-09-17 23:29:46 UTC (rev 913)
+++ phenote/trunk/doc/phenote-website/ontologies.shtml 2007-09-17 23:43:28 UTC (rev 914)
@@ -1,85 +0,0 @@
-<!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">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Open Biomedical Ontologies Foundry</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container_aux">
- <div id="main_content_aux">
- <div class="catch_phrase">
- The Ontologies of the OBO Foundry
- </div>
-
- <h3>
- <a href="crit.shtml">
- Current Principles
- </a>
- </h3>
- <p>
- OBO consists of ontologies which either conform to, or are
- committed to working towards conforming to, the OBO Foundry
- principles. The OBO coordinators are committed to working
- with ontology developers to aid this process, and they are
- also committed to keeping these Foundry Principles under
- review.
- </p>
-
- <h3>
- <a href="http://www.obofoundry.org">
- Ontology Table
- </a>
- </h3>
- <p>
- Our main page contains a tabular listing of the current set
- of ontologies in the OBO Foundry. The table can be sorted by
- clicking on column headings, and you can find further
- information by clicking on the ontology name.
- </p>
-
- <h3>
- <a href="browse.shtml">
- Ontology Browser
- </a>
- </h3>
- <p>
- An indexed view of the current set of ontologies in the OBO
- Foundry organized by domains. Nodes can be expanded and
- collapsed, and the leaf nodes link to further information.
- </p>
-
- <h3>
- <a href="http://www.berkeleybop.org/ontologies">
- Downloads
- </a>
- </h3>
- <p>
- All of the current set of ontologies in the OBO Foundry are
- available here to download in a variety of different
- representations: obo_xml, obo format, owl, chadoxml, rdf,
- tabular, prolog, and others. Updated nightly.
- </p>
-
- <h3>
- <a href="http://sourceforge.net/cvs/?group_id=76834">
- Ontology repository
- </a>
- </h3>
- <p>
- Many of the OBO Foundry ontologies are maintained in this
- CVS repository. You can browse and download the active
- versions of these ontologies here.
- </p>
-
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/ontologies.txt
===================================================================
Deleted: phenote/trunk/doc/phenote-website/participate.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/participate.shtml 2007-09-17 23:29:46 UTC (rev 913)
+++ phenote/trunk/doc/phenote-website/participate.shtml 2007-09-17 23:43:28 UTC (rev 914)
@@ -1,74 +0,0 @@
-<!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">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Open Biomedical Ontologies Foundry</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container_aux">
- <div id="main_content_aux">
- <div class="catch_phrase">
- Participation in the OBO Foundry
- </div>
-
- <h3><a href="join.shtml">Join</a></h3>
- <p>
- How any group that is in the process of developing an
- ontology and who would like to join the foundry can do this.
- </p>
-
- <h3>
- <a href="http://obofoundry.org/wiki/index.php/Main_Page">
- OBO Wiki
- </a>
- </h3>
- <p>
- Not much here yet, but contributions are welcome. If you
- would like an account on the wiki, please contact the
- <script type="text/javascript">
- obfuscate("lbl.gov","sjcarbon","OBO webmaster");
- </script>.
- </p>
-
- <h3>
- <a href="http://www.obofoundry.org/cgi-bin/discussion.cgi">
- Discussion
- </a>
- </h3>
- <p>
- A list of all of the OBO Foundry discussion lists, archives,
- and how to subscribe.
- </p>
-
- <h3>
- <a href="http://lists.sourceforge.net/lists/listinfo/obo-discuss">
- Subscribe
- </a>
- </h3>
- <p>
- Click here to subscribe (or unsubscribe) to the primary OBO
- discussion list.
- </p>
-
- <h3>
- <a href="mailto:obo...@li...">
- Contact
- </a>
- </h3>
- <p>
- Send us an e-mail with your questions, perspectives, and
- critiques.
- </p>
-
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/phenote-release-notes.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-09-17 23:29:46 UTC (rev 913)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-09-17 23:43:28 UTC (rev 914)
@@ -1,654 +0,0 @@
-<!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 Release Notes</title>
-</head>
-
-
-<body>
-
-<h1>Phenote Release Notes</h1>
-
-<h2>1.4 </h2>
-08.28.2007, version <a href="phenote/1.4-beta3/phenote.jnlp">1.4-beta3</a><br>
-<ul>
- <li>feature: Native look-and-feel enabled for interface. Users should now see Mac or Windows style depending on their system.</li>
- <li>feature: read-only field (needs work)</li>
- <li>feature: config disabling of copy of field (for db ids)</li>
- <li>feature: display property values of terms in term info</li>
- <li>feature: Phylogeny Chooser for NESCent/PhenoMap project. A user can import a phylogenetic tree in Newick format. The user can use the tree
- viewer to select rows within the character template - typically taxonomic groups.</li>
- <li>feature: term fields can be nullified</li>
- <li>feature: separate queries to backend for different groups, implemented in worm</li>
- <li>feature: ID field type, requires ":"</li>
- <li>feature: can get unique list of deleted annots</li>
- <li>feature: added group adapter framework</li>
- <li>feature: fly genotype group adapter makes fly genotype strings from tab/group</li>
- <li>feature: worm group adapter makes reference terms from ref query</li>
- <li>change: on term completion if adding a letter use previous completion list</li>
- <li>change: worm adapter query tab working properly</li>
- <li>change: build file takes param for webstart version deployment, and puts in jnlp</li>
- <li>change: group adapters can listen for CharList changes</li>
- <li>change: added/corrected birn ontologies</li>
- <li>bugfix: load of file doesnt crash on post comp parsing bug</li>
- <li>bugfix: doesnt load obo files specified twice twice</li>
- <li>bugfix: view menu show up at initialization</li>
- <li>bugfix: layout of term history with split pane proper</li>
-</ul>
-<br>
-07.20.2007, version <a href="phenote/1.4-beta2/phenote.jnlp">1.4-beta2</a><br>
-
-<ul>
-
- <li>feature: RESTful data input for BIRN's smart atlas</li>
-
- <li>feature: Character Template for NESCent/CToL (Jim Balhoff). This
-is an additional window which edits a separate list of characters using
-a subset of the fields in the main window. The fields to include are
-denoted by a group in the config file. This functionality will be used
-by the PhenoMap project to create a specimen list. The same EQ
-statement can be applied to many specimens at once by selecting the
-relevant specimens and generating characters in the main window with
-the template fields pre-filled. All the new characters are selected and
-can then be bulk edited.</li>
-
- <li>feature: Progress on gui for config (in progress)</li>
-
- <li>feature: Progress on field groups (genotype maker, pub querying...)</li>
-
- <li>feature: right-click editing functions for free-text fields in data input frame. right-click copy in table.</li>
-
- <li>feature: incorporation of help documentation into Phenote under menu item Help->PhenoteHelp </li>
-
- <li>feature: added plant_grammene.cfg configuration, plus appropriate obo files.</li>
-
- <li>feature: navigation bar added to top of term info; buttons to traverse worn paths; term name moved up to top of box [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1685540&group_id=76834&atid=887913">1685540</a>]</li>
-
- <li>feature: dbxrefs are listed in term info (no external links yet) [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1739399&group_id=76834&atid=887913">1739399</a>]</li>
-
- <li>change: ontology files can be read with dangling references</li>
-
- <li>change: Command line read & write of .tab</li>
-
- <li>change: 'use term' button moved and replaced with checkmark button in navigation bar</li>
-
- <li>change: ncbo.cfg changed to always update from master file at url</li>
-
- <li>change: birn2.cfg gene_ontology replaced with gene_ontology_edit.obo reference</li>
-
- <li>change: Windows splash screen text edited from 'biomedial' to 'biomedical'</li>
-
- <li>bugfix: obsolete terms were not being read in from annotation files as Ontology.getTerm was only looking at non obsoleted terms</li>
-
- <li>known bug: ontology files using import statements not properly read</li>
-
-</ul>
-
-
-<h3>version 1.4-beta1 - oops - skipped!</h3>
-
-
-
-<h2>1.3</h2>
-
-
-05.24.2007, version <a href="phenote/1.3/phenote.jnlp">1.3 release</a><br>
-
-<ul>
-
- <li>feature: <a href="http://www.phenote.org/help/">Web-based documentation and Help features.</a></li>
-
- <li>feature: Metadata fields added to configuration. User can name their configuration, add a description, and author [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1676756&group_id=76834&atid=887913">1676756</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1672080&group_id=76834&atid=887913">1672080</a>]</li>
-
- <li>feature: Descriptions can be added for fields </li>
-
- <li>feature: Master-to-local overwrite stuff</li>
-
- <li>feature: Dialog allows user to back out of exiting from File->Exit</li>
-
- <li>feature: Autocompletion search default settings configurable <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1677411&group_id=76834&atid=887913">1677411</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1669579&group_id=76834&atid=887913">1669579</a>]
- </li>
-
- <li>feature: User can save search setting defaults if changed during Phenote session</li>
-
- <li>change: File->New is disabled until next version</li>
-
- <li>change: ncbo, zfin-standalone, flybase, demo configurations
-modified to include master-overwrite feature; keeping track of revision
-history in file comments </li>
-
- <li>change: can read http, https, ftp, ftps for ontology update URLs, not just http [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1718945&group_id=76834&atid=887913">1718945</a>]</li>
-
- <li>bugfix: Bulk-editing functions are working again</li>
-
- <li>bugfix: Undo wasn't working for several functions due to a bug in the Copy function [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721044&group_id=76834&atid=887913"> 1721044</a>]</li>
-
- <li>bugfix: multi-select deletes free-text content replaces with * [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721032&group_id=76834&atid=887913">1721032</a>]</li>
-
- <li>bugfix: pre 1.2 post comp data wasnt able to load<big> </big>[<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721470&group_id=76834&atid=887913">1721470</a>]</li>
-
-</ul>
-
-
-
-
-05.09.2007, version <a href="phenote/1.3-beta1/phenote.jnlp">1.3-beta1</a><br>
-
-
-
-<ul>
-
- <li>feature: Added sample config for BIRN</li>
-
- <li>feature: Added SAO.obo ontology for BIRN</li>
-
- <li>feature: Namespace config writes back</li>
-
- <li>feature: Can specify more than one website for ontology update</li>
-
- <li>feature: Empty field shows all terms in ontology rather than none</li>
-
- <li>feature: Can add more differentia to post comp</li>
-
- <li>bugfix: Config update/merge bug where fields in wrong order fixed.</li>
-
- <li>known bug: can't read post-compositions from phenote versions 1.1 and prior</li>
-
-</ul>
-
-
-
-
-<h2>1.2
-<hr></h2>
-
-
-
-05.02.2007, version <a href="phenote/1.2/phenote.jnlp">1.2</a><br>
-
-
-<ul>
-
- <li>feature: Can post-compose with >2 terms </li>
-
- <li>feature: Term history display can be toggled on/off (Settings->Term History menu)</li>
-
- <li>feature: Synonyms delineated by scope in Term Info: Exact,
-Narrow, Broad, General, Related. If the synonym category is given, it
-is displayed. For example, the term 'water' has the <i>related</i> synonym H2O, which has the category of a chemical <i>formula</i>.</li>
-
- <li>feature: Obsolete replacements or consideration terms are displayed in term info with links</li>
-
- <li>feature: Display term comments in Term Info beneath relationships</li>
-
- <li>feature: Loading splash screen </li>
-
- <li>feature: Can configure by namespace for ontologies</li>
-
- <li>feature: Can automatically update ontologies during startup (configurable)</li>
-
- <li>feature: Timer added to configuration during ontology update check (configurable)</li>
-
- <li>feature: Can check which version of phenote is running by selecting Help->About.</li>
-
- <li>feature: Added common configuration for OMIM curation for use by NCBO (ncbo.cfg).</li>
-
- <li>feature: can forward and reverse sort columns by repeatedly clicking on column header [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574916&group_id=76834&atid=887913">1574916</a>]</li>
-
- <li>feature: display ontology namespace in term info box [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1598048&group_id=76834&atid=887913">1598048</a>]</li>
-
- <li>change: Search filters moved into menu </li>
-
- <li>change: Updates to the zfin-standalone.cfg for the zebrafish community annotation; only includes GO and ZFanatomy ontologies. </li>
-
- <li>bugfix: Free-text field text not sticking in "new" or blank rows </li>
-
-</ul>
-
-
-
-
-<h2>1.1
-<hr></h2>
-
-
-
-04.06.2007, version <a href="phenote/1.1/phenote.jnlp">1.1.3</a><br>
-
-
-<ul>
-
- <li>feature: User can change the configuration they want to use at
-initialization from file menu; change takes effect after restart.
