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[Obo-svn-commit] SF.net SVN: obo: [625] phenote/trunk/src/java/phenote/config/OntologyConfig .java

From: <nl...@us...> - 2007-05-24 19:09:03

Revision: 625
          http://svn.sourceforge.net/obo/?rev=625&view=rev
Author:   nlw
Date:     2007-05-24 12:09:04 -0700 (Thu, 24 May 2007)

Log Message:
-----------
added the ability to have ftp, sftp, and https as prefixes for downloading ontology files

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/config/OntologyConfig.java

Modified: phenote/trunk/src/java/phenote/config/OntologyConfig.java
===================================================================
--- phenote/trunk/src/java/phenote/config/OntologyConfig.java	2007-05-24 19:07:45 UTC (rev 624)
+++ phenote/trunk/src/java/phenote/config/OntologyConfig.java	2007-05-24 19:09:04 UTC (rev 625)
@@ -96,7 +96,8 @@
   /** File can be url(repos) or filename (from cache/jar/app), if url sets 
       reposUrlString and ontologyFile with end of url */
   private void setFile(String file) {
-    if (file.startsWith("http:")) {
+    if (file.startsWith("http:") || file.startsWith("https:") ||
+    		file.startsWith("ftp:") || file.startsWith("sftp:")) {
       reposUrlString = file;
       ontologyFile = file.substring(file.lastIndexOf('/')+1);
     }


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[Obo-svn-commit] SF.net SVN: obo: [624] phenote/trunk/conf

From: <nl...@us...> - 2007-05-24 19:07:46

Revision: 624
          http://svn.sourceforge.net/obo/?rev=624&view=rev
Author:   nlw
Date:     2007-05-24 12:07:45 -0700 (Thu, 24 May 2007)

Log Message:
-----------
changed most configuratios to be decorated with comments; changed to remove the old obo-repos config line and replaced each with the embedded link within the filename; removed nicole.cfg - not necessary anymore; added a new alternative for birn configuration - will use for access to my test data; note that these configurations require the use of 'ftp:' as a prefix for the filename, and can be used only after version 1.3beta2

Modified Paths:
--------------
    phenote/trunk/conf/demo.cfg
    phenote/trunk/conf/flybase.cfg
    phenote/trunk/conf/ncbo.cfg
    phenote/trunk/conf/zfin-standalone.cfg

Added Paths:
-----------
    phenote/trunk/conf/birn2.cfg

Removed Paths:
-------------
    phenote/trunk/conf/nicole.cfg

Added: phenote/trunk/conf/birn2.cfg
===================================================================
--- phenote/trunk/conf/birn2.cfg	                        (rev 0)
+++ phenote/trunk/conf/birn2.cfg	2007-05-24 19:07:45 UTC (rev 624)
@@ -0,0 +1,67 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<phenote-configuration version="1.3-beta1" xmlns="phenote/config/xml" 
+		       name="BIRN Test Config 2" 
+		       author="Nicole Washington"
+		       description="A test for finding a config for BIRN so I can test annotate from their spreadsheet.  It includes their converted brain subcellular anatomy ontology (SAO).">
+  <log config-file="conf/log4j-standalone.xml"/>
+
+
+  <!-- ********************* FILE ADAPTERS ************************** -->
+  <!-- be sure to include at least one enabled file adapter -->                                      
+  <dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>
+  <dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
+  <dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
+
+
+  <!-- ******************** FIELD DEFINITIONS *********************** --> 
+  <field name="Pub" syntax-abbrev="PUB" enable="true" desc="The provenance for this data"/>
+  <field name="Image" enable="true" desc="An image ID for reference"/>
+  <field name="Organism" enable="true" syntax-abbrev="GT" desc="This is like the genotype; its probably a
+    mouse strain or some other identifying factor"/>
+  <field name="Phenotypic Character" enable="true" desc="This is a free-text field for phenotype characters for now, not exactly sure what this captures; it might be just a grouping or it might be conclusions, or something else entirely"/>
+  <field name="Entity" syntax-abbrev="E" enable="true">
+     <ontology name="Relationship" is-postcomp-rel="true"
+      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
+    <ontology name="SAO" file="SAO.obo"/>
+    <ontology name="FMA" file="fma_obo.obo"/>
+    <ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
+    <ontology name="GO"
+       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
+    <ontology name="CL"
+        file="http://www.berkeleybop.org/ontologies/obo-all/cell/cell.obo" />
+    <ontology name="CHEBI"
+       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
+  </field>
+
+  <field name="Quality" syntax-abbrev="Q" enable="true">
+    <ontology file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo"/>
+  </field>
+
+  <field name="Add'l Entity" syntax-abbrev="E2" enable="true">
+     <ontology name="Relationship" is-postcomp-rel="true"
+      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
+    <ontology name="SAO" file="SAO.obo"/>
+    <ontology name="FMA" file="fma_obo.obo"/>
+    <ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
+    <ontology name="GO"
+     file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
+    <ontology name="CL"
+        file="http://www.berkeleybop.org/ontologies/obo-all/cell/cell.obo" />
+    <ontology name="CHEBI"
+       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
+  </field>
+
+  <field name="Compare To" syntax-abbrev="Compar" enable="true"/>
+
+  <field name="Description" syntax-abbrev="Desc" enable="true"/>
+
+
+  <!-- *********************** SETTINGS **************************** -->
+  <uvic-graph enable="false"/>
+  <term-history enable="false"/>
+  <auto-update-ontologies enable="true"/>  <!--true=update; false=don't update-->
+  <!--set to 0 if you want to bypass the check; time in seconds-->
+  <update-timer timer="10"/>
+
+
+</phenote-configuration>

Modified: phenote/trunk/conf/demo.cfg
===================================================================
--- phenote/trunk/conf/demo.cfg	2007-05-24 18:22:25 UTC (rev 623)
+++ phenote/trunk/conf/demo.cfg	2007-05-24 19:07:45 UTC (rev 624)
@@ -1,57 +1,78 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<ns:phenote-configuration version="1.3.1" xmlns:ns="phenote/config/xml">
+<!-- *********************** CONFIG INFO ************************** -->
+<ns:phenote-configuration xmlns:ns="phenote/config/xml" version="1.3.1"
+			  name="Demo Configuration"
+			  author="Phenote Developers"
+			  description="This is a configuration for demonstration purposes only.  It shows the different types of fields, ontologies, etc.  Use of the sample_data.xls can be loaded into this configuration.">
+
+  <!-- *********************** SETTINGS **************************** -->
+  <ns:master-to-local-config mode="WIPEOUT" when="ALWAYS" 
+     overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/demo.cfg" />
   <ns:log config-file="conf/log4j-standalone.xml"/>
 
-  <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>  <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>
+  <ns:uvic-graph enable="false"/>
+  <ns:term-history enable="false"/>
+  <ns:auto-update-ontologies enable="true"/>  
+    <!--true=update; false=don't update-->
+  <ns:update-timer timer="0"/>
+    <!--set to 0 if you want to bypass the check; time in seconds-->
+
+  <!-- ********************* FILE ADAPTERS ************************** -->
+  <!-- be sure to include at least one enabled file adapter -->
+  <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>  
+  <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>
   <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
   <ns:dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/>
 
