Menu
▾
▴
obo-svn-commit — sends mail for all commits to svn repository
You can subscribe to this list here.
| 2006 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
(18) |
Aug
(33) |
Sep
(30) |
Oct
(27) |
Nov
(59) |
Dec
(30) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2007 |
Jan
(67) |
Feb
(44) |
Mar
(70) |
Apr
(73) |
May
(119) |
Jun
(31) |
Jul
(92) |
Aug
(86) |
Sep
(76) |
Oct
(152) |
Nov
(156) |
Dec
(85) |
| 2008 |
Jan
(111) |
Feb
(121) |
Mar
(107) |
Apr
(102) |
May
(45) |
Jun
(65) |
Jul
(62) |
Aug
(133) |
Sep
(56) |
Oct
(56) |
Nov
(17) |
Dec
(15) |
| 2009 |
Jan
(10) |
Feb
(5) |
Mar
(10) |
Apr
(14) |
May
(49) |
Jun
(94) |
Jul
(67) |
Aug
(23) |
Sep
(9) |
Oct
(92) |
Nov
(26) |
Dec
(51) |
| 2010 |
Jan
(105) |
Feb
(83) |
Mar
(52) |
Apr
(59) |
May
(68) |
Jun
(71) |
Jul
(127) |
Aug
(49) |
Sep
(91) |
Oct
(27) |
Nov
(33) |
Dec
(26) |
| 2011 |
Jan
(26) |
Feb
(45) |
Mar
(26) |
Apr
(28) |
May
(17) |
Jun
(15) |
Jul
(45) |
Aug
(33) |
Sep
(50) |
Oct
(22) |
Nov
(10) |
Dec
(21) |
| 2012 |
Jan
(33) |
Feb
(24) |
Mar
(36) |
Apr
(60) |
May
(60) |
Jun
(43) |
Jul
(114) |
Aug
(19) |
Sep
(35) |
Oct
(24) |
Nov
(64) |
Dec
(12) |
| 2013 |
Jan
(54) |
Feb
(58) |
Mar
(51) |
Apr
(46) |
May
(21) |
Jun
(29) |
Jul
(25) |
Aug
(25) |
Sep
(13) |
Oct
(7) |
Nov
(14) |
Dec
(27) |
| 2014 |
Jan
(10) |
Feb
(7) |
Mar
(16) |
Apr
(14) |
May
(19) |
Jun
(8) |
Jul
(15) |
Aug
(11) |
Sep
(5) |
Oct
(11) |
Nov
(11) |
Dec
(4) |
| 2015 |
Jan
(52) |
Feb
(27) |
Mar
(22) |
Apr
(17) |
May
(2) |
Jun
(2) |
Jul
(2) |
Aug
(2) |
Sep
(2) |
Oct
|
Nov
(2) |
Dec
|
| 2016 |
Jan
(2) |
Feb
|
Mar
|
Apr
(2) |
May
(1) |
Jun
(1) |
Jul
(3) |
Aug
(2) |
Sep
(2) |
Oct
(2) |
Nov
(2) |
Dec
|
| 2017 |
Jan
|
Feb
|
Mar
(1) |
Apr
(1) |
May
(4) |
Jun
|
Jul
|
Aug
(1) |
Sep
(1) |
Oct
(2) |
Nov
|
Dec
(1) |
| 2018 |
Jan
|
Feb
|
Mar
(4) |
Apr
|
May
(2) |
Jun
(2) |
Jul
(2) |
Aug
(2) |
Sep
(1) |
Oct
(2) |
Nov
(1) |
Dec
|
| 2019 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
(2) |
Aug
|
Sep
|
Oct
|
Nov
|
Dec
(3) |
| 2020 |
Jan
|
Feb
|
Mar
|
Apr
|
May
(2) |
Jun
(3) |
Jul
|
Aug
|
Sep
(2) |
Oct
|
Nov
|
Dec
|
|
From: <nl...@us...> - 2007-09-15 00:36:03
|
Revision: 903
http://obo.svn.sourceforge.net/obo/?rev=903&view=rev
Author: nlw
Date: 2007-09-14 17:36:03 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
more validation fixes
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/contact.shtml
phenote/trunk/doc/phenote-website/new/download.shtml
phenote/trunk/doc/phenote-website/new/download.shtml~
phenote/trunk/doc/phenote-website/new/faq.shtml
phenote/trunk/doc/phenote-website/new/funding.shtml
phenote/trunk/doc/phenote-website/new/related.shtml
phenote/trunk/doc/phenote-website/new/users.shtml
Modified: phenote/trunk/doc/phenote-website/new/contact.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/contact.shtml 2007-09-15 00:17:58 UTC (rev 902)
+++ phenote/trunk/doc/phenote-website/new/contact.shtml 2007-09-15 00:36:03 UTC (rev 903)
@@ -64,7 +64,7 @@
<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>
+ <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">Request Tracker</a></p>
</div>
</div>
Modified: phenote/trunk/doc/phenote-website/new/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-15 00:17:58 UTC (rev 902)
+++ phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-15 00:36:03 UTC (rev 903)
@@ -24,9 +24,13 @@
</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>
+ <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>
+ </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>
Modified: phenote/trunk/doc/phenote-website/new/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-15 00:17:58 UTC (rev 902)
+++ phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-15 00:36:03 UTC (rev 903)
@@ -56,28 +56,28 @@
</div>
<div class="content_box_blue">
- <p>feature: Native look-and-feel enabled for interface. Users should now see Mac or Windows style depending on their system.</p>
- <p>feature: read-only field (needs work)</p>
- <p>feature: config disabpng of copy of field (for db ids)</p>
- <p>feature: display property values of terms in term info</p>
- <p>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.</p>
- <p>feature: term fields can be nullified</p>
- <p>feature: separate queries to backend for different groups, implemented in worm</p>
- <p>feature: ID field type, requires ":"</p>
- <p>feature: can get unique list of deleted annots</p>
- <p>feature: added group adapter framework</p>
- <p>feature: fly genotype group adapter makes fly genotype strings from tab/group</p>
- <p>feature: worm group adapter makes reference terms from ref query</p>
- <p>change: on term completion if adding a letter use previous completion list</p>
- <p>change: worm adapter query tab working properly</p>
- <p>change: build file takes param for webstart version deployment, and puts in jnlp</p>
- <p>change: group adapters can psten for CharList changes</p>
- <p>change: added/corrected BIRN ontologies</p>
- <p>bugfix: load of file doesnt crash on post comp parsing bug</p>
- <p>bugfix: doesnt load obo files specified twice twice</p>
- <p>bugfix: view menu show up at initialization</p>
- <p>bugfix: layout of term history with split pane proper</p>
+ <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>
Modified: phenote/trunk/doc/phenote-website/new/faq.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/faq.shtml 2007-09-15 00:17:58 UTC (rev 902)
+++ phenote/trunk/doc/phenote-website/new/faq.shtml 2007-09-15 00:36:03 UTC (rev 903)
@@ -27,11 +27,11 @@
</p>
<h3>I found a bug in Phenote. How do I report errors?</h3>
<p>
- We want to know if there's any errors. Please use our <a href="http://www.sourceforge.net/tracker/?group_id=76834&atid=887913">Bug Report tracker</a>.
+ We want to know if there's any errors. Please use our <a href="http://www.sourceforge.net/tracker/?group_id=76834&atid=887913">Bug Report tracker</a>.
</p>
<h3>There's a function/feature I wish Phenote had. Can you add it?</h3>
<p>
- You can request new features through our <a href="http://www.sourceforge.net/tracker/?group_id=76834&atid=887913">Feature Request tracker</a>. Please be sure to label the "Group" as a "new feature".
+ You can request new features through our <a href="http://www.sourceforge.net/tracker/?group_id=76834&atid=887913">Feature Request tracker</a>. Please be sure to label the "Group" as a "new feature".
</p>
<h1>Ontologies</h1>
<h3>What kinds of ontologies can I use?</h3>
@@ -59,12 +59,11 @@
</p>
<h3>Is there one place I can go to browse through all the available ontologies?</h3>
<p>
- Yep! There are several online resources that can help you learn more. Some of these include:
+ Yep! There are several online resources that can help you learn more. Some of these include:</p>
<ul>
<li><a href="http://www.bioontology.org/">National Center for Biomedical Ontology</a></li>
<li><a href="http://www.obofoundry.org/">OBO Foundry</a></li>
</ul>
- </p>
<h1>Using Phenote</h1>
<h3>Is there some online documentation?</h3>
<p>
Modified: phenote/trunk/doc/phenote-website/new/funding.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/funding.shtml 2007-09-15 00:17:58 UTC (rev 902)
+++ phenote/trunk/doc/phenote-website/new/funding.shtml 2007-09-15 00:36:03 UTC (rev 903)
@@ -25,24 +25,27 @@
<p> There are three funded groups driving the development of this
software project through the NCBO:</p>
- <table border="0">
- <tr>
- <td><a href="http://flybase.bio.indiana.edu/">
- <img class="portrait" height="50" border="0" src="/images/fly_logo.png"alt="Flybase" /></a>
- </td>
- <td><p><strong>Flybase: The Drosophila Genome Database</strong>[<a href="http://www.bioontology.org/dbp_drosophila.html">...</a>]</p></td>
- </tr>
- <tr>
- <td><a href="http://www.zfin.org/"><img class="portrait" border="0" src="/images/zfin_logo.gif" height="50" alt="Zfin" /></a>
- </td>
- <td><p><strong>Zfin: Zebrafish Information Network</strong> [<a href="http://www.bioontology.org/dbp_zfin.html">...</a>]</p></td>
- </tr>
- <td><a href="http://www.nbirn.net/research/mouse/index.shtm">
- <img class="portrait" height="50" border="0" src="/images/BIRN_logo.gif"alt="BIRN" /></a>
- </td>
- <td><p><strong>mouseBIRN: mouse Biomedical Informatics Research Network</strong></p></td>
- </tr>
- </table>
+ <table border="0">
+ <tr>
+ <td><a href="http://flybase.bio.indiana.edu/">
+ <img class="portrait" height="50" border="0" src="/images/fly_logo.png"alt="Flybase" /></a>
+ </td>
+ <td><p><strong>Flybase: The Drosophila Genome Database</strong>[<a href="http://www.bioontology.org/dbp_drosophila.html">...</a>]</p></td>
+ </tr>
+ <tr>
+ <td><a href="http://www.zfin.org/"><img class="portrait" border="0" src="/images/zfin_logo.gif" height="50" alt="Zfin" /></a>
+ </td>
+ <td><p><strong>Zfin: Zebrafish Information Network</strong> [<a href="http://www.bioontology.org/dbp_zfin.html">...</a>]</p>
+ </td>
+ </tr>
+ <tr>
+ <td><a href="http://www.nbirn.net/research/mouse/index.shtm">
+ <img class="portrait" height="50" border="0" src="/images/BIRN_logo.gif" alt="BIRN" /></a>
+ </td>
+ <td><p><strong>mouseBIRN: mouse Biomedical Informatics Research Network</strong></p>
+ </td>
+ </tr>
+ </table>
</div>
</div>
Modified: phenote/trunk/doc/phenote-website/new/related.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/related.shtml 2007-09-15 00:17:58 UTC (rev 902)
+++ phenote/trunk/doc/phenote-website/new/related.shtml 2007-09-15 00:36:03 UTC (rev 903)
@@ -16,10 +16,10 @@
Related Projects
</div>
<h1>Ontologies</h1>
- <h3>
+ <h2>
<a href="http://www.bioontology.org/wiki/index.php/PATO:Main_Page">
Phenotype and Trait Ontology (PATO)</a>
- </h3>
+ </h2>
<p>
An ontology of phenotypic qualities (properties). This ontology
can be used in conjunction with other ontologies such as GO or
@@ -27,10 +27,10 @@
qualities are red, ectopic, high temperature, fused, small,
edematous and arrested.
</p>
- <h3>
+ <h2>
<a href="http://www.geneontology.org/">
Gene Ontology (GO)</a>
- </h3>
+ </h2>
<p>
The Gene Ontology (GO) project is a collaborative effort to address
the need for consistent descriptions of gene products in different
@@ -39,11 +39,12 @@
describe gene and gene product attributes in any organism. There
are three distinct ontologies developed by GO: molecular function,
biological process, and cellular component.
- <h3>
+ </p>
+ <h2>
<a href="http://obi.sourceforge.net/">
Ontologies for Biomedical Investigations
</a>
- </h3>
+ </h2>
<p>
The Ontology for Biomedical Investigations (OBI) project is
developing an integrated ontology for the description of
@@ -55,10 +56,10 @@
<h1>Resources</h1>
- <h3>
+ <h2>
<a href="http://www.bioontology.org/">
National Center for Biomedical Ontology</a>
- </h3>
+ </h2>
<p>
The NCBO is a consortium of leading biologists, clinicians,
informaticians, and ontologists who develop innovative technology
@@ -66,10 +67,10 @@
manage biomedical information and knowledge in machine-processable
form.
</p>
- <h3>
+ <h2>
<a href="http://www.obofoundry.org/">
OBO Foundry</a>
- </h3>
+ </h2>
<p>
The OBO Foundry is an open, inclusive, and collaborative core of
interoperable ontologies developed by the research community. The
@@ -83,10 +84,10 @@
of data and information integration in the biomedical domain.
</p>
- <h3>
+ <h2>
<a href="http://www.gmod.org/">
Generic Model Organism Databases</a>
- </h3>
+ </h2>
<p>
The Generic Model Organism Project (GMOD) is a joint effort
by the model organism system databases WormBase, FlyBase,
@@ -95,12 +96,12 @@
community databases of biology.
</p>
- <h3>
+ <h2>
<a href="http://ifomis.org">
Institute for Formal Ontology and Medical Information
Science (IFOMIS)
</a>
- </h3>
+ </h2>
<p>
The Institute for Formal Ontology and Medical Information
Science (IFOMIS) comprehends an interdisciplinary research
@@ -110,11 +111,11 @@
applied ontology.
</p>
- <h3>
+ <h2>
<a href="http://mged.sf.net/">
MGED
</a>
- </h3>
+ </h2>
<p>
The Microarray Gene Expression Data (MGED) Society is an
international organisation of biologists, computer
@@ -123,11 +124,11 @@
and proteomics experiments.
</p>
- <h3>
+ <h2>
<a href="http://www.ebi.ac.uk/ontology-lookup/">
Ontology Lookup Service
</a>
- </h3>
+ </h2>
<p>
The Ontology Lookup Service is a spin-off of the PRIDE
project, which required a centralized query interface for
@@ -139,11 +140,11 @@
format.
</p>
- <h3>
+ <h2>
<a href="http://www.plantontology.org/">
Plant Ontology Consortium
</a>
- </h3>
+ </h2>
<p>
The Plant Ontology Consortium (POC) aims to develop, curate
and share structured controlled vocabularies (ontologies)
@@ -154,11 +155,11 @@
specific expression of genes, proteins and phenotypes.
</p>
- <h3>
+ <h2>
<a href="http://www.psidev.info/index.php?q=node/258">
Proteomics Standards Initiative
</a>
- </h3>
+ </h2>
<p>
Is also interested in guidelines for the development of
Controlled Vocabularies.
Modified: phenote/trunk/doc/phenote-website/new/users.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/users.shtml 2007-09-15 00:17:58 UTC (rev 902)
+++ phenote/trunk/doc/phenote-website/new/users.shtml 2007-09-15 00:36:03 UTC (rev 903)
@@ -30,6 +30,7 @@
</td>
<td>Zebrafish Information Network (Zfin)</td>
</tr>
+ <tr>
<td><a href="http://www.nbirn.net/research/mouse/index.shtm">
<img class="portrait" height="50" border="0" src="/images/BIRN_logo.gif"alt="BIRN" /></a>
</td>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-15 00:18:04
|
Revision: 902
http://obo.svn.sourceforge.net/obo/?rev=902&view=rev
Author: nlw
Date: 2007-09-14 17:17:58 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
fixed some w3c validation errors
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/resources.shtml
phenote/trunk/doc/phenote-website/new/ssi/header.html
phenote/trunk/doc/phenote-website/new/team.shtml
Modified: phenote/trunk/doc/phenote-website/new/resources.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/resources.shtml 2007-09-14 22:08:36 UTC (rev 901)
+++ phenote/trunk/doc/phenote-website/new/resources.shtml 2007-09-15 00:17:58 UTC (rev 902)
@@ -16,7 +16,7 @@
Ontology Resources
</div>
<p>You can find out more about available ontologies for use during
- annotation with Phenote software:<p>
+ annotation with Phenote software:</p>
<h3>
<a href="http://www.bioontology.org/ncbo/faces/pages/ontology_list.xhtml">
NCBO Bioportal
Modified: phenote/trunk/doc/phenote-website/new/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/new/ssi/header.html 2007-09-14 22:08:36 UTC (rev 901)
+++ phenote/trunk/doc/phenote-website/new/ssi/header.html 2007-09-15 00:17:58 UTC (rev 902)
@@ -96,7 +96,7 @@
title="User Guide">User Guide</a>
</li>
<li>
- <a href="http://sourceforge.net/tracker/?group_id=76834&atid=887913"
+ <a href="http://sourceforge.net/tracker/?group_id=76834&atid=887913"
title="Report a bug/Request a feature">Bug Reports / Feature Requests</a>
</li>
</ul>
Modified: phenote/trunk/doc/phenote-website/new/team.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/team.shtml 2007-09-14 22:08:36 UTC (rev 901)
+++ phenote/trunk/doc/phenote-website/new/team.shtml 2007-09-15 00:17:58 UTC (rev 902)
@@ -23,7 +23,7 @@
</div>
<div class="third_bio">
<p><img src="http://www.bioontology.org/images/team/washington.jpg" title="Nicole Washington" alt="Nicole Washington" height="130" /> </p>
- <p><a href="http://berkeleybop.org/content/about/people/nlwashington/" title="Nicole Washington">Nicole Washington</a></a>, PhD </p>
+ <p><a href="http://berkeleybop.org/content/about/people/nlwashington/" title="Nicole Washington">Nicole Washington</a>, PhD </p>
</div>
<div class="third_bio">
<p><img src="http://www.bioontology.org/images/team/mungall.jpg" title="Chris Mungall" alt="Chris Mungall" height="130" /></p>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-14 22:08:33
|
Revision: 901
http://obo.svn.sourceforge.net/obo/?rev=901&view=rev
Author: nlw
Date: 2007-09-14 15:08:36 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
website: another faq, making the main page pretty
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/faq.shtml
phenote/trunk/doc/phenote-website/new/index.shtml
Modified: phenote/trunk/doc/phenote-website/new/faq.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/faq.shtml 2007-09-14 21:38:59 UTC (rev 900)
+++ phenote/trunk/doc/phenote-website/new/faq.shtml 2007-09-14 22:08:36 UTC (rev 901)
@@ -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 Phenote link from the main page or the Downloads 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/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.
</p>
<h3>What's the best forum to ask my burning questions?</h3>
<p>
@@ -40,7 +40,7 @@
</p>
<h3>Can I use OBO and/or OWL format ontologies?</h3>
<p>
- Yes! However, there's a little catch. You will need to convert your OWL ontology to OBO format first.
+ Yes! However, there's a little catch. You will need to convert your OWL ontology to OBO format first. In the future, we plan to include a feature to convert on-the-fly.
</p>
<h3>How can I convert my OWL ontology to OBO format?</h3>
<p>
@@ -48,7 +48,7 @@
</p>
<h3>Can I use my own ontologies?</h3>
<p>
- Yes you can! You don't have to use ontologies that are in public repositories if you don't want to. Please consult the User Guide for more detailed instructions...
+ Yes you can! You don't have to use ontologies that are in public repositories if you don't want to. Please consult the <a href="http://www.phenote.org/help/">User Guide</a> for more detailed instructions...
</p>
<h3>Can I use my own pre-coordinated phenotype ontology?</h3>
<p>
@@ -71,13 +71,21 @@
You bet! Check out our <a href="http://www.phenote.org/help/">User's Guide</a></p>
<h3>When I'm annotating, I can't seem to find the right terms?</h3>
<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.
- If you still can't find it, it might be that the ontology is really missing a term. Ontologies 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.
+ 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.
</p>
+ <h3>Are there any tools that allow me to analyze my annotations?</h3>
+ <p> Presently Phenote does not include any analysis tools. However,
+ <a href="http://www.bioontology.org/wiki/index.php/OBD:Main_Page">tools</a>
+ are being developed within the NCBO that will allow
+ for data warehousing, querying, and analysis. Our hope is to have
+ them integrated in Phenote whenever possible. Please stay tuned
+ for future updates and take a look at our <a href="roadmap.shtml">
+ roadmap</a> to find out more.</p>
</div>
</div>
Modified: phenote/trunk/doc/phenote-website/new/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/index.shtml 2007-09-14 21:38:59 UTC (rev 900)
+++ phenote/trunk/doc/phenote-website/new/index.shtml 2007-09-14 22:08:36 UTC (rev 901)
@@ -16,7 +16,7 @@
Welcome to 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.
+ Phenote is both a complete piece of software and a software toolkit designed to facilitate the <b>annotation of biological phenotypes using ontologies</b>. It provides an interface and infrastructure 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 <b>user-friendly</b> and <b>computable</b> 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).