-(previously user had to edit the .phenote/conf/my-phenote file).</li>
-
-</ul>
-
-
-
-03.28.2007, version 1.1.1<br>
-
-
-
-<ul>
-
- <li>feature: Phenote is now a single webstart app; user chooses
-their configuration at startup (used to be hard wired to a
-configuration)</li>
-
- <li>feature: Phenote will merge its default configuration with users' configuration,
-preserving user changes as well as adding anything new from phenote
-upgrade.</li>
-
- <li>feature: Beginnings of term history to display recently used ontology terms. Will be clickable in future.</li>
-
- <li>feature: Data entry panel will spill over into multiple tabs if >12 fields included</li>
-
- <li>feature: Tab delimited data adapter; data in/output format compatible with excel and other spreadsheet software [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661778&group_id=76834&atid=887913">1661778</a>]</li>
-
- <li>feature: QueryableDataAdapter interface for developers; enables
-connection between input fields and a database backend for quering.
-Queryable fields get a retrieve button.</li>
-
- <li>feature: Autocompletion search with ALL ontologies in a field instead of just one [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1575241&group_id=76834&atid=887913">1575241</a>]</li>
-
- <li>feature: Retrieve ontology files from URL if more up to date or no local found; only from a single repository for all [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1648337&group_id=76834&atid=887913">1648337</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574906&group_id=76834&atid=887913">1574906</a>]</li>
-
- <li>feature: fixed releases available for checkout via sourceforge [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1670345&group_id=76834&atid=887913">1670345</a>]</li>
-
- <li>feature: display xtns in load/save menu choices [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1594508&group_id=76834&atid=887913">1594508</a>]</li>
-
- <li>change: Refactored code for field guis</li>
-
- <li>change: Layout improved</li>
-
- <li>change: OBSOLETE is displayed in red next to obsolete term in term info [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1581589&group_id=76834&atid=887913">1581589</a>]</li>
-
- <li>change: human.cfg configuration to include obo foundary ontologies GO, SO, CL, ChEBI, PATO, OBI, Relations, unit, and spatial [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1633287&group_id=76834&atid=887913">1633287</a>]</li>
-
- <li>bugfix: Ontology chooser reflects current term</li>
-
- <li>bugfix: phenosyntax reader broken [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1684591&group_id=76834&atid=887913">1684591</a>]</li>
-
- <li>bugfix: post-composed terms not loading [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661728&group_id=76834&atid=887913">1661728</a>]</li>
-
-</ul>
-
-
-
-<h2>1.0
-<hr></h2>
-
-
-
-02.06.2007, version <a href="phenote/1.0/phenote-flybase.jnlp">1.0.5-fly</a>, <a href="1.0/phenote-zfin.jnlp">1.0.5-zfin</a><br>
-
-
-
-01.12.2007, version1.0,
-<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby
-Phenote(components used by Zfin)</a><br>
-
-
-
-<ul>
-
-
-
- <li>change: refactoring of the data model to allow addition of any
-field desired, not just E,Q,GC,GT,Pub. Stage, Evidence, Description,
-Abnormal, and Absent have been added through this new mechanism in the
-newest configurations. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574912&group_id=76834&atid=887913">1574912</a>]</li>
-
- <li>change: Webby phenote is now using JSP and Spring.</li>
-
- <li>change: 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.</li>
-
- <li>bugfix: absent fields not displaying in human 1.03 [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661973&group_id=76834&atid=887913">1661973</a>]</li>
-
-</ul>
-
-
-
-<h2>0.9
-<hr></h2>
-
-
-
-11.15.2006, version <a href="phenote/0.9/phenote-flybase.jnlp">0.9-fly</a>,
-<a href="phenote/0.9/phenote-zfin.jnlp">0.9-zfin</a>,
-<a href="http://165.124.152.194/web/html/interface.html">DictyBase
-webby phenote</a><br>
-
-
-
-11.09.2006, version 0.9<br>
-
-
-
-<ul>
-
-
-
- <li>feature: Undo - can step backward through previous actions</li>
-
- <li>feature: Quartz scheduler used to schedule when to check for new obo files. Added by Christian Pich of Zfin. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1588669&group_id=76834&atid=887913">1588669</a>]</li>
-
- <li>change: upgraded PhenoteServlet to Spring framework. Added by Christian Pich [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1588670&group_id=76834&atid=887913">1588670</a>]</li>
-
- <li>feature: Synonyms are displayed from autocomplete with [syn]; when
-selected the term name (not the synonym) goes into the field and table (webby & standalone)</li>
-
- <li>feature: obsoletes are displayed from autocomplete with [obs]</li>
-
- <li>feature: Bulk update & copy in standalone. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1579885&group_id=76834&atid=887913">1579885</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1579882&group_id=76834&atid=887913">1579882</a>] </li>
-
- <li>change: search types interface changed from radio buttons to checkboxes (j. balhoff)</li>
-
- <li>bugfix: file-save button changed to say "save" not "load"</li>
-
- <li>feature: file-save recognizes and chooses appropriate data
-adapter based on file extension (.psx for phenosyntax and .xml for
-phenoxml)</li>
-
- <li>change: Single quotes escaped for javascript fns.</li>
-
-</ul>
-
-
-
-<h2>0.8
-<hr></h2>
-
-
-10.02.2006, version <a href="phenote/0.8/phenote-flybase.jnlp">0.8-fly</a>,
-<a href="phenote/0.8/phenote-zfin.jnlp">0.8-zfin</a>,
-<a href="http://165.124.152.194/web/html/interface.html">DictyBase
-webby phenote</a><br>
-
-
-
-<ul>
-
- <li>feature: Added post composition to standalone phenote. </li>
-
- <li>feature: Actions are logged for both webby/servlet & standalone.</li>
-
- <li>feature: Pheno-xml reader (thanks to Jim Balhoff) and improvements to pheno-xml
-writer (does pub & genetic context)</li>
-
- <li> feature: Command line reading & writing of phenoxml & phenosyntax.</li>
-
- <li>feature: Application exits on window exit (unless servlet)</li>
-
- <li>feature: Can filter out stage terms from zfin anatomy</li>
-
-</ul>
-
-
-
-
-<h2>0.7
-<hr></h2>
-
-
-
-08.23.2007, version <a href="phenote/0.7/phenote-flybase.jnlp">0.7-fly.</a>,
-<a href="0.7/phenote-zfin.jnlp">0.7-zfin</a><br>
-
-
-
-<ul>
-
-
-
- <li>feature: entity chooser (web)</li>
-
- <li>feature: 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).</li>
-
- <li>feature: entity field and term info installed into zfin (web)
-phenotype site. Term info & completion are scrollable.</li>
-
- <li>feature: standalone version can read & write pheno-syntax with ids & term names in comments</li>
-
- <li>feature: standalone entity chooser</li>
-
- <li>feature: added pub field</li>
-
- <li>feature: added 'use term' button in term info</li>
-
- <li>feature: can sort table by any field in forward order by clicking on headers</li>
-
- <li>change: personal config file gets copied out of jar</li>
-
- <li>change: directory for file load/save remembered</li>
-
- <li>change: layout fixed</li>
-
- <li>bugfix: paste for mac fixed</li>
-
-</ul>
-
-
-
-<h2>0.6
-<hr></h2>
-
-
-
-07.28.2006, version <a href="phenote/0.6/phenote-flybase.jnlp">0.6-fly</a>, <a href="phenote/0.6/phenote-zfin.jnlp">0.6-zfin</a>,
-<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote
-(0.6)</a><br>
-
-
-
-<ul>
-
-
-
- <li>new: webbified 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! </li>
-
- <li> feature: writing pheno-xml format, and uses the latest
-PATO ontology (as of July 28, 2006).</li>
-
-</ul>
-
-
-
-<h2>0.5
-<hr></h2>
-
-
-
-05.12.2006, version <a href="phenote/0.5/phenote-flybase.jnlp">0.5-FlyBase</a>, <a href="phenote/0.5/phenote-zfin.jnlp">0.5-ZFIN</a><br>
-
-
-
-<p>
-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
-adapters. The FlyBase data adapter simply cuts and pastes phenotype
-character objects to the system clipboard. The idea is that FlyBase's
-Proforma java application will also cut and paste to the clipboard.
-This is a simple way to pass objects between applications, to get us
-off the ground. Proforma is not there yet so this has not been
-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.</p>
-
-
-
-
-<h2>0.4
-<hr></h2>
-
-
-
-04.26.2006, version <a href="phenote/0.4/phenote-flybase.jnlp">0.4-flybase</a>, <a href="phenote/0.4/phenote-zfin.jnlp">0.4-zfin</a><br>
-
-
-<ul>
-
- <li>feature: Added Genetic Context field.</li>
-
- <li>feature: Parent & child terms in term info are now clickable/navigable.</li>
-
- <li>feature: HTML Links in descriptions are clickable (should bring up default browser)</li>
-
- <li>feature: configuration files 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.
