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[Obo-svn-commit] SF.net SVN: obo: [1033] phenote/trunk/doc/phenote-website/phenote-birn.jnlp

From: <mg...@us...> - 2007-10-11 15:07:26

Revision: 1033
          http://obo.svn.sourceforge.net/obo/?rev=1033&view=rev
Author:   mgibson
Date:     2007-10-11 08:07:27 -0700 (Thu, 11 Oct 2007)

Log Message:
-----------
phenote-smart-atlas.cfg moved to phenote-birn.jnlp

Added Paths:
-----------
    phenote/trunk/doc/phenote-website/phenote-birn.jnlp

Added: phenote/trunk/doc/phenote-website/phenote-birn.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-birn.jnlp	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/phenote-birn.jnlp	2007-10-11 15:07:27 UTC (rev 1033)
@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<jnlp
+spec="1.0+"
+codebase="http://phenote.org/phenote/@@phenote.version@@"
+href="phenote.jnlp">
+<information>
+	<title>Phenote @@phenote.version@@</title>
+	<vendor>National Center for Biomedical Ontology</vendor>
+	<icon href="/images/elephant_icon.jpg" />
+	<description>Phenote standalone app via webstart</description>
+ 	 <!-- Declares that the application can run without
+         access to the server it was downloaded from -->
+	<offline-allowed />
+</information>
+<security>
+      <!-- Request that the application be given full
+           access to the local (executing) machine,
+           as if it were a regular Java application.
+           Requires that all JAR files be signed
+           by a trusted party -->
+	<all-permissions />
+</security>
+<resources>
+  	<!-- Specify the versions of the Java Runtime Environment
+         (JRE) that are supported by the application.
+         Multiple entries of this kind are allowed, in which
+         case they are considered to be in order of preference -->
+	<j2se version="1.5+" initial-heap-size="64m" max-heap-size="600m" />
+	<jar href="jars/phenote.jar" />
+	<jar href="jars/oboedit.jar" />
+	<jar href="jars/org.geneontology.jar" />
+	<jar href="jars/BrowserLauncher2-10rc4.jar" />
+	<jar href="jars/jsr173_1.0_api.jar" />
+	<jar href="jars/phenoxmlbeans.jar" />
+	<jar href="jars/phenoteconfigbeans.jar" />
+	<jar href="jars/xbean.jar" />
+	<jar href="jars/tomcat-servlet.jar" />
+	<jar href="jars/te-common.jar" />
+	<jar href="jars/log4j-1.2.13.jar" />
+	<jar href="jars/jh.jar" />
+	<jar href="jars/jetty-6.1.4.jar" />
+	<jar href="jars/jetty-util-6.1.4.jar" />
+	<jar href="jars/swixml.jar" />
+	<jar href="jars/jdom.jar" />
+	<jar href="jars/quaqua.jar" />
+	<jar href="jars/jebl-0.4.jar" />
+	<jar href="jars/swing-layout.jar" />
+	<jar href="jars/glazedlists-1.7.0_java15.jar" />
+	<nativelib href="jars/phenote-nativelibs.jar"/>
+
+</resources>
+<!-- was smart-atlas.cfg, merged into birn.cfg  -->
+<application-desc main-class="phenote.main.Phenote">
+        <argument>-c</argument>
+        <argument>/birn.cfg</argument>
+</application-desc>
+</jnlp>


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[Obo-svn-commit] SF.net SVN: obo: [1032] phenote/trunk/doc/phenote-website

From: <mg...@us...> - 2007-10-11 14:41:20

Revision: 1032
          http://obo.svn.sourceforge.net/obo/?rev=1032&view=rev
Author:   mgibson
Date:     2007-10-11 07:41:21 -0700 (Thu, 11 Oct 2007)

Log Message:
-----------
smart atlas jnlp now points to birn.cfg instead of smart-atlas.cfg as maryann
has requested merging the configs - we'll see how that goes

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
    phenote/trunk/doc/phenote-website/phenote.html

Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp	2007-10-10 23:15:56 UTC (rev 1031)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp	2007-10-11 14:41:21 UTC (rev 1032)
@@ -49,9 +49,9 @@
 	<nativelib href="jars/phenote-nativelibs.jar"/>
 
 </resources>
-<!-- no cmd line param will ask user for config at initialization -->
+<!-- was smart-atlas.cfg, merged into birn.cfg  -->
 <application-desc main-class="phenote.main.Phenote">
-        <argument>-u</argument>
-        <argument>/smart-atlas.cfg</argument>
+        <argument>-c</argument>
+        <argument>/birn.cfg</argument>
 </application-desc>
 </jnlp>

Modified: phenote/trunk/doc/phenote-website/phenote.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.html	2007-10-10 23:15:56 UTC (rev 1031)
+++ phenote/trunk/doc/phenote-website/phenote.html	2007-10-11 14:41:21 UTC (rev 1032)
@@ -51,64 +51,12 @@
 email list</a><br>
 <a href="https://sourceforge.net/tracker/?group_id=76834&amp;atid=887913">Phenote
 bug tracker</a><br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-bug-tracker">Bug
 tracker email list</a><br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <a href="https://sourceforge.net/svn/?group_id=76834">Phenote source
 code (obo sourceforge svn)</a><br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <a href="https://lists.sourceforge.net/lists/listinfo/obo-svn-commit">Phenote
 svn commit email list</a><br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <a href="http://wiki.dictybase.org/dictywiki/index.php/Phenotype_Curation_Tool_Documentation#Usage">Dicty
 webby phenote wiki developer docs</a><br>
 


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[Obo-svn-commit] SF.net SVN: obo: [1031] phenote/trunk/doc/phenote-website

From: <nl...@us...> - 2007-10-10 23:15:52

Revision: 1031
          http://obo.svn.sourceforge.net/obo/?rev=1031&view=rev
Author:   nlw
Date:     2007-10-10 16:15:56 -0700 (Wed, 10 Oct 2007)

Log Message:
-----------
few minor changes to website

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/download.shtml
    phenote/trunk/doc/phenote-website/download.shtml~
    phenote/trunk/doc/phenote-website/events.shtml
    phenote/trunk/doc/phenote-website/events.shtml~
    phenote/trunk/doc/phenote-website/index.shtml
    phenote/trunk/doc/phenote-website/index.shtml~

Modified: phenote/trunk/doc/phenote-website/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml	2007-10-10 23:10:36 UTC (rev 1030)
+++ phenote/trunk/doc/phenote-website/download.shtml	2007-10-10 23:15:56 UTC (rev 1031)
@@ -16,7 +16,8 @@
 	</div>
 	<h2><a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Launch Phenote in your browser</a></h2>
 	<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
-<!--	<ul><li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></strong></li>-->
+	<ul>
+<!--	<li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></strong></li>-->
 	<li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp">1.4</a> </strong></li>
 	<li><a href="http://www.phenote.org/phenote/phenote.html">Older releases</a></li>
 	</ul>

Modified: phenote/trunk/doc/phenote-website/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml~	2007-10-10 23:10:36 UTC (rev 1030)
+++ phenote/trunk/doc/phenote-website/download.shtml~	2007-10-10 23:15:56 UTC (rev 1031)
@@ -16,17 +16,21 @@
 	</div>
 	<h2><a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Launch Phenote in your browser</a></h2>
 	<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
-	<ul><li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></strong></li>
-	<li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.3/phenote.jnlp">1.3</a> </strong></li>
+<!--	<ul><li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></strong></li>-->
+	<li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp">1.4</a> </strong></li>
 	<li><a href="http://www.phenote.org/phenote/phenote.html">Older releases</a></li>
 	</ul>
 	<p> You may be prompted to sign a certificate and allow the download.  This will take a few minutes the first time you do this.
 	</p>
 	<h2>Run Phenote at the command line</h2>
 	<p> To run phenote on the command line, linux or MacOSX users will need to checkout Phenote from the subversion repository.  This can be done with the following command:</p>
-	<ul><li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.4-beta3/ phenote</b> </li>
-	<li>Stable release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.3/ phenote</b>
-	<li>Latest: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote </b></li>
+	<ul>
+<!--	<li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.4-beta3/ phenote</b>
+	</li>-->
+	<li>Stable release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.4/ phenote</b>
+	</li>
+	<li>Latest: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote </b>
+	</li>
 	</ul>	
 	<p>Once you've got it, you can run Phenote with ant with the command:  <b>ant run</b>
 	</p>
@@ -52,32 +56,32 @@
       <div id="sidebar_content">
 
 	<div class="content_box_head_blue">
-	  Recently added features, version 1.4-beta3
+	  Recently added features, version 1.4
 	</div>
 
 	<div class="content_box_blue">
-  <b>feature</b>: Native look-and-feel enabled for interface.  Users should now see Mac or Windows style depending on their system.<br />
-  <b>feature</b>: read-only field (needs work)<br />
-  <b>feature</b>: config disabpng of copy of field (for db ids)<br />
-  <b>feature</b>: display property values of terms in term info<br />
-  <b>feature</b>: Phylogeny Chooser for NESCent/PhenoMap project. A user can import a phylogenetic tree in Newick format.  The user can use the tree
-  viewer to select rows within the character template - typically taxonomic groups.<br />
-  <b>feature</b>: term fields can be nullified<br />
-  <b>feature</b>: separate queries to backend for different groups, implemented in worm<br />
-  <b>feature</b>: ID field type, requires ":"<br />
-  <b>feature</b>: can get unique list of deleted annots<br />
-  <b>feature</b>: added group adapter framework<br />
-  <b>feature</b>: fly genotype group adapter makes fly genotype strings from tab/group<br />
-  <b>feature</b>: worm group adapter makes reference terms from ref query<br />
-  <b>change</b>: on term completion if adding a letter use previous completion list<br />
-  <b>change</b>: worm adapter query tab working properly<br />
-  <b>change</b>: build file takes param for webstart version deployment, and puts in jnlp<br />
-  <b>change</b>: group adapters can psten for CharList changes<br />
-  <b>change</b>: added/corrected BIRN ontologies<br />
-  <b>bugfix</b>: load of file doesnt crash on post comp parsing bug<br />
-  <b>bugfix</b>: doesnt load obo files specified twice twice<br />
-  <b>bugfix</b>: view menu show up at initialization<br />
-  <b>bugfix</b>: layout of term history with split pane proper<br />
+	 <b>feature</b>: Loading splash more informative about what's going on behind-the-scenes such as which ontologies are loading, if they are being updated, etc.<br />
+	<b>feature</b>: obo edit annotation model can now be optionally configured for backend, which will allow for more sophisticated data to be captured (like comparisons)<br />
+	<b>feature</b>: Error for obo parse failures to info panel <br />
+	<b>feature</b>: Delimited tab adapter uses column headings to map to table, rather than ordering <br />
+	<b>feature</b>: Autocompletion optimized with threading, cancels stale requests (min-comp-chars now pase) <br />
+	<b>feature</b>: Date created automatically added into data (under the hood) <br />
+	<b>feature</b>: If arrow hit with empty input then gets &amp; displays all terms (used to inefficiently pre-load) <br />
+	<b>feature</b>: Can sort completion list by ID, needed for zfin stages<br />
+	<b>feature</b>: Table preserves user ordering of columns, in addition to column widths.<br />
+	<b>feature</b>: Filter search field allows user to narrow down displayed data rows via matching text.<br />
+	<b>feature</b>: See actual value in input field when multiple rows are selected and have the same value.<br />
+	<b>feature</b>: Copy all taxon names in specimen list as an unresolved Newick tree (for PhenoMap/NESCent)<br />
+	<b>feature</b>: Automatically open specimen list and phylogenetic tree files when opening data file (for PhenoMap/NESCent)<br />
+	<b>change</b>: Moved test suites in with source to work with eclipse<br />
+	<b>change</b>: Took a lot of obos out of webstart jar - less bulky - as they get automatically downloaded<br />
+	<b>change</b>: Phenote now follows standard log4j configuration conventions.  Pass a custom log configuration to Phenote via the classpath or the system propery "log4j.configuration".<br />
+	<b>bugfix</b>: Terms not found are no longer dropped, a dangler is created, and error msg to info, show up in red<br />
+	<b>bugfix</b>: if log conf fails use backup default<br />
+	<b>bugfix</b>: Input fields now commit changes with either Return or Tab<br />
+	<b>bugfix</b>: Native lib is loaded properly for Mac interface on webstart, allowing traversal of aliases in file dialog, as well as user sidebar items in file dialog<br />
+	<b>bugfix</b>: Noncontiguous row selection works now on Mac<br />
+</ul>
 	</div>
       </div>
     </div>

Modified: phenote/trunk/doc/phenote-website/events.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml	2007-10-10 23:10:36 UTC (rev 1030)
+++ phenote/trunk/doc/phenote-website/events.shtml	2007-10-10 23:15:56 UTC (rev 1031)
@@ -39,8 +39,8 @@
 
 	<h1>Past News and Events, 2007</h1>
 	<h2>October</h2>
-	  <p>Oct 10, New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
-
+	  <li>Oct 10, New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
+	  </li>
 	  <li>Oct 2, Phenote Users Group, Online via WebEx
 	  </li>
 

Modified: phenote/trunk/doc/phenote-website/events.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml~	2007-10-10 23:10:36 UTC (rev 1030)
+++ phenote/trunk/doc/phenote-website/events.shtml~	2007-10-10 23:15:56 UTC (rev 1031)
@@ -39,6 +39,8 @@
 
 	<h1>Past News and Events, 2007</h1>
 	<h2>October</h2>
+	  <p>Oct 10, New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
+
 	  <li>Oct 2, Phenote Users Group, Online via WebEx
 	  </li>
 

Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml	2007-10-10 23:10:36 UTC (rev 1030)
+++ phenote/trunk/doc/phenote-website/index.shtml	2007-10-10 23:15:56 UTC (rev 1031)
@@ -129,12 +129,10 @@
 	  <!--No news is good news!-->
 	  
 	  <!-- Do not destry the following event template -->
-	  <p>10.10.2007 - New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
+	  <p>10.10.2007 - <b>New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a></b>
 	  <p>10.02.2007 - Phenote user's group to be moved to first Thursday of each month, 9am.  Join us for our next meeting on November 1st over WebEx!</p>
 	  <p>09.17.2007 - New website rolled out!  The website has the same
 	    content as the old one, just with a new look-and-feel.</p>
-	    <p> 08.28.2007 - 
-	    <a href="http://www.phenote.org/download.shtml">New Phenote Beta available: 1.4-beta3!</a> </p>
 	  <!--
 	  <h3>Event Title</h3>
 	  <ul class="events">

Modified: phenote/trunk/doc/phenote-website/index.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml~	2007-10-10 23:10:36 UTC (rev 1030)
+++ phenote/trunk/doc/phenote-website/index.shtml~	2007-10-10 23:15:56 UTC (rev 1031)
@@ -60,7 +60,7 @@
 
 	  <p class="quick_link">
 	    <img src="images/star.gif" alt=""  class="icon_green"/>
-	    <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp"
+	    <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp"
 	       title="Lauch Phenote via Webstart">
 		Launch Phenote via Webstart
 	    </a>
@@ -129,6 +129,7 @@
 	  <!--No news is good news!-->
 	  
 	  <!-- Do not destry the following event template -->
+	  <p>10.10.2007 - New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
 	  <p>10.02.2007 - Phenote user's group to be moved to first Thursday of each month, 9am.  Join us for our next meeting on November 1st over WebEx!</p>
 	  <p>09.17.2007 - New website rolled out!  The website has the same
 	    content as the old one, just with a new look-and-feel.</p>


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[Obo-svn-commit] SF.net SVN: obo: [1030] phenote/trunk/doc

From: <nl...@us...> - 2007-10-10 23:10:37

Revision: 1030
          http://obo.svn.sourceforge.net/obo/?rev=1030&view=rev
Author:   nlw
Date:     2007-10-10 16:10:36 -0700 (Wed, 10 Oct 2007)

Log Message:
-----------
updated links on phenote website to the newest release, 1.4.  also
touched up the instructions for making a release

Modified Paths:
--------------
    phenote/trunk/doc/making-a-phenote-release.html
    phenote/trunk/doc/phenote-website/download.shtml
    phenote/trunk/doc/phenote-website/events.shtml
    phenote/trunk/doc/phenote-website/events.shtml~
    phenote/trunk/doc/phenote-website/features.shtml
    phenote/trunk/doc/phenote-website/index.shtml
    phenote/trunk/doc/phenote-website/index.shtml~
    phenote/trunk/doc/phenote-website/phenote-release-notes.shtml

Modified: phenote/trunk/doc/making-a-phenote-release.html
===================================================================
--- phenote/trunk/doc/making-a-phenote-release.html	2007-10-10 23:08:29 UTC (rev 1029)
+++ phenote/trunk/doc/making-a-phenote-release.html	2007-10-10 23:10:36 UTC (rev 1030)
@@ -61,6 +61,9 @@
     <p>update the svn command under 'run phenote at the command   line'</p>
     <p>add the latest and/or sexiest features of the latest release</p>
     </li>
+    <li>features.shtml:
+    <p>update the link under the 'quick link' section</p>
+    </li>
   </ul>
   <li>to update the website:
   <p>then, to make sure all the changes are made to the website, be sure to first commit your changes to svn.  then run 'update_site' script that resides in the phenote/website dir.  this must be done from a berkeleybop machine.</p>

Modified: phenote/trunk/doc/phenote-website/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml	2007-10-10 23:08:29 UTC (rev 1029)
+++ phenote/trunk/doc/phenote-website/download.shtml	2007-10-10 23:10:36 UTC (rev 1030)
@@ -16,8 +16,8 @@
 	</div>
 	<h2><a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Launch Phenote in your browser</a></h2>
 	<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
-	<ul><li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></strong></li>
-	<li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.3/phenote.jnlp">1.3</a> </strong></li>
+<!--	<ul><li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp">1.4 beta3</a></strong></li>-->
+	<li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp">1.4</a> </strong></li>
 	<li><a href="http://www.phenote.org/phenote/phenote.html">Older releases</a></li>
 	</ul>
 	<p> You may be prompted to sign a certificate and allow the download.  This will take a few minutes the first time you do this.
@@ -25,10 +25,10 @@
 	<h2>Run Phenote at the command line</h2>
 	<p> To run phenote on the command line, linux or MacOSX users will need to checkout Phenote from the subversion repository.  This can be done with the following command:</p>
 	<ul>
-	<li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.4-beta3/ phenote</b> 
+<!--	<li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.4-beta3/ phenote</b>
+	</li>-->
+	<li>Stable release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.4/ phenote</b>
 	</li>
-	<li>Stable release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.3/ phenote</b>
-	</li>
 	<li>Latest: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote </b>
 	</li>
 	</ul>	
@@ -56,32 +56,32 @@
       <div id="sidebar_content">
 
 	<div class="content_box_head_blue">
-	  Recently added features, version 1.4-beta3
+	  Recently added features, version 1.4
 	</div>
 
 	<div class="content_box_blue">
-  <b>feature</b>: Native look-and-feel enabled for interface.  Users should now see Mac or Windows style depending on their system.<br />
-  <b>feature</b>: read-only field (needs work)<br />
-  <b>feature</b>: config disabpng of copy of field (for db ids)<br />
-  <b>feature</b>: display property values of terms in term info<br />
-  <b>feature</b>: Phylogeny Chooser for NESCent/PhenoMap project. A user can import a phylogenetic tree in Newick format.  The user can use the tree
-  viewer to select rows within the character template - typically taxonomic groups.<br />
-  <b>feature</b>: term fields can be nullified<br />
-  <b>feature</b>: separate queries to backend for different groups, implemented in worm<br />
-  <b>feature</b>: ID field type, requires ":"<br />
-  <b>feature</b>: can get unique list of deleted annots<br />
-  <b>feature</b>: added group adapter framework<br />
-  <b>feature</b>: fly genotype group adapter makes fly genotype strings from tab/group<br />
-  <b>feature</b>: worm group adapter makes reference terms from ref query<br />
-  <b>change</b>: on term completion if adding a letter use previous completion list<br />
-  <b>change</b>: worm adapter query tab working properly<br />
-  <b>change</b>: build file takes param for webstart version deployment, and puts in jnlp<br />
-  <b>change</b>: group adapters can psten for CharList changes<br />
-  <b>change</b>: added/corrected BIRN ontologies<br />
-  <b>bugfix</b>: load of file doesnt crash on post comp parsing bug<br />
-  <b>bugfix</b>: doesnt load obo files specified twice twice<br />
-  <b>bugfix</b>: view menu show up at initialization<br />
-  <b>bugfix</b>: layout of term history with split pane proper<br />
+	 <b>feature</b>: Loading splash more informative about what's going on behind-the-scenes such as which ontologies are loading, if they are being updated, etc.<br />
+	<b>feature</b>: obo edit annotation model can now be optionally configured for backend, which will allow for more sophisticated data to be captured (like comparisons)<br />
+	<b>feature</b>: Error for obo parse failures to info panel <br />
+	<b>feature</b>: Delimited tab adapter uses column headings to map to table, rather than ordering <br />
+	<b>feature</b>: Autocompletion optimized with threading, cancels stale requests (min-comp-chars now pase) <br />
+	<b>feature</b>: Date created automatically added into data (under the hood) <br />
+	<b>feature</b>: If arrow hit with empty input then gets &amp; displays all terms (used to inefficiently pre-load) <br />
+	<b>feature</b>: Can sort completion list by ID, needed for zfin stages<br />
+	<b>feature</b>: Table preserves user ordering of columns, in addition to column widths.<br />
+	<b>feature</b>: Filter search field allows user to narrow down displayed data rows via matching text.<br />
+	<b>feature</b>: See actual value in input field when multiple rows are selected and have the same value.<br />
+	<b>feature</b>: Copy all taxon names in specimen list as an unresolved Newick tree (for PhenoMap/NESCent)<br />
+	<b>feature</b>: Automatically open specimen list and phylogenetic tree files when opening data file (for PhenoMap/NESCent)<br />
+	<b>change</b>: Moved test suites in with source to work with eclipse<br />
+	<b>change</b>: Took a lot of obos out of webstart jar - less bulky - as they get automatically downloaded<br />
+	<b>change</b>: Phenote now follows standard log4j configuration conventions.  Pass a custom log configuration to Phenote via the classpath or the system propery "log4j.configuration".<br />
+	<b>bugfix</b>: Terms not found are no longer dropped, a dangler is created, and error msg to info, show up in red<br />
+	<b>bugfix</b>: if log conf fails use backup default<br />
+	<b>bugfix</b>: Input fields now commit changes with either Return or Tab<br />
+	<b>bugfix</b>: Native lib is loaded properly for Mac interface on webstart, allowing traversal of aliases in file dialog, as well as user sidebar items in file dialog<br />
+	<b>bugfix</b>: Noncontiguous row selection works now on Mac<br />
+</ul>
 	</div>
       </div>
     </div>

Modified: phenote/trunk/doc/phenote-website/events.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml	2007-10-10 23:08:29 UTC (rev 1029)
+++ phenote/trunk/doc/phenote-website/events.shtml	2007-10-10 23:10:36 UTC (rev 1030)
@@ -39,6 +39,8 @@
 
 	<h1>Past News and Events, 2007</h1>
 	<h2>October</h2>
+	  <p>Oct 10, New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
+
 	  <li>Oct 2, Phenote Users Group, Online via WebEx
 	  </li>
 

Modified: phenote/trunk/doc/phenote-website/events.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml~	2007-10-10 23:08:29 UTC (rev 1029)
+++ phenote/trunk/doc/phenote-website/events.shtml~	2007-10-10 23:10:36 UTC (rev 1030)
@@ -17,23 +17,16 @@
 	</div>
 
 	<h1>Upcoming Events, 2007</h1>
-	<h2>September</h2>
-	<ul>
-	  <li>
-	  </li>
-	</ul>
 
 	<h2>October</h2>
 	<ul>
-	  <li>Oct 2, Phenote Users Group, Online
-	  </li>
 	<li>Oct 23-25, Ontology Best Practices Workshop, <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">Biocurator Meeting</a>, Hayes Mansion, San Jose, CA
 	</li>
 	</ul>
 
 	<h2>November</h2>
 	<ul>
-	  <li>Nov 6, Phenote Users Group, Online
+	  <li>Nov 1, Phenote Users Group, Online via WebEx
 	  </li>
 	<li>Nov 27, <a href="http://www.bioontology.org/">NCBO</a> Scientific Advisory Board meeting</li>
 	</ul>
@@ -44,7 +37,11 @@
 	  </li>
 	</ul>
 
-	<h1>Past Events, 2007</h1>
+	<h1>Past News and Events, 2007</h1>
+	<h2>October</h2>
+	  <li>Oct 2, Phenote Users Group, Online via WebEx
+	  </li>
+
 	<h2>September</h2>
 	<ul>
 	  <li>Sept 17, New website released
@@ -58,8 +55,10 @@
 	  <li>Aug 28, new 1.4 beta 3 released [<a href="http://www.phenote.org/downloads.shtml">Release notes</a>...]</li>
 	  <li>Aug 22-24, Phenote Demo, <a href="http://wiki.modencode.org/index.php/White">K. White group, ModENCODE</a>, Chicago, IL
 	  </li>
-	  <li>Aug 13-14, site visit, <a href="http://www.nbirn.net/research/mouse/index.shtm">BIRN</a>, San Diego, CA
+	  <li>Apr 16, site visit, <a href="http://www.wormbase.org">Wormbase</a>, Pasadena, CA
 	  </li>
+	  <li>Aug 13-15, site visit, <a href="http://www.nbirn.net/research/mouse/index.shtm">BIRN</a>, San Diego, CA
+	  </li>
 	  <li>Aug 7, <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote:Agendas_.26_Transcripts">Phenote Users Group</a>, Online
 	  </li>
 	</ul>	
@@ -95,9 +94,7 @@
 	  <li>Mar 28-29, site visit, <a href="http://zfin.org">ZFin</a>, Eugene, OR
 	  </li>
 	</ul>
-	<h1>Past Events, 2007</h1>
 
-
       </div>
     </div>
 

Modified: phenote/trunk/doc/phenote-website/features.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/features.shtml	2007-10-10 23:08:29 UTC (rev 1029)
+++ phenote/trunk/doc/phenote-website/features.shtml	2007-10-10 23:10:36 UTC (rev 1030)
@@ -52,7 +52,7 @@
 
 	  <p class="quick_link">
 	    <img src="images/star.gif" alt=""  class="icon_green"/>
-	    <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp"
+	    <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp"
 	       title="Lauch Phenote via Webstart">
 		Launch Phenote v1.4-beta3
 	    </a> via webstart

Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml	2007-10-10 23:08:29 UTC (rev 1029)
+++ phenote/trunk/doc/phenote-website/index.shtml	2007-10-10 23:10:36 UTC (rev 1030)
@@ -60,7 +60,7 @@
 
 	  <p class="quick_link">
 	    <img src="images/star.gif" alt=""  class="icon_green"/>
-	    <a href="http://www.phenote.org/phenote/1.4-beta3/phenote.jnlp"
+	    <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp"
 	       title="Lauch Phenote via Webstart">
 		Launch Phenote via Webstart
 	    </a>
@@ -129,6 +129,7 @@
 	  <!--No news is good news!-->
 	  
 	  <!-- Do not destry the following event template -->
+	  <p>10.10.2007 - New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
 	  <p>10.02.2007 - Phenote user's group to be moved to first Thursday of each month, 9am.  Join us for our next meeting on November 1st over WebEx!</p>
 	  <p>09.17.2007 - New website rolled out!  The website has the same
 	    content as the old one, just with a new look-and-feel.</p>

Modified: phenote/trunk/doc/phenote-website/index.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml~	2007-10-10 23:08:29 UTC (rev 1029)
+++ phenote/trunk/doc/phenote-website/index.shtml~	2007-10-10 23:10:36 UTC (rev 1030)
@@ -79,7 +79,7 @@
 	  <img src="images/calendar.gif"
 	       alt="Upcoming Events" 
 	       class="icon_blue"/>
-	  Upcoming Events
+	  <a href="events.shtml">Upcoming Events</a>
 	</div>
 
 	<div class="content_box_green">
@@ -102,7 +102,7 @@
 	    <li class="events">
 	  <p class="quick_link">
 	    <img src="images/star.gif" alt=""  class="icon_green"/>	      
-	    <a href="http://www.phenote.org/irc_chat">User's Group Monthly Meeting</a>, October 4, 8:30am, Online 
+	    <a href="http://www.phenote.org/irc_chat">User's Group Monthly Meeting</a>, November 1, 9:00am, Online 
 	    </p>
 	    </li> 
 	  </ul>
@@ -115,12 +115,12 @@
 	    </p>
 	    </li>
 	  </ul>
-	  <h3><a href="http://www.phenote.org/events.shtml">Past Events...</a></h3>	  
+	  <!--h3><a href="http://www.phenote.org/events.shtml">Past Events...</a></h3-->	  
 	</div>
 
 	<div class="content_box_head_green">
 	  <img src="images/document.gif" alt="News" class="icon_blue" />
-	  News
+	  <a href="events.shtml">News</a>
 	</div>
 
 	<div class="content_box_green">
@@ -129,7 +129,8 @@
 	  <!--No news is good news!-->
 	  
 	  <!-- Do not destry the following event template -->
-	    <p>09.17.2007 - New website rolled out!  The website has the same
+	  <p>10.02.2007 - Phenote user's group to be moved to first Thursday of each month, 9am.  Join us for our next meeting on November 1st over WebEx!</p>
+	  <p>09.17.2007 - New website rolled out!  The website has the same
 	    content as the old one, just with a new look-and-feel.</p>
 	    <p> 08.28.2007 - 
 	    <a href="http://www.phenote.org/download.shtml">New Phenote Beta available: 1.4-beta3!</a> </p>

Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.shtml	2007-10-10 23:08:29 UTC (rev 1029)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.shtml	2007-10-10 23:10:36 UTC (rev 1030)
@@ -25,9 +25,7 @@
 <h1>1.4 </h1>
 
 	
-<h2>10.10.2007, version <a href="put.link.here">1.4 - release</a></h2>
-
-	
+<h2>10.10.2007, version <a href="phenote/1.4/phenote.jnlp">1.4 - release</a></h2>
 <ul>
 	<li>feature: Loading splash more informative about what's going on behind-the-scenes such as which ontologies are loading, if they are being updated, etc.</li>
 	<li>feature: obo edit annotation model can now be optionally configured for backend, which will allow for more sophisticated data to be captured (like comparisons)</li>
@@ -42,13 +40,9 @@
 	<li>feature: See actual value in input field when multiple rows are selected and have the same value.</li>
 	<li>feature: Copy all taxon names in specimen list as an unresolved Newick tree (for PhenoMap/NESCent)</li>
 	<li>feature: Automatically open specimen list and phylogenetic tree files when opening data file (for PhenoMap/NESCent)</li>
-</ul>
-<ul>
 	<li>change: Moved test suites in with source to work with eclipse</li>
 	<li>change: Took a lot of obos out of webstart jar - less bulky - as they get automatically downloaded</li>
 	<li>change: Phenote now follows standard log4j configuration conventions.  Pass a custom log configuration to Phenote via the classpath or the system propery "log4j.configuration".</li>
-</ul>
-<ul>
 	<li>bugfix: Terms not found are no longer dropped, a dangler is created, and error msg to info, show up in red</li>
 	<li>bugfix: if log conf fails use backup default</li>
 	<li>bugfix: Input fields now commit changes with either Return or Tab</li>


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[Obo-svn-commit] SF.net SVN: obo: [1029] phenote/trunk/doc/making-a-phenote-release.html

From: <nl...@us...> - 2007-10-10 23:08:26

Revision: 1029
          http://obo.svn.sourceforge.net/obo/?rev=1029&view=rev
Author:   nlw
Date:     2007-10-10 16:08:29 -0700 (Wed, 10 Oct 2007)

Log Message:
-----------
added details for how to update the website

Modified Paths:
--------------
    phenote/trunk/doc/making-a-phenote-release.html

Modified: phenote/trunk/doc/making-a-phenote-release.html
===================================================================
--- phenote/trunk/doc/making-a-phenote-release.html	2007-10-10 22:36:00 UTC (rev 1028)
+++ phenote/trunk/doc/making-a-phenote-release.html	2007-10-10 23:08:29 UTC (rev 1029)
@@ -43,8 +43,29 @@
 - ant webstart -Dphenote.version="versionNumber" (called from phenote root) should then install phenote webstart<br>
 version number is something like "1.5"<br>
 <br>
-- [Nicole then modifies some files and runs some script to update the
-phenote website download page - nicole could you fill that in here? ]<br>
+<ul>
+  <li>update the release notes:
+  <p> in phenote/doc/phenote-website there's a file called phenote-release-notes.shtml.  add any significant changes, bugfixes, or new features.  i try to put the most interesting (for the user) changes first, since they might read this to see what's new, but might stop reading after only a few.  When applicable, be sure to include a link to the tracker item that the item relates.</p>
+  </li>
+  <li>update the links on the website:
+  <ul>
+    <li>index.shtml:
+    <p>there's a 'quick link' - change to the latest version</p>
+    <p>add a note that there's been a new release to the 'news' section</p>
+    <p>remove the oldest release news item</p></li>
+    <li>events.shtml:
+    <p>add the same news item to this page (past events section)</p>
+    </li>
+    <li>download.shtml:
+    <p>update the link to the newest release under webstart </p>
+    <p>update the svn command under 'run phenote at the command   line'</p>
+    <p>add the latest and/or sexiest features of the latest release</p>
+    </li>
+  </ul>
+  <li>to update the website:
+  <p>then, to make sure all the changes are made to the website, be sure to first commit your changes to svn.  then run 'update_site' script that resides in the phenote/website dir.  this must be done from a berkeleybop machine.</p>
+  </li>
+</ul>
 <br>
 - make tag in sourceforge subversion
 </body>


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[Obo-svn-commit] SF.net SVN: obo: [1028] phenote/trunk/src/java/phenote/gui/HelpMenu.java

From: <nl...@us...> - 2007-10-10 22:35:56

Revision: 1028
          http://obo.svn.sourceforge.net/obo/?rev=1028&view=rev
Author:   nlw
Date:     2007-10-10 15:36:00 -0700 (Wed, 10 Oct 2007)

Log Message:
-----------
added a warning popup to the request-term item -before- the actual screen pops up

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/gui/HelpMenu.java

Modified: phenote/trunk/src/java/phenote/gui/HelpMenu.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/HelpMenu.java	2007-10-10 21:08:39 UTC (rev 1027)
+++ phenote/trunk/src/java/phenote/gui/HelpMenu.java	2007-10-10 22:36:00 UTC (rev 1028)
@@ -90,6 +90,11 @@
       	}
     	else if (e.getActionCommand().equals("request")) {
     		try {
+		    String m="This feature is still in development.  Any information\n"+
+			"you enter will be lost\n";
+			
+		    JOptionPane.showMessageDialog(null, m, "Phenote message", JOptionPane.PLAIN_MESSAGE);
+
     			termRequester = new TermRequestGUI();
     			termRequester.setVisible(true);
     		} catch (Exception ex) {


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[Obo-svn-commit] SF.net SVN: obo: [1024] obo-database/trunk

From: <cmu...@us...> - 2007-10-10 21:12:08

Revision: 1024
          http://obo.svn.sourceforge.net/obo/?rev=1024&view=rev
Author:   cmungall
Date:     2007-10-10 14:05:28 -0700 (Wed, 10 Oct 2007)

Log Message:
-----------


Added Paths:
-----------
    obo-database/trunk/build/README

Removed Paths:
-------------
    obo-database/trunk/xsl/oboxml_to_obd_prestore.xsl

Added: obo-database/trunk/build/README
===================================================================
--- obo-database/trunk/build/README	                        (rev 0)
+++ obo-database/trunk/build/README	2007-10-10 21:05:28 UTC (rev 1024)
@@ -0,0 +1,9 @@
+OBD Build process.
+
+* OBD-Phenotype : OBD Instance for representing phenotypes and phenotype associations
+
+Phenotype association files are first converted from the Phenote
+tabular format to .obo-xml using the configuration-specific mapping
+file and phenote-apply-template. See the Makefile for details.
+
+

Deleted: obo-database/trunk/xsl/oboxml_to_obd_prestore.xsl
===================================================================
--- obo-database/trunk/xsl/oboxml_to_obd_prestore.xsl	2007-10-10 20:46:57 UTC (rev 1023)
+++ obo-database/trunk/xsl/oboxml_to_obd_prestore.xsl	2007-10-10 21:05:28 UTC (rev 1024)
@@ -1 +0,0 @@
-link /Users/cjm/go-xsl/oboxml_to_obd_prestore.xsl
\ No newline at end of file


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[Obo-svn-commit] SF.net SVN: obo: [1026] obo-database/trunk/conf/fma-part-slim.obo

From: <cmu...@us...> - 2007-10-10 21:11:58

Revision: 1026
          http://obo.svn.sourceforge.net/obo/?rev=1026&view=rev
Author:   cmungall
Date:     2007-10-10 14:08:09 -0700 (Wed, 10 Oct 2007)

Log Message:
-----------


Removed Paths:
-------------
    obo-database/trunk/conf/fma-part-slim.obo

Deleted: obo-database/trunk/conf/fma-part-slim.obo
===================================================================
--- obo-database/trunk/conf/fma-part-slim.obo	2007-10-10 21:05:49 UTC (rev 1025)
+++ obo-database/trunk/conf/fma-part-slim.obo	2007-10-10 21:08:09 UTC (rev 1026)
@@ -1 +0,0 @@
-link /Users/cjm/cvs/fma-conversion/fma-part-slim.obo
\ No newline at end of file