@@ -29,7 +29,7 @@
</li>
<li>Use of any OBO-format ontology (or OWL->OBO converted)
</li>
- <li>Ontology navigation and term information display
+ <li>Ontology navigation and all-in-one term information display
</li>
<li>Bulk copy/edit/delete/sort of phenotype-genotype character entries
</li>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-14 21:38:56
|
Revision: 900
http://obo.svn.sourceforge.net/obo/?rev=900&view=rev
Author: nlw
Date: 2007-09-14 14:38:59 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
working on the website sidebar
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/download.shtml
phenote/trunk/doc/phenote-website/new/download.shtml~
Modified: phenote/trunk/doc/phenote-website/new/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-14 21:30:31 UTC (rev 899)
+++ phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-14 21:38:59 UTC (rev 900)
@@ -56,28 +56,28 @@
</div>
<div class="content_box_blue">
- <p>feature: Native look-and-feel enabled for interface. Users should now see Mac or Windows style depending on their system.</p>
- <p>feature: read-only field (needs work)</p>
- <p>feature: config disabpng of copy of field (for db ids)</p>
- <p>feature: display property values of terms in term info</p>
- <p>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.</p>
- <p>feature: term fields can be nullified</p>
- <p>feature: separate queries to backend for different groups, implemented in worm</p>
- <p>feature: ID field type, requires ":"</p>
- <p>feature: can get unique list of deleted annots</p>
- <p>feature: added group adapter framework</p>
- <p>feature: fly genotype group adapter makes fly genotype strings from tab/group</p>
- <p>feature: worm group adapter makes reference terms from ref query</p>
- <p>change: on term completion if adding a letter use previous completion list</p>
- <p>change: worm adapter query tab working properly</p>
- <p>change: build file takes param for webstart version deployment, and puts in jnlp</p>
- <p>change: group adapters can psten for CharList changes</p>
- <p>change: added/corrected BIRN ontologies</p>
- <p>bugfix: load of file doesnt crash on post comp parsing bug</p>
- <p>bugfix: doesnt load obo files specified twice twice</p>
- <p>bugfix: view menu show up at initialization</p>
- <p>bugfix: layout of term history with split pane proper</p>
+ <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>
Modified: phenote/trunk/doc/phenote-website/new/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-14 21:30:31 UTC (rev 899)
+++ phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-14 21:38:59 UTC (rev 900)
@@ -14,15 +14,15 @@
<div id="main_content">
<div class="catch_phrase">
</div>
- <h3>Launch Phenote in your browser</h3>
+ <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>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></li>
- <li>Stable release: <a href="http://www.phenote.org/phenote/1.3/phenote.jnlp">1.3</a> </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/1.3/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>
- <h3>Run Phenote at the command line</h3>
+ <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>
@@ -30,14 +30,14 @@
</ul>
<p>Once you've got it, you can run Phenote with ant with the command: <b>ant run</b>
</p>
- <h3>Hardware requirements</h3>
+ <h2>Hardware requirements</h2>
<ul>
<li> 400 Mhz processor or faster.</li>
<li> 500+ MB RAM </li>
- <li> ? MB free disk space on your computer </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>
- <h3>Software requirements</h3>
+ <h2>Software requirements</h2>
<ul>
<li> PC running Windows XP; Mac OSX; Linux </li>
<li> Webstart: Internet browser with webstart installed </li>
@@ -56,30 +56,28 @@
</div>
<div class="content_box_blue">
-<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>
+ <p>feature: Native look-and-feel enabled for interface. Users should now see Mac or Windows style depending on their system.</p>
+ <p>feature: read-only field (needs work)</p>
+ <p>feature: config disabpng of copy of field (for db ids)</p>
+ <p>feature: display property values of terms in term info</p>
+ <p>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.</p>
+ <p>feature: term fields can be nullified</p>
+ <p>feature: separate queries to backend for different groups, implemented in worm</p>
+ <p>feature: ID field type, requires ":"</p>
+ <p>feature: can get unique list of deleted annots</p>
+ <p>feature: added group adapter framework</p>
+ <p>feature: fly genotype group adapter makes fly genotype strings from tab/group</p>
+ <p>feature: worm group adapter makes reference terms from ref query</p>
+ <p>change: on term completion if adding a letter use previous completion list</p>
+ <p>change: worm adapter query tab working properly</p>
+ <p>change: build file takes param for webstart version deployment, and puts in jnlp</p>
+ <p>change: group adapters can psten for CharList changes</p>
+ <p>change: added/corrected BIRN ontologies</p>
+ <p>bugfix: load of file doesnt crash on post comp parsing bug</p>
+ <p>bugfix: doesnt load obo files specified twice twice</p>
+ <p>bugfix: view menu show up at initialization</p>
+ <p>bugfix: layout of term history with split pane proper</p>
</div>
</div>
</div>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-14 21:30:28
|
Revision: 899
http://obo.svn.sourceforge.net/obo/?rev=899&view=rev
Author: nlw
Date: 2007-09-14 14:30:31 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
website: a few more fixes
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/download.shtml
phenote/trunk/doc/phenote-website/new/download.shtml~
phenote/trunk/doc/phenote-website/new/team.shtml
Modified: phenote/trunk/doc/phenote-website/new/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-14 21:06:13 UTC (rev 898)
+++ phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-14 21:30:31 UTC (rev 899)
@@ -14,15 +14,15 @@
<div id="main_content">
<div class="catch_phrase">
</div>
- <h3>Launch Phenote in your browser</h3>
+ <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>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></li>
- <li>Stable release: <a href="http://www.phenote.org/phenote/1.3/phenote.jnlp">1.3</a> </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/1.3/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>
- <h3>Run Phenote at the command line</h3>
+ <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>
@@ -30,14 +30,14 @@
</ul>
<p>Once you've got it, you can run Phenote with ant with the command: <b>ant run</b>
</p>
- <h3>Hardware requirements</h3>
+ <h2>Hardware requirements</h2>
<ul>
<li> 400 Mhz processor or faster.</li>
<li> 500+ MB RAM </li>
- <li> ? MB free disk space on your computer </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>
- <h3>Software requirements</h3>
+ <h2>Software requirements</h2>
<ul>
<li> PC running Windows XP; Mac OSX; Linux </li>
<li> Webstart: Internet browser with webstart installed </li>
@@ -56,30 +56,28 @@
</div>
<div class="content_box_blue">
-<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>
+ <p>feature: Native look-and-feel enabled for interface. Users should now see Mac or Windows style depending on their system.</p>
+ <p>feature: read-only field (needs work)</p>
+ <p>feature: config disabpng of copy of field (for db ids)</p>
+ <p>feature: display property values of terms in term info</p>
+ <p>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.</p>
+ <p>feature: term fields can be nullified</p>
+ <p>feature: separate queries to backend for different groups, implemented in worm</p>
+ <p>feature: ID field type, requires ":"</p>
+ <p>feature: can get unique list of deleted annots</p>
+ <p>feature: added group adapter framework</p>
+ <p>feature: fly genotype group adapter makes fly genotype strings from tab/group</p>
+ <p>feature: worm group adapter makes reference terms from ref query</p>
+ <p>change: on term completion if adding a letter use previous completion list</p>
+ <p>change: worm adapter query tab working properly</p>
+ <p>change: build file takes param for webstart version deployment, and puts in jnlp</p>
+ <p>change: group adapters can psten for CharList changes</p>
+ <p>change: added/corrected BIRN ontologies</p>
+ <p>bugfix: load of file doesnt crash on post comp parsing bug</p>
+ <p>bugfix: doesnt load obo files specified twice twice</p>
+ <p>bugfix: view menu show up at initialization</p>
+ <p>bugfix: layout of term history with split pane proper</p>
</div>
</div>
</div>
Modified: phenote/trunk/doc/phenote-website/new/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-14 21:06:13 UTC (rev 898)
+++ phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-14 21:30:31 UTC (rev 899)
@@ -17,7 +17,7 @@
<h3>Launch Phenote in your browser</h3>
<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
<ul><li>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></li>
- <li>Stable release: <a href="http://www.phenote.org/1.3/phenote.jnlp">1.3</a> </li>
+ <li>Stable release: <a href="http://www.phenote.org/phenote/1.3/phenote.jnlp">1.3</a> </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.
Modified: phenote/trunk/doc/phenote-website/new/team.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/team.shtml 2007-09-14 21:06:13 UTC (rev 898)
+++ phenote/trunk/doc/phenote-website/new/team.shtml 2007-09-14 21:30:31 UTC (rev 899)
@@ -3,7 +3,7 @@
<head>
<!--#include virtual="ssi/head.html" -->
- <title>Phenote</title>
+ <title>Phenote: The Team</title>
</head>
<body>
@@ -19,11 +19,11 @@
Development</h2>
<div class="third_bio">
<p><img src="http://www.bioontology.org/images/team/gibson.jpg" title="Mark Gibson" alt="Mark Gibson" height="130"/></p>
- <p><a href="http://www.berkeleybop.org/mgibson/" title="Mark Gibson">Mark Gibson</a>, MSE</p>
+ <p><a href="http://www.berkeleybop.org/content/about/people/" title="Mark Gibson">Mark Gibson</a>, MSE</p>
</div>
<div class="third_bio">
<p><img src="http://www.bioontology.org/images/team/washington.jpg" title="Nicole Washington" alt="Nicole Washington" height="130" /> </p>
- <p><a href="http://berkeleybop.org/content/people/nlwashington/" title="Nicole Washington">Nicole Washington</a></a>, PhD </p>
+ <p><a href="http://berkeleybop.org/content/about/people/nlwashington/" title="Nicole Washington">Nicole Washington</a></a>, PhD </p>
</div>
<div class="third_bio">
<p><img src="http://www.bioontology.org/images/team/mungall.jpg" title="Chris Mungall" alt="Chris Mungall" height="130" /></p>
@@ -33,7 +33,7 @@
<div class="third_bio">
<p><img src="http://www.bioontology.org/images/team/lewis.jpg" title="Suzanna Lewis" alt="Suzanna Lewis" height="130" /> </p>
- <p><a href="http://www.berkeleybop.org/content/people/suzi/" title="Suzanna Lewis">Suzanna Lewis</a>, MS</p>
+ <p><a href="http://www.berkeleybop.org/content/about/people/" title="Suzanna Lewis">Suzanna Lewis</a>, MS</p>
</div>
<div class="clearall"></div>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-14 21:06:12
|
Revision: 898
http://obo.svn.sourceforge.net/obo/?rev=898&view=rev
Author: nlw
Date: 2007-09-14 14:06:13 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
new header pic, fix up upcoming events
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/index.shtml
phenote/trunk/doc/phenote-website/new/ssi/header.html
Modified: phenote/trunk/doc/phenote-website/new/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/index.shtml 2007-09-14 21:01:24 UTC (rev 897)
+++ phenote/trunk/doc/phenote-website/new/index.shtml 2007-09-14 21:06:13 UTC (rev 898)
@@ -92,7 +92,7 @@
<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="link">Event</a>, Date, Location
</p>
</li>
</ul>
@@ -105,18 +105,6 @@
<a href="http://www.phenote.org/irc_chat">User's Group Monthly Meeting</a>, October 4, 8:30am, Online
</p>
</li>
- <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 6, 8:30am, Online
- </p>
- </li>
- <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>, December 1, 8:30am, Online
- </p>
- </li>
<h3>Meetings/Demos</h3>
<ul class="events">
<li class="events">
@@ -127,10 +115,8 @@
</li>
</ul>
-
</div>
-
<div class="content_box_head_green">
<img src="images/document.gif" alt="News" class="icon_blue" />
News
Modified: phenote/trunk/doc/phenote-website/new/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/new/ssi/header.html 2007-09-14 21:01:24 UTC (rev 897)
+++ phenote/trunk/doc/phenote-website/new/ssi/header.html 2007-09-14 21:06:13 UTC (rev 898)
@@ -8,7 +8,7 @@
</span>
<a class="image" href="http://www.phenote.org"
title="Phenote: A Phenotype Annotation Tool">
- <img src="http://www.phenote.org/images/elephant_icon3.jpg"
+ <img src="http://www.phenote.org/images/elephant_header.jpg"
alt="Phenote"
class="image" />
</a>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-14 21:01:21
|
Revision: 897
http://obo.svn.sourceforge.net/obo/?rev=897&view=rev
Author: nlw
Date: 2007-09-14 14:01:24 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
working on the head/banner
Added Paths:
-----------
phenote/trunk/doc/phenote-website/images/elephant_header.jpg
Added: phenote/trunk/doc/phenote-website/images/elephant_header.jpg
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/elephant_header.jpg
___________________________________________________________________
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...> - 2007-09-14 20:46:05
|
Revision: 896
http://obo.svn.sourceforge.net/obo/?rev=896&view=rev
Author: nlw
Date: 2007-09-14 13:46:07 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
a few more website edits
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/index.shtml
phenote/trunk/doc/phenote-website/new/resources.shtml
Modified: phenote/trunk/doc/phenote-website/new/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/index.shtml 2007-09-14 19:53:38 UTC (rev 895)
+++ phenote/trunk/doc/phenote-website/new/index.shtml 2007-09-14 20:46:07 UTC (rev 896)
@@ -21,13 +21,13 @@
<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>
- <h2> Features included:</h2>
+ <h2>Features include:</h2>
<ul>
<li>Friendly spreadsheet-like interface
</li>
<li>Type-ahead-suggest (autocompletion) for terms within ontologies
</li>
- <li>Use of any OBO-format ontology
+ <li>Use of any OBO-format ontology (or OWL->OBO converted)
</li>
<li>Ontology navigation and term information display
</li>
@@ -102,10 +102,22 @@
<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, Online
+ <a href="http://www.phenote.org/irc_chat">User's Group Monthly Meeting</a>, October 4, 8:30am, Online
</p>
</li>
- <h3>Phenote demo</h3>
+ <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 6, 8:30am, Online
+ </p>
+ </li>
+ <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>, December 1, 8:30am, Online
+ </p>
+ </li>
+ <h3>Meetings/Demos</h3>
<ul class="events">
<li class="events">
<p class="quick_link">
Modified: phenote/trunk/doc/phenote-website/new/resources.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/resources.shtml 2007-09-14 19:53:38 UTC (rev 895)
+++ phenote/trunk/doc/phenote-website/new/resources.shtml 2007-09-14 20:46:07 UTC (rev 896)
@@ -3,7 +3,7 @@
<head>
<!--#include virtual="ssi/head.html" -->
- <title>Open Biomedical Ontologies Foundry</title>
+ <title>Phenote</title>
</head>
<body>
@@ -13,50 +13,55 @@
<div id="main_container_aux">
<div id="main_content_aux">
<div class="catch_phrase">
- OBO Foundry Resources
+ Ontology Resources
</div>
-
+ <p>You can find out more about available ontologies for use during
+ annotation with Phenote software:<p>
<h3>
- <a href="http://www.obofoundry.org/index.cgi?show=mappings">
- Mappings
+ <a href="http://www.bioontology.org/ncbo/faces/pages/ontology_list.xhtml">
+ NCBO Bioportal
</a>
</h3>
<p>
- On this page you can find bi-directional mappings between
- OBO ontologies and between an OBO ontology and other
- ontologies (or controlled vocabularies) that are critical to
- the biomedical research community. Useful for the
- integration of data.
+ On this page you can find a listing of biomedical ontologies
+ that have been submitted to the NCBO. From there you can link
+ to their project websites, download the ontology files, and search
+ their contents.
</p>
-
+
<h3>
- <a href="http://oboedit.org">Tools
+ <a href="http://www.obofoundry.org">OBO Foundry
</a>
</h3>
<p>
- Just one tool listed here now, OBO-Edit for the creation and
- maintenance of an ontology, more are coming soon.
+ The OBO Foundry is an open, inclusive, and collaborative core of
+ interoperable ontologies developed by the research community.
+ The goal is to facilitate the creation of consistent, compatible,
+ and unambiguous ontologies thereby supporting the biomedical
+ research community. The contributors are those biological
+ researchers and ontology developers who have agreed to work
+ together on an evolving set of design principles that can
+ foster interoperability of ontologies, and 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>
<h3>
- <a href="literature.shtml">
- Literature
+ <a href="http://www.ebi.ac.uk/ontology-lookup/">
+ Ontology Lookup Service (OLS)
</a>
</h3>
<p>
- A compendium of relevant publications.
+ 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://sourceforge.net/projects/obo">
- Project
- </a>
- </h3>
- <p>
- The OBO Foundry uses Sourceforge to manage this
- project. This is a link to these project pages.
- </p>
-
</div>
</div>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ba...@us...> - 2007-09-14 19:53:36
|
Revision: 895
http://obo.svn.sourceforge.net/obo/?rev=895&view=rev
Author: balhoff
Date: 2007-09-14 12:53:38 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
Major update to character selection and editing. In order to support text filtering and sorting of the character table contents, the table now shows a "view" of the character list instead of the direct character list. Features and fixes:
* Character table supports noncontiguous row selection
* Character table maintains identity of selected rows while sorting columns
* Character table shows triangle in column header indicating sorted row and direction
* FieldPanel properly handles no selection in character table by disabling field guis
* When multiple rows are selected, field guis show value if all rows have same value, or show "Multiple Values" placeholder otherwise
* Field guis support pressing either Return or Tab (generally, lose focus) to change value - previously FreeTextField supported only Tab while TermCompList supported only Return
* Filter search field restricts character table to show only matching rows
Many changes to Phenote classes. Importantly, SelectionManager no longer handles character selection notifications - this is provided by the EventList interface. CharacterList no longer handles sorting. Also, the controller code for the character table is no longer in a view class.
