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From: <nl...@us...> - 2007-07-19 23:10:49
|
Revision: 754
http://svn.sourceforge.net/obo/?rev=754&view=rev
Author: nlw
Date: 2007-07-19 16:10:36 -0700 (Thu, 19 Jul 2007)
Log Message:
-----------
*turned menu items to "true". (were dependent on dataadapters being loaded)
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 2007-07-19 23:07:05 UTC (rev 753)
+++ phenote/trunk/src/java/phenote/gui/HelpMenu.java 2007-07-19 23:10:36 UTC (rev 754)
@@ -39,7 +39,7 @@
help = new JMenuItem("Phenote Help");
- help.setEnabled(Config.inst().hasDataAdapters());
+ help.setEnabled(true);
help.setActionCommand("help");
HelpBroker hb = HelpManager.getHelpBroker();
if (hb == null) {
@@ -52,7 +52,7 @@
}
JMenuItem about = new JMenuItem("About");
- about.setEnabled(Config.inst().hasDataAdapters());
+ about.setEnabled(true);
about.setActionCommand("about");
about.addActionListener(actionListener);
add(about);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-07-19 23:07:08
|
Revision: 753
http://svn.sourceforge.net/obo/?rev=753&view=rev
Author: nlw
Date: 2007-07-19 16:07:05 -0700 (Thu, 19 Jul 2007)
Log Message:
-----------
need to include image heights in html to display them correctly in java help browser
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/help/JavaHelpSearch/POSITIONS
phenote/trunk/doc/phenote-website/help/html/Annotation_Spreadsheet.htm
phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Free_Text_fields.htm
phenote/trunk/doc/phenote-website/help/html/Phenote_from_the_Command_Line.htm
phenote/trunk/doc/phenote-website/help/html/Running_Phenote_for_the_First_Time.htm
phenote/trunk/doc/phenote-website/help/html/Sample_Configuration_1.htm
phenote/trunk/doc/phenote-website/help/html/Sample_Configuration_2.htm
phenote/trunk/doc/phenote-website/help/html/The_Phenote_Interface.htm
phenote/trunk/doc/phenote-website/help/indexer.log
Modified: phenote/trunk/doc/phenote-website/help/JavaHelpSearch/POSITIONS
===================================================================
(Binary files differ)
Modified: phenote/trunk/doc/phenote-website/help/html/Annotation_Spreadsheet.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Annotation_Spreadsheet.htm 2007-07-19 20:47:27 UTC (rev 752)
+++ phenote/trunk/doc/phenote-website/help/html/Annotation_Spreadsheet.htm 2007-07-19 23:07:05 UTC (rev 753)
@@ -7,8 +7,8 @@
</head>
<body bgcolor="#ffffff">
<h1>Annotation Spreadsheet</h1>
-<p><IMG src="../images/annotation_spreadsheet_blank.png" width="100%"
-border=0></p>
+<p><IMG height=180 src="../images/annotation_spreadsheet_blank.png" width=700
+ border=0 ></p>
<p> </p>
<p>In the bottom half of the Phenote window occupies the Annotation
Spreadsheet.</p>
Modified: phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Free_Text_fields.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Free_Text_fields.htm 2007-07-19 20:47:27 UTC (rev 752)
+++ phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Free_Text_fields.htm 2007-07-19 23:07:05 UTC (rev 753)
@@ -13,12 +13,12 @@
entry section, you will see a blinking cursor in the active field.</p>
<h3>Step 2: Begin typing...</h3>
<p>Go ahead...</p>
-<p><IMG src="../images/free-text-pretab.png" width=600 border=0></p>
+<p><IMG height=275 src="../images/free-text-pretab.png" width=500 border=0></p>
<h3>Step 3: "Tab" or mouse-click to insert into the spreadsheet</h3>
<p>Once you've typed all you want, be sure to hit tab
(which will also advance to the next field), or click on another field.
This will insert your entry into the <em>Annotation spreadsheet</em> down
below:</p>
-<p><IMG src="../images/free-text-posttab.png" width=600 border=0></p>
+<p><IMG height=275 src="../images/free-text-posttab.png" width=500 border=0></p>
</body>
</html>
\ No newline at end of file
Modified: phenote/trunk/doc/phenote-website/help/html/Phenote_from_the_Command_Line.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Phenote_from_the_Command_Line.htm 2007-07-19 20:47:27 UTC (rev 752)
+++ phenote/trunk/doc/phenote-website/help/html/Phenote_from_the_Command_Line.htm 2007-07-19 23:07:05 UTC (rev 753)
@@ -40,11 +40,11 @@
<h2>2) Get Phenote</h2>
<p>The latest development version of Phenote can be retrieved
from SourceForge.net Subversion repository through SVN with the following
-instruction set: </p><pre>svn co <A href="https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk">https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk</a> phenote </pre>
+instruction set: </p><pre>svn co <A href="https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk">https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk</A> phenote </pre>
<p>If you would like to check out a particular release, you will have to check
out that particular version from the "tags" directory. For example, to
checkout version 1.1 into your phenote1.1/ directory, you would use the
-following command:</p><pre>svn co <A href="https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.1/">https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.1/</a> phenote1.1</pre>
+following command:</p><pre>svn co <A href="https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.1/">https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.1/</A> phenote1.1</pre>
<p>Information about accessing this Subversion repository may be found in a
document titled "<a href="http://sourceforge.net/docs/E09">Subversion (Version
Control for Source Code)</a>". </p>
Modified: phenote/trunk/doc/phenote-website/help/html/Running_Phenote_for_the_First_Time.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Running_Phenote_for_the_First_Time.htm 2007-07-19 20:47:27 UTC (rev 752)
+++ phenote/trunk/doc/phenote-website/help/html/Running_Phenote_for_the_First_Time.htm 2007-07-19 23:07:05 UTC (rev 753)
@@ -20,7 +20,7 @@
newer versions of ontologies available for download. If so, it will
automatically download the newest versions to your local computer. (This
feature can be disabled in the future. See the <A
-href="What_is_a_Configuration_.htm">Customizing Phenote</a>
+href="What_is_a_Configuration_.htm">Customizing Phenote</A>
section for more
information.)</p>
Modified: phenote/trunk/doc/phenote-website/help/html/Sample_Configuration_1.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Sample_Configuration_1.htm 2007-07-19 20:47:27 UTC (rev 752)
+++ phenote/trunk/doc/phenote-website/help/html/Sample_Configuration_1.htm 2007-07-19 23:07:05 UTC (rev 753)
@@ -9,7 +9,7 @@
<h1>Sample Configuration 1</h1><pre><h2><font face="Arial">The Phenote window for sample.cfg</font></h2></pre>
<p>This interface is created with the configuration file sample.cfg shown
below:</p>
-<p><IMG src="../images/sample-config.png" width="100%" border=0></p>
+<p><IMG height=325 src="../images/sample-config.png" width=700 border=0></p>
<h2>The configuration file: sample.cfg</h2><pre><?xml version="1.0" encoding="UTF-8"?><br><ns:phenote-configuration version="1.3-beta1" xmlns:ns="phenote/config/xml"><br> <ns:log config-file="conf/log4j-standalone.xml"/><br> <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/></pre><pre><br> <ns:uvic-graph enable="false"/><br> <ns:term-history enable="false"/> <br> <ns:auto-update-ontologies enable="false"/> <<br> <ns:update-timer timer="15"/>< <br> <ns:field name="Example Free-text" syntax-abbrev="PUB" enable="true"/> <br> <ns:field name="Genotype" syntax-abbrev="GT" enable="false"/><br> <ns:field name="Example Multi-Ontology" syntax-abbrev="E" enable="true"> <br> <ns:ontology name="Relationship" file="relationship.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/> <br> <ns:ontology name="GO" file="gene_ontology.obo" repos-subdir="genomic-proteomic"/> <br> <ns:ontology name="CL" file="cell.obo" repos-subdir="anatomy/cell_type"/> <br> </ns:field><br> <ns:field name="Example Single-Ontology" syntax-abbrev="Q" enable="true"> <br> <ns:ontology name="PATO" file="quality.obo" repos-subdir="phenotype"/> <br> </ns:field><br> <ns:field name="Description" syntax-abbrev="Desc" enable="true"/></pre><pre></ns:phenote-configuration></pre><pre> </pre>
</body>
</html>
Modified: phenote/trunk/doc/phenote-website/help/html/Sample_Configuration_2.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Sample_Configuration_2.htm 2007-07-19 20:47:27 UTC (rev 752)
+++ phenote/trunk/doc/phenote-website/help/html/Sample_Configuration_2.htm 2007-07-19 23:07:05 UTC (rev 753)
@@ -9,7 +9,7 @@
<h1>Sample Configuration 2</h1>
<h2>The Phenote window for ncbo.cfg</h2>
<p>This interface is created with the configuration file ncbo.cfg shown below</p>
-<p><IMG src="../images/ncbo-config.png" width="100%" border=0> </p>
+<p><IMG height=480 src="../images/ncbo-config.png" width=720 border=0> </p>
<h2>The configuration file: ncbo.cfg</h2><pre><?xml version="1.3.1" encoding="UTF-8"?><br><ns:phenote-configuration version="1.1.2" xmlns:ns="phenote/config/xml"><br> <ns:log config-file="conf/log4j-standalone.xml"/></pre><pre> <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/> <br> <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/><br> <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="false"/><br> <ns:dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/></pre><pre> <ns:uvic-graph enable="false"/><br> <ns:term-history enable="false"/><br> <ns:auto-update-ontologies enable="true"/> <<br> <ns:update-timer timer="0"/><><br> <br> <ns:obo-repository url-dir="<A href="'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/" ??>http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/</a>><br> <ns:field name="Pub" syntax-abbrev="PUB" enable="true"/><br> <ns:field name="Genotype" syntax-abbrev="GT" enable="true"/><br> <ns:field name="Genetic Context" syntax-abbrev="GC" enable="true"><br> <ns:ontology name="Genetic Context" file="context.obo"/><br> </ns:field><br> <ns:field name="Entity" syntax-abbrev="E" enable="true"><br> <ns:ontology name="Relationship" file="relationship.obo" is-postcomp-rel="true"/><br> <ns:ontology name="FMA" file="fma_obo.obo"/><br> <ns:ontology name="EHDAA" file="human-dev-anat-abstract.obo"/><br> <ns:ontology name="GO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo" /><br> <ns:ontology name="CL" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo" /><br> <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo" /><br> </ns:field><br> <ns:field name="Quality" syntax-abbrev="Q" enable="true"><br> <ns:ontology name="PATO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo" /><br> <ns:ontology name="MP" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mammalian_phenotype.obo" /><br> </ns:field><br> <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true"><br> <ns:ontology name="Relationship" file="relationship.obo" is-postcomp-rel="true"/><br> <ns:ontology name="FMA" file="fma_obo.obo"/><br> <ns:ontology name="EHDAA" file="human-dev-anat-abstract.obo"/><br> <ns:ontology name="GO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo" /><br> <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo" /><br> <ns:ontology name="CL" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo" /><br> </ns:field><br> <ns:field name="Abnormal" syntax-abbrev="Tag" enable="true"><br> <ns:ontology name="Abnormal" file="quality.obo" slim="abnormal_slim"/><br> </ns:field><br> <ns:field name="Description" syntax-abbrev="Desc" enable="true"/><br></ns:phenote-configuration></pre> <pre></pre>
</body>
</html>
Modified: phenote/trunk/doc/phenote-website/help/html/The_Phenote_Interface.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The_Phenote_Interface.htm 2007-07-19 20:47:27 UTC (rev 752)
+++ phenote/trunk/doc/phenote-website/help/html/The_Phenote_Interface.htm 2007-07-19 23:07:05 UTC (rev 753)
@@ -10,7 +10,8 @@
<p>This screenshot is of Phenote when configured with the "demo" configuration and loaded
with data. It is a typical interface for phenotype
annotation. </p>
-<p><IMG src="../images/phenote-data-markup.png" width="100%" border=0> The Phenote application window is comprised of three main areas:</p>
+<IMG height=400 src="../images/phenote-data-markup.png" width=600 border=0>
+<p>The Phenote application window is comprised of three main areas:</p>
<ul>
<li>The Data Entry frame located in the upper left.
<li>The Term Info frame located in the upper right.
Modified: phenote/trunk/doc/phenote-website/help/indexer.log
===================================================================
--- phenote/trunk/doc/phenote-website/help/indexer.log 2007-07-19 20:47:27 UTC (rev 752)
+++ phenote/trunk/doc/phenote-website/help/indexer.log 2007-07-19 23:07:05 UTC (rev 753)
@@ -106,4 +106,4 @@
URL: 'html/The__phenote_configuration__Tag.htm'
File: 'html/XML_skeleton.htm'
URL: 'html/XML_skeleton.htm'
- Parse time: 0.921 s
+ Parse time: 0.791 s
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-07-19 21:40:13
|
Revision: 752
http://svn.sourceforge.net/obo/?rev=752&view=rev
Author: mgibson
Date: 2007-07-19 13:47:27 -0700 (Thu, 19 Jul 2007)
Log Message:
-----------
disclaimer popup elaboration that it takes a minute or so to parse all configs
Modified Paths:
--------------
phenote/trunk/src/java/phenote/gui/ConfigGui.java
Modified: phenote/trunk/src/java/phenote/gui/ConfigGui.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/ConfigGui.java 2007-07-19 20:30:57 UTC (rev 751)
+++ phenote/trunk/src/java/phenote/gui/ConfigGui.java 2007-07-19 20:47:27 UTC (rev 752)
@@ -65,7 +65,8 @@
String m="This is a mockup for gui configuration. This is very much under const"
+"ruction!\nPresently you can use it to browse configs, and you can see where "
+"I am going with editing(which doesnt work yet).\nFeedback would be great.\n"
- +"Thanks.\nWarning: it takes a while to load all the configs up";
+ +"Thanks.\nWarning: it takes a while(~1 minute) to load all the configs up\n"
+ +"during which time phenote will be frozen(but not dead) - this will be improved";
int ok =
JOptionPane.showConfirmDialog(null,m,"Under construction!",JOptionPane.OK_CANCEL_OPTION);
if (ok == JOptionPane.CANCEL_OPTION) return;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-07-19 21:39:57
|
Revision: 751
http://svn.sourceforge.net/obo/?rev=751&view=rev
Author: mgibson
Date: 2007-07-19 13:30:57 -0700 (Thu, 19 Jul 2007)
Log Message:
-----------
put in popup disclaimer for gui config soliciting for feedback
Modified Paths:
--------------
phenote/trunk/src/java/phenote/gui/ConfigGui.java
Modified: phenote/trunk/src/java/phenote/gui/ConfigGui.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/ConfigGui.java 2007-07-19 18:09:49 UTC (rev 750)
+++ phenote/trunk/src/java/phenote/gui/ConfigGui.java 2007-07-19 20:30:57 UTC (rev 751)
@@ -14,6 +14,7 @@
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JList;
+import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JSplitPane;
@@ -61,6 +62,14 @@
public ConfigGui() { init(); }
private void init() {
+ String m="This is a mockup for gui configuration. This is very much under const"
+ +"ruction!\nPresently you can use it to browse configs, and you can see where "
+ +"I am going with editing(which doesnt work yet).\nFeedback would be great.\n"
+ +"Thanks.\nWarning: it takes a while to load all the configs up";
+ int ok =
+ JOptionPane.showConfirmDialog(null,m,"Under construction!",JOptionPane.OK_CANCEL_OPTION);
+ if (ok == JOptionPane.CANCEL_OPTION) return;
+
JFrame frame = new JFrame("Phenote Configuration(under development)");
JComponent allConfigs = makeAllConfigsPanel();
@@ -99,7 +108,7 @@
frame.pack();
frame.setVisible(true);
- Config c2 = Config.newInstance("h2","2");//NO_NAME,noNameItalics); //??
+ //Config c2 = Config.newInstance("h2","2");//NO_NAME,noNameItalics); //??
//configList.setModel(getConfigListModel()); // ????