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[Obo-svn-commit] SF.net SVN: obo: [1027] obo-database/trunk/conf/fma-part-slim.obo

From: <cmu...@us...> - 2007-10-10 21:08:44

Revision: 1027
          http://obo.svn.sourceforge.net/obo/?rev=1027&view=rev
Author:   cmungall
Date:     2007-10-10 14:08:39 -0700 (Wed, 10 Oct 2007)

Log Message:
-----------


Added Paths:
-----------
    obo-database/trunk/conf/fma-part-slim.obo

Added: obo-database/trunk/conf/fma-part-slim.obo
===================================================================
--- obo-database/trunk/conf/fma-part-slim.obo	                        (rev 0)
+++ obo-database/trunk/conf/fma-part-slim.obo	2007-10-10 21:08:39 UTC (rev 1027)
@@ -0,0 +1,512948 @@
+format-version: 1.2
+
+[Term]
+id: FMA:10000
+name: Eighth thoracic vertebral arch
+namespace: fma
+synonym: "Arch of T8 vertebra" EXACT []
+synonym: "Arch of eighth thoracic vertebra" EXACT []
+is_a: FMA:9151  ! Thoracic vertebral arch
+relationship: part_of FMA:9991 ! Eighth thoracic vertebra
+
+[Term]
+id: FMA:10001
+name: Pedicle of eighth thoracic vertebra
+namespace: fma
+synonym: "Eighth thoracic vertebral pedicle" EXACT []
+synonym: "Pedicle of T8 vertebra" EXACT []
+is_a: FMA:9152  ! Pedicle of thoracic vertebra
+
+[Term]
+id: FMA:10002
+name: Superior vertebral notch of eighth thoracic vertebra
+namespace: fma
+synonym: "Superior vertebral incisure of pedicle of eighth thoracic vertebra" EXACT []
+is_a: FMA:9157  ! Superior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10003
+name: Inferior vertebral notch of eighth thoracic vertebra
+namespace: fma
+synonym: "Inferior vertebral incisure of pedicle of eighth thoracic vertebra" EXACT []
+is_a: FMA:9158  ! Inferior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10004
+name: Lamina of eighth thoracic vertebra
+namespace: fma
+synonym: "Eighth thoracic vertebral lamina" EXACT []
+is_a: FMA:9153  ! Lamina of thoracic vertebra
+
+[Term]
+id: FMA:10005
+name: Spinous process of eighth thoracic vertebra
+namespace: fma
+synonym: "Spinous process of T8 vertebra" EXACT []
+is_a: FMA:9149  ! Spinous process of thoracic vertebra
+relationship: part_of FMA:10000 ! Eighth thoracic vertebral arch
+
+[Term]
+id: FMA:10006
+name: Transverse process of eighth thoracic vertebra
+namespace: fma
+synonym: "Transverse process of T8 vertebra" EXACT []
+is_a: FMA:9150  ! Transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10007
+name: Costal facet of transverse process of eighth thoracic vertebra
+namespace: fma
+synonym: "Articular facet of transverse process of eighth thoracic vertebra" EXACT []
+is_a: FMA:10440  ! Costal facet of transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10008
+name: Vasculature of bony part of eighth thoracic vertebra
+namespace: fma
+is_a: FMA:9154  ! Vasculature of bony part of thoracic vertebra
+
+[Term]
+id: FMA:10009
+name: Superior articular process of eighth thoracic vertebra
+namespace: fma
+synonym: "Cranial articular process of eighth thoracic vertebra" EXACT []
+is_a: FMA:9155  ! Superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10010
+name: Articular facet of superior articular process of eighth thoracic vertebra
+namespace: fma
+is_a: FMA:10521  ! Articular facet of superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10011
+name: Inferior articular process of eighth thoracic vertebra
+namespace: fma
+synonym: "Caudal articular process of eighth thoracic vertebra" EXACT []
+is_a: FMA:9156  ! Inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10012
+name: Articular facet of inferior articular process of eighth thoracic vertebra
+namespace: fma
+is_a: FMA:9160  ! Articular facet of inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10013
+name: Intervertebral foramen of eighth thoracic vertebra
+namespace: fma
+is_a: FMA:9144  ! Intervertebral foramen of thoracic vertebra
+
+[Term]
+id: FMA:10014
+name: Ninth thoracic vertebra
+namespace: fma
+synonym: "Ninth dorsal vertebra" EXACT []
+synonym: "T9 vertebra" EXACT []
+is_a: FMA:9139  ! Thoracic vertebra
+
+[Term]
+id: FMA:10015
+name: Body of ninth thoracic vertebra
+namespace: fma
+synonym: "Body of T9 vertebra" EXACT []
+synonym: "Ninth thoracic vertebral body" EXACT []
+is_a: FMA:9141  ! Body of thoracic vertebra
+relationship: part_of FMA:10014 ! Ninth thoracic vertebra
+
+[Term]
+id: FMA:10016
+name: Anterior surface of body of ninth thoracic vertebra
+namespace: fma
+is_a: FMA:9147  ! Anterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10017
+name: Posterior surface of body of ninth thoracic vertebra
+namespace: fma
+is_a: FMA:9148  ! Posterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10018
+name: Lateral surface of body of ninth thoracic vertebra
+namespace: fma
+is_a: FMA:9162  ! Lateral surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10019
+name: Superior costal facet of body of ninth thoracic vertebra
+namespace: fma
+synonym: "Superior costocapitular demifacet of body of ninth thoracic vertebra" EXACT []
+synonym: "Upper costal facet of body of ninth thoracic vertebra" EXACT []
+is_a: FMA:9145  ! Superior costal facet of body of thoracic vertebra
+relationship: part_of FMA:8945 ! Joint of head of ninth rib
+
+[Term]
+id: FMA:10021
+name: Superior surface of body of ninth thoracic vertebra
+namespace: fma
+synonym: "Upper border of body of ninth thoracic vertebra" EXACT []
+is_a: FMA:9163  ! Superior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10022
+name: Inferior surface of body of ninth thoracic vertebra
+namespace: fma
+synonym: "Lower border of body of ninth thoracic vertebra" EXACT []
+is_a: FMA:9164  ! Inferior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10023
+name: Ninth thoracic vertebral arch
+namespace: fma
+synonym: "Arch of T9 vertebra" EXACT []
+synonym: "Arch of ninth thoracic vertebra" EXACT []
+is_a: FMA:9151  ! Thoracic vertebral arch
+relationship: part_of FMA:10014 ! Ninth thoracic vertebra
+
+[Term]
+id: FMA:10024
+name: Pedicle of ninth thoracic vertebra
+namespace: fma
+synonym: "Ninth thoracic vertebral pedicle" EXACT []
+synonym: "Pedicle of T9 vertebra" EXACT []
+is_a: FMA:9152  ! Pedicle of thoracic vertebra
+
+[Term]
+id: FMA:10025
+name: Superior vertebral notch of ninth thoracic vertebra
+namespace: fma
+synonym: "Superior vertebral incisure of pedicle of ninth thoracic vertebra" EXACT []
+is_a: FMA:9157  ! Superior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10026
+name: Inferior vertebral notch of ninth thoracic vertebra
+namespace: fma
+synonym: "Inferior vertebral incisure of pedicle of ninth thoracic vertebra" EXACT []
+is_a: FMA:9158  ! Inferior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10027
+name: Lamina of ninth thoracic vertebra
+namespace: fma
+synonym: "Ninth thoracic vertebral lamina" EXACT []
+is_a: FMA:9153  ! Lamina of thoracic vertebra
+
+[Term]
+id: FMA:10028
+name: Spinous process of ninth thoracic vertebra
+namespace: fma
+synonym: "Spinous process of T9 vertebra" EXACT []
+is_a: FMA:9149  ! Spinous process of thoracic vertebra
+relationship: part_of FMA:10023 ! Ninth thoracic vertebral arch
+
+[Term]
+id: FMA:10029
+name: Transverse process of ninth thoracic vertebra
+namespace: fma
+synonym: "Transverse process of T9 vertebra" EXACT []
+is_a: FMA:9150  ! Transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10030
+name: Costal facet of transverse process of ninth thoracic vertebra
+namespace: fma
+synonym: "Articular facet of transverse process of ninth thoracic vertebra" EXACT []
+is_a: FMA:10440  ! Costal facet of transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10031
+name: Vasculature of bony part of ninth thoracic vertebra
+namespace: fma
+is_a: FMA:9154  ! Vasculature of bony part of thoracic vertebra
+
+[Term]
+id: FMA:10032
+name: Superior articular process of ninth thoracic vertebra
+namespace: fma
+synonym: "Cranial articular process of ninth thoracic vertebra" EXACT []
+is_a: FMA:9155  ! Superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10033
+name: Articular facet of superior articular process of ninth thoracic vertebra
+namespace: fma
+is_a: FMA:10521  ! Articular facet of superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10034
+name: Inferior articular process of ninth thoracic vertebra
+namespace: fma
+synonym: "Caudal articular process of ninth thoracic vertebra" EXACT []
+is_a: FMA:9156  ! Inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10035
+name: Articular facet of inferior articular process of ninth thoracic vertebra
+namespace: fma
+is_a: FMA:9160  ! Articular facet of inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10036
+name: Intervertebral foramen of ninth thoracic vertebra
+namespace: fma
+is_a: FMA:9144  ! Intervertebral foramen of thoracic vertebra
+
+[Term]
+id: FMA:10037
+name: Tenth thoracic vertebra
+namespace: fma
+synonym: "T10 vertebra" EXACT []
+synonym: "Tenth dorsal vertebra" EXACT []
+is_a: FMA:9139  ! Thoracic vertebra
+
+[Term]
+id: FMA:10038
+name: Body of tenth thoracic vertebra
+namespace: fma
+synonym: "Body of T10 vertebra" EXACT []
+synonym: "Tenth thoracic vertebral body" EXACT []
+is_a: FMA:9141  ! Body of thoracic vertebra
+relationship: part_of FMA:10037 ! Tenth thoracic vertebra
+
+[Term]
+id: FMA:10039
+name: Anterior surface of body of tenth thoracic vertebra
+namespace: fma
+is_a: FMA:9147  ! Anterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10040
+name: Posterior surface of body of tenth thoracic vertebra
+namespace: fma
+is_a: FMA:9148  ! Posterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10041
+name: Lateral surface of body of tenth thoracic vertebra
+namespace: fma
+is_a: FMA:9162  ! Lateral surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10042
+name: Superior costal facet of body of tenth thoracic vertebra
+namespace: fma
+synonym: "Superior costocapitular demifacet of body of tenth thoracic vertebra" EXACT []
+synonym: "Upper costal facet of body of tenth thoracic vertebra" EXACT []
+is_a: FMA:9145  ! Superior costal facet of body of thoracic vertebra
+relationship: part_of FMA:8948 ! Joint of head of tenth rib
+
+[Term]
+id: FMA:10043
+name: Superior surface of body of tenth thoracic vertebra
+namespace: fma
+synonym: "Upper border of body of tenth thoracic vertebra" EXACT []
+is_a: FMA:9163  ! Superior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10044
+name: Inferior surface of body of tenth thoracic vertebra
+namespace: fma
+synonym: "Lower border of body of tenth thoracic vertebra" EXACT []
+is_a: FMA:9164  ! Inferior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10045
+name: Tenth thoracic vertebral arch
+namespace: fma
+synonym: "Arch of T10 vertebra" EXACT []
+synonym: "Arch of tenth thoracic vertebra" EXACT []
+is_a: FMA:9151  ! Thoracic vertebral arch
+relationship: part_of FMA:10037 ! Tenth thoracic vertebra
+
+[Term]
+id: FMA:10046
+name: Pedicle of tenth thoracic vertebra
+namespace: fma
+synonym: "Pedicle of T10 vertebra" EXACT []
+synonym: "Tenth thoracic vertebral pedicle" EXACT []
+is_a: FMA:9152  ! Pedicle of thoracic vertebra
+
+[Term]
+id: FMA:10047
+name: Superior vertebral notch of tenth thoracic vertebra
+namespace: fma
+synonym: "Superior vertebral incisure of pedicle of tenth thoracic vertebra" EXACT []
+is_a: FMA:9157  ! Superior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10048
+name: Inferior vertebral notch of tenth thoracic vertebra
+namespace: fma
+synonym: "Inferior vertebral incisure of pedicle of tenth thoracic vertebra" EXACT []
+is_a: FMA:9158  ! Inferior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10049
+name: Lamina of tenth thoracic vertebra
+namespace: fma
+synonym: "Tenth thoracic vertebral lamina" EXACT []
+is_a: FMA:9153  ! Lamina of thoracic vertebra
+
+[Term]
+id: FMA:10050
+name: Spinous process of tenth thoracic vertebra
+namespace: fma
+synonym: "Spinous process of T10 vertebra" EXACT []
+is_a: FMA:9149  ! Spinous process of thoracic vertebra
+relationship: part_of FMA:10045 ! Tenth thoracic vertebral arch
+
+[Term]
+id: FMA:10051
+name: Transverse process of tenth thoracic vertebra
+namespace: fma
+synonym: "Transverse process of T10 vertebra" EXACT []
+is_a: FMA:9150  ! Transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10052
+name: Costal facet of transverse process of tenth thoracic vertebra
+namespace: fma
+synonym: "Articular facet of transverse process of tenth thoracic vertebra" EXACT []
+is_a: FMA:10440  ! Costal facet of transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10053
+name: Vasculature of bony part of tenth thoracic vertebra
+namespace: fma
+is_a: FMA:9154  ! Vasculature of bony part of thoracic vertebra
+
+[Term]
+id: FMA:10054
+name: Superior articular process of tenth thoracic vertebra
+namespace: fma
+synonym: "Cranial articular process of tenth thoracic vertebra" EXACT []
+is_a: FMA:9155  ! Superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10055
+name: Articular facet of superior articular process of tenth thoracic vertebra
+namespace: fma
+is_a: FMA:10521  ! Articular facet of superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10056
+name: Inferior articular process of tenth thoracic vertebra
+namespace: fma
+synonym: "Caudal articular process of tenth thoracic vertebra" EXACT []
+is_a: FMA:9156  ! Inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10057
+name: Articular facet of inferior articular process of tenth thoracic vertebra
+namespace: fma
+is_a: FMA:9160  ! Articular facet of inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10058
+name: Intervertebral foramen of tenth thoracic vertebra
+namespace: fma
+is_a: FMA:9144  ! Intervertebral foramen of thoracic vertebra
+
+[Term]
+id: FMA:10059
+name: Eleventh thoracic vertebra
+namespace: fma
+synonym: "Eleventh dorsal vertebra" EXACT []
+synonym: "T11 vertebra" EXACT []
+is_a: FMA:9139  ! Thoracic vertebra
+
+[Term]
+id: FMA:10060
+name: Body of eleventh thoracic vertebra
+namespace: fma
+synonym: "Body of T11 vertebra" EXACT []
+synonym: "Eleventh thoracic vertebral body" EXACT []
+is_a: FMA:9141  ! Body of thoracic vertebra
+relationship: part_of FMA:10059 ! Eleventh thoracic vertebra
+
+[Term]
+id: FMA:10061
+name: Anterior surface of body of eleventh thoracic vertebra
+namespace: fma
+is_a: FMA:9147  ! Anterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10062
+name: Posterior surface of body of eleventh thoracic vertebra
+namespace: fma
+is_a: FMA:9148  ! Posterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10063
+name: Lateral surface of body of eleventh thoracic vertebra
+namespace: fma
+is_a: FMA:9162  ! Lateral surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10064
+name: Costal facet of body of eleventh thoracic vertebra
+namespace: fma
+synonym: "Costocapitular demifacet of body of eleventh thoracic vertebra" EXACT []
+is_a: FMA:13577  ! Costal facet of body of thoracic vertebra
+relationship: part_of FMA:8951 ! Joint of head of eleventh rib
+
+[Term]
+id: FMA:10065
+name: Superior surface of body of eleventh thoracic vertebra
+namespace: fma
+synonym: "Upper border of body of eleventh thoracic vertebra" EXACT []
+is_a: FMA:9163  ! Superior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10066
+name: Inferior surface of body of eleventh thoracic vertebra
+namespace: fma
+synonym: "Lower border of body of eleventh thoracic vertebra" EXACT []
+is_a: FMA:9164  ! Inferior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10067
+name: Eleventh thoracic vertebral arch
+namespace: fma
+synonym: "Arch of T11 vertebra" EXACT []
+synonym: "Arch of eleventh thoracic vertebra" EXACT []
+is_a: FMA:9151  ! Thoracic vertebral arch
+relationship: part_of FMA:10059 ! Eleventh thoracic vertebra
+
+[Term]
+id: FMA:10068
+name: Pedicle of eleventh thoracic vertebra
+namespace: fma
+synonym: "Eleventh thoracic vertebral pedicle" EXACT []
+synonym: "Pedicle of T11 vertebra" EXACT []
+is_a: FMA:9152  ! Pedicle of thoracic vertebra
+
+[Term]
+id: FMA:10069
+name: Superior vertebral notch of eleventh thoracic vertebra
+namespace: fma
+synonym: "Superior vertebral incisure of pedicle of eleventh thoracic vertebra" EXACT []
+is_a: FMA:9157  ! Superior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10070
+name: Inferior vertebral notch of eleventh thoracic vertebra
+namespace: fma
+synonym: "Inferior vertebral incisure of pedicle of eleventh thoracic vertebra" EXACT []
+is_a: FMA:9158  ! Inferior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10071
+name: Lamina of eleventh thoracic vertebra
+namespace: fma
+synonym: "Eleventh thoracic vertebral lamina" EXACT []
+is_a: FMA:9153  ! Lamina of thoracic vertebra
+
+[Term]
+id: FMA:10072
+name: Spinous process of eleventh thoracic vertebra
+namespace: fma
+synonym: "Spinous process of T11 vertebra" EXACT []
+is_a: FMA:9149  ! Spinous process of thoracic vertebra
+relationship: part_of FMA:10067 ! Eleventh thoracic vertebral arch
+
+[Term]
+id: FMA:10073
+name: Transverse process of eleventh thoracic vertebra
+namespace: fma
+synonym: "Transverse process of T11 vertebra" EXACT []
+is_a: FMA:9150  ! Transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10075
+name: Vasculature of bony part of eleventh thoracic vertebra
+namespace: fma
+is_a: FMA:9154  ! Vasculature of bony part of thoracic vertebra
+
+[Term]
+id: FMA:10076
+name: Superior articular process of eleventh thoracic vertebra
+namespace: fma
+synonym: "Cranial articular process of eleventh thoracic vertebra" EXACT []
+is_a: FMA:9155  ! Superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10077
+name: Articular facet of superior articular process of eleventh thoracic vertebra
+namespace: fma
+is_a: FMA:10521  ! Articular facet of superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10078
+name: Inferior articular process of eleventh thoracic vertebra
+namespace: fma
+synonym: "Caudal articular process of eleventh thoracic vertebra" EXACT []
+is_a: FMA:9156  ! Inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10079
+name: Articular facet of inferior articular process of eleventh thoracic vertebra
+namespace: fma
+is_a: FMA:9160  ! Articular facet of inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10080
+name: Intervertebral foramen of eleventh thoracic vertebra
+namespace: fma
+is_a: FMA:9144  ! Intervertebral foramen of thoracic vertebra
+
+[Term]
+id: FMA:10081
+name: Twelfth thoracic vertebra
+namespace: fma
+synonym: "T12 vertebra" EXACT []
+synonym: "Twelfth dorsal vertebra" EXACT []
+is_a: FMA:9139  ! Thoracic vertebra
+
+[Term]
+id: FMA:10082
+name: Body of twelfth thoracic vertebra
+namespace: fma
+synonym: "Body of T12 vertebra" EXACT []
+synonym: "Twelfth thoracic vertebral body" EXACT []
+is_a: FMA:9141  ! Body of thoracic vertebra
+relationship: part_of FMA:10081 ! Twelfth thoracic vertebra
+
+[Term]
+id: FMA:10083
+name: Anterior surface of body of twelfth thoracic vertebra
+namespace: fma
+is_a: FMA:9147  ! Anterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10084
+name: Posterior surface of body of twelfth thoracic vertebra
+namespace: fma
+is_a: FMA:9148  ! Posterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10085
+name: Lateral surface of body of twelfth thoracic vertebra
+namespace: fma
+is_a: FMA:9162  ! Lateral surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10087
+name: Superior surface of body of twelfth thoracic vertebra
+namespace: fma
+synonym: "Upper border of body of twelfth thoracic vertebra" EXACT []
+is_a: FMA:9163  ! Superior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10088
+name: Inferior surface of body of twelfth thoracic vertebra
+namespace: fma
+synonym: "Lower border of body of twelfth thoracic vertebra" EXACT []
+is_a: FMA:9164  ! Inferior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10089
+name: Twelfth thoracic vertebral arch
+namespace: fma
+synonym: "Arch of T12 vertebra" EXACT []
+synonym: "Arch of twelfth thoracic vertebra" EXACT []
+is_a: FMA:9151  ! Thoracic vertebral arch
+relationship: part_of FMA:10081 ! Twelfth thoracic vertebra
+
+[Term]
+id: FMA:10090
+name: Pedicle of twelfth thoracic vertebra
+namespace: fma
+synonym: "Pedicle of T12 vertebra" EXACT []
+synonym: "Twelfth thoracic vertebral pedicle" EXACT []
+is_a: FMA:9152  ! Pedicle of thoracic vertebra
+
+[Term]
+id: FMA:10091
+name: Superior vertebral notch of twelfth thoracic vertebra
+namespace: fma
+synonym: "Superior vertebral incisure of pedicle of twelfth thoracic vertebra" EXACT []
+is_a: FMA:9157  ! Superior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10092
+name: Inferior vertebral notch of twelfth thoracic vertebra
+namespace: fma
+synonym: "Inferior vertebral incisure of pedicle of twelfth thoracic vertebra" EXACT []
+is_a: FMA:9158  ! Inferior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10093
+name: Lamina of twelfth thoracic vertebra
+namespace: fma
+synonym: "Twelfth thoracic vertebral lamina" EXACT []
+is_a: FMA:9153  ! Lamina of thoracic vertebra
+
+[Term]
+id: FMA:10094
+name: Spinous process of twelfth thoracic vertebra
+namespace: fma
+synonym: "Spinous process of T12 vertebra" EXACT []
+is_a: FMA:9149  ! Spinous process of thoracic vertebra
+relationship: part_of FMA:10089 ! Twelfth thoracic vertebral arch
+
+[Term]
+id: FMA:10095
+name: Transverse process of twelfth thoracic vertebra
+namespace: fma
+synonym: "Transverse process of T12 vertebra" EXACT []
+is_a: FMA:9150  ! Transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10096
+name: Vasculature of bony part of twelfth thoracic vertebra
+namespace: fma
+is_a: FMA:9154  ! Vasculature of bony part of thoracic vertebra
+
+[Term]
+id: FMA:10097
+name: Superior articular process of twelfth thoracic vertebra
+namespace: fma
+synonym: "Cranial articular process of twelfth thoracic vertebra" EXACT []
+is_a: FMA:9155  ! Superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10098
+name: Articular facet of superior articular process of twelfth thoracic vertebra
+namespace: fma
+is_a: FMA:10521  ! Articular facet of superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10099
+name: Inferior articular process of twelfth thoracic vertebra
+namespace: fma
+synonym: "Caudal articular process of twelfth thoracic vertebra" EXACT []
+is_a: FMA:9156  ! Inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10100
+name: Articular facet of inferior articular process of twelfth thoracic vertebra
+namespace: fma
+is_a: FMA:9160  ! Articular facet of inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10101
+name: Intervertebral foramen of twelfth thoracic vertebra
+namespace: fma
+is_a: FMA:9144  ! Intervertebral foramen of thoracic vertebra
+
+[Term]
+id: FMA:10102
+name: First costochondral joint
+namespace: fma
+is_a: FMA:7956  ! Costochondral joint
+
+[Term]
+id: FMA:10103
+name: Right first costochondral joint
+namespace: fma
+is_a: FMA:10102  ! First costochondral joint
+relationship: part_of FMA:7857 ! Right first rib
+
+[Term]
+id: FMA:10104
+name: Left first costochondral joint
+namespace: fma
+is_a: FMA:10102  ! First costochondral joint
+relationship: part_of FMA:7987 ! Left first rib
+
+[Term]
+id: FMA:10105
+name: Second costochondral joint
+namespace: fma
+is_a: FMA:7956  ! Costochondral joint
+
+[Term]
+id: FMA:10106
+name: Right second costochondral joint
+namespace: fma
+is_a: FMA:10105  ! Second costochondral joint
+relationship: part_of FMA:7882 ! Right second rib
+
+[Term]
+id: FMA:10107
+name: Left second costochondral joint
+namespace: fma
+is_a: FMA:10105  ! Second costochondral joint
+relationship: part_of FMA:8012 ! Left second rib
+
+[Term]
+id: FMA:10108
+name: Third costochondral joint
+namespace: fma
+is_a: FMA:7956  ! Costochondral joint
+
+[Term]
+id: FMA:10109
+name: Right third costochondral joint
+namespace: fma
+is_a: FMA:10108  ! Third costochondral joint
+relationship: part_of FMA:7909 ! Right third rib
+
+[Term]
+id: FMA:10110
+name: Left third costochondral joint
+namespace: fma
+is_a: FMA:10108  ! Third costochondral joint
+relationship: part_of FMA:8039 ! Left third rib
+
+[Term]
+id: FMA:10111
+name: Fourth costochondral joint
+namespace: fma
+is_a: FMA:7956  ! Costochondral joint
+
+[Term]
+id: FMA:10112
+name: Right fourth costochondral joint
+namespace: fma
+is_a: FMA:10111  ! Fourth costochondral joint
+relationship: part_of FMA:7957 ! Right fourth rib
+
+[Term]
+id: FMA:10113
+name: Left fourth costochondral joint
+namespace: fma
+is_a: FMA:10111  ! Fourth costochondral joint
+relationship: part_of FMA:8148 ! Left fourth rib
+
+[Term]
+id: FMA:10114
+name: Fifth costochondral joint
+namespace: fma
+is_a: FMA:7956  ! Costochondral joint
+
+[Term]
+id: FMA:10115
+name: Right fifth costochondral joint
+namespace: fma
+is_a: FMA:10114  ! Fifth costochondral joint
+relationship: part_of FMA:8066 ! Right fifth rib
+
+[Term]
+id: FMA:10116
+name: Left fifth costochondral joint
+namespace: fma
+is_a: FMA:10114  ! Fifth costochondral joint
+relationship: part_of FMA:8093 ! Left fifth rib
+
+[Term]
+id: FMA:10117
+name: Sixth costochondral joint
+namespace: fma
+is_a: FMA:7956  ! Costochondral joint
+
+[Term]
+id: FMA:10118
+name: Right sixth costochondral joint
+namespace: fma
+is_a: FMA:10117  ! Sixth costochondral joint
+relationship: part_of FMA:8175 ! Right sixth rib
+
+[Term]
+id: FMA:10119
+name: Left sixth costochondral joint
+namespace: fma
+is_a: FMA:10117  ! Sixth costochondral joint
+relationship: part_of FMA:8202 ! Left sixth rib
+
+[Term]
+id: FMA:10120
+name: Seventh costochondral joint
+namespace: fma
+is_a: FMA:7956  ! Costochondral joint
+
+[Term]
+id: FMA:10121
+name: Right seventh costochondral joint
+namespace: fma
+is_a: FMA:10120  ! Seventh costochondral joint
+relationship: part_of FMA:8229 ! Right seventh rib
+
+[Term]
+id: FMA:10122
+name: Left seventh costochondral joint
+namespace: fma
+is_a: FMA:10120  ! Seventh costochondral joint
+relationship: part_of FMA:8256 ! Left seventh rib
+
+[Term]
+id: FMA:10123
+name: Eighth costochondral joint
+namespace: fma
+is_a: FMA:7956  ! Costochondral joint
+
+[Term]
+id: FMA:10124
+name: Right eighth costochondral joint
+namespace: fma
+is_a: FMA:10123  ! Eighth costochondral joint
+relationship: part_of FMA:8283 ! Right eighth rib
+
+[Term]
+id: FMA:10125
+name: Left eighth costochondral joint
+namespace: fma
+is_a: FMA:10123  ! Eighth costochondral joint
+relationship: part_of FMA:8310 ! Left eighth rib
+
+[Term]
+id: FMA:10126
+name: Ninth costochondral joint
+namespace: fma
+is_a: FMA:7956  ! Costochondral joint
+
+[Term]
+id: FMA:10127
+name: Right ninth costochondral joint
+namespace: fma
+is_a: FMA:10126  ! Ninth costochondral joint
+relationship: part_of FMA:8364 ! Right ninth rib
+
+[Term]
+id: FMA:10128
+name: Left ninth costochondral joint
+namespace: fma
+is_a: FMA:10126  ! Ninth costochondral joint
+relationship: part_of FMA:8391 ! Left ninth rib
+
+[Term]
+id: FMA:10129
+name: Tenth costochondral joint
+namespace: fma
+is_a: FMA:7956  ! Costochondral joint
+
+[Term]
+id: FMA:10130
+name: Right tenth costochondral joint
+namespace: fma
+is_a: FMA:10129  ! Tenth costochondral joint
+relationship: part_of FMA:8445 ! Right tenth rib
+
+[Term]
+id: FMA:10131
+name: Left tenth costochondral joint
+namespace: fma
+is_a: FMA:10129  ! Tenth costochondral joint
+relationship: part_of FMA:8472 ! Left tenth rib
+
+[Term]
+id: FMA:10132
+name: Eleventh costochondral joint
+namespace: fma
+is_a: FMA:7956  ! Costochondral joint
+
+[Term]
+id: FMA:10133
+name: Right eleventh costochondral joint
+namespace: fma
+is_a: FMA:10132  ! Eleventh costochondral joint
+relationship: part_of FMA:8531 ! Right eleventh rib
+
+[Term]
+id: FMA:10134
+name: Left eleventh costochondral joint
+namespace: fma
+is_a: FMA:10132  ! Eleventh costochondral joint
+relationship: part_of FMA:8532 ! Left eleventh rib
+
+[Term]
+id: FMA:10135
+name: Twelfth costochondral joint
+namespace: fma
+is_a: FMA:7956  ! Costochondral joint
+
+[Term]
+id: FMA:10136
+name: Right twelfth costochondral joint
+namespace: fma
+is_a: FMA:10135  ! Twelfth costochondral joint
+relationship: part_of FMA:8533 ! Right twelfth rib
+
+[Term]
+id: FMA:10137
+name: Left twelfth costochondral joint
+namespace: fma
+is_a: FMA:10135  ! Twelfth costochondral joint
+relationship: part_of FMA:8534 ! Left twelfth rib
+
+[Term]
+id: FMA:10138
+name: Accessory ligament
+namespace: fma
+is_a: FMA:11106  ! Ligament of costotransverse joint
+relationship: part_of FMA:7952 ! Costotransverse joint
+
+[Term]
+id: FMA:10139
+name: First costotransverse joint
+namespace: fma
+is_a: FMA:7952  ! Costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10140
+name: Capsule of costotransverse joint
+namespace: fma
+synonym: "Costotransverse joint capsule" EXACT []
+synonym: "Fibrous capsule of costotransverse joint" EXACT []
+is_a: FMA:34836  ! Articular capsule
+relationship: part_of FMA:7952 ! Costotransverse joint
+
+[Term]
+id: FMA:10141
+name: Second costotransverse joint
+namespace: fma
+is_a: FMA:7952  ! Costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10142
+name: Capsule of first costotransverse joint
+namespace: fma
+synonym: "First costotransverse joint capsule" EXACT []
+is_a: FMA:10140  ! Capsule of costotransverse joint
+relationship: part_of FMA:10139 ! First costotransverse joint
+
+[Term]
+id: FMA:10143
+name: Costotransverse foramen
+namespace: fma
+is_a: FMA:9338  ! Anatomical conduit
+
+[Term]
+id: FMA:10144
+name: Costotransverse ligament of first costotransverse joint
+namespace: fma
+is_a: FMA:12163  ! Costotransverse ligament
+relationship: part_of FMA:10139 ! First costotransverse joint
+
+[Term]
+id: FMA:10145
+name: Lateral costotransverse ligament of first costotransverse joint
+namespace: fma
+is_a: FMA:12162  ! Lateral costotransverse ligament
+relationship: part_of FMA:10139 ! First costotransverse joint