Modified Paths:
--------------
phenote/trunk/conf/character_template.xml
phenote/trunk/conf/phenomap.cfg
phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
phenote/trunk/src/java/phenote/dataadapter/CharacterListManager.java
phenote/trunk/src/java/phenote/datamodel/CharFieldValue.java
phenote/trunk/src/java/phenote/datamodel/CharacterList.java
phenote/trunk/src/java/phenote/datamodel/CharacterListI.java
phenote/trunk/src/java/phenote/gui/EditMenu.java
phenote/trunk/src/java/phenote/gui/TableRightClickMenu.java
phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java
phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java
phenote/trunk/src/java/phenote/gui/field/FieldPanel.java
phenote/trunk/src/java/phenote/gui/field/FreeTextField.java
phenote/trunk/src/java/phenote/gui/field/PostCompGui.java
phenote/trunk/src/java/phenote/gui/field/ReadOnlyFieldGui.java
phenote/trunk/src/java/phenote/gui/field/RelationCompList.java
phenote/trunk/src/java/phenote/gui/field/TermCompList.java
phenote/trunk/src/java/phenote/gui/selection/SelectionManager.java
phenote/trunk/src/java/phenote/main/Phenote.java
Added Paths:
-----------
phenote/trunk/conf/character_table_panel.xml
phenote/trunk/jars/glazedlists-1.7.0_java15.jar
phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableFormat.java
phenote/trunk/src/java/phenote/gui/CharacterTableController.java
phenote/trunk/src/java/phenote/gui/CharacterTableFormat.java
Removed Paths:
-------------
phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableModel.java
phenote/trunk/src/java/phenote/charactertemplate/SelectionManagerListSelectionModel.java
phenote/trunk/src/java/phenote/gui/CharacterTableModel.java
phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java
phenote/trunk/src/java/phenote/gui/SortableTableModel.java
phenote/trunk/src/java/phenote/gui/TableSortingAdapter.java
Added: phenote/trunk/conf/character_table_panel.xml
===================================================================
--- phenote/trunk/conf/character_table_panel.xml (rev 0)
+++ phenote/trunk/conf/character_table_panel.xml 2007-09-14 19:53:38 UTC (rev 895)
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+
+<panel id="characterTablePanel" constraints="BorderLayout.CENTER" layout="GridBagLayout">
+ <panel layout="GridBagLayout">
+ <gridbagconstraints gridx="0" gridy="0" weightx="1" weighty="0" fill="GridBagConstraints.HORIZONTAL"/>
+ <label text="Search:" horizontalAlignment="SwingConstants.RIGHT">
+ <gridbagconstraints gridx="0" gridy="0" weightx="1" weighty="0" anchor="GridBagConstraints.EAST"/>
+ </label>
+ <textfield id="filterField" columns="25">
+ <gridbagconstraints gridx="1" gridy="0" weightx="0" weighty="0" anchor="GridBagConstraints.EAST" insets="0,0,0,5"/>
+ </textfield>
+ </panel>
+ <scrollpane horizontalScrollBarPolicy="JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS">
+ <gridbagconstraints gridx="0" gridy="1" weightx="1" weighty="1" fill="GridBagConstraints.BOTH" insets="5,5,0,5"/>
+ <table id="characterTable"/>
+ </scrollpane>
+ <panel id="buttonPanel">
+ <gridbagconstraints gridx="0" gridy="2" weightx="1" insets="10,10,10,10" fill="GridBagConstraints.HORIZONTAL"/>
+ <button id="addButton" text="New" action="addNewCharacter" toolTipText="Add new row"/>
+ <button id="duplicateButton" text="Duplicate" action="duplicateSelectedCharacters" toolTipText="Duplicate selected rows"/>
+ <button id="deleteButton" text="Delete" action="deleteSelectedCharacters" toolTipText="Delete selected rows"/>
+ <panel size="20,1" preferredSize="20,1"/>
+ <button id="undoButton" text="Undo" action="undo" toolTipText="Undo previous action"/>
+ <panel size="80,1" preferredSize="80,1"/>
+ <button id="commitButton" text="Save Data" action="commitCharacters" toolTipText="Save Data"/>
+ <panel size="20,1" preferredSize="20,1"/>
+ <button id="graphButton" text="Graph" action="showGraph" toolTipText="Show Graph View"/>
+ </panel>
+</panel>
Modified: phenote/trunk/conf/character_template.xml
===================================================================
--- phenote/trunk/conf/character_template.xml 2007-09-14 19:28:52 UTC (rev 894)
+++ phenote/trunk/conf/character_template.xml 2007-09-14 19:53:38 UTC (rev 895)
@@ -7,12 +7,21 @@
</panel>
</splitpane>
<panel constraints="BorderLayout.CENTER" layout="GridBagLayout">
+ <panel layout="GridBagLayout">
+ <gridbagconstraints gridx="0" gridy="0" weightx="1" weighty="0" fill="GridBagConstraints.HORIZONTAL"/>
+ <label text="Search:" horizontalAlignment="SwingConstants.RIGHT">
+ <gridbagconstraints gridx="0" gridy="0" weightx="1" weighty="0" anchor="GridBagConstraints.EAST"/>
+ </label>
+ <textfield id="filterField" columns="25">
+ <gridbagconstraints gridx="1" gridy="0" weightx="0" weighty="0" anchor="GridBagConstraints.EAST" insets="0,0,0,10"/>
+ </textfield>
+ </panel>
<scrollpane horizontalScrollBarPolicy="JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS">
- <gridbagconstraints gridx="0" gridy="0" weightx="1" weighty="1" fill="GridBagConstraints.BOTH" insets="10,10,0,10"/>
+ <gridbagconstraints gridx="0" gridy="1" weightx="1" weighty="1" fill="GridBagConstraints.BOTH" insets="0,10,0,10"/>
<table id="characterTemplateTable"/>
</scrollpane>
<panel id="buttonPanel">
- <gridbagconstraints gridx="0" gridy="1" weightx="1" insets="10,10,10,10"/>
+ <gridbagconstraints gridx="0" gridy="2" weightx="1" insets="10,10,10,10"/>
<button id="addButton" text="New" action="addNewCharacter" toolTipText="Add new row"/>
<button id="duplicateButton" text="Duplicate" action="duplicateSelectedCharacters" toolTipText="Duplicate selected rows"/>
<button id="deleteButton" text="Delete" action="deleteSelectedCharacters" toolTipText="Delete selected rows"/>
Modified: phenote/trunk/conf/phenomap.cfg
===================================================================
--- phenote/trunk/conf/phenomap.cfg 2007-09-14 19:28:52 UTC (rev 894)
+++ phenote/trunk/conf/phenomap.cfg 2007-09-14 19:53:38 UTC (rev 895)
@@ -6,7 +6,7 @@
<ns:uvic-graph enable="false"/>
<ns:term-history enable="false"/>
<ns:auto-update-ontologies enable="true"/>
- <ns:update-timer timer="4"/>
+ <ns:update-timer timer="0"/>
<ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/>
<ns:obo-repository url-dir="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/>
Added: phenote/trunk/jars/glazedlists-1.7.0_java15.jar
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/jars/glazedlists-1.7.0_java15.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Modified: phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java 2007-09-14 19:28:52 UTC (rev 894)
+++ phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java 2007-09-14 19:53:38 UTC (rev 895)
@@ -1,10 +1,16 @@
package phenote.charactertemplate;
import java.awt.Component;
+import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashSet;
import java.util.List;
+import java.util.Set;
import javax.swing.JComponent;
import javax.swing.JFrame;
@@ -14,6 +20,7 @@
import javax.swing.JPanel;
import javax.swing.JSeparator;
import javax.swing.JTable;
+import javax.swing.JTextField;
import org.apache.log4j.Logger;
import org.swixml.SwingEngine;
@@ -25,16 +32,24 @@
import phenote.dataadapter.LoadSaveManager;
import phenote.datamodel.CharField;
import phenote.datamodel.CharacterI;
+import phenote.edit.CharChangeEvent;
+import phenote.edit.CharChangeListener;
import phenote.edit.EditManager;
import phenote.gui.MenuManager;
-import phenote.gui.TableSortingAdapter;
import phenote.gui.TermInfo;
import phenote.gui.field.FieldPanel;
import phenote.gui.selection.SelectionManager;
import phenote.main.Phenote;
import phenote.util.FileUtil;
+import ca.odell.glazedlists.FilterList;
+import ca.odell.glazedlists.SortedList;
+import ca.odell.glazedlists.TextFilterator;
+import ca.odell.glazedlists.swing.EventSelectionModel;
+import ca.odell.glazedlists.swing.EventTableModel;
+import ca.odell.glazedlists.swing.TableComparatorChooser;
+import ca.odell.glazedlists.swing.TextComponentMatcherEditor;
-public class CharacterTemplateController implements ActionListener, TemplateChoiceListener {
+public class CharacterTemplateController implements ActionListener, TemplateChoiceListener, CharChangeListener {
public static final String SHOW_CHARACTER_TEMPLATE_ACTION = "showCharacterTemplate";
public static final String IMPORT_TEMPLATE_CHARACTERS_ACTION = "importCharacters";
@@ -44,21 +59,26 @@
private EditManager editManager;
private SelectionManager selectionManager;
private LoadSaveManager loadSaveManager;
- private CharacterTemplateTableModel tableModel;
private JFrame window;
private JPanel charFieldPanelContainer; // initialized by swix
private JPanel termInfoPanelContainer; // initialized by swix
private JTable characterTemplateTable; // initialized by swix
+ private JTextField filterField; // initialized by swix
private List<TemplateChooser> templateChoosers = new ArrayList<TemplateChooser>();
+ private SortedList<CharacterI> sortedCharacters;
+ private FilterList<CharacterI> filteredCharacters;
+ private EventSelectionModel<CharacterI> selectionModel;
+ private Set<CharacterI> markedCharacters = new HashSet<CharacterI>();
public CharacterTemplateController(String groupName) {
super();
this.representedGroup = groupName;
this.characterListManager = new CharacterListManager();
this.editManager = new EditManager(this.characterListManager);
+ this.editManager.addCharChangeListener(this);
this.selectionManager = new SelectionManager();
- this.tableModel = new CharacterTemplateTableModel(this.representedGroup, this.characterListManager, this.editManager);
- this.addInitialBlankCharacter();
+ this.sortedCharacters = new SortedList<CharacterI>(this.characterListManager.getCharacterList().getList(), new EverythingEqualComparator<CharacterI>());
+ this.sortedCharacters.setMode(SortedList.AVOID_MOVING_ELEMENTS);
this.configureTemplateChoosers();
this.configureMenus();
}
@@ -92,22 +112,19 @@
}
public void deleteSelectedCharacters() {
- this.editManager.deleteChars(this.selectionManager.getSelectedChars());
- if (this.characterListManager.getCharacterList().isEmpty()) {
- this.addInitialBlankCharacter();
- }
+ this.editManager.deleteChars(this.selectionModel.getSelected());
}
public void duplicateSelectedCharacters() {
- this.editManager.copyChars(this.selectionManager.getSelectedChars());
+ this.editManager.copyChars(this.selectionModel.getSelected());
}
public void markSelectedCharacters() {
- this.tableModel.setCharactersInRowsAreMarked(this.characterTemplateTable.getSelectedRows(), true);
+ this.setCharactersAreMarked(this.selectionModel.getSelected(), true);
}
public void unmarkSelectedCharacters() {
- this.tableModel.setCharactersInRowsAreMarked(this.characterTemplateTable.getSelectedRows(), false);
+ this.setCharactersAreMarked(this.selectionModel.getSelected(), false);
}
public void undo() {
@@ -115,24 +132,87 @@
}
public void invertMarkedCharacters() {
- this.tableModel.invertCharacterMarks();
+ for (CharacterI character : this.getCurrentCharacters()) {
+ this.setCharacterIsMarked(character, !this.isCharacterMarked(character));
+ }
}
+ public boolean isCharacterMarked(CharacterI character) {
+ return this.markedCharacters.contains(character);
+ }
+
+ public void setCharacterIsMarked(CharacterI character, boolean selected) {
+ if (selected) {
+ this.markedCharacters.add(character);
+ } else {
+ this.markedCharacters.remove(character);
+ }
+ this.updateCharacterForGlazedLists(character);
+ }
+
+ public List<CharacterI> getMarkedCharacters() {
+ // make a list to make sure the characters are in the same order as they are in the character list
+ List<CharacterI> characters = new ArrayList<CharacterI>();
+ for (CharacterI character : this.getCurrentCharacters()) {
+ if (this.isCharacterMarked(character)){
+ characters.add(character);
+ }
+ }
+ return characters;
+ }
+
+ public void setMarkedCharacters(Collection<CharacterI> charactersToMark) {
+ for (CharacterI character : this.sortedCharacters) {
+ this.setCharacterIsMarked(character, charactersToMark.contains(character));
+ }
+ }
+
+ public void setCharactersAreMarked(List<CharacterI> characters, boolean marked) {
+ for (CharacterI character : characters) {
+ this.setCharacterIsMarked(character, marked);
+ }
+ }
+
public void generateCharacters() {
- final List<CharacterI> newCharacters = new ArrayList<CharacterI>();
- for (CharacterI character : this.tableModel.getMarkedCharacters()) {
- final CharacterI newCharacter = character.cloneCharacter();
- EditManager.inst().addCharacter(newCharacter);
- newCharacters.add(newCharacter);
- }
- SelectionManager.inst().selectCharacters(this, newCharacters);
+ EditManager.inst().copyChars(this.getMarkedCharacters());
Phenote.getPhenote().getFrame().toFront();
}
public void templateChoiceChanged(TemplateChooser source) {
+ this.setMarkedCharacters(source.getChosenTemplates(Collections.unmodifiableList(this.sortedCharacters)));
this.showCharacterTemplate();
}
+ public void charChanged(CharChangeEvent e) {
+ if (e.isUpdate()) {
+ for (CharacterI character : e.getTransaction().getCharacters()) {
+ this.updateCharacterForGlazedLists(character);
+ }
+ } else if (e.isAdd()) {
+ this.setSelectionWithCharacters(e.getTransaction().getCharacters());
+ }
+ }
+
+ private void setSelectionWithCharacters(List<CharacterI> characters) {
+ this.filterField.setText("");
+ this.selectionModel.clearSelection();
+ for (CharacterI character : characters) {
+ final int index = this.filteredCharacters.indexOf(character);
+ if (index > -1) {
+ this.selectionModel.addSelectionInterval(index, index);
+ Rectangle rect = this.characterTemplateTable.getCellRect(index, 0, false);
+ this.characterTemplateTable.scrollRectToVisible(rect);
+ }
+ }
+ }
+
+ private void updateCharacterForGlazedLists(CharacterI character) {
+ final int index = this.characterListManager.getCharacterList().getList().indexOf(character);
+ if (index > -1) {
+ this.characterListManager.getCharacterList().getList().set(index, character);
+ }
+ }
+
private String getGroupTitle() {
return Config.inst().getTitleForGroup(this.representedGroup);
}
@@ -198,11 +278,16 @@
SwingEngine swix = new SwingEngine(this);
try {
JComponent component = (JComponent)swix.render(FileUtil.findUrl("character_template.xml"));
- this.characterTemplateTable.setModel(this.tableModel);
- this.characterTemplateTable.setSelectionModel(new SelectionManagerListSelectionModel(this.characterListManager, this.editManager, this.selectionManager));
- this.characterTemplateTable.getTableHeader().addMouseListener(new TableSortingAdapter(this.characterTemplateTable, this.tableModel));
+ this.filteredCharacters = new FilterList<CharacterI>(this.sortedCharacters, new TextComponentMatcherEditor<CharacterI>(filterField, new CharacterFilterator()));
+ final CharacterTemplateTableFormat tableFormat = new CharacterTemplateTableFormat(this.representedGroup, this);
+ EventTableModel<CharacterI> eventTableModel = new EventTableModel<CharacterI>(this.filteredCharacters, tableFormat);
+ this.characterTemplateTable.setModel(eventTableModel);
+ new TableComparatorChooser<CharacterI>(this.characterTemplateTable, this.sortedCharacters, false);
+ this.selectionModel = new EventSelectionModel<CharacterI>(this.filteredCharacters);
+ this.characterTemplateTable.setSelectionModel(this.selectionModel);
this.characterTemplateTable.putClientProperty("Quaqua.Table.style", "striped");
- FieldPanel fieldPanel = new FieldPanel(true, false, this.representedGroup, this.selectionManager, this.editManager);
+ this.filterField.putClientProperty("Quaqua.TextField.style", "search");
+ FieldPanel fieldPanel = new FieldPanel(true, false, this.representedGroup, this.selectionManager, this.editManager, this.selectionModel);
this.charFieldPanelContainer.add(fieldPanel);
TermInfo termInfo = new TermInfo(this.selectionManager);
this.termInfoPanelContainer.add(termInfo.getComponent());
@@ -213,11 +298,6 @@
}
}
- private void addInitialBlankCharacter() {
- this.editManager.addInitialCharacter();
- this.selectionManager.selectCharacters(this, this.characterListManager.getCharacterList().getList());
- }
-
private void configureTemplateChoosers() {
for (Group group : Config.inst().getFieldGroups()) {
if (group.getName() == this.representedGroup) {
@@ -225,7 +305,6 @@
TemplateChooser chooser = this.createTemplateChooserInstance(chooserConfig.getAdapter());
chooser.setCharField(this.getCharFieldWithName(chooserConfig.getField()));
chooser.setTitle(chooserConfig.getTitle());
- chooser.addTemplateChoiceListener(this.tableModel);
chooser.addTemplateChoiceListener(this);
this.templateChoosers.add(chooser);
}
@@ -258,6 +337,10 @@
return null;
}
+ private List<CharacterI> getCurrentCharacters() {
+ return (this.filteredCharacters == null) ? this.sortedCharacters : this.filteredCharacters;
+ }
+
private LoadSaveManager getLoadSaveManager() {
if (this.loadSaveManager == null) {
this.loadSaveManager = new LoadSaveManager(this.characterListManager);
@@ -269,4 +352,18 @@
return Logger.getLogger(this.getClass());
}
+ private static class EverythingEqualComparator<T> implements Comparator<T> {
+ public int compare(T o1, T o2) {
+ return 0;
+ }
+ }
+
+ private static class CharacterFilterator implements TextFilterator<CharacterI> {
+ public void getFilterStrings(List<String> baseList, CharacterI character) {
+ for (CharField charField : character.getAllCharFields()) {
+ baseList.add(character.getValueString(charField));
+ }
+ }
+ }
+
}
Added: phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableFormat.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableFormat.java (rev 0)
+++ phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableFormat.java 2007-09-14 19:53:38 UTC (rev 895)
@@ -0,0 +1,67 @@
+package phenote.charactertemplate;
+
+import java.util.Comparator;
+
+import phenote.datamodel.CharacterI;
+import phenote.gui.CharacterTableFormat;
+import ca.odell.glazedlists.GlazedLists;
+import ca.odell.glazedlists.gui.WritableTableFormat;
+
+public class CharacterTemplateTableFormat extends CharacterTableFormat implements WritableTableFormat<CharacterI> {
+
+ private static final String SELECTED_COLUMN_NAME = "Use";
+ private final CharacterTemplateController controller;
+
+ public CharacterTemplateTableFormat(String groupName, CharacterTemplateController aController) {
+ super(groupName);
+ this.controller = aController;
+ }
+
+ public Class<?> getColumnClass(int columnIndex) {
+ if (columnIndex == 0) {
+ return Boolean.class;
+ } else {
+ return super.getColumnClass(columnIndex - 1);
+ }
+ }
+
+ public Comparator<?> getColumnComparator(int columnIndex) {
+ if (columnIndex == 0) {
+ return GlazedLists.booleanComparator();
+ } else {
+ return super.getColumnComparator(columnIndex - 1);
+ }
+ }
+
+ public int getColumnCount() {
+ return super.getColumnCount() + 1;
+ }
+
+ public String getColumnName(int column) {
+ if (column == 0) {
+ return CharacterTemplateTableFormat.SELECTED_COLUMN_NAME;
+ } else {
+ return super.getColumnName(column - 1);
+ }
+ }
+
+ public Object getColumnValue(CharacterI character, int column) {
+ if (column == 0) {
+ return this.controller.isCharacterMarked(character);
+ } else {
+ return super.getColumnValue(character, (column - 1));
+ }
+ }
+
+ public boolean isEditable(CharacterI character, int column) {
+ return column == 0;
+ }
+
+ public CharacterI setColumnValue(CharacterI character, Object editedValue, int column) {
+ if (column == 0) {
+ this.controller.setCharacterIsMarked(character, (Boolean)editedValue);
+ }
+ return character;
+ }
+
+}
Deleted: phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableModel.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableModel.java 2007-09-14 19:28:52 UTC (rev 894)
+++ phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableModel.java 2007-09-14 19:53:38 UTC (rev 895)
@@ -1,184 +0,0 @@
-package phenote.charactertemplate;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import javax.swing.table.AbstractTableModel;
-
-import org.apache.log4j.Logger;
-
-import phenote.config.Config;
-import phenote.dataadapter.CharListChangeEvent;
-import phenote.dataadapter.CharListChangeListener;
-import phenote.dataadapter.CharacterListManager;
-import phenote.datamodel.CharField;
-import phenote.datamodel.CharFieldException;
-import phenote.datamodel.CharacterI;
-import phenote.edit.CharChangeEvent;
-import phenote.edit.CharChangeListener;
-import phenote.edit.EditManager;
-import phenote.gui.SortableTableModel;
-
-@SuppressWarnings("serial")
-public class CharacterTemplateTableModel extends AbstractTableModel implements CharChangeListener, CharListChangeListener, TemplateChoiceListener, SortableTableModel {
-
- private String representedGroup;
- private CharacterListManager characterListManager;
- private EditManager editManager;
- private Set<CharacterI> markedCharacters;
- private static final String SELECTED_COLUMN_NAME = "Use";
-
- public CharacterTemplateTableModel(String groupName, CharacterListManager clManager, EditManager eManager) {
- super();
- this.representedGroup = groupName;
- this.characterListManager = clManager;
- this.characterListManager.addCharListChangeListener(this);
- this.editManager = eManager;
- this.editManager.addCharChangeListener(this);
- this.markedCharacters = new HashSet<CharacterI>();
- }
-
- public List<CharacterI> getMarkedCharacters() {
- // make a list to make sure the characters are in the same order as they are in the main character list
- List<CharacterI> characters = new ArrayList<CharacterI>();
- for (CharacterI character : this.getAllCharacters()) {
- if (this.isCharacterMarked(character)){
- characters.add(character);
- }
- }
- return characters;
- }
-
- public void setMarkedCharacters(Collection<CharacterI> charactersToMark) {
- for (CharacterI character : this.getAllCharacters()) {
- this.setCharacterIsMarked(character, charactersToMark.contains(character));
- }
- }
-
- public boolean isCharacterMarked(CharacterI character) {
- return this.markedCharacters.contains(character);
- }
-
- public void setCharacterIsMarked(CharacterI character, boolean selected) {
- if (selected) {
- this.markedCharacters.add(character);
- } else {
- this.markedCharacters.remove(character);
- }
- final int indexOfCharacter = this.getAllCharacters().indexOf(character);
- this.fireTableRowsUpdated(indexOfCharacter, indexOfCharacter);
- }
-
- public void invertCharacterMarks() {
- for (CharacterI character : this.getAllCharacters()) {
- this.setCharacterIsMarked(character, !this.isCharacterMarked(character));
- }
- }
-
- public void setCharactersInRowsAreMarked(int[] rows, boolean marked) {
- for (int row : rows) {
- this.setCharacterIsMarked(this.getCharacterAtRow(row), marked);
- }
- }
-
- public int getColumnCount() {
- return Config.inst().getFieldsInGroup(this.representedGroup).size() + 1;
- }
-
- public int getRowCount() {
- return this.getAllCharacters().size();
- }
-
- public Object getValueAt(int row, int column) {
- final CharacterI character = this.getCharacterAtRow(row);
- final String fieldName = this.getColumnName(column);
- if (fieldName == CharacterTemplateTableModel.SELECTED_COLUMN_NAME) {
- return this.isCharacterMarked(character);
- }
- try {
- return character.getValueString(fieldName);
- } catch (CharFieldException e) {
- this.getLogger().error("Failed to get value for table column", e);
- return "";
- }
- }
-
- public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
- if (this.getColumnName(columnIndex).equals(CharacterTemplateTableModel.SELECTED_COLUMN_NAME)) {
- this.setCharacterIsMarked(this.getCharacterAtRow(rowIndex), (Boolean)aValue);
- }
- }
-
- public Class<?> getColumnClass(int columnIndex) {
- if (columnIndex == 0) {
- return Boolean.class;
- } else {
- return super.getColumnClass(columnIndex);
- }
- }
-
- public String getColumnName(int column) {
- if (column == 0) {
- return CharacterTemplateTableModel.SELECTED_COLUMN_NAME;
- } else {
- return Config.inst().getFieldsInGroup(this.representedGroup).get(column - 1);
- }
- }
-
- public boolean isCellEditable(int rowIndex, int columnIndex) {
- return columnIndex == 0;
- }
-
- public void charChanged(CharChangeEvent e) {
- if (e.isUpdate()) {
- this.fireTableRowsUpdated(0, this.getRowCount() - 1);
- } else if (e.isAdd()) {
- this.fireTableRowsInserted(this.getRowCount() - 1, this.getRowCount() - 1);
- } else { // must be a deletion
- this.fireTableDataChanged();
- }
- }
-
- public void newCharList(CharListChangeEvent e) {
- this.fireTableDataChanged();
- }
-
- public void templateChoiceChanged(TemplateChooser source) {
- this.setMarkedCharacters(source.getChosenTemplates(Collections.unmodifiableList(this.getAllCharacters())));
- }
-
- public void sortOnColumn(int column) {
- final String fieldName = this.getColumnName(column);
- // right now we cannot sort by the checkmarked column, unfortunately
- if (fieldName.equals(CharacterTemplateTableModel.SELECTED_COLUMN_NAME)) return;
- final CharacterI aCharacter;
- if (this.getRowCount() < 1) {
- return;
- } else {
- aCharacter = this.getCharacterAtRow(0);
- }
- try {
- final CharField charField = aCharacter.getCharFieldForName(fieldName);
- this.characterListManager.getCharacterList().sortBy(charField);
- } catch (CharFieldException e) {
- this.getLogger().error("Could not find CharField to sort by", e);
- }
- }
-
- private CharacterI getCharacterAtRow(int row) {
- return this.characterListManager.getCharacterList().get(row);
- }
-
- private List<CharacterI> getAllCharacters() {
- return this.characterListManager.getCharacterList().getList();
- }
-
- private Logger getLogger() {
- return Logger.getLogger(this.getClass());
- }
-
-}
Deleted: phenote/trunk/src/java/phenote/charactertemplate/SelectionManagerListSelectionModel.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/SelectionManagerListSelectionModel.java 2007-09-14 19:28:52 UTC (rev 894)
+++ phenote/trunk/src/java/phenote/charactertemplate/SelectionManagerListSelectionModel.java 2007-09-14 19:53:38 UTC (rev 895)
@@ -1,101 +0,0 @@
-package phenote.charactertemplate;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.DefaultListSelectionModel;
-
-import phenote.dataadapter.CharacterListManager;
-import phenote.datamodel.CharacterI;
-import phenote.edit.CharChangeEvent;
-import phenote.edit.CharChangeListener;
-import phenote.edit.EditManager;
-import phenote.gui.selection.CharSelectionEvent;
-import phenote.gui.selection.CharSelectionListener;
-import phenote.gui.selection.SelectionManager;
-
-/**
- * List selection model which stays in sync with SelectionManager.
- * Also automatically selects newly inserted characters.
- * This list selection model does not support non-contiguous selection.