//getConfigListModel().list.add(c2);
configList.repaint();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-07-19 18:09:47
|
Revision: 750
http://svn.sourceforge.net/obo/?rev=750&view=rev
Author: mgibson
Date: 2007-07-19 11:09:49 -0700 (Thu, 19 Jul 2007)
Log Message:
-----------
ant jar is now putting help stuff into jar
just grabbing it from doc/phenote-website/help
puts in jar dir help
HelpManager checks 2 paths with findUrl
doc/phenote-website/help/Phenote.hs
and just help/Phenote.hs (for jar/webstart)
Modified Paths:
--------------
phenote/trunk/build.xml
phenote/trunk/src/java/phenote/main/HelpManager.java
phenote/trunk/src/java/phenote/util/FileUtil.java
Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml 2007-07-19 16:35:40 UTC (rev 749)
+++ phenote/trunk/build.xml 2007-07-19 18:09:49 UTC (rev 750)
@@ -201,12 +201,14 @@
<!-- JAR The jar target compiles everything, and produces a phenote.jar in
phenote/jars/phenote.jar. -->
<target name="jar" depends="compile">
+ <!-- copy file="doc/phenote-website/help/Phenote.hs" todir="conf" ?? -->
<jar destfile="${jarfile}">
<fileset dir="${classfiles}"/>
<fileset dir="." includes="obo-files/" excludes="obo-files/old"/>
<fileset file="${conf}/*.cfg"/>
<fileset dir="." includes="${conf}/*.xml"/>
<fileset dir="." includes="images/"/>
+ <fileset dir="doc/phenote-website" includes="help/**"/>
</jar>
</target>
Modified: phenote/trunk/src/java/phenote/main/HelpManager.java
===================================================================
--- phenote/trunk/src/java/phenote/main/HelpManager.java 2007-07-19 16:35:40 UTC (rev 749)
+++ phenote/trunk/src/java/phenote/main/HelpManager.java 2007-07-19 18:09:49 UTC (rev 750)
@@ -1,29 +1,50 @@
package phenote.main;
import java.io.File;
+import java.io.FileNotFoundException;
+import java.net.URL;
import javax.help.HelpBroker;
import javax.help.HelpSet;
+import javax.help.HelpSetException;
-public class HelpManager {
- protected static HelpBroker helpBroker;
- protected static String helpsetPath = "doc/phenote-website/help/Phenote.hs";
+import org.apache.log4j.Logger;
- public static HelpBroker getHelpBroker() {
- if (helpBroker == null) {
- HelpSet hs;
- File docsDir = new File(helpsetPath);
+import phenote.util.FileUtil;
- try {
- hs = new HelpSet(null, docsDir.toURL());
- } catch (Exception ee) {
- System.out.println("HelpSet " + ee.getMessage());
- System.out.println("HelpSet " + docsDir + " not found");
- return null;
- }
- helpBroker = hs.createHelpBroker();
- }
-
- return helpBroker;
- }
-}
\ No newline at end of file
+public class HelpManager {
+ protected static HelpBroker helpBroker;
+ protected static String helpsetPath = "doc/phenote-website/help/Phenote.hs";
+ private static String jarHelpsetPath = "help/Phenote.hs";
+ private static final Logger LOG = Logger.getLogger(HelpManager.class);
+
+ public static HelpBroker getHelpBroker() {
+ if (helpBroker == null) {
+ HelpSet hs;
+ //File docsDir = new File(helpsetPath);
+ URL url;
+ try { url = FileUtil.findUrl(helpsetPath); }
+ catch (FileNotFoundException e) { // try jar path (webstart)
+ try {
+ LOG.info("Didnt find help at "+helpsetPath+" trying "+jarHelpsetPath);
+ url = FileUtil.findUrl(jarHelpsetPath);
+ LOG.info("Found help at "+jarHelpsetPath);
+ }
+ catch (FileNotFoundException e2) {
+ LOG.error("phenote help not found "+e);
+ return null;
+ }
+ }
+
+ try {
+ hs = new HelpSet(null, url); //docsDir.toURL());
+ } catch (HelpSetException ee) {
+ LOG.error("HelpSet error: " + ee.getMessage());
+ return null;
+ }
+ helpBroker = hs.createHelpBroker();
+ }
+
+ return helpBroker;
+ }
+}
Modified: phenote/trunk/src/java/phenote/util/FileUtil.java
===================================================================
--- phenote/trunk/src/java/phenote/util/FileUtil.java 2007-07-19 16:35:40 UTC (rev 749)
+++ phenote/trunk/src/java/phenote/util/FileUtil.java 2007-07-19 18:09:49 UTC (rev 750)
@@ -85,7 +85,7 @@
//System.out.println(u+" url exists "+urlExists(u));
if (urlExists(u)) return u;
}
- System.out.println("Failed to find file "+filename);
+ //System.out.println("Failed to find file "+filename);
//LOG.error("Failed to find file "+filename);
throw new FileNotFoundException(filename+" not found");
}
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|
|
From: <mg...@us...> - 2007-07-19 16:35:38
|
Revision: 749
http://svn.sourceforge.net/obo/?rev=749&view=rev
Author: mgibson
Date: 2007-07-19 09:35:40 -0700 (Thu, 19 Jul 2007)
Log Message:
-----------
ant build now puts xmls from conf in jar - in conf dir
log4j and character template
Modified Paths:
--------------
phenote/trunk/build.xml
Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml 2007-07-19 15:21:41 UTC (rev 748)
+++ phenote/trunk/build.xml 2007-07-19 16:35:40 UTC (rev 749)
@@ -205,6 +205,7 @@
<fileset dir="${classfiles}"/>
<fileset dir="." includes="obo-files/" excludes="obo-files/old"/>
<fileset file="${conf}/*.cfg"/>
+ <fileset dir="." includes="${conf}/*.xml"/>
<fileset dir="." includes="images/"/>
</jar>
</target>
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|
|
From: <ba...@us...> - 2007-07-19 15:21:39
|
Revision: 748
http://svn.sourceforge.net/obo/?rev=748&view=rev
Author: balhoff
Date: 2007-07-19 08:21:41 -0700 (Thu, 19 Jul 2007)
Log Message:
-----------
Fixed finding of swixml file in jar.
Modified Paths:
--------------
phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
Modified: phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java 2007-07-19 14:20:42 UTC (rev 747)
+++ phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java 2007-07-19 15:21:41 UTC (rev 748)
@@ -4,7 +4,6 @@
import java.awt.Component;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.io.File;
import java.util.ArrayList;
import java.util.List;
@@ -28,6 +27,7 @@
import phenote.gui.field.FieldPanel;
import phenote.gui.selection.SelectionManager;
import phenote.main.Phenote;
+import phenote.util.FileUtil;
public class CharacterTemplateController implements ActionListener {
@@ -165,7 +165,7 @@
private JPanel createPanel() {
SwingEngine swix = new SwingEngine(this);
try {
- JPanel panel = (JPanel)swix.render(new File("conf/character_template.xml"));
+ JPanel panel = (JPanel)swix.render(FileUtil.findUrl("character_template.xml"));
this.characterTemplateTable.setModel(this.tableModel);
this.characterTemplateTable.setSelectionModel(new SelectionManagerListSelectionModel(this.characterListManager, this.editManager, this.selectionManager));
FieldPanel fieldPanel = new FieldPanel(true, false, this.representedGroup, this.selectionManager, this.editManager);
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|
|
From: <mg...@us...> - 2007-07-19 14:20:39
|
Revision: 747
http://svn.sourceforge.net/obo/?rev=747&view=rev
Author: mgibson
Date: 2007-07-19 07:20:42 -0700 (Thu, 19 Jul 2007)
Log Message:
-----------
swixml needs jdom
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-19 14:15:21 UTC (rev 746)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-19 14:20:42 UTC (rev 747)
@@ -40,6 +40,7 @@
<jar href="jars/jetty-6.1.4.jar" />
<jar href="jars/jetty-util-6.1.4.jar" />
<jar href="jars/swixml.jar" />
+ <jar href="jars/jdom.jar" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-19 14:15:21 UTC (rev 746)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-19 14:20:42 UTC (rev 747)
@@ -40,6 +40,7 @@
<jar href="jars/jetty-6.1.4.jar" />
<jar href="jars/jetty-util-6.1.4.jar" />
<jar href="jars/swixml.jar" />
+ <jar href="jars/jdom.jar" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
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|
|
From: <mg...@us...> - 2007-07-19 14:15:19
|
Revision: 746
http://svn.sourceforge.net/obo/?rev=746&view=rev
Author: mgibson
Date: 2007-07-19 07:15:21 -0700 (Thu, 19 Jul 2007)
Log Message:
-----------
added swixml jar to jnlp for jims new stuff
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-19 00:23:07 UTC (rev 745)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-19 14:15:21 UTC (rev 746)
@@ -39,6 +39,7 @@
<jar href="jars/jh.jar" />
<jar href="jars/jetty-6.1.4.jar" />
<jar href="jars/jetty-util-6.1.4.jar" />
+ <jar href="jars/swixml.jar" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-19 00:23:07 UTC (rev 745)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-19 14:15:21 UTC (rev 746)
@@ -39,6 +39,7 @@
<jar href="jars/jh.jar" />
<jar href="jars/jetty-6.1.4.jar" />
<jar href="jars/jetty-util-6.1.4.jar" />
+ <jar href="jars/swixml.jar" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
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|
|
From: <nl...@us...> - 2007-07-19 00:23:05
|
Revision: 745
http://svn.sourceforge.net/obo/?rev=745&view=rev
Author: nlw
Date: 2007-07-18 17:23:07 -0700 (Wed, 18 Jul 2007)
Log Message:
-----------
Modified Paths:
--------------
phenote/trunk/src/java/phenote/main/Phenote.java
Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java 2007-07-19 00:16:41 UTC (rev 744)
+++ phenote/trunk/src/java/phenote/main/Phenote.java 2007-07-19 00:23:07 UTC (rev 745)
@@ -42,6 +42,7 @@
import phenote.gui.SplashScreen;
import phenote.gui.TermInfo;
import phenote.gui.field.FieldPanel;
+import phenote.util.FileUtil;
public class Phenote {
@@ -56,8 +57,9 @@
private CommandLine commandLine = CommandLine.inst();
private JFrame frame;
public SplashScreen splashScreen;
- private String logoFile = "images/phenote_logo.jpg";
+ private String logoFile = "images/phenote_logo.jpg";
+
// public static Keymap defaultKeymap;
@@ -198,7 +200,12 @@
private void splashScreenInit(boolean enable) {
- ImageIcon myImage = new ImageIcon(logoFile);
+ ImageIcon myImage = new ImageIcon();
+ try {
+ myImage = new ImageIcon(FileUtil.findUrl(logoFile));
+ } catch (FileNotFoundException ex) { }
+
+// ImageIcon myImage = new ImageIcon(logoFile);
splashScreen = new SplashScreen(myImage,enable);
if (!enable) return;
splashScreen.setLocationRelativeTo(null);
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|
|
From: <nl...@us...> - 2007-07-19 00:16:38
|
Revision: 744
http://svn.sourceforge.net/obo/?rev=744&view=rev
Author: nlw
Date: 2007-07-18 17:16:41 -0700 (Wed, 18 Jul 2007)
Log Message:
-----------
*changed image file names to use the fileUrl method in file util class. this should make the image icons work for the browser now.
Modified Paths:
--------------
phenote/trunk/src/java/phenote/gui/TermInfo.java
phenote/trunk/src/java/phenote/util/FileUtil.java
Modified: phenote/trunk/src/java/phenote/gui/TermInfo.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/TermInfo.java 2007-07-18 23:43:32 UTC (rev 743)
+++ phenote/trunk/src/java/phenote/gui/TermInfo.java 2007-07-19 00:16:41 UTC (rev 744)
@@ -8,6 +8,8 @@
import java.awt.event.ActionListener;
import java.net.URL;
+import java.io.FileNotFoundException;
+
import javax.swing.BorderFactory;
import javax.swing.ImageIcon;
import javax.swing.JButton;
@@ -30,6 +32,7 @@
import phenote.gui.selection.UseTermEvent;
import phenote.gui.selection.UseTermListener;
import phenote.util.HtmlUtil;
+import phenote.util.FileUtil;
import edu.stanford.ejalbert.BrowserLauncher;
import edu.stanford.ejalbert.BrowserLauncherRunner;
import edu.stanford.ejalbert.exception.BrowserLaunchingInitializingException;
@@ -91,20 +94,30 @@
termInfoPanel.setBorder(BorderFactory.createTitledBorder("Term Info"));
termInfoPanel.add(scrollPane,BorderLayout.CENTER);
//Layout doesn't look good right now. Will fix
- ImageIcon ok = new ImageIcon("images/OK.GIF");
+ ImageIcon ok = new ImageIcon();
+ ImageIcon back = new ImageIcon();
+ ImageIcon forward = new ImageIcon();
+ try {
+ ok = new ImageIcon(FileUtil.findUrl("images/OK.GIF"));
+ } catch (FileNotFoundException ex) { }
+
useTermButton = new JButton(ok);
// JButton useTermButton = new JButton("Use Term");
useTermButton.addActionListener(new UseTermActionListener());
useTermButton.setPreferredSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
useTermButton.setMinimumSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
useTermButton.setToolTipText("Use Term");
- ImageIcon back = new ImageIcon("images/arrow.small.left.gif");
+ try {
+ back = new ImageIcon(FileUtil.findUrl("images/arrow.small.left.gif"));
+ } catch (FileNotFoundException ex) { }
JButton backButton = new JButton(back);
backButton.setToolTipText("Go back a term");
backButton.setPreferredSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
backButton.setMinimumSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
backButton.setMaximumSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
- ImageIcon forward = new ImageIcon("images/arrow.small.right.gif");
+ try {
+ forward = new ImageIcon(FileUtil.findUrl("images/arrow.small.right.gif"));
+ } catch (FileNotFoundException ex) { }
JButton forwardButton = new JButton(forward);
forwardButton.setToolTipText("Go forward a term");
forwardButton.setPreferredSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
Modified: phenote/trunk/src/java/phenote/util/FileUtil.java
===================================================================
--- phenote/trunk/src/java/phenote/util/FileUtil.java 2007-07-18 23:43:32 UTC (rev 743)
+++ phenote/trunk/src/java/phenote/util/FileUtil.java 2007-07-19 00:16:41 UTC (rev 744)
@@ -108,6 +108,7 @@
// jar as config files are in root(fix), obo files finally given dir
addFile(filename,urls); // full path or relative to pwd
addFile("conf/"+filename,urls);
+ addFile("images/"+filename,urls);
// ~/.phenote/obo-files cache for obo files - overrides phenote obo-files
// eventually may have configured obo dir as well...