+
+[Term]
+id: FMA:10146
+name: First costotransverse foramen
+namespace: fma
+is_a: FMA:10143  ! Costotransverse foramen
+
+[Term]
+id: FMA:10147
+name: Right first costotransverse joint
+namespace: fma
+is_a: FMA:10139  ! First costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10148
+name: Capsule of right first costotransverse joint
+namespace: fma
+synonym: "Right first costotransverse joint capsule" EXACT []
+is_a: FMA:10142  ! Capsule of first costotransverse joint
+relationship: part_of FMA:10147 ! Right first costotransverse joint
+
+[Term]
+id: FMA:10149
+name: Costotransverse ligament of right first costotransverse joint
+namespace: fma
+is_a: FMA:10144  ! Costotransverse ligament of first costotransverse joint
+relationship: part_of FMA:10147 ! Right first costotransverse joint
+
+[Term]
+id: FMA:10150
+name: Lateral costotransverse ligament of right first costotransverse joint
+namespace: fma
+is_a: FMA:10145  ! Lateral costotransverse ligament of first costotransverse joint
+relationship: part_of FMA:10147 ! Right first costotransverse joint
+
+[Term]
+id: FMA:10151
+name: Right first costotransverse foramen
+namespace: fma
+is_a: FMA:10146  ! First costotransverse foramen
+
+[Term]
+id: FMA:10152
+name: Left first costotransverse joint
+namespace: fma
+is_a: FMA:10139  ! First costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10153
+name: Capsule of left first costotransverse joint
+namespace: fma
+synonym: "Left first costotransverse joint capsule" EXACT []
+is_a: FMA:10142  ! Capsule of first costotransverse joint
+relationship: part_of FMA:10152 ! Left first costotransverse joint
+
+[Term]
+id: FMA:10154
+name: Costotransverse ligament of left first costotransverse joint
+namespace: fma
+is_a: FMA:10144  ! Costotransverse ligament of first costotransverse joint
+relationship: part_of FMA:10152 ! Left first costotransverse joint
+
+[Term]
+id: FMA:10155
+name: Lateral costotransverse ligament of left first costotransverse joint
+namespace: fma
+is_a: FMA:10145  ! Lateral costotransverse ligament of first costotransverse joint
+relationship: part_of FMA:10152 ! Left first costotransverse joint
+
+[Term]
+id: FMA:10156
+name: Left first costotransverse foramen
+namespace: fma
+is_a: FMA:10146  ! First costotransverse foramen
+
+[Term]
+id: FMA:10157
+name: Capsule of second costotransverse joint
+namespace: fma
+synonym: "Second costotransverse joint capsule" EXACT []
+is_a: FMA:10140  ! Capsule of costotransverse joint
+relationship: part_of FMA:10141 ! Second costotransverse joint
+
+[Term]
+id: FMA:10158
+name: Superior costotransverse ligament of second costotransverse joint
+namespace: fma
+is_a: FMA:8958  ! Superior costotransverse ligament
+relationship: part_of FMA:10141 ! Second costotransverse joint
+
+[Term]
+id: FMA:10159
+name: Costotransverse ligament of second costotransverse joint
+namespace: fma
+is_a: FMA:12163  ! Costotransverse ligament
+relationship: part_of FMA:10141 ! Second costotransverse joint
+
+[Term]
+id: FMA:10160
+name: Lateral costotransverse ligament of second costotransverse joint
+namespace: fma
+is_a: FMA:12162  ! Lateral costotransverse ligament
+relationship: part_of FMA:10141 ! Second costotransverse joint
+
+[Term]
+id: FMA:10161
+name: Accessory ligament of second costotransverse joint
+namespace: fma
+is_a: FMA:10138  ! Accessory ligament
+relationship: part_of FMA:10141 ! Second costotransverse joint
+
+[Term]
+id: FMA:10162
+name: Second costotransverse foramen
+namespace: fma
+is_a: FMA:10143  ! Costotransverse foramen
+
+[Term]
+id: FMA:10163
+name: Right second costotransverse joint
+namespace: fma
+is_a: FMA:10141  ! Second costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10164
+name: Capsule of right second costotransverse joint
+namespace: fma
+synonym: "Right second costotransverse joint capsule" EXACT []
+is_a: FMA:10157  ! Capsule of second costotransverse joint
+relationship: part_of FMA:10163 ! Right second costotransverse joint
+
+[Term]
+id: FMA:10165
+name: Superior costotransverse ligament of right second costotransverse joint
+namespace: fma
+is_a: FMA:10158  ! Superior costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10163 ! Right second costotransverse joint
+
+[Term]
+id: FMA:10166
+name: Costotransverse ligament of right second costotransverse joint
+namespace: fma
+is_a: FMA:10159  ! Costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10163 ! Right second costotransverse joint
+
+[Term]
+id: FMA:10167
+name: Lateral costotransverse ligament of right second costotransverse joint
+namespace: fma
+is_a: FMA:10160  ! Lateral costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10163 ! Right second costotransverse joint
+
+[Term]
+id: FMA:10168
+name: Accessory ligament of right second costotransverse joint
+namespace: fma
+is_a: FMA:10161  ! Accessory ligament of second costotransverse joint
+relationship: part_of FMA:10163 ! Right second costotransverse joint
+
+[Term]
+id: FMA:10169
+name: Right second costotransverse foramen
+namespace: fma
+is_a: FMA:10162  ! Second costotransverse foramen
+
+[Term]
+id: FMA:10170
+name: Left second costotransverse joint
+namespace: fma
+is_a: FMA:10141  ! Second costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10171
+name: Capsule of left second costotransverse joint
+namespace: fma
+synonym: "Left second costotransverse joint capsule" EXACT []
+is_a: FMA:10157  ! Capsule of second costotransverse joint
+relationship: part_of FMA:10170 ! Left second costotransverse joint
+
+[Term]
+id: FMA:10172
+name: Superior costotransverse ligament of left second costotransverse joint
+namespace: fma
+is_a: FMA:10158  ! Superior costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10170 ! Left second costotransverse joint
+
+[Term]
+id: FMA:10173
+name: Costotransverse ligament of left second costotransverse joint
+namespace: fma
+is_a: FMA:10159  ! Costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10170 ! Left second costotransverse joint
+
+[Term]
+id: FMA:10174
+name: Lateral costotransverse ligament of left second costotransverse joint
+namespace: fma
+is_a: FMA:10160  ! Lateral costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10170 ! Left second costotransverse joint
+
+[Term]
+id: FMA:10175
+name: Accessory ligament of left second costotransverse joint
+namespace: fma
+is_a: FMA:10161  ! Accessory ligament of second costotransverse joint
+relationship: part_of FMA:10170 ! Left second costotransverse joint
+
+[Term]
+id: FMA:10176
+name: Left second costotransverse foramen
+namespace: fma
+is_a: FMA:10162  ! Second costotransverse foramen
+
+[Term]
+id: FMA:10177
+name: Third costotransverse joint
+namespace: fma
+is_a: FMA:7952  ! Costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10178
+name: Capsule of third costotransverse joint
+namespace: fma
+synonym: "Third costotransverse joint capsule" EXACT []
+is_a: FMA:10140  ! Capsule of costotransverse joint
+relationship: part_of FMA:10177 ! Third costotransverse joint
+
+[Term]
+id: FMA:10179
+name: Superior costotransverse ligament of third costotransverse joint
+namespace: fma
+is_a: FMA:8958  ! Superior costotransverse ligament
+relationship: part_of FMA:10177 ! Third costotransverse joint
+
+[Term]
+id: FMA:10180
+name: Costotransverse ligament of third costotransverse joint
+namespace: fma
+is_a: FMA:12163  ! Costotransverse ligament
+relationship: part_of FMA:10177 ! Third costotransverse joint
+
+[Term]
+id: FMA:10181
+name: Lateral costotransverse ligament of third costotransverse joint
+namespace: fma
+is_a: FMA:12162  ! Lateral costotransverse ligament
+relationship: part_of FMA:10177 ! Third costotransverse joint
+
+[Term]
+id: FMA:10182
+name: Accessory ligament of third costotransverse joint
+namespace: fma
+is_a: FMA:10138  ! Accessory ligament
+relationship: part_of FMA:10177 ! Third costotransverse joint
+
+[Term]
+id: FMA:10183
+name: Third costotransverse foramen
+namespace: fma
+is_a: FMA:10143  ! Costotransverse foramen
+
+[Term]
+id: FMA:10184
+name: Right third costotransverse joint
+namespace: fma
+is_a: FMA:10177  ! Third costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10185
+name: Capsule of right third costotransverse joint
+namespace: fma
+synonym: "Right third costotransverse joint capsule" EXACT []
+is_a: FMA:10178  ! Capsule of third costotransverse joint
+relationship: part_of FMA:10184 ! Right third costotransverse joint
+
+[Term]
+id: FMA:10186
+name: Superior costotransverse ligament of right third costotransverse joint
+namespace: fma
+is_a: FMA:10179  ! Superior costotransverse ligament of third costotransverse joint
+relationship: part_of FMA:10184 ! Right third costotransverse joint
+
+[Term]
+id: FMA:10187
+name: Costotransverse ligament of right third costotransverse joint
+namespace: fma
+is_a: FMA:10180  ! Costotransverse ligament of third costotransverse joint
+
+[Term]
+id: FMA:10188
+name: Lateral costotransverse ligament of right third costotransverse joint
+namespace: fma
+is_a: FMA:10181  ! Lateral costotransverse ligament of third costotransverse joint
+relationship: part_of FMA:10184 ! Right third costotransverse joint
+
+[Term]
+id: FMA:10189
+name: Accessory ligament of right third costotransverse joint
+namespace: fma
+is_a: FMA:10182  ! Accessory ligament of third costotransverse joint
+relationship: part_of FMA:10184 ! Right third costotransverse joint
+
+[Term]
+id: FMA:10190
+name: Right third costotransverse foramen
+namespace: fma
+is_a: FMA:10183  ! Third costotransverse foramen
+
+[Term]
+id: FMA:10191
+name: Left third costotransverse joint
+namespace: fma
+is_a: FMA:10177  ! Third costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10192
+name: Capsule of left third costotransverse joint
+namespace: fma
+synonym: "Left third costotransverse joint capsule" EXACT []
+is_a: FMA:10178  ! Capsule of third costotransverse joint
+relationship: part_of FMA:10191 ! Left third costotransverse joint
+
+[Term]
+id: FMA:10193
+name: Superior costotransverse ligament of left third costotransverse joint
+namespace: fma
+is_a: FMA:10179  ! Superior costotransverse ligament of third costotransverse joint
+relationship: part_of FMA:10191 ! Left third costotransverse joint
+
+[Term]
+id: FMA:10194
+name: Costotransverse ligament of left third costotransverse joint
+namespace: fma
+is_a: FMA:10180  ! Costotransverse ligament of third costotransverse joint
+relationship: part_of FMA:10191 ! Left third costotransverse joint
+
+[Term]
+id: FMA:10195
+name: Lateral costotransverse ligament of left third costotransverse joint
+namespace: fma
+is_a: FMA:10181  ! Lateral costotransverse ligament of third costotransverse joint
+relationship: part_of FMA:10191 ! Left third costotransverse joint
+
+[Term]
+id: FMA:10196
+name: Accessory ligament of left third costotransverse joint
+namespace: fma
+is_a: FMA:10182  ! Accessory ligament of third costotransverse joint
+relationship: part_of FMA:10191 ! Left third costotransverse joint
+
+[Term]
+id: FMA:10197
+name: Left third costotransverse foramen
+namespace: fma
+is_a: FMA:10183  ! Third costotransverse foramen
+
+[Term]
+id: FMA:10198
+name: Fourth costotransverse joint
+namespace: fma
+is_a: FMA:7952  ! Costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10199
+name: Capsule of fourth costotransverse joint
+namespace: fma
+synonym: "Fourth costotransverse joint capsule" EXACT []
+is_a: FMA:10140  ! Capsule of costotransverse joint
+relationship: part_of FMA:10198 ! Fourth costotransverse joint
+
+[Term]
+id: FMA:10200
+name: Superior costotransverse ligament of fourth costotransverse joint
+namespace: fma
+is_a: FMA:8958  ! Superior costotransverse ligament
+relationship: part_of FMA:10198 ! Fourth costotransverse joint
+
+[Term]
+id: FMA:10201
+name: Lateral costotransverse ligament of fourth costotransverse joint
+namespace: fma
+is_a: FMA:12162  ! Lateral costotransverse ligament
+relationship: part_of FMA:10198 ! Fourth costotransverse joint
+
+[Term]
+id: FMA:10202
+name: Costotransverse ligament of fourth costotransverse joint
+namespace: fma
+is_a: FMA:12163  ! Costotransverse ligament
+relationship: part_of FMA:10198 ! Fourth costotransverse joint
+
+[Term]
+id: FMA:10203
+name: Accessory ligament of fourth costotransverse joint
+namespace: fma
+is_a: FMA:10138  ! Accessory ligament
+relationship: part_of FMA:10198 ! Fourth costotransverse joint
+
+[Term]
+id: FMA:10204
+name: Fourth costotransverse foramen
+namespace: fma
+is_a: FMA:10143  ! Costotransverse foramen
+
+[Term]
+id: FMA:10205
+name: Right fourth costotransverse joint
+namespace: fma
+is_a: FMA:10198  ! Fourth costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10206
+name: Capsule of right fourth costotransverse joint
+namespace: fma
+synonym: "Right fourth costotransverse joint capsule" EXACT []
+is_a: FMA:10199  ! Capsule of fourth costotransverse joint
+relationship: part_of FMA:10205 ! Right fourth costotransverse joint
+
+[Term]
+id: FMA:10207
+name: Superior costotransverse ligament of right fourth costotransverse joint
+namespace: fma
+is_a: FMA:10200  ! Superior costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10205 ! Right fourth costotransverse joint
+
+[Term]
+id: FMA:10208
+name: Costotransverse ligament of right fourth costotransverse joint
+namespace: fma
+is_a: FMA:10202  ! Costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10205 ! Right fourth costotransverse joint
+
+[Term]
+id: FMA:10209
+name: Lateral costotransverse ligament of right fourth costotransverse joint
+namespace: fma
+is_a: FMA:10201  ! Lateral costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10205 ! Right fourth costotransverse joint
+
+[Term]
+id: FMA:10210
+name: Accessory ligament of right fourth costotransverse joint
+namespace: fma
+is_a: FMA:10203  ! Accessory ligament of fourth costotransverse joint
+relationship: part_of FMA:10205 ! Right fourth costotransverse joint
+
+[Term]
+id: FMA:10211
+name: Right fourth costotransverse foramen
+namespace: fma
+is_a: FMA:10204  ! Fourth costotransverse foramen
+
+[Term]
+id: FMA:10212
+name: Left fourth costotransverse joint
+namespace: fma
+is_a: FMA:10198  ! Fourth costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10213
+name: Capsule of left fourth costotransverse joint
+namespace: fma
+synonym: "Left fourth costotransverse joint capsule" EXACT []
+is_a: FMA:10199  ! Capsule of fourth costotransverse joint
+relationship: part_of FMA:10212 ! Left fourth costotransverse joint
+
+[Term]
+id: FMA:10214
+name: Superior costotransverse ligament of left fourth costotransverse joint
+namespace: fma
+is_a: FMA:10200  ! Superior costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10212 ! Left fourth costotransverse joint
+
+[Term]
+id: FMA:10215
+name: Costotransverse ligament of left fourth costotransverse joint
+namespace: fma
+is_a: FMA:10202  ! Costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10212 ! Left fourth costotransverse joint
+
+[Term]
+id: FMA:10216
+name: Lateral costotransverse ligament of left fourth costotransverse joint
+namespace: fma
+is_a: FMA:10201  ! Lateral costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10212 ! Left fourth costotransverse joint
+
+[Term]
+id: FMA:10217
+name: Accessory ligament of left fourth costotransverse joint
+namespace: fma
+is_a: FMA:10203  ! Accessory ligament of fourth costotransverse joint
+relationship: part_of FMA:10212 ! Left fourth costotransverse joint
+
+[Term]
+id: FMA:10218
+name: Left fourth costotransverse foramen
+namespace: fma
+is_a: FMA:10204  ! Fourth costotransverse foramen
+
+[Term]
+id: FMA:10219
+name: Fifth costotransverse joint
+namespace: fma
+is_a: FMA:7952  ! Costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10220
+name: Capsule of fifth costotransverse joint
+namespace: fma
+synonym: "Fifth costotransverse joint capsule" EXACT []
+is_a: FMA:10140  ! Capsule of costotransverse joint
+relationship: part_of FMA:10219 ! Fifth costotransverse joint
+
+[Term]
+id: FMA:10221
+name: Superior costotransverse ligament of fifth costotransverse joint
+namespace: fma
+is_a: FMA:8958  ! Superior costotransverse ligament
+relationship: part_of FMA:10219 ! Fifth costotransverse joint
+
+[Term]
+id: FMA:10222
+name: Costotransverse ligament of fifth costotransverse joint
+namespace: fma
+is_a: FMA:12163  ! Costotransverse ligament
+relationship: part_of FMA:10219 ! Fifth costotransverse joint
+
+[Term]
+id: FMA:10223
+name: Lateral costotransverse ligament of fifth costotransverse joint
+namespace: fma
+is_a: FMA:12162  ! Lateral costotransverse ligament
+relationship: part_of FMA:10219 ! Fifth costotransverse joint
+
+[Term]
+id: FMA:10224
+name: Accessory ligament of fifth costotransverse joint
+namespace: fma
+is_a: FMA:10138  ! Accessory ligament
+relationship: part_of FMA:10219 ! Fifth costotransverse joint
+
+[Term]
+id: FMA:10225
+name: Fifth costotransverse foramen
+namespace: fma
+is_a: FMA:10143  ! Costotransverse foramen
+
+[Term]
+id: FMA:10226
+name: Right fifth costotransverse joint
+namespace: fma
+is_a: FMA:10219  ! Fifth costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10227
+name: Capsule of right fifth costotransverse joint
+namespace: fma
+synonym: "Right fifth costotransverse joint capsule" EXACT []
+is_a: FMA:10220  ! Capsule of fifth costotransverse joint
+relationship: part_of FMA:10226 ! Right fifth costotransverse joint
+
+[Term]
+id: FMA:10228
+name: Superior costotransverse ligament of right fifth costotransverse joint
+namespace: fma
+is_a: FMA:10221  ! Superior costotransverse ligament of fifth costotransverse joint
+relationship: part_of FMA:10226 ! Right fifth costotransverse joint
+
+[Term]
+id: FMA:10229
+name: Costotransverse ligament of right fifth costotransverse joint
+namespace: fma
+is_a: FMA:10222  ! Costotransverse ligament of fifth costotransverse joint
+relationship: part_of FMA:10226 ! Right fifth costotransverse joint
+
+[Term]
+id: FMA:10230
+name: Lateral costotransverse ligament of right fifth costotransverse joint
+namespace: fma
+is_a: FMA:10223  ! Lateral costotransverse ligament of fifth costotransverse joint
+relationship: part_of FMA:10226 ! Right fifth costotransverse joint
+
+[Term]
+id: FMA:10231
+name: Accessory ligament of right fifth costotransverse joint
+namespace: fma
+is_a: FMA:10224  ! Accessory ligament of fifth costotransverse joint
+relationship: part_of FMA:10226 ! Right fifth costotransverse joint
+
+[Term]
+id: FMA:10232
+name: Right fifth costotransverse foramen
+namespace: fma
+is_a: FMA:10225  ! Fifth costotransverse foramen
+
+[Term]
+id: FMA:10233
+name: Left fifth costotransverse joint
+namespace: fma
+is_a: FMA:10219  ! Fifth costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10234
+name: Capsule of left fifth costotransverse joint
+namespace: fma
+synonym: "Left fifth costotransverse joint capsule" EXACT []
+is_a: FMA:10220  ! Capsule of fifth costotransverse joint
+relationship: part_of FMA:10233 ! Left fifth costotransverse joint
+
+[Term]
+id: FMA:10235
+name: Superior costotransverse ligament of left fifth costotransverse joint
+namespace: fma
+is_a: FMA:10221  ! Superior costotransverse ligament of fifth costotransverse joint
+relationship: part_of FMA:10233 ! Left fifth costotransverse joint
+
+[Term]
+id: FMA:10236
+name: Costotransverse ligament of left fifth costotransverse joint
+namespace: fma
+is_a: FMA:10222  ! Costotransverse ligament of fifth costotransverse joint
+relationship: part_of FMA:10233 ! Left fifth costotransverse joint
+
+[Term]
+id: FMA:10237
+name: Lateral costotransverse ligament of left fifth costotransverse joint
+namespace: fma
+is_a: FMA:10223  ! Lateral costotransverse ligament of fifth costotransverse joint
+relationship: part_of FMA:10233 ! Left fifth costotransverse joint
+
+[Term]
+id: FMA:10238
+name: Accessory ligament of left fifth costotransverse joint
+namespace: fma
+is_a: FMA:10224  ! Accessory ligament of fifth costotransverse joint
+relationship: part_of FMA:10233 ! Left fifth costotransverse joint
+
+[Term]
+id: FMA:10239
+name: Left fifth costotransverse foramen
+namespace: fma
+is_a: FMA:10225  ! Fifth costotransverse foramen
+
+[Term]
+id: FMA:10240
+name: Sixth costotransverse joint
+namespace: fma
+is_a: FMA:7952  ! Costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10241
+name: Capsule of sixth costotransverse joint
+namespace: fma
+synonym: "Sixth costotransverse joint capsule" EXACT []
+is_a: FMA:10140  ! Capsule of costotransverse joint
+relationship: part_of FMA:10240 ! Sixth costotransverse joint
+
+[Term]
+id: FMA:10242
+name: Superior costotransverse ligament of sixth costotransverse joint
+namespace: fma
+is_a: FMA:8958  ! Superior costotransverse ligament
+relationship: part_of FMA:10240 ! Sixth costotransverse joint
+
+[Term]
+id: FMA:10243
+name: Costotransverse ligament of sixth costotransverse joint
+namespace: fma
+is_a: FMA:12163  ! Costotransverse ligament
+relationship: part_of FMA:10240 ! Sixth costotransverse joint
+
+[Term]
+id: FMA:10244
+name: Lateral costotransverse ligament of sixth costotransverse joint
+namespace: fma
+is_a: FMA:12162  ! Lateral costotransverse ligament
+relationship: part_of FMA:10240 ! Sixth costotransverse joint
+
+[Term]
+id: FMA:10245
+name: Accessory ligament of sixth costotransverse joint
+namespace: fma
+is_a: FMA:10138  ! Accessory ligament
+relationship: part_of FMA:10240 ! Sixth costotransverse joint
+
+[Term]
+id: FMA:10246
+name: Sixth costotransverse foramen
+namespace: fma
+is_a: FMA:10143  ! Costotransverse foramen
+
+[Term]
+id: FMA:10247
+name: Right sixth costotransverse joint
+namespace: fma
+is_a: FMA:10240  ! Sixth costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10248
+name: Capsule of right sixth costotransverse joint
+namespace: fma
+synonym: "Right sixth costotransverse joint capsule" EXACT []
+is_a: FMA:10241  ! Capsule of sixth costotransverse joint
+relationship: part_of FMA:10247 ! Right sixth costotransverse joint
+
+[Term]
+id: FMA:10249
+name: Superior costotransverse ligament of right sixth costotransverse joint
+namespace: fma
+is_a: FMA:10242  ! Superior costotransverse ligament of sixth costotransverse joint
+relationship: part_of FMA:10247 ! Right sixth costotransverse joint
+
+[Term]
+id: FMA:10250
+name: Costotransverse ligament of right sixth costotransverse joint
+namespace: fma
+is_a: FMA:10243  ! Costotransverse ligament of sixth costotransverse joint
+relationship: part_of FMA:10247 ! Right sixth costotransverse joint
+
+[Term]
+id: FMA:10251
+name: Lateral costotransverse ligament of right sixth costotransverse joint
+namespace: fma
+is_a: FMA:10244  ! Lateral costotransverse ligament of sixth costotransverse joint
+relationship: part_of FMA:10247 ! Right sixth costotransverse joint
+
+[Term]
+id: FMA:10252
+name: Accessory ligament of right sixth costotransverse joint
+namespace: fma
+is_a: FMA:10245  ! Accessory ligament of sixth costotransverse joint
+relationship: part_of FMA:10247 ! Right sixth costotransverse joint
+
+[Term]
+id: FMA:10253
+name: Right sixth costotransverse foramen
+namespace: fma
+is_a: FMA:10246  ! Sixth costotransverse foramen
+
+[Term]
+id: FMA:10254
+name: Left sixth costotransverse joint
+namespace: fma
+is_a: FMA:10240  ! Sixth costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10255
+name: Capsule of left sixth costotransverse joint
+namespace: fma
+synonym: "Left sixth costotransverse joint capsule" EXACT []
+is_a: FMA:10241  ! Capsule of sixth costotransverse joint
+relationship: part_of FMA:10254 ! Left sixth costotransverse joint
+
+[Term]
+id: FMA:10256
+name: Superior costotransverse ligament of left sixth costotransverse joint
+namespace: fma
+is_a: FMA:10242  ! Superior costotransverse ligament of sixth costotransverse joint
+relationship: part_of FMA:10254 ! Left sixth costotransverse joint
+
+[Term]
+id: FMA:10257
+name: Costotransverse ligament of left sixth costotransverse joint
+namespace: fma
+is_a: FMA:10243  ! Costotransverse ligament of sixth costotransverse joint
+relationship: part_of FMA:10254 ! Left sixth costotransverse joint
+
+[Term]
+id: FMA:10258
+name: Lateral costotransverse ligament of left sixth costotransverse joint
+namespace: fma
+is_a: FMA:10244  ! Lateral costotransverse ligament of sixth costotransverse joint
+relationship: part_of FMA:10254 ! Left sixth costotransverse joint
+
+[Term]
+id: FMA:10259
+name: Accessory ligament of left sixth costotransverse joint
+namespace: fma
+is_a: FMA:10245  ! Accessory ligament of sixth costotransverse joint
+relationship: part_of FMA:10254 ! Left sixth costotransverse joint
+
+[Term]
+id: FMA:10260
+name: Left sixth costotransverse foramen
+namespace: fma
+is_a: FMA:10246  ! Sixth costotransverse foramen
+
+[Term]
+id: FMA:10261
+name: Seventh costotransverse joint
+namespace: fma
+is_a: FMA:7952  ! Costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10262
+name: Capsule of seventh costotransverse joint
+namespace: fma
+synonym: "Seventh costotransverse joint capsule" EXACT []
+is_a: FMA:10140  ! Capsule of costotransverse joint
+relationship: part_of FMA:10261 ! Seventh costotransverse joint
+
+[Term]
+id: FMA:10263
+name: Superior costotransverse ligament of seventh costotransverse joint
+namespace: fma
+is_a: FMA:8958  ! Superior costotransverse ligament
+relationship: part_of FMA:10261 ! Seventh costotransverse joint
+
+[Term]
+id: FMA:10264
+name: Costotransverse ligament of seventh costotransverse joint
+namespace: fma
+is_a: FMA:12163  ! Costotransverse ligament
+relationship: part_of FMA:10261 ! Seventh costotransverse joint
+
+[Term]
+id: FMA:10265
+name: Lateral costotransverse ligament of seventh costotransverse joint
+namespace: fma
+is_a: FMA:12162  ! Lateral costotransverse ligament
+relationship: part_of FMA:10261 ! Seventh costotransverse joint
+
+[Term]
+id: FMA:10266
+name: Accessory ligament of seventh costotransverse joint
+namespace: fma
+is_a: FMA:10138  ! Accessory ligament
+relationship: part_of FMA:10261 ! Seventh costotransverse joint
+
+[Term]
+id: FMA:10267
+name: Seventh costotransverse foramen
+namespace: fma
+is_a: FMA:10143  ! Costotransverse foramen
+
+[Term]
+id: FMA:10268
+name: Right seventh costotransverse joint
+namespace: fma
+is_a: FMA:10261  ! Seventh costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10269
+name: Capsule of right seventh costotransverse joint
+namespace: fma
+synonym: "Right seventh costotransverse joint capsule" EXACT []
+is_a: FMA:10262  ! Capsule of seventh costotransverse joint
+relationship: part_of FMA:10268 ! Right seventh costotransverse joint
+
+[Term]
+id: FMA:10270
+name: Superior costotransverse ligament of right seventh costotransverse joint
+namespace: fma
+is_a: FMA:10263  ! Superior costotransverse ligament of seventh costotransverse joint
+relationship: part_of FMA:10268 ! Right seventh costotransverse joint
+
+[Term]
+id: FMA:10271
+name: Costotransverse ligament of right seventh costotransverse joint
+namespace: fma
+is_a: FMA:10264  ! Costotransverse ligament of seventh costotransverse joint
+relationship: part_of FMA:10268 ! Right seventh costotransverse joint
+
+[Term]
+id: FMA:10272
+name: Lateral costotransverse ligament of right seventh costotransverse joint
+namespace: fma
+is_a: FMA:10265  ! Lateral costotransverse ligament of seventh costotransverse joint
+relationship: part_of FMA:10268 ! Right seventh costotransverse joint
+
+[Term]
+id: FMA:10273
+name: Accessory ligament of right seventh costotransverse joint
+namespace: fma
+is_a: FMA:10266  ! Accessory ligament of seventh costotransverse joint
+relationship: part_of FMA:10268 ! Right seventh costotransverse joint
+
+[Term]
+id: FMA:10274
+name: Right seventh costotransverse foramen
+namespace: fma
+is_a: FMA:10267  ! Seventh costotransverse foramen
+
+[Term]
+id: FMA:10275
+name: Left seventh costotransverse joint
+namespace: fma
+is_a: FMA:10261  ! Seventh costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10276
+name: Capsule of left seventh costotransverse joint
+namespace: fma
+synonym: "Left seventh costotransverse joint capsule" EXACT []
+is_a: FMA:10262  ! Capsule of seventh costotransverse joint
+relationship: part_of FMA:10275 ! Left seventh costotransverse joint
+
+[Term]
+id: FMA:10277
+name: Superior costotransverse ligament of left seventh costotransverse joint
+namespace: fma
+is_a: FMA:10263  ! Superior costotransverse ligament of seventh costotransverse joint
+relationship: part_of FMA:10275 ! Left seventh costotransverse joint
+
+[Term]
+id: FMA:10278
+name: Costotransverse ligament of left seventh costotransverse joint
+namespace: fma
+is_a: FMA:10264  ! Costotransverse ligament of seventh costotransverse joint
+relationship: part_of FMA:10275 ! Left seventh costotransverse joint
+
+[Term]
+id: FMA:10279
+name: Lateral costotransverse ligament of left seventh costotransverse joint
+namespace: fma
+is_a: FMA:10265  ! Lateral costotransverse ligament of seventh costotransverse joint
+relationship: part_of FMA:10275 ! Left seventh costotransverse joint
+
+[Term]
+id: FMA:10280
+name: Accessory ligament of left seventh costotransverse joint
+namespace: fma
+is_a: FMA:10266  ! Accessory ligament of seventh costotransverse joint
+relationship: part_of FMA:10275 ! Left seventh costotransverse joint
+
+[Term]
+id: FMA:10281
+name: Left seventh costotransverse foramen
+namespace: fma
+is_a: FMA:10267  ! Seventh costotransverse foramen
+
+[Term]
+id: FMA:10282
+name: Eighth costotransverse joint
+namespace: fma
+is_a: FMA:7952  ! Costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10283
+name: Capsule of eighth costotransverse joint
+namespace: fma
+synonym: "Eighth costotransverse joint capsule" EXACT []
+is_a: FMA:10140  ! Capsule of costotr...
 