-This allows for having separate zf & fb releases without having to
-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.</li>
-
- <li>bugfix: can't delete to 0 rows</li>
-
- <li>bugfix: synonym search duplicates removed</li>
-
- <li>Development: 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.</li>
-
- <li>Development: Renamed Phenotype to Character. Added Character interface CharacterI.</li>
-
- <li>Development: Added tests to test suite.</li>
-
-</ul>
-
-
-
-
-<h2>0.3
-<hr></h2>
-
-
-
-04.07.2006, version <a href="phenote/0.3/phenote-webstart.jnlp">0.3</a>, <a href="phenote/0.3.1/phenote-webstart.jnlp">0.3.1 (for CToL)</a><br>
-
-
-
-<p>Note: 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.</p>
-
-
-
-<p> 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.</p>
-
-
-
-<ul>
-
- <li>feature: Completion terms now sorted alphabeitcally.</li>
-
- <li>feature: Obsoletes are now in addition to regular terms, not in lieu of.</li>
-
- <li>feature: Filtering out attribute values (todo: change to actually filter in
-values)</li>
-
- <li>change: Html formatting of term info (todo: make terms selectable)</li>
-
- <li>feature: Children relations are in term info</li>
-
- <li>change: Term info layout greatly improved</li>
-
- <li>change: Term info in scroller</li>
-
- <li>change: Border with label around term info</li>
-
- <li>change: Put definition at end of term info</li>
-
- <li>bugfix: Backspace in ontology combo box</li>
-
- <li>bugfix: Selection of item in comp list causing exception, not going in term box</li>
-
- <li>bugfix: No terms with just 1 char</li>
-
- <li>bugfix: Popup was staying up after selection</li>
-
- <li>development: Test suite added! (todo: add more tests)</li>
-
- <li>development: Migrated to jdk 1.5 (which caused some of the bugs above)</li>
-
- <li>development: Ant file made build.xml.</li>
-
- <li>development: CompletionList refactored into Ontology (prompted by sorting)</li>
-
-</ul>
-
-
-
-
-<h2>0.2
-<hr></h2>
-
-
-
-03.27.2006, version <a href="phenote/0.2/phenote-webstart.jnlp">0.2</a><br>
-
-
-
-<ul>
-
- <li>feature: term completion on Synonyms, Definitions and Obsoletes</li>
-
- <li>feature: mouse-over on term in completion list displays info in 'term info' text area</li>
-
- <li>Todo: layout, scrollbar, border w title, ordering & lumping
-parents
-& children, formatting. Also perhaps have children & parents be
-clickable in some fashion either html-like clickable text or as buttons.</li>
-
- <li>known bugs: If you hit backspace in term completion fields it gets wacky </li>
-
-</ul>
-
-
-
-<h2>0.1
-<hr></h2>
-
-
-
-03.01.2006, version <a href="phenote/0.1/phenote-webstart.jnlp">0.1</a><br>
-
-
-
-<p> 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.</p>
-
-
-</body>
-</html>
Copied: phenote/trunk/doc/phenote-website/phenote-release-notes.shtml (from rev 912, phenote/trunk/doc/phenote-website/release-notes.shtml)
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.shtml 2007-09-17 23:43:28 UTC (rev 914)
@@ -0,0 +1,579 @@
+<!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">
+ <head>
+
+ <!--#include virtual="ssi/head.html" -->
+ <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
+
+ </head>
+ <body>
+
+ <!--#include virtual="ssi/header.html" -->
+
+ <div id="main_container_aux">
+ <div id="main_content_aux">
+ <div class="catch_phrase">
+ Phenote Release Notes
+ </div>
+
+ <h1>1.4 </h1>
+ <h2>08.28.2007, version <a href="phenote/1.4-beta3/phenote.jnlp">1.4-beta3</a></h2>
+ <ul>
+ <li>feature: Native look-and-feel enabled for interface. Users should now see Mac or Windows style depending on their system.</li>
+ <li>feature: read-only field (needs work)</li>
+ <li>feature: config disabling of copy of field (for db ids)</li>
+ <li>feature: display property values of terms in term info</li>
+ <li>feature: Phylogeny Chooser for NESCent/PhenoMap project. A user can import a phylogenetic tree in Newick format. The user can use the tree
+ viewer to select rows within the character template - typically taxonomic groups.</li>
+ <li>feature: term fields can be nullified</li>
+ <li>feature: separate queries to backend for different groups, implemented in worm</li>
+ <li>feature: ID field type, requires ":"</li>
+ <li>feature: can get unique list of deleted annots</li>
+ <li>feature: added group adapter framework</li>
+ <li>feature: fly genotype group adapter makes fly genotype strings from tab/group</li>
+ <li>feature: worm group adapter makes reference terms from ref query</li>
+ <li>change: on term completion if adding a letter use previous completion list</li>
+ <li>change: worm adapter query tab working properly</li>
+ <li>change: build file takes param for webstart version deployment, and puts in jnlp</li>
+ <li>change: group adapters can listen for CharList changes</li>
+ <li>change: added/corrected birn ontologies</li>
+ <li>bugfix: load of file doesnt crash on post comp parsing bug</li>
+ <li>bugfix: doesnt load obo files specified twice twice</li>
+ <li>bugfix: view menu show up at initialization</li>
+ <li>bugfix: layout of term history with split pane proper</li>
+</ul>
+
+<h2>07.20.2007, version <a href="phenote/1.4-beta2/phenote.jnlp">1.4-beta2</a></h2>
+
+<ul>
+
+ <li>feature: RESTful data input for BIRN's smart atlas</li>
+
+ <li>feature: Character Template for NESCent/CToL (Jim Balhoff). This
+is an additional window which edits a separate list of characters using
+a subset of the fields in the main window. The fields to include are
+denoted by a group in the config file. This functionality will be used
+by the PhenoMap project to create a specimen list. The same EQ
+statement can be applied to many specimens at once by selecting the
+relevant specimens and generating characters in the main window with
+the template fields pre-filled. All the new characters are selected and
+can then be bulk edited.</li>
+
+ <li>feature: Progress on gui for config (in progress)</li>
+
+ <li>feature: Progress on field groups (genotype maker, pub querying...)</li>
+
+ <li>feature: right-click editing functions for free-text fields in data input frame. right-click copy in table.</li>
+
+ <li>feature: incorporation of help documentation into Phenote under menu item Help->PhenoteHelp </li>
+
+ <li>feature: added plant_grammene.cfg configuration, plus appropriate obo files.</li>
+
+ <li>feature: navigation bar added to top of term info; buttons to traverse worn paths; term name moved up to top of box [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1685540&group_id=76834&atid=887913">1685540</a>]</li>
+
+ <li>feature: dbxrefs are listed in term info (no external links yet) [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1739399&group_id=76834&atid=887913">1739399</a>]</li>
+
+ <li>change: ontology files can be read with dangling references</li>
+
+ <li>change: Command line read & write of .tab</li>
+
+ <li>change: 'use term' button moved and replaced with checkmark button in navigation bar</li>
+
+ <li>change: ncbo.cfg changed to always update from master file at url</li>
+
+ <li>change: birn2.cfg gene_ontology replaced with gene_ontology_edit.obo reference</li>
+
+ <li>change: Windows splash screen text edited from 'biomedial' to 'biomedical'</li>
+
+ <li>bugfix: obsolete terms were not being read in from annotation files as Ontology.getTerm was only looking at non obsoleted terms</li>
+
+ <li>known bug: ontology files using import statements not properly read</li>
+
+</ul>
+
+
+<h2>version 1.4-beta1 - oops - skipped!</h2>
+
+
+
+<h1>1.3</h1>
+
+
+<h2>05.24.2007, version <a href="phenote/1.3/phenote.jnlp">1.3 release</a></h2>
+
+<ul>
+
+ <li>feature: <a href="http://www.phenote.org/help/">Web-based documentation and Help features.</a></li>
+
+ <li>feature: Metadata fields added to configuration. User can name their configuration, add a description, and author [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1676756&group_id=76834&atid=887913">1676756</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1672080&group_id=76834&atid=887913">1672080</a>]</li>
+
+ <li>feature: Descriptions can be added for fields </li>
+
+ <li>feature: Master-to-local overwrite stuff</li>
+
+ <li>feature: Dialog allows user to back out of exiting from File->Exit</li>
+
+ <li>feature: Autocompletion search default settings configurable <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1677411&group_id=76834&atid=887913">1677411</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1669579&group_id=76834&atid=887913">1669579</a>]
+ </li>
+
+ <li>feature: User can save search setting defaults if changed during Phenote session</li>
+
+ <li>change: File->New is disabled until next version</li>
+
+ <li>change: ncbo, zfin-standalone, flybase, demo configurations
+modified to include master-overwrite feature; keeping track of revision
+history in file comments </li>
+
+ <li>change: can read http, https, ftp, ftps for ontology update URLs, not just http [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1718945&group_id=76834&atid=887913">1718945</a>]</li>
+
+ <li>bugfix: Bulk-editing functions are working again</li>
+
+ <li>bugfix: Undo wasn't working for several functions due to a bug in the Copy function [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721044&group_id=76834&atid=887913"> 1721044</a>]</li>
+
+ <li>bugfix: multi-select deletes free-text content replaces with * [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721032&group_id=76834&atid=887913">1721032</a>]</li>
+
+ <li>bugfix: pre 1.2 post comp data wasnt able to load<big> </big>[<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721470&group_id=76834&atid=887913">1721470</a>]</li>
+
+</ul>
+
+
+
+
+<h2>05.09.2007, version <a href="phenote/1.3-beta1/phenote.jnlp">1.3-beta1</a></h2>
+
+
+
+<ul>
+
+ <li>feature: Added sample config for BIRN</li>
+
+ <li>feature: Added SAO.obo ontology for BIRN</li>
+
+ <li>feature: Namespace config writes back</li>
+
+ <li>feature: Can specify more than one website for ontology update</li>
+
+ <li>feature: Empty field shows all terms in ontology rather than none</li>
+
+ <li>feature: Can add more differentia to post comp</li>
+
+ <li>bugfix: Config update/merge bug where fields in wrong order fixed.</li>
+
+ <li>known bug: can't read post-compositions from phenote versions 1.1 and prior</li>
+
+</ul>
+
+
+
+
+<h1>1.2</h1>
+
+<h2>05.02.2007, version <a href="phenote/1.2/phenote.jnlp">1.2</a></h2>
+<ul>
+
+ <li>feature: Can post-compose with >2 terms </li>
+
+ <li>feature: Term history display can be toggled on/off (Settings->Term History menu)</li>
+
+ <li>feature: Synonyms delineated by scope in Term Info: Exact,
+Narrow, Broad, General, Related. If the synonym category is given, it
+is displayed. For example, the term 'water' has the <i>related</i> synonym H2O, which has the category of a chemical <i>formula</i>.</li>
+
+ <li>feature: Obsolete replacements or consideration terms are displayed in term info with links</li>
+
+ <li>feature: Display term comments in Term Info beneath relationships</li>
+
+ <li>feature: Loading splash screen </li>
+
+ <li>feature: Can configure by namespace for ontologies</li>
+
+ <li>feature: Can automatically update ontologies during startup (configurable)</li>
+
+ <li>feature: Timer added to configuration during ontology update check (configurable)</li>
+
+ <li>feature: Can check which version of phenote is running by selecting Help->About.</li>
+
+ <li>feature: Added common configuration for OMIM curation for use by NCBO (ncbo.cfg).</li>
+
+ <li>feature: can forward and reverse sort columns by repeatedly clicking on column header [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574916&group_id=76834&atid=887913">1574916</a>]</li>
+
+ <li>feature: display ontology namespace in term info box [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1598048&group_id=76834&atid=887913">1598048</a>]</li>
+
+ <li>change: Search filters moved into menu </li>
+
+ <li>change: Updates to the zfin-standalone.cfg for the zebrafish community annotation; only includes GO and ZFanatomy ontologies. </li>
+
+ <li>bugfix: Free-text field text not sticking in "new" or blank rows </li>
+
+</ul>
+
+
+
+
+<h1>1.1</h1>
+
+
+
+<h2>04.06.2007, version <a href="phenote/1.1/phenote.jnlp">1.1.3</a></h2>
+
+
+<ul>
+
+ <li>feature: User can change the configuration they want to use at
+initialization from file menu; change takes effect after restart.
+(previously user had to edit the .phenote/conf/my-phenote file).</li>
+
+</ul>
+
+
+
+<h2>03.28.2007, version 1.1.1</h2>
+
+<ul>
+
+ <li>feature: Phenote is now a single webstart app; user chooses
+their configuration at startup (used to be hard wired to a
+configuration)</li>
+
+ <li>feature: Phenote will merge its default configuration with users' configuration,
+preserving user changes as well as adding anything new from phenote
+upgrade.</li>
+
+ <li>feature: Beginnings of term history to display recently used ontology terms. Will be clickable in future.</li>
+
+ <li>feature: Data entry panel will spill over into multiple tabs if >12 fields included</li>
+
+ <li>feature: Tab delimited data adapter; data in/output format compatible with excel and other spreadsheet software [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661778&group_id=76834&atid=887913">1661778</a>]</li>
+
+ <li>feature: QueryableDataAdapter interface for developers; enables
+connection between input fields and a database backend for quering.
+Queryable fields get a retrieve button.</li>
+
+ <li>feature: Autocompletion search with ALL ontologies in a field instead of just one [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1575241&group_id=76834&atid=887913">1575241</a>]</li>
+
+ <li>feature: Retrieve ontology files from URL if more up to date or no local found; only from a single repository for all [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1648337&group_id=76834&atid=887913">1648337</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574906&group_id=76834&atid=887913">1574906</a>]</li>
+
+ <li>feature: fixed releases available for checkout via sourceforge [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1670345&group_id=76834&atid=887913">1670345</a>]</li>
+
+ <li>feature: display xtns in load/save menu choices [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1594508&group_id=76834&atid=887913">1594508</a>]</li>
+
+ <li>change: Refactored code for field guis</li>
+
+ <li>change: Layout improved</li>
+
+ <li>change: OBSOLETE is displayed in red next to obsolete term in term info [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1581589&group_id=76834&atid=887913">1581589</a>]</li>
+
+ <li>change: human.cfg configuration to include obo foundary ontologies GO, SO, CL, ChEBI, PATO, OBI, Relations, unit, and spatial [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1633287&group_id=76834&atid=887913">1633287</a>]</li>
+
+ <li>bugfix: Ontology chooser reflects current term</li>
+
+ <li>bugfix: phenosyntax reader broken [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1684591&group_id=76834&atid=887913">1684591</a>]</li>
+
+ <li>bugfix: post-composed terms not loading [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661728&group_id=76834&atid=887913">1661728</a>]</li>
+
+</ul>
+
+
+
+<h1>1.0</h1>
+
+
+
+<h2>02.06.2007, version <a href="phenote/1.0/phenote-flybase.jnlp">1.0.5-fly</a>, <a href="1.0/phenote-zfin.jnlp">1.0.5-zfin</a></h2>
+
+
+
+<h2>01.12.2007, version1.0,
+<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby
+Phenote(components used by Zfin)</a></h2>
+
+<ul>
+ <li>change: refactoring of the data model to allow addition of any
+field desired, not just E,Q,GC,GT,Pub. Stage, Evidence, Description,
+Abnormal, and Absent have been added through this new mechanism in the
+newest configurations. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574912&group_id=76834&atid=887913">1574912</a>]</li>
+
+ <li>change: Webby phenote is now using JSP and Spring.</li>
+
+ <li>change: 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.</li>
+
+ <li>bugfix: absent fields not displaying in human 1.03 [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661973&group_id=76834&atid=887913">1661973</a>]</li>
+
+</ul>
+
+
+
+<h1>0.9</h1>
+
+<h2>11.15.2006, version <a href="phenote/0.9/phenote-flybase.jnlp">0.9-fly</a>,
+<a href="phenote/0.9/phenote-zfin.jnlp">0.9-zfin</a>,
+<a href="http://165.124.152.194/web/html/interface.html">DictyBase
+webby phenote</a></h2>
+
+<h2>11.09.2006, version 0.9</...