addFile(getDotPhenoteOboDir().getPath()+"/"+filename,urls);
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|
|
From: <nl...@us...> - 2007-07-18 23:43:30
|
Revision: 743
http://svn.sourceforge.net/obo/?rev=743&view=rev
Author: nlw
Date: 2007-07-18 16:43:32 -0700 (Wed, 18 Jul 2007)
Log Message:
-----------
added new path to build file for images/
Modified Paths:
--------------
phenote/trunk/build.xml
Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml 2007-07-18 22:18:01 UTC (rev 742)
+++ phenote/trunk/build.xml 2007-07-18 23:43:32 UTC (rev 743)
@@ -194,7 +194,7 @@
<fileset dir="${classfiles}"/>
<fileset file="${obo}/*.obo"/>
<fileset file="${conf}/*.cfg"/>
- <fileset dir="${images}"/>
+ <fileset dir="${images}/*"/>
</jar>
</target>
@@ -205,7 +205,7 @@
<fileset dir="${classfiles}"/>
<fileset dir="." includes="obo-files/" excludes="obo-files/old"/>
<fileset file="${conf}/*.cfg"/>
- <fileset dir="${images}"/>
+ <fileset dir="." includes="images/"/>
</jar>
</target>
@@ -216,7 +216,7 @@
<fileset dir="${classfiles}"/>
<fileset dir="." includes="obo-files/" excludes="obo-files/old,obo-files/fma_obo.obo,obo-files/gene_ontology.obo,obo-files/chebi.obo" />
<fileset file="${conf}/*.cfg"/>
- <fileset dir="${images}"/>
+ <fileset dir="." includes="images/"/>
</jar>
</target>
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|
|
From: <mg...@us...> - 2007-07-18 22:18:11
|
Revision: 742
http://svn.sourceforge.net/obo/?rev=742&view=rev
Author: mgibson
Date: 2007-07-18 15:18:01 -0700 (Wed, 18 Jul 2007)
Log Message:
-----------
brought back splash - but its back for cmd line usage as well (sorry chris)
will actually take some finnagling to figure out that its full read & write
before the read & write happens
Modified Paths:
--------------
phenote/trunk/src/java/phenote/main/Phenote.java
Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java 2007-07-18 20:10:26 UTC (rev 741)
+++ phenote/trunk/src/java/phenote/main/Phenote.java 2007-07-18 22:18:01 UTC (rev 742)
@@ -80,7 +80,8 @@
System.out.println("Failed to set to Java/Metal look & feel");
}
phenote = getPhenote();
- boolean enableSplashScreen = phenote.commandLine.writeIsSpecified();
+ boolean enableSplashScreen = !phenote.commandLine.writeIsSpecified();
+ //System.out.println("splash "+enableSplashScreen);
phenote.splashScreenInit(enableSplashScreen); //initialize the splash screen;
phenote.doCommandLine(args); // does config
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|
|
From: <mg...@us...> - 2007-07-18 20:10:23
|
Revision: 741
http://svn.sourceforge.net/obo/?rev=741&view=rev
Author: mgibson
Date: 2007-07-18 13:10:26 -0700 (Wed, 18 Jul 2007)
Log Message:
-----------
and jetty util jar
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-18 20:07:43 UTC (rev 740)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-18 20:10:26 UTC (rev 741)
@@ -38,6 +38,7 @@
<jar href="jars/log4j-1.2.13.jar" />
<jar href="jars/jh.jar" />
<jar href="jars/jetty-6.1.4.jar" />
+ <jar href="jars/jetty-util-6.1.4.jar" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-18 20:07:43 UTC (rev 740)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-18 20:10:26 UTC (rev 741)
@@ -38,6 +38,7 @@
<jar href="jars/log4j-1.2.13.jar" />
<jar href="jars/jh.jar" />
<jar href="jars/jetty-6.1.4.jar" />
+ <jar href="jars/jetty-util-6.1.4.jar" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
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|
|
From: <mg...@us...> - 2007-07-18 20:07:40
|
Revision: 740
http://svn.sourceforge.net/obo/?rev=740&view=rev
Author: mgibson
Date: 2007-07-18 13:07:43 -0700 (Wed, 18 Jul 2007)
Log Message:
-----------
jetty jar for smart atlas jnlp
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-18 20:06:17 UTC (rev 739)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-18 20:07:43 UTC (rev 740)
@@ -37,6 +37,7 @@
<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" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
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|
|
From: <mg...@us...> - 2007-07-18 20:06:13
|
Revision: 739
http://svn.sourceforge.net/obo/?rev=739&view=rev
Author: mgibson
Date: 2007-07-18 13:06:17 -0700 (Wed, 18 Jul 2007)
Log Message:
-----------
jar for servlet for smart atlas
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-18 19:56:33 UTC (rev 738)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-18 20:06:17 UTC (rev 739)
@@ -37,6 +37,7 @@
<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" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
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|
|
From: <azu...@us...> - 2007-07-18 19:56:44
|
Revision: 738
http://svn.sourceforge.net/obo/?rev=738&view=rev
Author: azurebrd
Date: 2007-07-18 12:56:33 -0700 (Wed, 18 Jul 2007)
Log Message:
-----------
Updated worm.cfg to put Reference data in Reference tab instead of Main tab
Modified Paths:
--------------
phenote/trunk/conf/worm.cfg
Modified: phenote/trunk/conf/worm.cfg
===================================================================
--- phenote/trunk/conf/worm.cfg 2007-07-18 19:48:09 UTC (rev 737)
+++ phenote/trunk/conf/worm.cfg 2007-07-18 19:56:33 UTC (rev 738)
@@ -20,23 +20,26 @@
<auto-update-ontologies enable="true"/> <!--true=update; false=don't update-->
<update-timer timer="0"/><!--set to 0 if you want to bypass the check; time in seconds-->
+ <group name="referenceMaker" title="Reference Maker" container="tab" interface="default"/>
+ <group name="default" title="Main" container="tab" interface="default"/>
+
<field name="Object Type" enable="true"/>
<field name="Object Name" enable="true"/>
- <field name="Pub" syntax-abbrev="T" enable="true">
+ <field name="Pub" syntax-abbrev="T" enable="true" groups="referenceMaker">
<ontology name="Pub" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_obo.cgi"/>
</field>
- <field name="Person" syntax-abbrev="T" enable="true">
+ <field name="Person" syntax-abbrev="T" enable="true" groups="referenceMaker">
<ontology name="Person" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person_obo.cgi"/>
</field>
- <field name="NBP" syntax-abbrev="PhenotypeTextRemark" enable="true"/>
+ <field name="NBP" syntax-abbrev="PhenotypeTextRemark" enable="true" groups="referenceMaker"/>
- <field name="Reference Remark" syntax-abbrev="OtherRemark" enable="true"/>
+ <field name="Reference Remark" syntax-abbrev="OtherRemark" enable="true" groups="referenceMaker"/>
<field name="Genetic Intx Desc" syntax-abbrev="IntxDesc" enable="true"/>
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|
|
From: <mg...@us...> - 2007-07-18 19:48:07
|
Revision: 737
http://svn.sourceforge.net/obo/?rev=737&view=rev
Author: mgibson
Date: 2007-07-18 12:48:09 -0700 (Wed, 18 Jul 2007)
Log Message:
-----------
up the mbs - what the hell
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-18 19:45:01 UTC (rev 736)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-18 19:48:09 UTC (rev 737)
@@ -24,7 +24,7 @@
(JRE) that are supported by the application.
Multiple entries of this kind are allowed, in which
case they are considered to be in order of preference -->
- <j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
+ <j2se version="1.5+" initial-heap-size="64m" max-heap-size="600m" />
<jar href="jars/phenote.jar" />
<jar href="jars/oboedit.jar" />
<jar href="jars/org.geneontology.jar" />
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-18 19:45:01 UTC (rev 736)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-18 19:48:09 UTC (rev 737)
@@ -24,7 +24,7 @@
(JRE) that are supported by the application.
Multiple entries of this kind are allowed, in which
case they are considered to be in order of preference -->
- <j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
+ <j2se version="1.5+" initial-heap-size="64m" max-heap-size="600m" />
<jar href="jars/phenote.jar" />
<jar href="jars/oboedit.jar" />
<jar href="jars/org.geneontology.jar" />
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|
|
From: <mg...@us...> - 2007-07-18 19:45:00
|
Revision: 736
http://svn.sourceforge.net/obo/?rev=736&view=rev
Author: mgibson
Date: 2007-07-18 12:45:01 -0700 (Wed, 18 Jul 2007)
Log Message:
-----------
ooh i hope this does the trick - im in webstart hell - but i think the issue
is that jh.jar already had a sun signfile in it and it was screwing everything
up - so i redid the jar and took out the sign file - hopefully this will work
Modified Paths:
--------------
phenote/trunk/jars/jh.jar
Modified: phenote/trunk/jars/jh.jar
===================================================================
(Binary files differ)
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|
|
From: <nl...@us...> - 2007-07-18 18:50:05
|
Revision: 735
http://svn.sourceforge.net/obo/?rev=735&view=rev
Author: nlw
Date: 2007-07-18 11:49:54 -0700 (Wed, 18 Jul 2007)
Log Message:
-----------
s
--This line, and those below, will be ignoredupdates to the release notes--
M phenote-website/phenote-release-notes.html
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-release-notes.html
Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-07-18 18:16:56 UTC (rev 734)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-07-18 18:49:54 UTC (rev 735)
@@ -57,6 +57,7 @@
<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>
</ul>
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|
|
From: <mg...@us...> - 2007-07-18 18:16:56
|
Revision: 734
http://svn.sourceforge.net/obo/?rev=734&view=rev
Author: mgibson
Date: 2007-07-18 11:16:56 -0700 (Wed, 18 Jul 2007)
Log Message:
-----------
jars for jnlp jh.jar
release notes,
for 1.4-beta2
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-release-notes.html
phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
phenote/trunk/doc/phenote-website/phenote.html
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-07-18 16:53:44 UTC (rev 733)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-07-18 18:16:56 UTC (rev 734)
@@ -2,350 +2,512 @@
<html>
<head>
+
+
<meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
+
+
<title>Phenote Release Notes</title>
</head>
<body>
+
<h1>Phenote Release Notes</h1>
+
<h2>1.4 </h2>
-<h3>version 1.4beta1 - in development</h3>
+<h3>version 1.4-beta2</h3>
<ul>
+ <li>feature: help </li>
+ <li>feature: RESTful data input for birn's smart atlas</li>
+ <li>feature: Character Template for nescent/ctol (Jim Balhoff)</li>
+ <li>feature: Progress on gui for config (in progress)</li>
+ <li>feature: Progress on field groups (genotype maker, pub querying...)</li>
+ <li>change: Command line read & write of .tab</li>
+ <li>change: Not dropping obsolete terms</li>
+ <li>.... and more...</li>
+</ul>
+<h3>version 1.4-beta1 - in development</h3>
+
+
+<ul>
+
<li>feature: right-click editing functions for free-text fields in data input frame. right-click copy in table.</li>
- <li>feature: incorporation of help documentation into Phenote under menu item Help->PhenoteHelp </li>
-<li>feature: added plant_grammene.cfg configuration, plus appropriate obo files.</li>
-<li>feature: navigation bar added to top of term info; buttons to traverse worn paths; term name moved up to top of box [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1685540&group_id=76834&atid=887913">1685540</a>]</li>
-<li>feature: dbxrefs are listed in term info (no external links yet) [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1739399&group_id=76834&atid=887913">1739399</a>]</li>
-<li>change: 'use term' button moved and replaced with checkmark button in navigation bar</li>
-<li>change: 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>feature: incorporation of help documentation into Phenote under menu item Help->PhenoteHelp </li>
+
+ <li>feature: added plant_grammene.cfg configuration, plus appropriate obo files.</li>
+
+ <li>feature: navigation bar added to top of term info; buttons to traverse worn paths; term name moved up to top of box [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1685540&group_id=76834&atid=887913">1685540</a>]</li>
+
+ <li>feature: dbxrefs are listed in term info (no external links yet) [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1739399&group_id=76834&atid=887913">1739399</a>]</li>
+
+ <li>change: 'use term' button moved and replaced with checkmark button in navigation bar</li>
+
+ <li>change: 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>
+
</ul>
+
<h2>1.3</h2>
+
05.24.2007, version <a href="phenote/1.3/phenote.jnlp">1.3 release</a><br>
+
<ul>
+
<li>feature: <a href="http://www.phenote.org/help/">Web-based documentation and Help features.</a></li>
+
<li>feature: Metadata fields added to configuration. User can name their configuration, add a description, and author [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1676756&group_id=76834&atid=887913">1676756</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1672080&group_id=76834&atid=887913">1672080</a>]</li>
+
<li>feature: Descriptions can be added for fields </li>
+
<li>feature: Master-to-local overwrite stuff</li>
+
<li>feature: Dialog allows user to back out of exiting from File->Exit</li>
+
<li>feature: Autocompletion search default settings configurable <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1677411&group_id=76834&atid=887913">1677411</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1669579&group_id=76834&atid=887913">1669579</a>]
</li>
+
<li>feature: User can save search setting defaults if changed during Phenote session</li>
+
<li>change: File->New is disabled until next version</li>
+
<li>change: ncbo, zfin-standalone, flybase, demo configurations
modified to include master-overwrite feature; keeping track of revision
history in file comments </li>
+
<li>change: can read http, https, ftp, ftps for ontology update URLs, not just http [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1718945&group_id=76834&atid=887913">1718945</a>]</li>
+
<li>bugfix: Bulk-editing functions are working again</li>
+
<li>bugfix: Undo wasn't working for several functions due to a bug in the Copy function [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721044&group_id=76834&atid=887913"> 1721044</a>]</li>
+
<li>bugfix: multi-select deletes free-text content replaces with * [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721032&group_id=76834&atid=887913">1721032</a>]</li>
+
<li>bugfix: pre 1.2 post comp data wasnt able to load<big> </big>[<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721470&group_id=76834&atid=887913">1721470</a>]</li>
+
</ul>
+
05.09.2007, version <a href="phenote/1.3-beta1/phenote.jnlp">1.3-beta1</a><br>
+
<ul>
+
<li>feature: Added sample config for BIRN</li>
+
<li>feature: Added SAO.obo ontology for BIRN</li>
+
<li>feature: Namespace config writes back</li>
+
<li>feature: Can specify more than one website for ontology update</li>
+
<li>feature: Empty field shows all terms in ontology rather than none</li>
+
<li>feature: Can add more differentia to post comp</li>
+
<li>bugfix: Config update/merge bug where fields in wrong order fixed.</li>
+
<li>known bug: can't read post-compositions from phenote versions 1.1 and prior</li>
+
</ul>
+
<h2>1.2
<hr></h2>
+
05.02.2007, version <a href="phenote/1.2/phenote.jnlp">1.2</a><br>
+
<ul>
+
<li>feature: Can post-compose with >2 terms </li>
+
<li>feature: Term history display can be toggled on/off (Settings->Term History menu)</li>
+
<li>feature: Synonyms delineated by scope in Term Info: Exact,
Narrow, Broad, General, Related. If the synonym category is given, it
is displayed. For example, the term 'water' has the <i>related</i> synonym H2O, which has the category of a chemical <i>formula</i>.</li>
+
<li>feature: Obsolete replacements or consideration terms are displayed in term info with links</li>
+
<li>feature: Display term comments in Term Info beneath relationships</li>
-<li>feature: Loading splash screen </li>
+ <li>feature: Loading splash screen </li>
+
+
<li>feature: Can configure by namespace for ontologies</li>
+
<li>feature: Can automatically update ontologies during startup (configurable)</li>
+
<li>feature: Timer added to configuration during ontology update check (configurable)</li>
+
<li>feature: Can check which version of phenote is running by selecting Help->About.</li>
+
<li>feature: Added common configuration for OMIM curation for use by NCBO (ncbo.cfg).</li>
+
<li>feature: can forward and reverse sort columns by repeatedly clicking on column header [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574916&group_id=76834&atid=887913">1574916</a>]</li>
+
<li>feature: display ontology namespace in term info box [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1598048&group_id=76834&atid=887913">1598048</a>]</li>
+
<li>change: Search filters moved into menu </li>
+
<li>change: Updates to the zfin-standalone.cfg for the zebrafish community annotation; only includes GO and ZFanatomy ontologies. </li>
+
<li>bugfix: Free-text field text not sticking in "new" or blank rows </li>
+
</ul>
+
<h2>1.1
<hr></h2>
+
04.06.2007, version <a href="phenote/1.1/phenote.jnlp">1.1.3</a><br>
+
<ul>
+
<li>feature: User can change the configuration they want to use at
initialization from file menu; change takes effect after restart.
(previously user had to edit the .phenote/conf/my-phenote file).</li>
+
</ul>
+
03.28.2007, version 1.1.1<br>
+
<ul>
+
<li>feature: Phenote is now a single webstart app; user chooses
their configuration at startup (used to be hard wired to a
configuration)</li>
+
<li>feature: Phenote will merge its default configuration with users' configuration,
preserving user changes as well as adding anything new from phenote
upgrade.</li>
+
<li>feature: Beginnings of term history to display recently used ontology terms. Will be clickable in future.</li>
+
<li>feature: Data entry panel will spill over into multiple tabs if >12 fields included</li>
+
<li>feature: Tab delimited data adapter; data in/output format compatible with excel and other spreadsheet software [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661778&group_id=76834&atid=887913">1661778</a>]</li>
+
<li>feature: QueryableDataAdapter interface for developers; enables
connection between input fields and a database backend for quering.