[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [1025] obo-database/trunk/xsl/oboxml_to_obd_prestore.xsl

From: <cmu...@us...> - 2007-10-10 21:05:56

Revision: 1025
          http://obo.svn.sourceforge.net/obo/?rev=1025&view=rev
Author:   cmungall
Date:     2007-10-10 14:05:49 -0700 (Wed, 10 Oct 2007)

Log Message:
-----------


Added Paths:
-----------
    obo-database/trunk/xsl/oboxml_to_obd_prestore.xsl

Added: obo-database/trunk/xsl/oboxml_to_obd_prestore.xsl
===================================================================
--- obo-database/trunk/xsl/oboxml_to_obd_prestore.xsl	                        (rev 0)
+++ obo-database/trunk/xsl/oboxml_to_obd_prestore.xsl	2007-10-10 21:05:49 UTC (rev 1025)
@@ -0,0 +1,1141 @@
+<?xml version = "1.0"?>
+<!DOCTYPE stylesheet [
+  <!ENTITY oboInOwl "http://www.geneontology.org/formats/oboInOwl#">
+  <!ENTITY oboContent "http://purl.org/obo/owl/">
+  <!ENTITY xref "http://purl.org/obo/owl/">
+  <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#">
+  ]>
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
+
+  <!-- this transforms oboxml into obdxml -->
+  <!-- obdxml can be loaded into an obd db using DBIx::DBStag -->
+  <xsl:param name="source"/>
+
+  <xsl:output indent="yes" method="xml"/>
+
+  <!-- *********************************************** -->
+  <!-- Parameters -->
+  <!-- *********************************************** -->
+  <xsl:param name="localid_prefix"/>
+  <xsl:param name="default_idspace"/>
+
+  <!-- *********************************************** -->
+  <!-- Indexes -->
+  <!-- *********************************************** -->
+  <xsl:key name="k_idspace" match="obo/header/idspace" use="local"/>
+  <xsl:key name="k_entity" match="term|typedef|instance" use="id"/>
+
+  <xsl:variable name="unique_namespace" select="//namespace[not(.=preceding::namespace)]"/>
+  <xsl:variable name="source_id" select="//source/source_id"/>
+
+  <xsl:template match="/">
+    <obd>
+      <xsl:comment>
+        <xsl:text>XORT macros - we can refer to these later by stag??</xsl:text>
+      </xsl:comment>
+
+      <!-- set macros; ensure the basic stuff is there -->
+
+      <node op="force" id="OBO_REL">
+        <uid>OBO_REL</uid>
+        <label>OBO_REL</label>
+        <uri>http://www.obofoundry.org/ro#</uri>
+        <metatype><xsl:text>I</xsl:text></metatype>
+      </node>
+
+      <node op="force" id="_default_idspace">
+        <uid>
+          <xsl:choose>
+            <xsl:when test="$default_idspace">
+              <xsl:value-of select="$default_idspace"/>
+            </xsl:when>
+            <xsl:otherwise>
+              <xsl:text>_global</xsl:text>
+            </xsl:otherwise>
+          </xsl:choose>
+        </uid>
+      </node>
+
+      <node op="force" id="is_a">
+        <uid>OBO_REL:is_a</uid>
+        <metatype><xsl:text>R</xsl:text></metatype>
+      </node>
+
+      <node op="force" id="instance_of">
+        <uid>OBO_REL:instance_of</uid>
+        <metatype><xsl:text>R</xsl:text></metatype>
+      </node>
+
+      <node op="force" id="owl:inverseOf">
+        <uid>owl:inverseOf</uid>
+        <metatype><xsl:text>R</xsl:text></metatype>
+      </node>
+
+      <node op="force" id="in_organism">
+        <uid>oban:in_organism</uid>
+        <metatype><xsl:text>R</xsl:text></metatype>
+      </node>
+
+      <node op="force" id="influences">
+        <uid>oban:influences</uid>
+        <metatype><xsl:text>R</xsl:text></metatype>
+      </node>
+
+      <!-- ID only appears as an attribute in trailing qualifiers -->
+      <xsl:for-each select="//@id">
+        <node id="{.}">
+          <is_reiflink><xsl:text>t</xsl:text></is_reiflink>
+          <is_anonymous><xsl:text>t</xsl:text></is_anonymous>
+        </node>
+      </xsl:for-each>
+
+      <xsl:call-template name="embed-delete-directives"/>
+      <xsl:apply-templates select="*/source"/>
+      <xsl:apply-templates select="*/header/subsetdef"/>
+
+      <!-- terms can appear in different obo file types -->
+      <xsl:comment>relationship types</xsl:comment>
+      <xsl:apply-templates select="*/typedef"/>
+
+      <xsl:comment>terms</xsl:comment>
+      <xsl:apply-templates select="*/term"/>
+
+      <xsl:comment>instances</xsl:comment>
+      <xsl:apply-templates select="*/instance"/>
+
+      <xsl:comment>annotations</xsl:comment>
+      <xsl:apply-templates select="*/annotation"/>
+
+
+      <xsl:comment>is_a relationship types</xsl:comment>
+      <xsl:apply-templates select="*/term/is_a"/>
+      <xsl:apply-templates select="*/typedef/is_a"/>
+      <xsl:apply-templates select="*/typedef/inverse_of"/>
+
+      <xsl:comment>other relationship types</xsl:comment>
+      <xsl:apply-templates select="*/term/relationship"/>
+
+      <xsl:comment>
+        logical definitions (by intersection or union)
+      </xsl:comment>
+      <xsl:apply-templates select="*/term/intersection_of"/>
+      <xsl:apply-templates select="*/term/union_of"/>
+
+      <xsl:comment>instance-level relations</xsl:comment>
+      <xsl:apply-templates select="*/instance/property_value"/>
+
+      <!-- old-style obo-xml annotations -->
+      <xsl:apply-templates select="//prod"/>
+
+    </obd>
+  </xsl:template>
+
+  <!-- todo -->
+  <xsl:template name="embed-delete-directives">
+    <xsl:comment>
+      <xsl:text>
+        Update policy: all links from this source are deleted and repopulated
+      </xsl:text>
+    </xsl:comment>
+    <_sql op="delete" from="link" match="loaded_from_id" pkey="link_id">
+      <xsl:call-template name="sql-for-namespaces"/>
+    </_sql>
+    <_sql op="delete" from="tagval" match="loaded_from_id" pkey="tagval_id">
+      <xsl:call-template name="sql-for-namespaces"/>
+    </_sql>
+    <_sql op="delete" from="sameas" match="loaded_from_id" pkey="sameas_id">
+      <xsl:call-template name="sql-for-namespaces"/>
+    </_sql>
+    <_sql op="delete" from="alias" match="loaded_from_id" pkey="alias_id">
+      <xsl:call-template name="sql-for-namespaces"/>
+    </_sql>
+    <_sql op="delete" from="description" match="loaded_from_id" pkey="description_id">
+      <xsl:call-template name="sql-for-namespaces"/>
+    </_sql>
+    <!-- annotation nodes too? -->
+  </xsl:template>
+
+  <xsl:template name="sql-for-namespaces">
+    <_sql op="select" from="node" col="node_id" match="uid">
+      <xsl:value-of select="//source/source_id"/>
+    </_sql>
+  </xsl:template>
+
+  <xsl:template name="xxxx-sql-for-namespaces">
+    <xsl:for-each select="$unique_namespace">
+      <_sql op="select" from="node" col="node_id" match="uid">
+        <xsl:value-of select="."/>
+      </_sql>
+    </xsl:for-each>
+  </xsl:template>
+
+  <xsl:template match="term">
+    <node id="{id}">
+      <xsl:apply-templates select="id" mode="id"/>
+      <xsl:call-template name="node_audit"/>
+
+      <xsl:choose>
+        <xsl:when test="is_anonymous=1">
+          <is_anonymous>
+            <xsl:text>t</xsl:text>
+          </is_anonymous>
+        </xsl:when>
+        <xsl:otherwise>
+          <xsl:apply-templates select="id" mode="uri"/>
+        </xsl:otherwise>
+      </xsl:choose>
+
+      <metatype><xsl:text>C</xsl:text></metatype>
+      <xsl:if test="is_obsolete=1">
+        <is_obsolete>t</is_obsolete>
+      </xsl:if>
+      <xsl:if test="name">
+        <label>
+          <xsl:value-of select="name"/>
+        </label>
+      </xsl:if>
+
+      <!-- when no namespace, use string before ':' in id for source  if any -->
+      <xsl:apply-templates mode="source_id" select="."/>
+
+      <xsl:apply-templates select="def"/>
+      <xsl:apply-templates select="comment"/>
+      <xsl:apply-templates select="synonym"/>
+      <xsl:apply-templates select="alt_id"/>
+      <xsl:apply-templates select="xref_analog"/>
+      <xsl:apply-templates select="subset"/>
+    </node>
+  </xsl:template>
+
+  <!-- in oboxml, a typedef element is used for relations and slots. these map to nodes in obd -->
+  <xsl:template match="typedef">
+    <node id="{id}">
+      <xsl:apply-templates select="id" mode="id"/>
+      <metatype>
+        <xsl:text>R</xsl:text>
+      </metatype>
+      <label>
+        <!-- note: earlier versions of ontologies had ad-hoc names -->
+        <!-- we want to use the ID of the name here -->
+        <xsl:choose>
+          <xsl:when test="contains(id,':')">
+            <!-- we have a 'real' ID, which means the name is real -->
+            <xsl:value-of select="name"/>
+          </xsl:when>
+          <xsl:otherwise>
+            <!-- old ontology: ID is actually the name -->
+            <xsl:value-of select="id"/>
+          </xsl:otherwise>
+        </xsl:choose>
+      </label>
+
+      <!-- by default, relations go in the relationship
+           namespace, even though they may not be defined in
+           official obo relations ontology -->
+      <xsl:choose>
+        <xsl:when test="namespace and contains(id,':')">
+          <source_id>
+            <node>
+              <uid>
+                <xsl:value-of select="namespace"/>
+              </uid>
+              <metatype><xsl:text>I</xsl:text></metatype>
+            </node>
+          </source_id>
+        </xsl:when>
+        <xsl:otherwise>
+          <source_id>_default_idspace</source_id>
+        </xsl:otherwise>
+      </xsl:choose>
+
+      <xsl:if test="is_obsolete">
+        <is_obsolete>t</is_obsolete>
+      </xsl:if>
+      <xsl:apply-templates select="is_symmetric|is_cyclic|is_anti_symmetric|is_reflexive|is_transitive"/>
+      <xsl:apply-templates select="def"/>
+      <xsl:apply-templates select="synonym"/>
+      <xsl:apply-templates select="alt_id"/>
+      <xsl:apply-templates select="xref_analog"/>
+    </node>
+  </xsl:template>
+
+  <!-- more work needed here!! -->
+  <xsl:template match="instance">
+    <node id="{id}">
+      <xsl:apply-templates select="id" mode="id"/>
+      <xsl:choose>
+        <xsl:when test="is_anonymous=1">
+          <is_anonymous>
+            <xsl:text>t</xsl:text>
+          </is_anonymous>
+        </xsl:when>
+        <xsl:otherwise>
+          <xsl:apply-templates select="id" mode="uri"/>
+        </xsl:otherwise>
+      </xsl:choose>
+      <xsl:apply-templates select="name" mode="label"/>
+      <metatype><xsl:text>I</xsl:text></metatype>
+      
+      <xsl:if test="namespace">
+        <source_id>
+          <node>
+            <uid>
+              <xsl:value-of select="namespace"/>
+            </uid>
+          </node>
+        </source_id>
+      </xsl:if>
+
+      <xsl:apply-templates select="instance_of"/>
+      <xsl:apply-templates select="comment"/>
+      <xsl:apply-templates select="synonym"/>
+      <xsl:apply-templates select="alt_id"/>
+      <xsl:apply-templates select="xref_analog"/>
+      <xsl:apply-templates select="subset"/>
+
+    </node>
+  </xsl:template>
+
+  <xsl:template match="subsetdef">
+    <node>
+      <uid>
+        <xsl:value-of select="id"/>
+      </uid>
+      <label>
+        <xsl:value-of select="name"/>
+      </label>
+      <metatype><xsl:text>I</xsl:text></metatype>
+      <source_id>
+        <node>
+          <uid>subset</uid>
+        </node>
+      </source_id>
+    </node>
+  </xsl:template>
+
+  <xsl:template match="is_symmetric|is_cyclic|is_anti_symmetric|is_reflexive|is_transitive">
+    <xsl:if test="../is_transitive">
+      <is_transitive>t</is_transitive>
+    </xsl:if>
+    <!-- what about other rel property?? -->
+  </xsl:template>
+
+  <!-- reference to a node
+       assumed to be inside a foreign key element -->
+  <xsl:template match="*" mode="node_ref">
+    <xsl:if test="not(.)">
+      <xsl:message terminate="yes">
+        <xsl:copy select="."/>
+        <xsl:text>No ID</xsl:text>
+      </xsl:message>
+    </xsl:if>
+    <xsl:choose>
+      <!-- we've already referenced this node -
+           we assume it has already been loaded -->
+      <xsl:when test="key('k_entity',.)">
+        <xsl:value-of select="."/>
+      </xsl:when>
+      <!-- convention: bNodes are in _ idspace -->
+      <!-- is there a term or typedef by this ID in this file? -->
+      <xsl:when test="substring-before(.,':') = '_'">
+        <!-- use a XORT id -->
+        <xsl:value-of select="."/>
+      </xsl:when>
+      <xsl:otherwise>
+        <!-- explicit node reference -->
+        <node>
+          <uid>
+            <xsl:value-of select="."/>
+          </uid>
+        </node>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:template>
+
+  <xsl:template name="link_audit">
+    <link_audit op="insert">
+      <source_id>__source</source_id>
+      <loadtime>now</loadtime>
+    </link_audit>
+  </xsl:template>
+  <xsl:template name="node_audit">
+    <node_audit op="insert">
+      <source_id>__source</source_id>
+      <loadtime>now</loadtime>
+    </node_audit>
+  </xsl:template>
+
+  <xsl:template match="*" mode="id">
+    <xsl:if test="not(.)">
+      <xsl:message terminate="yes">
+        <xsl:copy select="."/>
+        <xsl:text>No ID</xsl:text>
+      </xsl:message>
+    </xsl:if>
+    <xsl:choose>
+      <!-- convention: bNodes are in _ idspace -->
+      <xsl:when test="substring-before(.,':') = '_'">
+      </xsl:when>
+      <xsl:otherwise>
+        <!-- not a bNode -->
+        <uid>
+          <xsl:value-of select="."/>
+        </uid>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:template>
+
+  <!-- not the ones under def -->
+  <xsl:template match="*" mode="dbxref">
+    <sameas>
+      <object_id>
+        <xsl:apply-templates select="." mode="node_ref"/>
+      </object_id>
+    </sameas>
+  </xsl:template>
+
+  <xsl:template match="is_a|instance_of">
+    <link>
+      <xsl:call-template name="link_audit"/>
+      <xsl:apply-templates select="@implied"/>
+      <node_id>
+        <xsl:apply-templates select="../id" mode="node_ref"/>
+      </node_id>
+      <predicate_id>
+        <xsl:value-of select="name(.)"/>
+      </predicate_id>
+      <object_id>
+        <xsl:apply-templates select="." mode="node_ref"/>
+      </object_id>
+      <xsl:apply-templates mode="source_id" select=".."/>
+    </link>
+  </xsl:template>
+
+  <xsl:template match="inverse_of">
+    <link>
+      <xsl:apply-templates select="@implied"/>
+      <node_id>
+        <xsl:apply-templates select="../id" mode="node_ref"/>
+      </node_id>
+      <predicate_id>
+        <xsl:text>owl:inverseOf</xsl:text>
+      </predicate_id>
+      <object_id>
+        <xsl:apply-templates select="." mode="node_ref"/>
+      </object_id>
+      <xsl:apply-templates mode="source_id" select=".."/>
+    </link>
+  </xsl:template>
+
+  <xsl:template match="relationship">
+    <link>
+      <xsl:if test="@id">
+        <!-- if the link is identified, we also create or reference a tuple in the node table -->
+        <reiflink_node_id>
+          <!-- use a macro lookup -->
+          <xsl:value-of select="@id"/>
+        </reiflink_node_id>
+      </xsl:if>
+      <xsl:apply-templates select="@implied"/>
+      <node_id>
+        <xsl:apply-templates select="../id" mode="node_ref"/>
+      </node_id>
+      <predicate_id>
+        <xsl:apply-templates select="type" mode="node_ref"/>
+      </predicate_id>
+      <object_id>
+        <xsl:apply-templates select="to" mode="node_ref"/>
+      </object_id>
+      <xsl:apply-templates mode="source_id" select=".."/>
+    </link>
+  </xsl:template>
+
+  <!-- for instances: slot-values and relationships between instances -->
+  <xsl:template match="property_value">
+    <xsl:choose>
+      <xsl:when test="datatype">
+        <!-- slots -->
+        <tagval>
+          <node_id>
+            <xsl:value-of select="../id"/>
+          </node_id>
+          <tag_id>
+            <xsl:apply-templates select="type" mode="node_ref"/>
+          </tag_id>
+          <val>
+            <xsl:value-of select="value"/>
+          </val>
+          <xsl:apply-templates mode="source_id" select=".."/>
+        </tagval>
+      </xsl:when>
+      <xsl:otherwise>
+        <!-- instance to instance links -->
+        <link>
+          <xsl:if test="@id">
+            <!-- if the link is identified, we also create or reference a tuple in the node table -->
+            <reiflink_node_id>
+              <!-- use a macro lookup -->
+              <xsl:value-of select="@id"/>
+            </reiflink_node_id>
+          </xsl:if>
+          <xsl:apply-templates select="@implied"/>
+          <node_id>
+            <xsl:apply-templates select="../id" mode="node_ref"/>
+          </node_id>
+          <predicate_id>
+            <xsl:apply-templates select="type" mode="node_ref"/>
+          </predicate_id>
+          <object_id>
+            <xsl:apply-templates select="to" mode="node_ref"/>
+          </object_id>
+          <xsl:apply-templates mode="source_id" select=".."/>
+        </link>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:template>
+
+  <!-- intersection_ofs: collection of links -->
+  <xsl:template match="intersection_of|union_of">
+    <link>
+      <xsl:apply-templates select="@implied"/>
+      <node_id>
+        <xsl:apply-templates select="../id" mode="node_ref"/>
+      </node_id>
+      <combinator>
+        <xsl:choose>
+          <xsl:when test="name(.)='intersection_of'">
+            <xsl:text>I</xsl:text>
+          </xsl:when>
+          <xsl:otherwise>
+            <xsl:text>U</xsl:text>
+          </xsl:otherwise>
+        </xsl:choose>
+      </combinator>
+      <xsl:if test="@implied and @implied!='false'">
+        <is_inferred>
+          <xsl:text>t</xsl:text>
+        </is_inferred>
+      </xsl:if>
+      <predicate_id>
+        <xsl:choose>
+          <xsl:when test="type">
+            <xsl:apply-templates select="type" mode="node_ref"/>
+          </xsl:when>
+          <xsl:otherwise>
+            <xsl:text>is_a</xsl:text>
+          </xsl:otherwise>
+        </xsl:choose>
+      </predicate_id>
+      <object_id>
+        <xsl:apply-templates select="to" mode="node_ref"/>
+      </object_id>
+      <xsl:apply-templates mode="source_id" select=".."/>
+    </link>
+  </xsl:template>
+
+  <xsl:template name="make-anon-node-attrs">
+    <xsl:param name="anon_id"/>
+    <uid><xsl:value-of select="$anon_id"/></uid>
+    <metatype><xsl:text>I</xsl:text></metatype>
+    <is_anonymous>t</is_anonymous>
+  </xsl:template>
+
+  <xsl:template match="synonym">
+    <alias>
+      <label>
+        <xsl:value-of select="synonym_text"/>
+      </label>
+      <xsl:if test="@scope">
+        <scope>
+          <xsl:value-of select="@scope"/>
+        </scope>
+      </xsl:if>
+      <xsl:apply-templates mode="source_id" select=".."/>
+    </alias>
+  </xsl:template>
+
+  <xsl:template match="comment">
+    <description>
+      <type_id>
+        <node>
+          <uid>comment</uid>
+          <metatype><xsl:text>R</xsl:text></metatype>
+        </node>
+      </type_id>
+      <label>
+        <xsl:value-of select="."/>
+      </label>
+      <xsl:apply-templates mode="source_id" select=".."/>
+    </description>
+  </xsl:template>
+
+  <xsl:template match="description">
+    <description>
+      <type_id>
+        <node>
+          <uid>oboMetaModel:description</uid>
+          <metatype><xsl:text>R</xsl:text></metatype>
+        </node>
+      </type_id>
+      <label>
+        <xsl:value-of select="."/>
+      </label>
+      <xsl:apply-templates mode="source_id" select=".."/>
+    </description>
+  </xsl:template>
+
+  <xsl:template match="creator">
+    <tagval>
+      <tag_id>
+        <node>
+          <uid>dc:creator</uid>
+          <metatype><xsl:text>R</xsl:text></metatype>
+        </node>
+      </tag_id>
+      <val>
+        <xsl:value-of select="."/>
+      </val>
+      <xsl:apply-templates mode="source_id" select=".."/>
+    </tagval>
+  </xsl:template>
+
+  <xsl:template match="annotation_date">
+    <tagval>
+      <tag_id>
+        <node>
+          <uid>dc:date</uid>
+          <metatype><xsl:text>R</xsl:text></metatype>
+        </node>
+      </tag_id>
+      <val>
+        <xsl:value-of select="."/>
+      </val>
+      <xsl:apply-templates mode="source_id" select=".."/>
+    </tagval>
+  </xsl:template>
+
+  <xsl:template match="provenance">
+    <link>
+      <predicate_id>
+        <node>
+          <uid>oboMetaModel:provenance</uid>
+          <metatype><xsl:text>R</xsl:text></metatype>
+        </node>
+      </predicate_id>
+      <object_id>
+        <xsl:apply-templates mode="id-or-expression" select="."/>
+      </object_id>
+      <xsl:apply-templates mode="source_id" select=".."/>
+      <is_metadata>
+        <xsl:text>t</xsl:text>
+      </is_metadata>
+    </link>
+  </xsl:template>
+
+  <xsl:template mode="xref" match="*">
+    <xsl:choose>
+      <!-- typically OBO xrefs are in the form DB:ID - eg EC:1.1.1.1
+           on occasion the xref is also a URI. This this case it may be
+           mistakenly mis-parsed as DB=http, ID=//xxx.yyy.zzz/foo
+           we correct for that here -->
+      <xsl:when test="dbname='URL'">
+        <xsl:value-of select="acc"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="dbname"/>
+        <xsl:text>:</xsl:text>
+        <xsl:value-of select="acc"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:template>
+
+  <xsl:template match="xref_analog">
+    <link>
+      <predicate_id>
+        <node>
+          <uid>oboMetaModel:xref</uid>
+        </node>
+      </predicate_id>
+      <object_id>
+        <node>
+          <uid>
+            <xsl:apply-templates mode="xref" select="."/>
+          </uid>
+        </node>
+      </object_id>
+      <xsl:apply-templates mode="source_id" select=".."/>
+      <is_metadata>
+        <xsl:text>t</xsl:text>
+      </is_metadata>
+    </link>
+  </xsl:template>
+
+  <xsl:template match="OLD--xref_analog">
+    <node_xref>
+      <xref_id>
+        <node>
+          <uid>
+            <xsl:value-of select="acc"/>
+          </uid>
+          <source_id>
+            <node>
+              <uid>
+                <xsl:value-of select="dbname"/>
+              </uid>
+            </node>
+          </source_id>
+        </node>
+      </xref_id>
+    </node_xref>
+  </xsl:template>
+
+  <!-- only dbxref under def -->
+  <xsl:template match="dbxref" mode="is_for_definition">
+    <description_xref>
+      <xref_id>
+        <node>
+          <uid>
+            <xsl:apply-templates mode="xref" select="."/>
+          </uid>
+        </node>
+      </xref_id>
+    </description_xref>
+  </xsl:template>
+
+  <!-- TODO: fix this -->
+  <!-- treat alt_id as alias -->
+  <xsl:template match="alt_id">
+    <alias>
+      <type_id>
+        <node>
+          <uid>alt_id</uid>
+        </node>
+      </type_id>
+      <label>
+        <xsl:value-of select="."/>
+      </label>
+      <xsl:apply-templates mode="source_id" select=".."/>
+    </alias>
+  </xsl:template>
+  
+  <xsl:template match="def">
+    <description>
+      <type_id>
+        <node>
+          <uid>definition</uid>
+          <metatype><xsl:text>R</xsl:text></metatype>
+        </node>
+      </type_id>
+      <label>
+        <xsl:value-of select="defstr"/>
+      </label>
+      <xsl:if test="string-length(dbxref/acc) > 0 and string-length(dbxref/dbname) > 0">
+        <xsl:apply-templates select="dbxref" mode="is_for_definition"/>
+      </xsl:if>
+      <xsl:apply-templates mode="source_id" select=".."/>
+    </description>
+  </xsl:template>
+
+  <xsl:template match="subset">
+    <link>
+      <predicate_id>
+        <node>
+          <uid>oboMetaModel:inSubset</uid>
+        </node>
+      </predicate_id>
+      <object_id>
+        <node>
+          <uid>
+            <xsl:value-of select="."/>
+          </uid>
+        </node>
+      </object_id>
+      <is_metadata>
+        <xsl:text>t</xsl:text>
+      </is_metadata>
+      <xsl:apply-templates mode="source_id" select=".."/>
+    </link>
+  </xsl:template>
+
+  <!-- implied links (inferred by reasoner) -->
+  <xsl:template match="@implied">
+    <xsl:if test=". != 'false'">
+      <is_inferred>
+        <xsl:text>t</xsl:text>
+      </is_inferred>
+    </xsl:if>
+  </xsl:template>
+
+  <xsl:template match="*" mode="label">
+    <xsl:if test=".">
+      <label>
+        <xsl:value-of select="."/>
+      </label>
+    </xsl:if>
+  </xsl:template>
+
+
+  <!-- also parse go_assoc xml -->
+  <xsl:template match="prod">
+    <node>
+      <xsl:comment>
+        <xsl:text>annotated entity</xsl:text>
+      </xsl:comment>
+      <source_id>
+        <node>
+          <uid>
+            <xsl:value-of select="../proddb"/>
+          </uid>
+        </node>
+      </source_id>
+      <uid>
+        <xsl:value-of select="../proddb"/>
+        <xsl:text>:</xsl:text>
+        <xsl:value-of select="prodacc"/>
+      </uid>
+      <xsl:call-template name="node_audit"/>
+      <label>
+        <xsl:value-of select="prodsymbol"/>
+      </label>
+      <xsl:if test="prodname">
+        <alias>
+          <type_id>
+            <node>
+              <uid>full_name</uid>
+            </node>
+          </type_id>
+          <label>
+            <xsl:value-of select="prodname"/>
+          </label>
+        </alias>
+      </xsl:if>
+      <xsl:for-each select="prodsyn">
+        <alias>
+          <type_id>
+            <node>
+              <uid>synonym</uid>
+            </node>
+          </type_id>
+          <label>
+            <xsl:value-of select="."/>
+          </label>
+        </alias>
+      </xsl:for-each>
+      <xsl:if test="prodtaxa">
+        <link>
+          <predicate_id>
+            <xsl:text>in_organism</xsl:text> <!-- TODO -->
+          </predicate_id>
+          <object_id>
+            <node>
+              <uid>
+                <xsl:text>NCBITaxon:</xsl:text>
+                <xsl:value-of select="prodtaxa"/>
+              </uid>
+            </node>
+          </object_id>
+        </link>
+      </xsl:if>
+      <xsl:if test="prodtype">
+        <link>
+          <predicate_id>
+            <xsl:text>is_a</xsl:text> <!-- TODO: is_a vs instance_of -->
+          </predicate_id>
+          <object_id>
+            <node>
+              <uid>
+                <xsl:value-of select="prodtype"/>
+              </uid>
+            </node>
+          </object_id>
+        </link>
+      </xsl:if>
+      <xsl:comment>
+        <xsl:text>annotations</xsl:text>
+      </xsl:comment>
+      <xsl:for-each select="assoc">
+        <link>
+          <predicate_id>
+            <xsl:text>influences</xsl:text> <!-- TODO -->
+          </predicate_id>
+          <object_id>
+            <node>
+              <uid>
+                <xsl:value-of select="termacc"/>
+              </uid>
+            </node>
+          </object_id>
+          <source_id>
+            <node>
+              <uid>
+                <xsl:value-of select="../proddb"/>
+              </uid>
+            </node>
+          </source_id>
+          <xsl:call-template name="link_audit"/>
+          <xsl:if test="is_not=1">
+            <is_negated><xsl:text>t</xsl:text></is_negated>
+          </xsl:if>
+          <xsl:comment>the annotation is the attribution for the link</xsl:comment>
+          <reiflink_node_id>
+            <node>
+              <!-- id is optional -->
+              <xsl:apply-templates select="id" mode="id"/>
+              <is_anonymous><xsl:text>t</xsl:text></is_anonymous>
+              <is_reiflink><xsl:text>t</xsl:text></is_reiflink>
+              <metatype><xsl:text>I</xsl:text></metatype>
+              <!-- type -->
+              <link>
+                <predicate_id>
+                  <xsl:text>instance_of</xsl:text>
+                </predicate_id>
+                <object_id>
+                  <node>
+                    <uid>oban:Annotation</uid>
+                  </node>
+                </object_id>
+              </link>
+              <!-- assocdata -->
+              <xsl:if test="assocdate">
+                <!-- TODO -->
+              </xsl:if>
+            </node>
+          </reiflink_node_id>
+        </link>
+      </xsl:for-each>
+    </node>
+    <!-- xsl:value-of select="../proddb"/?? -->
+    <!-- xsl:value-of select="prodtype"/?? -->
+    <!-- xsl:value-of select="prodtaxa"/?? -->
+  </xsl:template>
+
+  <!-- obo-format 1.3 annotation extension -->
+  <xsl:template match="annotation">
+    <link>
+      <predicate_id>
+        <node>
+          <uid>
+            <xsl:value-of select="relation"/>
+          </uid>
+        </node>
+      </predicate_id>
+      <node_id>
+        <node>
+          <uid>
+            <xsl:value-of select="subject"/>
+          </uid>
+        </node>
+      </node_id>
+      <object_id>
+        <xsl:apply-templates select="object" mode="id-or-expression"/>
+      </object_id>
+      <source_id>
+        <node>
+          <uid>
+            <xsl:value-of select="namespace"/>
+          </uid>
+        </node>
+      </source_id>
+      <xsl:call-template name="link_audit"/>
+      <xsl:if test="is_negated=1">
+        <is_negated>
+          <xsl:text>t</xsl:text>
+        </is_negated>
+      </xsl:if>
+      <xsl:comment>the annotation is the attributation for the link</xsl:comment>
+      <reiflink_node_id>
+        <node>
+          
+          <is_anonymous><xsl:text>t</xsl:text></is_anonymous>
+          <metatype><xsl:text>I</xsl:text></metatype>
+          <!-- type -->
+          <link>
+            <predicate_id>
+              <xsl:text>instance_of</xsl:text>
+            </predicate_id>
+            <object_id>
+              <node>
+                <uid>oban:Annotation</uid>
+              </node>
+            </object_id>
+          </link>
+          <!-- note: duplicated in node and link -->
+          
+          <xsl:apply-templates mode="source_id" select="."/>
+          <xsl:apply-templates select="description"/>
+          <xsl:apply-templates select="annotation_date"/>
+          <xsl:apply-templates select="provenance"/>
+          <xsl:apply-templates select="context"/>
+          <xsl:apply-templates select="creator"/>
+        </node>
+      </reiflink_node_id>
+    </link>
+  </xsl:template>
+
+  <xsl:template mode="source_id" match="*">
+    <source_id>
+      <node>
+        <uid>
+          <xsl:choose>
+            <xsl:when test="namespace">
+              <xsl:value-of select="namespace"/>
+            </xsl:when>
+            <xsl:when test="contains(id,':')">
+              <xsl:value-of select="substring-before(id,':')"/>
+            </xsl:when>
+            <xsl:otherwise>
+              <xsl:value-of select="//header/default-namespace"/>
+            </xsl:otherwise>
+          </xsl:choose>
+        </uid>
+        <metatype><xsl:text>I</xsl:text></metatype>
+      </node>
+    </source_id>
+    <loaded_from_id>
+      <xsl:text>__source</xsl:text>
+    </loaded_from_id>
+  </xsl:template>
+
+  <!-- auditing -->
+  <!-- audit source - not to be confused with namespace source... -->
+  <xsl:template match="source">
+    <node id="__source">
+      <xsl:apply-templates select="source_id" mode="id"/>
+      <xsl:apply-templates select="name" mode="label"/>
+      <metatype><xsl:text>I</xsl:text></metatype>
+      
+      <xsl:if test="namespace">
+        <source_id>
+          <node>
+            <uid>
+              <xsl:value-of select="source_path"/>
+            </uid>
+          </node>
+        </source_id>
+      </xsl:if>
+
+      <link>
+        <predicate_id>
+          <xsl:text>instance_of</xsl:text>
+        </predicate_id>
+        <object_id>
+          <node>
+            <uid>obd_meta:Document</uid>
+          </node>
+        </object_id>
+      </link>
+      <tagval>
+        <tag_id>
+          <node>
+            <uid>obd_meta:md5</uid>
+          </node>
+        </tag_id>
+        <val>
+          <xsl:value-of select="source_md5"/>
+        </val>
+      </tagval>
+      <tagval>
+        <tag_id>
+          <node>
+            <uid>obd_meta:modification_time</uid>
+          </node>
+        </tag_id>
+        <val>
+          <xsl:value-of select="source_mtime"/>
+        </val>
+      </tagval>
+      <tagval>
+        <tag_id>
+          <node>
+            <uid>obd_meta:source_fullpath</uid>
+          </node>
+        </tag_id>
+        <val>
+          <xsl:value-of select="source_fullpath"/>
+        </val>
+      </tagval>
+    </node>
+  </xsl:template>
+
+  <xsl:template match="*" mode="id-or-expression">
+    <xsl:choose>
+      <xsl:when test="intersection/link">
+        <node>
+          <is_anonymous>
+            <xsl:text>t</xsl:text>
+          </is_anonymous>
+          <metatype>
+            <xsl:text>C</xsl:text>
+          </metatype>
+          <xsl:for-each select="intersection/link">
+            <link>
+              <combinator>
+                <xsl:text>I</xsl:text>
+              </combinator>
+              <predicate_id>
+                <xsl:choose>
+                  <xsl:when test="type">
+                    <xsl:apply-templates select="type" mode="node_ref"/>
+                  </xsl:when>
+                  <xsl:otherwise>
+                    <xsl:text>is_a</xsl:text>
+                  </xsl:otherwise>
+                </xsl:choose>
+              </predicate_id>
+              <object_id>
+                <xsl:apply-templates select="to" mode="id-or-expression"/>
+              </object_id>
+            </link>
+          </xsl:for-each>
+        </node>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:apply-templates select="." mode="node_ref"/> 
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:template>
+
+  <xsl:template mode="uri" match="*">
+    <uri>
+      <xsl:apply-templates mode="translate-id" select="."/>
+    </uri>
+  </xsl:template>
+
+  <xsl:template mode="translate-id" match="*">
+    <xsl:choose>
+      <xsl:when test="key('k_idspace',substring-before(.,':'))">
+        <xsl:value-of select="key('k_idspace',substring-before(.,':'))/global"/>
+        <xsl:if test="$localid_prefix">
+          <xsl:value-of select="$localid_prefix"/>
+        </xsl:if>
+        <xsl:value-of select="substring-after(.,':')"/>
+      </xsl:when>
+      <xsl:when test="substring-before(.,':')">
+        <xsl:text>&oboContent;</xsl:text>
+        <xsl:value-of select="substring-before(.,':')"/>
+        <xsl:text>#</xsl:text>
+        <xsl:value-of select="substring-before(.,':')"/>
+        <xsl:text>_</xsl:text>
+        <xsl:if test="$localid_prefix">
+          <xsl:value-of select="$localid_prefix"/>
+        </xsl:if>
+        <xsl:value-of select="substring-after(.,':')"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:text>&oboContent;</xsl:text>
+        <xsl:text>_global/</xsl:text>
+        <xsl:if test="$localid_prefix">
+          <xsl:value-of select="$localid_prefix"/>
+        </xsl:if>
+        <xsl:value-of select="."/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:template>
+
+  <xsl:template match="text()|@*">
+  </xsl:template>
+
+
+</xsl:stylesheet>
+
+


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[Obo-svn-commit] SF.net SVN: obo: [1023] obo-database/trunk

From: <cmu...@us...> - 2007-10-10 20:46:55

Revision: 1023
          http://obo.svn.sourceforge.net/obo/?rev=1023&view=rev
Author:   cmungall
Date:     2007-10-10 13:46:57 -0700 (Wed, 10 Oct 2007)

Log Message:
-----------


Modified Paths:
--------------
    obo-database/trunk/sql/obd-core-views.sql

Added Paths:
-----------
    obo-database/trunk/xsl/
    obo-database/trunk/xsl/oboxml_to_obd_prestore.xsl

Modified: obo-database/trunk/sql/obd-core-views.sql
===================================================================
--- obo-database/trunk/sql/obd-core-views.sql	2007-10-10 20:46:17 UTC (rev 1022)
+++ obo-database/trunk/sql/obd-core-views.sql	2007-10-10 20:46:57 UTC (rev 1023)
@@ -111,7 +111,6 @@
 CREATE OR REPLACE VIEW reified_link AS SELECT * FROM link WHERE reiflink_node_id IS NOT NULL;
 COMMENT ON VIEW reified_link IS 'A link that has a link pointing to it';
 
-
 -- instance_of
 CREATE OR REPLACE VIEW instance_of_relation AS SELECT * FROM relation_node WHERE uid='OBO_REL:instance_of';
 COMMENT ON VIEW instance_of_relation IS 'A relation node for the OBO_REL relation "instance_of"';
@@ -159,6 +158,15 @@
 CREATE OR REPLACE VIEW implied_is_a_link AS SELECT * FROM is_a_link WHERE is_inferred='t';
 COMMENT ON VIEW implied_is_a_link IS 'An is_a_link that is inferred (ie it is not directly asserted)';
 
+-- todo: generalise to any irreflexive relation
+CREATE OR REPLACE VIEW implied_equivalent_class_link AS 
+ SELECT 
+  x.node_id AS node1_id,
+  y.node_id AS node2_id
+ FROM is_a_link AS x INNER JOIN is_a_link AS y ON (x.object_id=y.node_id AND y.object_id=x.node_id)
+ WHERE x.node_id != x.object_id;
+
+
 CREATE OR REPLACE VIEW genus_link AS
  SELECT link.*
  FROM link INNER JOIN is_a_relation ON (predicate_id=is_a_relation.node_id)

Added: obo-database/trunk/xsl/oboxml_to_obd_prestore.xsl
===================================================================
--- obo-database/trunk/xsl/oboxml_to_obd_prestore.xsl	                        (rev 0)
+++ obo-database/trunk/xsl/oboxml_to_obd_prestore.xsl	2007-10-10 20:46:57 UTC (rev 1023)
@@ -0,0 +1 @@
+link /Users/cjm/go-xsl/oboxml_to_obd_prestore.xsl
\ No newline at end of file


Property changes on: obo-database/trunk/xsl/oboxml_to_obd_prestore.xsl
___________________________________________________________________
Name: svn:special
   + *


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[Obo-svn-commit] SF.net SVN: obo: [1022] phenote/trunk/src/java/phenote/main/PhenoteVersion. java

From: <mg...@us...> - 2007-10-10 20:46:13

Revision: 1022
          http://obo.svn.sourceforge.net/obo/?rev=1022&view=rev
Author:   mgibson
Date:     2007-10-10 13:46:17 -0700 (Wed, 10 Oct 2007)

Log Message:
-----------
thanks jim for reminder - forgot - flakyflaky

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/main/PhenoteVersion.java

Modified: phenote/trunk/src/java/phenote/main/PhenoteVersion.java
===================================================================
--- phenote/trunk/src/java/phenote/main/PhenoteVersion.java	2007-10-10 20:43:11 UTC (rev 1021)
+++ phenote/trunk/src/java/phenote/main/PhenoteVersion.java	2007-10-10 20:46:17 UTC (rev 1022)
@@ -9,7 +9,7 @@
 
 public class PhenoteVersion {
 
-  private static String hardwiredDefaultVersion = "1.4-beta3";
+  private static String hardwiredDefaultVersion = "1.4";
 
   public static String versionString() {
     final String version = System.getProperty("phenote.version");
@@ -33,7 +33,7 @@
   }
 
   public static Date getDateOfVersion(){
-    GregorianCalendar cal = new GregorianCalendar(2007, GregorianCalendar.JULY, 17);
+    GregorianCalendar cal = new GregorianCalendar(2007, GregorianCalendar.OCTOBER, 10);
     return cal.getTime();
   }
 


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[Obo-svn-commit] SF.net SVN: obo: [1021] phenote/trunk/doc/making-a-phenote-release.html

From: <ba...@us...> - 2007-10-10 20:43:10

Revision: 1021
          http://obo.svn.sourceforge.net/obo/?rev=1021&view=rev
Author:   balhoff
Date:     2007-10-10 13:43:11 -0700 (Wed, 10 Oct 2007)

Log Message:
-----------
Reminder to update "hardwiredDefaultVersion" in PhenoteVersion.java before release.

Modified Paths:
--------------
    phenote/trunk/doc/making-a-phenote-release.html

Modified: phenote/trunk/doc/making-a-phenote-release.html
===================================================================
--- phenote/trunk/doc/making-a-phenote-release.html	2007-10-10 15:35:12 UTC (rev 1020)
+++ phenote/trunk/doc/making-a-phenote-release.html	2007-10-10 20:43:11 UTC (rev 1021)
@@ -33,6 +33,8 @@
 it "phenote-webstart". This will be used by ant<br>
 make sure you have write permission to this directory and permission to mkdird<br>
 <br>
+- set "hardwiredDefaultVersion" in PhenoteVersion.java to the current version of phenote
+<br>
 (this is no longer true - but we may bring this back) [- set
 environment variable PHENOTE_VERSION to the current version of phenote,
 e.g. "1.5". ant will deploy phenote to


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[Obo-svn-commit] SF.net SVN: obo: [1020] phenote/trunk/conf/FB_camcur.cfg

From: <mg...@us...> - 2007-10-10 15:35:08

Revision: 1020
          http://obo.svn.sourceforge.net/obo/?rev=1020&view=rev
Author:   mgibson
Date:     2007-10-10 08:35:12 -0700 (Wed, 10 Oct 2007)

Log Message:
-----------
syntax-abbrev -> datatag

Modified Paths:
--------------
    phenote/trunk/conf/FB_camcur.cfg

Modified: phenote/trunk/conf/FB_camcur.cfg
===================================================================
--- phenote/trunk/conf/FB_camcur.cfg	2007-10-10 14:57:25 UTC (rev 1019)
+++ phenote/trunk/conf/FB_camcur.cfg	2007-10-10 15:35:12 UTC (rev 1020)
@@ -44,35 +44,35 @@
 
   <ns:field name="Genotype" datatag="GT"/>
   
-  <ns:field name="Dominance" syntax-abbrev="dom">
+  <ns:field name="Dominance" datatag="dom">
 	  <ns:ontology name="Dominance" file="flybase_controlled_vocabulary.obo" namespace="dominance_qualifier" slim="camcur"/>
 </ns:field>
 c
 <!-- Note - namespace for clone qualifier not yet implemented -->
-<ns:field name="Clonal qualifier" syntax-abbrev="cq">
+<ns:field name="Clonal qualifier" datatag="cq">
 	<ns:ontology name="clonal qualifier" file="flybase_controlled_vocabulary.obo" namespace="genotype_to_phenotype_relation" slim="camcur"/>
 </ns:field>
 
-<ns:field name="Gen to Phen" syntax-abbrev="g2p">
+<ns:field name="Gen to Phen" datatag="g2p">
 	<ns:ontology name="Gen to Phen" file="flybase_controlled_vocabulary.obo" namespace="genotype_to_phenotype_relation" slim="camcur"/>
 </ns:field>
 
-<ns:field name="Environment" syntax-abbrev="env">
+<ns:field name="Environment" datatag="env">
 	<ns:ontology name="Environment" file="flybase_controlled_vocabulary.obo" namespace="environmental_qualifier" slim="camcur"/>
 </ns:field>
 
-  <ns:field name="Stage" syntax-abbrev="stage">
+  <ns:field name="Stage" datatag="stage">
 		  <ns:ontology name="stage" file="fly_development.obo"/>
 	  </ns:field>
 	  
-	  <ns:field name="Entity" syntax-abbrev="E">
+	  <ns:field name="Entity" datatag="E">
 		  <ns:ontology name="Relationship" is-postcomp-rel="true"
 			       file="ro.obo"/>
 		  <ns:ontology name="Anatomy" file="fly_anatomy.obo" />
 		  <ns:ontology name="Subcell" file="gene_ontology.obo" namespace="cellular_component" />
 		  <ns:ontology name="Process" file="gene_ontology.obo" namespace="biological_process" />
 	  </ns:field>
-	  <ns:field name="Spatial Q" syntax-abbrev="spatial">
+	  <ns:field name="Spatial Q" datatag="spatial">
 		  <ns:ontology name="Spatial qualifier" file="flybase_controlled_vocabulary.obo" namespace="spatial_qualifier" slim="camcur"/>
 </ns:field>
 


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[Obo-svn-commit] SF.net SVN: obo: [1019] phenote/trunk/doc/phenote-website/phenote.html

From: <mg...@us...> - 2007-10-10 14:57:32

Revision: 1019
          http://obo.svn.sourceforge.net/obo/?rev=1019&view=rev
Author:   mgibson
Date:     2007-10-10 07:57:25 -0700 (Wed, 10 Oct 2007)

Log Message:
-----------
relaease notes link

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/phenote.html

Modified: phenote/trunk/doc/phenote-website/phenote.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.html	2007-10-10 14:41:46 UTC (rev 1018)
+++ phenote/trunk/doc/phenote-website/phenote.html	2007-10-10 14:57:25 UTC (rev 1019)
@@ -1,408 +1,54 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-
-
-
-
-
-
-
-
-
-
-
-
-
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
+<html><head>
   <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
+  <title>Phenote</title></head>
 
-
-
-
-
-
-
-
-
-
-
-
-
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  <title>Phenote</title>
-</head>
-
-
 <body>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <h1 style="text-align: left;"><span style="font-weight: bold;"></span>Phenote<br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 </h1>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 Phenote is a tool to annotate phenotypes using the Entity Quality
 paradigm. It takes advantage of
 ontologies. It uses term completion to allow curators quick access to
 the ontology terms they want to use. <br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <br>
 <a href="1.4/phenote.jnlp">Phenote 1.4</a><br>
-
-
 <br>
-
 <br>
-
-
-
-
-
-
-
 After phenote downloads the java jar files (takes a while) it will ask
 you what configuration you would like to use, fly, zfin, human,worm,birn....<br>
-
-
-
 <br>
-
-
-
-
-
-
-
-
-
-
-
-
-
-<a href="phenote-release-notes.html">Phenote Release Notes and old
+<a href="phenote-release-notes.shtml">Phenote Release Notes and old
 webstart releases</a><br>
 
 
 
 Please see the release notes for recent changes.<br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 Zebrafish requires
 components of phenote(to plug into their non-public
 website), not a full web app. Here is a proof of concept of some of
 those
 components:<br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby
 Phenote(components used by Zfin)</a><br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 Webby phenote is a collaboration with Sohel Merchant at dictyBase, and Christian Pich &amp; Kevin Schaper at zfin.
 Here is what Dicty has done:<br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DictyBase
 webby phenote</a><br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 We would love to get your&nbsp;feedback! Please report any bugs (ideally through the <a href="https://sourceforge.net/tracker/?group_id=76834&amp;atid=887913">bug
 tracker</a>) and let us know what you
 think (email:<a href="mailto:mg...@be..."> mg...@be...</a>, email list: <a href="mailto:obo...@li...">obo...@li...</a>).<br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <h4>Phenote links:<br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 </h4>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Phenote
 email list</a><br>
-
-
-
-
-
-
-
-
-
-
-
-
-
 <a href="https://sourceforge.net/tracker/?group_id=76834&amp;atid=887913">Phenote
 bug tracker</a><br>
 
@@ -1154,5 +800,4 @@
 
 
 
-</body>
-</html>
+</body></html>
\ No newline at end of file


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[Obo-svn-commit] SF.net SVN: obo: [1018] phenote/trunk/doc/phenote-website/ phenote-release-notes.shtml

From: <ba...@us...> - 2007-10-10 14:41:50

Revision: 1018
          http://obo.svn.sourceforge.net/obo/?rev=1018&view=rev
Author:   balhoff
Date:     2007-10-10 07:41:46 -0700 (Wed, 10 Oct 2007)

Log Message:
-----------
Updated release notes.