- */
-@SuppressWarnings("serial")
-public class SelectionManagerListSelectionModel extends DefaultListSelectionModel implements CharChangeListener, CharSelectionListener {
-
- private CharacterListManager characterListManager;
- private EditManager editManager;
- private SelectionManager selectionManager;
-
- public SelectionManagerListSelectionModel(CharacterListManager clManager, EditManager eManager, SelectionManager selManager) {
- super();
- this.characterListManager = clManager;
- this.editManager = eManager;
- this.editManager.addCharChangeListener(this);
- this.selectionManager = selManager;
- this.selectionManager.addCharSelectionListener(this);
- this.setSelectionInterval(this.selectionManager.getSelectedChars());
- }
-
- public void charChanged(CharChangeEvent e) {
- if (e.isAdd()) {
- this.setSelectionInterval(e.getTransaction().getCharacters());
- }
- }
-
- public void setSelectionInterval(int index0, int index1) {
- super.setSelectionInterval(index0, index1);
- final int firstIndex = index0 > index1 ? index1 : index0;
- final int secondIndex = index0 > index1 ? index0 : index1;
- final List<CharacterI> selectedCharacters = this.characterListManager.getCharacterList().getList().subList(firstIndex, secondIndex + 1);
- this.selectionManager.selectCharacters(this, new ArrayList<CharacterI>(selectedCharacters));
- }
-
- public void clearSelection() {
- // only clear the selection if there are no characters
- if (this.getCharacterCount() == 0) {
- super.clearSelection();
- return;
- }
- // otherwise select a character
- final int selectedIndex = this.getMinSelectionIndex();
- if (selectedIndex > -1) {
- final int maximumSelectedIndex = selectedIndex < this.getCharacterCount() ? selectedIndex : (this.getCharacterCount() - 1);
- this.setSelectionInterval(maximumSelectedIndex, maximumSelectedIndex);
- } else {
- this.setSelectionInterval(0, 0);
- }
- }
-
- public void charactersSelected(CharSelectionEvent e) {
- if (e.getSource() == this) {
- return;
- } else {
- this.setSelectionInterval(e.getChars());
- }
- }
-
- private int getCharacterCount() {
- return this.characterListManager.getCharacterList().size();
- }
-
- private void setSelectionInterval(List<CharacterI> characters) {
- if ((characters == null) || (characters.isEmpty()) || (!this.characterListManager.getCharacterList().getList().containsAll(characters))) {
- this.clearSelection();
- return;
- }
- int minIndex = Integer.MAX_VALUE;
- int maxIndex = Integer.MIN_VALUE;
- final List<CharacterI> allCharacters = this.characterListManager.getCharacterList().getList();
- for (CharacterI character : characters) {
- final int characterIndex = allCharacters.indexOf(character);
- if (characterIndex < minIndex) {
- minIndex = characterIndex;
- }
- if (characterIndex > maxIndex) {
- maxIndex = characterIndex;
- }
- }
- this.setSelectionInterval(minIndex, maxIndex);
- }
-
-}
Modified: phenote/trunk/src/java/phenote/dataadapter/CharacterListManager.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/CharacterListManager.java 2007-09-14 19:28:52 UTC (rev 894)
+++ phenote/trunk/src/java/phenote/dataadapter/CharacterListManager.java 2007-09-14 19:53:38 UTC (rev 895)
@@ -56,7 +56,9 @@
JOptionPane.showMessageDialog(null,m,"Load failure",JOptionPane.ERROR_MESSAGE);
return;
}
- characterList = charList;
+ characterList.getList().clear();
+ characterList.getList().addAll(charList.getList());
+ //characterList = charList;
fireChangeEvent(source,charList);
}
Modified: phenote/trunk/src/java/phenote/datamodel/CharFieldValue.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharFieldValue.java 2007-09-14 19:28:52 UTC (rev 894)
+++ phenote/trunk/src/java/phenote/datamodel/CharFieldValue.java 2007-09-14 19:53:38 UTC (rev 895)
@@ -88,7 +88,7 @@
if (isOboClass)
return oboClassValue == null;
else
- return stringValue == null;
+ return ((stringValue == null) || (stringValue.equals("")));
}
// maybe this should be called getString??? why getName???
@@ -126,8 +126,8 @@
}
public String toString() { return getName(); }
-}
+
// if (charFieldEnum == null)
// System.out.println("ERROR no datamodel associated with configuration, cant set"+
// " value");
@@ -139,4 +139,23 @@
//System.out.println("CFV editMod "+getName());
// phase out...
//public CharFieldEnum getCharFieldEnum() { return charFieldEnum; }
+
+ public boolean equals(Object o) {
+ final CharFieldValue otherValue = (CharFieldValue)o;
+ if (this == otherValue) return true;
+ if (this.isEmpty()) {
+ return otherValue.isEmpty();
+ }
+ if (this.isTerm()) {
+ return ((otherValue.isTerm()) && (this.getTerm().equals(otherValue.getTerm())));
+ }
+ return this.getName().equals(otherValue.getName());
+ }
+
+ public int hashCode() {
+ if (this.oboClassValue != null) return this.oboClassValue.hashCode();
+ if ((this.stringValue != null) || (!this.stringValue.equals(""))) return this.stringValue.hashCode();
+ return 0;
+ }
+}
Modified: phenote/trunk/src/java/phenote/datamodel/CharacterList.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharacterList.java 2007-09-14 19:28:52 UTC (rev 894)
+++ phenote/trunk/src/java/phenote/datamodel/CharacterList.java 2007-09-14 19:53:38 UTC (rev 895)
@@ -1,9 +1,7 @@
package phenote.datamodel;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Collections;
-import java.util.Comparator;
+import ca.odell.glazedlists.BasicEventList;
+import ca.odell.glazedlists.EventList;
/** i made this as a transferable when i didnt get the whole transferable thing
and now i dont whether to scrap it or not. all it is at the moment is a
@@ -11,24 +9,17 @@
functionality - i guess ill keep it for now */
public class CharacterList implements CharacterListI {
- private List<CharacterI> characterList = new ArrayList<CharacterI>();
- public int sorted;
- public CharField cf_sorted = null;
- public static int UNSORTED = 0; //constants to explain sorting
- public static int FORWARD_SORT = 1;
- public static int REV_SORT = 2;
+ private EventList<CharacterI> characterList = new BasicEventList<CharacterI>();
public CharacterI get(int i) {
// should this check if i is out of range - throw ex, or print error msg??
return characterList.get(i);
}
- public void add(CharacterI c) {//once a new char is added, any sorts are voided
- characterList.add(c);
- sorted=UNSORTED;
+ public void add(CharacterI c) {
+ characterList.add(c);
}
- public void add(int i, CharacterI c) {//once a new char is added, any sorts are voided
+ public void add(int i, CharacterI c) {
characterList.add(i,c);
- sorted=UNSORTED;
}
public void remove(int i) { characterList.remove(i); }
public void remove(CharacterI c) { characterList.remove(c); }
@@ -36,7 +27,7 @@
public int size() { return characterList.size(); }
public boolean isEmpty() { return characterList.isEmpty(); }
public int indexOf(CharacterI c) { return characterList.indexOf(c); }
- public List<CharacterI> getList() { return characterList; }
+ public EventList<CharacterI> getList() { return characterList; }
public boolean equals(CharacterListI cl) {
if (size() != cl.size()) return false;
@@ -47,69 +38,4 @@
return true;
}
- // ??
- public void sortBy(CharField cf) {
- if (cf_sorted!=cf) {sorted=UNSORTED;} //newly selected cf
- if ((sorted==UNSORTED) || (sorted==REV_SORT)) {
-// Collections.sort(characterList,getComparator(cf));
- Collections.sort(characterList,getForwardComparator(cf));
- sorted = FORWARD_SORT;
-// System.out.println("forward sort!");
- } else if ((sorted == FORWARD_SORT)) {
- sorted = REV_SORT;
- Collections.sort(characterList,getReverseComparator(cf));
-// System.out.println("need to reverse sort!");
- }
- cf_sorted = cf; //remember the last col that was sorted
- }
-
-// private Comparator<CharacterI> getComparator(final CharField cf) {
-// return new Comparator<CharacterI>() {
-// public int compare(CharacterI c1, CharacterI c2) {
-// String s1 = c1.getValueString(cf);//cf.getValue(c1).getName();
-// String s2 = c2.getValueString(cf);
-// return s1.compareTo(s2);
-// }
-// };
-// }
-
- private Comparator<CharacterI> getForwardComparator(final CharField cf) {
- return new Comparator<CharacterI>() {
- public int compare(CharacterI c1, CharacterI c2) {
- String s1 = c1.getValueString(cf);//cf.getValue(c1).getName();
- String s2 = c2.getValueString(cf);
- return s1.compareToIgnoreCase(s2);
- }
- };
- }
-
- private Comparator<CharacterI> getReverseComparator(final CharField cf) {
- return new Comparator<CharacterI>() {
- public int compare(CharacterI c1, CharacterI c2) {
- String s1 = c1.getValueString(cf);//cf.getValue(c1).getName();
- String s2 = c2.getValueString(cf);
- return s2.compareToIgnoreCase(s1);
- }
- };
- }
-
}
-
-// private class CharFieldComparator<CharacterI> implements Comparator {
-// private CharFieldEnum charFieldEnum;
-// private CharFieldComparator(CharFieldEnum cfe) {
-// charFieldEnum = cfe;
-// }
-// public int compare(CharacterI c1, CharacterI c2) {
-// String s1 = charFieldEnum.getValue(c1).getName();
-// String s2 = charFieldEnum.getValue(c2).getName();
-// return s1.compareTo(s2);
-// }
-// }
-
-
-// Comparator<String> comparator = new Comparator<String>() {
-// public int compare(String s1, String s2) { // Ignore null for brevity
-// return -s1.compareTo(s2);
-// }
-// };
Modified: phenote/trunk/src/java/phenote/datamodel/CharacterListI.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharacterListI.java 2007-09-14 19:28:52 UTC (rev 894)
+++ phenote/trunk/src/java/phenote/datamodel/CharacterListI.java 2007-09-14 19:53:38 UTC (rev 895)
@@ -1,6 +1,6 @@
package phenote.datamodel;
-import java.util.List;
+import ca.odell.glazedlists.EventList;
/** holds a list of Characters - rename phenotype? i dont think so - can have
multiple genotypes in it - transfreable allows it to be plopped on the
@@ -17,8 +17,6 @@
public int size();
public boolean isEmpty();
public int indexOf(CharacterI c);
- public List<CharacterI> getList();
+ public EventList<CharacterI> getList();
public boolean equals(CharacterListI cl);
- /** Sort data by char field/column */
- public void sortBy(CharField cf);
}
Added: phenote/trunk/src/java/phenote/gui/CharacterTableController.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTableController.java (rev 0)
+++ phenote/trunk/src/java/phenote/gui/CharacterTableController.java 2007-09-14 19:53:38 UTC (rev 895)
@@ -0,0 +1,270 @@
+package phenote.gui;
+
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.Comparator;
+import java.util.List;
+
+import javax.swing.JButton;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.table.TableColumn;
+
+import org.apache.log4j.Logger;
+import org.swixml.SwingEngine;
+
+import phenote.config.Config;
+import phenote.dataadapter.CharacterListManager;
+import phenote.dataadapter.LoadSaveManager;
+import phenote.datamodel.CharField;
+import phenote.datamodel.CharacterI;
+import phenote.edit.CharChangeEvent;
+import phenote.edit.CharChangeListener;
+import phenote.edit.EditManager;
+import phenote.util.FileUtil;
+import ca.odell.glazedlists.FilterList;
+import ca.odell.glazedlists.SortedList;
+import ca.odell.glazedlists.TextFilterator;
+import ca.odell.glazedlists.swing.EventSelectionModel;
+import ca.odell.glazedlists.swing.EventTableModel;
+import ca.odell.glazedlists.swing.TableComparatorChooser;
+import ca.odell.glazedlists.swing.TextComponentMatcherEditor;
+
+public class CharacterTableController {
+
+ private static int DEFAULT_COLWIDTH=150; //default column width for table
+ private static int INIT_TABLE_WIDTH=1400;
+ private static int DEFAULT_VIEW_WIDTH=500;
+ private int tableWidth=INIT_TABLE_WIDTH;
+ private static final String SAVE_STRING = "Save Data";
+ private String representedGroup = "default";
+ private SortedList<CharacterI> sortedCharacters;
+ private FilterList<CharacterI> filteredCharacters;
+ private EventSelectionModel<CharacterI> selectionModel;
+ private CharacterTableFormat tableFormat;
+ private LoadSaveManager loadSaveManager;
+ private JPanel characterTablePanel; // initialized by swix
+ private JTable characterTable; // initialized by swix
+ private JTextField filterField; // initialized by swix
+ private JButton commitButton; // initialized by swix
+ private JButton graphButton; // initialized by swix
+
+ public CharacterTableController(String groupName) {
+ if (groupName != null) this.representedGroup = groupName;
+ this.loadPanelLayout();
+ this.sortedCharacters = new SortedList<CharacterI>(this.getCharacterListManager().getCharacterList().getList(), new EverythingEqualComparator<CharacterI>());
+ this.sortedCharacters.setMode(SortedList.AVOID_MOVING_ELEMENTS);
+ this.filteredCharacters = new FilterList<CharacterI>(this.sortedCharacters, new TextComponentMatcherEditor<CharacterI>(this.filterField, new CharacterFilterator()));
+ this.selectionModel = new EventSelectionModel<CharacterI>(this.filteredCharacters);
+ this.tableFormat = new CharacterTableFormat(this.representedGroup);
+ this.getEditManager().addCharChangeListener(new CharacterChangeListener());
+ this.initializeInterface();
+ }
+
+ public JPanel getCharacterTablePanel() {
+ return this.characterTablePanel;
+ }
+
+ public void addNewCharacter() {
+ this.getEditManager().addNewCharacter();
+ }
+
+ public void duplicateSelectedCharacters() {
+ this.getEditManager().copyChars(this.selectionModel.getSelected());
+ }
+
+ public void deleteSelectedCharacters() {
+ this.getEditManager().deleteChars(this.selectionModel.getSelected());
+ }
+
+ public void undo() {
+ this.getEditManager().undo();
+ }
+
+ public void commitCharacters() {
+ if (Config.inst().hasQueryableDataAdapter()) {
+ Config.inst().getQueryableDataAdapter().commit(this.getCharacterListManager().getCharacterList());
+ }
+ else {
+ this.getLoadSaveManager().saveData();
+ }
+ }
+
+ public EventSelectionModel<CharacterI> getSelectionModel() {
+ return this.selectionModel;
+ }
+
+ private void loadPanelLayout() {
+ SwingEngine swix = new SwingEngine(this);
+ try {
+ this.characterTablePanel = (JPanel)swix.render(FileUtil.findUrl("character_table_panel.xml"));
+ } catch (Exception e) {
+ log().fatal("Unable to render character table interface", e);
+ }
+ }
+
+ private void initializeInterface() {
+ final EventTableModel<CharacterI> eventTableModel = new EventTableModel<CharacterI>(this.filteredCharacters, this.tableFormat);
+ this.characterTable.setModel(eventTableModel);
+ new TableComparatorChooser<CharacterI>(characterTable, this.sortedCharacters, false);
+ this.characterTable.setSelectionModel(this.selectionModel);
+ this.characterTable.putClientProperty("Quaqua.Table.style", "striped");
+ this.commitButton.setText(this.getCommitButtonString());
+ if (!Config.inst().uvicGraphIsEnabled()) {
+ this.graphButton.getParent().remove(this.graphButton);
+ }
+ this.filterField.putClientProperty("Quaqua.TextField.style", "search");
+ this.setColumnWidths();
+ if (tableWidth>DEFAULT_VIEW_WIDTH) this.characterTable.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
+ this.characterTable.addMouseListener(new PopupListener(new TableRightClickMenu(this.characterTable)));
+ this.characterTablePanel.validate();
+ }
+
+ private void setColumnWidths() {
+ //this method sets the column widths according to those in the configuration
+ //will determine the total table width according to dimensions in config
+ final int columnCount = this.tableFormat.getColumnCount();
+ int totalWidth = 0;
+ for (int i = 0; i < columnCount; i++) {
+ TableColumn column = this.characterTable.getColumnModel().getColumn(i);
+ int width = this.getWidthOfColumn(i);
+ if (width==0) //-1 is no display
+ {width=DEFAULT_COLWIDTH;}
+ column.setPreferredWidth(width);
+ column.addPropertyChangeListener(new ColwidthChangeListener());
+ this.characterTable.getTableHeader().setResizingColumn(column);
+ column.setWidth(width);
+ totalWidth+=width;
+ }
+ tableWidth=totalWidth;
+ }
+
+ private int getWidthOfColumn(int columnIndex) {
+ return Config.inst().getFieldColwidth(columnIndex);
+ }
+
+ private void setSelectionWithCharacters(List<CharacterI> characters) {
+ this.filterField.setText("");
+ this.selectionModel.clearSelection();
+ for (CharacterI character : characters) {
+ final int index = this.filteredCharacters.indexOf(character);
+ if (index > -1) {
+ this.selectionModel.addSelectionInterval(index, index);
+ Rectangle rect = this.characterTable.getCellRect(index, 0, false);
+ this.characterTable.scrollRectToVisible(rect);
+ }
+ }
+ }
+
+ private void updateCharacterForGlazedLists(CharacterI character) {
+ final int index = this.getCharacterListManager().getCharacterList().getList().indexOf(character);
+ if (index > -1) {
+ this.getCharacterListManager().getCharacterList().getList().set(index, character);
+ }
+ }
+
+ private EditManager getEditManager() {
+ return EditManager.getEditManager(this.representedGroup);
+ }
+
+ private CharacterListManager getCharacterListManager() {
+ return CharacterListManager.getCharListMan(this.representedGroup);
+ }
+
+ private LoadSaveManager getLoadSaveManager() {
+ if (this.loadSaveManager == null) {
+ this.loadSaveManager = new LoadSaveManager(this.getCharacterListManager());
+ }
+ return this.loadSaveManager;
+ }
+
+ private String getCommitButtonString() {
+ if (Config.inst().hasQueryableDataAdapter())
+ return Config.inst().getQueryableDataAdapter().getCommitButtonLabel();
+ else return CharacterTableController.SAVE_STRING;
+ }
+
+ private static Logger log() {
+ return Logger.getLogger(CharacterTableController.class);
+ }
+
+ private class CharacterChangeListener implements CharChangeListener {
+ public void charChanged(CharChangeEvent e) {
+ if (e.isUpdate()) {
+ for (CharacterI character : e.getTransaction().getCharacters()) {
+ CharacterTableController.this.updateCharacterForGlazedLists(character);
+ }
+ } else if (e.isAdd()) {
+ CharacterTableController.this.setSelectionWithCharacters(e.getTransaction().getCharacters());
+ }
+ }
+ }
+
+ private static class EverythingEqualComparator<T> implements Comparator<T> {
+ public int compare(T o1, T o2) {
+ return 0;
+ }
+ }
+
+ private static class CharacterFilterator implements TextFilterator<CharacterI> {
+ public void getFilterStrings(List<String> baseList, CharacterI character) {
+ for (CharField charField : character.getAllCharFields()) {
+ baseList.add(character.getValueString(charField));
+ }
+ }
+ }
+
+ private static class ColwidthChangeListener implements PropertyChangeListener {
+ public void propertyChange(PropertyChangeEvent e)
+ {
+ //listens for changes to the column widths, makes changes to config,
+ //and flags that there's been changes (so that they'll be saved)
+ if (e.getPropertyName().equals("width")) {
+ TableColumn col = (TableColumn)e.getSource();
+ int colIndex = col.getModelIndex();
+ Integer newWidth = (Integer)e.getNewValue();
+ int w = newWidth.intValue();
+ if (w!=(Config.inst().getFieldColwidth(colIndex))) {
+ //only flag modified if changed from original settings
+ Config.inst().setFieldColwidth(colIndex, w);
+ Config.inst().setConfigModified(true);
+ }
+ }
+ }
+ }
+
+ private class PopupListener extends MouseAdapter {
+ JPopupMenu popup;
+ int col; int row;
+ Point p;
+ PopupListener(JPopupMenu popupMenu) {
+ popup = popupMenu;
+ }
+
+ public void mousePressed(MouseEvent e) {
+ maybeShowPopup(e);
+ }
+
+ public void mouseReleased(MouseEvent e) {
+ maybeShowPopup(e);
+ }
+
+ private void maybeShowPopup(MouseEvent e) {
+ p= e.getPoint();
+ col = CharacterTableController.this.characterTable.getTableHeader().columnAtPoint(p);
+ row = CharacterTableController.this.characterTable.rowAtPoint(p);
+ if (e.isPopupTrigger()) {
+ popup.show(e.getComponent(),
+ e.getX(), e.getY());
+ }
+ }
+ }
+
+}
+
\ No newline at end of file
Added: phenote/trunk/src/java/phenote/gui/CharacterTableFormat.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTableFormat.java (rev 0)
+++ phenote/trunk/src/java/phenote/gui/CharacterTableFormat.java 2007-09-14 19:53:38 UTC (rev 895)
@@ -0,0 +1,54 @@
+package phenote.gui;
+
+import java.util.Comparator;
+
+import org.apache.log4j.Logger;
+
+import phenote.config.Config;
+import phenote.datamodel.CharField;
+import phenote.datamodel.CharacterI;
+import phenote.datamodel.OntologyException;
+import phenote.datamodel.OntologyManager;
+import ca.odell.glazedlists.GlazedLists;
+import ca.odell.glazedlists.gui.AdvancedTableFormat;
+
+public class CharacterTableFormat implements AdvancedTableFormat<CharacterI> {
+
+ private String representedGroup = "default";
+
+ public CharacterTableFormat(String groupName) {
+ if (representedGroup != null) this.representedGroup = groupName;
+ }
+
+ public int getColumnCount() {
+ return Config.inst().getEnbldFieldsNum(this.representedGroup);
+ }
+
+ public String getColumnName(int column) {
+ return Config.inst().getFieldLabel(column, this.representedGroup);
+ }
+
+ public Object getColumnValue(CharacterI character, int column) {
+ try {
+ CharField cf = OntologyManager.inst().getCharField(column, this.representedGroup);
+ return character.getValueString(cf);
+ }
+ catch (OntologyException e) {
+ log().error("Column " + column + " not configured properly in " + "character table, can't retrieve value ", e);
+ return "";
+ }
+ }
+
+ public Class<?> getColumnClass(int column) {
+ return String.class;
+ }
+
+ public Comparator<?> getColumnComparator(int column) {
+ return GlazedLists.caseInsensitiveComparator();
+ }
+
+ private static Logger log() {
+ return Logger.getLogger(CharacterTableFormat.class);
+ }
+
+}
Deleted: phenote/trunk/src/java/phenote/gui/CharacterTableModel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTableModel.java 2007-09-14 19:28:52 UTC (rev 894)
+++ phenote/trunk/src/java/phenote/gui/CharacterTableModel.java 2007-09-14 19:53:38 UTC (rev 895)
@@ -1,223 +0,0 @@
-package phenote.gui;
-
-import java.util.List;
-
-import javax.swing.table.AbstractTableModel;
-
-import org.apache.log4j.Logger;
-
-import phenote.config.Config;
-import phenote.dataadapter.CharacterListManager;
-import phenote.datamodel.CharField;
-import phenote.datamodel.CharacterI;
-import phenote.datamodel.CharacterListI;
-import phenote.datamodel.OntologyManager;
-import phenote.edit.EditManager;
-
-/**
- * table model for table of characters. currently holds list of characters - this should
- be moved to datamodel - CharacterList object? CharacterSession? Phenotype?
- */
-class CharacterTableModel extends AbstractTableModel implements SortableTableModel {
-
- //private int rowCount = 0;
- // todo - get this from data adapter/model - especially for loaded
- private CharacterListI characterList;// = new CharacterList();
- private CharacterListManager characterListManager;
- private EditManager editManager;
- private String group = "default";
- //private Config config = Config.inst(); cant cache - may change!
-
- CharacterTableModel(String group, CharacterListManager clManager,
- EditManager eManager) {
- if (group != null) this.group = group;
- this.characterList = clManager.getCharacterList();
- this.characterListManager = clManager;
- this.editManager = eManager;
- // should supress editing model for this i think???