[truncated message content] |
|
From: <nl...@us...> - 2007-09-17 23:50:41
|
Revision: 915
http://obo.svn.sourceforge.net/obo/?rev=915&view=rev
Author: nlw
Date: 2007-09-17 16:50:43 -0700 (Mon, 17 Sep 2007)
Log Message:
-----------
ok, last change for awhile... bad link
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/faq.shtml
phenote/trunk/doc/phenote-website/faq.shtml~
Modified: phenote/trunk/doc/phenote-website/faq.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/faq.shtml 2007-09-17 23:43:28 UTC (rev 914)
+++ phenote/trunk/doc/phenote-website/faq.shtml 2007-09-17 23:50:43 UTC (rev 915)
@@ -18,8 +18,8 @@
<h1>General</h1>
<h3>How do I get started?</h3>
- <p>
- You can lauch Phenote directly from your browser. Simply click on the Launch Phenote 'quick link' from the <a href="http://www.phenote.org/">main page</a> or the <a href="http://www.phenote.org/software.shtml">Software</a> page, and it will launch directly from your browser. It will take a couple of minutes to download all the components, but that's it.
+
+ You can lauch Phenote directly from your browser. Simply click on the Launch Phenote 'quick link' from the <a href="http://www.phenote.org/">main page</a> or the <a href="http://www.phenote.org/download.shtml">Downloads</a> page, and it will launch directly from your browser. It will take a couple of minutes to download all the components, but that's it.
</p>
<h3>What's the best forum to ask my burning questions?</h3>
<p>
Modified: phenote/trunk/doc/phenote-website/faq.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/faq.shtml~ 2007-09-17 23:43:28 UTC (rev 914)
+++ phenote/trunk/doc/phenote-website/faq.shtml~ 2007-09-17 23:50:43 UTC (rev 915)
@@ -19,7 +19,7 @@
<h1>General</h1>
<h3>How do I get started?</h3>
<p>
- You can lauch Phenote directly from your browser. Simply click on the Launch Phenote 'quick link' from the <a href="http://www.phenote.org/">main page</a> or the <a href="http://www.phenote.org/downloads.shtml">Downloads</a> page, and it will launch directly from your browser. It will take a couple of minutes to download all the components, but that's it.
+ You can lauch Phenote directly from your browser. Simply click on the Launch Phenote 'quick link' from the <a href="http://www.phenote.org/">main page</a> or the <a href="http://www.phenote.org/software.shtml">Software</a> page, and it will launch directly from your browser. It will take a couple of minutes to download all the components, but that's it.
</p>
<h3>What's the best forum to ask my burning questions?</h3>
<p>
@@ -72,7 +72,6 @@
<p>
Sometimes a term you are looking for is really just a synonym of another term. Make sure you have "synonyms" selected under the "Settings" menu. </p>
<p>If you still can't find it, it might be that the ontology is really missing a term. Ontologies, while extensive, are never complete, and are under active development. There are usually online term request resources for each ontology. You will need to contact each ontology resource separately. </p>
- </p>
<h3>Can I output my data in RDF-OWL?</h3>
<p>
Not yet, but that feature is coming soon.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-18 00:03:25
|
Revision: 916
http://obo.svn.sourceforge.net/obo/?rev=916&view=rev
Author: nlw
Date: 2007-09-17 17:03:29 -0700 (Mon, 17 Sep 2007)
Log Message:
-----------
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/faq.shtml
phenote/trunk/doc/phenote-website/faq.shtml~
Modified: phenote/trunk/doc/phenote-website/faq.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/faq.shtml 2007-09-17 23:50:43 UTC (rev 915)
+++ phenote/trunk/doc/phenote-website/faq.shtml 2007-09-18 00:03:29 UTC (rev 916)
@@ -18,7 +18,7 @@
<h1>General</h1>
<h3>How do I get started?</h3>
-
+ <p>
You can lauch Phenote directly from your browser. Simply click on the Launch Phenote 'quick link' from the <a href="http://www.phenote.org/">main page</a> or the <a href="http://www.phenote.org/download.shtml">Downloads</a> page, and it will launch directly from your browser. It will take a couple of minutes to download all the components, but that's it.
</p>
<h3>What's the best forum to ask my burning questions?</h3>
Modified: phenote/trunk/doc/phenote-website/faq.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/faq.shtml~ 2007-09-17 23:50:43 UTC (rev 915)
+++ phenote/trunk/doc/phenote-website/faq.shtml~ 2007-09-18 00:03:29 UTC (rev 916)
@@ -18,8 +18,8 @@
<h1>General</h1>
<h3>How do I get started?</h3>
- <p>
- You can lauch Phenote directly from your browser. Simply click on the Launch Phenote 'quick link' from the <a href="http://www.phenote.org/">main page</a> or the <a href="http://www.phenote.org/software.shtml">Software</a> page, and it will launch directly from your browser. It will take a couple of minutes to download all the components, but that's it.
+
+ You can lauch Phenote directly from your browser. Simply click on the Launch Phenote 'quick link' from the <a href="http://www.phenote.org/">main page</a> or the <a href="http://www.phenote.org/download.shtml">Downloads</a> page, and it will launch directly from your browser. It will take a couple of minutes to download all the components, but that's it.
</p>
<h3>What's the best forum to ask my burning questions?</h3>
<p>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-10-08 19:11:43
|
Revision: 978
http://obo.svn.sourceforge.net/obo/?rev=978&view=rev
Author: nlw
Date: 2007-10-08 12:10:44 -0700 (Mon, 08 Oct 2007)
Log Message:
-----------
revise
website: revised dates/notes, etc.
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/events.shtml
phenote/trunk/doc/phenote-website/index.shtml
Modified: phenote/trunk/doc/phenote-website/events.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml 2007-10-08 16:04:33 UTC (rev 977)
+++ phenote/trunk/doc/phenote-website/events.shtml 2007-10-08 19:10:44 UTC (rev 978)
@@ -17,23 +17,16 @@
</div>
<h1>Upcoming Events, 2007</h1>
- <h2>September</h2>
- <ul>
- <li>
- </li>
- </ul>
<h2>October</h2>
<ul>
- <li>Oct 2, Phenote Users Group, Online
- </li>
<li>Oct 23-25, Ontology Best Practices Workshop, <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">Biocurator Meeting</a>, Hayes Mansion, San Jose, CA
</li>
</ul>
<h2>November</h2>
<ul>
- <li>Nov 6, Phenote Users Group, Online
+ <li>Nov 1, Phenote Users Group, Online via WebEx
</li>
<li>Nov 27, <a href="http://www.bioontology.org/">NCBO</a> Scientific Advisory Board meeting</li>
</ul>
@@ -45,6 +38,10 @@
</ul>
<h1>Past News and Events, 2007</h1>
+ <h2>October</h2>
+ <li>Oct 2, Phenote Users Group, Online via WebEx
+ </li>
+
<h2>September</h2>
<ul>
<li>Sept 17, New website released
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2007-10-08 16:04:33 UTC (rev 977)
+++ phenote/trunk/doc/phenote-website/index.shtml 2007-10-08 19:10:44 UTC (rev 978)
@@ -102,7 +102,7 @@
<li class="events">
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://www.phenote.org/irc_chat">User's Group Monthly Meeting</a>, October 4, 8:30am, Online
+ <a href="http://www.phenote.org/irc_chat">User's Group Monthly Meeting</a>, November 1, 9:00am, Online
</p>
</li>
</ul>
@@ -129,7 +129,8 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
- <p>09.17.2007 - New website rolled out! The website has the same
+ <p>10.02.2007 - Phenote user's group to be moved to first Thursday of each month, 9am. Join us for our next meeting on November 1st over WebEx!</p>
+ <p>09.17.2007 - New website rolled out! The website has the same
content as the old one, just with a new look-and-feel.</p>
<p> 08.28.2007 -
<a href="http://www.phenote.org/download.shtml">New Phenote Beta available: 1.4-beta3!</a> </p>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-10-09 20:31:00
|
Revision: 1002
http://obo.svn.sourceforge.net/obo/?rev=1002&view=rev
Author: nlw
Date: 2007-10-09 13:30:59 -0700 (Tue, 09 Oct 2007)
Log Message:
-----------
alrighty, made the imports list for smart-atlas and regular phenote
jnlps the same. also have put the elephant pic as the icon. hee hee...
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-10-09 20:24:40 UTC (rev 1001)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-10-09 20:30:59 UTC (rev 1002)
@@ -6,6 +6,7 @@
<information>
<title>Phenote @@phenote.version@@</title>
<vendor>National Center for Biomedical Ontology</vendor>
+ <icon href="images/elephant_icon.jpg" />
<description>Phenote standalone app via webstart</description>
<!-- Declares that the application can run without
access to the server it was downloaded from -->
@@ -43,6 +44,10 @@
<jar href="jars/jdom.jar" />
<jar href="jars/quaqua.jar" />
<jar href="jars/jebl-0.4.jar" />
+ <jar href="jars/swing-layout.jar" />
+ <jar href="jars/glazedlists-1.7.0_java15.jar" />
+ <nativelib href="jars/phenote-nativelibs.jar"/>
+
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-10-09 20:24:40 UTC (rev 1001)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-10-09 20:30:59 UTC (rev 1002)
@@ -45,9 +45,10 @@
<jar href="jars/quaqua.jar" />
<jar href="jars/jebl-0.4.jar" />
<jar href="jars/glazedlists-1.7.0_java15.jar" />
+ <jar href="jars/swing-layout.jar"/>
<nativelib href="jars/phenote-nativelibs.jar"/>
- <nativelib href="jars/swing-layout.jar"/>
+
<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...> - 2007-10-10 23:15:52
|
Revision: 1031
http://obo.svn.sourceforge.net/obo/?rev=1031&view=rev
Author: nlw
Date: 2007-10-10 16:15:56 -0700 (Wed, 10 Oct 2007)
Log Message:
-----------
few minor changes to website
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/download.shtml
phenote/trunk/doc/phenote-website/download.shtml~
phenote/trunk/doc/phenote-website/events.shtml
phenote/trunk/doc/phenote-website/events.shtml~
phenote/trunk/doc/phenote-website/index.shtml
phenote/trunk/doc/phenote-website/index.shtml~
Modified: phenote/trunk/doc/phenote-website/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml 2007-10-10 23:10:36 UTC (rev 1030)
+++ phenote/trunk/doc/phenote-website/download.shtml 2007-10-10 23:15:56 UTC (rev 1031)
@@ -16,7 +16,8 @@
</div>
<h2><a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Launch Phenote in your browser</a></h2>
<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
-<!-- <ul><li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></strong></li>-->
+ <ul>
+<!-- <li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></strong></li>-->
<li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp">1.4</a> </strong></li>
<li><a href="http://www.phenote.org/phenote/phenote.html">Older releases</a></li>
</ul>
Modified: phenote/trunk/doc/phenote-website/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml~ 2007-10-10 23:10:36 UTC (rev 1030)
+++ phenote/trunk/doc/phenote-website/download.shtml~ 2007-10-10 23:15:56 UTC (rev 1031)
@@ -16,17 +16,21 @@
</div>
<h2><a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Launch Phenote in your browser</a></h2>
<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
- <ul><li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></strong></li>
- <li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.3/phenote.jnlp">1.3</a> </strong></li>
+<!-- <ul><li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></strong></li>-->
+ <li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp">1.4</a> </strong></li>
<li><a href="http://www.phenote.org/phenote/phenote.html">Older releases</a></li>
</ul>
<p> You may be prompted to sign a certificate and allow the download. This will take a few minutes the first time you do this.