 
-  <ns:uvic-graph enable="false"/>
 
-  <ns:term-history enable="false"/>
+  <!-- ******************** FIELD DEFINITIONS *********************** --> 
+  <!--The order of the fields is important, and will display in the order 
+  listed here.  If a repository location is given as the filename (ie 
+  "http://www.your-repository.com/your_obo_file.obo"), then this site 
+  will be checked for updates -->
   
-  <ns:auto-update-ontologies enable="true"/>  <!--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:obo-repository url-dir="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/>
-
   <ns:field name="Pub" syntax-abbrev="PUB" enable="true"/>
   <ns:field name="Genotype" syntax-abbrev="GT" enable="true"/>
   <ns:field name="Genetic Context" syntax-abbrev="GC" enable="true">
     <ns:ontology name="Genetic Context" file="context.obo"/>
   </ns:field>
   <ns:field name="Entity" syntax-abbrev="E" enable="true">
-    <ns:ontology name="Relationship" file="relationship.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/>
+    <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/>
     <ns:ontology name="FMA" file="fma_obo.obo"/>
-    <ns:ontology name="GO" file="gene_ontology.obo" repos-subdir="genomic-proteomic"/>
-    <ns:ontology name="CL" file="cell.obo" repos-subdir="anatomy/cell_type"/>
-    <ns:ontology name="SO" file="so.obo" repos-subdir="genomic-proteomic"/>
-    <ns:ontology name="CHEBI" file="chebi.obo" repos-subdir="chemical"/>
+    <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
+    <ns:ontology name="CL" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo"/>
+    <ns:ontology name="SO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo"/>
+    <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
   </ns:field>
   <ns:field name="Quality" syntax-abbrev="Q" enable="true">
-    <ns:ontology name="PATO" file="quality.obo" repos-subdir="phenotype"/>
-    <ns:ontology name="MP" file="mammalian_phenotype.obo" repos-subdir="phenotype"/>
+    <ns:ontology name="PATO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
+    <ns:ontology name="MP" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mammalian_phenotype.obo"/>
   </ns:field>
   <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true">
-    <ns:ontology name="Relationship" file="relationship.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/>
+    <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" is-postcomp-rel="true"/>
     <ns:ontology name="FMA" file="fma_obo.obo"/>
-    <ns:ontology name="GO" file="gene_ontology.obo" repos-subdir="genomic-proteomic"/>
-    <ns:ontology name="CL" file="cell.obo" repos-subdir="anatomy/cell_type"/>
-    <ns:ontology name="SO" file="so.obo" repos-subdir="genomic-proteomic"/>
-    <ns:ontology name="CHEBI" file="chebi.obo" repos-subdir="chemical"/>
+    <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo" />
+    <ns:ontology name="CL" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo"/>
+    <ns:ontology name="SO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo"/>
+    <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
   </ns:field>
   <ns:field name="Time" syntax-abbrev="T" enable="true"/>
   <ns:field name="Count" syntax-abbrev="C" enable="true"/>
   <ns:field name="Unit" syntax-abbrev="U" enable="true">
-    <ns:ontology name="Unit" file="unit.obo" repos-subdir="phenotype"/>
+    <ns:ontology name="Unit" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
   </ns:field>
   <ns:field name="Abnormal" syntax-abbrev="Tag" enable="true">
     <ns:ontology name="Abnormal" file="quality.obo" slim="abnormal_slim"/>
   </ns:field>
   <ns:field name="Description" syntax-abbrev="Desc" enable="true"/>
   <ns:field name="Evidence" syntax-abbrev="EC" enable="false">
-    <ns:ontology name="Evidence" file="evidence_code.obo" repos-subdir="."/>
+    <ns:ontology name="Evidence" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/evidence_code.obo"/>
   </ns:field>
+  <!-- ******************** REVISION HISTORY *********************** --> 
+  <!-- 05.24.2007 - Latest update changes relationship.obo to ro.obo; included ehdaa repository; 
+       removed obo-repository url-dir and incorporated into each filename; added in comments; 
+       Changed GO to gene_ontology_edit.obo file;
+       Added in local-to-master overwrite config to ALWAYS overwrite -->
+
 </ns:phenote-configuration>
\ No newline at end of file

Modified: phenote/trunk/conf/flybase.cfg
===================================================================
--- phenote/trunk/conf/flybase.cfg	2007-05-24 18:22:25 UTC (rev 623)
+++ phenote/trunk/conf/flybase.cfg	2007-05-24 19:07:45 UTC (rev 624)
@@ -1,12 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<ns:phenote-configuration version="1.3.1" xmlns:ns="phenote/config/xml">
+<!-- *********************** CONFIG INFO ************************** -->
+<ns:phenote-configuration version="1.3.1" xmlns:ns="phenote/config/xml"
+			  name="Flybase"
+			  author="Nicole Washington"
+			  description="This configuration is for the curators working at Flybase, or others in the Drosophila community for phenotype annotation.  This does not yet have a genotype maker.">
+>
 
-  <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"/>
-
+  <!-- *********************** 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"/>
@@ -14,11 +16,17 @@
   
   <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-->
+
+  <!-- ********************* 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:obo-repository url-dir="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/>
-
   <ns:field name="Pub" syntax-abbrev="PUB"/>                      
 
   <ns:field name="Genotype" syntax-abbrev="GT" type="free_text"/>
@@ -30,16 +38,16 @@
   <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="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/relationship.obo"/>
+      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
      <ns:ontology name="Fly" file="fly_anatomy.obo" />
         <!--repos-subdir="anatomy/gross_anatomy/animal_gross_anatomy/fly"-->
      <ns:ontology name="Human Anatomy" file="fma_obo.obo"/>	
-     <ns:ontology name="GO" file="gene_ontology.obo" repos-subdir="genomic-proteomic"/>
+     <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
      <ns:ontology name="SP" file="spatial.obo"/>
   </ns:field>
 
   <ns:field name="Quality"  syntax-abbrev="Q">
-    <ns:ontology file="quality.obo" repos-subdir="phenotype" />
+    <ns:ontology file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo" />
   </ns:field>
 
   <ns:field name="Absent" syntax-abbrev="Tag">
@@ -52,4 +60,11 @@
 
   <ns:field name="Description" syntax-abbrev="Desc"/>
 
+  <!-- ******************** REVISION HISTORY *********************** --> 
+  <!-- 05.24.2007 - Latest update changes relationship.obo to ro.obo;  
+       removed obo-repository url-dir and incorporated into each filename; added in comments; 
+       Changed GO to gene_ontology_edit.obo file;
+       Added in local-to-master overwrite config to UPDATE on VERSION_CHANGE
+       removed fly from repository update -->
+
 </ns:phenote-configuration>