Queryable fields get a retrieve button.</li>
+
<li>feature: Autocompletion search with ALL ontologies in a field instead of just one [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1575241&group_id=76834&atid=887913">1575241</a>]</li>
+
<li>feature: Retrieve ontology files from URL if more up to date or no local found; only from a single repository for all [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1648337&group_id=76834&atid=887913">1648337</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574906&group_id=76834&atid=887913">1574906</a>]</li>
+
<li>feature: fixed releases available for checkout via sourceforge [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1670345&group_id=76834&atid=887913">1670345</a>]</li>
+
<li>feature: display xtns in load/save menu choices [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1594508&group_id=76834&atid=887913">1594508</a>]</li>
+
<li>change: Refactored code for field guis</li>
+
<li>change: Layout improved</li>
+
<li>change: OBSOLETE is displayed in red next to obsolete term in term info [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1581589&group_id=76834&atid=887913">1581589</a>]</li>
+
<li>change: human.cfg configuration to include obo foundary ontologies GO, SO, CL, ChEBI, PATO, OBI, Relations, unit, and spatial [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1633287&group_id=76834&atid=887913">1633287</a>]</li>
+
<li>bugfix: Ontology chooser reflects current term</li>
+
<li>bugfix: phenosyntax reader broken [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1684591&group_id=76834&atid=887913">1684591</a>]</li>
+
<li>bugfix: post-composed terms not loading [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661728&group_id=76834&atid=887913">1661728</a>]</li>
+
</ul>
+
<h2>1.0
<hr></h2>
+
02.06.2007, version <a href="phenote/1.0/phenote-flybase.jnlp">1.0.5-fly</a>, <a href="1.0/phenote-zfin.jnlp">1.0.5-zfin</a><br>
+
01.12.2007, version1.0,
<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby
Phenote(components used by Zfin)</a><br>
+
<ul>
+
<li>change: refactoring of the data model to allow addition of any
field desired, not just E,Q,GC,GT,Pub. Stage, Evidence, Description,
Abnormal, and Absent have been added through this new mechanism in the
newest configurations. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574912&group_id=76834&atid=887913">1574912</a>]</li>
+
<li>change: Webby phenote is now using JSP and Spring.</li>
+
<li>change: There has been some recent work with UVictoria for ontology graph
visualization. This is coming along well and hopefully will be seen in
the next release.</li>
+
<li>bugfix: absent fields not displaying in human 1.03 [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661973&group_id=76834&atid=887913">1661973</a>]</li>
+
</ul>
+
<h2>0.9
<hr></h2>
+
11.15.2006, version <a href="phenote/0.9/phenote-flybase.jnlp">0.9-fly</a>,
<a href="phenote/0.9/phenote-zfin.jnlp">0.9-zfin</a>,
<a href="http://165.124.152.194/web/html/interface.html">DictyBase
webby phenote</a><br>
+
11.09.2006, version 0.9<br>
+
<ul>
+
<li>feature: Undo - can step backward through previous actions</li>
+
<li>feature: Quartz scheduler used to schedule when to check for new obo files. Added by Christian Pich of Zfin. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1588669&group_id=76834&atid=887913">1588669</a>]</li>
+
<li>change: upgraded PhenoteServlet to Spring framework. Added by Christian Pich [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1588670&group_id=76834&atid=887913">1588670</a>]</li>
+
<li>feature: Synonyms are displayed from autocomplete with [syn]; when
selected the term name (not the synonym) goes into the field and table (webby & standalone)</li>
+
<li>feature: obsoletes are displayed from autocomplete with [obs]</li>
+
<li>feature: Bulk update & copy in standalone. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1579885&group_id=76834&atid=887913">1579885</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1579882&group_id=76834&atid=887913">1579882</a>] </li>
+
<li>change: search types interface changed from radio buttons to checkboxes (j. balhoff)</li>
+
<li>bugfix: file-save button changed to say "save" not "load"
</li>
+
<li>feature: file-save recognizes and chooses appropriate data
adapter based on file extension (.psx for phenosyntax and .xml for
phenoxml)</li>
+
<li>change: Single quotes escaped for javascript fns.</li>
+
</ul>
+
<h2>0.8
<hr></h2>
+
10.02.2006, version <a href="phenote/0.8/phenote-flybase.jnlp">0.8-fly</a>,
<a href="phenote/0.8/phenote-zfin.jnlp">0.8-zfin</a>,
<a href="http://165.124.152.194/web/html/interface.html">DictyBase
webby phenote</a><br>
+
<ul>
+
<li>feature: Added post composition to standalone phenote. </li>
+
<li>feature: Actions are logged for both webby/servlet & standalone.</li>
+
<li>feature: Pheno-xml reader (thanks to Jim Balhoff) and improvements to pheno-xml
writer (does pub & genetic context)</li>
+
<li> feature: Command line reading & writing of phenoxml & phenosyntax.</li>
+
<li>feature: Application exits on window exit (unless servlet)</li>
+
<li>feature: Can filter out stage terms from zfin anatomy</li>
+
</ul>
+
<h2>0.7
<hr></h2>
+
08.23.2007, version <a href="phenote/0.7/phenote-flybase.jnlp">0.7-fly.</a>,
<a href="0.7/phenote-zfin.jnlp">0.7-zfin</a><br>
+
<ul>
+
<li>feature: entity chooser (web)</li>
+
<li>feature: can configure to check for new obo files and load
them. (These are installed at zfin, if anyone would like to see them
publicly let me know).</li>
+
<li>feature: entity field and term info installed into zfin (web)
phenotype site. Term info & completion are scrollable.</li>
+
<li>feature: standalone version can read & write pheno-syntax with ids & term names in comments</li>
+
<li>feature: standalone entity chooser</li>
+
<li>feature: added pub field</li>
+
<li>feature: added 'use term' button in term info</li>
+
<li>feature: can sort table by any field in forward order by clicking on headers</li>
+
<li>change: personal config file gets copied out of jar
</li>
+
<li>change: directory for file load/save remembered</li>
+
<li>change: layout fixed</li>
+
<li>bugfix: paste for mac fixed</li>
+
</ul>
+
<h2>0.6
<hr></h2>
+
07.28.2006, version <a href="phenote/0.6/phenote-flybase.jnlp">0.6-fly</a>, <a href="phenote/0.6/phenote-zfin.jnlp">0.6-zfin</a>,
<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote
(0.6)</a><br>
+
<ul>
+
<li>new: webbified phenote. This is in its extremely early stages
(very little functionality and buggy). At this point it only does
Entity and Quality fields and term info and thats it, and even thats
buggy, but more coming soon! </li>
+
<li> feature: writing pheno-xml format, and uses the latest
PATO ontology (as of July 28, 2006).</li>
+
</ul>
+
<h2>0.5
<hr></h2>
+
05.12.2006, version <a href="phenote/0.5/phenote-flybase.jnlp">0.5-FlyBase</a>, <a href="phenote/0.5/phenote-zfin.jnlp">0.5-ZFIN</a><br>
+
<p>
No new additions to the gui here. In preparation for my visit to
Cambridge/FlyBase, I worked on a FlyBase dataadapter. This is phenote
@@ -360,19 +522,26 @@
character strings.</p>
+
<h2>0.4
<hr></h2>
+
04.26.2006, version <a href="phenote/0.4/phenote-flybase.jnlp">0.4-flybase</a>, <a href="phenote/0.4/phenote-zfin.jnlp">0.4-zfin</a><br>
+
<ul>
+
<li>feature: Added Genetic Context field.</li>
+
<li>feature: Parent & child terms in term info are now clickable/navigable.</li>
+
<li>feature: HTML Links in descriptions are clickable (should bring up default browser)</li>
+
<li>feature: configuration files to configure ontologies & fields. This is
currently at a devloper level (xml file) not a user level(gui - todo).
There is a command line argument for which configuration file to use.
@@ -381,10 +550,13 @@
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 & adding field.
Made the internal code much more generic for adding new fields from
configuration, got rid of a lot of hard wiring. Part of this was
@@ -393,96 +565,134 @@
easier to plop a web gui on top of the current phenote model &
controller.</li>
+
<li>Development: Renamed Phenotype to Character. Added Character interface CharacterI.</li>
+
<li>Development: Added tests to test suite.</li>
+
</ul>
+
<h2>0.3
<hr></h2>
+
04.07.2006, version <a href="phenote/0.3/phenote-webstart.jnlp">0.3</a>, <a href="phenote/0.3.1/phenote-webstart.jnlp">0.3.1 (for CToL)</a><br>
+
<p>Note: 0.3.1 is identical to 0.3 except that it has ontologies for CToL
(fish evolution group). In particular it uses a fish taxonomy<br>
+
ontology for the id (in this taxonomy) choosing. On the todo is the
ability to configure ontologies, but not there yet, so for now need to
hardwire with seaparate jar file. This clearly makes the todo item a
bit more pressing.</p>
+
<p> Release for NESCent fish eveolution meeting. No major new functionality
here. Cleaned up and fixed a lot of the bugs in 0.2, which was rather
buggy.</p>
+
<ul>
+
<li>feature: Completion terms now sorted alphabeitcally.</li>
+
<li>feature: Obsoletes are now in addition to regular terms, not in lieu of.</li>
+
<li>feature: Filtering out attribute values (todo: change to actually filter in
values)</li>
+
<li>change: Html formatting of term info (todo: make terms selectable)</li>
+
<li>feature: Children relations are in term info</li>
+
<li>change: Term info layout greatly improved</li>
+
<li>change: Term info in scroller</li>
+
<li>change: Border with label around term info</li>
+
<li>change: Put definition at end of term info</li>
+
<li>bugfix: Backspace in ontology combo box</li>
+
<li>bugfix: Selection of item in comp list causing exception, not going in term box</li>
+
<li>bugfix: No terms with just 1 char</li>
+
<li>bugfix: Popup was staying up after selection</li>
+
<li>development: Test suite added! (todo: add more tests)</li>
+
<li>development: Migrated to jdk 1.5 (which caused some of the bugs above)</li>
+
<li>development: Ant file made build.xml.</li>
+
<li>development: CompletionList refactored into Ontology (prompted by sorting)</li>
+
</ul>
+
<h2>0.2
<hr></h2>
+
03.27.2006, version <a href="phenote/0.2/phenote-webstart.jnlp">0.2</a><br>
+
<ul>
+
<li>feature: term completion on Synonyms, Definitions and Obsoletes</li>
+
<li>feature: mouse-over on term in completion list displays info in 'term info' text area</li>
+
<li>Todo: layout, scrollbar, border w title, ordering & lumping
parents
& children, formatting. Also perhaps have children & parents be
clickable in some fashion either html-like clickable text or as buttons.</li>
+
<li>known bugs: If you hit backspace in term completion fields it gets wacky </li>
+
</ul>
+
<h2>0.1
<hr></h2>
+
03.01.2006, version <a href="phenote/0.1/phenote-webstart.jnlp">0.1</a><br>
+
<p> 0.1 was the initial phenote release (known briefly as the plumper at
the time). It just had a genotype, anatomy and pato fields, where
anatomy and pato did term completion (just on term names) with there
@@ -491,5 +701,6 @@
limited functionality was demo'd at the cbio meeting 3/3/06 at Stanford.</p>
+
</body>
</html>
Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-18 16:53:44 UTC (rev 733)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-18 18:16:56 UTC (rev 734)
@@ -36,6 +36,7 @@
<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" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
Modified: phenote/trunk/doc/phenote-website/phenote.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.html 2007-07-18 16:53:44 UTC (rev 733)
+++ phenote/trunk/doc/phenote-website/phenote.html 2007-07-18 18:16:56 UTC (rev 734)
@@ -11,6 +11,7 @@
+
@@ -21,6 +22,7 @@
+
<meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
@@ -32,6 +34,7 @@
+
@@ -42,6 +45,7 @@
+
<title>Phenote</title>
</head>
@@ -57,6 +61,7 @@
+
<h1 style="text-align: left;"><span style="font-weight: bold;"></span>Phenote<br>
@@ -68,6 +73,7 @@
+
</h1>
@@ -79,6 +85,7 @@
+
<br>
@@ -90,6 +97,7 @@
+
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
@@ -104,7 +112,10 @@
+
<br>
+<a href="1.4-beta2/phenote.jnlp">Phenote 1.4-beta2</a><br>
+<br>
@@ -114,16 +125,20 @@
+
<a href="1.3/phenote.jnlp">Phenote 1.3</a><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>
@@ -135,9 +150,12 @@
+
<a href="phenote-release-notes.html">Phenote Release Notes and old
webstart releases</a><br>
+
<br>
+
Recent addditions include the ability to update config while preserving
your changes, change config, tab delimited format, tabbed field panel,
retrieve ontologies from web, retrieve from field to database, search
@@ -154,6 +172,7 @@
+
<br>
@@ -165,6 +184,7 @@
+
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
@@ -180,6 +200,7 @@
+
<br>
@@ -191,6 +212,7 @@
+
<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby
Phenote(components used by Zfin)</a><br>
@@ -203,6 +225,7 @@
+
<br>
@@ -214,6 +237,7 @@
+
Webby phenote is a collaboration with Sohel Merchant at dictyBase, and Christian Pich & Kevin Schaper at zfin.
Here is what Dicty has done:<br>
@@ -226,6 +250,7 @@
+
<br>
@@ -237,6 +262,7 @@
+
<a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DictyBase
webby phenote</a><br>
@@ -249,6 +275,7 @@
+
<br>
@@ -260,6 +287,7 @@
+
<br>
@@ -271,6 +299,7 @@
+
We would love to get your feedback! Please report any bugs (ideally through the <a href="https://sourceforge.net/tracker/?group_id=76834&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>
@@ -284,6 +313,7 @@
+
<br>
@@ -295,6 +325,7 @@
+
<h4>Phenote links:<br>
@@ -306,6 +337,7 @@
+
</h4>
@@ -317,6 +349,7 @@
+
<a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Phenote
email list</a><br>
@@ -329,6 +362,7 @@
+
<a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">Phenote
bug tracker</a><br>
@@ -341,6 +375,7 @@
+
<a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-bug-tracker">Bug
tracker email list</a><br>
@@ -353,6 +388,7 @@
+
<a href="https://sourceforge.net/svn/?group_id=76834">Phenote source
code (obo sourceforge svn)</a><br>
@@ -365,6 +401,7 @@
+
<a href="https://lists.sourceforge.net/lists/listinfo/obo-svn-commit">Phenote
svn commit email list</a><br>
@@ -377,6 +414,7 @@
+
<a href="http://wiki.dictybase.org/dictywiki/index.php/Phenotype_Curation_Tool_Documentation#Usage">Dicty
webby phenote wiki developer docs</a><br>
@@ -389,6 +427,7 @@
+
<a href="http://www.bioontology.org/wiki-internal/index.php/Phenotype_Annotation_Tool">Phenote
ncbo internal wiki (ncbo folk only)</a><br>
@@ -396,10 +435,12 @@
+
<a href="developer-docs/dataadapter.html">Phenote dataadapter developer doc</a><br>
+
<a href="developer-docs/developer-docs.html">More developer docs</a><br>
@@ -411,6 +452,7 @@
+
<br>
@@ -422,6 +464,7 @@
+
<br>
@@ -433,6 +476,7 @@
+
If the Phenote webstart link fails to do anything, then there are
probably problems
with webstart and/or java(has to be jdk 1.5). Take a look at the <a href="webstart-troubleshooting.html">webstart troubleshooting</a><br>
@@ -446,6 +490,7 @@
+
page.<br>
@@ -457,6 +502,7 @@
+
<br>
@@ -468,6 +514,7 @@
+
Click here for <a href="phenote-java-requirements.html">phenote java
requirements</a><br>
@@ -480,6 +527,7 @@
+
<br>
@@ -491,6 +539,7 @@
+
<br>
@@ -502,6 +551,7 @@
+
<br>
@@ -513,6 +563,7 @@
+
Old releases: <br>
@@ -524,11 +575,15 @@
+
<a href="1.3-beta1/phenote.jnlp">Phenote 1.3-beta1</a><br>
+
<a href="1.2/phenote.jnlp">Phenote 1.2</a><br>
+
<a href="1.1/phenote.jnlp">Phenote 1.1</a><br>
+
<a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br>
@@ -540,6 +595,7 @@
+
<a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br>
@@ -550,6 +606,7 @@
+
<a href="1.0/phenote-human.jnlp">Phenote 1.0 for human</a><br>
@@ -558,6 +615,7 @@
+
<br>
@@ -569,6 +627,7 @@
+
<a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br>
@@ -580,6 +639,7 @@
+
<a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br>
@@ -590,6 +650,7 @@
+
<br>
@@ -600,6 +661,7 @@
+
<a href="0.8/phenote-flybase.jnlp">Phenote 0.8 for fly.</a><br>
@@ -611,6 +673,7 @@
+
<a href="0.8/phenote-zfin.jnlp">Phenote (standalone) 0.8 for zfin</a><br>
@@ -622,6 +685,7 @@
+
<br>
@@ -633,6 +697,7 @@
+
<a href="0.7/phenote-flybase.jnlp">Phenote 0.7 for fly.</a><br>
@@ -644,6 +709,7 @@
+
<a href="0.7/phenote-zfin.jnlp">Phenote (standalone) 0.7 for zfin</a><br>
@@ -655,6 +721,7 @@
+
<br>
@@ -666,6 +733,7 @@
+
<a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br>
@@ -677,6 +745,7 @@
+
<br>
@@ -688,6 +757,7 @@
+
<a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br>
@@ -699,6 +769,7 @@
+
<br>
@@ -710,6 +781,7 @@
+
<a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br>
@@ -721,6 +793,7 @@
+
<br>
@@ -732,6 +805,7 @@
+
<a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br>
@@ -743,6 +817,7 @@
+
<br>
@@ -754,6 +829,7 @@
+
<a href="0.4/phenote-flybase.jnlp">Phenote 0.4 webstart for FlyBase</a><br>
@@ -765,6 +841,7 @@
+
<br>
@@ -776,6 +853,7 @@
+
<a href="0.4/phenote-zfin.jnlp">Phenote 0.4 webstart for ZFIN</a><br>
@@ -787,6 +865,7 @@
+
<br>
@@ -798,6 +877,7 @@
+
<a href="0.3.1/phenote-webstart.jnlp">Phenote for CToL group (0.3.1)</a>
(a special release for the CToL group that uses fish
taxonomy)<br>
@@ -811,6 +891,7 @@
+
<br>
@@ -822,6 +903,7 @@
+
<a href="0.3/phenote-webstart.jnlp">Phenote 0.3</a><br>
@@ -833,6 +915,7 @@
+
<br>
@@ -844,6 +927,7 @@
+
<a href="0.2/phenote-webstart.jnlp">Phenote 0.2</a><br>
@@ -855,6 +939,7 @@
+
<br>
@@ -866,6 +951,7 @@
+
<a href="0.1/phenote-webstart.jnlp">Phenote 0.1</a><br>
@@ -877,6 +963,7 @@
+
<br>
@@ -888,6 +975,7 @@
+
<br>
@@ -899,5 +987,6 @@
+
</body>
</html>
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-18 16:53:44 UTC (rev 733)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-18 18:16:56 UTC (rev 734)
@@ -36,6 +36,7 @@
<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" />
</resources>
<!-- no cmd line param will ask user for config at initialization -->
<application-desc main-class="phenote.main.Phenote">
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <dj...@us...> - 2007-07-18 16:53:50
|
Revision: 733
http://svn.sourceforge.net/obo/?rev=733&view=rev
Author: djs93
Date: 2007-07-18 09:53:44 -0700 (Wed, 18 Jul 2007)
Log Message:
-----------
fly development and fly controlled vocabulary ontologies added to obo files
Added Paths:
-----------
phenote/trunk/obo-files/fly_development.obo
phenote/trunk/obo-files/flybase_controlled_vocabulary.obo
Added: phenote/trunk/obo-files/fly_development.obo
===================================================================
--- phenote/trunk/obo-files/fly_development.obo (rev 0)
+++ phenote/trunk/obo-files/fly_development.obo 2007-07-18 16:53:44 UTC (rev 733)
@@ -0,0 +1,803 @@
+format-version: 1.0
+date: 22:09:2006 17:12
+saved-by: David
+auto-generated-by: OBO-Edit 1.002
+default-namespace: fly_development.ontology
+remark: made from FlyBase: Version 480.