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/phenote-release-notes.shtml

Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.shtml	2007-10-10 14:21:57 UTC (rev 1017)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.shtml	2007-10-10 14:41:46 UTC (rev 1018)
@@ -29,17 +29,32 @@
 
 	
 <ul>
-
-	<li>feature: Loading splash more informative about what's going on
-behind-the-scenes such as which ontologies are loading, if they are
-being updated, etc.</li>
-  <li>feature: obo edit annotation model can now be optionally configured for
-backend, which will allow for more sophisticated data to be captured (like
-comparisons)</li>
-  <li>feature: Error for obo parse failures to info panel</li><li>feature: Delimited tab adapter uses column headings to map to table, rather than ordering</li><li>feature: Autocompletion optimized with threading, cancels stale requests (min-comp-chars now pase)</li><li>feature: Date created automatically added into data (under the hood)</li><li>feature: If arrow hit with empty input then gets &amp; displays all terms (used to inefficiently pre-load)</li><li>feature: Can sort completion list by ID, needed for zfin stages</li><li>change: Moved test suites in with source to work with eclipse</li><li>change: Took a lot of obos out of webstart jar - less bulky - as they get automatically downloaded</li></ul><ul><li>bugfix: Terms not found are no longer dropped, a dangler is created, and error msg to info, show up in red</li><li>bugfix: if log conf fails use backup default</li>
-
-	
+	<li>feature: Loading splash more informative about what's going on behind-the-scenes such as which ontologies are loading, if they are being updated, etc.</li>
+	<li>feature: obo edit annotation model can now be optionally configured for backend, which will allow for more sophisticated data to be captured (like comparisons)</li>
+	<li>feature: Error for obo parse failures to info panel</li>
+	<li>feature: Delimited tab adapter uses column headings to map to table, rather than ordering</li>
+	<li>feature: Autocompletion optimized with threading, cancels stale requests (min-comp-chars now pase)</li>
+	<li>feature: Date created automatically added into data (under the hood)</li>
+	<li>feature: If arrow hit with empty input then gets &amp; displays all terms (used to inefficiently pre-load)</li>
+	<li>feature: Can sort completion list by ID, needed for zfin stages</li>
+	<li>feature: Table preserves user ordering of columns, in addition to column widths.</li>
+	<li>feature: Filter search field allows user to narrow down displayed data rows via matching text.</li>
+	<li>feature: See actual value in input field when multiple rows are selected and have the same value.</li>
+	<li>feature: Copy all taxon names in specimen list as an unresolved Newick tree (for PhenoMap/NESCent)</li>
+	<li>feature: Automatically open specimen list and phylogenetic tree files when opening data file (for PhenoMap/NESCent)</li>
 </ul>
+<ul>
+	<li>change: Moved test suites in with source to work with eclipse</li>
+	<li>change: Took a lot of obos out of webstart jar - less bulky - as they get automatically downloaded</li>
+	<li>change: Phenote now follows standard log4j configuration conventions.  Pass a custom log configuration to Phenote via the classpath or the system propery "log4j.configuration".</li>
+</ul>
+<ul>
+	<li>bugfix: Terms not found are no longer dropped, a dangler is created, and error msg to info, show up in red</li>
+	<li>bugfix: if log conf fails use backup default</li>
+	<li>bugfix: Input fields now commit changes with either Return or Tab</li>
+	<li>bugfix: Native lib is loaded properly for Mac interface on webstart, allowing traversal of aliases in file dialog, as well as user sidebar items in file dialog</li>
+	<li>bugfix: Noncontiguous row selection works now on Mac</li>
+</ul>
 
 	
 <h2>08.28.2007, version <a href="phenote/1.4-beta3/phenote.jnlp">1.4-beta3</a></h2>


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[Obo-svn-commit] SF.net SVN: obo: [1015] phenote/trunk/doc/phenote-website/ phenote-release-notes.shtml

From: <mg...@us...> - 2007-10-10 14:38:22

Revision: 1015
          http://obo.svn.sourceforge.net/obo/?rev=1015&view=rev
Author:   mgibson
Date:     2007-10-10 07:02:46 -0700 (Wed, 10 Oct 2007)

Log Message:
-----------
added in some release notes - more coming
jim you should add in yours

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/phenote-release-notes.shtml

Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.shtml	2007-10-09 23:41:21 UTC (rev 1014)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.shtml	2007-10-10 14:02:46 UTC (rev 1015)
@@ -1,17 +1,14 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<!--#include virtual="ssi/head.html" -->
+<html xmlns="http://www.w3.org/1999/xhtml"><head><!--#include virtual="ssi/head.html" -->
 
+
     
     
-  <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
-</head>
+  <title>Phenote: A Phenotype Annotation Tool using Ontologies</title></head>
 
+<body>
 
-  <body>
 
-
     <!--#include virtual="ssi/header.html" -->
 
     
@@ -28,7 +25,7 @@
 <h1>1.4 </h1>
 
 	
-<h2>10.09.2007, version <a href="put.link.here">1.4 - release</a></h2>
+<h2>10.10.2007, version <a href="put.link.here">1.4 - release</a></h2>
 
 	
 <ul>
@@ -36,10 +33,10 @@
 	<li>feature: Loading splash more informative about what's going on
 behind-the-scenes such as which ontologies are loading, if they are
 being updated, etc.</li>
-  <li>obo edit annotation model can now be optionally configured for
-backend, which will allow for more sophistaicated to be captured (like
+  <li>feature: obo edit annotation model can now be optionally configured for
+backend, which will allow for more sophisticated data to be captured (like
 comparisons)</li>
-  <li></li>
+  <li>feature: Error for obo parse failures to info panel</li><li>feature: Delimited tab adapter uses column headings to map to table, rather than ordering</li><li>change: Moved test suites in with source to work with eclipse</li></ul><ul><li>bugfix: Terms not found are no longer dropped, a dangler is created, and error msg to info, show up in red</li><li>bugfix: if log conf fails use backup default</li>
 
 	
 </ul>
@@ -833,5 +830,4 @@
 
     <!--#include virtual="ssi/footer.html" -->
 
-</body>
-</html>
+</body></html>
\ No newline at end of file


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[Obo-svn-commit] SF.net SVN: obo: [1016] phenote/trunk/doc/phenote-website/ phenote-release-notes.shtml

From: <mg...@us...> - 2007-10-10 14:15:39

Revision: 1016
          http://obo.svn.sourceforge.net/obo/?rev=1016&view=rev
Author:   mgibson
Date:     2007-10-10 07:15:43 -0700 (Wed, 10 Oct 2007)

Log Message:
-----------
ok done with my part of release notes - its ready for ya jim

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/phenote-release-notes.shtml

Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.shtml	2007-10-10 14:02:46 UTC (rev 1015)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.shtml	2007-10-10 14:15:43 UTC (rev 1016)
@@ -36,7 +36,7 @@
   <li>feature: obo edit annotation model can now be optionally configured for
 backend, which will allow for more sophisticated data to be captured (like
 comparisons)</li>
-  <li>feature: Error for obo parse failures to info panel</li><li>feature: Delimited tab adapter uses column headings to map to table, rather than ordering</li><li>change: Moved test suites in with source to work with eclipse</li></ul><ul><li>bugfix: Terms not found are no longer dropped, a dangler is created, and error msg to info, show up in red</li><li>bugfix: if log conf fails use backup default</li>
+  <li>feature: Error for obo parse failures to info panel</li><li>feature: Delimited tab adapter uses column headings to map to table, rather than ordering</li><li>feature: Autocompletion optimized with threading, cancels stale requests (min-comp-chars now pase)</li><li>feature: Date created automatically added into data (under the hood)</li><li>feature: If arrow hit with empty input then gets &amp; displays all terms (used to inefficiently pre-load)</li><li>feature: Can sort completion list by ID, needed for zfin stages</li><li>change: Moved test suites in with source to work with eclipse</li><li>change: Took a lot of obos out of webstart jar - less bulky - as they get automatically downloaded</li></ul><ul><li>bugfix: Terms not found are no longer dropped, a dangler is created, and error msg to info, show up in red</li><li>bugfix: if log conf fails use backup default</li>
 
 	
 </ul>


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[Obo-svn-commit] SF.net SVN: obo: [1014] phenote/trunk/doc/phenote-website/ phenote-release-notes.shtml

From: <mg...@us...> - 2007-10-09 23:41:25

Revision: 1014
          http://obo.svn.sourceforge.net/obo/?rev=1014&view=rev
Author:   mgibson
Date:     2007-10-09 16:41:21 -0700 (Tue, 09 Oct 2007)

Log Message:
-----------
i need a new html composer - Nvu does this silly thing of putting in lots of 
blank lines
does anyone have any suggestions?

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/phenote-release-notes.shtml

Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.shtml	2007-10-09 23:39:13 UTC (rev 1013)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.shtml	2007-10-09 23:41:21 UTC (rev 1014)
@@ -1,58 +1,112 @@
 <!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>
+<head>
+<!--#include virtual="ssi/head.html" -->
 
-    <!--#include virtual="ssi/head.html" -->
-    <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
+    
+    
+  <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
+</head>
 
-  </head>
+
   <body>
 
+
     <!--#include virtual="ssi/header.html" -->
 
-    <div id="main_container_aux">
-      <div id="main_content_aux">
-	<div class="catch_phrase">
+    
+<div id="main_container_aux">
+      
+<div id="main_content_aux">
+	
+<div class="catch_phrase">
 	  Phenote Release Notes
 	</div>
 
-	<h1>1.4 </h1>
-	<h2>10.09.2007, version <a href="put.link.here">1.4 - release</a></h2>
-	<ul>
-	<li>feature: Loading splash more informative about what's going on behind-the-scenes such as which ontologies are loading, if they are being updated, etc.</li>
-	</ul>
-	<h2>08.28.2007, version <a href="phenote/1.4-beta3/phenote.jnlp">1.4-beta3</a></h2>
-	<ul>
+
+	
+<h1>1.4 </h1>
+
+	
+<h2>10.09.2007, version <a href="put.link.here">1.4 - release</a></h2>
+
+	
+<ul>
+
+	<li>feature: Loading splash more informative about what's going on
+behind-the-scenes such as which ontologies are loading, if they are
+being updated, etc.</li>
+  <li>obo edit annotation model can now be optionally configured for
+backend, which will allow for more sophistaicated to be captured (like
+comparisons)</li>
+  <li></li>
+
+	
+</ul>
+
+	
+<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: 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
@@ -63,380 +117,530 @@
 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-&gt;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&amp;aid=1685540&amp;group_id=76834&amp;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&amp;aid=1739399&amp;group_id=76834&amp;atid=887913">1739399</a>]</li>
 
+
   <li>change: ontology files can be read with dangling references</li>
 
+
   <li>change: Command line read &amp; 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&amp;aid=1676756&amp;group_id=76834&amp;atid=887913">1676756</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&amp;aid=1672080&amp;group_id=76834&amp;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-&gt;Exit</li>
 
+
   <li>feature:  Autocompletion search default settings configurable <a href="https://sourceforge.net/tracker/index.php?func=detail&amp;aid=1677411&amp;group_id=76834&amp;atid=887913">1677411</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&amp;aid=1669579&amp;group_id=76834&amp;atid=887913">1669579</a>]
   </li>
 
+
   <li>feature:  User can save search setting defaults if changed during Phenote session</li>
 
+
   <li>change:  File-&gt;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&amp;aid=1718945&amp;group_id=76834&amp;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&amp;aid=1721044&amp;group_id=76834&amp;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&amp;aid=1721032&amp;group_id=76834&amp;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&amp;aid=1721470&amp;group_id=76834&amp;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 &gt;2 terms </li>
 
+
   <li>feature:  Term history display can be toggled on/off (Settings-&gt;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-&gt;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&amp;aid=1574916&amp;group_id=76834&amp;atid=887913">1574916</a>]</li>
 
+
   <li>feature:  display ontology namespace in term info box [<a href="https://sourceforge.net/tracker/index.php?func=detail&amp;aid=1598048&amp;group_id=76834&amp;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 &gt;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&amp;aid=1661778&amp;group_id=76834&amp;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&amp;aid=1575241&amp;group_id=76834&amp;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&amp;aid=1648337&amp;group_id=76834&amp;atid=887913">1648337</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&amp;aid=1574906&amp;group_id=76834&amp;atid=887913">1574906</a>]</li>
 
+
   <li>feature:  fixed releases available for checkout via sourceforge [<a href="https://sourceforge.net/tracker/index.php?func=detail&amp;aid=1670345&amp;group_id=76834&amp;atid=887913">1670345</a>]</li>
 
+
   <li>feature:  display xtns in load/save menu choices [<a href="https://sourceforge.net/tracker/index.php?func=detail&amp;aid=1594508&amp;group_id=76834&amp;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&amp;aid=1581589&amp;group_id=76834&amp;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&amp;aid=1633287&amp;group_id=76834&amp;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&amp;aid=1684591&amp;group_id=76834&amp;atid=887913">1684591</a>]</li>
 
+
   <li>bugfix:  post-composed terms not loading [<a href="https://sourceforge.net/tracker/index.php?func=detail&amp;aid=1661728&amp;group_id=76834&amp;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&amp;aid=1574912&amp;group_id=76834&amp;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&amp;aid=1661973&amp;group_id=76834&amp;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&amp;aid=1588669&amp;group_id=76834&amp;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&amp;aid=1588670&amp;group_id=76834&amp;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 &amp; standalone)</li>
 
+
   <li>feature:  obsoletes are displayed from autocomplete with [obs]</li>
 
+
   <li>feature:  Bulk update &amp; copy in standalone. [<a href="https://sourceforge.net/tracker/index.php?func=detail&amp;aid=1579885&amp;group_id=76834&amp;atid=887913">1579885</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&amp;aid=1579882&amp;group_id=76834&amp;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 &amp; standalone.</li>
 
+
   <li>feature:  Pheno-xml reader (thanks to Jim Balhoff) and improvements to pheno-xml
 writer (does pub &amp; genetic context)</li>
 
+
   <li> feature:  Command line reading &amp; writing of phenoxml &amp; 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 &amp; completion are scrollable.</li>
 
+
   <li>feature: standalone version can read &amp; write pheno-syntax with ids &amp; 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
@@ -451,17 +655,24 @@
 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 &amp; 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 &amp; 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.
@@ -470,10 +681,13 @@
 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 &amp; adding field.
 Made the internal code much more generic for adding new fields from
 configuration, got rid of a lot of hard wiring.&nbsp; Part of this was
@@ -482,101 +696,141 @@
 easier to plop a web gui on top of the current phenote model &amp;
 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 &amp; lumping
 parents
 &amp; children, formatting. Also perhaps have children &amp; 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>


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[Obo-svn-commit] SF.net SVN: obo: [1013] phenote/trunk

From: <nl...@us...> - 2007-10-09 23:39:09

Revision: 1013
          http://obo.svn.sourceforge.net/obo/?rev=1013&view=rev
Author:   nlw
Date:     2007-10-09 16:39:13 -0700 (Tue, 09 Oct 2007)

Log Message:
-----------
added correct path to icon in jnlps;
added warning message to termrequester to indicate that the functionality is not yet in place

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
    phenote/trunk/doc/phenote-website/phenote.jnlp
    phenote/trunk/src/java/phenote/gui/TermRequestGUI.java

Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp	2007-10-09 23:18:25 UTC (rev 1012)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp	2007-10-09 23:39:13 UTC (rev 1013)
@@ -6,7 +6,7 @@
 <information>
 	<title>Phenote @@phenote.version@@</title>
 	<vendor>National Center for Biomedical Ontology</vendor>
-	<icon href="images/elephant_icon.jpg" />
+	<icon href="/images/elephant_icon.jpg" />
 	<description>Phenote standalone app via webstart</description>
  	 <!-- Declares that the application can run without
          access to the server it was downloaded from -->

Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp	2007-10-09 23:18:25 UTC (rev 1012)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp	2007-10-09 23:39:13 UTC (rev 1013)
@@ -6,7 +6,7 @@
 <information>
 	<title>Phenote @@phenote.version@@</title>
 	<vendor>National Center for Biomedical Ontology</vendor>
-	<icon href="images/elephant_icon.jpg" />
+	<icon href="/images/elephant_icon.jpg" />
 	<description>Phenote standalone app via webstart</description>
  	 <!-- Declares that the application can run without
          access to the server it was downloaded from -->

Modified: phenote/trunk/src/java/phenote/gui/TermRequestGUI.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/TermRequestGUI.java	2007-10-09 23:18:25 UTC (rev 1012)
+++ phenote/trunk/src/java/phenote/gui/TermRequestGUI.java	2007-10-09 23:39:13 UTC (rev 1013)
@@ -270,13 +270,15 @@
 		  m+="[DEF] "+ newtermDef.getText()+"\n";
 		  m+="[COMMENT] "+ newtermComment.getText()+"\n";
 		  String newtermID = submitNewTermViaREST();
-		  if (newRadioButton.isSelected()) {
-		  	m = "<html><body>Your term <bold>"+newtermName.getText()+"</bold> has been successfully created.\n";
-		  	m+= "It has been given a temporary ID <font color=red>"+newtermID+"</font></body></html>";
-		  }
+//		  if (newRadioButton.isSelected()) {
+//		  	m = "<html><body>Your term <bold>"+newtermName.getText()+"</bold> has been successfully created.\n";
+//		  	m+= "It has been given a temporary ID <font color=red>"+newtermID+"</font></body></html>";
+//		  }
 		  if (newtermID!=null) {
 		  }
-      JOptionPane.showMessageDialog(null, m, "Submission Successful", JOptionPane.PLAIN_MESSAGE);
+		  m="This feature has not yet been implemented!";
+		  JOptionPane.showMessageDialog(null, m, "Submission Error", JOptionPane.ERROR_MESSAGE);
+		  //      JOptionPane.showMessageDialog(null, m, "Submission Successful", JOptionPane.PLAIN_MESSAGE);
 			thisframe.setVisible(false);
 		}
 	}


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[Obo-svn-commit] SF.net SVN: obo: [1011] phenote/trunk/obo-files/worm_anatomy.obo

From: <mg...@us...> - 2007-10-09 23:09:32

Revision: 1011
          http://obo.svn.sourceforge.net/obo/?rev=1011&view=rev
Author:   mgibson
Date:     2007-10-09 16:09:33 -0700 (Tue, 09 Oct 2007)

Log Message:
-----------
worm anatomy being automatically retreived from sourceforge 
taking out of repos

Removed Paths:
-------------
    phenote/trunk/obo-files/worm_anatomy.obo

Deleted: phenote/trunk/obo-files/worm_anatomy.obo
===================================================================
--- phenote/trunk/obo-files/worm_anatomy.obo	2007-10-09 22:57:10 UTC (rev 1010)
+++ phenote/trunk/obo-files/worm_anatomy.obo	2007-10-09 23:09:33 UTC (rev 1011)
@@ -1,37046 +0,0 @@
-format-version: 1.0
-date: 26:02:2007 17:08
-saved-by: raymond
-auto-generated-by: DAG-Edit 1.417
-default-namespace: WORManat1_1417
-remark: autogenerated-by 1.1 $
-
-[Term]
-id: WBbt:0001001
-name: AB
-def: "nucleus of embryonic cell AB." [WB:rynl]
-relationship: DESCENDENTOF WBbt:0000102
-
-[Term]
-id: WBbt:0004015
-name: AB
-def: "Embryonic founder cell" [ISBN:0-87969-307-X]
-synonym: "AB blastomere" []
-synonym: "lineage name\: P0.a" []
-is_a: WBbt:0007028
-
-[Term]
-id: WBbt:0005434
-name: AB lineage
-alt_id: WBbt:0005436
-synonym: "AB cells" []
-is_obsolete: true
-
-[Term]
-id: WBbt:0001002
-name: AB.a
-relationship: DESCENDENTOF WBbt:0001001
-
-[Term]
-id: WBbt:0005432
-name: AB.a lineage
-def: "cells in the AB.a lineage" [WB:rynl]
-is_obsolete: true
-
-[Term]
-id: WBbt:0001003
-name: AB.al
-relationship: DESCENDENTOF WBbt:0001002
-
-[Term]
-id: WBbt:0001004
-name: AB.ala
-relationship: DESCENDENTOF WBbt:0001003
-
-[Term]
-id: WBbt:0001005
-name: AB.alaa
-relationship: DESCENDENTOF WBbt:0001004
-
-[Term]
-id: WBbt:0001006
-name: AB.alaaa
-relationship: DESCENDENTOF WBbt:0001005
-
-[Term]
-id: WBbt:0001007
-name: AB.alaaaa
-relationship: DESCENDENTOF WBbt:0001006
-
-[Term]
-id: WBbt:0001008
-name: AB.alaaaal
-relationship: DESCENDENTOF WBbt:0001007
-
-[Term]
-id: WBbt:0001009
-name: AB.alaaaala
-relationship: DESCENDENTOF WBbt:0001008
-
-[Term]
-id: WBbt:0001641
-name: AB.alaaaalal
-relationship: DESCENDENTOF WBbt:0001009
-
-[Term]
-id: WBbt:0001010
-name: AB.alaaaalar
-relationship: DESCENDENTOF WBbt:0001009
-
-[Term]
-id: WBbt:0001011
-name: AB.alaaaalp
-relationship: DESCENDENTOF WBbt:0001008
-
-[Term]
-id: WBbt:0001012
-name: AB.alaaaalpa
-relationship: DESCENDENTOF WBbt:0001011
-
-[Term]
-id: WBbt:0002119
-name: AB.alaaaalpp
-relationship: DESCENDENTOF WBbt:0001011
-
-[Term]
-id: WBbt:0001013
-name: AB.alaaaar
-relationship: DESCENDENTOF WBbt:0001007
-
-[Term]
-id: WBbt:0001014
-name: AB.alaaaarl
-relationship: DESCENDENTOF WBbt:0001013
-
-[Term]
-id: WBbt:0001015
-name: AB.alaaaarla
-relationship: DESCENDENTOF WBbt:0001014
-
-[Term]
-id: WBbt:0002728
-name: AB.alaaaarlp
-relationship: DESCENDENTOF WBbt:0001014
-
-[Term]
-id: WBbt:0001016
-name: AB.alaaaarr
-relationship: DESCENDENTOF WBbt:0001013
-
-[Term]
-id: WBbt:0001017
-name: AB.alaaaarra
-relationship: DESCENDENTOF WBbt:0001016
-
-[Term]
-id: WBbt:0002729
-name: AB.alaaaarrp
-relationship: DESCENDENTOF WBbt:0001016
-
-[Term]
-id: WBbt:0001018
-name: AB.alaaap
-relationship: DESCENDENTOF WBbt:0001006
-
-[Term]
-id: WBbt:0001019
-name: AB.alaaapa
-relationship: DESCENDENTOF WBbt:0001018
-
-[Term]
-id: WBbt:0001020
-name: AB.alaaapal
-relationship: DESCENDENTOF WBbt:0001019
-
-[Term]
-id: WBbt:0002125
-name: AB.alaaapall
-relationship: DESCENDENTOF WBbt:0001020
-
-[Term]
-id: WBbt:0001695
-name: AB.alaaapalr
-relationship: DESCENDENTOF WBbt:0001020
-
-[Term]
-id: WBbt:0001021
-name: AB.alaaapar
-relationship: DESCENDENTOF WBbt:0001019
-
-[Term]
-id: WBbt:0001022
-name: AB.alaaaparl
-relationship: DESCENDENTOF WBbt:0001021
-
-[Term]
-id: WBbt:0002117
-name: AB.alaaaparr
-relationship: DESCENDENTOF WBbt:0001021
-
-[Term]
-id: WBbt:0001023
-name: AB.alaaapp
-relationship: DESCENDENTOF WBbt:0001018
-
-[Term]
-id: WBbt:0001024
-name: AB.alaaappl
-relationship: DESCENDENTOF WBbt:0001023
-
-[Term]
-id: WBbt:0002118
-name: AB.alaaappll
-relationship: DESCENDENTOF WBbt:0001024
-
-[Term]
-id: WBbt:0001025
-name: AB.alaaapplr
-relationship: DESCENDENTOF WBbt:0001024
-
-[Term]
-id: WBbt:0001026
-name: AB.alaaappr
-relationship: DESCENDENTOF WBbt:0001023
-
-[Term]
-id: WBbt:0001696
-name: AB.alaaapprl
-relationship: DESCENDENTOF WBbt:0001026
-
-[Term]
-id: WBbt:0002126
-name: AB.alaaapprr
-relationship: DESCENDENTOF WBbt:0001026
-
-[Term]
-id: WBbt:0001027
-name: AB.alaap
-relationship: DESCENDENTOF WBbt:0001005
-
-[Term]
-id: WBbt:0001028
-name: AB.alaapa
-relationship: DESCENDENTOF WBbt:0001027
-
-[Term]
-id: WBbt:0001029
-name: AB.alaapaa
-relationship: DESCENDENTOF WBbt:0001028
-
-[Term]
-id: WBbt:0001030
-name: AB.alaapaaa
-relationship: DESCENDENTOF WBbt:0001029
-
-[Term]
-id: WBbt:0001031
-name: AB.alaapaaal
-relationship: DESCENDENTOF WBbt:0001030
-
-[Term]
-id: WBbt:0001642
-name: AB.alaapaaar
-relationship: DESCENDENTOF WBbt:0001030
-
-[Term]
-id: WBbt:0001032
-name: AB.alaapaap
-relationship: DESCENDENTOF WBbt:0001029
-
-[Term]
-id: WBbt:0001033
-name: AB.alaapaapa
-relationship: DESCENDENTOF WBbt:0001032
-
-[Term]
-id: WBbt:0002120
-name: AB.alaapaapp
-relationship: DESCENDENTOF WBbt:0001032
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[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [1009] phenote/trunk/obo-files/wbpaper.obo

From: <mg...@us...> - 2007-10-09 22:42:38

Revision: 1009
          http://obo.svn.sourceforge.net/obo/?rev=1009&view=rev
Author:   mgibson
Date:     2007-10-09 15:42:40 -0700 (Tue, 09 Oct 2007)