Modified: phenote/trunk/conf/ncbo.cfg
===================================================================
--- phenote/trunk/conf/ncbo.cfg	2007-05-24 18:22:25 UTC (rev 623)
+++ phenote/trunk/conf/ncbo.cfg	2007-05-24 19:07:45 UTC (rev 624)
@@ -42,7 +42,7 @@
     <ns:ontology name="FMA" file="fma_obo.obo"/>
     <ns:ontology name="EHDAA" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo"/>
     <ns:ontology name="GO"
-      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
+      file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
     <ns:ontology name="CL"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo"/>
     <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
@@ -58,7 +58,7 @@
     <ns:ontology name="FMA" file="fma_obo.obo"/>
     <ns:ontology name="EHDAA" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo"/>
     <ns:ontology name="GO"
-      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
+      file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
     <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
     <ns:ontology name="CL"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo"/>
@@ -74,5 +74,6 @@
   <!-- 05.20.2007 - Latest update changes relationship.obo to ro.obo; included ehdaa repository; 
        removed obo-repository url-dir and incorporated into each filename; added in comments; 
        removed the nexus adapter...it won't ever be used by this group.-->
+  <!-- 05.24.2007 - Changed GO to gene_ontology_edit.obo file -->
 
 </ns:phenote-configuration>
\ No newline at end of file

Deleted: phenote/trunk/conf/nicole.cfg
===================================================================
--- phenote/trunk/conf/nicole.cfg	2007-05-24 18:22:25 UTC (rev 623)
+++ phenote/trunk/conf/nicole.cfg	2007-05-24 19:07:45 UTC (rev 624)
@@ -1,52 +0,0 @@
-<?xml version="1.2beta1" encoding="UTF-8"?>
-<ns:phenote-configuration version="1.1.2b" xmlns:ns="phenote/config/xml">
-  <ns:log config-file="conf/log4j-standalone.xml"/>
-
-  <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter"
-                   enable="true"/>  
-  <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter"
-                  enable="true"/>
-  <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
-  <ns:dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/>
-
-  <ns:uvic-graph enable="false"/>
-  <ns:term-history enable="false"/>
-  <ns:obo-repository url-dir="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/>
-  <ns:field name="Pub" syntax-abbrev="PUB" enable="true"/>
-  <ns:field name="Genotype" syntax-abbrev="GT" enable="true"/>
-  <ns:field name="Genetic Context" syntax-abbrev="GC" enable="true">
-    <ns:ontology name="Genetic Context" file="context.obo"/>
-  </ns:field>
-  <ns:field name="Entity" syntax-abbrev="E" enable="true">
-    <ns:ontology name="Relationship" file="relationship.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/>
-    <ns:ontology name="FMA" file="fma_obo.obo"/>
-    <ns:ontology name="GO" file="gene_ontology.obo" repos-subdir="genomic-proteomic"/>
-    <ns:ontology name="CL" file="cell.obo" repos-subdir="anatomy/cell_type"/>
-    <ns:ontology name="SO" file="so.obo" repos-subdir="genomic-proteomic"/>
-    <ns:ontology name="CHEBI" file="chebi.obo" repos-subdir="chemical"/>
-  </ns:field>
-  <ns:field name="Quality" syntax-abbrev="Q" enable="true">
-    <ns:ontology name="PATO" file="quality.obo" repos-subdir="phenotype"/>
-    <ns:ontology name="MP" file="mammalian_phenotype.obo" repos-subdir="phenotype"/>
-  </ns:field>
-  <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true">
-    <ns:ontology name="Relationship" file="relationship.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/>
-    <ns:ontology name="FMA" file="fma_obo.obo"/>
-    <ns:ontology name="GO" file="gene_ontology.obo" repos-subdir="genomic-proteomic"/>
-    <ns:ontology name="CL" file="cell.obo" repos-subdir="anatomy/cell_type"/>
-    <ns:ontology name="SO" file="so.obo" repos-subdir="genomic-proteomic"/>
-    <ns:ontology name="CHEBI" file="chebi.obo" repos-subdir="chemical"/>
-  </ns:field>
-  <ns:field name="Time" syntax-abbrev="T" enable="true"/>
-  <ns:field name="Count" syntax-abbrev="C" enable="true"/>
-  <ns:field name="Unit" syntax-abbrev="U" enable="true">
-    <ns:ontology name="Unit" file="unit.obo" repos-subdir="phenotype"/>
-  </ns:field>
-  <ns:field name="Abnormal" syntax-abbrev="Tag" enable="true">
-    <ns:ontology name="Abnormal" file="quality.obo" slim="abnormal_slim"/>
-  </ns:field>
-  <ns:field name="Description" syntax-abbrev="Desc" enable="true"/>
-  <ns:field name="Evidence" syntax-abbrev="EC" enable="false">
-    <ns:ontology name="Evidence" file="evidence_code.obo" repos-subdir="."/>
-  </ns:field>
-</ns:phenote-configuration>
\ No newline at end of file

Modified: phenote/trunk/conf/zfin-standalone.cfg
===================================================================
--- phenote/trunk/conf/zfin-standalone.cfg	2007-05-24 18:22:25 UTC (rev 623)
+++ phenote/trunk/conf/zfin-standalone.cfg	2007-05-24 19:07:45 UTC (rev 624)
@@ -1,27 +1,28 @@
 <?xml version="1.3.1" encoding="UTF-8"?>
+<!-- *********************** CONFIG INFO ************************** -->
+<ns:phenote-configuration xmlns:ns="phenote/config/xml"
+			  name="Zebrafish Community"
+			  author="Mark Gibson, Nicole Washington"
+			  description="This configuration is for the curators and research community working with Zebrafish.  This tools provides for phenotype annotation.  It updates to the current ontologies.">
 
-<ns:phenote-configuration xmlns:ns="phenote/config/xml">
-
+  <!-- *********************** 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/zfin-standalone.cfg" />
 
   <ns:log config-file="conf/log4j-standalone.xml"/>
+  <ns:uvic-graph enable="false"/>
+  <ns:term-history enable="false"/>
+  <ns:auto-update-ontologies enable="true"/>  <!--true=update; false=don't update-->
+  <ns:update-timer timer="4"/><!--set to 0 if you want to bypass the check; time in seconds-->
 
-
+  <!-- ********************* FILE ADAPTERS ************************** -->
   <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter"
                   enable="true"/>
   <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter"
                   enable="true"/>
   <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
-  <ns:dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/>
-
-  <ns:uvic-graph enable="false"/>
-  <ns:term-history enable="false"/>
-  <ns:auto-update-ontologies enable="true"/>  <!--true=update; false=don't update-->
-  <ns:update-timer timer="4"/><!--set to 0 if you want to bypass the check; time in seconds-->
   
-  <ns:obo-repository url-dir="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/>
-
+  <!-- ******************** FIELD DEFINITIONS *********************** --> 
   <ns:field name="Pub" syntax-abbrev="PUB" enable="true"/>
 
   <ns:field name="Genotype" syntax-abbrev="GT" enable="true"/>
@@ -31,13 +32,12 @@
   </ns:field>
 