- addInitialBlankRow(); // add blank row to start off
- //getCharListManager().addCharListChangeListener(new TableCharListChangeListener());
- // --> panel
- //EditManager.inst().addCharChangeListener(new TableCharChangeListener());
- }
-
-// public CharacterTableModel() {
-// this(null,CharacterListManager.inst(), EditManager.inst());
-// }
-
- private Config cfg() { return Config.inst(); }
-
- private CharacterListManager getCharListManager() {
- return this.characterListManager;
- }
-
- CharacterI getCharacter(int i) {
- // check out of bounds
- if (characterList == null) return null; // ex?
- return characterList.get(i);
- }
-
- /** returns -1 if not found */
- int indexOf(CharacterI ch) {
- return getCharacterList().indexOf(ch);
- }
-
- // this should come from datamodel not here - refactor
- CharacterListI getCharacterList() {
- return getCharListManager().getCharacterList();
- }
-
- void setCharacterList(CharacterListI charList) {
- characterList = charList;
- fireTableDataChanged();
- }
-
- public String getColumnName(int col) {
- return cfg().getFieldLabel(col,group);
- }
-
- public int getColwidth(int col) {
- return cfg().getFieldColwidth(col);
- }
-
- public int getColumnCount() {
- return cfg().getEnbldFieldsNum(group);
- }
-
- public int getRowCount() {
- //return rowCount;
- if (getCharacterList() == null) return 1; // or 0?? always have 1 blank row?
- return getCharacterList().size();
- }
-
- boolean hasRows() { return getRowCount() > 0; }
-
- void addInitialBlankRow() {
- this.editManager.addInitialCharacter();
- fireTableRowsInserted(getRowCount(),getRowCount());
- }
-
- /** Returns row # of new row - handy for selection */
- int addNewBlankRow() {
- this.editManager.addNewCharacter();
- fireTableRowsInserted(getRowCount(),getRowCount());
- return getRowCount() - 1; // last row
- //return addCharacter(new Character());
- }
-
-
-// /** returns row # of new copied into row */
-// int copyRow(int rowToCopy) {
-// if (!hasRows())
-// return -1; // err msg?
-// CharacterI copy = getCharacter(rowToCopy).cloneCharacter();
-// return addCharacter(copy);
-// }
-
- /** return RowInterval of all new rows to be selected? yes i think so
- the caller (CharTablePanel) wants to know what rows were created
- (so it can selection them) */
- RowInterval copyChars(List<CharacterI> charsToCopy) {
- if (charsToCopy.isEmpty()) {
- log().error("No chars selected to make copy of");
- return new RowInterval(-1,-1); // ex?
- }
- this.editManager.copyChars(charsToCopy); // edits model
- //CompoundTransaction ct = CompoundTransaction.makeCopyTrans(charsToCopy);
- //ct.editModel(); // clones & adds char to char list
- fireTableRowsInserted(getRowCount(),getRowCount()); // updates table view
- int rowEnd = getRowCount() - 1; // -1 -> 0 based
- int rowStart = rowEnd - charsToCopy.size() + 1; // +1 inclusive
- return new RowInterval(rowStart,rowEnd);
- }
-
-// /** Returns row # of row inserted */
-// private int addCharacter(CharacterI character) {
-// //++rowCount;
-// // changes data model (fire event?) add transaction for undo! edit man?
-// characterList.add(character);
-// fireTableRowsInserted(getRowCount(),getRowCount());
-// return getRowCount() -1;
-// }
-
-// void deleteSelectedRow(int deleteRow) {
-// if (!hasRows())
-// return; // err msg?
-// // This needs to make a delete transaction for undo! edit man?
-// characterList.remove(deleteRow);
-// fireTableRowsDeleted(deleteRow,deleteRow);
-// }
-
- void deleteChars(List<CharacterI> chars) {
- if (chars.isEmpty()) {
- log().error("No rows/chars to delete");
- return;
- }
- this.editManager.deleteChars(chars);
- fireTableRowsDeleted(0,getRowCount()); // could be more savvy
- }
-
-
- public Object getValueAt(int row, int col) {
- CharacterI chr = getCharacter(row);
- if (chr == null) {
- log().error("character is null for row "+row+" in table");
- return null;
- }
- try {
- CharField cf = OntologyManager.inst().getCharField(col,group);
- if (!chr.hasValue(cf))
- return null;
- return chr.getValue(cf);
- }
- catch (Exception e) {
- log().error("column "+col+" not configured properly in "+
- ...
[truncated message content] |
|
From: <nl...@us...> - 2007-09-14 19:28:50
|
Revision: 894
http://obo.svn.sourceforge.net/obo/?rev=894&view=rev
Author: nlw
Date: 2007-09-14 12:28:52 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
couple of minor fixes
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/download.shtml
phenote/trunk/doc/phenote-website/new/download.shtml~
phenote/trunk/doc/phenote-website/new/funding.shtml
Modified: phenote/trunk/doc/phenote-website/new/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-14 19:12:33 UTC (rev 893)
+++ phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-14 19:28:52 UTC (rev 894)
@@ -17,7 +17,7 @@
<h3>Launch Phenote in your browser</h3>
<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
<ul><li>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></li>
- <li>Stable release: <a href="http://www.phenote.org/1.3/phenote.jnlp">1.3</a> </li>
+ <li>Stable release: <a href="http://www.phenote.org/phenote/1.3/phenote.jnlp">1.3</a> </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.
Modified: phenote/trunk/doc/phenote-website/new/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-14 19:12:33 UTC (rev 893)
+++ phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-14 19:28:52 UTC (rev 894)
@@ -18,7 +18,7 @@
<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
<ul><li>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></li>
<li>Stable release: <a href="http://www.phenote.org/1.3/phenote.jnlp">1.3</a> </li>
- <li><a href="http://www.phenote.org/old.shtml">Older releases</a></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>
Modified: phenote/trunk/doc/phenote-website/new/funding.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/funding.shtml 2007-09-14 19:12:33 UTC (rev 893)
+++ phenote/trunk/doc/phenote-website/new/funding.shtml 2007-09-14 19:28:52 UTC (rev 894)
@@ -41,7 +41,8 @@
<img class="portrait" height="50" border="0" src="/images/BIRN_logo.gif"alt="BIRN" /></a>
</td>
<td><p><strong>mouseBIRN: mouse Biomedical Informatics Research Network</strong></p></td>
- </tr>
+ </tr>
+ </table>
</div>
</div>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-14 19:12:31
|
Revision: 893
http://obo.svn.sourceforge.net/obo/?rev=893&view=rev
Author: nlw
Date: 2007-09-14 12:12:33 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
again, more website changes
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/contact.shtml
phenote/trunk/doc/phenote-website/new/download.shtml
phenote/trunk/doc/phenote-website/new/download.shtml~
phenote/trunk/doc/phenote-website/new/ssi/header.html
Added Paths:
-----------
phenote/trunk/doc/phenote-website/new/funding.shtml
phenote/trunk/doc/phenote-website/new/help.shtml
Modified: phenote/trunk/doc/phenote-website/new/contact.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/contact.shtml 2007-09-14 18:37:39 UTC (rev 892)
+++ phenote/trunk/doc/phenote-website/new/contact.shtml 2007-09-14 19:12:33 UTC (rev 893)
@@ -37,37 +37,34 @@
<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">
+ [ <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>
+ </script> ]
+ [ <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Join</a> ]</p>
<p>Phenote software development
- [<script type="text/javascript">
+ [ <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>
+ </script> ]
+ [ <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-dev">Join</a> ]</p>
<p>Phenotype annotation discussion list
- [<script type="text/javascript">
+ [ <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>
+ </script> ]
+ [ <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenotype">Join</a> ]</p>
<p>General OBO ontology discussion
- [<script type="text/javascript">
+ [ <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>
+ </script> ]
+ [ <a href="https://lists.sourceforge.net/lists/listinfo/obo-discuss">Join</a> ]</p>
<p>General NCBO discussion
- [<script type="text/javascript">
+ [ <script type="text/javascript">
obfuscate("lists.stanford.edu", "cbio-everyone", "Email");
- </script>]</p>
+ </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 of sourceforge to log your request:
- <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">Bug Tracker</a></p>
+ tracker on sourceforge to log your request:
+ <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">Request Tracker</a></p>
</div>
</div>
Modified: phenote/trunk/doc/phenote-website/new/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-14 18:37:39 UTC (rev 892)
+++ phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-14 19:12:33 UTC (rev 893)
@@ -18,7 +18,7 @@
<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
<ul><li>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></li>
<li>Stable release: <a href="http://www.phenote.org/1.3/phenote.jnlp">1.3</a> </li>
- <li><a href="http://www.phenote.org/old.shtml">Older releases</a></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>
Modified: phenote/trunk/doc/phenote-website/new/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-14 18:37:39 UTC (rev 892)
+++ phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-14 19:12:33 UTC (rev 893)
@@ -16,7 +16,7 @@
</div>
<h3>Launch Phenote in your browser</h3>
<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
- <ul><li>Beta release: <a href="http://www.phenote.org/1.4-beta3/phenote.jnlp">1.4 beta3</a></li>
+ <ul><li>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></li>
<li>Stable release: <a href="http://www.phenote.org/1.3/phenote.jnlp">1.3</a> </li>
<li><a href="http://www.phenote.org/old.shtml">Older releases</a></li>
</ul>
Added: phenote/trunk/doc/phenote-website/new/funding.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/funding.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/new/funding.shtml 2007-09-14 19:12:33 UTC (rev 893)
@@ -0,0 +1,52 @@
+<!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">
+ Phenote Funding and Support
+ </div>
+ <p>Phenote is being developed by the <a href="http://www.berkeleybop.org/">
+ Bioinformatics Core</a> of the <a href="http://www.bioontology.org/">
+ National Center for Biomedical Ontology</a>, which is part of the
+ <a href="http://www.bisti.nih.gov/ncbc/index.cfm">
+ National Center for Biomedical Computing</a> network.
+ Funding is given by the <a href="http://nihroadmap.nih.gov/">NIH Roadmap</a> initiative. </p>
+
+ <p> There are three funded groups driving the development of this
+ software project through the NCBO:</p>
+
+ <table border="0">
+ <tr>
+ <td><a href="http://flybase.bio.indiana.edu/">
+ <img class="portrait" height="50" border="0" src="/images/fly_logo.png"alt="Flybase" /></a>
+ </td>
+ <td><p><strong>Flybase: The Drosophila Genome Database</strong>[<a href="http://www.bioontology.org/dbp_drosophila.html">...</a>]</p></td>
+ </tr>
+ <tr>
+ <td><a href="http://www.zfin.org/"><img class="portrait" border="0" src="/images/zfin_logo.gif" height="50" alt="Zfin" /></a>
+ </td>
+ <td><p><strong>Zfin: Zebrafish Information Network</strong> [<a href="http://www.bioontology.org/dbp_zfin.html">...</a>]</p></td>
+ </tr>
+ <td><a href="http://www.nbirn.net/research/mouse/index.shtm">
+ <img class="portrait" height="50" border="0" src="/images/BIRN_logo.gif"alt="BIRN" /></a>
+ </td>
+ <td><p><strong>mouseBIRN: mouse Biomedical Informatics Research Network</strong></p></td>
+ </tr>
+
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
+
+ </body>
+</html>
Added: phenote/trunk/doc/phenote-website/new/help.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/help.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/new/help.shtml 2007-09-14 19:12:33 UTC (rev 893)
@@ -0,0 +1,33 @@
+<!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">
+ Getting Help with Phenote
+ </div>
+ <h2><a href="http://www.phenote.org/faq.shtml/">Frequently Asked Questions (FAQs)</a></h2>
+ <p>A resource for some basic questions and those we are most frequently asked</p>
+ <h2><a href="http://www.phenote.org/help/">Online Help</a></h2>
+ <p>We provide a searchable online help tool to help answer your questions. This is the same help content provided in the software.</p>
+ <h2><a href="http://www.phenote.org/contact.shtml">Contact Us</a></h2>
+ <p>We are here to help you whenever you might need it. You can contact
+ us directly or pose your questions to our user community with the links provided here.
+ </p>
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
+
+ </body>
+</html>
Modified: phenote/trunk/doc/phenote-website/new/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/new/ssi/header.html 2007-09-14 18:37:39 UTC (rev 892)
+++ phenote/trunk/doc/phenote-website/new/ssi/header.html 2007-09-14 19:12:33 UTC (rev 893)
@@ -37,7 +37,7 @@
title="Phenote Project Team">Team</a>
</li>
<li>
- <a href="http://www.obofoundry.org/related.shtml"
+ <a href="http://www.phenote.org/related.shtml"
title="Projects related to Phenote">Related Projects</a>
</li>
</ul>
@@ -84,7 +84,7 @@
</ul>
</li>
<li>
- <a href="http://www.phenote.org/"
+ <a href="http://www.phenote.org/help.shtml"
title="Phenote Help">Help</a>
<ul>
<li>
@@ -112,7 +112,7 @@
</li>
<li>
<a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page"
- title="Join the Phenote Working Group">Working Group</a>
+ title="Join the Phenote Working Group">Working Group Wiki</a>
</li>
<li>
<a href="http://www.phenote.org/contact.shtml"
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-14 18:37:36
|
Revision: 892
http://obo.svn.sourceforge.net/obo/?rev=892&view=rev
Author: nlw
Date: 2007-09-14 11:37:39 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
lots of changes to new website pages
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/about.shtml
phenote/trunk/doc/phenote-website/new/contact.shtml
phenote/trunk/doc/phenote-website/new/download.shtml
phenote/trunk/doc/phenote-website/new/download.shtml~
phenote/trunk/doc/phenote-website/new/index.shtml
phenote/trunk/doc/phenote-website/new/ssi/header.html
Modified: phenote/trunk/doc/phenote-website/new/about.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/about.shtml 2007-09-14 15:25:58 UTC (rev 891)
+++ phenote/trunk/doc/phenote-website/new/about.shtml 2007-09-14 18:37:39 UTC (rev 892)
@@ -24,8 +24,8 @@
</p>
<h3>
- <a href="coordination.shtml">
- Coordination
+ <a href="contact.shtml">
+ Contact us
</a>
</h3>
<p>
Modified: phenote/trunk/doc/phenote-website/new/contact.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/contact.shtml 2007-09-14 15:25:58 UTC (rev 891)
+++ phenote/trunk/doc/phenote-website/new/contact.shtml 2007-09-14 18:37:39 UTC (rev 892)
@@ -15,8 +15,8 @@
<div class="catch_phrase">
Contact Us
- </div>
-
+ </div>
+ <h1>Email us</h1>
<p>Software Development:
<script type="text/javascript">
obfuscate("berkeleybop.org", "mgibson", "Mark Gibson");
@@ -33,7 +33,42 @@
<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 of sourceforge to log your request:
+ <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">Bug Tracker</a></p>
+
</div>
</div>
Modified: phenote/trunk/doc/phenote-website/new/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-14 15:25:58 UTC (rev 891)
+++ phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-14 18:37:39 UTC (rev 892)
@@ -16,7 +16,7 @@
</div>
<h3>Launch Phenote in your browser</h3>
<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
- <ul><li>Beta release: <a href="http://www.phenote.org/1.4-beta3/phenote.jnlp">1.4 beta3</a></li>
+ <ul><li>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></li>
<li>Stable release: <a href="http://www.phenote.org/1.3/phenote.jnlp">1.3</a> </li>
<li><a href="http://www.phenote.org/old.shtml">Older releases</a></li>
</ul>
Modified: phenote/trunk/doc/phenote-website/new/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-14 15:25:58 UTC (rev 891)
+++ phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-14 18:37:39 UTC (rev 892)
@@ -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/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/index.shtml 2007-09-14 15:25:58 UTC (rev 891)
+++ phenote/trunk/doc/phenote-website/new/index.shtml 2007-09-14 18:37:39 UTC (rev 892)
@@ -15,14 +15,36 @@
<div class="catch_phrase">
Welcome to 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>
- <p>
- </p>
-
+ <h2> Features included:</h2>
+ <ul>
+ <li>Friendly spreadsheet-like interface
+ </li>
+ <li>Type-ahead-suggest (autocompletion) for terms within ontologies
+ </li>
+ <li>Use of any OBO-format ontology
+ </li>
+ <li>Ontology navigation and term information display
+ </li>
+ <li>Bulk copy/edit/delete/sort of phenotype-genotype character entries
+ </li>
+ <li>Excel-compatible output format (tab-delimited)
+ </li>
+ <li>Additional export formats: phenosyntax, xml
+ </li>
+ <li>configurable input fields to allow custom data entry and user-specified ontologies
+ </li>
+ <li>Preconfigurations available for different communities
+ </li>
+ <li>Customized configurations easily added
+ </li>
+ </ul>
+
</div>
</div>
@@ -38,7 +60,7 @@
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://www.phenote.org/phenote.jnlp"
+ <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp"
title="Lauch Phenote via Webstart">
Launch Phenote via Webstart
</a>
@@ -74,12 +96,20 @@
</p>
</li>
</ul>
- -->
- <h3>Event Title</h3>
+ -->
+ <h3>Phenote User's Group IRC</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>, October 4, Online
+ </p>
+ </li>
+ <h3>Phenote demo</h3>
+ <ul class="events">
+ <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
</p>
</li>
@@ -100,7 +130,7 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
- New Phenote Beta available: 1.4-beta3!
+ <a href="http://www.phenote.org/download.shtml">New Phenote Beta available: 1.4-beta3!</a>
<!--
<h3>Event Title</h3>
<ul class="events">
Modified: phenote/trunk/doc/phenote-website/new/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/new/ssi/header.html 2007-09-14 15:25:58 UTC (rev 891)
+++ phenote/trunk/doc/phenote-website/new/ssi/header.html 2007-09-14 18:37:39 UTC (rev 892)
@@ -52,7 +52,7 @@
title="Phenote Software Download Page">Download</a>
</li>
<li>
- <a href="http://www.phenote.org/phenote-release-notes.html"
+ <a href="http://www.phenote.org/release-notes.shtml"
title="Phenote Release Notes">Release Notes</a>
</li>
<li>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-09-14 15:26:01
|
Revision: 891
http://obo.svn.sourceforge.net/obo/?rev=891&view=rev
Author: mgibson
Date: 2007-09-14 08:25:58 -0700 (Fri, 14 Sep 2007)
Log Message:
-----------
took out genetic context
per melissa request
Modified Paths:
--------------
phenote/trunk/conf/zfin-standalone.cfg
Modified: phenote/trunk/conf/zfin-standalone.cfg
===================================================================
--- phenote/trunk/conf/zfin-standalone.cfg 2007-09-14 01:51:57 UTC (rev 890)
+++ phenote/trunk/conf/zfin-standalone.cfg 2007-09-14 15:25:58 UTC (rev 891)
@@ -31,15 +31,12 @@
<ns:field name="Image File" enable="true" desc="The image filename to attribute this phenotype character."/>
- <ns:field name="Genetic Context" syntax-abbrev="GC" enable="true">
- <ns:ontology name="Genetic Context" file="context.obo"/>
- </ns:field>
<ns:field name="Entity" syntax-abbrev="E" enable="true">
- <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"
- is-postcomp-rel="true"/>
- <ns:ontology name="ZF" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/zebrafish_anatomy.obo"
- namespace="zebrafish_anatomy"/>
+ <ns:ontology name="Relationship" is-postcomp-rel="true"
+ file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" />
+ <ns:ontology name="ZF" namespace="zebrafish_anatomy"
+ file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/zebrafish_anatomy.obo"/>
<ns:ontology name="GO"
file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
</ns:field>
@@ -78,5 +75,6 @@
Added in autocompletion setting defaults; Terms&Synonyms -->
<!-- 06.14.07 - Added 'image name' free-text field as an additional provenance field
changed settings to ALWAYS WIPEOUT in master-to-local config option -->
+ <!-- 09.14.07 - (MG) per melissas request - took out genetic context -->
</ns:phenote-configuration>
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-14 01:51:55
|
Revision: 890
http://obo.svn.sourceforge.net/obo/?rev=890&view=rev
Author: nlw
Date: 2007-09-13 18:51:57 -0700 (Thu, 13 Sep 2007)
Log Message:
-----------
fixed a couple of links, etc.
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/team.shtml
phenote/trunk/doc/phenote-website/new/users.shtml
Modified: phenote/trunk/doc/phenote-website/new/team.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/team.shtml 2007-09-14 01:44:39 UTC (rev 889)
+++ phenote/trunk/doc/phenote-website/new/team.shtml 2007-09-14 01:51:57 UTC (rev 890)
@@ -15,8 +15,7 @@
<div class="catch_phrase">
Project Team
</div>
- <div class="clearall"></div>
- <h2 class="bio"><a name="exec" id="exec"></a>
+ <h2 class="bio"><a name="exec" id="exec"></a>
Development</h2>
<div class="third_bio">
<p><img src="http://www.bioontology.org/images/team/gibson.jpg" title="Mark Gibson" alt="Mark Gibson" height="130"/></p>
@@ -33,7 +32,7 @@
<div class="clearall"></div>
<div class="third_bio">
- <p><img src="images/team/lewis.jpg" title="Suzanna Lewis" alt="Suzanna Lewis" height="130" /> </p>
+ <p><img src="http://www.bioontology.org/images/team/lewis.jpg" title="Suzanna Lewis" alt="Suzanna Lewis" height="130" /> </p>
<p><a href="http://www.berkeleybop.org/content/people/suzi/" title="Suzanna Lewis">Suzanna Lewis</a>, MS</p>
</div>
<div class="clearall"></div>
@@ -65,7 +64,8 @@
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
+ for Biomedical Ontology, the Model Organism Encyclopedia
+ of DNA Elements (modENCODE), and the Generic Model Organism
Database Project.