+remark: Corrections to ma...@ge...
+remark: Drosophila temporal ontology.
+
+[Term]
+id: FBdv:00000054
+name: cleavage stage
+def: "A collective term for stages 1-4." [FB:DJS]
+relationship: part_of FBdv:00005289 ! embryonic stage
+
+[Term]
+id: FBdv:00004450
+name: late extended germ band stage
+def: "A collective term for stages 11 and 12." [FB:DJS]
+relationship: part_of FBdv:00005321 ! extended germ band stage
+relationship: preceded_by FBdv:00014201 ! early extended germ band stage
+
+[Term]
+id: FBdv:00004886
+name: oogenesis stage
+relationship: part_of FBdv_root:00000000 ! Drosophila life cycle
+
+[Term]
+id: FBdv:00005261
+name: oogenesis stage S1
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00004886 ! oogenesis stage
+
+[Term]
+id: FBdv:00005262
+name: oogenesis stage S2
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00004886 ! oogenesis stage
+relationship: preceded_by FBdv:00005261 ! oogenesis stage S1
+
+[Term]
+id: FBdv:00005263
+name: oogenesis stage S3
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00004886 ! oogenesis stage
+relationship: preceded_by FBdv:00005262 ! oogenesis stage S2
+
+[Term]
+id: FBdv:00005264
+name: oogenesis stage S4
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00004886 ! oogenesis stage
+relationship: preceded_by FBdv:00005263 ! oogenesis stage S3
+
+[Term]
+id: FBdv:00005265
+name: oogenesis stage S5
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00004886 ! oogenesis stage
+relationship: preceded_by FBdv:00005264 ! oogenesis stage S4
+
+[Term]
+id: FBdv:00005266
+name: oogenesis stage S6
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00004886 ! oogenesis stage
+relationship: preceded_by FBdv:00005265 ! oogenesis stage S5
+
+[Term]
+id: FBdv:00005267
+name: oogenesis stage S7
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00004886 ! oogenesis stage
+relationship: preceded_by FBdv:00005266 ! oogenesis stage S6
+
+[Term]
+id: FBdv:00005268
+name: oogenesis stage S8
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00004886 ! oogenesis stage
+relationship: preceded_by FBdv:00005267 ! oogenesis stage S7
+
+[Term]
+id: FBdv:00005269
+name: oogenesis stage S9
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00004886 ! oogenesis stage
+relationship: preceded_by FBdv:00005268 ! oogenesis stage S8
+
+[Term]
+id: FBdv:00005270
+name: oogenesis stage S10
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00004886 ! oogenesis stage
+
+[Term]
+id: FBdv:00005271
+name: oogenesis stage S10A
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00005270 ! oogenesis stage S10
+relationship: preceded_by FBdv:00005269 ! oogenesis stage S9
+
+[Term]
+id: FBdv:00005272
+name: oogenesis stage S10B
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00005270 ! oogenesis stage S10
+relationship: preceded_by FBdv:00005271 ! oogenesis stage S10A
+
+[Term]
+id: FBdv:00005273
+name: oogenesis stage S11
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00004886 ! oogenesis stage
+relationship: preceded_by FBdv:00005272 ! oogenesis stage S10B
+
+[Term]
+id: FBdv:00005274
+name: oogenesis stage S12
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00004886 ! oogenesis stage
+
+[Term]
+id: FBdv:00005275
+name: oogenesis stage S12A
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00005274 ! oogenesis stage S12
+relationship: preceded_by FBdv:00005273 ! oogenesis stage S11
+
+[Term]
+id: FBdv:00005276
+name: oogenesis stage S12B
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00005274 ! oogenesis stage S12
+relationship: preceded_by FBdv:00005275 ! oogenesis stage S12A
+
+[Term]
+id: FBdv:00005277
+name: oogenesis stage S12C
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00005274 ! oogenesis stage S12
+relationship: preceded_by FBdv:00005276 ! oogenesis stage S12B
+
+[Term]
+id: FBdv:00005278
+name: oogenesis stage S13
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00004886 ! oogenesis stage
+relationship: preceded_by FBdv:00005274 ! oogenesis stage S12
+
+[Term]
+id: FBdv:00005279
+name: oogenesis stage S13A
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00005278 ! oogenesis stage S13
+relationship: preceded_by FBdv:00005277 ! oogenesis stage S12C
+
+[Term]
+id: FBdv:00005280
+name: oogenesis stage S13B
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00005278 ! oogenesis stage S13
+relationship: preceded_by FBdv:00005279 ! oogenesis stage S13A
+
+[Term]
+id: FBdv:00005281
+name: oogenesis stage S13C
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00005278 ! oogenesis stage S13
+relationship: preceded_by FBdv:00005280 ! oogenesis stage S13B
+
+[Term]
+id: FBdv:00005282
+name: oogenesis stage S13D
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00005278 ! oogenesis stage S13
+relationship: preceded_by FBdv:00005281 ! oogenesis stage S13C
+
+[Term]
+id: FBdv:00005283
+name: oogenesis stage S14
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00004886 ! oogenesis stage
+relationship: preceded_by FBdv:00005278 ! oogenesis stage S13
+
+[Term]
+id: FBdv:00005284
+name: oogenesis stage S14A
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00005283 ! oogenesis stage S14
+relationship: preceded_by FBdv:00005282 ! oogenesis stage S13D
+
+[Term]
+id: FBdv:00005285
+name: oogenesis stage S14B
+def: "." [FB:FBrf0021038]
+relationship: part_of FBdv:00005283 ! oogenesis stage S14
+relationship: preceded_by FBdv:00005284 ! oogenesis stage S14A
+
+[Term]
+id: FBdv:00005286
+name: egg stage
+relationship: part_of FBdv_root:00000000 ! Drosophila life cycle
+
+[Term]
+id: FBdv:00005287
+name: unfertilized egg stage
+relationship: part_of FBdv:00005286 ! egg stage
+relationship: preceded_by FBdv:00005283 ! oogenesis stage S14
+relationship: preceded_by FBdv:00005285 ! oogenesis stage S14B
+
+[Term]
+id: FBdv:00005288
+name: fertilized egg stage
+relationship: part_of FBdv:00005286 ! egg stage
+relationship: preceded_by FBdv:00005287 ! unfertilized egg stage
+
+[Term]
+id: FBdv:00005289
+name: embryonic stage
+relationship: part_of FBdv_root:00000000 ! Drosophila life cycle
+
+[Term]
+id: FBdv:00005290
+name: pre-blastoderm stage
+related_synonym: "pre-blastoderm" []
+relationship: part_of FBdv:00005289 ! embryonic stage
+
+[Term]
+id: FBdv:00005291
+name: embryonic stage 1
+def: "Nuclear divisions 1 and 2. Duration at 25 degrees C\\: approximately 25 minutes (0-25 minutes after egg laying)" [FB:FBrf0089570]
+relationship: part_of FBdv:00000054 ! cleavage stage
+relationship: part_of FBdv:00005290 ! pre-blastoderm stage
+relationship: preceded_by FBdv:00005288 ! fertilized egg stage
+
+[Term]
+id: FBdv:00005292
+name: embryonic cycle 1
+relationship: part_of FBdv:00005291 ! embryonic stage 1
+
+[Term]
+id: FBdv:00005293
+name: embryonic stage 2
+def: "Nuclear divisions 3-8. The egg cytoplasm contracts producing a clear separation from the vitelline membrane and empty spaces at the anterior and posterior. The cleavage nuclei migrate towards the periphery. Duration at 25 degrees C approximately 40 minutes (25-65 minutes AEL)." [FB:FBrf0089570]
+relationship: part_of FBdv:00000054 ! cleavage stage
+relationship: part_of FBdv:00005290 ! pre-blastoderm stage
+relationship: preceded_by FBdv:00005291 ! embryonic stage 1
+
+[Term]
+id: FBdv:00005294
+name: embryonic cycle 2
+relationship: part_of FBdv:00005293 ! embryonic stage 2
+
+[Term]
+id: FBdv:00005295
+name: embryonic cycle 3
+relationship: part_of FBdv:00005293 ! embryonic stage 2
+relationship: preceded_by FBdv:00005294 ! embryonic cycle 2
+
+[Term]
+id: FBdv:00005296
+name: embryonic cycle 4
+relationship: part_of FBdv:00005293 ! embryonic stage 2
+relationship: preceded_by FBdv:00005295 ! embryonic cycle 3
+
+[Term]
+id: FBdv:00005297
+name: embryonic cycle 5
+relationship: part_of FBdv:00005293 ! embryonic stage 2
+relationship: preceded_by FBdv:00005296 ! embryonic cycle 4
+
+[Term]
+id: FBdv:00005298
+name: embryonic cycle 6
+relationship: part_of FBdv:00005293 ! embryonic stage 2
+relationship: preceded_by FBdv:00005297 ! embryonic cycle 5
+
+[Term]
+id: FBdv:00005299
+name: embryonic cycle 7
+relationship: part_of FBdv:00005293 ! embryonic stage 2
+relationship: preceded_by FBdv:00005298 ! embryonic cycle 6
+
+[Term]
+id: FBdv:00005300
+name: embryonic cycle 8
+relationship: part_of FBdv:00005293 ! embryonic stage 2
+relationship: preceded_by FBdv:00005299 ! embryonic cycle 7
+
+[Term]
+id: FBdv:00005301
+name: embryonic stage 3
+def: "Nuclear division 9. The cleavage nuclei complete their migration to the periphery. Polar buds form at the posterior pole and divide once. Duration at 25 degrees C: approximately 15 minutes (65-80 minutes after egg laying)." [FB:FBrf0089570]
+relationship: part_of FBdv:00000054 ! cleavage stage
+relationship: part_of FBdv:00005290 ! pre-blastoderm stage
+relationship: preceded_by FBdv:00005293 ! embryonic stage 2
+
+[Term]
+id: FBdv:00005302
+name: embryonic cycle 9
+relationship: part_of FBdv:00005301 ! embryonic stage 3
+
+[Term]
+id: FBdv:00005303
+name: embryonic cycle 10
+relationship: part_of FBdv:00005301 ! embryonic stage 3
+relationship: preceded_by FBdv:00005302 ! embryonic cycle 9
+
+[Term]
+id: FBdv:00005304
+name: blastoderm stage
+related_synonym: "blastoderm" []
+relationship: part_of FBdv:00005289 ! embryonic stage
+
+[Term]
+id: FBdv:00005305
+name: syncytial blastoderm stage
+is_obsolete: true
+
+[Term]
+id: FBdv:00005306
+name: embryonic stage 4
+def: "Nuclear division 10-13. Polar buds divide twice and become tightly grouped at the posterior pole by the end of this stage. Nuclei visible at the rim of the embryo. Stage 4 ends with the begining of cellularization. Duration at 25 degrees C: approx. 50 minutes (80-130 minutes after egg laying)." [FB:FBrf0089570]
+related_synonym: "syncytial blastoderm" []
+related_synonym: "syncytial blastoderm stage" []
+relationship: part_of FBdv:00000054 ! cleavage stage
+relationship: part_of FBdv:00005304 ! blastoderm stage
+relationship: preceded_by FBdv:00005301 ! embryonic stage 3
+
+[Term]
+id: FBdv:00005307
+name: embryonic cycle 11
+relationship: part_of FBdv:00005306 ! embryonic stage 4
+
+[Term]
+id: FBdv:00005308
+name: embryonic cycle 12
+relationship: part_of FBdv:00005306 ! embryonic stage 4
+relationship: preceded_by FBdv:00005307 ! embryonic cycle 11
+
+[Term]
+id: FBdv:00005309
+name: embryonic cycle 13
+relationship: part_of FBdv:00005306 ! embryonic stage 4
+relationship: preceded_by FBdv:00005308 ! embryonic cycle 12
+
+[Term]
+id: FBdv:00005310
+name: cellular blastoderm stage
+is_obsolete: true
+
+[Term]
+id: FBdv:00005311
+name: embryonic stage 5
+def: "Cellularization. Stage 5 begins when cellularization starts. Near the end of this stage the pole cells begin to migrate dorsally and ventral midline cells acquire an irregular, wavy appearance. Stage 5 ends when ventral furrow formation becomes apparent. Duration at 25 degrees: approximately 40 minutes (130-170 minutes after egg laying)." [FB:FBrf0089570]
+related_synonym: "cellular blastoderm" []
+related_synonym: "cellular blastoderm stage" []
+relationship: part_of FBdv:00005304 ! blastoderm stage
+relationship: preceded_by FBdv:00005306 ! embryonic stage 4
+
+[Term]
+id: FBdv:00005312
+name: embryonic cycle 14
+relationship: part_of FBdv:00005289 ! embryonic stage
+
+[Term]
+id: FBdv:00005313
+name: embryonic cycle 14A
+relationship: part_of FBdv:00005312 ! embryonic cycle 14
+
+[Term]
+id: FBdv:00005314
+name: embryonic cycle 14B
+relationship: part_of FBdv:00005312 ! embryonic cycle 14
+relationship: preceded_by FBdv:00005313 ! embryonic cycle 14A
+
+[Term]
+id: FBdv:00005315
+name: embryonic cycle 15
+relationship: part_of FBdv:00005289 ! embryonic stage
+relationship: preceded_by FBdv:00005312 ! embryonic cycle 14
+
+[Term]
+id: FBdv:00005316
+name: embryonic cycle 16
+relationship: part_of FBdv:00005289 ! embryonic stage
+relationship: preceded_by FBdv:00005315 ! embryonic cycle 15
+
+[Term]
+id: FBdv:00005317
+name: gastrula stage
+related_synonym: "gastrula" []
+relationship: part_of FBdv:00005289 ! embryonic stage
+relationship: preceded_by FBdv:00005310 ! cellular blastoderm stage
+
+[Term]
+id: FBdv:00005318
+name: embryonic stage 6
+def: "Stage 6 begins when the ventral furrow becomes apparent, an event which is followed rapidly by the formation of the cephalic furrow. Stage 6 ends when the pole cells have adopted a dorsal (horizontal) position at the posterior. Duration at 25 degrees C: approximately 10 minutes (170-180 minutes after egg laying)." [FB:FBrf0089570]
+relationship: part_of FBdv:00005317 ! gastrula stage
+relationship: preceded_by FBdv:00005311 ! embryonic stage 5
+
+[Term]
+id: FBdv:00005319
+name: embryonic stage 7
+def: "Stage 7 begins when the pole cells have adopted a dorsal (horizontal) position at the posterior. Invagination of the anterior and posterior midgut and hindgut follows. The 'discoid plate' that carries the pole cells forms a pocket. Transverse furrows (dorsal folds) form on the dorsal surface. This stage ends when the anterior wall of the amnioproctodeal invagination starts moving anteriorly and the pole cells are no longer visible externally. Duration at 25 degrees C: approximately 10 minutes (180-190 minutes after egg laying)." [FB:FBrf0089570]
+relationship: part_of FBdv:00005317 ! gastrula stage
+relationship: preceded_by FBdv:00005318 ! embryonic stage 6
+
+[Term]
+id: FBdv:00005320
+name: germ band stage
+is_obsolete: true
+
+[Term]
+id: FBdv:00005321
+name: extended germ band stage
+relationship: part_of FBdv:00005289 ! embryonic stage
+
+[Term]
+id: FBdv:00005322
+name: embryonic stage 8
+def: "Stage 8 starts with the rapid phase of germ band extension and ends with the beginning of mesodermal segmentation. By the end of this stage germ band extension has progressed to the point where the proctodeal opening is at about 60% egg length and the dorsal folds (transverse furrows) are no longer visible. Duration at 25 degrees C: approximately 30 minutes (190-220 minutes after egg laying)." [FB:FBrf0089570]
+related_synonym: "rapidly extending germ band stage" []
+relationship: part_of FBdv:00005317 ! gastrula stage
+relationship: preceded_by FBdv:00005319 ! embryonic stage 7
+
+[Term]
+id: FBdv:00005323
+name: embryonic stage 9
+def: "Stage 9 begins when mesodermal segmentation becomes (transiently) visible\\, and ends with the appearance of the stomodeal invagination slightly ventral to the anterior pole. Duration at 25 degrees C: approximately 40 minutes (220-260 minutes after egg laying)." [FB:FBrf0089570]
+relationship: part_of FBdv:00014201 ! early extended germ band stage
+relationship: preceded_by FBdv:00005322 ! embryonic stage 8
+
+[Term]