   <ns:field name="Entity" syntax-abbrev="E" enable="true">
-    <ns:ontology name="Relationship" file="relationship.obo"
-                 repos-subdir="OBO_REL" is-postcomp-rel="true"/>
-    <ns:ontology name="ZF" file="zebrafish_anatomy.obo"
-                  repos-subdir="anatomy/gross_anatomy/animal_gross_anatomy/fish"
-                  namespace="zebrafish_anatomy"/>
+    <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"
+                 is-postcomp-rel="true"/>
+    <ns:ontology name="ZF" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/zebrafish_anatomy.obo"
+		 namespace="zebrafish_anatomy"/>
     <ns:ontology name="GO"
-      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
+      file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
   </ns:field>
 
   <ns:field name="Stage" syntax-abbrev="T" enable="true">
@@ -52,10 +52,10 @@
 
   <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true">
     <ns:ontology name="Relationship" is-postcomp-rel="true"
-      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/relationship.obo"/>
+      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
     <ns:ontology name="ZF" namespace="zebrafish_anatomy"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/zebrafish_anatomy.obo"/>
-    <ns:ontology name="GO" file="gene_ontology.obo"/>
+    <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
   </ns:field>
 
   <ns:field name="Abnormal" syntax-abbrev="Tag" enable="true">
@@ -64,4 +64,12 @@
 
   <ns:field name="Description" syntax-abbrev="Desc" enable="true"/>
 
+  <!-- ******************** REVISION HISTORY *********************** --> 
+  <!-- 05.20.2007 - Added master-to-local config option to UPDATE on VERSION_CHANGE
+       Added timer to 4 sec. (mgibson) -->
+  <!-- 05.24.2007 - Latest update changes relationship.obo to ro.obo; 
+       removed obo-repository url-dir and incorporated into each filename; added in comments; 
+       removed the nexus adapter...it won't ever be used by this group.
+       Changed GO to gene_ontology_edit.obo file (nlw) -->
+
 </ns:phenote-configuration>
\ No newline at end of file


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [619] phenote/trunk/doc/phenote-website/help

From: <nl...@us...> - 2007-05-24 00:45:12

Revision: 619
          http://svn.sourceforge.net/obo/?rev=619&view=rev
Author:   nlw
Date:     2007-05-23 17:40:18 -0700 (Wed, 23 May 2007)

Log Message:
-----------
Phenote help docs:  added in post-composition with screenshots; is-queryable to datadapter parameter

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/help/Phenote.jhm
    phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak
    phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml
    phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml.bak
    phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html
    phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html.tmp
    phenote/trunk/doc/phenote-website/help/html/Editing_Functions.htm
    phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Free_Text_fields.htm
    phenote/trunk/doc/phenote-website/help/html/The__dataadapter__Tag.htm
    phenote/trunk/doc/phenote-website/help/html/Writing_a_Data_Adapter.htm

Added Paths:
-----------
    phenote/trunk/doc/phenote-website/help/html/Entity_Composition_Refinement.htm
    phenote/trunk/doc/phenote-website/help/images/Refine-expand.png
    phenote/trunk/doc/phenote-website/help/images/Refine-spreadsheet.png
    phenote/trunk/doc/phenote-website/help/images/Refine-threeterm.png
    phenote/trunk/doc/phenote-website/help/images/Refine-twoterm.png
    phenote/trunk/doc/phenote-website/help/images/Refine-window.png
    phenote/trunk/doc/phenote-website/help/images/free-text-posttab.png
    phenote/trunk/doc/phenote-website/help/images/free-text-pretab.png

Modified: phenote/trunk/doc/phenote-website/help/Phenote.jhm
===================================================================
--- phenote/trunk/doc/phenote-website/help/Phenote.jhm	2007-05-23 22:59:47 UTC (rev 618)
+++ phenote/trunk/doc/phenote-website/help/Phenote.jhm	2007-05-24 00:40:18 UTC (rev 619)
@@ -51,6 +51,7 @@
    <mapID target="Editing_Obsoletes" url="html/Editing_Obsoletes.htm"/>
    <mapID target="Entering_data_into_Free_Text_fields" url="html/Entering_data_into_Free_Text_fields.htm"/>
    <mapID target="Entering_data_into_Ontology_Fields" url="html/Entering_data_into_Ontology_Fields.htm"/>
+   <mapID target="Entity_Composition_Refinement" url="html/Entity_Composition_Refinement.htm"/>
    <mapID target="Example_Layouts" url="html/Example_Layouts.htm"/>
    <mapID target="Example_Scripts" url="html/Example_Scripts.htm"/>
    <mapID target="Exiting_Phenote" url="html/Exiting_Phenote.htm"/>

Modified: phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak
===================================================================
--- phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak	2007-05-23 22:59:47 UTC (rev 618)
+++ phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak	2007-05-24 00:40:18 UTC (rev 619)
@@ -51,6 +51,7 @@
    <mapID target="Editing_Obsoletes" url="html/Editing_Obsoletes.htm"/>
    <mapID target="Entering_data_into_Free_Text_fields" url="html/Entering_data_into_Free_Text_fields.htm"/>
    <mapID target="Entering_data_into_Ontology_Fields" url="html/Entering_data_into_Ontology_Fields.htm"/>
+   <mapID target="Entity_Composition_Refinement" url="html/Entity_Composition_Refinement.htm"/>
    <mapID target="Example_Layouts" url="html/Example_Layouts.htm"/>
    <mapID target="Example_Scripts" url="html/Example_Scripts.htm"/>
    <mapID target="Exiting_Phenote" url="html/Exiting_Phenote.htm"/>