</p>
Modified: phenote/trunk/doc/phenote-website/new/users.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/users.shtml 2007-09-14 01:44:39 UTC (rev 889)
+++ phenote/trunk/doc/phenote-website/new/users.shtml 2007-09-14 01:51:57 UTC (rev 890)
@@ -46,6 +46,11 @@
<td>The Gene Ontology</td>
</tr>
<tr>
+ <td><a href="http://www.wormbase.org/"><img class="portrait" border="0" src="/images/worm_logo.jpg" height="50" alt="WB" /></a>
+ </td>
+ <td>The <i>C. elegans</i> Genome Database (Wormbase)</td>
+ </tr>
+ <tr>
<td><a href="http://www.nescent.org/">
<img class="portrait" border="0" src="/images/nescent_logo.gif" height="50" alt="Nescent" /></a>
</td>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-14 01:44:35
|
Revision: 889
http://obo.svn.sourceforge.net/obo/?rev=889&view=rev
Author: nlw
Date: 2007-09-13 18:44:39 -0700 (Thu, 13 Sep 2007)
Log Message:
-----------
modifications to logo pics
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/images/BIRN_logo.gif
phenote/trunk/doc/phenote-website/images/xenbase_logo.gif
Added Paths:
-----------
phenote/trunk/doc/phenote-website/images/worm_logo.jpg
Modified: phenote/trunk/doc/phenote-website/images/BIRN_logo.gif
===================================================================
(Binary files differ)
Added: phenote/trunk/doc/phenote-website/images/worm_logo.jpg
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/worm_logo.jpg
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Modified: phenote/trunk/doc/phenote-website/images/xenbase_logo.gif
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-14 01:33:44
|
Revision: 888
http://obo.svn.sourceforge.net/obo/?rev=888&view=rev
Author: nlw
Date: 2007-09-13 18:33:45 -0700 (Thu, 13 Sep 2007)
Log Message:
-----------
added related projects page
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/related.shtml
phenote/trunk/doc/phenote-website/new/screenshots.shtml
phenote/trunk/doc/phenote-website/new/ssi/header.html
phenote/trunk/doc/phenote-website/new/users.shtml
Modified: phenote/trunk/doc/phenote-website/new/related.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/related.shtml 2007-09-14 00:23:09 UTC (rev 887)
+++ phenote/trunk/doc/phenote-website/new/related.shtml 2007-09-14 01:33:45 UTC (rev 888)
@@ -3,7 +3,7 @@
<head>
<!--#include virtual="ssi/head.html" -->
- <title>Open Biomedical Ontologies Foundry</title>
+ <title>Phenote</title>
</head>
<body>
@@ -15,19 +15,30 @@
<div class="catch_phrase">
Related Projects
</div>
-
+ <h1>Ontologies</h1>
<h3>
- <a href="http://www.gmod.org/">
- Generic Model Organism Databases</a>
+ <a href="http://www.bioontology.org/wiki/index.php/PATO:Main_Page">
+ Phenotype and Trait Ontology (PATO)</a>
+ </h3>
+ <p>
+ An ontology of phenotypic qualities (properties). This ontology
+ can be used in conjunction with other ontologies such as GO or
+ anatomical ontologies to refer to phenotypes. Examples of
+ qualities are red, ectopic, high temperature, fused, small,
+ edematous and arrested.
+ </p>
+ <h3>
+ <a href="http://www.geneontology.org/">
+ Gene Ontology (GO)</a>
</h3>
<p>
- 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>
-
+ The Gene Ontology (GO) project is a collaborative effort to address
+ the need for consistent descriptions of gene products in different
+ databases.
+ The Gene Ontology project provides a controlled vocabulary to
+ describe gene and gene product attributes in any organism. There
+ are three distinct ontologies developed by GO: molecular function,
+ biological process, and cellular component.
<h3>
<a href="http://obi.sourceforge.net/">
Ontologies for Biomedical Investigations
@@ -42,7 +53,49 @@
field of study.
</p>
+
+ <h1>Resources</h1>
<h3>
+ <a href="http://www.bioontology.org/">
+ National Center for Biomedical Ontology</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://www.obofoundry.org/">
+ OBO Foundry</a>
+ </h3>
+ <p>
+ The OBO Foundry is an open, inclusive, and collaborative core of
+ interoperable ontologies developed by the research community. The
+ goal is to facilitate the creation of consistent, compatible, and
+ unambiguous ontologies thereby supporting the biomedical research
+ community. The contributors are those biological researchers and
+ ontology developers who have agreed to work together on an evolving
+ set of design principles that can foster interoperability of
+ ontologies, and 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>
+ <h3>
+ <a href="http://www.gmod.org/">
+ Generic Model Organism Databases</a>
+ </h3>
+ <p>
+ 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)
@@ -111,19 +164,6 @@
Controlled Vocabularies.
</p>
- <h3>
- <a href="http://www.sofg.org/">
- Standards and Ontologies for Functional Genomics
- </a>
- </h3>
- <p>
- 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>
Modified: phenote/trunk/doc/phenote-website/new/screenshots.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/screenshots.shtml 2007-09-14 00:23:09 UTC (rev 887)
+++ phenote/trunk/doc/phenote-website/new/screenshots.shtml 2007-09-14 01:33:45 UTC (rev 888)
@@ -16,7 +16,7 @@
Phenote Screenshots
</div>
<div class="clearall"></div>
- <p><img src="http://www.phenote.org/images/phenote_screenshot.jpg" title="Phenote in action" alt="Phenote screenshot" width="100%"/></p>
+ <p><img src="http://www.phenote.org/images/phenote_screenshot.png" title="Phenote in action" alt="Phenote screenshot" width="100%"/></p>
</div>
</div>
Modified: phenote/trunk/doc/phenote-website/new/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/new/ssi/header.html 2007-09-14 00:23:09 UTC (rev 887)
+++ phenote/trunk/doc/phenote-website/new/ssi/header.html 2007-09-14 01:33:45 UTC (rev 888)
@@ -25,7 +25,7 @@
title="Phenote Features">Features</a>
</li>
<li>
- <a href="http://www.phenote.org/faq.shtml"
+ <a href="http://www.phenote.org/screenshots.shtml"
title="Phenote Screenshot">Screenshots</a>
</li>
<li>
@@ -44,7 +44,7 @@
</li>
<li>
- <a href="http://www.phenote.org/info.shtml"
+ <a href="http://www.phenote.org/download.shtml"
title="Phenote Software">Software</a>
<ul>
<li>
@@ -103,7 +103,7 @@
</li>
<li>
- <a href="http://www.phenote.org/participate.shtml"
+ <a href="http://www.phenote.org/users.shtml"
title="How to participate in the Phenote Community">Community</a>
<ul>
<li>
@@ -115,7 +115,7 @@
title="Join the Phenote Working Group">Working Group</a>
</li>
<li>
- <a href="http://www.phenote.org/content/about/#lists"
+ <a href="http://www.phenote.org/contact.shtml"
title="Phenote Mailing Lists">Mailing Lists</a>
</li>
<li>
Modified: phenote/trunk/doc/phenote-website/new/users.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/users.shtml 2007-09-14 00:23:09 UTC (rev 887)
+++ phenote/trunk/doc/phenote-website/new/users.shtml 2007-09-14 01:33:45 UTC (rev 888)
@@ -13,31 +13,8 @@
<div id="main_container_aux">
<div id="main_content_aux">
<div class="catch_phrase">
- Project Team
+ Phenote User Community
</div>
- <div class="clearall"></div>
- <h2 class="bio"><a name="exec" id="exec"></a>
- Development</h2>
- <div class="third_bio">
- <p><img src="http://www.bioontology.org/images/team/gibson.jpg" title="Mark Gibson" alt="Mark Gibson" height="130"/></p>
- <p><a href="http://www.berkeleybop.org/mgibson/" title="Mark Gibson">Mark Gibson</a>, MSE</p>
- </div>
- <div class="third_bio">
- <p><img src="http://www.bioontology.org/images/team/washington.jpg" title="Nicole Washington" alt="Nicole Washington" height="130" /> </p>
- <p><a href="http://berkeleybop.org/content/people/nlwashington/" title="Nicole Washington">Nicole Washington</a></a>, PhD </p>
- </div>
- <div class="third_bio">
- <p><img src="http://www.bioontology.org/images/team/mungall.jpg" title="Chris Mungall" alt="Chris Mungall" height="130" /></p>
- <p><a href="http://www.fruitfly.org/%7Ecjm/" title="Chris Mungall">Chris Mungall</a>, BSc</p>
- </div>
- <div class="clearall"></div>
-
- <div class="third_bio">
- <p><img src="images/team/lewis.jpg" title="Suzanna Lewis" alt="Suzanna Lewis" height="130" /> </p>
- <p><a href="http://www.berkeleybop.org/content/people/suzi/" title="Suzanna Lewis">Suzanna Lewis</a>, MS</p>
- </div>
- <div class="clearall"></div>
-
<h1>Collaborations</h1>
<p>Phenote development is a community effort. We welcome input and feedback from our users. The following groups are using Phenote:</p>
@@ -80,7 +57,7 @@
<td>PharmacoGenomics KnowledgeBase (PharmGKB)</td>
</tr>
<tr>
- <td><a href="http://www.xenbase.org"><img class="portrait" border="0" src="/images/xenbase_logo.png" height="50" alt="Xenbase" /></a>
+ <td><a href="http://www.xenbase.org/"><img class="portrait" border="0" src="/images/xenbase_logo.gif" height="50" alt="Xenbase" /></a>
</td>
<td>Xenopus Model Organism Database (Xenbase)</td>
</tr>
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" -->
-
- <div id="main_container_aux">
- <div id="main_content_aux">
- <div class="catch_phrase">
- Ontology Browser
- </div>
-
- <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="http://www.obofoundry.org/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="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>
-
- <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">
-
- <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>
-
-
-
-
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/new/browse.shtml.~1.3.~
===================================================================
--- phenote/trunk/doc/phenote-website/new/browse.shtml.~1.3.~ 2007-09-13 23:39:28 UTC (rev 886)
+++ phenote/trunk/doc/phenote-website/new/browse.shtml.~1.3.~ 2007-09-14 00:23:09 UTC (rev 887)
@@ -1,347 +0,0 @@
-<!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">
- @page { size: 8.5inch 11inch; margin-top: 1inch; margin-bottom: 1inch; margin-left: 1.25inch; margin-right: 1.25inch }
- table { border-collapse:collapse; border-spacing:0; empty-cells:show }
- td, th { vertical-align:top; }
- h1, h2, h3, h4, h5, h6 { clear:both }
- ol, ul { padding:0; }
- * { margin:0; }
- *.Frame { font-size:12pt; vertical-align:top; text-align:center; }
- *.Graphics { font-size:12pt; vertical-align:top; text-align:center; }
- *.OLE { font-size:12pt; vertical-align:top; text-align:center; }
- *.Arial10BoldText { font-family:Arial; font-size:10pt; margin-top:0.0138in; margin-bottom:0.0138in; font-weight:bold; }
- *.body { font-family:'Palatino Linotype'; font-size:10pt; margin-top:0.0417in; margin-bottom:0.0417in; text-align:justify ! important; }
- *.bodyIndent { font-family:'Palatino Linotype'; font-size:10pt; margin-top:0.0417in; margin-bottom:0.0417in; text-align:justify ! important; margin-left:0in; margin-right:0in; text-indent:0.25inch; }
- *.Caption { font-family:Times; font-size:12pt; margin-top:0.0835in; margin-bottom:0.0835in; font-style:italic; }
- *.CM14 { font-family:'PICDE L+ Adv PS Tim', 'Adv PS Tim'; font-size:10pt; margin-top:0in; margin-bottom:0.1654in; text-align:justify ! important; }
- *.Commentaire { font-family:'Palatino Linotype'; font-size:10pt; }
- *.Contents1 { font-family:'Palatino Linotype'; font-size:10pt; text-align:justify ! important; }
- *.Contents2 { font-family:'Palatino Linotype'; font-size:10pt; margin-left:0.1528in; margin-right:0in; text-align:justify ! important; text-indent:0inch; }
- *.Contents3 { font-family:'Palatino Linotype'; font-size:10pt; margin-left:0.3055in; margin-right:0in; text-align:justify ! important; text-indent:0inch; }
- *.Corpsdetexte3 { font-family:Arial; font-size:8pt; margin-top:0in; margin-bottom:0.0835in; }
- *.DataField10pt { font-family:Arial; font-size:10pt; }
- *.DataField11pt { font-family:Arial; font-size:10pt; line-height:0.2083in; }
- *.DataField11pt-Single { font-family:Arial; font-size:10pt; }
- *.Endnote { font-family:Arial; font-size:10pt; margin-left:0.248in; margin-right:0in; margin-top:0.1in; margin-bottom:0.1in; text-align:justify ! important; text-indent:-0.248inch; }
- *.Footer { font-family:Arial; font-size:10pt; }
- *.Footnote { font-family:Arial; font-size:10pt; text-align:justify ! important; }
- *.FormFieldCaption { font-family:Arial; font-size:8pt; }
- *.FormFieldCaption7pt { font-family:Arial; font-size:7pt; }
- *.FormFooter { font-family:Arial; font-size:8pt; margin-left:0.0402in; margin-right:0in; text-indent:0inch; }
- *.FormFooterBorder { font-family:Arial; font-size:8pt; padding-left:0in; padding-right:0in; padding-top:0.0138in; padding-bottom:0in; border-left-style:none; border-right-style:none; border-top-width:0.018cm; border-top-style:solid; border-top-color:#000000; border-bottom-style:none; }
- *.Header { font-family:Arial; font-size:10pt; }
- *.Heading { font-family:Helvetica; font-size:14pt; margin-top:0.1665in; margin-bottom:0.0835in; }
- *.Heading1 { font-family:'Palatino Linotype'; font-size:10pt; text-align:center ! important; font-weight:bold; }
- *.Heading2 { font-family:'Palatino Linotype'; font-size:14pt; text-align:center ! important; font-weight:bold; }
- *.Heading3 { font-family:'Palatino Linotype'; font-size:13pt; margin-top:0.1665in; margin-bottom:0.0417in; font-weight:bold; }
- *.Heading4 { font-family:'Palatino Linotype'; font-size:10pt; margin-top:0.1665in; margin-bottom:0.0417in; text-align:justify ! important; font-style:italic; }
- *.Heading5 { font-family:Arial; font-size:10pt; margin-top:0.1665in; margin-bottom:0.0417in; text-align:justify ! important; font-style:italic; }
- *.Heading6 { font-family:Arial; font-size:10pt; margin-top:0.1665in; margin-bottom:0.0417in; text-align:justify ! important; font-weight:bold; }
- *.Heading7 { font-family:Arial; font-size:10pt; margin-top:0.1665in; margin-bottom:0.0417in; text-align:justify ! important; }
- *.Heading8 { font-family:Arial; font-size:10pt; margin-top:0.1665in; margin-bottom:0.0417in; text-align:justify ! important; font-style:italic; }
- *.Heading9 { font-family:Arial; font-size:10pt; margin-top:0.1665in; margin-bottom:0.0417in; text-align:justify ! important; }
- *.HeadingNote { font-family:Arial; font-size:8pt; margin-top:0.028in; margin-bottom:0.028in; text-align:center ! important; font-style:italic; }
- *.HeadNoteNotItalics { font-family:Arial; font-size:8pt; margin-top:0.028in; margin-bottom:0.028in; text-align:center ! important; font-style:normal; }
- *.Index { font-family:Times; font-size:10pt; }
- *.Légende { font-family:'Palatino Linotype'; font-size:10pt; margin-top:0.1665in; margin-bottom:0in; text-align:center ! important; font-weight:bold; }
- *.List { font-family:Times; font-size:10pt; margin-top:0in; margin-bottom:0.0835in; }
- *.Listeànuméros { font-family:Times; font-size:10pt; }
- *.Listeànuméros2 { font-family:Times; font-size:10pt; }
- *.Listeànuméros3 { font-family:Times; font-size:10pt; }
- *.Listeànuméros4 { font-family:Times; font-size:10pt; }
- *.Listeànuméros5 { font-family:Times; font-size:10pt; }
- *.Listeàpuces { font-family:Times; font-size:10pt; margin-left:0in; margin-right:0in; text-indent:0inch; }
- *.Listeàpuces2 { font-family:Times; font-size:10pt; margin-left:0in; margin-right:0in; text-indent:0inch; }
- *.Listeàpuces3 { font-family:Times; font-size:10pt; }
- *.Listeàpuces4 { font-family:Times; font-size:10pt; }
- *.Listeàpuces5 { font-family:Times; font-size:10pt; }
- *.MIAPEFootnote { font-family:'Palatino Linotype'; font-size:9pt; text-align:justify ! important; }
- *.NameofApplicant { font-family:Arial; font-size:8pt; }
- *.NormalWeb { font-family:'Palatino Linotype'; font-size:10pt; margin-top:0.1945in; margin-bottom:0.1945in; }
- *.Normalcentré { font-family:Arial; font-size:10pt; margin-left:1in; margin-right:1in; margin-top:0in; margin-bottom:0.0835in; text-align:justify ! important; text-indent:0inch; }
- *.Objetducommentaire { font-family:Arial; font-size:11pt; }
- *.P1 { font-family:'Palatino Linotype'; font-size:10pt; margin-top:0.0835in; margin-bottom:0.0835in; }
- *.P2 { font-family:'Times New Roman'; font-size:12pt; margin-top:0.0835in; margin-bottom:0.0835in; }
- *.P3 { font-family:'Times New Roman'; font-size:12pt; margin-top:0.0835in; margin-bottom:0.0835in; color:#000000; }
- *.P4 { font-family:'Times New Roman'; font-size:12pt; margin-top:0.0835in; margin-bottom:0.0835in; color:#000000; }
- *.PIHeader { font-family:'Palatino Linotype'; font-size:8pt; margin-left:0.6in; margin-right:0in; margin-top:0in; margin-bottom:0.028in; text-indent:0inch; }
- *.QuickA { font-family:'Palatino Linotype'; font-size:10pt; }
- *.reference { font-family:'Palatino Linotype'; font-size:10pt; margin-left:0.3744in; margin-right:0in; margin-top:0in; margin-bottom:0.0835in; text-align:justify ! important; text-indent:-0.3744inch; }
- *.References { font-family:'Palatino Linotype'; font-size:9pt; margin-top:0in; margin-bottom:0.0555in; }
- *.ReminderList1 { font-family:Helvetica; font-size:10pt; margin-top:0in; margin-bottom:0.0835in; color:#000000; font-weight:bold; }
- *.ReminderList2 { font-family:Helvetica; font-size:10pt; margin-top:0in; margin-bottom:0.0417in; color:#000000; }
- *.ReminderList3 { font-family:Helvetica; font-size:10pt; margin-top:0in; margin-bottom:0.0417in; }
- *.Standard { font-family:'Palatino Linotype'; font-size:10pt; }
- *.StyleLatinArialComplexArialJustified { font-family:'Palatino Linotype'; font-size:10pt; text-align:justify ! important; }
- *.StyleBefore:3ptAfter:3pt { font-family:'Palatino Linotype'; font-size:10pt; margin-top:0.0417in; margin-bottom:0.0417in; text-align:justify ! important; }
- *.StylebodyLatinArialComplexArial { font-family:'Palatino Linotype'; font-size:10pt; margin-top:0.0417in; margin-bottom:0.0417in; text-align:justify ! important; }
- *.StylebodyLatinArialComplexArialComplexBold { font-family:'Palatino Linotype'; font-size:10pt; margin-top:0.0417in; margin-bottom:0.0417in; text-align:justify ! important; }
- *.StylebodyIndentLatinArialComplexArial { font-family:'Palatino Linotype'; font-size:10pt; margin-left:0in; margin-right:0in; margin-top:0.0417in; margin-bottom:0.0417in; text-align:justify ! important; text-indent:0.25inch; }
- *.StyleHeading112ptLeft { font-family:'Palatino Linotype'; font-size:14pt; text-align:left ! important; font-weight:bold; }
- *.StyleHeading114ptLeft { font-family:'Palatino Linotype'; font-size:14pt; text-align:left ! important; font-weight:bold; margin-left:0in; margin-right:0in; text-indent:0inch; }
- *.StyleHeading1JustifiedBefore:12ptAfter:3pt { font-family:'Palatino Linotype'; font-size:14pt; text-align:justify ! important; font-weight:bold; margin-top:0.1665in; margin-bottom:0.0417in; }
- *.StyleHeading2Justified { font-family:'Palatino Linotype'; font-size:11pt; text-align:justify ! important; font-weight:bold; margin-top:0.1665in; margin-bottom:0.0417in; font-style:italic; }
- *.StyleHeading2JustifiedBefore:12ptAfter:3pt { font-family:'Palatino Linotype'; font-size:13pt; text-align:justify ! important; font-weight:bold; margin-top:0.1665in; margin-bottom:0.0417in; }
- *.StyleHeading2LeftBefore:12ptAfter:3pt { font-family:'Palatino Linotype'; font-size:12pt; text-align:left ! important; font-weight:bold; margin-top:0.1665in; margin-bottom:0.0417in; }
- *.StyleHeading2TimesNewRoman10pt { font-family:'Palatino Linotype'; font-size:10pt; text-align:center ! important; font-weight:bold; }
- *.StyleHeading3Justified { font-family:'Palatino Linotype'; font-size:13pt; margin-top:0.1665in; margin-bottom:0.0417in; font-weight:bold; text-align:justify ! important; }
- *.StyleHeading3Left { font-family:'Palatino Linotype'; font-size:11pt; margin-top:0.1665in; margin-bottom:0.0417in; font-weight:bold; }
- *.StyleNormalWeb9pt { font-family:'Palatino Linotype'; font-size:9pt; margin-top:0.1945in; margin-bottom:0.1945in; text-align:justify ! important; }
- *.StyleNormalWebBefore:AutoAfter:Auto { font-family:'Palatino Linotype'; font-size:10pt; margin-top:0.0417in; margin-bottom:0.0417in; text-align:justify ! important; }
- *.Table { font-family:'Palatino Linotype'; font-size:10pt; margin-top:0.0417in; margin-bottom:0.0417in; text-align:justify ! important; }
- *.Textbody { font-family:'Palatino Linotype'; font-size:10pt; margin-top:0in; margin-bottom:0.0835in; }
- *.Textbodyindent { font-family:Arial; font-size:10pt; margin-left:0.5in; margin-right:0in; text-align:justify ! important; text-indent:0inch; color:#ff0000; }
- *.Textedebulles { font-family:Tahoma; font-size:8pt; }
- *.WW-Default { font-family:Arial; font-size:12pt; color:#000000; }
- *.black101 { color:#000000; font-family:Arial; font-size:10pt; font-weight:normal; }
- *.black81 { color:#000000; font-family:Arial; font-size:8pt; }
- *.bodyCharChar { font-size:11pt; }
- *.BodyTextIndentChar { }
- *.bodytextnormal { }
- *.EndnoteSymbol { }
- *.FootnoteSymbol { vertical-align:sup; }
- *.Internetlink { color:#000066; background-color:#e9effa; }
- *.Marquedecommentaire { font-size:9pt; }
- *.PageNumber { font-family:Arial; font-size:10pt; text-decoration:underline; }
- *.Policepardéfaut { }
- *.QuickFormat4 { font-size:10pt; }
- *.sa { }
- *.sb { }
- *.sd { }
- *.smalltext { }
- *.st { }
- *.StrongEmphasis { font-weight:bold; }
- *.StyleLatinArialComplexArial { font-family:Arial; font-size:11pt; }
- *.StylebodyLatinArialComplexArialComplexBoldChar { font-family:Arial; font-size:11pt; }
- *.StylebodyLatinArialComplexArialChar { font-family:Arial; font-size:11pt; }
- *.StylebodyIndentLatinArialComplexArialChar { font-family:Arial; font-size:11pt; }
- *.T1 { font-family:'Times New Roman'; font-size:12pt; }
- *.T2 { font-family:'Times New Roman'; font-size:12pt; background-color:transparent; }
- *.T3 { font-family:'Times New Roman'; font-size:12pt; background-color:transparent; }
- *.T4 { color:#000000; font-family:'Times New Roman'; font-size:12pt; }
- *.T5 { color:#000000; font-family:'Times New Roman'; font-size:12pt; background-color:#ffff00; }
- *.T6 { color:#000000; font-family:'Times New Roman'; font-size:12pt; }
- *.T7 { }
- *.T8 { color:#000080; font-family:'Times New Roman'; font-size:12pt; background-color:transparent; }
- *.VisitedInternetLink { color:#800080; text-decoration:underline; }
- *.WW8Num10z0 { font-family:Symbol; }
- *.WW8Num14z0 { font-family:'Times New Roman'; font-size:9pt; font-style:normal; font-weight:normal; }
- *.WW8Num15z0 { font-family:Symbol; }
- *.WW8Num5z0 { font-family:Symbol; }
- *.WW8Num6z0 { font-family:Symbol; }
- *.WW8Num7z0 { font-family:Symbol; }
- *.WW8Num8z0 { font-family:Symbol; }
- *.xcitationtitle { }
- *.xpapertitle1 { color:#000000; font-family:Verdana; font-size:12pt; }
- </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...