+id: FBdv:00005324
+name: embryonic stage 10
+def: "Stage 10 begins with the appearance of the stomodeal invagination, slightly ventral to the anterior pole. Periodic furrows appear in the embryonic epidermis around the middle of the stage. The germ band continues to extend, reaching its maximum extent of 75% egg length towards the end of the stage. The end of the stage is marked by the beginning of invagination of the tracheal placodes. Duration at 25 degrees : approximately 60 minutes (260-320 minutes after egg laying)." [FB:FBrf0089570]
+relationship: part_of FBdv:00014201 ! early extended germ band stage
+relationship: preceded_by FBdv:00005323 ! embryonic stage 9
+
+[Term]
+id: FBdv:00005325
+name: embryonic stage 11
+def: "Stage 11 begins with the invagination of the tracheal placodes. Para-segmental furrow form and segment boundary furrows become deep folds. Within the head, gnathal protuberances become apparent. The end of this stage is signaled by the appearance of a distinct cleft at the posterior pole of the embryo, which becomes detached from the vitelline membrane. This marks the beginning of germ-band retraction. Duration at 25 degrees C: approximately 120 minutes (320-440 minutes after egg laying)" [FB:FBrf0089570]
+relationship: part_of FBdv:00004450 ! late extended germ band stage
+relationship: preceded_by FBdv:00005324 ! embryonic stage 10
+
+[Term]
+id: FBdv:00005326
+name: contracted germ band stage
+is_obsolete: true
+
+[Term]
+id: FBdv:00005327
+name: embryonic stage 12
+def: "Germ band retraction. Stage 12 begins when germ-band retraction starts and ends when this process is complete so that the prospective anal plate occupies the posterior pole. During this stage the posterior and anterior hindgut primordia meet and fuse and the tracheal pits fuse to form the tracheal tree. Duration at 25 degrees C: approximately 120 minutes (440-560 minutes after egg laying)." [FB:FBrf0089570]
+related_synonym: "retracting germ band stage" []
+relationship: part_of FBdv:00004450 ! late extended germ band stage
+relationship: preceded_by FBdv:00005325 ! embryonic stage 11
+
+[Term]
+id: FBdv:00005328
+name: embryonic stage 13
+def: "Stage 13 begins at the completion of germ-band retraction, when the prospective anal plate occupy the posterior pole. The dorsal ridge becomes apparent externally; the clypeolabrum retracts, leaving a triangular shaped gap at the anterior pole; the labium moves to the ventral midline. This stage ends when head involution begins. Duration at 25 degrees C: Approximately 60 minutes (560-620 minutes after egg laying)." [FB:FBrf0089570]
+related_synonym: "contracted germ band stage" []
+relationship: part_of FBdv:00005331 ! dorsal closure stage
+relationship: preceded_by FBdv:00005327 ! embryonic stage 12
+
+[Term]
+id: FBdv:00005329
+name: head involution stage
+is_obsolete: true
+
+[Term]
+id: FBdv:00005330
+name: embryonic stage 14
+def: "Stage 14 begins with the initiation of head involution. Closure of the midgut around the yolk and dorsal closure continue. Dorsal closure is 80% complete by the end of this stage. This stage ends with the appearance of the second midgut constriction. Duration at 25 degrees C: approximately 60 minutes (620-680 minutes after egg laying)" [FB:FBrf0089570]
+related_synonym: "head involution stage" []
+relationship: part_of FBdv:00005331 ! dorsal closure stage
+relationship: preceded_by FBdv:00005328 ! embryonic stage 13
+
+[Term]
+id: FBdv:00005331
+name: dorsal closure stage
+def: "A collective term for stages 13-15." [FB:DJS]
+relationship: part_of FBdv:00005289 ! embryonic stage
+relationship: preceded_by FBdv:00004450 ! late extended germ band stage
+
+[Term]
+id: FBdv:00005332
+name: embryonic stage 15
+def: "Stage 15 begins with the appearance of the second midgut constriction. During this stage the 1st and 3rd midgut constrictions form, dorsal closure is completed, and epidermal segmentation is accomplished. This stage ends when the intersegmental grooves can be distinguished at mid-dorsal level. Duration at 25 degrees C: approximately 100 minutes (680-780 minutes after egg laying)." [FB:FBrf0089570]
+relationship: part_of FBdv:00005331 ! dorsal closure stage
+relationship: preceded_by FBdv:00005330 ! embryonic stage 14
+
+[Term]
+id: FBdv:00005333
+name: late embryonic stage
+relationship: part_of FBdv:00005289 ! embryonic stage
+
+[Term]
+id: FBdv:00005334
+name: embryonic stage 16
+def: "Stage 16 begins when the intersegmental grooves can be distinguished at mid-dorsal level, and ends when the dorsal ridge (frontal sac) has overgrown the tip of the cylpeolabrum, which is thereby enclosed in the atrium. During this stage the ventral cord retracts to about 60% egg length. Duration at 25 degrees C: approximately 180 minutes (780-960 minutes after egg laying)." [FB:FBrf0089570]
+relationship: part_of FBdv:00005333 ! late embryonic stage
+relationship: preceded_by FBdv:00005332 ! embryonic stage 15
+
+[Term]
+id: FBdv:00005335
+name: embryonic stage 17
+def: "Stage 17 begins when the dorsal ridge (frontal sac) has overgrown the tip of the cylpeolabrum, which is thereby enclosed in the atrium. It asts until hatching of the embryo (approximately 24 hours after egg laying), during which time much terminal differentiation occurs, the tracheal tree fills with air, so becoming completely visible, and the ventral cord continues to retract. Duration at 25 degrees C: approximately 8 hours (960-1440 minutes after egg laying)." [FB:FBrf0089570]
+relationship: part_of FBdv:00005333 ! late embryonic stage
+relationship: preceded_by FBdv:00005334 ! embryonic stage 16
+
+[Term]
+id: FBdv:00005336
+name: larval stage
+relationship: part_of FBdv_root:00000000 ! Drosophila life cycle
+
+[Term]
+id: FBdv:00005337
+name: first instar larval stage
+xref_analog: abbrev:L1
+relationship: part_of FBdv:00005336 ! larval stage
+relationship: preceded_by FBdv:00005335 ! embryonic stage 17
+
+[Term]
+id: FBdv:00005338
+name: second instar larval stage
+xref_analog: abbrev:L2
+relationship: part_of FBdv:00005336 ! larval stage
+relationship: preceded_by FBdv:00005337 ! first instar larval stage
+
+[Term]
+id: FBdv:00005339
+name: third instar larval stage
+xref_analog: abbrev:L3
+relationship: part_of FBdv:00005336 ! larval stage
+
+[Term]
+id: FBdv:00005340
+name: third instar larval stage 1
+xref_analog: abbrev:L3-1
+relationship: part_of FBdv:00005336 ! larval stage
+relationship: preceded_by FBdv:00005338 ! second instar larval stage
+
+[Term]
+id: FBdv:00005341
+name: third instar larval stage 2
+xref_analog: abbrev:L3-2
+relationship: part_of FBdv:00005336 ! larval stage
+relationship: preceded_by FBdv:00005340 ! third instar larval stage 1
+
+[Term]
+id: FBdv:00005342
+name: prepupal stage
+relationship: part_of FBdv_root:00000000 ! Drosophila life cycle
+
+[Term]
+id: FBdv:00005343
+name: prepupal stage P1
+xref_analog: abbrev:L3-2
+relationship: part_of FBdv:00005342 ! prepupal stage
+relationship: preceded_by FBdv:00005339 ! third instar larval stage
+relationship: preceded_by FBdv:00005341 ! third instar larval stage 2
+
+[Term]
+id: FBdv:00005344
+name: prepupal stage P2
+relationship: part_of FBdv:00005342 ! prepupal stage
+relationship: preceded_by FBdv:00005343 ! prepupal stage P1
+
+[Term]
+id: FBdv:00005345
+name: prepupal stage P3
+relationship: part_of FBdv:00005342 ! prepupal stage
+relationship: preceded_by FBdv:00005344 ! prepupal stage P2
+
+[Term]
+id: FBdv:00005346
+name: prepupal stage P4
+relationship: part_of FBdv:00005342 ! prepupal stage
+
+[Term]
+id: FBdv:00005347
+name: prepupal stage P4(i)
+relationship: part_of FBdv:00005346 ! prepupal stage P4
+relationship: preceded_by FBdv:00005345 ! prepupal stage P3
+
+[Term]
+id: FBdv:00005348
+name: prepupal stage P4(ii)
+relationship: part_of FBdv:00005346 ! prepupal stage P4
+relationship: preceded_by FBdv:00005347 ! prepupal stage P4(i)
+
+[Term]
+id: FBdv:00005349
+name: pupal stage
+relationship: part_of FBdv_root:00000000 ! Drosophila life cycle
+
+[Term]
+id: FBdv:00005350
+name: pupal stage P5
+relationship: part_of FBdv:00005349 ! pupal stage
+
+[Term]
+id: FBdv:00005351
+name: pupal stage P5(i)
+relationship: part_of FBdv:00005350 ! pupal stage P5
+relationship: preceded_by FBdv:00005348 ! prepupal stage P4(ii)
+
+[Term]
+id: FBdv:00005352
+name: pupal stage P5(ii)
+relationship: part_of FBdv:00005350 ! pupal stage P5
+relationship: preceded_by FBdv:00005351 ! pupal stage P5(i)
+
+[Term]
+id: FBdv:00005353
+name: pupal stage P6
+relationship: part_of FBdv:00005349 ! pupal stage
+relationship: preceded_by FBdv:00005350 ! pupal stage P5
+relationship: preceded_by FBdv:00005352 ! pupal stage P5(ii)
+
+[Term]
+id: FBdv:00005354
+name: pupal stage P7
+relationship: part_of FBdv:00005349 ! pupal stage
+relationship: preceded_by FBdv:00005353 ! pupal stage P6
+
+[Term]
+id: FBdv:00005355
+name: pharate adult stage P8
+def: "." [FB:FBrf0049147]
+related_synonym: "pupal stage P8" []
+relationship: part_of FBdv:00006011 ! pharate adult stage
+relationship: preceded_by FBdv:00005354 ! pupal stage P7
+
+[Term]
+id: FBdv:00005356
+name: pharate adult stage P9
+def: "." [FB:FBrf0049147]
+related_synonym: "pupal stage P9" []
+relationship: part_of FBdv:00006011 ! pharate adult stage
+relationship: preceded_by FBdv:00005355 ! pharate adult stage P8
+
+[Term]
+id: FBdv:00005357
+name: pharate adult stage P10
+def: "." [FB:FBrf0049147]
+related_synonym: "pupal stage P10" []
+relationship: part_of FBdv:00006011 ! pharate adult stage
+relationship: preceded_by FBdv:00005356 ! pharate adult stage P9
+
+[Term]
+id: FBdv:00005358
+name: pharate adult stage P11
+def: "." [FB:FBrf0049147]
+related_synonym: "pupal stage P11" []
+relationship: part_of FBdv:00006011 ! pharate adult stage
+
+[Term]
+id: FBdv:00005359
+name: pharate adult stage P11(i)
+def: "." [FB:FBrf0049147]
+related_synonym: "pupal stage P11(i)" []
+relationship: part_of FBdv:00005358 ! pharate adult stage P11
+relationship: preceded_by FBdv:00005357 ! pharate adult stage P10
+
+[Term]
+id: FBdv:00005360
+name: pharate adult stage P11(ii)
+def: "." [FB:FBrf0049147]
+related_synonym: "pupal stage P11(ii)" []
+relationship: part_of FBdv:00005358 ! pharate adult stage P11
+relationship: preceded_by FBdv:00005359 ! pharate adult stage P11(i)
+
+[Term]
+id: FBdv:00005361
+name: pharate adult stage P12
+def: "." [FB:FBrf0049147]
+related_synonym: "pupal stage P12" []
+relationship: part_of FBdv:00006011 ! pharate adult stage
+
+[Term]
+id: FBdv:00005362
+name: pharate adult stage P12(i)
+def: "." [FB:FBrf0049147]
+related_synonym: "pupal stage P12(i)" []
+relationship: part_of FBdv:00005361 ! pharate adult stage P12
+relationship: preceded_by FBdv:00005360 ! pharate adult stage P11(ii)
+
+[Term]
+id: FBdv:00005363
+name: pharate adult stage P12(ii)
+def: "." [FB:FBrf0049147]
+related_synonym: "pupal stage P12(ii)" []
+relationship: part_of FBdv:00005361 ! pharate adult stage P12
+relationship: preceded_by FBdv:00005362 ! pharate adult stage P12(i)
+
+[Term]
+id: FBdv:00005364
+name: pharate adult stage P13
+def: "." [FB:FBrf0049147]
+related_synonym: "pupal stage P13" []
+relationship: part_of FBdv:00006011 ! pharate adult stage
+relationship: preceded_by FBdv:00005363 ! pharate adult stage P12(ii)
+
+[Term]
+id: FBdv:00005365
+name: pharate adult stage P14
+def: "." [FB:FBrf0049147]
+related_synonym: "pupal stage P14" []
+relationship: part_of FBdv:00006011 ! pharate adult stage
+relationship: preceded_by FBdv:00005364 ! pharate adult stage P13
+
+[Term]
+id: FBdv:00005366
+name: pharate adult stage P15
+alt_id: FBdv:00005372
+def: "." [FB:FBrf0049147]
+related_synonym: "adult stage 0" []
+related_synonym: "pupal stage P15" []
+relationship: part_of FBdv:00006011 ! pharate adult stage
+
+[Term]
+id: FBdv:00005367
+name: pharate adult stage P15(i)
+related_synonym: "pupal stage P15(i)" []
+relationship: part_of FBdv:00005366 ! pharate adult stage P15
+relationship: preceded_by FBdv:00005365 ! pharate adult stage P14
+
+[Term]
+id: FBdv:00005368
+name: pharate adult stage P15(ii)
+def: "." [FB:FBrf0049147]
+related_synonym: "pupal stage P15(ii)" []
+relationship: part_of FBdv:00005366 ! pharate adult stage P15
+relationship: preceded_by FBdv:00005367 ! pharate adult stage P15(i)
+
+[Term]
+id: FBdv:00005369
+name: adult stage
+relationship: part_of FBdv_root:00000000 ! Drosophila life cycle
+
+[Term]
+id: FBdv:00005370
+name: adult stage A1
+alt_id: FBdv:00005373
+def: "Newly eclosed - wings unfold flattern and harden. Abdomen becomes broader." [FB:FBrf0049147]
+related_synonym: "adult stage I" []
+relationship: part_of FBdv:00005369 ! adult stage
+relationship: preceded_by FBdv:00005368 ! pharate adult stage P15(ii)
+
+[Term]
+id: FBdv:00005371
+name: adult stage A2
+alt_id: FBdv:00005374
+def: "Wings extended. Abdominal tergites tan to shiny brown." [FB:FBrf0049147]
+related_synonym: "adult stage II" []
+relationship: part_of FBdv:00005369 ! adult stage
+relationship: preceded_by FBdv:00005370 ! adult stage A1
+
+[Term]
+id: FBdv:00005412
+name: gamete
+is_obsolete: true
+
+[Term]
+id: FBdv:00006011
+name: pharate adult stage
+def: "The developing adult after pupal-adult apolysis , i.e.- from stage P8 (when yellow eye color first becomes visible through the pupal case), to eclosion." [FB:FBrf0049147]
+relationship: part_of FBdv_root:00000000 ! Drosophila life cycle
+
+[Term]
+id: FBdv:00006012
+name: adult stage A3
+alt_id: FBdv:00005375
+def: "tergites tanned" [FB:FBrf0049147]
+related_synonym: "adult stage III" []
+relationship: part_of FBdv:00005369 ! adult stage
+relationship: preceded_by FBdv:00005371 ! adult stage A2
+
+[Term]
+id: FBdv:00014201
+name: early extended germ band stage
+def: "A collective term for stages 9 and 10." [FB:DJS]
+relationship: part_of FBdv:00005321 ! extended germ band stage
+
+[Term]
+id: FBdv_root:00000000
+name: Drosophila life cycle
+
+[Typedef]
+id: part_of
+name: part of
+
+[Typedef]
+id: preceded_by
+name: preceded_by
+
Added: phenote/trunk/obo-files/flybase_controlled_vocabulary.obo
===================================================================
--- phenote/trunk/obo-files/flybase_controlled_vocabulary.obo (rev 0)
+++ phenote/trunk/obo-files/flybase_controlled_vocabulary.obo 2007-07-18 16:53:44 UTC (rev 733)
@@ -0,0 +1,5284 @@
+format-version: 1.0
+date: 10:04:2007 13:20
+saved-by: djs93
+auto-generated-by: OBO-Edit 1.002
+subsetdef: camcur "camcur"
+default-namespace: FlyBase miscellaneous CV
+namespace-id-rule: * FBcv:$sequence(7,0,9999999)$
+
+[Term]
+id: FBcv:0000000
+name: FlyBase CV
+
+[Term]
+id: FBcv:0000001
+name: death certificate
+namespace: pub_type
+comment: Proforma field: P1.