</p>
<h2>Run Phenote at the command line</h2>
<p> To run phenote on the command line, linux or MacOSX users will need to checkout Phenote from the subversion repository. This can be done with the following command:</p>
- <ul><li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.4-beta3/ phenote</b> </li>
- <li>Stable release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.3/ phenote</b>
- <li>Latest: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote </b></li>
+ <ul>
+<!-- <li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.4-beta3/ phenote</b>
+ </li>-->
+ <li>Stable release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.4/ phenote</b>
+ </li>
+ <li>Latest: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote </b>
+ </li>
</ul>
<p>Once you've got it, you can run Phenote with ant with the command: <b>ant run</b>
</p>
@@ -52,32 +56,32 @@
<div id="sidebar_content">
<div class="content_box_head_blue">
- Recently added features, version 1.4-beta3
+ Recently added features, version 1.4
</div>
<div class="content_box_blue">
- <b>feature</b>: Native look-and-feel enabled for interface. Users should now see Mac or Windows style depending on their system.<br />
- <b>feature</b>: read-only field (needs work)<br />
- <b>feature</b>: config disabpng of copy of field (for db ids)<br />
- <b>feature</b>: display property values of terms in term info<br />
- <b>feature</b>: Phylogeny Chooser for NESCent/PhenoMap project. A user can import a phylogenetic tree in Newick format. The user can use the tree
- viewer to select rows within the character template - typically taxonomic groups.<br />
- <b>feature</b>: term fields can be nullified<br />
- <b>feature</b>: separate queries to backend for different groups, implemented in worm<br />
- <b>feature</b>: ID field type, requires ":"<br />
- <b>feature</b>: can get unique list of deleted annots<br />
- <b>feature</b>: added group adapter framework<br />
- <b>feature</b>: fly genotype group adapter makes fly genotype strings from tab/group<br />
- <b>feature</b>: worm group adapter makes reference terms from ref query<br />
- <b>change</b>: on term completion if adding a letter use previous completion list<br />
- <b>change</b>: worm adapter query tab working properly<br />
- <b>change</b>: build file takes param for webstart version deployment, and puts in jnlp<br />
- <b>change</b>: group adapters can psten for CharList changes<br />
- <b>change</b>: added/corrected BIRN ontologies<br />
- <b>bugfix</b>: load of file doesnt crash on post comp parsing bug<br />
- <b>bugfix</b>: doesnt load obo files specified twice twice<br />
- <b>bugfix</b>: view menu show up at initialization<br />
- <b>bugfix</b>: layout of term history with split pane proper<br />
+ <b>feature</b>: Loading splash more informative about what's going on behind-the-scenes such as which ontologies are loading, if they are being updated, etc.<br />
+ <b>feature</b>: obo edit annotation model can now be optionally configured for backend, which will allow for more sophisticated data to be captured (like comparisons)<br />
+ <b>feature</b>: Error for obo parse failures to info panel <br />
+ <b>feature</b>: Delimited tab adapter uses column headings to map to table, rather than ordering <br />
+ <b>feature</b>: Autocompletion optimized with threading, cancels stale requests (min-comp-chars now pase) <br />
+ <b>feature</b>: Date created automatically added into data (under the hood) <br />
+ <b>feature</b>: If arrow hit with empty input then gets & displays all terms (used to inefficiently pre-load) <br />
+ <b>feature</b>: Can sort completion list by ID, needed for zfin stages<br />
+ <b>feature</b>: Table preserves user ordering of columns, in addition to column widths.<br />
+ <b>feature</b>: Filter search field allows user to narrow down displayed data rows via matching text.<br />
+ <b>feature</b>: See actual value in input field when multiple rows are selected and have the same value.<br />
+ <b>feature</b>: Copy all taxon names in specimen list as an unresolved Newick tree (for PhenoMap/NESCent)<br />
+ <b>feature</b>: Automatically open specimen list and phylogenetic tree files when opening data file (for PhenoMap/NESCent)<br />
+ <b>change</b>: Moved test suites in with source to work with eclipse<br />
+ <b>change</b>: Took a lot of obos out of webstart jar - less bulky - as they get automatically downloaded<br />
+ <b>change</b>: Phenote now follows standard log4j configuration conventions. Pass a custom log configuration to Phenote via the classpath or the system propery "log4j.configuration".<br />
+ <b>bugfix</b>: Terms not found are no longer dropped, a dangler is created, and error msg to info, show up in red<br />
+ <b>bugfix</b>: if log conf fails use backup default<br />
+ <b>bugfix</b>: Input fields now commit changes with either Return or Tab<br />
+ <b>bugfix</b>: Native lib is loaded properly for Mac interface on webstart, allowing traversal of aliases in file dialog, as well as user sidebar items in file dialog<br />
+ <b>bugfix</b>: Noncontiguous row selection works now on Mac<br />
+</ul>
</div>
</div>
</div>
Modified: phenote/trunk/doc/phenote-website/events.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml 2007-10-10 23:10:36 UTC (rev 1030)
+++ phenote/trunk/doc/phenote-website/events.shtml 2007-10-10 23:15:56 UTC (rev 1031)
@@ -39,8 +39,8 @@
<h1>Past News and Events, 2007</h1>
<h2>October</h2>
- <p>Oct 10, New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
-
+ <li>Oct 10, New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
+ </li>
<li>Oct 2, Phenote Users Group, Online via WebEx
</li>
Modified: phenote/trunk/doc/phenote-website/events.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml~ 2007-10-10 23:10:36 UTC (rev 1030)
+++ phenote/trunk/doc/phenote-website/events.shtml~ 2007-10-10 23:15:56 UTC (rev 1031)
@@ -39,6 +39,8 @@
<h1>Past News and Events, 2007</h1>
<h2>October</h2>
+ <p>Oct 10, New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
+
<li>Oct 2, Phenote Users Group, Online via WebEx
</li>
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2007-10-10 23:10:36 UTC (rev 1030)
+++ phenote/trunk/doc/phenote-website/index.shtml 2007-10-10 23:15:56 UTC (rev 1031)
@@ -129,12 +129,10 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
- <p>10.10.2007 - New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
+ <p>10.10.2007 - <b>New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a></b>
<p>10.02.2007 - Phenote user's group to be moved to first Thursday of each month, 9am. Join us for our next meeting on November 1st over WebEx!</p>
<p>09.17.2007 - New website rolled out! The website has the same
content as the old one, just with a new look-and-feel.</p>
- <p> 08.28.2007 -
- <a href="http://www.phenote.org/download.shtml">New Phenote Beta available: 1.4-beta3!</a> </p>
<!--
<h3>Event Title</h3>
<ul class="events">
Modified: phenote/trunk/doc/phenote-website/index.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml~ 2007-10-10 23:10:36 UTC (rev 1030)
+++ phenote/trunk/doc/phenote-website/index.shtml~ 2007-10-10 23:15:56 UTC (rev 1031)
@@ -60,7 +60,7 @@
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp"
+ <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp"
title="Lauch Phenote via Webstart">
Launch Phenote via Webstart
</a>
@@ -129,6 +129,7 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
+ <p>10.10.2007 - New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
<p>10.02.2007 - Phenote user's group to be moved to first Thursday of each month, 9am. Join us for our next meeting on November 1st over WebEx!</p>
<p>09.17.2007 - New website rolled out! The website has the same
content as the old one, just with a new look-and-feel.</p>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-10-11 14:41:20
|
Revision: 1032
http://obo.svn.sourceforge.net/obo/?rev=1032&view=rev
Author: mgibson
Date: 2007-10-11 07:41:21 -0700 (Thu, 11 Oct 2007)
Log Message:
-----------
smart atlas jnlp now points to birn.cfg instead of smart-atlas.cfg as maryann
has requested merging the configs - we'll see how that goes
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
phenote/trunk/doc/phenote-website/phenote.html
Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-10-10 23:15:56 UTC (rev 1031)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-10-11 14:41:21 UTC (rev 1032)
@@ -49,9 +49,9 @@
<nativelib href="jars/phenote-nativelibs.jar"/>
</resources>
-<!-- no cmd line param will ask user for config at initialization -->
+<!-- was smart-atlas.cfg, merged into birn.cfg -->
<application-desc main-class="phenote.main.Phenote">
- <argument>-u</argument>
- <argument>/smart-atlas.cfg</argument>
+ <argument>-c</argument>
+ <argument>/birn.cfg</argument>
</application-desc>
</jnlp>
Modified: phenote/trunk/doc/phenote-website/phenote.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.html 2007-10-10 23:15:56 UTC (rev 1031)
+++ phenote/trunk/doc/phenote-website/phenote.html 2007-10-11 14:41:21 UTC (rev 1032)
@@ -51,64 +51,12 @@
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
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">Dicty
webby phenote wiki developer docs</a><br>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-10-30 16:45:02
|
Revision: 1085
http://obo.svn.sourceforge.net/obo/?rev=1085&view=rev
Author: nlw
Date: 2007-10-30 09:44:49 -0700 (Tue, 30 Oct 2007)
Log Message:
-----------
updates to website; adding the talk from biocrators meeting
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/events.shtml
phenote/trunk/doc/phenote-website/index.shtml
Added Paths:
-----------
phenote/trunk/doc/phenote-website/resources/
phenote/trunk/doc/phenote-website/resources/Biocurator_2007.ppt
Modified: phenote/trunk/doc/phenote-website/events.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml 2007-10-29 23:43:28 UTC (rev 1084)
+++ phenote/trunk/doc/phenote-website/events.shtml 2007-10-30 16:44:49 UTC (rev 1085)
@@ -18,16 +18,12 @@
<h1>Upcoming Events, 2007</h1>
- <h2>October</h2>
- <ul>
- <li>Oct 23-25, Ontology Best Practices Workshop, <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">Biocurator Meeting</a>, Hayes Mansion, San Jose, CA
- </li>
- </ul>
-
<h2>November</h2>
<ul>
<li>Nov 1, Phenote Users Group, Online via WebEx
</li>
+ <li>Nov 4, Talk, <a href="http://meetings.cshl.edu/meetings/info07.shtml">Genome Informatics</a>
+ </li>
<li>Nov 27, <a href="http://www.bioontology.org/">NCBO</a> Scientific Advisory Board meeting</li>
</ul>
@@ -39,15 +35,19 @@
<h1>Past News and Events, 2007</h1>
<h2>October</h2>
+ <ul>
+ <li>Oct 23-25, Ontology Best Practices Workshop, <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">Biocurator Meeting</a>, Hayes Mansion, San Jose, CA [<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]
+ </li>
<li>Oct 10, New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
</li>
<li>Oct 2, Phenote Users Group, Online via WebEx
</li>
+ </ul>
+
<h2>September</h2>
<ul>
- <li>Sept 17, New website released
- </li>
+ <li>Sept 17, - New website rolled out! The website has the same content as the old one, just with a new look-and-feel.</li>
<li>Sept 4, Phenote Users Group, Online
</li>
</ul>
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2007-10-29 23:43:28 UTC (rev 1084)
+++ phenote/trunk/doc/phenote-website/index.shtml 2007-10-30 16:44:49 UTC (rev 1085)
@@ -111,7 +111,7 @@
<li class="events">
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">BioCurator meeting</a>, October 23-25, San Jose, CA
+ <a href="http://meetings.cshl.edu/meetings/info07.shtml">Genome Informatics</a>, November 1-5, Cold Spring Harbor, NY
</p>
</li>
</ul>
@@ -129,10 +129,10 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
- <p>10.10.2007 - <b>New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a></b>
+ <p><a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">BioCurator meeting</a>, October 23-25, San Jose, CA
+ [<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]</p>
+ <p>10.10.2007 - <b>New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a></b></p>
<p>10.02.2007 - Phenote user's group to be moved to first Thursday of each month, 9am. Join us for our next meeting on November 1st over WebEx!</p>