Modified: phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml	2007-05-23 22:59:47 UTC (rev 618)
+++ phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml	2007-05-24 00:40:18 UTC (rev 619)
@@ -34,9 +34,10 @@
 </tocitem>
 <tocitem text="Creating Annotations">
      <tocitem text="Editing Functions" target="Editing_Functions"/>
-     <tocitem text="Changing your Autocompletion Settings" target="Changing_your_Autocompletion_Settings"/>
      <tocitem text="Entering data into Free-Text fields" target="Entering_data_into_Free_Text_fields"/>
      <tocitem text="Entering data into Ontology Fields" target="Entering_data_into_Ontology_Fields"/>
+     <tocitem text="Term Composition/Refinement" target="Entity_Composition_Refinement"/>
+     <tocitem text="Changing your Autocompletion Settings" target="Changing_your_Autocompletion_Settings"/>
      <tocitem text="Sample Annotations" target="Sample_Annotations"/>
 </tocitem>
 <tocitem text="Information for Developers">
@@ -69,29 +70,6 @@
      <tocitem text="Basic Concepts and Vocabulary" target="Basic_Concepts_and_Vocabulary"/>
 </tocitem>
 <tocitem text="from OBOedit">
-     <tocitem text="Customizing OBO-Edit">
-          <tocitem text="The Configuration Plugin" target="The_Configuration_Plugin"/>
-          <tocitem text="Customizing the Interface">
-               <tocitem text="Working with XML Layouts" target="Working_with_XML_Layouts"/>
-               <tocitem text="Common Parameters" target="Common_Parameters"/>
-               <tocitem text="The &lt;glue&gt; Tag" target="The_Glue_Tag"/>
-               <tocitem text="The &lt;spacer&gt; Tag" target="The_Spacer_Tag"/>
-               <tocitem text="The &lt;label&gt; Tag" target="The_Label_Tag"/>
-               <tocitem text="The &lt;box&gt; Tag" target="The_Box_Tag"/>
-               <tocitem text="The &lt;grid&gt; Tag" target="The_Grid_Tag"/>
-               <tocitem text="The &lt;panel&gt; Tag" target="The_Panel_Tag"/>
-               <tocitem text="The &lt;compactgrid&gt; Tag" target="The_Compactgrid_Tag"/>
-               <tocitem text="The &lt;divider&gt; Tag" target="The_Divider_Tag"/>
-               <tocitem text="The &lt;tabs&gt; Tag" target="The_Tabs_Tag"/>
-               <tocitem text="The &lt;window&gt; Tag" target="The_Window_Tag"/>
-               <tocitem text="The &lt;if&gt; Tag" target="The_If_Tag"/>
-               <tocitem text="The &lt;component&gt; Tag" target="The_Component_Tag"/>
-               <tocitem text="Example Layouts" target="Example_Layouts">
-                    <tocitem text="The Default Layout" target="The_Default_Layout"/>
-               </tocitem>
-          </tocitem>
-     </tocitem>
-     <tocitem text="New Topic"/>
      <tocitem text="Working with Data Adapters">
           <tocitem text="The Basic Flat File Interface" target="The_Scroller_Tag"/>
           <tocitem text="The OBO Adapter" target="The_OBO_Adapter"/>
@@ -99,5 +77,27 @@
           <tocitem text="The Serial Adapter" target="The_Serial_Adapter"/>
           <tocitem text="Custom Data Adapters" target="Custom_Data_Adapters"/>
      </tocitem>
+     <tocitem text="Customizing the Interface">
+          <tocitem text="Working with XML Layouts" target="Working_with_XML_Layouts"/>
+          <tocitem text="Common Parameters" target="Common_Parameters"/>
+          <tocitem text="The &lt;glue&gt; Tag" target="The_Glue_Tag"/>
+          <tocitem text="The &lt;spacer&gt; Tag" target="The_Spacer_Tag"/>
+          <tocitem text="The &lt;label&gt; Tag" target="The_Label_Tag"/>
+          <tocitem text="The &lt;box&gt; Tag" target="The_Box_Tag"/>
+          <tocitem text="The &lt;grid&gt; Tag" target="The_Grid_Tag"/>
+          <tocitem text="The &lt;panel&gt; Tag" target="The_Panel_Tag"/>
+          <tocitem text="The &lt;compactgrid&gt; Tag" target="The_Compactgrid_Tag"/>
+          <tocitem text="The &lt;divider&gt; Tag" target="The_Divider_Tag"/>
+          <tocitem text="The &lt;tabs&gt; Tag" target="The_Tabs_Tag"/>
+          <tocitem text="The &lt;window&gt; Tag" target="The_Window_Tag"/>
+          <tocitem text="The &lt;if&gt; Tag" target="The_If_Tag"/>
+          <tocitem text="The &lt;component&gt; Tag" target="The_Component_Tag"/>
+          <tocitem text="Example Layouts" target="Example_Layouts">
+               <tocitem text="The Default Layout" target="The_Default_Layout"/>
+          </tocitem>
+     </tocitem>
+     <tocitem text="Customizing OBO-Edit">
+          <tocitem text="The Configuration Plugin" target="The_Configuration_Plugin"/>
+     </tocitem>
 </tocitem>
 </toc>

Modified: phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml.bak
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml.bak	2007-05-23 22:59:47 UTC (rev 618)
+++ phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml.bak	2007-05-24 00:40:18 UTC (rev 619)
@@ -37,10 +37,11 @@
      <tocitem text="Changing your Autocompletion Settings" target="Changing_your_Autocompletion_Settings"/>
      <tocitem text="Entering data into Free-Text fields" target="Entering_data_into_Free_Text_fields"/>
      <tocitem text="Entering data into Ontology Fields" target="Entering_data_into_Ontology_Fields"/>
+     <tocitem text="Entity Composition/Refinement" target="Entity_Composition_Refinement"/>
      <tocitem text="Sample Annotations" target="Sample_Annotations"/>
 </tocitem>
 <tocitem text="Information for Developers">
-     <tocitem text="Writing a Data Adapter"/>
+     <tocitem text="Writing a Data Adapter" target="Writing_a_Data_Adapter"/>
      <tocitem text="Connecting to a Database" target="Connecting_to_a_Database"/>
      <tocitem text="Adding configurability" target="Adding_configurability"/>
 </tocitem>
@@ -69,29 +70,6 @@
      <tocitem text="Basic Concepts and Vocabulary" target="Basic_Concepts_and_Vocabulary"/>
 </tocitem>
 <tocitem text="from OBOedit">
-     <tocitem text="Customizing OBO-Edit">
-          <tocitem text="The Configuration Plugin" target="The_Configuration_Plugin"/>
-          <tocitem text="Customizing the Interface">
-               <tocitem text="Working with XML Layouts" target="Working_with_XML_Layouts"/>
-               <tocitem text="Common Parameters" target="Common_Parameters"/>
-               <tocitem text="The &lt;glue&gt; Tag" target="The_Glue_Tag"/>
-               <tocitem text="The &lt;spacer&gt; Tag" target="The_Spacer_Tag"/>
-               <tocitem text="The &lt;label&gt; Tag" target="The_Label_Tag"/>
-               <tocitem text="The &lt;box&gt; Tag" target="The_Box_Tag"/>
-               <tocitem text="The &lt;grid&gt; Tag" target="The_Grid_Tag"/>
-               <tocitem text="The &lt;panel&gt; Tag" target="The_Panel_Tag"/>
-               <tocitem text="The &lt;compactgrid&gt; Tag" target="The_Compactgrid_Tag"/>
-               <tocitem text="The &lt;divider&gt; Tag" target="The_Divider_Tag"/>
-               <tocitem text="The &lt;tabs&gt; Tag" target="The_Tabs_Tag"/>
-               <tocitem text="The &lt;window&gt; Tag" target="The_Window_Tag"/>
-               <tocitem text="The &lt;if&gt; Tag" target="The_If_Tag"/>
-               <tocitem text="The &lt;component&gt; Tag" target="The_Component_Tag"/>
-               <tocitem text="Example Layouts" target="Example_Layouts">
-                    <tocitem text="The Default Layout" target="The_Default_Layout"/>
-               </tocitem>
-          </tocitem>
-     </tocitem>
-     <tocitem text="New Topic"/>
      <tocitem text="Working with Data Adapters">
           <tocitem text="The Basic Flat File Interface" target="The_Scroller_Tag"/>
           <tocitem text="The OBO Adapter" target="The_OBO_Adapter"/>
@@ -99,5 +77,27 @@
           <tocitem text="The Serial Adapter" target="The_Serial_Adapter"/>
           <tocitem text="Custom Data Adapters" target="Custom_Data_Adapters"/>
      </tocitem>
+     <tocitem text="Customizing the Interface">
+          <tocitem text="Working with XML Layouts" target="Working_with_XML_Layouts"/>
+          <tocitem text="Common Parameters" target="Common_Parameters"/>
+          <tocitem text="The &lt;glue&gt; Tag" target="The_Glue_Tag"/>
+          <tocitem text="The &lt;spacer&gt; Tag" target="The_Spacer_Tag"/>
+          <tocitem text="The &lt;label&gt; Tag" target="The_Label_Tag"/>
+          <tocitem text="The &lt;box&gt; Tag" target="The_Box_Tag"/>
+          <tocitem text="The &lt;grid&gt; Tag" target="The_Grid_Tag"/>
+          <tocitem text="The &lt;panel&gt; Tag" target="The_Panel_Tag"/>
+          <tocitem text="The &lt;compactgrid&gt; Tag" target="The_Compactgrid_Tag"/>
+          <tocitem text="The &lt;divider&gt; Tag" target="The_Divider_Tag"/>
+          <tocitem text="The &lt;tabs&gt; Tag" target="The_Tabs_Tag"/>
+          <tocitem text="The &lt;window&gt; Tag" target="The_Window_Tag"/>
+          <tocitem text="The &lt;if&gt; Tag" target="The_If_Tag"/>
+          <tocitem text="The &lt;component&gt; Tag" target="The_Component_Tag"/>
+          <tocitem text="Example Layouts" target="Example_Layouts">
+               <tocitem text="The Default Layout" target="The_Default_Layout"/>
+          </tocitem>
+     </tocitem>
+     <tocitem text="Customizing OBO-Edit">
+          <tocitem text="The Configuration Plugin" target="The_Configuration_Plugin"/>
+     </tocitem>
 </tocitem>
 </toc>