+subset: camcur
+is_a: FBcv:0000189 ! publication class
+
+[Term]
+id: FBcv:0000002
+name: thermotaxis behavior defective
+namespace: phenotypic_class
+comment: Proforma field: GA56. Proforma field: GA28a. Proforma field: GA29a.
+subset: camcur
+exact_synonym: "thermotaxis behaviour defective" []
+is_a: FBcv:0000387 ! behavioral
+
+[Term]
+id: FBcv:0000003
+name: In transgenic Drosophila (intraspecific)
+namespace: mode_of_assay
+comment: Proforma field: GA19.
+subset: camcur
+xref_analog: abbrev:1
+is_a: FBcv:0000607 ! In transgenic Drosophila
+
+[Term]
+id: FBcv:0000004
+name: Whole-organism transient assay (intraspecific)
+namespace: mode_of_assay
+comment: Proforma field: GA19.
+subset: camcur
+xref_analog: abbrev:2
+is_a: FBcv:0000608 ! Whole-organism transient assay
+
+[Term]
+id: FBcv:0000005
+name: qualifier
+is_a: FBcv:0000000 ! FlyBase CV
+
+[Term]
+id: FBcv:0000006
+name: male semi-fertile
+namespace: phenotypic_class
+comment: Proforma field: GA56. Proforma field: GA28a. Proforma field: GA29a.
+subset: camcur
+is_a: FBcv:0000375 ! semi-fertile
+is_a: FBcv:0000376 ! male fertile
+
+[Term]
+id: FBcv:0000007
+name: female semi-fertile
+namespace: phenotypic_class
+comment: Proforma field: GA56. Proforma field: GA28a. Proforma field: GA29a.
+subset: camcur
+is_a: FBcv:0000375 ! semi-fertile
+is_a: FBcv:0000377 ! female fertile
+
+[Term]
+id: FBcv:0000008
+name: variegation
+namespace: phenotypic_class
+subset: camcur
+is_a: FBcv:0000347 ! phenotypic class
+
+[Term]
+id: FBcv:0000009
+name: temporal stage qualifier
+namespace: temporal_qualifier
+is_a: FBcv:0000176 ! temporal qualifier
+
+[Term]
+id: FBcv:0000010
+name: monophasic
+namespace: temporal_qualifier
+comment: Deprecated: Use of this term is discouraged as there is no way to decide how to group anatomy terms combined with this qualifier with other terms in the anatomy ontology. Subject to discussion and once its usage in old curation is removed, this term will be obsoleted. DS
+is_a: FBcv:0000009 ! temporal stage qualifier
+
+[Term]
+id: FBcv:0000011
+name: relative temporal qualifier
+namespace: temporal_qualifier
+is_a: FBcv:0000176 ! temporal qualifier
+
+[Term]
+id: FBcv:0000012
+name: absolute temporal qualifier
+namespace: temporal_qualifier
+is_a: FBcv:0000176 ! temporal qualifier
+
+[Term]
+id: FBcv:0000013
+name: descriptor
+is_a: FBcv:0000000 ! FlyBase CV
+
+[Term]
+id: FBcv:0000014
+name: structural qualifier
+namespace: structural_qualifier
+is_a: FBcv:0000809 ! phenotype qualifier
+
+[Term]
+id: FBcv:0000015
+name: postage stamp
+namespace: pub_type
+comment: Proforma field: P1.
+subset: camcur
+is_a: FBcv:0000189 ! publication class
+
+[Term]
+id: FBcv:0000016
+name: Baylor TE recombination mapping kit stock
+is_a: FBcv:0000648 ! mapping stock
+
+[Term]
+id: FBcv:0000017
+name: penetrance qualifier
+def: "Penetrance is the fraction of individuals of a given genotype who exhibit the phenotype associated with that genotype." [ISBN:0716735202]
+is_a: FBcv:0000005 ! qualifier
+
+[Term]
+id: FBcv:0000018
+name: penetrance complete
+def: "Penetrance is the fraction of individuals of a given genotype who exhibit the phenotype associated with that genotype. Penetrance is complete when all the individuals of a given genotype exhibit the phenotype associated with that genotype." [ISBN:0716735202]
+is_a: FBcv:0000017 ! penetrance qualifier
+
+[Term]
+id: FBcv:0000019
+name: penetrance incomplete
+def: "Penetrance is the fraction of individuals of a given genotype who exhibit the phenotype associated with that genotype. Penetrance is incomplete when only some the individuals of a given genotype exhibit the phenotype associated with that genotype." [ISBN:0716735202]
+is_a: FBcv:0000017 ! penetrance qualifier
+
+[Term]
+id: FBcv:0000020
+name: penetrance percent
+def: "Penetrance is the fraction of individuals of a given genotype who exhibit the phenotype associated with that genotype. Penetrance is incomplete when only a percentage of the individuals of a given genotype exhibit the phenotype associated with that genotype." [ISBN:0716735202]
+comment: This term modifed by a % value.
+is_a: FBcv:0000019 ! penetrance incomplete
+
+[Term]
+id: FBcv:0000021
+name: expressivity qualifier
+def: "Expressivity measures the extent to which a given genotype is expressed at the phenotypic level." [ISBN:0716735202]
+is_a: FBcv:0000005 ! qualifier
+
+[Term]
+id: FBcv:0000022
+name: expressivity complete
+def: "Expressivity measures the extent to which a given genotype is expressed at the phenotypic level. Expressivity is complete when an individual of a given genotype expresses the full phenotype associated with that genotype." [ISBN:0716735202]
+is_a: FBcv:0000021 ! expressivity qualifier
+
+[Term]
+id: FBcv:0000023
+name: expressivity incomplete
+def: "Expressivity measures the extent to which a given genotype is expressed at the phenotypic level. Expressivity is incomplete when an individual of a given genotype expresses only partially the phenotype associated with that genotype." [ISBN:0716735202]
+is_a: FBcv:0000021 ! expressivity qualifier
+
+[Term]
+id: FBcv:0000024
+name: expressivity high
+def: "Expressivity measures the extent to which a given genotype is expressed at the phenotypic level. \"High expressivity\" conveys that while expressivity is not complete, the phenotype expressed is approaching that of complete expressivity." [ISBN:0716735202]
+is_a: FBcv:0000023 ! expressivity incomplete
+
+[Term]
+id: FBcv:0000025
+name: expressivity low
+def: "Expressivity measures the extent to which a given genotype is expressed at the phenotypic level. \"Low expressivity\" conveys that phenotype expressed is a much reduced version compared to complete expressivity." [ISBN:0716735202]
+is_a: FBcv:0000023 ! expressivity incomplete
+
+[Term]
+id: FBcv:0000026
+name: recessive visible allele recombination mapping stock
+is_a: FBcv:0000649 ! visible allele recombination mapping stock
+
+[Term]
+id: FBcv:0000027
+name: dominant visible allele recombination mapping stock
+is_a: FBcv:0000649 ! visible allele recombination mapping stock
+
+[Term]
+id: FBcv:0000028
+name: SNP recombination mapping stock
+is_a: FBcv:0000648 ! mapping stock
+
+[Term]
+id: FBcv:0000029
+name: transposable element mutagenesis stock
+is_a: FBcv:0010000 ! living stock
+
+[Term]
+id: FBcv:0000030
+name: compartment
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000031
+name: anterior compartment
+namespace: spatial_qualifier
+def: "Restricted to the anterior compartment of some specified type" [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000030 ! compartment
+
+[Term]
+id: FBcv:0000032
+name: compartment boundary
+namespace: spatial_qualifier
+def: "Restricted to some compartment boundary within a specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000030 ! compartment
+
+[Term]
+id: FBcv:0000033
+name: anterior/posterior compartment boundary
+namespace: spatial_qualifier
+def: "Restricted to an anterior/posterior compartment boundary within a specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000032 ! compartment boundary
+
+[Term]
+id: FBcv:0000034
+name: dorsal/ventral compartment boundary
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000032 ! compartment boundary
+
+[Term]
+id: FBcv:0000035
+name: dorsal compartment
+namespace: spatial_qualifier
+def: "Restricted to the dorsal compartment of some specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000030 ! compartment
+
+[Term]
+id: FBcv:0000036
+name: posterior compartment
+namespace: spatial_qualifier
+def: "Restricted to the posterior compartment of some specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000030 ! compartment
+
+[Term]
+id: FBcv:0000037
+name: ventral compartment
+namespace: spatial_qualifier
+def: "Restricted to the ventral compartment of some specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000030 ! compartment
+
+[Term]
+id: FBcv:0000038
+name: relative spatial qualifier
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000039
+name: anterior to
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.\n\nDeprecated: Use of this term is discouraged as there is no way to decide how to group anatomy terms combined with this qualifier with other terms in the anatomy ontology. Once its usage in old curation is removed, this term will be obsoleted. DS
+is_a: FBcv:0000038 ! relative spatial qualifier
+
+[Term]
+id: FBcv:0000040
+name: distal to
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.\n\nDeprecated: Use of this term is discouraged as there is no way to decide how to group anatomy terms combined with this qualifier with other terms in the anatomy ontology. Once its usage in old curation is removed, this term will be obsoleted. DS
+is_a: FBcv:0000038 ! relative spatial qualifier
+
+[Term]
+id: FBcv:0000041
+name: dorsal to
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.\n\nDeprecated: Use of this term is discouraged as there is no way to decide how to group anatomy terms combined with this qualifier with other terms in the anatomy ontology. Once its usage in old curation is removed, this term will be obsoleted. DS
+is_a: FBcv:0000038 ! relative spatial qualifier
+
+[Term]
+id: FBcv:0000042
+name: deficiency kit stock
+related_synonym: "deletion kit stock" []
+is_a: FBcv:0010000 ! living stock
+
+[Term]
+id: FBcv:0000043
+name: transposase source for transposable element mutagenesis
+is_a: FBcv:0000029 ! transposable element mutagenesis stock
+
+[Term]
+id: FBcv:0000044
+name: ammunition source for transposable element mutagenesis
+is_a: FBcv:0000029 ! transposable element mutagenesis stock
+
+[Term]
+id: FBcv:0000045
+name: posterior to
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.\n\nDeprecated: Use of this term is discouraged as there is no way to decide how to group anatomy terms combined with this qualifier with other terms in the anatomy ontology. Once its usage in old curation is removed, this term will be obsoleted. DS
+is_a: FBcv:0000038 ! relative spatial qualifier
+
+[Term]
+id: FBcv:0000046
+name: precursor
+namespace: temporal_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.\n\nDeprecated: Use of this term is discouraged as there is no way to decide how to group anatomy terms combined with this qualifier with other terms in the anatomy ontology. Once its usage in old curation is removed, this term will be obsoleted. DS
+is_a: FBcv:0000176 ! temporal qualifier
+
+[Term]
+id: FBcv:0000047
+name: proximal to
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.\n\nDeprecated: Use of this term is discouraged as there is no way to decide how to group anatomy terms combined with this qualifier with other terms in the anatomy ontology. Once its usage in old curation is removed, this term will be obsoleted. DS
+is_a: FBcv:0000038 ! relative spatial qualifier
+
+[Term]
+id: FBcv:0000048
+name: surrounding
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.\n\nDeprecated: Use of this term is discouraged as there is no way to decide how to group anatomy terms combined with this qualifier with other terms in the anatomy ontology. Once its usage in old curation is removed, this term will be obsoleted. DS
+is_a: FBcv:0000038 ! relative spatial qualifier
+
+[Term]
+id: FBcv:0000049
+name: ventral to
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.\n\nDeprecated: Use of this term is discouraged as there is no way to decide how to group anatomy terms combined with this qualifier with other terms in the anatomy ontology. Once its usage in old curation is removed, this term will be obsoleted. DS
+is_a: FBcv:0000038 ! relative spatial qualifier
+
+[Term]
+id: FBcv:0000050
+name: vicinity of
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.\n\nDeprecated: Use of this term is discouraged as there is no way to decide how to group anatomy terms combined with this qualifier with other terms in the anatomy ontology. Once its usage in old curation is removed, this term will be obsoleted. DS
+is_a: FBcv:0000038 ! relative spatial qualifier
+
+[Term]
+id: FBcv:0000051
+name: segment boundary
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000052
+name: spatial qualifier
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+is_a: FBcv:0000005 ! qualifier
+
+[Term]
+id: FBcv:0000053
+name: anterior
+namespace: spatial_qualifier
+def: "Restricted to anterior region of some specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000054
+name: apical
+namespace: spatial_qualifier
+def: "Restricted to apical region of some specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAP6-q. Proforma field: GAT23-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000055
+name: basal
+namespace: spatial_qualifier
+def: "Restricted to basal region of some specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAP6-q. Proforma field: GAT23-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000056
+name: central
+namespace: spatial_qualifier
+def: "Restricted to central region of some specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000057
+name: contralateral
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.\n\nDeprecated: Contralateral means - on the oppsoite side from .... In curation usage: on the oppsoite side froms what ? Will be obsoleted once a replacement term agreed upon (if needed) and any old usage retrofitted. DS
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000058
+name: distal
+namespace: spatial_qualifier
+def: "Restricted to distsal region of some specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000059
+name: dorsal
+namespace: spatial_qualifier
+def: "Restricted to dorsal region of some specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000060
+name: dorso-lateral
+namespace: spatial_qualifier
+def: "Restricted to dorso-lateral region of some specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000061
+name: ectopic
+namespace: structural_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000014 ! structural qualifier
+
+[Term]
+id: FBcv:0000062
+name: ipsilateral
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.\n\nDeprecated: As far as I can tell, ipsilateral means - on the same side as .... In curation usage: on the same side as what ? Will be obsoleted once a replacement term agreed upon (if needed) and any old usage retrofitted. DS
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000063
+name: lateral
+namespace: spatial_qualifier
+def: "Restricted to lateral region(s) of some specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAP6-q. Proforma field: GAT23-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000064
+name: medial
+namespace: spatial_qualifier
+def: "Restricted to medial region of some specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000065
+name: posterior
+namespace: spatial_qualifier
+def: "Restricted to posterior region of some specified type." [FB:DS]
+comment: Proforma field: GA56-q. Proforma field: GA28a-q. Proforma field: GA29a-q. Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000066
+name: proximal
+namespace: spatial_qualifier
+def: "Restricted to proximal region of some specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000067
+name: restricted
+namespace: spatial_qualifier
+def: "Restricted to unknown part(s) of a specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000068
+name: supernumerary
+namespace: structural_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000014 ! structural qualifier
+
+[Term]
+id: FBcv:0000069
+name: ubiquitous
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000070
+name: ventral
+namespace: spatial_qualifier
+def: "Restricted to ventral region of some specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000071
+name: ventro-lateral
+namespace: spatial_qualifier
+def: "Restricted to ventro-lateral region of some specified type." [FB:DS]
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000072
+name: gene expression qualifier
+is_obsolete: true
+
+[Term]
+id: FBcv:0000073
+name: embryonic expression pattern
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+is_obsolete: true
+
+[Term]
+id: FBcv:0000074
+name: egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000052 ! spatial qualifier
+
+[Term]
+id: FBcv:0000075
+name: 0% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000076
+name: 0-10% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000077
+name: 0-100% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000078
+name: 0-20% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000079
+name: 0-30% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000080
+name: 0-40% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000081
+name: 0-50% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000082
+name: 0-60% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000083
+name: 0-70% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000084
+name: 0-80% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000085
+name: 0-90% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000086
+name: 10% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000087
+name: 10-100% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000088
+name: 10-20% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000089
+name: 10-30% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000090
+name: 10-40% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000091
+name: 10-50% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000092
+name: 10-60% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000093
+name: 10-70% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000094
+name: 10-80% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000095
+name: 10-90% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000096
+name: 100% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000097
+name: 20% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000098
+name: 20-100% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000099
+name: 20-30% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000100
+name: 20-40% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000101
+name: 20-50% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000102
+name: 20-60% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000103
+name: 20-70% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000104
+name: 20-80% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000105
+name: 20-90% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: camcur
+is_a: FBcv:0000074 ! egg length
+
+[Term]
+id: FBcv:0000106
+name: 30% egg length
+namespace: spatial_qualifier
+comment: Proforma field: GA17-q. Proforma field: GA28b-q. Proforma field: GA29b-q. Proforma field: GAT6-q. Proforma field: GAP5-q.