- <p>09.17.2007 - New website rolled out! The website has the same
- content as the old one, just with a new look-and-feel.</p>
<!--
<h3>Event Title</h3>
<ul class="events">
Added: phenote/trunk/doc/phenote-website/resources/Biocurator_2007.ppt
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/resources/Biocurator_2007.ppt
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-10-30 17:24:51
|
Revision: 1086
http://obo.svn.sourceforge.net/obo/?rev=1086&view=rev
Author: nlw
Date: 2007-10-30 10:24:54 -0700 (Tue, 30 Oct 2007)
Log Message:
-----------
a couple more website changes
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/events.shtml
phenote/trunk/doc/phenote-website/events.shtml~
phenote/trunk/doc/phenote-website/index.shtml
phenote/trunk/doc/phenote-website/index.shtml~
Modified: phenote/trunk/doc/phenote-website/events.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml 2007-10-30 16:44:49 UTC (rev 1085)
+++ phenote/trunk/doc/phenote-website/events.shtml 2007-10-30 17:24:54 UTC (rev 1086)
@@ -36,7 +36,7 @@
<h1>Past News and Events, 2007</h1>
<h2>October</h2>
<ul>
- <li>Oct 23-25, Ontology Best Practices Workshop, <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">Biocurator Meeting</a>, Hayes Mansion, San Jose, CA [<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]
+ <li>Oct 23-25, <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">Biocurator Meeting</a>, Hayes Mansion, San Jose, CA [<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]
</li>
<li>Oct 10, New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
</li>
Modified: phenote/trunk/doc/phenote-website/events.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml~ 2007-10-30 16:44:49 UTC (rev 1085)
+++ phenote/trunk/doc/phenote-website/events.shtml~ 2007-10-30 17:24:54 UTC (rev 1086)
@@ -18,16 +18,12 @@
<h1>Upcoming Events, 2007</h1>
- <h2>October</h2>
- <ul>
- <li>Oct 23-25, Ontology Best Practices Workshop, <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">Biocurator Meeting</a>, Hayes Mansion, San Jose, CA
- </li>
- </ul>
-
<h2>November</h2>
<ul>
<li>Nov 1, Phenote Users Group, Online via WebEx
</li>
+ <li>Nov 4, Talk, <a href="http://meetings.cshl.edu/meetings/info07.shtml">Genome Informatics</a>
+ </li>
<li>Nov 27, <a href="http://www.bioontology.org/">NCBO</a> Scientific Advisory Board meeting</li>
</ul>
@@ -39,15 +35,19 @@
<h1>Past News and Events, 2007</h1>
<h2>October</h2>
- <p>Oct 10, New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
-
+ <ul>
+ <li>Oct 23-25, Ontology Best Practices Workshop, <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">Biocurator Meeting</a>, Hayes Mansion, San Jose, CA [<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]
+ </li>
+ <li>Oct 10, New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
+ </li>
<li>Oct 2, Phenote Users Group, Online via WebEx
</li>
+ </ul>
+
<h2>September</h2>
<ul>
- <li>Sept 17, New website released
- </li>
+ <li>Sept 17, - New website rolled out! The website has the same content as the old one, just with a new look-and-feel.</li>
<li>Sept 4, Phenote Users Group, Online
</li>
</ul>
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2007-10-30 16:44:49 UTC (rev 1085)
+++ phenote/trunk/doc/phenote-website/index.shtml 2007-10-30 17:24:54 UTC (rev 1086)
@@ -129,7 +129,7 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
- <p><a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">BioCurator meeting</a>, October 23-25, San Jose, CA
+ <p>10.23-25.2007 - <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">BioCurator meeting</a>, San Jose, CA
[<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]</p>
<p>10.10.2007 - <b>New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a></b></p>
<p>10.02.2007 - Phenote user's group to be moved to first Thursday of each month, 9am. Join us for our next meeting on November 1st over WebEx!</p>
Modified: phenote/trunk/doc/phenote-website/index.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml~ 2007-10-30 16:44:49 UTC (rev 1085)
+++ phenote/trunk/doc/phenote-website/index.shtml~ 2007-10-30 17:24:54 UTC (rev 1086)
@@ -111,7 +111,7 @@
<li class="events">
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">BioCurator meeting</a>, October 23-25, San Jose, CA
+ <a href="http://meetings.cshl.edu/meetings/info07.shtml">Genome Informatics</a>, November 1-5, Cold Spring Harbor, NY
</p>
</li>
</ul>
@@ -129,12 +129,10 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
- <p>10.10.2007 - New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
+ <p><a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">BioCurator meeting</a>, October 23-25, San Jose, CA
+ [<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]</p>
+ <p>10.10.2007 - <b>New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a></b></p>
<p>10.02.2007 - Phenote user's group to be moved to first Thursday of each month, 9am. Join us for our next meeting on November 1st over WebEx!</p>
- <p>09.17.2007 - New website rolled out! The website has the same
- content as the old one, just with a new look-and-feel.</p>
- <p> 08.28.2007 -
- <a href="http://www.phenote.org/download.shtml">New Phenote Beta available: 1.4-beta3!</a> </p>
<!--
<h3>Event Title</h3>
<ul class="events">
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-11-29 22:11:35
|
Revision: 1244
http://obo.svn.sourceforge.net/obo/?rev=1244&view=rev
Author: nlw
Date: 2007-11-29 14:11:39 -0800 (Thu, 29 Nov 2007)
Log Message:
-----------
moving some of the events around, updating for the next user group
meeting
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/events.shtml
phenote/trunk/doc/phenote-website/events.shtml~
phenote/trunk/doc/phenote-website/index.shtml
phenote/trunk/doc/phenote-website/index.shtml~
Modified: phenote/trunk/doc/phenote-website/events.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml 2007-11-29 16:48:38 UTC (rev 1243)
+++ phenote/trunk/doc/phenote-website/events.shtml 2007-11-29 22:11:39 UTC (rev 1244)
@@ -18,22 +18,30 @@
<h1>Upcoming Events, 2007</h1>
- <h2>November</h2>
+ <h2>December</h2>
<ul>
- <li>Nov 1, Phenote Users Group, Online via WebEx
+ <li>Dec 6, Phenote Users Group, Online
</li>
- <li>Nov 4, Talk, <a href="http://meetings.cshl.edu/meetings/info07.shtml">Genome Informatics</a>
- </li>
- <li>Nov 27, <a href="http://www.bioontology.org/">NCBO</a> Scientific Advisory Board meeting</li>
</ul>
- <h2>December</h2>
+ <h1>2008</h1>
+ <h2>January</h2>
<ul>
- <li>Dec 4, Phenote Users Group, Online
+ <li>Major release scheduled</li>
+ </ul>
+
+ <h1>Past News and Events, 2007</h1>
+ <h2>November</h2>
+ <ul>
+ <li>Nov 1, Phenote Users Group, Online via WebEx
</li>
+ <li>Nov 4, Talk, <a href="http://meetings.cshl.edu/meetings/info07.shtml">Genome Informatics</a>, Cold Spring Harbor, NY
+ </li>
+ <li>Nov 6-9, Site Visit, <a href="http://www.flybase.org">Flybase</a>, Cambridge, UK
+ </li>
+ <li>Nov 27, <a href="http://www.bioontology.org/">NCBO</a> Scientific Advisory Board meeting</li>, Stanford, CA
</ul>
- <h1>Past News and Events, 2007</h1>
<h2>October</h2>
<ul>
<li>Oct 23-25, <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">Biocurator Meeting</a>, Hayes Mansion, San Jose, CA [<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]
Modified: phenote/trunk/doc/phenote-website/events.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml~ 2007-11-29 16:48:38 UTC (rev 1243)
+++ phenote/trunk/doc/phenote-website/events.shtml~ 2007-11-29 22:11:39 UTC (rev 1244)
@@ -36,7 +36,7 @@
<h1>Past News and Events, 2007</h1>
<h2>October</h2>
<ul>
- <li>Oct 23-25, Ontology Best Practices Workshop, <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">Biocurator Meeting</a>, Hayes Mansion, San Jose, CA [<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]
+ <li>Oct 23-25, <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">Biocurator Meeting</a>, Hayes Mansion, San Jose, CA [<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]
</li>
<li>Oct 10, New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
</li>
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2007-11-29 16:48:38 UTC (rev 1243)
+++ phenote/trunk/doc/phenote-website/index.shtml 2007-11-29 22:11:39 UTC (rev 1244)
@@ -97,12 +97,12 @@
</li>
</ul>
-->
- <h3>Phenote User's Group IRC</h3>
+ <h3>Phenote User's Group</h3>
<ul class="events">
<li class="events">
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://www.phenote.org/irc_chat">User's Group Monthly Meeting</a>, November 1, 9:00am, Online
+ <a href="http://www.phenote.org/irc_chat">User's Group Monthly Meeting</a>, December 6, 8:30am, Online
</p>
</li>
</ul>
@@ -111,7 +111,7 @@
<li class="events">
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://meetings.cshl.edu/meetings/info07.shtml">Genome Informatics</a>, November 1-5, Cold Spring Harbor, NY
+ (none scheduled at this time)
</p>
</li>
</ul>
Modified: phenote/trunk/doc/phenote-website/index.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml~ 2007-11-29 16:48:38 UTC (rev 1243)
+++ phenote/trunk/doc/phenote-website/index.shtml~ 2007-11-29 22:11:39 UTC (rev 1244)
@@ -129,7 +129,7 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
- <p><a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">BioCurator meeting</a>, October 23-25, San Jose, CA
+ <p>10.23-25.2007 - <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">BioCurator meeting</a>, San Jose, CA
[<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]</p>
<p>10.10.2007 - <b>New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a></b></p>
<p>10.02.2007 - Phenote user's group to be moved to first Thursday of each month, 9am. Join us for our next meeting on November 1st over WebEx!</p>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2008-01-03 00:32:13
|
Revision: 1339
http://obo.svn.sourceforge.net/obo/?rev=1339&view=rev
Author: nlw
Date: 2008-01-02 16:32:15 -0800 (Wed, 02 Jan 2008)
Log Message:
-----------
adding the new beta release to the website
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/download.shtml
phenote/trunk/doc/phenote-website/download.shtml~
phenote/trunk/doc/phenote-website/index.shtml
phenote/trunk/doc/phenote-website/index.shtml~
phenote/trunk/doc/phenote-website/phenote-release-notes.shtml
Modified: phenote/trunk/doc/phenote-website/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml 2008-01-03 00:21:43 UTC (rev 1338)
+++ phenote/trunk/doc/phenote-website/download.shtml 2008-01-03 00:32:15 UTC (rev 1339)
@@ -17,7 +17,7 @@
<h2><a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Launch Phenote in your browser</a></h2>
<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
<ul>
-<!-- <li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></strong></li>-->
+ <li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.5-beta2/phenote.jnlp">1.5 beta2</a></strong></li>-->
<li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp">1.4</a> </strong></li>
<li><a href="http://www.phenote.org/phenote/phenote.html">Older releases</a></li>
</ul>
@@ -26,8 +26,8 @@
<h2>Run Phenote at the command line</h2>
<p> To run phenote on the command line, linux or MacOSX users will need to checkout Phenote from the subversion repository. This can be done with the following command:</p>
<ul>
-<!-- <li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.4-beta3/ phenote</b>
- </li>-->
+ <li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.5-beta2/ phenote</b>
+ </li>
<li>Stable release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.4/ phenote</b>
</li>
<li>Latest: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote </b>
Modified: phenote/trunk/doc/phenote-website/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml~ 2008-01-03 00:21:43 UTC (rev 1338)
+++ phenote/trunk/doc/phenote-website/download.shtml~ 2008-01-03 00:32:15 UTC (rev 1339)
@@ -16,7 +16,8 @@
</div>
<h2><a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Launch Phenote in your browser</a></h2>
<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
-<!-- <ul><li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></strong></li>-->
+ <ul>
+<!-- <li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></strong></li>-->