Modified: phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html	2007-05-23 22:59:47 UTC (rev 618)
+++ phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html	2007-05-24 00:40:18 UTC (rev 619)
@@ -261,171 +261,171 @@
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Editing_Functions.htm" target=bodyframe>Editing Functions</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt122>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Changing_your_Autocompletion_Settings.htm" target=bodyframe>Changing your Autocompletion Settings</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Entering_data_into_Free_Text_fields.htm" target=bodyframe>Entering data into Free-Text fields</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt123>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Entering_data_into_Free_Text_fields.htm" target=bodyframe>Entering data into Free-Text fields</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Entering_data_into_Ontology_Fields.htm" target=bodyframe>Entering data into Ontology Fields</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt124>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Entering_data_into_Ontology_Fields.htm" target=bodyframe>Entering data into Ontology Fields</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Entity_Composition_Refinement.htm" target=bodyframe>Term Composition/Refinement</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt125>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Changing_your_Autocompletion_Settings.htm" target=bodyframe>Changing your Autocompletion Settings</font></a>
+</td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt126>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Sample_Annotations.htm" target=bodyframe>Sample Annotations</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Information for Developers</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt126>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt127>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Writing_a_Data_Adapter.htm" target=bodyframe>Writing a Data Adapter</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt127>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt128>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Connecting_to_a_Database.htm" target=bodyframe>Connecting to a Database</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt128>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt129>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Adding_configurability.htm" target=bodyframe>Adding configurability</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>What to do after Phenote</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt129>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt130>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>I've entered my data, now what?</face>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt130>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt131>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Other_Uses_for_Phenote.htm" target=bodyframe>Other Uses for Phenote</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing Phenote</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt131>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt132>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/What_is_a_Configuration_.htm" target=bodyframe>What is a Configuration?</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt132>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt133>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/How_To_Edit_a_Configuration_File.htm" target=bodyframe>How To Edit a Configuration File</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt133>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt134>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Sample_Configuration_1.htm" target=bodyframe>Sample Configuration 1</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt134>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt135>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Sample_Configuration_2.htm" target=bodyframe>Sample Configuration 2</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt135>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt136>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/XML_skeleton.htm" target=bodyframe>XML skeleton</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt136>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt137>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__phenote_configuration__Tag.htm" target=bodyframe>The &amp;lt;phenote-configuration&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt137>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt138>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__tab__Tag.htm" target=bodyframe>The &amp;lt;tab&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt138>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt139>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__dataadapter__Tag.htm" target=bodyframe>The &amp;lt;dataadapter&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt139>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt140>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__master_to_local_config__Tag.htm" target=bodyframe>The &amp;lt;master-to-local-config&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt140>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt141>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__field__Tag.htm" target=bodyframe>The &amp;lt;field&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt141>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt142>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__ontology__Tag.htm" target=bodyframe>The &amp;lt;ontology&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt142>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt143>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__auto_update_ontologies__Tag.htm" target=bodyframe>The &amp;lt;auto-update-ontologies&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt143>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt144>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__update_timer__Tag.htm" target=bodyframe>The &amp;lt;update-timer&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt144>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt145>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__term_history__Tag.htm" target=bodyframe>The &amp;lt;term-history&amp;gt; Tag</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Appendix</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt145>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt146>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/An_Introduction_to_OBO_Ontologies.htm" target=bodyframe>An Introduction to OBO Ontologies</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt146>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt147>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Basic_Concepts_and_Vocabulary.htm" target=bodyframe>Basic Concepts and Vocabulary</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>from OBOedit</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt147>
-<tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing OBO-Edit</face>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt148>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Configuration_Plugin.htm" target=bodyframe>The Configuration Plugin</font></a>
+<tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Working with Data Adapters</face>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt149>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Basic_Flat_File_Interface.htm" target=bodyframe>The Basic Flat File Interface</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt149>
-<tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing the Interface</face>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt150>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Working_with_XML_Layouts.htm" target=bodyframe>Working with XML Layouts</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_OBO_Adapter.htm" target=bodyframe>The OBO Adapter</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt151>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Common_Parameters.htm" target=bodyframe>Common Parameters</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_GO_Flat_File_Adapter.htm" target=bodyframe>The GO Flat File Adapter</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt152>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Glue_Tag.htm" target=bodyframe>The &amp;lt;glue&amp;gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Serial_Adapter.htm" target=bodyframe>The Serial Adapter</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt153>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Spacer_Tag.htm" target=bodyframe>The &amp;lt;spacer&amp;gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Custom_Data_Adapters.htm" target=bodyframe>Custom Data Adapters</font></a>
 </td></tr></table>
+</td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt154>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Label_Tag.htm" target=bodyframe>The &amp;lt;label&amp;gt; Tag</font></a>
-</td></tr></table>
+<tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing the Interface</face>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt155>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Box_Tag.htm" target=bodyframe>The &amp;lt;box&amp;gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Working_with_XML_Layouts.htm" target=bodyframe>Working with XML Layouts</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt156>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Grid_Tag.htm" target=bodyframe>The &amp;lt;grid&amp;gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Common_Parameters.htm" target=bodyframe>Common Parameters</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt157>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Panel_Tag.htm" target=bodyframe>The &amp;lt;panel&amp;gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Glue_Tag.htm" target=bodyframe>The &amp;lt;glue&amp;gt; Tag</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt158>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Compactgrid_Tag.htm" target=bodyframe>The &amp;lt;compactgrid&amp;gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Spacer_Tag.htm" target=bodyframe>The &amp;lt;spacer&amp;gt; Tag</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt159>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Divider_Tag.htm" target=bodyframe>The &amp;lt;divider&amp;gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Label_Tag.htm" target=bodyframe>The &amp;lt;label&amp;gt; Tag</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt160>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Tabs_Tag.htm" target=bodyframe>The &amp;lt;tabs&amp;gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Box_Tag.htm" target=bodyframe>The &amp;lt;box&amp;gt; Tag</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt161>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Window_Tag.htm" target=bodyframe>The &amp;lt;window&amp;gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Grid_Tag.htm" target=bodyframe>The &amp;lt;grid&amp;gt; Tag</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt162>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_If_Tag.htm" target=bodyframe>The &amp;lt;if&amp;gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Panel_Tag.htm" target=bodyframe>The &amp;lt;panel&amp;gt; Tag</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt163>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Component_Tag.htm" target=bodyframe>The &amp;lt;component&amp;gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Compactgrid_Tag.htm" target=bodyframe>The &amp;lt;compactgrid&amp;gt; Tag</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt164>
-<tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Example_Layouts.htm" target=bodyframe>Example Layouts</face></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Divider_Tag.htm" target=bodyframe>The &amp;lt;divider&amp;gt; Tag</font></a>
+</td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt165>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Introduction.htm" target=bodyframe>The Default Layout</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Tabs_Tag.htm" target=bodyframe>The &amp;lt;tabs&amp;gt; Tag</font></a>
 </td></tr></table>
-</td></tr></table>
-</td></tr></table>
-</td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt166>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>New Topic</face>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Window_Tag.htm" target=bodyframe>The &amp;lt;window&amp;gt; Tag</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt167>
-<tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Working with Data Adapters</face>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_If_Tag.htm" target=bodyframe>The &amp;lt;if&amp;gt; Tag</font></a>
+</td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt168>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Basic_Flat_File_Interface.htm" target=bodyframe>The Basic Flat File Interface</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Component_Tag.htm" target=bodyframe>The &amp;lt;component&amp;gt; Tag</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt169>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_OBO_Adapter.htm" target=bodyframe>The OBO Adapter</font></a>
-</td></tr></table>
+<tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Example_Layouts.htm" target=bodyframe>Example Layouts</face></a>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt170>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_GO_Flat_File_Adapter.htm" target=bodyframe>The GO Flat File Adapter</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Introduction.htm" target=bodyframe>The Default Layout</font></a>
 </td></tr></table>
+</td></tr></table>
+</td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt171>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Serial_Adapter.htm" target=bodyframe>The Serial Adapter</font></a>
-</td></tr></table>
+<tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing OBO-Edit</face>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt172>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Custom_Data_Adapters.htm" target=bodyframe>Custom Data Adapters</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Configuration_Plugin.htm" target=bodyframe>The Configuration Plugin</font></a>
 </td></tr></table>
 </td></tr></table>
 </td></tr></table>