[truncated message content] |
|
From: <nl...@us...> - 2007-09-13 23:39:34
|
Revision: 886
http://obo.svn.sourceforge.net/obo/?rev=886&view=rev
Author: nlw
Date: 2007-09-13 16:39:28 -0700 (Thu, 13 Sep 2007)
Log Message:
-----------
release notes in new fancy format, update to download page
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/download.shtml
phenote/trunk/doc/phenote-website/new/download.shtml~
Added Paths:
-----------
phenote/trunk/doc/phenote-website/new/release-notes.shtml
Modified: phenote/trunk/doc/phenote-website/new/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-13 23:16:20 UTC (rev 885)
+++ phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-13 23:39:28 UTC (rev 886)
@@ -82,6 +82,7 @@
</ul>
</div>
</div>
+ </div>
<!--#include virtual="ssi/footer.html" -->
Modified: phenote/trunk/doc/phenote-website/new/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-13 23:16:20 UTC (rev 885)
+++ phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-13 23:39:28 UTC (rev 886)
@@ -47,6 +47,42 @@
</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">
+<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>
+ </div>
+ </div>
+
<!--#include virtual="ssi/footer.html" -->
</body>
Added: phenote/trunk/doc/phenote-website/new/release-notes.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/release-notes.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/new/release-notes.shtml 2007-09-13 23:39:28 UTC (rev 886)
@@ -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">
+ <div id="main_content">
+ <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</h2>
+
+
+
+<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>
+
+
+
+<h1>0.8</h1>
+
+
+<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></h2>
+<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>
+
+
+
+
+<h1>0.7</h1>
+
+
+
+<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></h2>
+
+<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>
+
+
+
+<h1>0.6</h1>
+
+
+
+<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></h2>
+<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>
+
+<h1>0.5</h1>
+
+<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></h2>
+<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>
+
+
+<h1>0.4</h1>
+<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></h2>
+
+<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>
+
+
+<h1>0.3</h1>
+
+
+
+<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></h2>
+
+<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
+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>
+
+
+
+
+<h1>0.2</h1>
+
+<h2>03.27.2006, version <a href="phenote/0.2/phenote-webstart.jnlp">0.2</a></h2>
+<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>
+
+<h1>0.1</h1>
+
+<h2>03.01.2006, version <a href="phenote/0.1/phenote-webstart.jnlp">0.1</a></h2>
+<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>
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
+
+</body>
+</html>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-13 23:16:20
|
Revision: 885
http://obo.svn.sourceforge.net/obo/?rev=885&view=rev
Author: nlw
Date: 2007-09-13 16:16:20 -0700 (Thu, 13 Sep 2007)
Log Message:
-----------
edits to various pages
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/download.shtml
phenote/trunk/doc/phenote-website/new/download.shtml~
Added Paths:
-----------
phenote/trunk/doc/phenote-website/new/contact.shtml
phenote/trunk/doc/phenote-website/new/features.shtml
phenote/trunk/doc/phenote-website/new/team.shtml
Added: phenote/trunk/doc/phenote-website/new/contact.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/contact.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/new/contact.shtml 2007-09-13 23:16:20 UTC (rev 885)
@@ -0,0 +1,43 @@
+<!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>
+
+ <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>
+
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
+
+ </body>
+</html>
Modified: phenote/trunk/doc/phenote-website/new/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-13 00:58:56 UTC (rev 884)
+++ phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-13 23:16:20 UTC (rev 885)
@@ -15,12 +15,13 @@
<div class="catch_phrase">
</div>
<h3>Launch Phenote in your browser</h3>
- <p> You can run phenote directly from your web browser without a separate installation.</p>
+ <p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
<ul><li>Beta release: <a href="http://www.phenote.org/1.4-beta3/phenote.jnlp">1.4 beta3</a></li>
<li>Stable release: <a href="http://www.phenote.org/1.3/phenote.jnlp">1.3</a> </li>
<li><a href="http://www.phenote.org/old.shtml">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>
<h3>Run Phenote at the command line</h3>
<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>
@@ -32,7 +33,7 @@
<h3>Hardware requirements</h3>
<ul>
<li> 400 Mhz processor or faster.</li>
- <li> 500 MB RAM </li>
+ <li> 500+ MB RAM </li>
<li> ? 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>
@@ -46,6 +47,42 @@
</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">
+<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>
+ </div>
+ </div>
+
<!--#include virtual="ssi/footer.html" -->
</body>
Modified: phenote/trunk/doc/phenote-website/new/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-13 00:58:56 UTC (rev 884)
+++ phenote/trunk/doc/phenote-website/new/download.shtml~ 2007-09-13 23:16:20 UTC (rev 885)
@@ -3,7 +3,7 @@
<head>
<!--#include virtual="ssi/head.html" -->
- <title>Open Biomedical Ontologies Foundry</title>
+ <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
</head>
<body>
@@ -13,17 +13,36 @@
<div id="main_container_aux">
<div id="main_content_aux">
<div class="catch_phrase">
- Title
</div>
-
- <h3>
- <a href=".shtml">
- Header
- </a>
- </h3>
- <p>
- Body
+ <h3>Launch Phenote in your browser</h3>
+ <p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
+ <ul><li>Beta release: <a href="http://www.phenote.org/1.4-beta3/phenote.jnlp">1.4 beta3</a></li>
+ <li>Stable release: <a href="http://www.phenote.org/1.3/phenote.jnlp">1.3</a> </li>
+ <li><a href="http://www.phenote.org/old.shtml">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>
+ <h3>Run Phenote at the command line</h3>
+ <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>
+ <h3>Hardware requirements</h3>
+ <ul>
+ <li> 400 Mhz processor or faster.</li>
+ <li> 500+ MB RAM </li>
+ <li> ? 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>
+ <h3>Software requirements</h3>
+ <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>
Added: phenote/trunk/doc/phenote-website/new/features.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/features.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/new/features.shtml 2007-09-13 23:16:20 UTC (rev 885)
@@ -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: 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">
+ Phenote Features
+ </div>
+ <ul>
+ <li>Friendly spreadsheet-like interface
+ </li>
+ <li>Type-ahead-suggest (autocompletion) for terms within ontologies
+ </li>
+ <li>Use of any OBO-format ontology
+ </li>
+ <li>Ontology navigation and term information display
+ </li>
+ <li>Bulk copy/edit/delete/sort of phenotype-genotype character entries
+ </li>
+ <li>Excel-compatible output format (tab-delimited)
+ </li>
+ <li>Additional export formats: phenosyntax, xml
+ </li>
+ <li>configurable input fields to allow custom data entry and user-specified ontologies
+ </li>
+ <li>Preconfigurations available for different communities
+ </li>
+ <li>Customized configurations easily added
+ </li>
+ </ul>
+ </div>
+ </div>
+
+ <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://www.phenote.org/phenote.jnlp"
+ title="Lauch Phenote via Webstart">
+ Launch Phenote v1.4-beta3 via Webstart
+ </a>
+ </p>
+ <p class="quick_link">
+ <img src="images/star.gif" alt="" class="icon_green"/>
+ <a href="http://obo.svn.sourceforge.net/viewvc/obo/phenote/" title="Browse Repository"> Browse Repository
+ </a>
+ </p>
+
+ </div>
+
+
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
+
+ </body>
+</html>
Added: phenote/trunk/doc/phenote-website/new/team.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/team.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/new/team.shtml 2007-09-13 23:16:20 UTC (rev 885)
@@ -0,0 +1,79 @@
+<!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">
+ Project Team
+ </div>
+ <h2 class="bio"><a name="exec" id="exec"></a>
+ Development</h2>
+ <div class="third_bio">
+ <p><img src="http://www.bioontology.org/images/team/gibson.jpg" title="Mark Gibson" alt="Mark Gibson" height="130"/></p>
+ <p><a href="http://www.berkeleybop.org/mgibson/" title="Mark Gibson">Mark Gibson</a>, MSE</p>
+ </div>
+ <div class="third_bio">
+ <p><img src="http://www.bioontology.org/images/team/washington.jpg" title="Nicole Washington" alt="Nicole Washington" height="130" /> </p>
+ <p><a href="http://berkeleybop.org/content/people/nlwashington/" title="Nicole Washington">Nicole Washington</a></a>, PhD </p>
+ <var>Software Developer</var>
+ </div>
+ <div class="third_bio">
+ <p><img src="http://www.bioontology.org/images/team/mungall.jpg" title="Chris Mungall" alt="Chris Mungall" height="130" /></p>
+ <p><a href="http://www.fruitfly.org/%7Ecjm/" title="Chris Mungall">Chris Mungall</a>, BSc</p>
+ <var>Bioinformatics Specialist, BDGP</var>
+ </div>
+ <div class="clearall"></div>
+
+ <div class="third_bio">
+ <p><img src="images/team/lewis.jpg" title="Suzanna Lewis" alt="Suzanna Lewis" height="130" /> </p>
+ <p><a href="http://www.berkeleybop.org/content/people/suzi/" title="Suzanna Lewis">Suzanna Lewis</a>, MS</p>
+ <var>Co-principal Investigator</var> </div>
+
+ <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://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>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-13 00:58:53
|
Revision: 884
http://obo.svn.sourceforge.net/obo/?rev=884&view=rev
Author: nlw
Date: 2007-09-12 17:58:56 -0700 (Wed, 12 Sep 2007)
Log Message:
-----------
added download page
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/download.shtml
phenote/trunk/doc/phenote-website/new/faq.shtml
phenote/trunk/doc/phenote-website/new/ssi/header.html
Modified: phenote/trunk/doc/phenote-website/new/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-13 00:12:46 UTC (rev 883)
+++ phenote/trunk/doc/phenote-website/new/download.shtml 2007-09-13 00:58:56 UTC (rev 884)
@@ -3,7 +3,7 @@
<head>
<!--#include virtual="ssi/head.html" -->
- <title>Phenote</title>
+ <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
</head>
<body>
@@ -13,22 +13,35 @@
<div id="main_container_aux">
<div id="main_content_aux">
<div class="catch_phrase">
- Download Software
</div>
-
- <h3>
- <a href="ssi/header.shtml">
- Header
- </a>
- </h3>
- <p>Use phenote with webstart</p>
- <h4>Hardware requirements
- </h4>
- <h4>Software requirements
- </h4>
- <p>
- Body
+ <h3>Launch Phenote in your browser</h3>
+ <p> You can run phenote directly from your web browser without a separate installation.</p>
+ <ul><li>Beta release: <a href="http://www.phenote.org/1.4-beta3/phenote.jnlp">1.4 beta3</a></li>
+ <li>Stable release: <a href="http://www.phenote.org/1.3/phenote.jnlp">1.3</a> </li>
+ <li><a href="http://www.phenote.org/old.shtml">Older releases</a></li>
+ </ul>
+
+ <h3>Run Phenote at the command line</h3>
+ <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>
+ <h3>Hardware requirements</h3>
+ <ul>
+ <li> 400 Mhz processor or faster.</li>
+ <li> 500 MB RAM </li>
+ <li> ? 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>
+ <h3>Software requirements</h3>
+ <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>
Modified: phenote/trunk/doc/phenote-website/new/faq.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/faq.shtml 2007-09-13 00:12:46 UTC (rev 883)
+++ phenote/trunk/doc/phenote-website/new/faq.shtml 2007-09-13 00:58:56 UTC (rev 884)
@@ -3,7 +3,7 @@
<head>
<!--#include virtual="ssi/head.html" -->
- <title>Open Biomedical Ontologies Foundry</title>
+ <title>Phenote: A Phenotype Annotation Tool</title>
</head>
<body>
@@ -16,7 +16,7 @@
Frequently Asked Questions (FAQ)
</div>
- <h2>General</h2>
+ <h1>General</h1>
<h3>How do I get started?</h3>
<p>
You can lauch Phenote directly from your browser. Simply click on the Phenote link from the main page or the Downloads 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.
@@ -33,7 +33,7 @@
<p>
You can request new features through our <a href="http://www.sourceforge.net/tracker/?group_id=76834&atid=887913">Feature Request tracker</a>. Please be sure to label the "Group" as a "new feature".
</p>
- <h2>Ontologies</h2>
+ <h1>Ontologies</h1>
<h3>What kinds of ontologies can I use?</h3>
<p>
You can use any kind of domain specific ontologies. While Phenote is a tool being developed for annotation of biological phenotypes, it can certainly be adapted to any domain whose knowledge is captured with ontologies.
@@ -65,7 +65,7 @@
<li><a href="http://www.obofoundry.org/">OBO Foundry</a></li>
</ul>
</p>
- <h2>Using Phenote</h2>
+ <h1>Using Phenote</h1>
<h3>Is there some online documentation?</h3>
<p>
You bet! Check out our <a href="http://www.phenote.org/help/">User's Guide</a></p>
Modified: phenote/trunk/doc/phenote-website/new/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/new/ssi/header.html 2007-09-13 00:12:46 UTC (rev 883)
+++ phenote/trunk/doc/phenote-website/new/ssi/header.html 2007-09-13 00:58:56 UTC (rev 884)
@@ -56,7 +56,7 @@
title="Phenote Release Notes">Release Notes</a>
</li>
<li>
- <a href="http://www.phenote.org/"
+ <a href="https://obo.svn.sourceforge.net/viewvc/obo/phenote/"
title="Browse the Subversion Repository">Repository</a>
</li>
<li>
@@ -96,12 +96,8 @@
title="User Guide">User Guide</a>
</li>
<li>
- <a href="http://www.phenote.org/literature.shtml"
- title="OBO Foundry references">Literature</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>
+ title="Report a bug/Request a feature">Bug Reports / Feature Requests</a>
</li>
</ul>
</li>
@@ -123,9 +119,8 @@
title="Phenote Mailing Lists">Mailing Lists</a>
</li>
<li>
- <script type="text/javascript">
- obfuscate("lists.sourceforge.net","obo-phenote","Contact");
- </script>
+ <a href="http://www.phenote.org/contact.shtml"
+ title="Contact us">Contact us</a>
</li>
</ul>
</li>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-13 00:12:44
|
Revision: 883
http://obo.svn.sourceforge.net/obo/?rev=883&view=rev
Author: nlw
Date: 2007-09-12 17:12:46 -0700 (Wed, 12 Sep 2007)
Log Message:
-----------
a bunch of faq's
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/faq.shtml
Modified: phenote/trunk/doc/phenote-website/new/faq.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/faq.shtml 2007-09-12 23:05:35 UTC (rev 882)
+++ phenote/trunk/doc/phenote-website/new/faq.shtml 2007-09-13 00:12:46 UTC (rev 883)
@@ -16,27 +16,68 @@
Frequently Asked Questions (FAQ)
</div>
- <h3>How do I join?</h3>
+ <h2>General</h2>
+ <h3>How do I get started?</h3>
<p>
- Joining is easy! Just follow the steps on our
- <a href="join.shtml"><b>join</b></a> page. We look forward to hearing
- from you.
+ You can lauch Phenote directly from your browser. Simply click on the Phenote link from the main page or the Downloads 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>How should we resolve conflicts when ontologies overlap?</h3>
+ <h3>What's the best forum to ask my burning questions?</h3>
<p>
- Make every attempt to resolve inconsistencies and merge the
- ontologies. Tools are available for aiding this process
- (such as <a href="http://www.berkeleybop.org/obol/">OBOL</a>
- and <a
- href="http://protege.cim3.net/cgi-bin/wiki.pl?Prompt">Prompt</a>)
- and the community can be used to help clarify best
- practices.
-
- Also, face-to-face meetings can helpful to resolve details
- that cannot be covered through email.
+ There's several discussion groups that are relevant to Phenote users. You'll find a list on our <a href="http://www.phenote.org/contact.shmtl">Contact</a> page.
</p>
-
+ <h3>I found a bug in Phenote. How do I report errors?</h3>
+ <p>
+ We want to know if there's any errors. Please use our <a href="http://www.sourceforge.net/tracker/?group_id=76834&atid=887913">Bug Report tracker</a>.
+ </p>
+ <h3>There's a function/feature I wish Phenote had. Can you add it?</h3>
+ <p>
+ You can request new features through our <a href="http://www.sourceforge.net/tracker/?group_id=76834&atid=887913">Feature Request tracker</a>. Please be sure to label the "Group" as a "new feature".
+ </p>
+ <h2>Ontologies</h2>
+ <h3>What kinds of ontologies can I use?</h3>
+ <p>
+ You can use any kind of domain specific ontologies. While Phenote is a tool being developed for annotation of biological phenotypes, it can certainly be adapted to any domain whose knowledge is captured with ontologies.
+ </p>
+ <h3>Can I use OBO and/or OWL format ontologies?</h3>
+ <p>
+ Yes! However, there's a little catch. You will need to convert your OWL ontology to OBO format first.
+ </p>
+ <h3>How can I convert my OWL ontology to OBO format?</h3>
+ <p>
+ There's an online tool to help with this conversion: <a href="http://www.berkeleybop.org/obo-conv.cgi">OWL-OBO converter</a>
+ </p>
+ <h3>Can I use my own ontologies?</h3>
+ <p>
+ Yes you can! You don't have to use ontologies that are in public repositories if you don't want to. Please consult the User Guide for more detailed instructions...
+ </p>
+ <h3>Can I use my own pre-coordinated phenotype ontology?</h3>
+ <p>
+ Yes! Phenote is a generic tool that allows you to use any kind of ontology. Its simplicity allows the user to mix and match different kinds of annotations from different kinds of ontologies. So, you might use your pre-coordinated phenotype ontology for one kind of statement, and then combine a different entity+quality ontology for another statement.
+ </p>
+ <h3>What's the difference between using a pre-coordinated phenotype ontology, and E+Q statements?</h3>
+ <p>
+ </p>
+ <h3>Is there one place I can go to browse through all the available ontologies?</h3>
+ <p>
+ Yep! There are several online resources that can help you learn more. Some of these include:
+ <ul>
+ <li><a href="http://www.bioontology.org/">National Center for Biomedical Ontology</a></li>
+ <li><a href="http://www.obofoundry.org/">OBO Foundry</a></li>
+ </ul>
+ </p>
+ <h2>Using Phenote</h2>
+ <h3>Is there some online documentation?</h3>
+ <p>
+ You bet! Check out our <a href="http://www.phenote.org/help/">User's Guide</a></p>
+ <h3>When I'm annotating, I can't seem to find the right terms?</h3>
+ <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.
+ If you still can't find it, it might be that the ontology is really missing a term. Ontologies 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>
+ <h3>Can I output my data in RDF-OWL?</h3>
+ <p>
+ Not yet, but that feature is coming soon.
+ </p>
</div>
</div>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-12 23:05:35
|
Revision: 882
http://obo.svn.sourceforge.net/obo/?rev=882&view=rev
Author: nlw
Date: 2007-09-12 16:05:35 -0700 (Wed, 12 Sep 2007)
Log Message:
-----------
fixing up phenote front page
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/new/index.shtml
phenote/trunk/doc/phenote-website/new/ssi/header.html
Modified: phenote/trunk/doc/phenote-website/new/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/index.shtml 2007-09-12 22:43:51 UTC (rev 881)
+++ phenote/trunk/doc/phenote-website/new/index.shtml 2007-09-12 23:05:35 UTC (rev 882)
@@ -38,22 +38,17 @@
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="faq.shtml" title="Frequently asked questions">
- Frequently asked questions (FAQ)
- </a>
- </p>
-
- <p class="quick_link">
- <img src="images/star.gif" alt="" class="icon_green"/>
<a href="http://www.phenote.org/phenote.jnlp"
title="Lauch Phenote via Webstart">
- Launch phenote
+ Launch Phenote via Webstart
</a>
</p>
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="join.shtml" title="Join us">Join the OBO Foundry</a>
+ <a href="faq.shtml" title="Frequently asked questions">
+ Frequently asked questions (FAQ)
+ </a>
</p>
</div>
@@ -68,19 +63,28 @@
<div class="content_box_green">
<!-- Comment this out instead of erasing it. -->
- There are no upcoming events at this time.
+ <!--There are no upcoming events at this time.-->
<!-- Do not destry the following event template -->
- <!--
+<!-- <ul class="events">
+ <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
+ </p>
+ </li>
+ </ul>
+ -->
<h3>Event Title</h3>
<ul class="events">
<li class="events">
-
- Event Information
-
+ <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
+ </p>
</li>
</ul>
- -->
+
</div>
@@ -93,9 +97,10 @@
<div class="content_box_green">
<!-- Comment this out instead of erasing it. -->
- No news is good news!
+ <!--No news is good news!-->
<!-- Do not destry the following event template -->
+ New Phenote Beta available: 1.4-beta3!