+subset: ...
[truncated message content] |
|
From: <dj...@us...> - 2007-07-18 15:33:58
|
Revision: 732
http://svn.sourceforge.net/obo/?rev=732&view=rev
Author: djs93
Date: 2007-07-18 08:31:26 -0700 (Wed, 18 Jul 2007)
Log Message:
-----------
FlyBase expression curation config added
Added Paths:
-----------
phenote/trunk/conf/FlyBaseTAP.cfg
Added: phenote/trunk/conf/FlyBaseTAP.cfg
===================================================================
--- phenote/trunk/conf/FlyBaseTAP.cfg (rev 0)
+++ phenote/trunk/conf/FlyBaseTAP.cfg 2007-07-18 15:31:26 UTC (rev 732)
@@ -0,0 +1,59 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- *********************** CONFIG INFO ************************** -->
+<ns:phenote-configuration version="1.3.1" xmlns:ns="phenote/config/xml"
+ name="Flybase"
+ author="David Sutherland"
+ description="This configuration is expression pattern annotation by curators working at Flybase, or others in the Drosophila community.">
+
+
+ <!-- *********************** SETTINGS **************************** -->
+ <!--ns:master-to-local-config mode="UPDATE" when="ON_VERSION_CHANGE"
+ overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/flybase.cfg" /-->
+ <ns:log config-file="conf/log4j-standalone.xml" />
+
+ <ns:uvic-graph enable="false"/>
+ <ns:term-history enable="false"/>
+
+ <ns:auto-update-ontologies enable="false"/> <!--true=update; false=don't update-->
+ <ns:update-timer timer="0"/><!--set to 0 if you want to bypass the check; time in seconds-->
+ <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/>
+
+
+ <!-- ********************* FILE ADAPTERS ************************** -->
+ <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter"
+ enable="true"/>
+ <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter"
+ enable="false"/>
+ <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="false"/>
+
+
+ <!-- ******************** FIELD DEFINITIONS *********************** -->
+
+<ns:field name="Pub" syntax-abbrev="PUB"/>
+
+<ns:field name="Trans/Pep" syntax-abbrev="T-P" type="free_text"/>
+
+<ns:field name="Stage" syntax-abbrev="stage">
+ <ns:ontology name="stage" file="fly_development.obo"/>
+</ns:field>
+
+<ns:field name="Entity" syntax-abbrev="E">
+ <!-- postcomp relationship-ontology="relationship.obo" repos-subdir="OBO_REL"/ -->
+ <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:field>
+
+<ns:field name="Spatial Q" syntax-abbrev="spatial">
+ <ns:ontology name="Spatial qualifier" file="flybase_controlled_vocabulary.obo" namespace="spatial_qualifier" slim="camcur"/>
+</ns:field>
+
+<ns:field name="Description" syntax-abbrev="Desc"/>
+
+ <!-- ******************** REVISION HISTORY *********************** -->
+ <!-- 1st version constructed by DOS on 16th July 2007-->
+
+</ns:phenote-configuration>
+
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-07-17 22:05:07
|
Revision: 731
http://svn.sourceforge.net/obo/?rev=731&view=rev
Author: mgibson
Date: 2007-07-17 15:05:09 -0700 (Tue, 17 Jul 2007)
Log Message:
-----------
added some docs on datamodel & config to datamodel - more to add
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/developer-docs/developer-docs.html
Modified: phenote/trunk/doc/phenote-website/developer-docs/developer-docs.html
===================================================================
--- phenote/trunk/doc/phenote-website/developer-docs/developer-docs.html 2007-07-17 20:45:27 UTC (rev 730)
+++ phenote/trunk/doc/phenote-website/developer-docs/developer-docs.html 2007-07-17 22:05:09 UTC (rev 731)
@@ -4,16 +4,20 @@
+
+
<meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
+
+
<title>Developer docs</title>
</head>
@@ -22,14 +26,17 @@
+
<h3><span style="text-decoration: underline;">Editing the model</span></h3>
+
So a phenote.edit.CharChangeEvent has a phenote.edit.TransactionI. <br>
+
so when a gui component like CharFieldGui wants to edit the model
it calls a method on the EditManager. For instance, for updating
multiple fields at once CharFieldGui makes a bunch of
@@ -44,194 +51,290 @@
+
A phenote.edit.TransactionI knows how to edit and undo its edit to the datamodel.<br>
+
<br>
+
<h3><span style="text-decoration: underline;">Adding new configuration params</span></h3>
+
Phenote configuration is done with a xml file, that xml file is read
& written with apaches xml beans. Xml beans code generates java
classes from an xsd file. <br>
+
<br>
+
1) Add your new config item to the config/phenote-config.rnc file. An
rnc file is (i think) a handier way of specifying xml schemas. The best
thing to do there is to look how other elements are configured and just
copy & tweek.<br>
+
<br>
+
2) trang the rnc file into an xsd file. <br>
+
2a) To do this you first need to download the trang jar file see:
http://www.thaiopensource.com/relaxng/trang.html and its download dir
http://www.thaiopensource.com/download/ where you can download a zip
file like <a href="http://www.thaiopensource.com/download/trang-20030619.zip">trang-20030619.zip<span style="text-decoration: underline;"> </span></a><br>
+
and unzip which should give you the jar - and put that jar whereever you like.<br>
+
<span style="font-family: monospace;"></span>2b) cd to conf directory and run trang with rnc as input and xsd as output like so and this will recreate the xsd:<br>
+
java -jar /path/to/trang/trang.jar phenote-config.rnc phenote-config.xsd<br>
+
You can check the xsd to see if it has the element that you added in the rnc if you like.<br>
+
<br>
+
3) generate xmlbeans from xsd. <br>
+
3a) You need to download scomp, and jsr-api.jar and xbean.jar jar files from apache xml beans<br>
+
see http://xmlbeans.apache.org/ and its download dir http://www.apache.org/dyn/closer.cgi/xmlbeans<br>
+
current tgz or zip - and unzip and/or untar it. The relevant bits are bin/scomp and the jsrwithnumbers.jar and xbean.jar <br>
+
make sure to change the permissions on scomp so its executable.<br>
+
3b) Before we run scomp we need to set envrionment vars something like so (for unix/linux at least):<br>
+
<pre class="code">export XMLBEANS_HOME=/home/me/xmlbeans-2.1.0<br>export PATH=$PATH:$XMLBEANS_HOME/bin<br>export CLASSPATH=$XMLBEANS_HOME/lib/xbean.jar:$XMLBEANS_HOME/lib/jsr173_1.0_api.jar:$CLASSPATH</pre>
+
3c) Then run scomp using the above jars and the xsd file to create jars/phenote (all on one line):<br>
+
<br>
+
scomp -out /path/to/phenote/jars/phenoteconfigbeans.jar /home/mgibson/p/conf/phenote-config.xsd<br>
+
<br>
+
Now you should have a phenoteconfigbeans.jar file. With this jar we can now write java config code.<br>
+
<br>
+
4) Modify java config files. Go to the file src/java/phenote/config/Config.java.<br>
+
<br>
+
a) First put in the appropriate import statement from the xmlbean jar, something like<br>
+
import phenote.config.xml.TermHistoryDocument.TermHistory;<br>
+
<br>
+
b) The simple case is just adding a top level config boolean option - like enabling term history - so ill go with that. <br>
+
- the new parameter would automatically be read into an xml bean -
write a private getter for the new bean value like so (putting in
default value if null)<br>
+
private TermHistory getHistoryBean() {<br>
+
TermHistory history = phenoConfigBean.getTermHistory();<br>
+
if (history == null) {<br>
+
history = phenoConfigBean.addNewTermHistory();<br>
+
history.setEnable(false); // default false<br>
+
}<br>
+
return history;<br>
+
}<br>
+
<br>
+
- add a public getter method like:<br>
+
public boolean termHistoryIsEnabled() { <br>
+
return getHistoryBean().getEnable();<br>
+
}<br>
+
<br>
+
- setters are used by merge code and will be used in future by gui config:<br>
+
public void setTermHistory(boolean setter) { <br>
+
getHistoryBean().setEnable(setter);<br>
+
}<br>
+
<br>
+
- you need to deal with config upgrades to make sure youre new param
gets merged into old configs without wiping out a user previous config
settings (the default and -u option run by webstart)<br>
+
if you dont want the master/template config file to alter the value of
a users local config then nothing needs to be done here. but if you do
then...<br>
+
so in this method:<br>
+
<br>
+
void mergeNewWithOld(URL newConfig,File oldDotConfFile)<br>
+
<br>
+
where you need to add something like<br>
+
<br>
+
oldCfg.setAutoUpdate(newCfg.autoUpdateIsEnabled());<br>
+
<br>
+
notice this just wipes out the new with the old - you may actually want
to ask the user if they want this to happen (with a popup box or
something) - this example is for auto update.<br>
+
<br style="text-decoration: underline;">
+
<big style="text-decoration: underline;"><span style="font-weight: bold;">Source for generate xml beans:</span></big><br>
+
It can be handy to look at the actual source of the xmlbeans created by scomp, and scomp has such an option:<br>
+
instead of the -out used above, use -src, and tell scomp where you would like the source plopped:<br>
+
scomp -src ~/phenote/config-xmlbeans-src /home/mgibson/p/conf/phenote-config.xsd<br>
+<br>
+<big style="font-weight: bold; text-decoration: underline;">Datamodel</big><br>
+Each row is represented by a phenote.datamodel.CharacterI interface,
+the implementation of which is phenote.datamodel.Character. The whole
+table is just a list of Characters: CharacterList.
+phenote.dataadapter.CharacterListManager manages the CharacterLists for
+each table (groups of fields spurn separate tables), and sends out
+CharChangeEvents when a new CharacterList is loaded.<br>
+A Character is actually rather generic. Its really just a hash with
+CharField keys and CharFieldValue values. So a CharField represents a
+whole column/field of the table (eg Quality) and CharFieldValue
+represent a cell - a column/field of a row.<br>
+<br>
+<big><span style="text-decoration: underline;"><span style="font-weight: bold;">So what happens to a field from config to datamodel to gui?<br>
+</span></span><small>So I dont know if this is the best way to explain
+this but what the heck. So the fields in the rnc as explained above get
+tranged into xsd and then scomped (code generated) into java xml beans.
+phenote.config.Config makes the call to parse the config xml file into
+xml bean objects. One field xml bean object is created for each field
+in the config file. Config wraps the field xml bean with the
+FieldConfig object (just for convenience - may want to strip out
+FieldConfig at some point?). The OntologyDataAdapter iterates through
+FieldConfig objects and creates a CharField for each one. A CharField
+is a datmodel object that represents a column of the table basically (a
+field - see above). </small><span style="text-decoration: underline;"><span style="font-weight: bold;"><br>
+</span></span></big>
<br>
+
</body>
</html>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-07-17 20:45:40
|
Revision: 730
http://svn.sourceforge.net/obo/?rev=730&view=rev
Author: mgibson
Date: 2007-07-17 13:45:27 -0700 (Tue, 17 Jul 2007)
Log Message:
-----------
if only 1 tabbed group configured dont make tabs
version -> 1.4-beta2
Modified Paths:
--------------
phenote/trunk/src/java/phenote/gui/ConfigGui.java
phenote/trunk/src/java/phenote/gui/SettingsMenu.java
phenote/trunk/src/java/phenote/main/Phenote.java
phenote/trunk/src/java/phenote/main/PhenoteVersion.java
Modified: phenote/trunk/src/java/phenote/gui/ConfigGui.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/ConfigGui.java 2007-07-17 20:41:14 UTC (rev 729)
+++ phenote/trunk/src/java/phenote/gui/ConfigGui.java 2007-07-17 20:45:27 UTC (rev 730)
@@ -61,7 +61,7 @@
public ConfigGui() { init(); }
private void init() {
- JFrame frame = new JFrame("Phenote Configuration");
+ JFrame frame = new JFrame("Phenote Configuration(under development)");
JComponent allConfigs = makeAllConfigsPanel();
allConfigs.setPreferredSize(new Dimension(300,300));
Modified: phenote/trunk/src/java/phenote/gui/SettingsMenu.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/SettingsMenu.java 2007-07-17 20:41:14 UTC (rev 729)
+++ phenote/trunk/src/java/phenote/gui/SettingsMenu.java 2007-07-17 20:45:27 UTC (rev 730)
@@ -82,7 +82,7 @@
add(loadConfig);
// proto gui config
- JMenuItem browseConfig = new JMenuItem("Browse configuration");
+ JMenuItem browseConfig = new JMenuItem("Browse configuration(dev)");
browseConfig.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) { new ConfigGui(); } } );
add(browseConfig);
Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java 2007-07-17 20:41:14 UTC (rev 729)
+++ phenote/trunk/src/java/phenote/main/Phenote.java 2007-07-17 20:45:27 UTC (rev 730)
@@ -176,6 +176,11 @@
return !getGroupTabs().isEmpty();
}
+ private int getNumGroupTabs() {
+ if (getGroupTabs() == null) return 0;
+ return getGroupTabs().size();
+ }
+
private List<Group> getGroupTabs() {
return getGroupsByContainer(Group.Container.TAB);
}
@@ -228,7 +233,7 @@
private void makeMainWindow() {
// this may be changed to applet...
frame = new JFrame("Phenote "+PhenoteVersion.versionString());
- if (!hasGroupTabs()) {
+ if (getNumGroupTabs() < 2) {
frame.getContentPane().add(makeGroupPanel(OntologyManager.DEFAULT_GROUP));
}
else {
Modified: phenote/trunk/src/java/phenote/main/PhenoteVersion.java
===================================================================
--- phenote/trunk/src/java/phenote/main/PhenoteVersion.java 2007-07-17 20:41:14 UTC (rev 729)
+++ phenote/trunk/src/java/phenote/main/PhenoteVersion.java 2007-07-17 20:45:27 UTC (rev 730)
@@ -9,7 +9,7 @@
//private static final float MAJOR_VERSION_NUM = 0.8f;
//private static final float SUB_VERSION_NUM = .3f;
- private static final String VERSION = "1.4-beta1"; // ??
+ private static final String VERSION = "1.4-beta2"; // ??
// type is "dev" or "release"
//private static final String type = " dev"; // "release"
@@ -19,7 +19,7 @@
}
public static Date getDateOfVersion(){
- GregorianCalendar cal = new GregorianCalendar(2007, GregorianCalendar.MAY, 25);
+ GregorianCalendar cal = new GregorianCalendar(2007, GregorianCalendar.JULY, 17);
return cal.getTime();
}
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