Modified: phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html.tmp
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html.tmp	2007-05-23 22:59:47 UTC (rev 618)
+++ phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html.tmp	2007-05-24 00:40:18 UTC (rev 619)
@@ -81,171 +81,171 @@
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Editing_Functions.htm" target=bodyframe>Editing Functions</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt122>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Changing_your_Autocompletion_Settings.htm" target=bodyframe>Changing your Autocompletion Settings</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Entering_data_into_Free_Text_fields.htm" target=bodyframe>Entering data into Free-Text fields</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt123>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Entering_data_into_Free_Text_fields.htm" target=bodyframe>Entering data into Free-Text fields</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Entering_data_into_Ontology_Fields.htm" target=bodyframe>Entering data into Ontology Fields</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt124>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Entering_data_into_Ontology_Fields.htm" target=bodyframe>Entering data into Ontology Fields</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Entity_Composition_Refinement.htm" target=bodyframe>Term Composition/Refinement</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt125>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Changing_your_Autocompletion_Settings.htm" target=bodyframe>Changing your Autocompletion Settings</font></a>
+</td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt126>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Sample_Annotations.htm" target=bodyframe>Sample Annotations</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Information for Developers</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt126>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt127>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Writing_a_Data_Adapter.htm" target=bodyframe>Writing a Data Adapter</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt127>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt128>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Connecting_to_a_Database.htm" target=bodyframe>Connecting to a Database</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt128>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt129>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Adding_configurability.htm" target=bodyframe>Adding configurability</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>What to do after Phenote</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt129>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt130>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>I've entered my data, now what?</face>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt130>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt131>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Other_Uses_for_Phenote.htm" target=bodyframe>Other Uses for Phenote</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing Phenote</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt131>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt132>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/What_is_a_Configuration_.htm" target=bodyframe>What is a Configuration?</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt132>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt133>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/How_To_Edit_a_Configuration_File.htm" target=bodyframe>How To Edit a Configuration File</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt133>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt134>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Sample_Configuration_1.htm" target=bodyframe>Sample Configuration 1</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt134>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt135>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Sample_Configuration_2.htm" target=bodyframe>Sample Configuration 2</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt135>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt136>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/XML_skeleton.htm" target=bodyframe>XML skeleton</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt136>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt137>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__phenote_configuration__Tag.htm" target=bodyframe>The &amp;lt;phenote-configuration&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt137>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt138>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__tab__Tag.htm" target=bodyframe>The &amp;lt;tab&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt138>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt139>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__dataadapter__Tag.htm" target=bodyframe>The &amp;lt;dataadapter&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt139>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt140>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__master_to_local_config__Tag.htm" target=bodyframe>The &amp;lt;master-to-local-config&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt140>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt141>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__field__Tag.htm" target=bodyframe>The &amp;lt;field&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt141>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt142>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__ontology__Tag.htm" target=bodyframe>The &amp;lt;ontology&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt142>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt143>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__auto_update_ontologies__Tag.htm" target=bodyframe>The &amp;lt;auto-update-ontologies&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt143>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt144>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__update_timer__Tag.htm" target=bodyframe>The &amp;lt;update-timer&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt144>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt145>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__term_history__Tag.htm" target=bodyframe>The &amp;lt;term-history&amp;gt; Tag</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Appendix</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt145>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt146>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/An_Introduction_to_OBO_Ontologies.htm" target=bodyframe>An Introduction to OBO Ontologies</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt146>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt147>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Basic_Concepts_and_Vocabulary.htm" target=bodyframe>Basic Concepts and Vocabulary</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>from OBOedit</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt147>
-<tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing OBO-Edit</face>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt148>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Configuration_Plugin.htm" target=bodyframe>The Configuration Plugin</font></a>
+<tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Working with Data Adapters</face>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt149>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Basic_Flat_File_Interface.htm" target=bodyframe>The Basic Flat File Interface</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt149>
-<tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing the Interface</face>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt150>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Working_with_XML_Layouts.htm" target=bodyframe>Working with XML Layouts</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_OBO_Adapter.htm" target=bodyframe>The OBO Adapter</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt151>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Common_Parameters.htm" target=bodyframe>Common Parameters</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_GO_Flat_File_Adapter.htm" target=bodyframe>The GO Flat File Adapter</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt152>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Glue_Tag.htm" target=bodyframe>The &amp;lt;glue&amp;gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 ...
 