<!--
<h3>Event Title</h3>
<ul class="events">
Modified: phenote/trunk/doc/phenote-website/new/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/new/ssi/header.html 2007-09-12 22:43:51 UTC (rev 881)
+++ phenote/trunk/doc/phenote-website/new/ssi/header.html 2007-09-12 23:05:35 UTC (rev 882)
@@ -21,12 +21,12 @@
title="About Phenote">About</a>
<ul>
<li>
- <a href="http://www.obofoundry.org/related.shtml"
- title="Projects related to Phenote">Related Projects</a>
+ <a href="http://www.phenote.org/features.shtml"
+ title="Phenote Features">Features</a>
</li>
<li>
<a href="http://www.phenote.org/faq.shtml"
- title="Frequently asked questions">FAQs</a>
+ title="Phenote Screenshot">Screenshots</a>
</li>
<li>
<a href="http://www.phenote.org/funding.shtml"
@@ -36,6 +36,10 @@
<a href="http://www.phenote.org/team.shtml"
title="Phenote Project Team">Team</a>
</li>
+ <li>
+ <a href="http://www.obofoundry.org/related.shtml"
+ title="Projects related to Phenote">Related Projects</a>
+ </li>
</ul>
</li>
@@ -55,11 +59,15 @@
<a href="http://www.phenote.org/"
title="Browse the Subversion Repository">Repository</a>
</li>
+ <li>
+ <a href="http://www.phenote.org/roadmap.shtml"
+ title="Phenote Software Roadmap">Roadmap</a>
+ </li>
</ul>
</li>
<li>
<a href="http://www.phenote.org/resources.shtml"
- title="Ontology Resources">Ontologies</a>
+ title="Ontology Resources">Ontology Resources</a>
<ul>
<li>
<a href="http://www.bioontology.org/tools/portal/bioportal.html"
@@ -80,6 +88,10 @@
title="Phenote Help">Help</a>
<ul>
<li>
+ <a href="http://www.phenote.org/faq.shtml"
+ title="Frequently asked questions">FAQs</a>
+ </li>
+ <li>
<a href="http://www.phenote.org/help/"
title="User Guide">User Guide</a>
</li>
@@ -89,7 +101,7 @@
</li>
<li>
<a href="http://sourceforge.net/tracker/?group_id=76834&atid=887913"
- title="Report a bug/Request a feature">Bug Reports</a>
+ title="Report a bug/Request a feature">Bug Reports/Feature Requests</a>
</li>
</ul>
</li>
@@ -104,13 +116,9 @@
</li>
<li>
<a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page"
- title="Join the Phenote Working Group">Join</a>
+ title="Join the Phenote Working Group">Working Group</a>
</li>
<li>
- <a href="http://www.phenote.org/irc_chat/"
- title="Phenote Discussion Forum">Discuss</a>
- </li>
- <li>
<a href="http://www.phenote.org/content/about/#lists"
title="Phenote Mailing Lists">Mailing Lists</a>
</li>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-12 22:43:48
|
Revision: 881
http://obo.svn.sourceforge.net/obo/?rev=881&view=rev
Author: nlw
Date: 2007-09-12 15:43:51 -0700 (Wed, 12 Sep 2007)
Log Message:
-----------
website:trying out new index page
Added Paths:
-----------
phenote/trunk/doc/phenote-website/new/index.shtml
Added: phenote/trunk/doc/phenote-website/new/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/index.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/new/index.shtml 2007-09-12 22:43:51 UTC (rev 881)
@@ -0,0 +1,119 @@
+<!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">
+ Welcome to Phenote
+ </div>
+
+ <p>
+ </p>
+ <p>
+ </p>
+ <p>
+ </p>
+
+ </div>
+ </div>
+
+ <div id="sidebar_container">
+
+ <div id="sidebar_content">
+
+ <div class="content_box_head_blue">
+ Frequently Used Links
+ </div>
+
+ <div class="content_box_blue">
+
+ <p class="quick_link">
+ <img src="images/star.gif" alt="" class="icon_green"/>
+ <a href="faq.shtml" title="Frequently asked questions">
+ Frequently asked questions (FAQ)
+ </a>
+ </p>
+
+ <p class="quick_link">
+ <img src="images/star.gif" alt="" class="icon_green"/>
+ <a href="http://www.phenote.org/phenote.jnlp"
+ title="Lauch Phenote via Webstart">
+ Launch phenote
+ </a>
+ </p>
+
+ <p class="quick_link">
+ <img src="images/star.gif" alt="" class="icon_green"/>
+ <a href="join.shtml" title="Join us">Join the OBO Foundry</a>
+ </p>
+
+ </div>
+
+ <div class="content_box_head_green">
+ <img src="images/calendar.gif"
+ alt="Upcoming Events"
+ class="icon_blue"/>
+ Upcoming Events
+ </div>
+
+ <div class="content_box_green">
+
+ <!-- Comment this out instead of erasing it. -->
+ There are no upcoming events at this time.
+
+ <!-- Do not destry the following event template -->
+ <!--
+ <h3>Event Title</h3>
+ <ul class="events">
+ <li class="events">
+
+ Event Information
+
+ </li>
+ </ul>
+ -->
+
+ </div>
+
+
+ <div class="content_box_head_green">
+ <img src="images/document.gif" alt="News" class="icon_blue" />
+ News
+ </div>
+
+ <div class="content_box_green">
+
+ <!-- Comment this out instead of erasing it. -->
+ No news is good news!
+
+ <!-- Do not destry the following event template -->
+ <!--
+ <h3>Event Title</h3>
+ <ul class="events">
+ <li class="events">
+
+ Event Information
+
+ </li>
+ </ul>
+ -->
+
+ </div>
+
+
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
+
+ </body>
+</html>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-09-12 22:38:51
|
Revision: 880
http://obo.svn.sourceforge.net/obo/?rev=880&view=rev
Author: nlw
Date: 2007-09-12 15:38:54 -0700 (Wed, 12 Sep 2007)
Log Message:
-----------
adding new website based on obofoundry/ncbo skins
Added Paths:
-----------
phenote/trunk/doc/phenote-website/new/LiteTemplate
phenote/trunk/doc/phenote-website/new/about.shtml
phenote/trunk/doc/phenote-website/new/browse.shtml
phenote/trunk/doc/phenote-website/new/browse.shtml.~1.3.~
phenote/trunk/doc/phenote-website/new/coordination.shtml
phenote/trunk/doc/phenote-website/new/crit.shtml
phenote/trunk/doc/phenote-website/new/crit.shtml.~1.1.~
phenote/trunk/doc/phenote-website/new/css/
phenote/trunk/doc/phenote-website/new/css/detail.css
phenote/trunk/doc/phenote-website/new/css/enhancer.css
phenote/trunk/doc/phenote-website/new/css/list.css
phenote/trunk/doc/phenote-website/new/css/main.css
phenote/trunk/doc/phenote-website/new/css/menu.css
phenote/trunk/doc/phenote-website/new/css/table.css
phenote/trunk/doc/phenote-website/new/download.shtml
phenote/trunk/doc/phenote-website/new/download.shtml~
phenote/trunk/doc/phenote-website/new/faq.shtml
phenote/trunk/doc/phenote-website/new/images/
phenote/trunk/doc/phenote-website/new/images/about_section.jpg
phenote/trunk/doc/phenote-website/new/images/arrow.gif
phenote/trunk/doc/phenote-website/new/images/arrow1_se.gif
phenote/trunk/doc/phenote-website/new/images/back.gif
phenote/trunk/doc/phenote-website/new/images/calendar.gif
phenote/trunk/doc/phenote-website/new/images/document.gif
phenote/trunk/doc/phenote-website/new/images/down.gif
phenote/trunk/doc/phenote-website/new/images/email.gif
phenote/trunk/doc/phenote-website/new/images/favicon.ico
phenote/trunk/doc/phenote-website/new/images/favicon.xcf
phenote/trunk/doc/phenote-website/new/images/minus.gif
phenote/trunk/doc/phenote-website/new/images/nav_bg.gif
phenote/trunk/doc/phenote-website/new/images/nihlogo.gif
phenote/trunk/doc/phenote-website/new/images/obo.gif
phenote/trunk/doc/phenote-website/new/images/obofoundry_logo.gif
phenote/trunk/doc/phenote-website/new/images/obofoundry_logo.xcf
phenote/trunk/doc/phenote-website/new/images/plus.gif
phenote/trunk/doc/phenote-website/new/images/spacer.gif
phenote/trunk/doc/phenote-website/new/images/star.gif
phenote/trunk/doc/phenote-website/new/images/tools.gif
phenote/trunk/doc/phenote-website/new/images/x.gif
phenote/trunk/doc/phenote-website/new/index.cgi
phenote/trunk/doc/phenote-website/new/index.shtml.hiding
phenote/trunk/doc/phenote-website/new/index.shtml.~1.4.~
phenote/trunk/doc/phenote-website/new/javascript/
phenote/trunk/doc/phenote-website/new/join.shtml
phenote/trunk/doc/phenote-website/new/js/
phenote/trunk/doc/phenote-website/new/js/enhancer.js
phenote/trunk/doc/phenote-website/new/js/menu.js
phenote/trunk/doc/phenote-website/new/js/obfuscate.js
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
phenote/trunk/doc/phenote-website/new/old-relationship/
phenote/trunk/doc/phenote-website/new/old-relationship/Makefile
phenote/trunk/doc/phenote-website/new/old-relationship/relationship.xsl
phenote/trunk/doc/phenote-website/new/ontologies.shtml
phenote/trunk/doc/phenote-website/new/ontologies.txt
phenote/trunk/doc/phenote-website/new/participate.shtml
phenote/trunk/doc/phenote-website/new/related.shtml
phenote/trunk/doc/phenote-website/new/relatedprojects.shtml
phenote/trunk/doc/phenote-website/new/relationship/
phenote/trunk/doc/phenote-website/new/resources.shtml
phenote/trunk/doc/phenote-website/new/ro/
phenote/trunk/doc/phenote-website/new/ro/index.html
phenote/trunk/doc/phenote-website/new/ro/ro.html
phenote/trunk/doc/phenote-website/new/ro/ro.obo
phenote/trunk/doc/phenote-website/new/ro/ro.obo-xml
phenote/trunk/doc/phenote-website/new/ro/ro.owl
phenote/trunk/doc/phenote-website/new/ro/ro.pellet
phenote/trunk/doc/phenote-website/new/ro/ro.pro
phenote/trunk/doc/phenote-website/new/ro/ro_bfo_bridge.obo
phenote/trunk/doc/phenote-website/new/ro/ro_bfo_bridge.obo-xml
phenote/trunk/doc/phenote-website/new/ro/ro_bfo_bridge.owl
phenote/trunk/doc/phenote-website/new/ro/stylesheet-old.css
phenote/trunk/doc/phenote-website/new/ro/stylesheet.css
phenote/trunk/doc/phenote-website/new/ssi/
phenote/trunk/doc/phenote-website/new/ssi/footer.html
phenote/trunk/doc/phenote-website/new/ssi/head.html
phenote/trunk/doc/phenote-website/new/ssi/header.html
phenote/trunk/doc/phenote-website/new/ssi/side.html
phenote/trunk/doc/phenote-website/new/template.shtml
phenote/trunk/doc/phenote-website/new/utils/
phenote/trunk/doc/phenote-website/new/utils/archive-file.pl
phenote/trunk/doc/phenote-website/new/utils/chado_cv_schema.sql
phenote/trunk/doc/phenote-website/new/utils/download.sh
phenote/trunk/doc/phenote-website/new/utils/example-metadata.xml
phenote/trunk/doc/phenote-website/new/utils/js/
phenote/trunk/doc/phenote-website/new/utils/js/sorttable.js
phenote/trunk/doc/phenote-website/new/utils/metadata-to-download-html.xsl
phenote/trunk/doc/phenote-website/new/utils/metadata-to-html.xsl
phenote/trunk/doc/phenote-website/new/utils/metadata-to-rdf.xsl
phenote/trunk/doc/phenote-website/new/utils/obo-downloader.pl
phenote/trunk/doc/phenote-website/new/utils/obo-metadata.xsd
phenote/trunk/doc/phenote-website/new/utils/owl.obo
phenote/trunk/doc/phenote-website/new/utils/rdfs.obo
phenote/trunk/doc/phenote-website/new/utils/stats-to-tbl.pl
phenote/trunk/doc/phenote-website/new/utils/tbl2html
Added: phenote/trunk/doc/phenote-website/new/LiteTemplate
===================================================================
Added: phenote/trunk/doc/phenote-website/new/about.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/about.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/new/about.shtml 2007-09-12 22:38:54 UTC (rev 880)
@@ -0,0 +1,60 @@
+<!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="coordination.shtml">
+ Coordination
+ </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/new/browse.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/browse.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/new/browse.shtml 2007-09-12 22:38:54 UTC (rev 880)
@@ -0,0 +1,397 @@
+<!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" -->
+
+ <div id="main_container_aux">
+ <div id="main_content_aux">
+ <div class="catch_phrase">
+ Ontology Browser
+ </div>
+
+ <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="http://www.obofoundry.org/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="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>
+
+ <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">
+
+ <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>
+
+
+
+
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
+
+ </body>
+</html>
Added: phenote/trunk/doc/phenote-website/new/browse.shtml.~1.3.~
===================================================================
--- phenote/trunk/doc/phenote-website/new/browse.shtml.~1.3.~ (rev 0)
+++ phenote/trunk/doc/phenote-website/new/browse.shtml.~1.3.~ 2007-09-12 22:38:54 UTC (rev 880)
@@ -0,0 +1,347 @@
+<!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>
Added: phenote/trunk/doc/phenote-website/new/coordination.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/coordination.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/new/coordination.shtml 2007-09-12 22:38:54 UTC (rev 880)
@@ -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/new/crit.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/new/crit.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/new/crit.shtml 2007-09-12 22:38:54 UTC (rev 880)
@@ -0,0 +1,162 @@
+<!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">
+ OBO Foundry Principles
+ </div>
+
+ <p>
+ OBO is an open community and, by joining the initiative, the
+ authors of an ontology commit to its maintenance in light of
+ scientific advance and to working with other members to
+ ensure the improvement of these principles over time. The
+ OBO Foundry is an attempt to apply the scientific method to
+ the task of ontology development, and the scientific method
+ rests on constant criticism and on the assumption that no
+ resource will ever exist in a form in which it cannot be
+ further improved.
+ </p>
+ <p>
+ To comment on, or ask questions about, any of these
+ principles please send e-mail to
+ the
+ <a href="mailto:obo...@li...">
+ OBO discussion list
+ </a>.
+ To propose new principles please use the
+ <a href="http://obofoundry.org/wiki/index.php/OBO_Foundry_Principles">
+ OBO wiki
+ </a>.
+ </p>
+
+ <br />
+
+ <h1> Version as of 24 April 2006 </h1>
+
+ <p>
+
+ <ol>
+
+ <li>
+ <h3 class="crit">The ontology must be <em>open</em> and available to be
+ used by all without any constraint other than (a) its
+ origin must be acknowledged and (b) it is not to be
+ altered and subsequently redistributed under the
+ original name or with the same identifiers.</h3>
+
+ <p>
+ The OBO ontologies are for sharing and are resources
+ for the entire community. For this reason, they must
+ be available to all without any constraint or license
+ on their use or redistribution. However, it is proper
+ that their original source is always credited and that
+ after any external alterations, they must never be
+ redistributed under the same name or with the same
+ identifiers.
+ </p>
+ </li>
+
+ <li>
+ <h3 class="crit">The ontology is in, or can be expressed in,
+ a <em>common shared syntax</em>. This may be either the
+ OBO syntax, extensions of this syntax, or OWL. </h3>
+ <p>
+ The reason for this is that the same tools can then be
+ usefully applied. This facilitates shared software
+ implementations. This criterion is not met in all of
+ the ontologies currently listed, but we are working
+ with the ontology developers to have them available in
+ a common OBO syntax.
+ </p>
+ </li>
+
+ <li>
+ <h3 class="crit">The ontologies possesses a <em>unique identifier
+ space</em> within the OBO Foundry.</h3>
+ <p>
+ The source of concepts from any ontology can be
+ immediately identified by the prefix of the identifier
+ of each concept. It is, therefore, important that this
+ prefix be unique.
+ </p>
+ </li>
+
+ <li>
+ <h3 class="crit">The ontology provider has procedures for identifying
+ distinct successive <em>versions</em>.</h3>
+ </li>
+
+ <li>
+ <h3 class="crit">The ontology has a clearly specified and
+ clearly <em>delineated content</em>.</h3>
+ <p>The ontology must be orthogonal to other ontologies
+ already lodged within OBO.
+ </p>
+ <p>
+ The major reason for this principle is to allow two
+ different ontologies, for example anatomy and process,
+ to be combined through additional relationships. These
+ relationships could then be used to constrain when
+ terms could be jointly applied to describe
+ complementary (but distinguishable) perspectives on
+ the same biological or medical entity.
+ </p>
+ <p>
+ As a corollary to this, we would strive for community
+ acceptance of a single ontology for one domain, rather
+ than encouraging rivalry between ontologies.
+ </p>
+ </li>
+
+ <li>
+ <h3 class="crit">The ontologies include textual <em>definitions</em>
+ for all terms. </h3>
+ <p>
+ Many biological and medical terms may be ambiguous, so
+ concepts should be defined so that their precise
+ meaning within the context of a particular ontology is
+ clear to a human reader.
+ </p>
+ </li>
+
+ <li>
+ <h3 class="crit">The ontology uses relations which are unambiguously
+ defined following the pattern of definitions laid down
+ in the <em>OBO Relation Ontology</em>.</h3>
+ </li>
+
+ <li>
+ <h3 class="crit">The ontology is <em>well documented</em>.</h3>
+ </li>
+
+ <li>
+ <h3 class="crit">The ontology has a plurality of
+ independent <em>users</em>.</h3>
+ </li>
+
+ <li>
+ <h3 class="crit">The ontology will be
+ developed <em>collaboratively</em> with other OBO
+ Foundry members.</h3>
+ </li>
+ </ol>
+ </p>
+
+ </div>
+ </div>
+
+ <!--#include virtual="ssi/footer.html" -->
+
+ </body>
+</html>
Added: phenote/trunk/doc/phenote-website/new/crit.shtml.~1.1.~
===================================================================
--- phenote/trunk/doc/phenote-website/new/crit.shtml.~1.1.~ (rev 0)
+++ phenote/trunk/doc/phenote-website/new/crit.shtml.~1.1.~ 2007-09-12 22:38:54 UTC (rev 880)
@@ -0,0 +1,82 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
+ "http://www.w3.org/TR/html4/strict.dtd">
+<html>
+<head>
+ <title> OBO Inclusion Criteria </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="Criteria for membership of Open Biomedical Ontologies">
+ <script src="obfuscate.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" id="crit">
+ <h2>OBO Foundry Principles</h2>
+ <p>
+ For an ontology to be accepted as one of the Open Biomedical Ontologies in the Foundry, the following criteria must be met (further principles will be added over time):
+</p>
+<p>
+Version as of 24 April 2006
+</p>
+<ol>
+ <li>
+ <h4>The ontology must be <b>open</b> and available to be used by all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed under the original name or with the same identifiers.</h4>
+ <p>
+ The OBO ontologies are for sharing and are resources for the entire community. For this reason, they must be available to all without any constraint or license on their use or redistribution. However, it is proper that their original source is always credited and that after any external alterations, they must never be redistributed under the same name or with the same identifiers.
+ </p>
+ </li>
+ <li>
+ <h4>The ontology is in, or can be expressed in, a <b>common shared syntax</b>. This may be either the OBO syntax, extensions of this syntax, or OWL. </h4>
+ <p>
+ The reason for this is that the same tools can then be usefully applied. This facilitates shared software implementations. This criterion is not met in all of the ontologies currently listed, but we are working with the ontology developers to have them available in a common OBO syntax.
+ </p>
+ </li>
+ <li>
+ <h4>The ontologies possesses a <b>unique identifier space</b> within the OBO Foundry.</h4>
+ <p>
+ The source of concepts from any ontology can be immediately identified by the prefix of the identifier of each concept. It is, therefore, important that this prefix be unique.
+ </p>
+ </li>
+ <li>
+ <h4>The ontology provider has procedures for identifying distinct successive <b>versions</b>.</h4>
+ </li>
+ <li>
+ <h4>The ontology has a clearly specified and clearly <b>delineated content</b>.</h4>
+ <p>The ontology must be orthogonal to other ontologies already lodged within OBO. </p>
+ <p>
+ The major reason for this principle is to allow two different ontologies, for example anatomy and process, to be combined through additional relationships. These relationships could then be used to constrain when terms could be jointly applied to describe complementary (but distinguishable) perspectives on the same biological or medical entity. </p>
+ <p>
+ As a corollary to this, we would strive for community acceptance of a single ontology for one domain, rather than encouraging rivalry between ontologies.
+ </p>
+ </li>
+ <li>
+ <h4>The ontologies include textual <b>definitions</b> for all terms. </h4>
+ <p>
+ Many biological and medical terms may be ambiguous, so concepts should be defined so that their precise meaning within the context of a particular ontology is clear to a human reader.
+ </p>
+ </li>
+ <li>
+ <h4>The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the <b>OBO Relation Ontology</b>.</h4>
+ </li>
+ <li>
+ <h4>The ontology is <b>well documented</b>.</h4>
+ </li>
+ <li>
+ <h4>The ontology has a plurality of independent <b>users</b>.</h4>
+ </li>
+ <li>
+ <h4>The ontology will be developed <b>collaboratively</b> with other OBO Foundry members.</h4>
+ </li>
+</ol>
+</div>
+</div>
+</body>
+</html>
Added: phenote/trunk/doc/phenote-website/new/css/detail.css
===================================================================
--- phenote/trunk/doc/phenote-website/new/css/detail.css (rev 0)
+++ phenote/trunk/doc/phenote-website/new/css/detail.css 2007-09-12 22:38:54 UTC (rev 880)
@@ -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/new/css/enhancer.css
===================================================================
--- phenote/trunk/doc/phenote-website/new/css/enhancer.css (rev 0)
+++ phenote/trunk/doc/phenote-website/new/css/enhancer.css 2007-09-12 22:38:54 UTC (rev 880)
@@ -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/new/css/list.css
===================================================================
--- phenote/trunk/doc/phenote-website/new/css/list.css (rev 0)
+++ phenote/trunk/doc/phenote-website/new/css/list.css 2007-09-12 22:38:54 UTC (rev 880)
@@ -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/new/css/main.css
===================================================================
--- phenote/trunk/doc/phenote-website/new/css/main.css (rev 0)
+++ phenote/trunk/doc/phenote-website/new/css/main.css 2007-09-12 22:38:54 UTC (rev 880)
@@ -0,0 +1,625 @@
+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;
+}
+
+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-ali...
[truncated message content] |
|
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.
|
363 messages has been excluded from this view by a project administrator.
![http://www.bioontology.org/images/team/washington.jpg"](http://www.bioontology.org/images/team/washington.jpg"){kind=link}
![http://www.bioontology.org/images/team/mungall.jpg"](http://www.bioontology.org/images/team/mungall.jpg"){kind=link}
![http://www.bioontology.org/images/team/gibson.jpg"](http://www.bioontology.org/images/team/gibson.jpg"){kind=link}
![http://www.bioontology.org/images/team/lewis.jpg"](http://www.bioontology.org/images/team/lewis.jpg"){kind=link}
![http://www.phenote.org/images/elephant_icon3.jpg"](http://www.phenote.org/images/elephant_icon3.jpg"){kind=link}
![http://www.phenote.org/images/elephant_header.jpg"](http://www.phenote.org/images/elephant_header.jpg"){kind=link}
![http://www.phenote.org/images/phenote_screenshot.jpg"](http://www.phenote.org/images/phenote_screenshot.jpg"){kind=link}
![http://www.phenote.org/images/phenote_screenshot.png"](http://www.phenote.org/images/phenote_screenshot.png"){kind=link}