Log Message:
-----------
dont need womr paper anymore - dynamic

Removed Paths:
-------------
    phenote/trunk/obo-files/wbpaper.obo

Deleted: phenote/trunk/obo-files/wbpaper.obo
===================================================================
--- phenote/trunk/obo-files/wbpaper.obo	2007-10-09 21:57:08 UTC (rev 1008)
+++ phenote/trunk/obo-files/wbpaper.obo	2007-10-09 22:42:40 UTC (rev 1009)
@@ -1,133471 +0,0 @@
-default-namespace: WBPaper
-
-[Term]
-id: WBPaper00000003
-name: Induction, detection and isolation of temperature-sensitive lethal and/or sterile mutants in nematodes. I. The free-living nematode C. elegans.
-synonym: "cgc3" []
-
-[Term]
-id: WBPaper00000005
-name: Etude ultrastructurale des relations entre ovocytes et rachis au cours de l'Sovogenese du nematode C. elegans.
-synonym: "cgc5" []
-
-[Term]
-id: WBPaper00000006
-name: Ultrastructural changes in the nuclear and perinuclear regions of the oogonia and primary oocytes of C. elegans, Bergerac strain.
-synonym: "cgc6" []
-
-[Term]
-id: WBPaper00000007
-name: Changes in the synaptonemal complex in the oocyte nucleus in meiotic prophase of C. elegans.
-synonym: "cgc7" []
-
-[Term]
-id: WBPaper00000008
-name: Cell cycling and DNA replication in a mutant blocked in cell division in the nematode C. elegans.
-synonym: "cgc8" []
-synonym: "pmid631425" []
-
-[Term]
-id: WBPaper00000009
-name: The pharynx of C. elegans.
-synonym: "cgc9" []
-synonym: "pmid8805" []
-
-[Term]
-id: WBPaper00000010
-name: Nematodes associated with Coleoptera species in Egypt Part 2.
-synonym: "cgc10" []
-
-[Term]
-id: WBPaper00000011
-name: Responses of dauerlarvae of C. elegans (Nematoda: Rhabditidae) to thermal stress and oxygen deprivation.
-synonym: "cgc11" []
-
-[Term]
-id: WBPaper00000012
-name: Critical oxygen tension of C. elegans.
-synonym: "cgc12" []
-
-[Term]
-id: WBPaper00000014
-name: Effect of bacteria on dispersal of C. elegans (Rhabditidae).
-synonym: "cgc14" []
-
-[Term]
-id: WBPaper00000015
-name: Genetic studies of chemotaxis mutants in nematodes.
-synonym: "cgc15" []
-
-[Term]
-id: WBPaper00000016
-name: Biochemical genetics of C. elegans.
-synonym: "cgc16" []
-
-[Term]
-id: WBPaper00000021
-name: The persistence of processes regulating the level of reproduction in the herm nematode C. elegans, despite parental aging/
-synonym: "cgc21" []
-synonym: "pmid5047816" []
-
-[Term]
-id: WBPaper00000022
-name: Un exemple de derive meiotique chez un nematode libre autofecond C. elegans.
-synonym: "cgc22" []
-
-[Term]
-id: WBPaper00000023
-name: Cryoconservation de mutants femelle-steriles d'un nematode libre hermaphrodite C. elegans a la temperature de l'azote liquide.
-synonym: "cgc23" []
-
-[Term]
-id: WBPaper00000024
-name: Genetique de la physiologie ovocytaire chez un nematode libre autofecond C. elegans. I. Influence du genotype et selection/
-synonym: "cgc24" []
-
-[Term]
-id: WBPaper00000025
-name: Etude genetique d'un mutant meiotique dominant chez C. elegans, souche Bergerac.
-synonym: "cgc25" []
-
-[Term]
-id: WBPaper00000026
-name: Influence of parental aging on the reproduction of the F1 generation in a hermaphrodite nematode C. elegans.
-synonym: "cgc26" []
-synonym: "pmid5047815" []
-
-[Term]
-id: WBPaper00000027
-name: Obtaining a self-fertilizing hermaphrodite mutant with a male copulatory bursa in the free-living nematode C. elegans var. Bergerac.
-synonym: "cgc27" []
-
-[Term]
-id: WBPaper00000028
-name: DNA base composition of some free living nematode species.
-synonym: "cgc28" []
-
-[Term]
-id: WBPaper00000029
-name: A method of distinguishing between living and dead nematodes by enzymatically induced fluorescence.
-synonym: "cgc29" []
-
-[Term]
-id: WBPaper00000030
-name: The genetics of behaviour.
-synonym: "cgc30" []
-
-[Term]
-id: WBPaper00000031
-name: The genetics of Caenorhabditis elegans.
-synonym: "cgc31" []
-synonym: "pmid4366476" []
-
-[Term]
-id: WBPaper00000033
-name: Evolution de la prophase meiotique chez C. elegans Maupas 1900, sous l'influence de temperature elevees.
-synonym: "cgc33" []
-
-[Term]
-id: WBPaper00000034
-name: Genetic adaptation of C. elegans (Nematoda) to high temperatures.
-synonym: "cgc34" []
-
-[Term]
-id: WBPaper00000036
-name: L'adaptation aux temperatures elevees chez un nematode C. elegans Maupas 1900. I. L'adaptation et son evolution.
-synonym: "cgc36" []
-
-[Term]
-id: WBPaper00000037
-name: L'adptation aux temperatures elevees chez un nematode C. elegans Maupas 1900. II. Stabilite et physiologie de l'adaptation.
-synonym: "cgc37" []
-
-[Term]
-id: WBPaper00000038
-name: L'adaptation aux temperatures elevees chez un nematode C. elegans Maupas 1900. III. Role des facteurs autres que la temperature/
-synonym: "cgc38" []
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-[Term]
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-name: Influence des conditions de milieu sur la fecondite de C. elegans a diferentes temperatures.
-synonym: "cgc39" []
-
-[Term]
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-name: Structure, organisation et variation du materiel genetique du nematode libre hermaphrodite autofecond C. elegans.
-synonym: "cgc41" []
-
-[Term]
-id: WBPaper00000042
-name: Influence of parental aging on the fecundity of 1st generation descendants in a self-fertilizing hermaphrodite nematode: C. elegans.
-synonym: "cgc42" []
-
-[Term]
-id: WBPaper00000044
-name: Some aspects of the respiratory metabolism of C. briggsae (Rhabditidae).
-synonym: "cgc44" []
-
-[Term]
-id: WBPaper00000045
-name: Yeast extract as a supplement to chemically defined medium for axenic culture of C. briggsae.
-synonym: "cgc45" []
-
-[Term]
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-name: Mass culture of axenic nematodes using continuous aeration.
-synonym: "cgc46" []
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-name: Yeast ribosomes as a source of growth factor for nematodes.
-synonym: "cgc47" []
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-synonym: "cgc48" []
-
-[Term]
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-name: Ficoll activation of a protein essential for maturation of the free-living nematode Caenorhabditis briggsae.
-synonym: "cgc49" []
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-name: Growth of nematodes in defined medium containing hemin and supplemented with commercially available proteins.
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-
-[Term]
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-name: Cultivation of C. briggsae and Turbatrix aceti with defined proteins.
-synonym: "cgc51" []
-
-[Term]
-id: WBPaper00000052
-name: The role of precipitation during activation treatments of growth factor for C. briggsae.
-synonym: "cgc52" []
-
-[Term]
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-name: Machine for rapidly counting and measuring the size of small nematodes.
-synonym: "cgc53" []
-
-[Term]
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-name: The life cycle of the nematode C. elegans. I. Wild type growth and reproduction.
-synonym: "cgc54" []
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-[Term]
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-synonym: "pmid988846" []
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-[Term]
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-synonym: "pmid1183723" []
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-name: Studies on the effects of 2 procaine preparations on C. briggsae.
-synonym: "cgc60" []
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-[Term]
-id: WBPaper00000061
-name: Etude, a differentes temperatures, de l'activite predatrice de quelques champignons nematophages vis-a-vis du nematode C. elegans/
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-[Term]
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-name: Etudes preliminaires sur les relations entre nematodes libres et bacteri es dans le sol.
-synonym: "cgc63" []
-
-[Term]
-id: WBPaper00000065
-name: Organization of neuronal microtubules in the nematode C. elegans.
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-synonym: "pmid479300" []
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-name: Effect of particulate materials on population growth of the free living nematode C. briggsae.
-synonym: "cgc66" []
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-[Term]
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-name: Studies on some physiological functions and morphological characters of Rhabditis (Rhabditidae, Nematoda).
-synonym: "cgc67" []
-
-[Term]
-id: WBPaper00000069
-name: Isocitrate lyase from parasitic and free living nematodes.
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-synonym: "cgc70" []
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-synonym: "cgc74" []
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-synonym: "cgc75" []
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-id: WBPaper00000076
-name: Indolealkylamines in the coordination of nematode behavioral activities.
-synonym: "cgc76" []
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-synonym: "cgc77" []
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-name: Sensory mechanisms in nematodes.
-synonym: "cgc79" []
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-name: Integrated behaviour in the feeding phase of C. elegans (Nematoda).
-synonym: "cgc80" []
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-name: Croissance des ovotestis puis des ovaires chez un nematode libre hermaphrodite: C. elegans Maupas 1900.
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-id: WBPaper00000105
-name: The axenic cultivation of Rhabditis briggsae Dougherty & Nigon, 1949 (Nematoda: Rhabditidae) IV. Plasma protein fractions with various supplementations.
-synonym: "cgc105" []
-
-[Term]
-id: WBPaper00000106
-name: The effect of acriflavine (a mixture of 2,8-diaminoacridine and 2,8-diamino-10-methyl-acridinium-chloride) on the growth of the nematode C. elegans.
-synonym: "cgc106" []
-
-[Term]
-id: WBPaper00000107
-name: The axenic cultivation of Rhabditis briggsae I. Experiments with chick embryo juice and chemically defined media/
-synonym: "cgc107" []
-
-[Term]
-id: WBPaper00000108
-name: A new species of Stylopage preying on nematodes.
-synonym: "cgc108" []
-
-[Term]
-id: WBPaper00000109
-name: Three fungi destructive to free-living terricolous nematodes.
-synonym: "cgc109" []
-
-[Term]
-id: WBPaper00000110
-name: Three new Hyphomycetes preying on free-living terricolous nematodes.
-synonym: "cgc110" []
-
-[Term]
-id: WBPaper00000111
-name: Some hyphomycetes parasitic on free-living terricolous nematodes.
-synonym: "cgc111" []
-
-[Term]
-id: WBPaper00000112
-name: Three hyphomycetes that capture nematodes in adhesive networks.
-synonym: "cgc112" []
-
-[Term]
-id: WBPaper00000113
-name: A species of Harposporium invading its nematode host from the stoma.
-synonym: "cgc113" []
-
-[Term]
-id: WBPaper00000114
-name: Growth inhibition of C. elegans and Panagrellus redivivus by selected mammalian and insect hormones.
-synonym: "cgc114" []
-
-[Term]
-id: WBPaper00000115
-name: Countercurrent separation: A new method for studying behavior of small aquatic organisms.
-synonym: "cgc115" []
-
-[Term]
-id: WBPaper00000116
-name: Analysis of chemotaxis in the nematode C. elegans by countercurrent separation.
-synonym: "cgc116" []
-synonym: "pmid4822548" []
-
-[Term]
-id: WBPaper00000117
-name: The avoidance of D-Tryptophan by the nematode C. elegans.
-synonym: "cgc117" []
-synonym: "pmid1176914" []
-
-[Term]
-id: WBPaper00000118
-name: Attraction of the nematode C. elegans to pyridine.
-synonym: "cgc118" []
-synonym: "pmid3374" []
-
-[Term]
-id: WBPaper00000119
-name: Chemotactic behavior of mutants of the nematode C. elegans that are defective in their attraction to NaCl.
-synonym: "cgc119" []
-
-[Term]
-id: WBPaper00000120
-name: Chemotactic responses of male C. elegans.
-synonym: "cgc120" []
-
-[Term]
-id: WBPaper00000121
-name: Thermal acclimation more extensive for behavioral parameters than for oxygen consumption in the nematode C. elegans.
-synonym: "cgc121" []
-
-[Term]
-id: WBPaper00000122
-name: Chemotaxis-defective mutants of the nematode C. elegans.
-synonym: "cgc122" []
-synonym: "pmid1132687" []
-
-[Term]
-id: WBPaper00000123
-name: The nematode C. elegans a new organism for intensive biological study.
-synonym: "cgc123" []
-synonym: "pmid929205" []
-
-[Term]
-id: WBPaper00000124
-name: Analysis of the constancy of DNA sequences during development and evolution of the nematode C. elegans.
-synonym: "cgc124" []
-synonym: "pmid286315" []
-
-[Term]
-id: WBPaper00000125
-name: Molecular genetics of nematode myosin.
-synonym: "cgc125" []
-
-[Term]
-id: WBPaper00000126
-name: Genetic and molecular studies of nematode myosin.
-synonym: "cgc126" []
-
-[Term]
-id: WBPaper00000127
-name: Kinetics of movement of normal and mutant nematodes.
-synonym: "cgc127" []
-
-[Term]
-id: WBPaper00000128
-name: Temperature sensitive mutation affecting myofilament assembly in C. elegans.
-synonym: "cgc128" []
-synonym: "med74284321" []
-synonym: "pmid4845659" []
-
-[Term]
-id: WBPaper00000129
-name: A mutant affecting the heavy chain of myosin in C. elegans.
-synonym: "cgc129" []
-synonym: "pmid4453018" []
-
-[Term]
-id: WBPaper00000130
-name: Ultrastructural studies on C. briggsae.
-synonym: "cgc130" []
-
-[Term]
-id: WBPaper00000131
-name: Studies on ageing in nematodes IV. The effect of antioxidants on cellular damage and life span.
-synonym: "cgc131" []
-
-[Term]
-id: WBPaper00000132
-name: Studies on ageing in nematodes III. Electronmicroscopical studies on age-associated cellular damage.
-synonym: "cgc132" []
-
-[Term]
-id: WBPaper00000135
-name: Nutritional requirements for reproduction of a temperature-sensitive nematode, reared in axenic culture.
-synonym: "cgc135" []
-
-[Term]
-id: WBPaper00000137
-name: Genetic control of differential heat tolerance in two strains of the nematode C. elegans.
-synonym: "cgc137" []
-
-[Term]
-id: WBPaper00000138
-name: Some effects of piperazine and methyridine on the free-living nematode C. briggsae (Rhabditidae).
-synonym: "cgc138" []
-
-[Term]
-id: WBPaper00000140
-name: Species differentiation in C. briggsae and C. elegans.
-synonym: "cgc140" []
-
-[Term]
-id: WBPaper00000141
-name: Neue parasitische und halbparasitische Nematoden bei Borkenkafern und einige andere Nematoden I. Teil.
-synonym: "cgc141" []
-
-[Term]
-id: WBPaper00000142
-name: A bioassay for measuring crude nematode extract which induced trap formation in a predaceous fungus.
-synonym: "cgc142" []
-
-[Term]
-id: WBPaper00000143
-name: Coordinate synthesis of two myosins in wild-type and mutant nematode muscle during larval development.
-synonym: "cgc143" []
-
-[Term]
-id: WBPaper00000146
-name: The evolution of hermaphroditism among animals.
-synonym: "cgc146" []
-
-[Term]
-id: WBPaper00000147
-name: Nabliudeniia nad nematodami (Okonchanie).
-synonym: "cgc147" []
-
-[Term]
-id: WBPaper00000148
-name: Responses of a soil nematode. Rhabditis briggsae to antibiotics.
-synonym: "cgc148" []
-
-[Term]
-id: WBPaper00000149
-name: Ascaris suum: Immune reactions in mice II. Metabolic and somatic antigens from in vitro cultured larvae.
-synonym: "cgc149" []
-
-[Term]
-id: WBPaper00000151
-name: Freeze-thaw survival of the free-living nematode C. briggsae.
-synonym: "cgc151" []
-
-[Term]
-id: WBPaper00000152
-name: Development of C. briggsae and Hymenolepsis nana in interchanged media.
-synonym: "cgc152" []
-
-[Term]
-id: WBPaper00000153
-name: Biochemical approach to systematic studies with axenic nematodes.
-synonym: "cgc153" []
-
-[Term]
-id: WBPaper00000154
-name: Effect of insect hormones on nematodes in axenic culture.
-synonym: "cgc154" []
-
-[Term]
-id: WBPaper00000155
-name: Development and maturation of C. briggsae in response to growth factor.
-synonym: "cgc155" []
-
-[Term]
-id: WBPaper00000156
-name: Continuous axenic culture of free-living nematodes.
-synonym: "cgc156" []
-
-[Term]
-id: WBPaper00000157
-name: Glycogen as a supplement in media for axenic cultivation of nematodes.
-synonym: "cgc157" []
-
-[Term]
-id: WBPaper00000158
-name: Actin and myosin-linked calcium regulation in C. elegans. Biochemical and structural properties of native filaments and purified proteins.
-synonym: "cgc158" []
-synonym: "pmid139159" []
-
-[Term]
-id: WBPaper00000159
-name: Myosin and paramyosin of C. elegans: Biochemical and structural properties of wild-type and mutant proteins.
-synonym: "cgc159" []
-synonym: "pmid140764" []
-
-[Term]
-id: WBPaper00000160
-name: The mating system of C. elegans: Evolutionary equilibrium between self- and cross-fertilization in a facultative hermaphrodite.
-synonym: "cgc160" []
-
-[Term]
-id: WBPaper00000161
-name: Normal and mutant thermotaxis in the nematode C. elegans.
-synonym: "cgc161" []
-synonym: "pmid1060088" []
-
-[Term]
-id: WBPaper00000162
-name: Chromosome rearrangements in C. elegans.
-synonym: "cgc162" []
-synonym: "pmid1269921" []
-
-[Term]
-id: WBPaper00000163
-name: Crossover suppressors and balanced recessive lethals in C. elegans.
-synonym: "cgc163" []
-synonym: "pmid631558" []
-
-[Term]
-id: WBPaper00000164
-name: Duplications in C. elegans.
-synonym: "cgc164" []
-synonym: "pmid573721" []
-
-[Term]
-id: WBPaper00000165
-name: Sterol requirement for reproduction of a free-living nematode.
-synonym: "cgc165" []
-
-[Term]
-id: WBPaper00000166
-name: Isolation from liver of a heat-stable requirement for reproduction of a free-living nematode.
-synonym: "cgc166" []
-
-[Term]
-id: WBPaper00000167
-name: Heme requirement for reproduction of a free-living nematode.
-synonym: "cgc167" []
-
-[Term]
-id: WBPaper00000168
-name: Roller mutants of the nematode C. elegans.
-synonym: "cgc168" []
-synonym: "pmid834177" []
-
-[Term]
-id: WBPaper00000169
-name: C. briggsae: Aging and the structural turnover of the outer cuticle surface and the intestine.
-synonym: "cgc169" []
-
-[Term]
-id: WBPaper00000170
-name: C. briggsae: Electron microscope analysis of changes in negative surface charge density of the outer cuticular membrane.
-synonym: "cgc170" []
-
-[Term]
-id: WBPaper00000172
-name: Patterns of gene expression during development of the nematode C. eleganss.
-synonym: "cgc172" []
-
-[Term]
-id: WBPaper00000174
-name: Development of the reproductive system of C. elegans.
-synonym: "cgc174" []
-synonym: "pmid943344" []
-
-[Term]
-id: WBPaper00000175
-name: Temperature-sensitive developmental mutants of C. elegans.
-synonym: "cgc175" []
-synonym: "pmid943345" []
-
-[Term]
-id: WBPaper00000176
-name: Expression of genes essential for early development in the nematode, C. elegans.
-synonym: "cgc176" []
-
-[Term]
-id: WBPaper00000177
-name: Behavior of free-living and plant-parasitic nematodes in a thermal gradient.
-synonym: "cgc177" []
-
-[Term]
-id: WBPaper00000178
-name: Mutations causing transformation of sexual phenotype in the nematode C. elegans.
-synonym: "cgc178" []
-synonym: "pmid560330" []
-
-[Term]
-id: WBPaper00000179
-name: Nondisjunction mutants of the nematode C. elegans.
-synonym: "cgc179" []
-
-[Term]
-id: WBPaper00000180
-name: A rapid, simple radiometric assay for cholinesterase, suitable for multiple determinations.
-synonym: "cgc180" []
-
-[Term]
-id: WBPaper00000181
-name: Cryofracturing for scanning electron microscope observations of internal structures of nematodes.
-synonym: "cgc181" []
-
-[Term]
-id: WBPaper00000182
-name: Surface scanning observations of changes in C. briggsae during aging.
-synonym: "cgc182" []
-
-[Term]
-id: WBPaper00000183
-name: Experimental and cytological studies on bisexual and hermaphroditic free-living nematodes with special reference to the problem of sex.
-synonym: "cgc183" []
-
-[Term]
-id: WBPaper00000184
-name: A uniform genetic nomenclature for the nematode C. elegans.
-synonym: "cgc184" []
-synonym: "pmid292825" []
-
-[Term]
-id: WBPaper00000185
-name: Age dependent changes in the behavior of C. elegans on attraction to Escherichia coli.
-synonym: "cgc185" []
-synonym: "pmid346360" []
-
-[Term]
-id: WBPaper00000186
-name: Sterilization and growth inhibition of C. elegans by 5-fluorodeoxyuridine.
-synonym: "cgc186" []
-synonym: "pmid153845" []
-
-[Term]
-id: WBPaper00000187
-name: Sinusoidal movement of C. elegans in liquid phase.
-synonym: "cgc187" []
-
-[Term]
-id: WBPaper00000188
-name: Freezing and storage of nematodes in liquid nitrogen.
-synonym: "cgc188" []
-
-[Term]
-id: WBPaper00000189
-name: Effect of heterologous antibody on Haemonchus contortus development in vitro.
-synonym: "cgc189" []
-
-[Term]
-id: WBPaper00000190
-name: Moulting of C. briggsae (Rhabditidae).
-synonym: "cgc190" []
-
-[Term]
-id: WBPaper00000191
-name: Patterns of proteins synthesized during development of C. elegans.
-synonym: "cgc191" []
-synonym: "pmid456742" []
-
-[Term]
-id: WBPaper00000192
-name: Recherches sur les ennemis du champignon de couche. I. Zoocenose des composts de champignonniere a Agaricus bisporus Lange/
-synonym: "cgc192" []
-
-[Term]
-id: WBPaper00000193
-name: Post-embryonic cell lineages of the hermaphrodite and male gonads in C. elegans.
-synonym: "cgc193" []
-synonym: "pmid478167" []
-
-[Term]
-id: WBPaper00000194
-name: Nematodes associated with vegetables in Prince Edward Island Canada.
-synonym: "cgc194" []
-
-[Term]
-id: WBPaper00000196
-name: Studies on ageing Turbatrix aceti.
-synonym: "cgc196" []
-
-[Term]
-id: WBPaper00000197
-name: Biogenic amines in the free-living nematode C. briggsae.
-synonym: "cgc197" []
-
-[Term]
-id: WBPaper00000198
-name: C. briggsae: Effects of aminopterin.
-synonym: "cgc198" []
-
-[Term]
-id: WBPaper00000199
-name: Influence of a growth factor from bacteria on the morphology of C. briggsae.
-synonym: "cgc199" []
-
-[Term]
-id: WBPaper00000200
-name: Effects of DNA synthesis inhibitors on C. briggsae and Turbatrix aceti.
-synonym: "cgc200" []
-
-[Term]
-id: WBPaper00000202
-name: Effects of centrophenoxine on the nematode C. briggsae.
-synonym: "cgc202" []
-
-[Term]
-id: WBPaper00000203
-name: Aging in the nematode C. elegans: Major biological and environmental factors influencing life span.
-synonym: "cgc203" []
-synonym: "pmid926867" []
-
-[Term]
-id: WBPaper00000204
-name: Nonaging developmental variant of C. elegans.
-synonym: "cgc204" []
-synonym: "pmid1264206" []
-
-[Term]
-id: WBPaper00000205
-name: Development of the male reproductive system and sexual transformation in the nematode C. elegans.
-synonym: "cgc205" []
-synonym: "pmid986968" []
-
-[Term]
-id: WBPaper00000206
-name: Further characterization of a temperature-sensitive transformation mutant in C. elegans.
-synonym: "cgc206" []
-synonym: "pmid446897" []
-
-[Term]
-id: WBPaper00000207
-name: Review: a comparative analysis of studies of enzyme changes with age, with comments on possible sources of error.
-synonym: "cgc207" []
-
-[Term]
-id: WBPaper00000208
-name: Die Nematoden-fauna des vergehenden Holzes und ihre Beziehungen zu den Insekten.
-synonym: "cgc208" []
-
-[Term]
-id: WBPaper00000209
-name: Freilebende terristrische Nematoden aus der Umgebung von Peking (China).
-synonym: "cgc209" []
-
-[Term]
-id: WBPaper00000210
-name: A. Freilebende terrestrische Nematoden aus der Umgebung von Peking (China) II.
-synonym: "cgc210" []
-
-[Term]
-id: WBPaper00000211
-name: Two new species of Rhabditis (R macrocerca & R clavopapillata) assoc with dogs and monkeys in experimental Strongyloides studies.
-synonym: "cgc211" []
-
-[Term]
-id: WBPaper00000212
-name: The cellular anatomy of embryos of the nematode C. elegans. Analysis and reconstruction of serial section electron micrographs.
-synonym: "cgc212" []
-synonym: "pmid567146" []
-
-[Term]
-id: WBPaper00000214
-name: Specific neuroanatomical changes in chemosensory mutants of the nematode C. elegans.
-synonym: "cgc214" []
-synonym: "pmid838889" []
-
-[Term]
-id: WBPaper00000215
-name: Nematode biochemistry XV. Enzyme changes related to glycerol excretion in C. briggsae.
-synonym: "cgc215" []
-
-[Term]
-id: WBPaper00000217
-name: Axenic culturing of nematodes: an easily prepared medium containing yeast extract.
-synonym: "cgc217" []
-
-[Term]
-id: WBPaper00000218
-name: Assay of a proteinaceous growth factor required for maturation of the free-living nematode, C. briggsae.
-synonym: "cgc218" []
-
-[Term]
-id: WBPaper00000219
-name: The use of nematodes cultured axenically on defined medium for biological studies.
-synonym: "cgc219" []
-
-[Term]
-id: WBPaper00000220
-name: Selection for adaptation to increased temperatures in free-living nematodes.
-synonym: "cgc220" []
-
-[Term]
-id: WBPaper00000223
-name: Accumulation of formimino-L-glutamic acid in the free-living nematode C. briggsae as related to folic acid deficiency.
-synonym: "cgc223" []
-
-[Term]
-id: WBPaper00000224
-name: Effect of vitamin B-12 & folate on biosynthesis of methionine from homocysteine in the nematode C. briggsae.
-synonym: "cgc224" []
-
-[Term]
-id: WBPaper00000225
-name: The growth-promoting activity of several lipid-related compounds in the free-living nematode C. briggsae.
-synonym: "cgc225" []
-
-[Term]
-id: WBPaper00000226
-name: The requirement of sterol and various sterol precursors in free-living nematodes.
-synonym: "cgc226" []
-
-[Term]
-id: WBPaper00000228
-name: Temperature-induced phase transitions in nematode lipids and their influence on respiration.
-synonym: "cgc228" []
-
-[Term]
-id: WBPaper00000230
-name: Muscle development in C. elegans mutants exhibiting retarded sarcomere construction.
-synonym: "cgc230" []
-synonym: "pmid728988" []
-
-[Term]
-id: WBPaper00000231
-name: Immunocytochemical localization of two myosins within the same muscle cells in C. elegans.
-synonym: "cgc231" []
-synonym: "pmid363276" []
-
-[Term]
-id: WBPaper00000232
-name: An internal deletion mutant of a myosin heavy chain in C. elegans.
-synonym: "cgc232" []
-synonym: "pmid271956" []
-
-[Term]
-id: WBPaper00000233
-name: Identification of the structural gene for a myosin heavy-chain in C. elegans.
-synonym: "cgc233" []
-synonym: "pmid909083" []
-
-[Term]
-id: WBPaper00000235
-name: The place of genetics in the study of behaviour.
-synonym: "cgc235" []
-
-[Term]
-id: WBPaper00000236
-name: Respiration responses of a Caenorhabditis sp. and Aphelencus avenae to the nematicide 1,2-dibromoethane (EDB).
-synonym: "cgc236" []
-
-[Term]
-id: WBPaper00000237
-name: Measurement of nematode respiration with the biological oxygen monitor.
-synonym: "cgc237" []
-
-[Term]
-id: WBPaper00000239
-name: Modes et formes de reproduction des nematodes.
-synonym: "cgc239" []
-
-[Term]
-id: WBPaper00000240
-name: Essais d'hybridisation chez les nematodes.
-synonym: "cgc240" []
-
-[Term]
-id: WBPaper00000241
-name: Lethals, steriles and deficiencies in a region of the X chromosome of C. elegans.
-synonym: "cgc241" []
-synonym: "pmid574105" []
-
-[Term]
-id: WBPaper00000242
-name: The histochemical evidence of peroxidase in invertebrate animals (nematoda and insecta).
-synonym: "cgc242" []
-
-[Term]
-id: WBPaper00000244
-name: Synchronous growth and aging of C. elegans in the presence of fluorodeoxyuridine.
-synonym: "cgc244" []
-synonym: "pmid153363" []
-
-[Term]
-id: WBPaper00000245
-name: Genetic organization in C. elegans: Fine-structure analysis of the unc-22 gene.
-synonym: "cgc245" []
-
-[Term]
-id: WBPaper00000247
-name: Endoparasitic nematode-trapping fungi of Mason State Forest.
-synonym: "cgc247" []
-
-[Term]
-id: WBPaper00000248
-name: Studies on the ability of various nematodes to induce trap formation in a nematode-trapping fungus Monacrosporium doedycoides.
-synonym: "cgc248" []
-
-[Term]
-id: WBPaper00000250
-name: Oogenesis in some free-living nematodes.
-synonym: "cgc250" []
-
-[Term]
-id: WBPaper00000251
-name: Characterization of the mitochondria of the free-living nematode, C. elegans.
-synonym: "cgc251" []
-synonym: "pmid131020" []
-
-[Term]
-id: WBPaper00000252
-name: Intersex, a temperature-sensitive mutant of the nematode C. elegans.
-synonym: "cgc252" []
-synonym: "pmid700253" []
-
-[Term]
-id: WBPaper00000253
-name: Axenic culture of free living nematodes a literature review.
-synonym: "cgc253" []
-
-[Term]
-id: WBPaper00000254
-name: The cultural and nutritional requirements of free-living nematodes of the genus Rhabditis and related genera.
-synonym: "cgc254" []
-
-[Term]
-id: WBPaper00000255
-name: The biology of free-living nematodes
-synonym: "cgc255" []
-
-[Term]
-id: WBPaper00000256
-name: Axenische Kultivierung freilebender Nematoden.
-synonym: "cgc256" []
-
-[Term]
-id: WBPaper00000257
-name: Axenic cultivation of C. briggsae (Nematoda: Rhabditidae) with chemically undefined supplements; comparative studies with related nematodes.
-synonym: "cgc257" []