<li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp">1.4</a> </strong></li>
<li><a href="http://www.phenote.org/phenote/phenote.html">Older releases</a></li>
</ul>
@@ -25,9 +26,9 @@
<h2>Run Phenote at the command line</h2>
<p> To run phenote on the command line, linux or MacOSX users will need to checkout Phenote from the subversion repository. This can be done with the following command:</p>
<ul>
-<!-- <li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.4-beta3/ phenote</b>
+<!-- <li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.4-beta3/ phenote</b>
</li>-->
- <li>Stable release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.4/ phenote</b>
+ <li>Stable release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.4/ phenote</b>
</li>
<li>Latest: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote </b>
</li>
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2008-01-03 00:21:43 UTC (rev 1338)
+++ phenote/trunk/doc/phenote-website/index.shtml 2008-01-03 00:32:15 UTC (rev 1339)
@@ -102,7 +102,7 @@
<li class="events">
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote_Working_Group">User's Group Monthly Meeting</a>, December 6, 8:30am, Online
+ <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote_Working_Group">User's Group Monthly Meeting</a>, January 3, 8:30am, Online
</p>
</li>
</ul>
@@ -129,10 +129,10 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
- <p>10.23-25.2007 - <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">BioCurator meeting</a>, San Jose, CA
+ <p>01.10.2008 - Seminar presentation at <a href="http://www.nescent.org/">NESCent</a></p>
+ <p>12.20.2007 - <b>New Phenote Beta Release - <a href="http://www.phenote.org/download.shtml">version 1.5-beta2</a></b></p>
+ <p>10.23-25.2007 - <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">BioCurator meeting</a>, San Jose, CA
[<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]</p>
- <p>10.10.2007 - <b>New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a></b></p>
- <p>10.02.2007 - Phenote user's group to be moved to first Thursday of each month, 9am. Join us for our next meeting on November 1st over WebEx!</p>
<!--
<h3>Event Title</h3>
<ul class="events">
Modified: phenote/trunk/doc/phenote-website/index.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml~ 2008-01-03 00:21:43 UTC (rev 1338)
+++ phenote/trunk/doc/phenote-website/index.shtml~ 2008-01-03 00:32:15 UTC (rev 1339)
@@ -97,12 +97,12 @@
</li>
</ul>
-->
- <h3>Phenote User's Group IRC</h3>
+ <h3>Phenote User's Group</h3>
<ul class="events">
<li class="events">
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://www.phenote.org/irc_chat">User's Group Monthly Meeting</a>, November 1, 9:00am, Online
+ <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote_Working_Group">User's Group Monthly Meeting</a>, December 6, 8:30am, Online
</p>
</li>
</ul>
@@ -111,7 +111,7 @@
<li class="events">
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://meetings.cshl.edu/meetings/info07.shtml">Genome Informatics</a>, November 1-5, Cold Spring Harbor, NY
+ (none scheduled at this time)
</p>
</li>
</ul>
Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.shtml 2008-01-03 00:21:43 UTC (rev 1338)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.shtml 2008-01-03 00:32:15 UTC (rev 1339)
@@ -20,9 +20,10 @@
Phenote Release Notes
</div>
-
+<h1>1.5</h1>
+<h2>12.20.2007, version <a href="phenote/1.5-beta2/phenote.jnlp">1.5 - beta2</a></h2>
-<h1>1.4 </h1>
+<h1>1.4</h1>
<h2>10.10.2007, version <a href="phenote/1.4/phenote.jnlp">1.4 - release</a></h2>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2008-01-03 00:35:23
|
Revision: 1340
http://obo.svn.sourceforge.net/obo/?rev=1340&view=rev
Author: nlw
Date: 2008-01-02 16:35:21 -0800 (Wed, 02 Jan 2008)
Log Message:
-----------
additional modifications to website
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/index.shtml
phenote/trunk/doc/phenote-website/index.shtml~
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2008-01-03 00:32:15 UTC (rev 1339)
+++ phenote/trunk/doc/phenote-website/index.shtml 2008-01-03 00:35:21 UTC (rev 1340)
@@ -111,7 +111,8 @@
<li class="events">
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- (none scheduled at this time)
+ <p>01.10.2008 - Seminar presentation at <a href="http://www.nescent.org/">NESCent</a></p>
+ <!-- (none scheduled at this time)-->
</p>
</li>
</ul>
@@ -129,7 +130,6 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
- <p>01.10.2008 - Seminar presentation at <a href="http://www.nescent.org/">NESCent</a></p>
<p>12.20.2007 - <b>New Phenote Beta Release - <a href="http://www.phenote.org/download.shtml">version 1.5-beta2</a></b></p>
<p>10.23-25.2007 - <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">BioCurator meeting</a>, San Jose, CA
[<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]</p>
Modified: phenote/trunk/doc/phenote-website/index.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml~ 2008-01-03 00:32:15 UTC (rev 1339)
+++ phenote/trunk/doc/phenote-website/index.shtml~ 2008-01-03 00:35:21 UTC (rev 1340)
@@ -102,7 +102,7 @@
<li class="events">
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote_Working_Group">User's Group Monthly Meeting</a>, December 6, 8:30am, Online
+ <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote_Working_Group">User's Group Monthly Meeting</a>, January 3, 8:30am, Online
</p>
</li>
</ul>
@@ -129,10 +129,10 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
- <p>10.23-25.2007 - <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">BioCurator meeting</a>, San Jose, CA
+ <p>01.10.2008 - Seminar presentation at <a href="http://www.nescent.org/">NESCent</a></p>
+ <p>12.20.2007 - <b>New Phenote Beta Release - <a href="http://www.phenote.org/download.shtml">version 1.5-beta2</a></b></p>
+ <p>10.23-25.2007 - <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">BioCurator meeting</a>, San Jose, CA
[<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]</p>
- <p>10.10.2007 - <b>New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a></b></p>
- <p>10.02.2007 - Phenote user's group to be moved to first Thursday of each month, 9am. Join us for our next meeting on November 1st over WebEx!</p>
<!--
<h3>Event Title</h3>
<ul class="events">
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2008-02-07 23:34:37
|
Revision: 1479
http://obo.svn.sourceforge.net/obo/?rev=1479&view=rev
Author: nlw
Date: 2008-02-07 15:34:38 -0800 (Thu, 07 Feb 2008)
Log Message:
-----------
some minor website edits
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/developer-docs/getting-source-code-in-eclipse.shtml
phenote/trunk/doc/phenote-website/download.shtml
phenote/trunk/doc/phenote-website/download.shtml~
Modified: phenote/trunk/doc/phenote-website/developer-docs/getting-source-code-in-eclipse.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/developer-docs/getting-source-code-in-eclipse.shtml 2008-02-07 23:22:59 UTC (rev 1478)
+++ phenote/trunk/doc/phenote-website/developer-docs/getting-source-code-in-eclipse.shtml 2008-02-07 23:34:38 UTC (rev 1479)
@@ -1,5 +1,6 @@
<!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"><head><!--#include virtual="ssi/head.html" -->
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head><!--#include virtual="..ssi/head.html" -->
@@ -9,7 +10,7 @@
<body>
- <!--#include virtual="ssi/header.html" -->
+ <!--#include virtual="../ssi/header.html" -->
<div id="main_container_aux">
@@ -131,6 +132,6 @@
</div>
- <!--#include virtual="ssi/footer.html" -->
+ <!--#include virtual="../ssi/footer.html" -->
</body></html>
\ No newline at end of file
Modified: phenote/trunk/doc/phenote-website/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml 2008-02-07 23:22:59 UTC (rev 1478)
+++ phenote/trunk/doc/phenote-website/download.shtml 2008-02-07 23:34:38 UTC (rev 1479)
@@ -14,6 +14,7 @@
<div id="main_content">
<div class="catch_phrase">
</div>
+ <h2>For Users</h2>
<h2><a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Launch Phenote in your browser</a></h2>
<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
<ul>
@@ -23,18 +24,9 @@
</ul>
<p> You may be prompted to sign a certificate and allow the download. This will take a few minutes the first time you do this.
</p>
- <h2>Run Phenote at the command line</h2>
- <p> To run phenote on the command line, linux or MacOSX users will need to checkout Phenote from the subversion repository. This can be done with the following command:</p>
- <ul>
- <li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.5-beta2/ phenote</b>
- </li>
- <li>Stable release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.4/ phenote</b>
- </li>
- <li>Latest: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote </b>
- </li>
- </ul>
- <p>Once you've got it, you can run Phenote with ant with the command: <b>ant run</b>
- </p>
+ <h2>For Developers</h2>
+ Check out our special documentation for running either on the <a href="developer-docs/getting-source-code-in-eclilpse.shtml">command line or in Eclipse</a>
+
<h2>Hardware requirements</h2>
<ul>
<li> 400 Mhz processor or faster.</li>
Modified: phenote/trunk/doc/phenote-website/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml~ 2008-02-07 23:22:59 UTC (rev 1478)
+++ phenote/trunk/doc/phenote-website/download.shtml~ 2008-02-07 23:34:38 UTC (rev 1479)
@@ -17,7 +17,7 @@
<h2><a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Launch Phenote in your browser</a></h2>
<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
<ul>
-<!-- <li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></strong></li>-->
+ <li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.5-beta2/phenote.jnlp">1.5 beta2</a></strong></li>-->
<li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp">1.4</a> </strong></li>
<li><a href="http://www.phenote.org/phenote/phenote.html">Older releases</a></li>
</ul>
@@ -26,8 +26,8 @@
<h2>Run Phenote at the command line</h2>
<p> To run phenote on the command line, linux or MacOSX users will need to checkout Phenote from the subversion repository. This can be done with the following command:</p>
<ul>
-<!-- <li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.4-beta3/ phenote</b>
- </li>-->
+ <li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.5-beta2/ phenote</b>
+ </li>
<li>Stable release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.4/ phenote</b>
</li>
<li>Latest: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote </b>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2008-02-08 00:18:58
|
Revision: 1481
http://obo.svn.sourceforge.net/obo/?rev=1481&view=rev
Author: nlw
Date: 2008-02-07 16:19:02 -0800 (Thu, 07 Feb 2008)
Log Message:
-----------
small web edits
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/download.shtml
phenote/trunk/doc/phenote-website/download.shtml~
Modified: phenote/trunk/doc/phenote-website/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml 2008-02-07 23:38:17 UTC (rev 1480)
+++ phenote/trunk/doc/phenote-website/download.shtml 2008-02-08 00:19:02 UTC (rev 1481)
@@ -25,7 +25,7 @@
<p> You may be prompted to sign a certificate and allow the download. This will take a few minutes the first time you do this.
</p>
<h2>For Developers</h2>
- Check out our special documentation for running either on the <a href="developer-docs/getting-source-code-in-eclilpse.shtml">command line or in Eclipse</a>
+ Check out our special documentation for running either on the <a href="developer-docs/getting-source-code-in-eclipse.shtml">command line or in Eclipse</a>
<h2>Hardware requirements</h2>
<ul>
Modified: phenote/trunk/doc/phenote-website/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml~ 2008-02-07 23:38:17 UTC (rev 1480)
+++ phenote/trunk/doc/phenote-website/download.shtml~ 2008-02-08 00:19:02 UTC (rev 1481)
@@ -14,6 +14,7 @@
<div id="main_content">
<div class="catch_phrase">
</div>
+ <h2>For Users</h2>
<h2><a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Launch Phenote in your browser</a></h2>
<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
<ul>
@@ -23,18 +24,9 @@
</ul>
<p> You may be prompted to sign a certificate and allow the download. This will take a few minutes the first time you do this.
</p>
- <h2>Run Phenote at the command line</h2>
- <p> To run phenote on the command line, linux or MacOSX users will need to checkout Phenote from the subversion repository. This can be done with the following command:</p>
- <ul>
- <li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.5-beta2/ phenote</b>
- </li>
- <li>Stable release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.4/ phenote</b>
- </li>
- <li>Latest: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote </b>
- </li>
- </ul>
- <p>Once you've got it, you can run Phenote with ant with the command: <b>ant run</b>
- </p>
+ <h2>For Developers</h2>
+ Check out our special documentation for running either on the <a href="developer-docs/getting-source-code-in-eclilpse.shtml">command line or in Eclipse</a>
+
<h2>Hardware requirements</h2>
<ul>
<li> 400 Mhz processor or faster.</li>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2008-02-08 01:24:51
|
Revision: 1484
http://obo.svn.sourceforge.net/obo/?rev=1484&view=rev
Author: nlw
Date: 2008-02-07 17:24:56 -0800 (Thu, 07 Feb 2008)
Log Message:
-----------
more website changes
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/developer-docs/dataadapter.shtml
phenote/trunk/doc/phenote-website/ssi/header.html
Added Paths:
-----------
phenote/trunk/doc/phenote-website/developer-docs/index.shtml
phenote/trunk/doc/phenote-website/developer-docs/web-developer-docs
Modified: phenote/trunk/doc/phenote-website/developer-docs/dataadapter.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/developer-docs/dataadapter.shtml 2008-02-08 01:05:12 UTC (rev 1483)
+++ phenote/trunk/doc/phenote-website/developer-docs/dataadapter.shtml 2008-02-08 01:24:56 UTC (rev 1484)
@@ -274,10 +274,10 @@
<br></constraint-list>
</code>
<p>(this isnt implemented yet) Alternative is to hardwire the adding of your constraint with <code>ConstraintManager.inst().addConstraint(Constraint)</code>. If you add more than one constraint, the messages from all the failing constraints will be appended and displayed together.</p>
-<code>ConstraintStatus</code> also has a warning state - this causes a warning to display and
+<p><code>ConstraintStatus</code> also has a warning state - this causes a warning to display and
lets user decide whether to to go through with commit. use
<code>ConstraintStatus.Status.WARNING</code>. and likewise all warning messages from
-all constraints get lumped into one message.
+all constraints get lumped into one message.</p>
</div>
</div>
Added: phenote/trunk/doc/phenote-website/developer-docs/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/developer-docs/index.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/developer-docs/index.shtml 2008-02-08 01:24:56 UTC (rev 1484)
@@ -0,0 +1,61 @@
+<!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">
+ <head>
+
+ <!--#include virtual="ssi/head.html" -->
+ <title>Phenote Developer Docs</title>
+
+ </head>
+ <body>
+
+ <!--#include virtual="ssi/header.html" -->
+
+ <div id="main_container">
+ <div id="main_content">
+ <div class="catch_phrase">
+ Welcome to the Phenote Developer Documentation Resource Page
+ </div>
+ <p>This page is your starting point if you are a developer on the Phenote project. Some interesting articles can be found below:</p>
+ <ul>
+ <li><a href="getting-source-code-in-eclipse.shtml">Getting the Source code</a> (command line or in Eclipse)
+ </li>
+ <li><a href="dataadapter.shtml">Working with Data Adapters</a>
+ </li>
+ <li><a href="developer-docs.shtml">Adding new configuration parameters</a>
+ </li>
+ </ul>
+
+ <div id="sidebar_container">
+
+ <div id="sidebar_content">
+
+ <div class="content_box_head_blue">
+ Quick Links
+ </div>
+
+ <div class="content_box_blue">
+
+ <p class="quick_link">
+ <img src="images/star.gif" alt="" class="icon_green"/>
+ <a href="http://sourceforge.net/tracker/?group_id=76834&atid=887913"
+ title="Bug Tracker">
+ Bug Tracker
+ </a>
+ </p>
+
+ <p class="quick_link">
+ <img src="images/star.gif" alt="" class="icon_green"/>
+ <a href="" title="Java API docs">
+ Java API docs
+ </a>
+ </p>
+
+ </div>
+
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
+
+ </body>
+</html>
Added: phenote/trunk/doc/phenote-website/developer-docs/web-developer-docs
===================================================================
--- phenote/trunk/doc/phenote-website/developer-docs/web-developer-docs (rev 0)
+++ phenote/trunk/doc/phenote-website/developer-docs/web-developer-docs 2008-02-08 01:24:56 UTC (rev 1484)
@@ -0,0 +1,177 @@
+heres how PhenoteServlet makes the auto completion response:
+
+ private String getCompletionList(String userInput,String ontol,String field) {
+ StringBuffer sb = new StringBuffer("<ul>");
+ try {
+ Vector<CompletionTerm> v =
+getCompListSearcher(ontol).getStringMatchTerms(userInput);
+ //Vector<OBOClass> v = ontology.getStringMatchTerms(userInput,
+getSearchParams());
+ for (CompletionTerm ct : v)
+ sb.append(makeCompListHtmlItem(ct, ontol, field));
+ }
+ catch (OntologyException e) { sb.append(e.getMessage()); }
+ sb.append("</ul>");
+ return sb.toString();
+ }
+ private String makeCompListHtmlItem(CompletionTerm term, String ontol,String
+field) {
+ String id = term.getID(), name=term.getName();
+ String display = term.getCompListDisplayString();
+ // pass in id, name & ontology - name for setting field on UseTerm
+ StringBuffer info = dq(fn("getTermInfo",new String[]{id,name,ontol,field}));
+ StringBuffer select = dq(fn("selectTerm",new String[]{name,field}));
+ //String info = "\"getTermInfo("+id +","+q(name)+","+ q(ontol) + ")\"";
+ return "<li onmouseover=" + info + " id=" + q(id) + " " +
+ "onclick=" + select + ">" + display + "</li>\n";
+ }
+
+ private static StringBuffer fn(String fnName, String[] params) {
+ return HtmlUtil.fn(fnName,params);
+ }
+
+
+so basically the ajax autocompleter expects a <ul> list - not a page, not a
+single string. furthermore the <li> elements of the list have onMouseOver
+getTermInfo javascript functions wired into them. Im working on a selectTerm
+fuction on mouse click to get term names to show up on synonym select but that
+isnt working yet. So the response needs to look like this:
+
+<ul>
+ <li onmouseover=getTermInfo('id','name','ontol','field') id='id'
+ onclick=selectTerm('name','field') > termName </li>
+ <li ...
+</ul>
+
+
+so if you just want to grab pieces of the javascript
+
+ajax scripts:
+<script src="../javascript/ajax-lib/prototype.js" type="text/javascript"></script>
+<script src="../javascript/ajax-lib/effects.js" type="text/javascript"></script>
+<script src="../javascript/ajax-lib/dragdrop.js" type="text/javascript"></script>
+<script src="../javascript/ajax-lib/controls.js" type="text/javascript"></script>
+
+
+EntityOntology Chooser:
+<script type="text/javascript">
+ function setEntityOntology(selectedOntology) {
+ if (selectedOntology == 'AO') {
+ ontologyName = 'ZF'; <!-- ZF Anatomy -->
+ } else if (selectedOntology == 'GO') {
+ ontologyName = 'GO';
+ }
+
+<!-- entityAutoCompleter.options.parameters = "ontologyName=" + ontologyName; -->
+ entityAutoCompleter.options.defaultParams = "ontologyName="+ontologyName+"&field=ENTITY";
+ <!-- alert(entityAutoCompleter.options.defaultParams); -->
+
+ }
+
+</script>
+
+
+src/web documentation of js,html,ajax...:
+
+This is a web widget to search ontologies dynamically using Ajax. The
+following describes the various compoents of the widget and how to use it.
+
+Style sheet: /css/control.js
+This contains all the styles used in the widget
+
+Javascript:
+/javascript/dichty-term-info.js contains a method to call Ajax to
+update the Ontology information in the term info panel.
+In this javascript the "var url" should point to the processing script.
+
+/javascript/ajax-lib contains Ajax libraries from Prototype
+for ajax and its auto completer
+http://prototype.conio.net/
+
+Perl
+/perl contains an example of a Ajax request processing script.
+It is written in CGI perl.
+
+
+-------------------
+src/web/html Files:
+-------------------
+dichty.html interface.html ncbo.html term_completer.html
+
+dichty.html: I think this is old and should be deleted - sohel? replaced by interface.html
+
+
+interface.html:
+---------------
+This should be renamed dichty-top.html as this is dichty base's new
+top level html page. The improvement over dichty.html (amongst other additions) is
+that it generically creates fields using the Sever Side Includes(SSI) file
+term_completer.html. Also has commit & retrieve buttons, that call javascript functions.
+
+term_completer.html
+-------------------
+This is generic server side include stuff for interface.html. It takes vars tag, title,
+ & url. see interface.html for use. This should be renamed term_completion_field.ssi
+ or just field.ssi (are all fields term completion - some may be free text) or
+ field_template.ssi?
+
+
+ncbo.html
+---------
+This is the top html page for ncbo/zfin (rename zfin.html?). It should use the new
+SSI paradigm and use the term_completer.html SSI stuff. But this does have stuff that
+interface/term_completer lacks. That is it has an entity chooser (dichtybase has no
+need for one), and a UseTerm button. These require both an ontology name and field
+name to be passed into the auto completion function. Also method names are renamed
+for clarity sake.
+
+
+So in summary ncbo.html & interface.html need to grab stuff from each other. Both of which
+serve as templates for new groups coming up with there own top level page (mod.html)
+
+
+
+--------------------------
+src/web/javascript readme
+--------------------------
+3 files: dichty-term-info.js ncbo-term-info.js term-completer.js
+one sub directory: ajax-lib
+
+ajax-lib is open source ajax code from scriptaculous that the above files use.
+in theory these shouldnt need to be modified (though ive had my temptations)
+
+The 3 scripts are all for term info retrieval from the backend. They should
+probably be merged & deleted. The main variant is the backend url to get term info
+from and that url should come from the top page where all mod specific stuff is set,
+rather than here. Once that is done should be able to merge.
+
+These scripts are called with onMouseOver that is in the completion list that is
+returned by the backend server(be it perl servlet or whatnot) for autocompletion.
+
+dichty-term-info.js might be old and if so should be deleted? sohel?
+
+term_completer.js is the new dichty base script (or old??) should be merged
+with ncbo-term-info.js. Sohel that would require you to change your mouseOver
+function call from the completion list to getTermInfo - would that be ok?
+
+ncbo-term-info.js
+-----------------
+is used for zfin/ncbo. There are some difference to dichty here.
+The method is called getTermInfo which is a clearer name then set_ontology or
+set_ontology_term. The url is different and as said above should be set in
+the top mod specific page not here.
+
+OntologyName & field are passed as
+parameters. Ontology name is needed for cases where theres an ontology chooser
+(zfin entity - dichty can ignore this). field is needed so the Use Term button
+of TermInfo knows which field to update (its the field the original term came from).
+
+In the top level html (ncbo.html) the form with the terms is given the name
+termForm and that is used instead of forms[0] which can be presumptious if plugging
+into a mods web page.
+
+The checking of the length of the ontologyid array was scrapped as it was unnecasary.
+
+So these scripts should be merged, and I think the ncbo changes should be incorporated.
+Would you agree sohel?
+
Modified: phenote/trunk/doc/phenote-website/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/header.html 2008-02-08 01:05:12 UTC (rev 1483)
+++ phenote/trunk/doc/phenote-website/ssi/header.html 2008-02-08 01:24:56 UTC (rev 1484)
@@ -96,6 +96,10 @@
title="User Guide">User Guide</a>
</li>
<li>
+ <a href="http://www.phenote.org/developer-docs/"
+ title="Developer Docs">Developer Docs</a>
+ </li>
+ <li>
<a href="http://sourceforge.net/tracker/?group_id=76834&atid=887913"
title="Report a bug/Request a feature">Bug Reports / Feature Requests</a>
</li>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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