-
-[Term]
-id: WBPaper00000258
-name: The incorporation of 14C from sodium acetate-2-14C into the amino acids of the soil-inhabiting nematode, Caenorhabditis briggsae.
-synonym: "cgc258" []
-
-[Term]
-id: WBPaper00000259
-name: The efficiency with which C. briggsae (Rhabditidae) feeds on the bacterium, Escherichia coli.
-synonym: "cgc259" []
-
-[Term]
-id: WBPaper00000260
-name: The B-Vitamins required by Caenorhabditis briggsae (Rhabditidae).
-synonym: "cgc260" []
-
-[Term]
-id: WBPaper00000261
-name: A biotin requirement for C. briggsae (Rhabditidae).
-synonym: "cgc261" []
-
-[Term]
-id: WBPaper00000262
-name: C. briggsae (Rhabditidae) under anaerobic conditions.
-synonym: "cgc262" []
-
-[Term]
-id: WBPaper00000263
-name: The effect of different concentrations of oxygen and of carbon dioxide on the growth and reproduction of C. briggsae (Rhabditidae).
-synonym: "cgc263" []
-
-[Term]
-id: WBPaper00000264
-name: A technique for obtaining axenic cultures of rhabditid nematodes.
-synonym: "cgc264" []
-
-[Term]
-id: WBPaper00000265
-name: The calorific value of C. elegans (Rhabditidae).
-synonym: "cgc265" []
-
-[Term]
-id: WBPaper00000266
-name: A study of the nutrition of C. briggsae (Rhabditidae) fed on Carbon-14 and Phosphorus-32 labelled bacteria.
-synonym: "cgc266" []
-
-[Term]
-id: WBPaper00000267
-name: C. dolichura in the head glands of the ants Camponotus herculeanus (L.) and Acanthomyops claviger (Roger) in Ontario/
-synonym: "cgc267" []
-
-[Term]
-id: WBPaper00000269
-name: Le determinisme du sexe chez un Nematode libre hermaphrodite Rhabditis dolichura Schneider.
-synonym: "cgc269" []
-
-[Term]
-id: WBPaper00000270
-name: Effects de la polyploidie chez un nematode libre.
-synonym: "cgc270" []
-
-[Term]
-id: WBPaper00000271
-name: Les modalites de la reproduction et le determinisme du sexe chez quelques nematodes libres.
-synonym: "cgc271" []
-
-[Term]
-id: WBPaper00000272
-name: Contributions a la critique experimentale des theories de la continuite germinale et de la lignee pure.
-synonym: "cgc272" []
-
-[Term]
-id: WBPaper00000273
-name: Developpement et reproduction des nematodes.
-synonym: "cgc273" []
-
-[Term]
-id: WBPaper00000274
-name: Effets d'une elevation de temperature sur la prophase meiotique d'un nematode libre.
-synonym: "cgc274" []
-
-[Term]
-id: WBPaper00000275
-name: L'evolution des structures nucleaires dans l'ovogenese de C. elegans Maupas 1900.
-synonym: "cgc275" []
-
-[Term]
-id: WBPaper00000276
-name: Genetique et evolution des nematodes libres. Perspectives tirees de l'etude de C. elegans.
-synonym: "cgc276" []
-synonym: "pmid6055883" []
-
-[Term]
-id: WBPaper00000277
-name: Reproduct patterns and attempts at recip crossing of Rhabditis elegans Maupas, 1900, and Rhabditis briggsae Dougherty & Nigon/
-synonym: "cgc277" []
-
-[Term]
-id: WBPaper00000278
-name: A dwarf mutation in a nematode. A morphological mutant of Rhabditis briggsae, a free-living soil nematode.
-synonym: "cgc278" []
-
-[Term]
-id: WBPaper00000280
-name: L'Architecture polaire de l'oeuf et les movements des constituants cellulaires au cour des premieres etapes du developpement chez quelques nematodes.
-synonym: "cgc280" []
-
-[Term]
-id: WBPaper00000281
-name: Asteromyces cruciatus from North America.
-synonym: "cgc281" []
-
-[Term]
-id: WBPaper00000282
-name: Incorporation of tritiated thymidine in the cells of C. briggsae (Nematoda) reared in axenic culture.
-synonym: "cgc282" []
-
-[Term]
-id: WBPaper00000283
-name: High-resolution two-dimensional electrophoresis of proteins.
-synonym: "cgc283" []
-
-[Term]
-id: WBPaper00000284
-name: Systematik und phylogenie der gattung Rhabditis (Nematoda).
-synonym: "cgc284" []
-
-[Term]
-id: WBPaper00000287
-name: A morphological temperature-sensitive mutant of the nematode C. elegans var. Bergerac.
-synonym: "cgc287" []
-
-[Term]
-id: WBPaper00000288
-name: Intracistronic recombination at a dwarfing locus in the free living self fertilizing nematode C. elegans.
-synonym: "cgc288" []
-synonym: "pmid807379" []
-
-[Term]
-id: WBPaper00000289
-name: Effect of dumpiness on the development and functioning of eutelic and noneutelic organs in the nematode C. elegans.
-synonym: "cgc289" []
-
-[Term]
-id: WBPaper00000290
-name: Cuticular collagen composition of the nematode C. elegans, Bergerac wild-type strain.
-synonym: "cgc290" []
-
-[Term]
-id: WBPaper00000291
-name: Exsheathment phenomenon in the infective-stage larvae of Haemonchus contortus.
-synonym: "cgc291" []
-
-[Term]
-id: WBPaper00000292
-name: Genetic approach to the study of the nervous system.
-synonym: "cgc292" []
-
-[Term]
-id: WBPaper00000294
-name: A simple spectrophotometric method for measurement of nematode populations.
-synonym: "cgc294" []
-
-[Term]
-id: WBPaper00000295
-name: Particulate isocitrate lyase and malate synthase in C. elegans.
-synonym: "cgc295" []
-synonym: "pmid907353" []
-
-[Term]
-id: WBPaper00000296
-name: Axenic and synchronous cultures of C. elegans.
-synonym: "cgc296" []
-
-[Term]
-id: WBPaper00000297
-name: C. elegans and Ascaris suum: Fragmentation of isocitrate lyase in crude extracts.
-synonym: "cgc297" []
-synonym: "pmid627278" []
-
-[Term]
-id: WBPaper00000298
-name: C. elegans and Ascaris suum: Inhibition of isocitrate lyase by itaconate.
-synonym: "cgc298" []
-synonym: "pmid658222" []
-
-[Term]
-id: WBPaper00000299
-name: Axenic cultivation of two species of rhabditid nematodes on a commercial medium.
-synonym: "cgc299" []
-
-[Term]
-id: WBPaper00000302
-name: C. elegans: Localization of cholinesterase associated with anterior nematode structures.
-synonym: "cgc302" []
-synonym: "pmid1269584" []
-
-[Term]
-id: WBPaper00000303
-name: Histamine content of the nematode, C. elegans.
-synonym: "cgc303" []
-synonym: "pmid4617652" []
-
-[Term]
-id: WBPaper00000305
-name: A mass culture bioassay method for C. briggsae using population growth rate as a response parameter.
-synonym: "cgc305" []
-
-[Term]
-id: WBPaper00000306
-name: Stimulatory effects of peptides on growth of the free-living nematode C. briggsae.
-synonym: "cgc306" []
-
-[Term]
-id: WBPaper00000307
-name: The effect of heme source on growth of C. briggsae in peptide and carbohydrate supplemented chemically defined medium.
-synonym: "cgc307" []
-
-[Term]
-id: WBPaper00000310
-name: An alternative interpretation of the fine structure of the basal zone of the cuticle of the dauerlarva of the nematode C. elegans (Nematoda).
-synonym: "cgc310" []
-synonym: "pmid688112" []
-
-[Term]
-id: WBPaper00000311
-name: Aspects of the fine structure of the dauer larva of the nematode C. elegans.
-synonym: "cgc311" []
-
-[Term]
-id: WBPaper00000312
-name: The use of osmium mixtures in localizing ions in C. elegans.
-synonym: "cgc312" []
-
-[Term]
-id: WBPaper00000313
-name: Notes on the free-living nematodes I. The hermaphrodite species.
-synonym: "cgc313" []
-
-[Term]
-id: WBPaper00000314
-name: Nerves and genes.
-synonym: "cgc314" []
-
-[Term]
-id: WBPaper00000315
-name: Harposporium anguillulae Lohde (moniliales), espece nematophage, trouve en Belgique.
-synonym: "cgc315" []
-
-[Term]
-id: WBPaper00000316
-name: A genetic pathway for dauer larva formation in C. elegans.
-synonym: "cgc316" []
-
-[Term]
-id: WBPaper00000317
-name: The genetics of development and behavior in C. elegans.
-synonym: "cgc317" []
-
-[Term]
-id: WBPaper00000318
-name: Indirect suppression in C. elegans.
-synonym: "cgc318" []
-synonym: "pmid669254" []
-
-[Term]
-id: WBPaper00000320
-name: The effect of temperature and parental age on recombination and nondisjunction in C. elegans.
-synonym: "cgc320" []
-
-[Term]
-id: WBPaper00000321
-name: A mutation in C. elegans that increases recombination frequency more then threefold.
-synonym: "cgc321" []
-synonym: "med80032926" []
-synonym: "pmid492325" []
-
-[Term]
-id: WBPaper00000323
-name: Nematode biochemistry - III. Excretion products.
-synonym: "cgc323" []
-
-[Term]
-id: WBPaper00000324
-name: Nematode biochemistry - V. Intermediary metabolism and amino acid interconversions in C. briggsae.
-synonym: "cgc324" []
-
-[Term]
-id: WBPaper00000325
-name: Nematode biochemistry - IX. Lack of sterol biosynthesis in free-living nematodes.
-synonym: "cgc325" []
-
-[Term]
-id: WBPaper00000326
-name: Nematode biochemistry - X. Excretion of glycerol by free-living nematodes.
-synonym: "cgc326" []
-
-[Term]
-id: WBPaper00000327
-name: Nematode biochemistry XI, biosynthesis of fatty acids by C. briggsae and Panagrellus redivivus.
-synonym: "cgc327" []
-
-[Term]
-id: WBPaper00000328
-name: Practical methods for the axenic culture of the free-living nematodes Turbatrix aceti and C. briggsae.
-synonym: "cgc328" []
-
-[Term]
-id: WBPaper00000330
-name: Nematode biochemistry - VI. Conditions for axenic culture of Turbatrix aceti, Panagrellus redivivus, Rhabditis anomala and C. briggsae.
-synonym: "cgc330" []
-
-[Term]
-id: WBPaper00000331
-name: Nutritional factors and conditions for the axenic culture of free-living nematodes.
-synonym: "cgc331" []
-synonym: "pmid318368" []
-
-[Term]
-id: WBPaper00000332
-name: Glycine synthesis and isocitrate lyase in the nematode, C. briggsae.
-synonym: "cgc332" []
-
-[Term]
-id: WBPaper00000333
-name: Nematode biochemistry IV. On isocitrate lyase in C. briggsae.
-synonym: "cgc333" []
-
-[Term]
-id: WBPaper00000334
-name: Nematode biochemistry - VIII. Malate synthetase.
-synonym: "cgc334" []
-
-[Term]
-id: WBPaper00000335
-name: Culture methods and nutrition of nematodes and Acanthocephala.
-synonym: "cgc335" []
-
-[Term]
-id: WBPaper00000336
-name: Biosynthesis of amino acids by the nematode C. briggsae.
-synonym: "cgc336" []
-
-[Term]
-id: WBPaper00000337
-name: Nematode biochemistry II. Biosynthesis of amino acids.
-synonym: "cgc337" []
-
-[Term]
-id: WBPaper00000338
-name: Mutants of acetylcholine metabolism in the nematode C. elegans.
-synonym: "cgc338" []
-
-[Term]
-id: WBPaper00000339
-name: Wave forms of C. elegans in a chemical attractant and repellent and in thermal gradients.
-synonym: "cgc339" []
-
-[Term]
-id: WBPaper00000341
-name: Growth factor studies; changes in reactivity of sulfhydryl groups with activation.
-synonym: "cgc341" []
-
-[Term]
-id: WBPaper00000342
-name: Isolation and partial characterization of a growth-control factor.
-synonym: "cgc342" []
-
-[Term]
-id: WBPaper00000343
-name: Biochemical aspects of the nutrition of Caenorhabditis briggsae.
-synonym: "cgc343" []
-
-[Term]
-id: WBPaper00000344
-name: Studies of a growth factor: Fractionation studies and amino acid composition of derived fractions.
-synonym: "cgc344" []
-
-[Term]
-id: WBPaper00000345
-name: Myosins exist as homodimers of heavy chains: Demonstration with specific antibody purified by nematode mutant myosin affinity chromatography.
-synonym: "cgc345" []
-
-[Term]
-id: WBPaper00000346
-name: Actin from the nematode, C. elegans, is a single electrofocusing species.
-synonym: "cgc346" []
-synonym: "pmid889873" []
-
-[Term]
-id: WBPaper00000347
-name: Two homogeneous myosins in body-wall muscle of C. elegans.
-synonym: "cgc347" []
-synonym: "pmid862026" []
-
-[Term]
-id: WBPaper00000348
-name: Studies on two body-wall myosins in wild type and mutant nematodes.
-synonym: "cgc348" []
-
-[Term]
-id: WBPaper00000349
-name: The moderately repetitive DNA sequences of C. elegans do not show short-period interspersion.
-synonym: "cgc349" []
-synonym: "pmid718922" []
-
-[Term]
-id: WBPaper00000350
-name: Nematode parasites of Oceanica. XVIII. C. avicola sp. n. (Rhabditidae) found in a bird from Taiwan.
-synonym: "cgc350" []
-
-[Term]
-id: WBPaper00000351
-name: Monographie der Nematoden
-synonym: "cgc351" []
-
-[Term]
-id: WBPaper00000352
-name: Age-related increase of cuticle permeability in the nematode C. briggsae.
-synonym: "cgc352" []
-
-[Term]
-id: WBPaper00000353
-name: Measurements by DNA renaturation of the genetic basis of parasitic reduction.
-synonym: "cgc353" []
-
-[Term]
-id: WBPaper00000354
-name: Some observations on molting in C. elegans.
-synonym: "cgc354" []
-
-[Term]
-id: WBPaper00000355
-name: Oligomycin, a new antifungal antibiotic.
-synonym: "cgc355" []
-
-[Term]
-id: WBPaper00000356
-name: Rhabditis carpathicus spec. nov. eine neue in Sphagnum-Mooren lebende Nematode/
-synonym: "cgc356" []
-
-[Term]
-id: WBPaper00000357
-name: Qualitative and quantitative distribution of soil nematodes of Signy Island South Orkney Islands.
-synonym: "cgc357" []
-
-[Term]
-id: WBPaper00000358
-name: Radioautographic study of RNA synthesis in C. elegans (Bergerac variety) oogenesis.
-synonym: "cgc358" []
-
-[Term]
-id: WBPaper00000359
-name: Heterologous helminth induced resistance to Ascaris suum in Guinea pigs.
-synonym: "cgc359" []
-
-[Term]
-id: WBPaper00000361
-name: Zur Systematik, Verbreitung, Okologie und Biologie neuer und wenig bekannter Rhabditiden (Nematoda) 2. Teil.
-synonym: "cgc361" []
-
-[Term]
-id: WBPaper00000362
-name: Influence of potential difference and current on the electrotaxis of C. elegans.
-synonym: "cgc362" []
-
-[Term]
-id: WBPaper00000363
-name: Post-embryonic development in the ventral cord of C. elegans.
-synonym: "cgc363" []
-synonym: "pmid8804" []
-
-[Term]
-id: WBPaper00000364
-name: The DNA of C. elegans.
-synonym: "cgc364" []
-synonym: "pmid4858229" []
-
-[Term]
-id: WBPaper00000365
-name: Dopaminergic neurons in the nematode C. elegans.
-synonym: "cgc365" []
-synonym: "pmid240872" []
-
-[Term]
-id: WBPaper00000366
-name: Post-embryonic cell lineages of the nematode, C. elegans.
-synonym: "cgc366" []
-synonym: "pmid838129" []
-
-[Term]
-id: WBPaper00000367
-name: Apparent nondestructive penetration of C. elegans by microelectrodes.
-synonym: "cgc367" []
-
-[Term]
-id: WBPaper00000368
-name: Nematode ageing. Automatic maintenance of age synchrony without inhibitors.
-synonym: "cgc368" []
-
-[Term]
-id: WBPaper00000369
-name: A preliminary in vitro test for anthelminthic activity.
-synonym: "cgc369" []
-
-[Term]
-id: WBPaper00000371
-name: Nematode Biochemistry I. Culture Methods.
-synonym: "cgc371" []
-
-[Term]
-id: WBPaper00000372
-name: Preparation of biological material for scanning electron microscopy by critical point drying from water miscible solvents.
-synonym: "cgc372" []
-
-[Term]
-id: WBPaper00000373
-name: Temperature-sensitive zygote defective mutants of C. elegans.
-synonym: "cgc373" []
-synonym: "pmid943346" []
-
-[Term]
-id: WBPaper00000374
-name: Amino acid requirements of the free-living nematode C. briggsae.
-synonym: "cgc374" []
-
-[Term]
-id: WBPaper00000375
-name: Nematode growth factor.
-synonym: "cgc375" []
-synonym: "med74132550" []
-
-[Term]
-id: WBPaper00000376
-name: The nature of a nematode growth factor I. Growth and maturation of C. briggsae on ribonucleoprotein particles.
-synonym: "cgc376" []
-
-[Term]
-id: WBPaper00000377
-name: The nature of a nematode growth factor II. Growth and maturation of C. briggsae on haem proteins.
-synonym: "cgc377" []
-
-[Term]
-id: WBPaper00000378
-name: The nature of a nematode growth factor. III. Growth and maturation of C. briggsae on protein-haemin co-precipitates.
-synonym: "cgc378" []
-
-[Term]
-id: WBPaper00000379
-name: Large scale cultivation of a free-living nematode (C. elegans).
-synonym: "cgc379" []
-synonym: "pmid955027" []
-
-[Term]
-id: WBPaper00000380
-name: Axenic culture of free-living, plant-parasitic, and insect-parasitic nematodes.
-synonym: "cgc380" []
-
-[Term]
-id: WBPaper00000381
-name: Selective inhibition of reproduction in aminopterin-treated nematodes.
-synonym: "cgc381" []
-
-[Term]
-id: WBPaper00000382
-name: Nematode chromosomal proteins-I. Isolation of chromatin and preliminary characterization of the chromosomal proteins of C. elegans.
-synonym: "cgc382" []
-synonym: "pmid95693" []
-
-[Term]
-id: WBPaper00000383
-name: The influence of some anthelmintic drugs on the population growth of the free-living nematodes C. briggsae and Turbatrix aceti (Nematoda: Rhabditida).
-synonym: "cgc383" []
-
-[Term]
-id: WBPaper00000385
-name: A model system for developmental biology and behavioral genetics.
-synonym: "cgc385" []
-
-[Term]
-id: WBPaper00000386
-name: Untersuchungen uber Nematoden in den Drusen des Kopfes der Ameisen (Formicidae).
-synonym: "cgc386" []
-
-[Term]
-id: WBPaper00000387
-name: Chemotaxis by the nematode C. elegans: Identification of attractants and analysis of the response by use of mutants.
-synonym: "cgc387" []
-synonym: "pmid4351805" []
-
-[Term]
-id: WBPaper00000388
-name: The use of mutants to analyze the sensory nervous system of C. elegans.
-synonym: "cgc388" []
-
-[Term]
-id: WBPaper00000389
-name: Invertebrate neurogenetics.
-synonym: "cgc389" []
-
-[Term]
-id: WBPaper00000390
-name: Use of nematode behavioral mutants for analysis of neural function and development.
-synonym: "cgc390" []
-
-[Term]
-id: WBPaper00000391
-name: Nematode chemotaxis and chemoreceptors.
-synonym: "cgc391" []
-
-[Term]
-id: WBPaper00000392
-name: Fertilization and sperm competition in the nematode C. elegans.
-synonym: "cgc392" []
-synonym: "pmid499670" []
-
-[Term]
-id: WBPaper00000393
-name: Characterization of temperature-sensitive, fertilization-defective mutants of the nematode C. elegans.
-synonym: "cgc393" []
-synonym: "pmid580424" []
-
-[Term]
-id: WBPaper00000394
-name: Electron microscopical reconstruction of the anterior sensory anatomy of the nematode C. elegans.
-synonym: "cgc394" []
-synonym: "pmid1112927" []
-
-[Term]
-id: WBPaper00000395
-name: The nerve ring of the nematode C. elegans: Sensory input and motor output.
-synonym: "cgc395" []
-
-[Term]
-id: WBPaper00000397
-name: A suppressor mutation in the nematode acting on specific alleles of many genes.
-synonym: "cgc397" []
-synonym: "med79032165" []
-synonym: "pmid703836" []
-
-[Term]
-id: WBPaper00000398
-name: Paramyosin of C. elegans.
-synonym: "cgc398" []
-synonym: "pmid4217841" []
-
-[Term]
-id: WBPaper00000399
-name: Mutants affecting paramyosin in C. elegans.
-synonym: "cgc399" []
-synonym: "pmid564970" []
-
-[Term]
-id: WBPaper00000400
-name: A nephelometer for measurement of nematode populations.
-synonym: "cgc400" []
-
-[Term]
-id: WBPaper00000401
-name: Connectivity changes in a class of motoneurone during the development of a nematode.
-synonym: "cgc401" []
-synonym: "med78114101" []
-
-[Term]
-id: WBPaper00000402
-name: The structure of the ventral nerve cord of C. elegans.
-synonym: "cgc402" []
-synonym: "pmid8806" []
-
-[Term]
-id: WBPaper00000403
-name: Nematode growth patterns and the moulting cycle: the population growth profile.
-synonym: "cgc403" []
-
-[Term]
-id: WBPaper00000404
-name: Spermatogenesis in males of the free-living nematode, C. elegans.
-synonym: "cgc404" []
-synonym: "pmid671581" []
-
-[Term]
-id: WBPaper00000405
-name: Summary of workshop on nematodes.
-synonym: "cgc405" []
-
-[Term]
-id: WBPaper00000406
-name: Acetylcholinesterase activity in the region of the nematode nerve ring: Improved histochemical specificity using ultrasonic pretreatment.
-synonym: "cgc406" []
-
-[Term]
-id: WBPaper00000407
-name: Dauer larvae of Caenorhabditis briggsae in axenic culture.
-synonym: "cgc407" []
-
-[Term]
-id: WBPaper00000409
-name: The effects of procaine on aging and development of a nematode.
-synonym: "cgc409" []
-
-[Term]
-id: WBPaper00000410
-name: Nematodes as models for aging studies.
-synonym: "cgc410" []
-
-[Term]
-id: WBPaper00000411
-name: Effects of P-chlorophenoxy acetic acid and dimethylaminoethanol on the nematode C. briggsae.
-synonym: "cgc411" []
-
-[Term]
-id: WBPaper00000412
-name: Studies on a growth supplement for C. briggsae from freeze-dried bacteria.
-synonym: "cgc412" []
-
-[Term]
-id: WBPaper00000415
-name: Fine structure changes in the cuticle of adult C. briggsae with age.
-synonym: "cgc415" []
-
-[Term]
-id: WBPaper00000417
-name: Aging in C. briggsae.
-synonym: "cgc417" []
-
-[Term]
-id: WBPaper00000419
-name: C. briggsae and C. elegans: Partial characterization of cuticle surface carbohydrates.
-synonym: "cgc419" []
-synonym: "pmid446589" []
-
-[Term]
-id: WBPaper00000420
-name: Specific gravity increase of C. briggsae with age.
-synonym: "cgc420" []
-
-[Term]
-id: WBPaper00000422
-name: Cloning of nematode tRNA genes and their expression in the frog oocyte.
-synonym: "cgc422" []
-synonym: "pmid370775" []
-
-[Term]
-id: WBPaper00000424
-name: The dauerlarva of C. elegans: A specific developmental arrest, inducible environmentally and genetically.
-synonym: "cgc424" []
-
-[Term]
-id: WBPaper00000425
-name: Transcription of cloned tRNA genes and the nuclear partitioning of a tRNA precursor.
-synonym: "cgc425" []
-
-[Term]
-id: WBPaper00000426
-name: Parental effects and phenotypic characterization of mutations that affect early development in C. elegans.
-synonym: "cgc426" []
-synonym: "pmid7371984" []
-
-[Term]
-id: WBPaper00000427
-name: Genetic organization of the region around unc-15(I), a gene affecting paramyosin in C. elegans.
-synonym: "cgc427" []
-synonym: "pmid7262541" []
-
-[Term]
-id: WBPaper00000429
-name: The consumption of oxygen by nematodes as a characteristic of zootic activity.
-synonym: "cgc429" []
-
-[Term]
-id: WBPaper00000430
-name: Controle genetique de la gametogenese et de la differenciation ovocytaire chez C. elegans, souche Bergerac.
-synonym: "cgc430" []
-
-[Term]
-id: WBPaper00000431
-name: Differential nutritional requirements for reproduction of two strains of Caenorhabditis elegans in axenic culture.
-synonym: "cgc431" []
-
-[Term]
-id: WBPaper00000432
-name: Large scale preparation of liver growth factor for cultivation of nematodes.
-synonym: "cgc432" []
-
-[Term]
-id: WBPaper00000433
-name: Temperature sensitive maternal effect mutants of early development in C. elegans.
-synonym: "cgc433" []
-
-[Term]
-id: WBPaper00000434
-name: A method for direct or microscopic observation and photography of nematode tracks during orientation behaviour studies.
-synonym: "cgc434" []
-
-[Term]
-id: WBPaper00000435
-name: Genes in development.
-synonym: "cgc435" []
-
-[Term]
-id: WBPaper00000436
-name: The unc-54 myosin heavy chain gene of C. elegans: A model system for the study of genetic suppression in higher eukaryotes.
-synonym: "cgc436" []
-
-[Term]
-id: WBPaper00000437
-name: Cadmium toxicity in the free living nematode C. elegans.
-synonym: "cgc437" []
-synonym: "pmid499167" []
-
-[Term]
-id: WBPaper00000438
-name: The structural gene for myosin, a closer look.
-synonym: "cgc438" []
-synonym: "med79010541" []
-
-[Term]
-id: WBPaper00000439
-name: A diet of worms.
-synonym: "cgc439" []
-
-[Term]
-id: WBPaper00000440
-name: Cell lineages of wild type and temperature sensitive embryonic arrest mutants of C. elegans.
-synonym: "cgc440" []
-
-[Term]
-id: WBPaper00000442
-name: Mutants altering coordinate synthesis of specific myosins during nematode muscle development.
-synonym: "cgc442" []
-synonym: "pmid6928685" []
-
-[Term]
-id: WBPaper00000443
-name: The nematode Caenorhabditis elegans.
-synonym: "cgc443" []
-
-[Term]
-id: WBPaper00000444
-name: Regulative development in the post-embryonic lineages of Caenorhabditis elegans.
-synonym: "cgc444" []
-
-[Term]
-id: WBPaper00000445
-name: Laser microbeam techniques in biological research.
-synonym: "cgc445" []
-
-[Term]
-id: WBPaper00000446
-name: Stability of the C. elegans genome during development and evolution.
-synonym: "cgc446" []
-
-[Term]
-id: WBPaper00000447
-name: Vesicle fusion, pseudopod extension and amoeboid motility are induced in nematode spermatids by the ionophore monensin.
-synonym: "cgc447" []
-synonym: "pmid7357613" []
-
-[Term]
-id: WBPaper00000448
-name: Cell lineages and developmental defects of temperature-sensitive embryonic arrest mutants in C. elegans.
-synonym: "cgc448" []
-synonym: "pmid7380087" []
-
-[Term]
-id: WBPaper00000449
-name: Genetics and mode of expression of temperature-sensitive mutations arresting embryonic development in C. elegans.
-synonym: "cgc449" []
-synonym: "pmid7380089" []
-
-[Term]
-id: WBPaper00000450
-name: Segregation of developmental potential in early embryos of C. elegans.
-synonym: "cgc450" []
-synonym: "pmid7363324" []
-
-[Term]
-id: WBPaper00000451
-name: A method for axenizing large numbers of nematodes.
-synonym: "cgc451" []
-
-[Term]
-id: WBPaper00000452
-name: Studies on the mechanism of action of avermectin B1a: Stimulation of release of GABA from brain synaptosomes.
-synonym: "cgc452" []
-
-[Term]
-id: WBPaper00000453
-name: Polyploids and sex determination in C. elegans.
-synonym: "cgc453" []
-synonym: "pmid295035" []
-
-[Term]
-id: WBPaper00000455
-name: Responses of nematode C. elegans to controlled chemical stimulation.
-synonym: "cgc455" []
-
-[Term]
-id: WBPaper00000456
-name: Appetitive response of the nematode C. elegans to oxygen.
-synonym: "cgc456" []
-
-[Term]
-id: WBPaper00000457
-name: Commentary on the uses of small nematode worms.
-synonym: "cgc457" []
-
-[Term]
-id: WBPaper00000458
-name: A squash technique demonstrating embryonic nuclear cleavage of the nematode C. elegans.
-synonym: "cgc458" []
-synonym: "pmid6993551" []
-
-[Term]
-id: WBPaper00000459
-name: Caracterist genet et physiol de thermosensibilite du developpement embryon chz un mutant a letalite condition C. elegans/
-synonym: "cgc459" []
-
-[Term]
-id: WBPaper00000460
-name: A simple method for maintaining large aging populations of C. elegans.
-synonym: "cgc460" []
-synonym: "pmid6445025" []
-
-[Term]
-id: WBPaper00000461
-name: Mutants with altered muscle structure in C. elegans.
-synonym: "cgc461" []
-synonym: "pmid7190524" []
-
-[Term]
-id: WBPaper00000462
-name: The C. elegans male: Postembryonic development of nongonadal structures.
-synonym: "cgc462" []
-synonym: "pmid7409314" []
-
-[Term]
-id: WBPaper00000463
-name: Regulation and cell autonomy during postembryonic development of C. elegans.
-synonym: "cgc463" []
-synonym: "pmid7190941" []
-
-[Term]
-id: WBPaper00000464
-name: Levamisole-resistant mutants of the nematode C. elegans appear to lack pharmacological acetylcholine receptors.
-synonym: "cgc464" []
-synonym: "pmid7402460" []
-
-[Term]
-id: WBPaper00000465
-name: Genetic and phenotypic characterization of roller mutants of C. elegans.
-synonym: "cgc465" []
-
-[Term]
-id: WBPaper00000466
-name: A temperature-sensitive mutant of C. elegans var Bergerac affecting morphological and embryonic development.
-synonym: "cgc466" []
-
-[Term]
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-name: Thermal limits and chemotaxis in mutants of the nematode C. elegans defective in thermotaxis.
-synonym: "cgc467" []
-
-[Term]
-id: WBPaper00000468
-name: A study of morphology of C. elegans: A mutant of C. elegans with dumpy and temperature-sensitive roller phenotype.
-synonym: "cgc468" []
-
-[Term]
-id: WBPaper00000469
-name: Age-dependent changes in mobility and separation of the nematode C. elegans.
-synonym: "cgc469" []
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-
-[Term]
-id: WBPaper00000470
-name: Genetic mosaics of C. elegans: A tissue-specific fluorescent mutant.
-synonym: "cgc470" []
-synonym: "pmid7423194" []
-
-[Term]
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-name: Novel bacteriophage lambda cloning vector.
-synonym: "cgc471" []
-synonym: "pmid6254062" []
-
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-name: Cell lineages and development of C. elegans and other nematodes.
-synonym: "cgc473" []
-
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-id: WBPaper00000474
-name: Muscle development in C. elegans: A molecular genetic approach.
-synonym: "cgc474" []
-
-[Term]
-id: WBPaper00000475
-name: Behavior of free-living nematodes.
-synonym: "cgc475" []
-
-[Term]
-id: WBPaper00000476
-name: Neural control of locomotion in Ascaris: anatomy, electrophysiology, and biochemistry.
-synonym: "cgc476" []
-
-[Term]
-id: WBPaper00000477
-name: Control mechanisms in nematodes.
-synonym: "cgc477" []
-
-[Term]
-id: WBPaper00000478
-name: Genetic analysis of C. elegans.
-synonym: "cgc478" []
-
-[Term]
-id: WBPaper00000479
-name: Developmental genetics of C. elegans.
-synonym: "cgc479" []
-
-[Term]
-id: WBPaper00000480
-name: Biochemical genetics of C. elegans.
-synonym: "cgc480" []
-
-[Term]
-id: WBPaper00000481
-name: Chemotactic behavior of mutants of the nematode C. elegans that are defective in osmotic avoidance.
-synonym: "cgc481" []
-
-[Term]
-id: WBPaper00000482
-name: Avermectin B1a, a paralyzing anthelmintic that affects interneurons and inhibitory motoneurons in Ascaris.
-synonym: "cgc482" []
-
-[Term]
-id: WBPaper00000483
-name: Eukaryotic DNA segments capable of autonomous replication in yeast.
-synonym: "cgc483" []
-synonym: "pmid6449009" []
-
-[Term]
-id: WBPaper00000484
-name: The genetics of levamisole resistance in the nematode C. elegans.
-synonym: "cgc4...
 
[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [1008] phenote/trunk/obo-files/mammalian_phenotype.obo

From: <mg...@us...> - 2007-10-09 21:57:05

Revision: 1008
          http://obo.svn.sourceforge.net/obo/?rev=1008&view=rev
Author:   mgibson
Date:     2007-10-09 14:57:08 -0700 (Tue, 09 Oct 2007)

Log Message:
-----------
next biggest obo - get it out - auto retrieve

Removed Paths:
-------------
    phenote/trunk/obo-files/mammalian_phenotype.obo

Deleted: phenote/trunk/obo-files/mammalian_phenotype.obo
===================================================================
--- phenote/trunk/obo-files/mammalian_phenotype.obo	2007-10-09 21:54:44 UTC (rev 1007)
+++ phenote/trunk/obo-files/mammalian_phenotype.obo	2007-10-09 21:57:08 UTC (rev 1008)
@@ -1,36377 +0,0 @@
-format-version: 1.2
-date: 30:01:2007 16:56
-saved-by: csmith
-auto-generated-by: OBO-Edit 1.002
-default-namespace: MPheno.ontology
-
-[Term]
-id: MP:0000001
-name: Phenotype Ontology
-
-[Term]
-id: MP:0000002
-name: Morphology
-synonym: "Anatomy" EXACT []
-is_obsolete: true
-
-[Term]
-id: MP:0000003
-name: abnormal adipose tissue morphology
-alt_id: MP:0000011
-def: "structural anomaly of the connective tissue composed of fat cells enmeshed in areolar tissue" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator, MeSH:National Library of Medicine_Medical Subject Headings]
-synonym: "adipose tissue abnormalities" EXACT []
-is_a: MP:0005375 ! adipose tissue phenotype
-
-[Term]
-id: MP:0000005
-name: increased brown fat amount
-alt_id: MP:0001779
-def: "increased amount of thermogenic tissue in the body that is composed of cells containing multiple small fat droplets" [J:14208, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "increased brown fat" EXACT []
-is_a: MP:0001778 ! abnormal brown fat amount
-
-[Term]
-id: MP:0000008
-name: increased white fat amount
-alt_id: MP:0001782
-def: "increased quantity of fat-storing cells/tissue" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-synonym: "increased white fat" EXACT []
-is_a: MP:0001781 ! abnormal white fat amount
-
-[Term]
-id: MP:0000010
-name: abnormal abdominal fat pads
-def: "malformed or aberrant size of the encapsulated adipose tissue in the abdomen" [J:65146]
-is_a: MP:0005334 ! abnormal fat pad
-
-[Term]
-id: MP:0000012
-name: loss of subcutaneous adipose tissue
-def: "reduction in amount or absence of adipose tissue beneath the skin" [J:65146]
-is_a: MP:0000013 ! abnormal fat distribution
-
-[Term]
-id: MP:0000013
-name: abnormal fat distribution
-def: "alterations in the normal placement and amount of body fat" [J:57315]
-is_a: MP:0000003 ! abnormal adipose tissue morphology
-
-[Term]
-id: MP:0000015
-name: abnormal ear pigmentation
-def: "anomaly in the coloration of the ear" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-is_a: MP:0002095 ! abnormal skin pigmentation
-is_a: MP:0002177 ! abnormal outer ear morphology
-
-[Term]
-id: MP:0000017
-name: big ears
-def: "outer ears of a greater than normal size" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-is_a: MP:0002177 ! abnormal outer ear morphology
-
-[Term]
-id: MP:0000018
-name: small ears
-def: "outer ears of a smaller than normal size" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-synonym: "microtia" EXACT []
-is_a: MP:0002177 ! abnormal outer ear morphology
-
-[Term]
-id: MP:0000019
-name: thick ears
-def: "increased width of the epidermal and cartilaginous tissue that makes up the ear" [J:65045]
-is_a: MP:0002177 ! abnormal outer ear morphology
-
-[Term]
-id: MP:0000020
-name: scaly ears
-def: "ears covered with shedding scales or flakes" [J:65045]
-is_a: MP:0002177 ! abnormal outer ear morphology
-
-[Term]
-id: MP:0000021
-name: prominent ears
-def: "protuberant outer ears" [J:61768]
-is_a: MP:0002177 ! abnormal outer ear morphology
-
-[Term]
-id: MP:0000022
-name: abnormal ear shape
-def: "malformation of the pattern of the external ear" [J:65038]
-is_a: MP:0002177 ! abnormal outer ear morphology
-
-[Term]
-id: MP:0000023
-name: abnormal ear distance/ position
-def: "anomaly in the space between or the placement of the outer ears " [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-is_a: MP:0002177 ! abnormal outer ear morphology
-
-[Term]
-id: MP:0000024
-name: lowered ear position
-def: "outer ears which are situated below the normal location " [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-is_a: MP:0000023 ! abnormal ear distance/ position
-
-[Term]
-id: MP:0000025
-name: otic hypertelorism
-def: "greater than normal space between the outer ears" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-synonym: "hypertelorism of ears" EXACT []
-synonym: "increased distance between the ears" EXACT []
-is_a: MP:0000023 ! abnormal ear distance/ position
-
-[Term]
-id: MP:0000026
-name: abnormal inner ear morphology
-def: "any structural anomaly of any components of the labyrinth, including the semicircular canals, vestibule and cochlea" [J:1776, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-xref: GO:0042472
-is_a: MP:0002102 ! abnormal ear morphology
-
-[Term]
-id: MP:0000027
-name: horizontal canal defects
-is_obsolete: true
-
-[Term]
-id: MP:0000028
-name: abnormal pars superior vestibularis morphology
-def: "structural anomaly in the part of the vestibular ganglion that receives fibers from the maculae of the utricle and the sacculae and the ampullae of the anterior and lateral semicircular ducts" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal pars superior vestibularis" EXACT []
-is_a: MP:0000026 ! abnormal inner ear morphology
-is_a: MP:0002856 ! abnormal vestibular ganglion morphology
-
-[Term]
-id: MP:0000029
-name: abnormal malleus morphology
-def: "structural anomaly in the largest of the three auditory ossicles, which resembles a club or hammer " [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal malleus" EXACT []
-is_a: MP:0005105 ! abnormal middle ear ossicle morphology
-
-[Term]
-id: MP:0000030
-name: abnormal tympanic ring morphology
-def: "any structural anomaly in the bony ring at the ear canal to which the tympanic membrane is attached" [J:23837, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal tympanic ring" EXACT []
-is_a: MP:0000049 ! abnormal middle ear morphology
-
-[Term]
-id: MP:0000031
-name: abnormal cochlea morphology
-def: "any structural anomaly of the  spiral-shaped bony canal in the inner ear containing the hair cells that transduce sound" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0000026 ! abnormal inner ear morphology
-
-[Term]
-id: MP:0000032
-name: cochlear degeneration
-def: "a retrogressive impairment of function or destruction of the part of the inner ear forms the anterior part of the labyrinth, is conical, and is concerned with hearing" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator, MeSH:National Library of Medicine_Medical Subject Headings]
-is_a: MP:0000031 ! abnormal cochlea morphology
-
-[Term]
-id: MP:0000033
-name: absent scala media
-def: "missing spiral tube within the cochlea that contains the organ of Corti, the neuroepithelial receptor organ for hearing" [J:23837, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "absent cochlear duct" EXACT []
-is_a: MP:0003169 ! abnormal scala media morphology
-
-[Term]
-id: MP:0000034
-name: abnormal vestibule morphology
-def: "any structural anomaly of the cavity between the semicircular canals and the cochlea of the inner ear" [J:1776, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0000026 ! abnormal inner ear morphology
-
-[Term]
-id: MP:0000035
-name: abnormal membranous labyrinth
-def: "any structural anomaly in the complex arrangement of communicating canaliculi and sacs suspended within the cavity of the bony labyrinth of the inner ear" [J:23837, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0000026 ! abnormal inner ear morphology
-
-[Term]
-id: MP:0000036
-name: absent semicircular canals
-def: "missing organ of balance; consists of three bony tubes within which the semicircular ducts are located" [J:23837, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0002428 ! abnormal semicircular canal
-
-[Term]
-id: MP:0000037
-name: abnormal lateral semicircular canal
-def: "anomaly of the lateral long bony tube of the labyrinth that is involved in the sense of balance " [anna:Anna V. Anagnostopoulos_Mouse Genome Informatics Curator, cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator, smb:Susan M. Bello_Mouse Genome Informatics Curator]
-synonym: "abnormal horizontal semicircular canal" EXACT []
-is_a: MP:0002428 ! abnormal semicircular canal
-
-[Term]
-id: MP:0000038
-name: thin semicircular canals
-def: "decreased diameter of the three long bony tubes of the labyrinth that are involved in the sense of balance" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-is_obsolete: true
-
-[Term]
-id: MP:0000039
-name: abnormal otic capsule morphology
-def: "any structural anomaly of the cartilage or bony capsule surrounding the inner ear mechanism" [J:23837, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal periotic capsule" EXACT []
-is_a: MP:0000026 ! abnormal inner ear morphology
-
-[Term]
-id: MP:0000040
-name: absent middle ear ossicles
-def: "missing small bones of the tympanic cavity" [J:1776, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0005105 ! abnormal middle ear ossicle morphology
-
-[Term]
-id: MP:0000041
-name: absent endolymphatic duct
-def: "missing small membranous canal of the inner ear; connecting membranous labyrinth with the endolymphatic sac" [J:1776, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0006011 ! abnormal endolymphatic duct morphology
-
-[Term]
-id: MP:0000042
-name: abnormal organ of Corti
-def: "abnormalities associated with the highly specialized epithelium in the floor of the ductus cochlearis; also referred to a spiral organ (organum spirale), or acoustic papilla" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal spiral organ" EXACT []
-is_a: MP:0003169 ! abnormal scala media morphology
-
-[Term]
-id: MP:0000043
-name: organ of Corti degeneration
-def: "a retrogressive impairment of function or destruction of the highly specialized epithelium in the floor of the ductus cochlearis" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-synonym: "degeneration of organ of Corti" EXACT []
-is_a: MP:0000042 ! abnormal organ of Corti
-
-[Term]
-id: MP:0000044
-name: absent organ of Corti
-def: "absence of the highly specialized epithelium in the floor of the ductus cochlearis" [J:54408]
-synonym: "absent acoustic papilla" EXACT []
-synonym: "absent spiral organ" EXACT []
-is_a: MP:0000042 ! abnormal organ of Corti
-
-[Term]
-id: MP:0000045
-name: abnormal hair cell morphology
-def: "any structural anomaly of the sensory epithelial cells of the inner ear" [pvb:Pierre Vanden Borre_Mouse Genome Informatics Curator, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal hair cells" EXACT []
-is_a: MP:0000026 ! abnormal inner ear morphology
-is_a: MP:0000972 ! abnormal mechanoreceptor morphology
-
-[Term]
-id: MP:0000046
-name: abnormal sulcus ampullaris morphology
-def: "anomaly in the structure of the transverse groove on the membranous amupulla of each semicircular duct, where the nerve enters the ampullary crest" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal ampullary groove" EXACT []
-synonym: "abnormal ampullary sulcus" EXACT []
-is_a: MP:0000026 ! abnormal inner ear morphology
-
-[Term]
-id: MP:0000047
-name: abnormal interdental cells
-is_obsolete: true
-
-[Term]
-id: MP:0000048
-name: abnormal stria vascularis
-def: "any structural abnormality in the stratified, secretory epithelium which lines the upper part of the cochlear spiral ligament and maintains K+ homeostasis in the endolymph; stria vascularis normally consists of marginal, intermediate, and basal cells: basal and marginal cell tight junctions preclude paracellular diffusion into and out of the intrastrial space while basal and intermediate cells secrete into this space K+ derived from fibrocytes through gap junctions" [anna:Anna V. Anagnostopoulos_Mouse Genome Informatics Curator, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal psalterial cord" EXACT []
-synonym: "abnormal stria vascularis ductus cochlearis" EXACT []
-synonym: "abnormal vascular stripe" EXACT []
-is_a: MP:0003169 ! abnormal scala media morphology
-
-[Term]
-id: MP:0000049
-name: abnormal middle ear morphology
-def: "any structural anomaly of any components of the tympanic cavity or its ossicles" [csmith:Cynthia L. Smith_Mouse Genome Informatics Curator, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0002102 ! abnormal ear morphology
-
-[Term]
-id: MP:0000051
-name: absent process brevus
-is_obsolete: true
-
-[Term]
-id: MP:0000052
-name: early ear unfolding
-def: "early onset of the opening and spreading out of the outer ear" [J:39752]
-is_a: MP:0002177 ! abnormal outer ear morphology
-
-[Term]
-id: MP:0000053
-name: excessive ear growth
-def: "overly robust development of the ear" [J:39752]
-is_a: MP:0002177 ! abnormal outer ear morphology
-
-[Term]
-id: MP:0000054
-name: delayed ear emergence
-def: "late onset of the growth of the outer ear" [J:49421]
-synonym: "delayed ear elevation" EXACT []
-synonym: "delayed ear extroversion" EXACT []
-is_a: MP:0002177 ! abnormal outer ear morphology
-
-[Term]
-id: MP:0000057
-name: abnormal osteogenesis
-alt_id: MP:0001535
-alt_id: MP:0001536
-def: "anomalous process of bone formation" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal bone formation" EXACT []
-synonym: "abnormal osteogenesis" EXACT []
-synonym: "abnormal skeletogenesis" EXACT []
-synonym: "osteogenesis abnormalities" EXACT []
-synonym: "skeletogenesis abnormalities" EXACT []
-is_a: MP:0002113 ! abnormal skeleton development
-
-[Term]
-id: MP:0000058
-name: reduced osteoblast formation
-def: "fewer than normal numbers of bone-forming cells that develop into osteocytes" [J:61509]
-is_a: MP:0005008 ! abnormal osteoblast formation
-
-[Term]
-id: MP:0000059
-name: abnormal osteoclast formation
-def: "anomalous development of this multinucleated cell, which normally functions in the absorption and removal of osseous tissue" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal osteophage formation" EXACT []
-is_a: MP:0000057 ! abnormal osteogenesis
-
-[Term]
-id: MP:0000060
-name: delayed bone ossification
-def: "late onset of the formation of bone" [J:40203]
-is_a: MP:0000057 ! abnormal osteogenesis
-
-[Term]
-id: MP:0000061
-name: fragile skeleton
-alt_id: MP:0001543
-def: "easily damaged or broken bones" [J:14208]
-synonym: "brittle bones" EXACT []
-synonym: "general bone weakness" EXACT []
-is_a: MP:0001542 ! abnormal bone strength
-
-[Term]
-id: MP:0000062
-name: increased bone density
-def: "increased mineral content of bone; indicator of bone strength" [J:61295, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0005007 ! abnormal bone density
-
-[Term]
-id: MP:0000063
-name: reduced bone density
-def: "decreased mineral content of bone; indicator of bone strength" [csmith:Cynthia L. Smith_Mouse Genome Informatics Curator, J:57315, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "osteopenia" EXACT []
-is_a: MP:0005007 ! abnormal bone density
-
-[Term]
-id: MP:0000064
-name: failure of secondary bone resorption
-def: "inability of osteoclasts to degrade the organic and inorganic phases of bone by absorption" [J:61295, J:67040]
-is_a: MP:0001541 ! abnormal osteoclast physiology
-
-[Term]
-id: MP:0000065
-name: abnormal bone marrow cavities
-def: "absence or abnormal size or shape of the medullary cavities of the bones" [J:61295, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0000168 ! abnormal bone marrow development
-
-[Term]
-id: MP:0000066
-name: osteoporosis
-def: "reduction in bone mass or atrophy of skeletal tissue; may lead to skeletal fragility" [csmith:Cynthia L. Smith_Mouse Genome Informatics Curator, J:57315, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "reduced bone mass" EXACT []
-is_a: MP:0004016 ! decreased bone mass
-
-[Term]
-id: MP:0000067
-name: osteopetrosis
-def: "excessive formation of dense trabecular bone and excessive calcified cartilage formation; may lead to anemia and extramedullary hematopoiesis " [MeSH:National Library of Medicine_Medical Subject Headings, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0003795 ! abnormal bone structure
-is_a: MP:0005605 ! increased bone mass
-
-[Term]
-id: MP:0000069
-name: kyphoscoliosis
-def: "kyphosis combined with scoliosis" [cml:Cathleen M. Lutz_Mouse Genome Informatics Curator, J:66943]
-is_a: MP:0004174 ! abnormal spine curvature
-
-[Term]
-id: MP:0000071
-name: axial skeleton hypoplasia
-def: "reduced cell number in the skeletal elements of the trunk usually resulting in smaller size" [csmith:Cynthia L. Smith_Mouse Genome Informatics Curator, J:55583, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "hypoplastic axial skeleton" EXACT []
-is_a: MP:0002114 ! abnormal axial skeleton morphology
-
-[Term]
-id: MP:0000073
-name: absent craniofacial bones
-def: "missing skeletal elements comprising the cranium and face" [J:35802]
-synonym: "absence of craniofacial bones" EXACT []
-is_a: MP:0002116 ! abnormal craniofacial bone morphology
-
-[Term]
-id: MP:0000074
-name: abnormal neurocranium morphology
-def: "malformed bones of the skull enclosing the brain" [J:55583, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal neurocranium" EXACT []
-is_a: MP:0000438 ! abnormal skull morphology
-
-[Term]
-id: MP:0000075
-name: absent neurocranium
-def: "missing bones of the skull enclosing the brain" [J:49840, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "absence of neurocranium" EXACT []
-synonym: "acrania" EXACT []
-is_a: MP:0000074 ! abnormal neurocranium morphology
-
-[Term]
-id: MP:0000076
-name: abnormal calvaria morphology
-def: "malformed upper domelike portion of the skull" [J:61509]
-synonym: "abnormal calvaria" EXACT []
-synonym: "abnormal cranial vault" EXACT []
-is_a: MP:0000074 ! abnormal neurocranium morphology
-
-[Term]
-id: MP:0000077
-name: abnormal interparietal bone morphology
-alt_id: MP:0000110
-def: "any structural anomaly of the bone of the cranium that lies above and anterior to the occipital bone in some mammals" [csmith:Cynthia L. Smith_Mouse Genome Informatics Curator, J:61509]
-synonym: "abnormal interparietal bone" EXACT []
-is_a: MP:0000076 ! abnormal calvaria morphology
-
-[Term]
-id: MP:0000078
-name: abnormal supraoccipital bone morphology
-def: "any structural anomaly of the bone on the dorsal side of the great foramen of the skull, usually forming a part of the occipital in the adult, but distinct in the young" [J:61509]
-synonym: "abnormal supraoccipital bone" EXACT []
-is_a: MP:0005269 ! abnormal occipital bone morphology
-
-[Term]
-id: MP:0000079
-name: abnormal basioccipital bone morphology
-def: "any structural anomaly of the basilar process of the occipital bone in the base of the cranium, frequently forming a direct part of the occipital in the adult, but usually distinct in the young " [J:55583, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal basioccipital bone" EXACT []
-is_a: MP:0005269 ! abnormal occipital bone morphology
-
-[Term]
-id: MP:0000080
-name: abnormal exoccipital bone morphology
-def: "any structural anomaly of the bone or region on the lateral sides of the great foremen of the skull, which often forms a part of the occipital in the adult, but is usually distinct in the young" [J:23837, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal exoccipital bone" EXACT []
-is_a: MP:0005269 ! abnormal occipital bone morphology
-
-[Term]
-id: MP:0000081
-name: premature suture closure
-alt_id: MP:0005268
-def: "early fusion of the bones of the skull" [J:26513]
-synonym: "craniostosis" EXACT []
-synonym: "craniosynostosis" EXACT []
-is_a: MP:0003418 ! premature intramembranous bone ossification
-
-[Term]
-id: MP:0000082
-name: overlapping parietal bones
-def: "parietal bones of the skull partly coincide instead of articulating" [J:26513]
-is_a: MP:0000109 ! abnormal parietal bone morphology
-
-[Term]
-id: MP:0000083
-name: ectopic cranial bone growth
-def: "growth of extra bony structures in or near the cranium" [J:26513]
-synonym: "heterotopic cranial bone growth" EXACT []
-is_a: MP:0000076 ! abnormal calvaria morphology
-
-[Term]
-id: MP:0000084
-name: abnormal fontanelle morphology
-def: "structural defect in the membranous interval at the margins of cranial bones in neonates" [J:53370, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal fontanel" EXACT []
-synonym: "abnormal fontanelle" EXACT []
-is_a: MP:0000076 ! abnormal calvaria morphology
-is_a: MP:0002113 ! abnormal skeleton development
-
-[Term]
-id: MP:0000085
-name: large anterior fontanelle
-def: "enlarged diamond-shaped membranous interval at the junction of the coronal, sagittal and metopic sutures of the cranium" [J:53370, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "large anterior fontanel" EXACT []
-is_a: MP:0000084 ! abnormal fontanelle morphology
-
-[Term]
-id: MP:0000087
-name: absent mandible
-def: "missing the lower bony framework of the mouth where the inferior teeth are held" [csmith:Cynthia L. Smith_Mouse Genome Informatics Curator, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "absence of mandible" EXACT []
-synonym: "agnathia" EXACT []
-is_a: MP:0000458 ! abnormal mandible morphology
-
-[Term]
-id: MP:0000088
-name: short mandible
-def: "reduced length of the lower bony framework of the mouth where the inferior teeth are held" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-synonym: "reduced mandible length" EXACT []
-synonym: "truncated mandible" EXACT []
-is_a: MP:0000458 ! abnormal mandible morphology
-
-[Term]
-id: MP:0000090
-name: absent premaxilla
-def: "missing anterior and interior portion of the maxilla" [J:17489, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "absence of premaxilla" EXACT []
-is_a: MP:0002820 ! abnormal premaxilla morphology
-
-[Term]
-id: MP:0000091
-name: short premaxilla
-def: "reduced length of the anterior and interior portion of the maxilla" [J:53370, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "short incisive bone" EXACT []
-synonym: "truncated maxilla" EXACT []
-is_a: MP:0002820 ! abnormal premaxilla morphology
-
-[Term]
-id: MP:0000094
-name: absent alveolar process
-def: "missing projecting ridge on the inferior surface of the body of the maxilla and mandible containing the tooth sockets" [J:17489, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "absence of alveolar process" EXACT []
-is_a: MP:0004189 ! abnormal alveolar process
-
-[Term]
-id: MP:0000097
-name: short maxilla
-alt_id: MP:0000093
-def: "reduced length of the upper jaw bone" [J:53370, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "reduced upper jaw length" EXACT []
-is_a: MP:0000455 ! abnormal maxilla morphology
-
-[Term]
-id: MP:0000098
-name: abnormal vomer bone morphology
-def: "missing triangular flat bone of the nasal septum" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal vomer bone" EXACT []
-is_a: MP:0005274 ! abnormal viscerocranium morphology
-
-[Term]
-id: MP:0000099
-name: absent vomer bone
-def: "missing triangular flat bone of the nasal septum" [J:49840, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "absence of vomer bone" EXACT []
-is_a: MP:0000098 ! abnormal vomer bone morphology
-
-[Term]
-id: MP:0000100
-name: abnormal ethmoidal bone morphology
-def: "defect in the midline facial bone that encloses the nasal cavity" [csmith:Cynthia L. Smith_Mouse Genome Informatics Curator, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal ethmoid bone" EXACT []
-synonym: "abnormal ethmoidal bone" EXACT []
-is_a: MP:0005273 ! abnormal cranial base morphology
-is_a: MP:0005552 ! abnormal orbital bone morphology
-
-[Term]
-id: MP:0000101
-name: absent ethmoidal bone
-def: "missing midline facial bone that encloses the nasal cavity" [csmith:Cynthia L. Smith_Mouse Genome Informatics Curator, J:49840, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "absent ethmoidal bone" EXACT []
-is_a: MP:0000100 ! abnormal ethmoidal bone morphology
-
-[Term]
-id: MP:0000102
-name: abnormal nasal bone morphology
-def: "any structural anomaly of either of two rectangular bone plates forming the bridge of the nose" [J:17489, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal nasal bone" EXACT []
-is_a: MP:0005274 ! abnormal viscerocranium morphology
-
-[Term]
-id: MP:0000103
-name: nasal bone hypoplasia
-def: "reduced cell number in the bone which forms the nasal bridge" [J:53370]
-synonym: "hypoplastic nasal bone" EXACT []
-is_a: MP:0004470 ! small nasal bone
-
-[Term]
-id: MP:0000104
-name: abnormal sphenoid bone morphology
-def: "malformed irregularly shaped bone of the base of the skull" [J:49840, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal sphenoid bone" EXACT []
-is_a: MP:0005273 ! abnormal cranial base morphology
-is_a: MP:0005552 ! abnormal orbital bone morphology
-
-[Term]
-id: MP:0000105
-name: defective ossification of basisphenoid
-def: "abnormal formation of the bone at the base of the sphenoid bone; arises from an ossification center independent of the remainder of the sphenoid bone" [J:49840, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0000106 ! abnormal basisphenoid bone morphology
-
-[Term]
-id: MP:0000106
-name: abnormal basisphenoid bone morphology
-def: "any structural anomaly of part of the base of the cranium between the basioccipital and the presphenoid, which usually ossifies separately in the embryo or in the young, and becomes a part of the sphenoid in the adult; in many animals it persists as a separate bone between the basioccipital bone and the presphenoidal bone" [J:55583, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal basisphenoid bone" EXACT []
-is_a: MP:0000104 ! abnormal sphenoid bone morphology
-
-[Term]
-id: MP:0000107
-name: abnormal frontal bone morphology
-def: "any structural anomaly of the bone forming the forehead and roof of the eye orbit" [J:17489, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal frontal bone" EXACT []
-is_a: MP:0000076 ! abnormal calvaria morphology
-is_a: MP:0005274 ! abnormal viscerocranium morphology
-is_a: MP:0005552 ! abnormal orbital bone morphology
-
-[Term]
-id: MP:0000108
-name: midline facial cleft
-def: "incomplete merging or fusion of the tissues normally uniting to form the face" [J:49840, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0002116 ! abnormal craniofacial bone morphology
-
-[Term]
-id: MP:0000109
-name: abnormal parietal bone morphology
-def: "malformed curved bone forming part of the vault of the cranium" [J:17489]
-synonym: "abnormal parietal bone" EXACT []
-is_a: MP:0000076 ! abnormal calvaria morphology
-
-[Term]
-id: MP:0000111
-name: cleft palate
-alt_id: MP:0000429
-def: "congenital fissure of the tissues normally uniting to form the palate" [J:49840, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0003755 ! abnormal palate
-
-[Term]
-id: MP:0000114
-name: cleft chin
-def: "incomplete fusion of the chin; usually a fissure" [J:42035, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0000458 ! abnormal mandible morphology
-
-[Term]
-id: MP:0000116
-name: abnormal tooth development
-def: "anomalous formation of the teeth" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-synonym: "tooth development abnormalities" EXACT []
-is_a: MP:0002100 ! abnormal tooth morphology
-is_a: MP:0002113 ! abnormal skeleton development
-is_a: MP:0003935 ! abnormal craniofacial development
-
-[Term]
-id: MP:0000117
-name: absent tooth primordium
-def: "missing the cells that will give rise to teeth" [J:54637, tc:Teresa Chu_Mouse Genome Informatics Curator]
-synonym: "absence of tooth anlage" EXACT []
-synonym: "absence of tooth primordium" EXACT []
-is_a: MP:0000116 ! abnormal tooth development
-
-[Term]
-id: MP:0000118
-name: arrest of tooth development
-def: "failure of differentiation of the teeth" [J:18378]
-is_a: MP:0000116 ! abnormal tooth development
-
-[Term]
-id: MP:0000119
-name: abnormal tooth eruption
-def: "anomalies in the passage of a tooth through the alveolar process and perforation of the gums" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "tooth eruption abnormalities" EXACT []
-is_a: MP:0002100 ! abnormal tooth morphology
-
-[Term]
-id: MP:0000120
-name: malocclusion
-def: "perturbations in the normal patterned arrangement of the teeth or alignment of the jaw, resulting in the incorrect position of biting or chewing surfaces of the upper and lower teeth" [J:61509]
-synonym: "misaligned teeth" EXACT []
-is_a: MP:0000438 ! abnormal skull morphology
-
-[Term]
-id: MP:0000121
-name: failure of tooth eruption
-def: "inability of the teeth to grow into the oral cavity" [J:61295, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0000119 ! abnormal tooth eruption
-is_a: MP:0000124 ! absent teeth
-
-[Term]
-id: MP:0000122
-name: accelerated tooth eruption
-def: "early onset of the growth of the teeth out of the gums" [J:65045]
-is_a: MP:0000119 ! abnormal tooth eruption
-
-[Term]
-id: MP:0000124
-name: absent teeth
-def: "missing bony structures of the upper and lower jaws used in mastication" [J:61295, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "absence of all teeth" EXACT []
-is_a: MP:0002100 ! abnormal tooth morphology
-
-[Term]
-id: MP:0000125
-name: absent incisors
-def: "missing long pointed teeth; most anterior and prominent in the jaw" [J:17489]
-synonym: "absence of incisors" EXACT []
-is_a: MP:0000124 ! absent teeth
-is_a: MP:0005358 ! abnormal incisor morphology
-
-[Term]
-id: MP:0000126
-name: brittle teeth
-def: "fragile and likely to break teeth" [J:61509]
-is_a: MP:0002100 ! abnormal tooth morphology
-
-[Term]
-id: MP:0000127
-name: degenerated molars
-def: "atrophy of the molars" [J:61509]
-is_a: MP:0002689 ! abnormal molar morphology
-
-[Term]
-id: MP:0000128
-name: growth retardation of molars
-def: "developmental delay of the growth of the molars" [J:17489]
-is_a: MP:0000118 ! arrest of tooth development
-
-[Term]
-id: MP:0000129
-name: ameloblast degeneration
-def: "a retrogressive impairment of function or destruction of the epithelial cells of the inner later of the enamel organ of the developing tooth" [J:61509, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "degeneration of ameloblasts" EXACT []
-is_a: MP:0002650 ! abnormal ameloblast morphology
-
-[Term]
-id: MP:0000130
-name: abnormal cancellous bone morphology
-def: "structural anomaly of bone that has a lattice-like or spongy structure" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal cancellous bone" EXACT []
-synonym: "abnormal spongy bone" EXACT []
-synonym: "abnormal spongy spongiosa" EXACT []
-synonym: "abnormal spongy substance" EXACT []
-synonym: "abnormal substantia trabecularis" EXACT []
-synonym: "abnormal trabecular bone" EXACT []
-is_a: MP:0003795 ! abnormal bone structure
-
-[Term]
-id: MP:0000131
-name: abnormal long bone epiphysis morphology
-def: "the head of a developing long bone that is separated from the shaft by the epiphyseal plate" [J:61509]
-synonym: "abnormal epiphysis" EXACT []
-synonym: "abnormal long bone epiphysis morphology" EXACT []
-is_a: MP:0002113 ! abnormal skeleton development
-is_a: MP:0003723 ! abnormal long bone morphology
-
-[Term]
-id: MP:0000132
-name: thickened epiphysis
-def: "wider than normal part of the long bones that initially develops from a distinct ossification center than the shaft" [J:61295, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0000131 ! abnormal long bone epiphysis morphology
-
-[Term]
-id: MP:0000133
-name: abnormal long bone metaphysis morphology
-def: "malformed conical section of bone between the epiphysis and diaphysis of the long bones" [J:61295, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal long bone metaphysis" EXACT []
-synonym: "abnormal metaphysis" EXACT []
-is_a: MP:0003723 ! abnormal long bone morphology
-
-[Term]
-id: MP:0000134
-name: abnormal cortical bone thickness
-def: "reduced or increased width of the superficial layer of compact bone" [J:58795, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "cortical bone thickness abnormalities" EXACT []
-is_a: MP:0003796 ! abnormal cortical bone morphology
-
-[Term]
-id: MP:0000135
-name: reduced cortical bone thickness
-def: "thinner than normal superficial layer of compact bone " [J:61509]
-is_a: MP:0000134 ! abnormal cortical bone thickness
-
-[Term]
-id: MP:0000136
-name: abnormal microglial cell morphology
-def: "anomalous structure, number, or composition of the small neuroglial cells, possibly of mesodermal origin, which may become phagocytic, in areas of neural damage or inflammation" [anna:Anna V. Anagnostopoulos_Mouse Genome Informatics Curator, J:71688]
-is_a: MP:0000952 ! abnormal CNS glia
-
-[Term]
-id: MP:0000137
-name: abnormal vertebrae morphology
-alt_id: MP:0001538
-def: "any structural anomaly of the bony segments of the spinal column" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal vertebrae" EXACT []
-synonym: "vertebra defect" EXACT []
-is_a: MP:0004703 ! abnormal vertebral column
-
-[Term]
-id: MP:0000138
-name: absent vertebrae
-def: "missing all of the bony segments of the spinal column" [J:35802]
-synonym: "absence of vertebrae" EXACT []
-is_a: MP:0000137 ! abnormal vertebrae morphology
-
-[Term]
-id: MP:0000139
-name: absent vertebral transverse processes
-def: "loss of the bony protrusions on either side of the arch of a vertebrae at the point where the lamina joins the pedicle, between the superior and inferior articular processes; muscles and ligaments attach to these processes" [J:62022, J:62023]
-synonym: "absence of transverse processes" EXACT []
-is_a: MP:0004600 ! abnormal vertebral transverse process
-
-[Term]
-id: MP:0000140
-name: absent vertebral pedicles
-def: "loss of the two short, thick processes, which project backward, one on either side, from the upper part of the body to the laminae" [J:62022, J:62023, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "absence of pedicles" EXACT []
-is_a: MP:0004604 ! abnormal vertebral pedicle morphology
-
-[Term]
-id: MP:0000141
-name: abnormal vertebral body morphology
-def: "any structural anomaly of the main cylindrical portion of the vertebra ventral to the vertebral canal" [J:55583, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal vertebral bodies" EXACT []
-is_a: MP:0000137 ! abnormal vertebrae morphology
-
-[Term]
-id: MP:0000142
-name: An Extra Piece of Bone Rostral to C1
-is_obsolete: true
-
-[Term]
-id: MP:0000143
-name: Broadening/Splitting of the Neural Arch of C2
-is_obsolete: true
-
-[Term]
-id: MP:0000148
-name: abnormal shoulder/ pelvic girdle morphology
-alt_id: MP:0001540
-def: "anomalous structure of the bones of the shoulder or of the bones of the pelvis by which the limbs attach to the axial skeleton " [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal shoulder/ pelvic girdle" EXACT []
-synonym: "shoulder/ pelvic girdle defect" EXACT []
-is_obsolete: true
-
-[Term]
-id: MP:0000149
-name: abnormal scapula morphology
-def: "any structural anomaly of either or both of the large, flat bones of the back part of the shoulder" [J:13049]
-synonym: "abnormal scapula" EXACT []
-is_a: MP:0004508 ! abnormal shoulder bone morphology
-
-[Term]
-id: MP:0000150
-name: abnormal rib morphology
-def: "any structural anomaly of the bones forming the bony wall of the chest" [J:50311, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal ribs" EXACT []
-synonym: "rib defect" EXACT []
-is_a: MP:0002114 ! abnormal axial skeleton morphology
-
-[Term]
-id: MP:0000151
-name: absent ribs
-def: "missing all the pairs of bony structures that make up the body wall" [J:19212]
-synonym: "absence of ribs" EXACT []
-is_a: MP:0000150 ! abnormal rib morphology
-
-[Term]
-id: MP:0000152
-name: absent proximal rib
-def: "missing part of rib structures near the spine, ribs do not contact vertebrae" [J:62022, J:62023]
-synonym: "absence of proximal ribs" EXACT []
-is_a: MP:0000151 ! absent ribs
-
-[Term]
-id: MP:0000153
-name: rib bifurcation
-def: "forking or division of ribs, may be a result of partial rib fusions" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0000150 ! abnormal rib morphology
-
-[Term]
-id: MP:0000154
-name: rib fusion
-def: "appearance of one or more ribs as a single structure" [J:62022, J:62023]
-synonym: "fusion of ribs" EXACT []
-is_a: MP:0000150 ! abnormal rib morphology
-
-[Term]
-id: MP:0000155
-name: asymmetric rib attachment
-def: "loss of bilateral symmetry in rib attachments to the vertebral column or to the sternum" [J:19212]
-is_a: MP:0004625 ! abnormal rib attachment
-
-[Term]
-id: MP:0000156
-name: Presence of 6 Vertebrosternal Ribs instead of 7
-is_obsolete: true
-
-[Term]
-id: MP:0000157
-name: abnormal sternum morphology
-def: "malformed long flat bone of the chest; articulates with clavicle and first seven rib pairs" [J:19212, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal sternum" EXACT []
-synonym: "sternum defect" EXACT []
-is_a: MP:0002114 ! abnormal axial skeleton morphology
-
-[Term]
-id: MP:0000158
-name: absent sternum
-def: "missing long flat bone of the chest; articulates with clavicle and first seven rib pairs" [J:62577, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0000157 ! abnormal sternum morphology
-
-[Term]
-id: MP:0000159
-name: abnormal xiphoid process
-def: "any structural anomaly of the posterior tip of the sternum" [J:42932, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal xiphisternum" EXACT []
-synonym: "abnormal xiphoid cartilage" EXACT []
-synonym: "abnormal xyphoid process" EXACT []
-synonym: "xiphoid process defect" EXACT []
-is_a: MP:0000157 ! abnormal sternum morphology
-
-[Term]
-id: MP:0000160
-name: kyphosis
-alt_id: MP:0000068
-def: "forward curvature of the spine, characterized by extensive flexion. " [cml:Cathleen M. Lutz_Mouse Genome Informatics Curator, J:62023, J:66943, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "humpback" EXACT []
-synonym: "hunchback" EXACT []
-is_a: MP:0004174 ! abnormal spine curvature
-
-[Term]
-id: MP:0000161
-name: scoliosis
-alt_id: MP:0000070
-def: "lateral and rotational curvature of the spine" [J:53770, J:66943, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0004174 ! abnormal spine curvature
-
-[Term]
-id: MP:0000162
-name: lordosis
-def: "anteriorly convex curvature of the spine" [J:62022, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "saddle back" EXACT []
-is_a: MP:0004174 ! abnormal spine curvature
-
-[Term]
-id: MP:0000163
-name: abnormal cartilage morphology
-def: "any structural anomaly of the nonvascular, resilient, flexible connective tissue found primarily in joints, walls of the thorax, and tubular structures, but which also comprises most of the skeleton in early fetal life " [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal cartilage" EXACT []
-is_a: MP:0005508 ! abnormal skeleton morphology
-
-[Term]
-id: MP:0000164
-name: abnormal cartilage development
-def: "anomalous formation of the nonvascular, resilient, flexible connective tissue found primarily in joints, walls of the thorax, and tubular structures, but which also comprises most of the skeleton in early fetal life " [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal cartilage formation" EXACT []
-is_a: MP:0000163 ! abnormal cartilage morphology
-is_a: MP:0002113 ! abnormal skeleton development
-
-[Term]
-id: MP:0000165
-name: abnormal hypertrophic chondrocyte zone
-def: "anomaly of the cartilage cell matrix layer " [J:58795, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0000164 ! abnormal cartilage development
-is_a: MP:0003055 ! abnormal epiphyseal plate morphology
-
-[Term]
-id: MP:0000166
-name: abnormal chondrocyte morphology
-def: "anomalous structure, organization, or differentiation of nondividing cartilage cells" [J:40203, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal chondrocytes" EXACT []
-is_a: MP:0000163 ! abnormal cartilage morphology
-
-[Term]
-id: MP:0000167
-name: reduced chondrocyte numbers
-def: "fewer than normal numbers of nondividing cartilage cells" [J:61509, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0000166 ! abnormal chondrocyte morphology
-
-[Term]
-id: MP:0000168
-name: abnormal bone marrow development
-def: "malformation or anomalous differentiation of the soft, pulpy tissue filling the medullary cavities of bones" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal bone marrow formation/ structure" EXACT []
-is_a: MP:0002113 ! abnormal skeleton development
-
-[Term]
-id: MP:0000172
-name: abnormal bone marrow cell number
-def: "increased or decreased number of cells that make up the core cavities of bones when compared to controls" [tc:Teresa Chu_Mouse Genome Informatics Curator]
-is_a: MP:0002398 ! abnormal bone marrow cell morphology/development
-
-[Term]
-id: MP:0000175
-name: absent bone marrow cell
-alt_id: MP:0000342
-def: "lack of cells that make up the core cavities of bones" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-synonym: "absence of bone marrow cell" EXACT []
-synonym: "Loss of bone marrow cell" EXACT []
-synonym: "loss of bone marrow cell" EXACT []
-is_a: MP:0000172 ! abnormal bone marrow cell number
-
-[Term]
-id: MP:0000176
-name: bone marrow occupied by adipocytes
-def: "anomalous appearance of fat-forming cells in the bone marrow" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-is_a: MP:0000168 ! abnormal bone marrow development
-
-[Term]
-id: MP:0000179
-name: abnormal blood chemistry
-alt_id: MP:0001546
-def: "anomalous concentrations of proteins, minerals, nutrients, gases, or other substances in the blood" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-synonym: "blood chemistry abnormalities" EXACT []
-is_a: MP:0005428 ! abnormal clinical chemistry
-
-[Term]
-id: MP:0000180
-name: abnormal circulating cholesterol level
-def: "anomalous concentration in the blood of these most abundant steroids in animal tissues, and precursors to steroid hormones and bile salts; also components of plasma membranes" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal cholesterol level" EXACT []
-is_a: MP:0003947 ! abnormal cholesterol level
-is_a: MP:0003949 ! abnormal circulating lipid level
-
-[Term]
-id: MP:0000181
-name: abnormal circulating LDL cholesterol level
-def: "anomalous concentration in the blood of low density lipoprotein, which normally transports cholesterol to tissues other than the liver" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal LDL cholesterol level" EXACT []
-is_a: MP:0000180 ! abnormal circulating cholesterol level
-
-[Term]
-id: MP:0000182
-name: increased circulating LDL cholesterol level
-def: "greater than average concentration in the blood of low density lipoprotein, which normally transports cholesterol to tissues other than the liver" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "elevated circulating LDL cholesterol level" EXACT []
-synonym: "elevated LDL cholesterol level" EXACT []
-synonym: "high LDL cholesterol level" EXACT []
-synonym: "increased LDL cholesterol level" EXACT []
-is_a: MP:0000181 ! abnormal circulating LDL cholesterol level
-is_a: MP:0003982 ! increased cholesterol level
-
-[Term]
-id: MP:0000183
-name: decreased circulating LDL cholesterol level
-def: "less than average concentration in the blood of low density lipoprotein, which normally transports cholesterol to tissues other than the liver" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "decreased LDL cholesterol level" EXACT []
-synonym: "low circulating LDL cholesterol level" EXACT []
-synonym: "low LDL cholesterol level" EXACT []
-is_a: MP:0000181 ! abnormal circulating LDL cholesterol level
-is_a: MP:0003983 ! decreased cholesterol level
-
-[Term]
-id: MP:0000184
-name: abnormal circulating HDL cholesterol level
-alt_id: MP:0001555
-def: "anomalous concentration in the blood of high density lipoprotein; this molecule transports cholesterol to the liver for excretion in bile" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal HDL cholesterol level" EXACT []
-synonym: "Abnormal HDL Levels" EXACT []
-is_a: MP:0000180 ! abnormal circulating cholesterol level
-
-[Term]
-id: MP:0000186
-name: decreased circulating HDL cholesterol level
-alt_id: MP:0002618
-def: "lower than average level of high density lipoprotein in blood; this molecule transports cholesterol to the liver for excretion in bile" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "decreased HDL cholesterol level" EXACT []
-synonym: "low circulating HDL cholesterol level" EXACT []
-synonym: "low HDL cholesterol level" EXACT []
-synonym: "low serum HDL level" EXACT []
-is_a: MP:0000184 ! abnormal circulating HDL cholesterol level
-is_a: MP:0003983 ! decreased cholesterol level
-
-[Term]
-id: MP:0000187
-name: abnormal triglyceride level
-alt_id: MP:0001551
-def: "anomalous concentration of this molecule, glycerol esterified at each of its three hydroxyl groups by a fatty acid; triglyceride is an important molecule for storage of fatty acids in adipose tissue" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal triacylglycerol level" EXACT []
-is_a: MP:0001547 ! abnormal lipid level
-
-[Term]
-id: MP:0000188
-name: abnormal circulating glucose level
-alt_id: MP:0001557
-def: "anomalous concentration in the blood of this major monosaccharide of the body; it is an important energy source" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-synonym: "abnormal blood glucose level" EXACT []
-is_a: MP:0002078 ! abnormal glucose homeostasis
-
-[Term]
-id: MP:0000189
-name: hypoglycemia
-alt_id: MP:0001558
-alt_id: MP:0002613
-def: "low levels of plasma glucose in the circulating blood; this generally refers to a pathological state" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "Decreased Blood Glucose Level" EXACT []
-synonym: "low blood glucose levels" EXACT []
-is_a: MP:0005560 ! decreased circulating glucose level
-
-[Term]
-id: MP:0000192
-name: abnormal mineral level
-alt_id: MP:0001561
-def: "anomalous concentration of any inorganic substance that has importance in body functions" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0005636 ! abnormal mineral homeostasis
-
-[Term]
-id: MP:0000194
-name: hypercalcemia
-alt_id: MP:0001563
-alt_id: MP:0001768
-def: "abnormally high concentration of calcium ions in the circulating blood " [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "increased circulating calcium" EXACT []
-is_a: MP:0001562 ! abnormal circulating calcium level
-
-[Term]
-id: MP:0000195
-name: hypocalcemia
-alt_id: MP:0001564
-alt_id: MP:0001769
-def: "subnormal concentrations of calcium ions in the circulating blood	" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "decreased circulating calcium" EXACT []
-is_a: MP:0001562 ! abnormal circulating calcium level
-
-[Term]
-id: MP:0000198
-name: hypophosphatemia
-alt_id: MP:0001567
-alt_id: MP:0001774
-def: "abnormally low concentrations of phosphates in the circulating blood" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0001565 ! abnormal circulating phosphate level
-
-[Term]
-id: MP:0000199
-name: abnormal circulating albumin level
-alt_id: MP:0001568
-def: "aberrant concentration in the blood of this most abundant of the plasma proteins " [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-synonym: "abnormal albumin level" EXACT []
-synonym: "analbuminemia" EXACT []
-is_a: MP:0005416 ! abnormal circulating protein level
-
-[Term]
-id: MP:0000202
-name: abnormal circulating alkaline phosphatase level
-alt_id: MP:0001571
-def: "anomalous concentration in the blood of this enzyme, which hydrolyzes orthophosphoric monoesters; low levels are seen in cases of hypophosphatasia" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal alkaline phosphatase activity" EXACT []
-synonym: "abnormal alkaline phosphatase level" EXACT []
-synonym: "abnormal AP level" EXACT []
-synonym: "abnormal circulating ALP levels" EXACT []
-xref: GO:0004035
-is_a: MP:0001570 ! abnormal circulating enzyme level
-
-[Term]
-id: MP:0000203
-name: abnormal circulating aspartate transaminase level
-alt_id: MP:0001572
-def: "anomalous concentration in the blood of this enzyme, which catalyzes the reversible transfer of an amine group from l-glutamic acid to oxaloacetic acid, forming alpha-ketoglutaric acid and l-aspartic acid; aids in diagnosis of viral hepatitis and myocardial infarction" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-synonym: "abnormal aspartate aminotransferase level" EXACT []
-synonym: "abnormal aspartate transaminase level" EXACT []
-synonym: "abnormal AST level" EXACT []
-is_a: MP:0001570 ! abnormal circulating enzyme level
-
-[Term]
-id: MP:0000208
-name: decreased hematocrit
-alt_id: MP:0001580
-def: "less than the average percentage of a volume of a blood sample occupied by red blood cells" [MeSH:National Library of Medicine_Medical Subject Headings]
-synonym: "decreased hematocrit" EXACT []
-is_a: MP:0002596 ! abnormal hematocrit
-
-[Term]
-id: MP:0000215
-name: absent erythrocytes
-def: "lack of mature red blood cells" [J:23061]
-synonym: "absence of erythrocytes" EXACT []
-synonym: "absence of RBCs" EXACT []
-synonym: "absence of red blood cells" EXACT []
-is_a: MP:0001586 ! abnormal erythrocyte count
-
-[Term]
-id: MP:0000216
-name: absent erythrocyte precursors
-def: "lack of progenitors of the erythrocyte lineage" [J:23061]
-synonym: "absence of erythrocyte precursors" EXACT []
-is_a: MP:0002424 ! abnormal reticulocyte morphology/development
-
-[Term]
-id: MP:0000217
-name: abnormal white blood cell count
-alt_id: MP:0001587
-def: "anomalies in the number of leukocytes" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator, MeSH:National Library of Medicine_Medical Subject Headings]
-synonym: "abnormal WBC cell" EXACT []
-synonym: "abnormal white blood cell number" EXACT []
-synonym: "leukocyte count abnormalities" EXACT []
-synonym: "white blood cell count abnormalities" EXACT []
-synonym: "white blood cell number abnormalities" EXACT []
-is_a: MP:0000716 ! abnormal immune system cell morphology
-is_a: MP:0002429 ! abnormal blood cell morphology/development
-
-[Term]
-id: MP:0000218
-name: increased WBC count
-def: "greater than normal WBC numbers" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator, MeSH:National Library of Medicine_Medical Subject Headings]
-synonym: "increased leukocyte count" EXACT []
-synonym: "increased WBC number" EXACT []
-synonym: "leukocytosis" EXACT []
-is_a: MP:0000217 ! abnormal white blood cell count
-
-[Term]
-id: MP:0000219
-name: increased neutrophil count
-def: "greater than normal neutrophil numbers" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-synonym: "increased neutrophil number" EXACT []
-synonym: "neutrophilia" EXACT []
-is_a: MP:0000322 ! increased granulocyte number
-is_a: MP:0002415 ! abnormal neutrophil morphology/development
-
-[Term]
-id: MP:0000220
-name: increased monocyte count
-def: "greater than normal monocyte numbers" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-synonym: "increased monocyte number" EXACT []
-is_a: MP:0000218 ! increased WBC count
-is_a: MP:0002620 ! abnormal monocyte morphology
-
-[Term]
-id: MP:0000221
-name: decreased WBC count
-def: "fewer than normal numbers of WBCs" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator, MeSH:National Library of Medicine_Medical Subject Headings]
-synonym: "decreased leukocyte count" EXACT []
-synonym: "decreased WBC number" EXACT []
-synonym: "leukocytopenia" EXACT []
-synonym: "leukopenia" EXACT []
-synonym: "lymphopenia" EXACT []
-is_a: MP:0000217 ! abnormal white blood cell count
-
-[Term]
-id: MP:0000222
-name: decreased neutrophil count
-def: "fewer than normal neutrophil numbers" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-synonym: "decreased neutrophil number" EXACT []
-synonym: "neutropenia" EXACT []
-is_a: MP:0000334 ! decreased granulocyte number
-is_a: MP:0002415 ! abnormal neutrophil morphology/development
-
-[Term]
-id: MP:0000223
-name: decreased monocyte count
-def: "fewer than normal monocyte numbers" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-synonym: "decreased monocyte number" EXACT []
-synonym: "monocytopenia" EXACT []
-is_a: MP:0000221 ! decreased WBC count
-is_a: MP:0002620 ! abnormal monocyte morphology
-
-[Term]
-id: MP:0000226
-name: abnormal mean corpuscular volume
-alt_id: MP:0001590
-def: "deviation from normal for the average amount of space occupied by each red blood cell, calculated from the hematocrit and red cell count, in erythrocyte indices" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator, MeSH:National Library of Medicine_Medical Subject Headings]
-comment: MCV is calculated by dividing the hematocrit by the total number of RBCs and multiplying this number by ten (10). This was found on medfriendly.com. cwg 3/10/03
-synonym: "abnormal MCV" EXACT []
-synonym: "abnormal mean cell volume" EXACT []
-is_a: MP:0002124 ! abnormal red blood cell
-
-[Term]
-id: MP:0000228
-name: abnormal thrombopoiesis
-alt_id: MP:0000211
-alt_id: MP:0000227
-alt_id: MP:0001583
-alt_id: MP:0001591
-alt_id: MP:0001592
-alt_id: MP:0002448
-def: "abnormal development of the non-nucleated cells of the blood (platelets, thrombocytes) involved in blood coagulation" [MeSH:National Library of Medicine_Medical Subject Headings]
-synonym: "abnormal platelet development" EXACT []
-synonym: "abnormal platelet morphology/development" EXACT []
-synonym: "abnormal platelets" EXACT []
-synonym: "platelet abnormalities" EXACT []
-synonym: "platelet development abnormalities" EXACT []
-synonym: "thrombocyte abnormalities" EXACT []
-is_a: MP:0002123 ! abnormal hematopoiesis
-is_a: MP:0002417 ! abnormal megakaryocyte morphology/development
-
-[Term]
-id: MP:0000229
-name: abnormal megakaryocyte differentiation
-alt_id: MP:0001593
-def: "atypical process of formation and development these very large bone marrow cells which release mature platelets" [MeSH:National Library of Medicine_Medical Subject Headings]
-is_a: MP:0000228 ! abnormal thrombopoiesis
-
-[Term]
-id: MP:0000230
-name: abnormal blood pressure
-alt_id: MP:0001594
-alt_id: MP:0002129
-def: "altered tension of the blood within the systemic arteries" [csmith:Cynthia L. Smith_Mouse Genome Informatics Curator]
-synonym: "heart/cardiovascular system: blood pressure anomalies" EXACT []
-xref: MGI:2173589
-is_a: MP:0001544 ! abnormal cardiovascular system physiology
-
-[Term]
-id: MP:0000231
-name: hypertension
-alt_id: MP:0001595
-def: "sustained high blood pressure at a level that is likely to result in cardiovascular disease and/or other pathological states" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0002842 ! increased blood pressure
-
-[Term]
-id: MP:0000233
-name: abnormal blood flow velocity
-alt_id: MP:0001597
-def: "anomalous rate of flow of the blood through vessels" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator]
-is_a: MP:0002128 ! abnormal blood circulation
-
-[Term]
-id: MP:0000237
-name: decreased blood cell numbers
-def: "fewer than the normal numbers of the various types of blood cells" [J:60630]
-synonym: "reduction in hematopoietic cell types" EXACT []
-synonym: "reduction in hemopoietic cell types" EXACT []
-is_a: MP:0002123 ! abnormal hematopoiesis
-
-[Term]
-id: MP:0000238
-name: deficiency of pre-B cells
-alt_id: MP:0000349
-def: "lack of progenitor cells that form the B cell component of the immune system" [J:60630, tc:Teresa Chu_Mouse Genome Informatics Curator]
-synonym: "Absence of pre-B cell" EXACT []
-synonym: "absence of pre-B cell" EXACT []
-synonym: "Loss of pre-B cell" EXACT []
-synonym: "loss of pre-B cell" EXACT []
-is_a: MP:0002403 ! abnormal pre-B cell
-
-[Term]
-id: MP:0000239
-name: deficiency of myeloid colony forming progenitor cells
-def: "lack of precursors of the myeloid cell types" [J:60630, tc:Teresa Chu_Mouse Genome Informatics Curator]
-is_a: MP:0002123 ! abnormal hematopoiesis
-
-[Term]
-id: MP:0000240
-name: extramedullary hematopoiesis
-def: "formation and development of blood cells outside the bone marrow, e.g., in the spleen, liver, or lymph nodes" [MeSH:National Library of Medicine_Medical Subject Headings]
-synonym: "EMH" EXACT []
-synonym: "extramedullary hemopoiesis" EXACT []
-is_a: MP:0002123 ! abnormal hematopoiesis
-
-[Term]
-id: MP:0000242
-name: impaired fertilization
-def: "defect or reduced ability in the process beginning with penetration of the secondary oocyte by the spermatozoon and completed by fusion of the male and female pronuclei" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0005410 ! abnormal fertilization
-
-[Term]
-id: MP:0000243
-name: myoclonus
-def: "involuntary shock-like contractions, variable in rhythm and amplitude, followed by relaxation, of a muscle or a group of muscles; generally due to a central nervous system lesion" [MeSH:National Library of Medicine_Medical Subject Headings, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8]
-is_a: MP:0000743 ! muscle spasms
-is_a: MP:0000947 ! convulsive seizures
-
-[Term]
-id: MP:0000245
-name: abnormal erythropoiesis
-alt_id: MP:0001608
-def: "atypical process of red blood cell formation" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8, tc:Teresa Chu_Mouse Genome Informatics Curator]
-synonym: "abnormal erythrocytopoiesis" EXACT []
-synonym: "erythropoiesis abnormalities" EXACT []
-is_a: MP:0002123 ! abnormal hematopoiesis
-
-[Term]
-id: MP:0000247
-name: abnormal IL-10 physiology
-def: "functional anomaly of this factor that is a co-regulator of mast cell growth and produced by T and B cells" [MeSH:National Library of Medicine_Medical Subject Headings, pvb:Pierre Vanden Borre_Mouse Genome Informatics Curator]
-synonym: "interleukin 10" EXACT []
-is_a: MP:0002529 ! abnormal interleukin physiology
-
-[Term]
-id: MP:0000248
-name: macrocytosis
-alt_id: MP:0001610
-def: "condition in which erythrocytes are larger than normal in size" [cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator, S...
 
[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [1007] phenote/trunk/obo-files/anatomy.obo

From: <mg...@us...> - 2007-10-09 21:54:40

Revision: 1007
          http://obo.svn.sourceforge.net/obo/?rev=1007&view=rev
Author:   mgibson
Date:     2007-10-09 14:54:44 -0700 (Tue, 09 Oct 2007)

Log Message:
-----------
not sure what this is doing here

Removed Paths:
-------------
    phenote/trunk/obo-files/anatomy.obo

Deleted: phenote/trunk/obo-files/anatomy.obo
===================================================================
--- phenote/trunk/obo-files/anatomy.obo	2007-10-09 21:49:36 UTC (rev 1006)
+++ phenote/trunk/obo-files/anatomy.obo	2007-10-09 21:54:44 UTC (rev 1007)
@@ -1 +0,0 @@
-link fly_anatomy.obo
\ No newline at end of file


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[Obo-svn-commit] SF.net SVN: obo: [1006] phenote/trunk/images/elephant_icon.jpg

From: <nl...@us...> - 2007-10-09 21:49:33

Revision: 1006
          http://obo.svn.sourceforge.net/obo/?rev=1006&view=rev
Author:   nlw
Date:     2007-10-09 14:49:36 -0700 (Tue, 09 Oct 2007)

Log Message:
-----------
added the icon for fun

Added Paths:
-----------
    phenote/trunk/images/elephant_icon.jpg

Added: phenote/trunk/images/elephant_icon.jpg
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/images/elephant_icon.jpg
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream


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