[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [618] phenote/trunk/src/java/phenote/datamodel

From: <mg...@us...> - 2007-05-23 22:59:46

Revision: 618
          http://svn.sourceforge.net/obo/?rev=618&view=rev
Author:   mgibson
Date:     2007-05-23 15:59:47 -0700 (Wed, 23 May 2007)

Log Message:
-----------
well this bug took some digging but i nabbed it -
undo was all wack - if you did a copy and then edited on the copy
undo would actually undo on the original not the copy
which was hard to even realize thats what was going on
it turns out it was a cloning issue - it was only doing a shallow copy of the
hash of char field values - that meant the old char field values for undo were
still pointing to the old oricginal characters not the new ones

nicole i think this fixes all the undo bugs you put in the tracker item
i fiddled with it and it seems so - let me know if you still see undo bugs

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/datamodel/CharFieldValue.java
    phenote/trunk/src/java/phenote/datamodel/Character.java

Modified: phenote/trunk/src/java/phenote/datamodel/CharFieldValue.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharFieldValue.java	2007-05-22 18:48:36 UTC (rev 617)
+++ phenote/trunk/src/java/phenote/datamodel/CharFieldValue.java	2007-05-23 22:59:47 UTC (rev 618)
@@ -11,7 +11,7 @@
     should this be merged with CharField? im forgetting the rationale for having it be
     separate??? oh wait CharField is the generic field, CharFieldValue is an actual
     instance of data within the CharField - linked via CharFieldEnum & Character*/
-public class CharFieldValue {
+public class CharFieldValue implements Cloneable {
 
   private OBOClass oboClassValue=null;
   private String stringValue=null;
@@ -56,6 +56,11 @@
     charField = cf;
   }
 
+  CharFieldValue cloneCharFieldValue() {
+    try { return (CharFieldValue)clone(); }
+    catch (CloneNotSupportedException x) { return null; }
+  }
+
   // hmmmmm.... needed if post comp done inframe
 //   public CharFieldValue(OBOClass o,CharacterI c,CharFieldEnum e, boolean isDifferentia) {
 //     this(o,c,e);
@@ -69,6 +74,8 @@
       return new CharFieldValue((String)null,c,cf); // ""?
   }
 
+  void setCharacter(CharacterI c) { character = c; }
+
   boolean isEmpty() {
     if (isOboClass)
       return oboClassValue == null;

Modified: phenote/trunk/src/java/phenote/datamodel/Character.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/Character.java	2007-05-22 18:48:36 UTC (rev 617)
+++ phenote/trunk/src/java/phenote/datamodel/Character.java	2007-05-23 22:59:47 UTC (rev 618)
@@ -10,7 +10,7 @@
     was called a Phenotype which was a misnomer 
     Should the Character datamodel be a generic hash of CharField-CharFieldValues?
     That can be free text or from ontologies? */
-public class Character implements CharacterI, Cloneable {
+public class Character implements CharacterI {
 
   private HashMap<CharField,CharFieldValue> charFieldToValue =
     new HashMap<CharField,CharFieldValue>();
@@ -27,6 +27,7 @@
 
   /** for generic fields its just a map from char field to char field value */
   public void setValue(CharField cf, CharFieldValue cfv) {
+    cfv.setCharacter(this);
     charFieldToValue.put(cf,cfv);
     //System.out.println("Char setVal "+cf+" val "+cfv);
     // setOboEditModel(oboEditAnnotation,cf,cfv);
@@ -196,12 +197,19 @@
   }
 
   public CharacterI cloneCharacter() {
-    try {
-      // do OBOClasses clone? do we need to clone them?
-      Character clone = (Character)clone();
-      clone.charFieldToValue = (HashMap<CharField,CharFieldValue>)charFieldToValue.clone();
-      return clone;
-    } catch (CloneNotSupportedException e) { return null; }
+    //try {
+    // do OBOClasses clone? do we need to clone them? dont think so - immutable
+    Character charClone = new Character(); //(Character)clone();
+    // WRONG - will use same charFieldVal which points to old char!!
+//    clone.charFieldToValue =(HashMap<CharField,CharFieldValue>)charFieldToValue.clone();
+    // clone.setCharFieldValuesCharacterToSelf(); ???
+    for (CharFieldValue v : charFieldToValue.values()) {
+      CharFieldValue cfvClone = v.cloneCharFieldValue();
+      // cfvClone.setCharacter(charClone); done by setValue
+      charClone.setValue(cfvClone.getCharField(),cfvClone);
+    }
+    return charClone;
+      //} catch (CloneNotSupportedException e) { return null; }
   }
 
   // used by character table panel


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[Obo-svn-commit] SF.net SVN: obo: [617] phenote/trunk/src/java/phenote/gui

From: <mg...@us...> - 2007-05-22 18:48:35

Revision: 617
          http://svn.sourceforge.net/obo/?rev=617&view=rev
Author:   mgibson
Date:     2007-05-22 11:48:36 -0700 (Tue, 22 May 2007)

Log Message:
-----------
fixed heinous bug where mutli select *'s were making it into the model for
free text fields 
this happened due to a bug fix where selection of another row in table was
causing free text edit to not go through
but the fix cirumvented the catch for the multi
so now free text field only notes if gui has changed if not in multi setting -
setUpdateGuiOnly is true in that case

i also got rid of superfluous table list selection events which i actually
thought would fix the problem as well but didnt - but nonetheless we dont need
the superfluous events

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java
    phenote/trunk/src/java/phenote/gui/field/FreeTextField.java

Modified: phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java	2007-05-21 23:21:56 UTC (rev 616)
+++ phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java	2007-05-22 18:48:36 UTC (rev 617)
@@ -315,6 +315,8 @@
    notifies selectionManager of new char selection */
   private class CharacterSelectionListener implements ListSelectionListener {
     public void valueChanged(ListSelectionEvent e) {
+      // selection sends out many spurious events, the only one we want is non-adjust
+      if (e.getValueIsAdjusting()) return;
       if (ignoreSelectionChange) return; // for bulk delete error out of synch
       if (!hasSelection()) // this can happen with a delete row
         return;

Modified: phenote/trunk/src/java/phenote/gui/field/FreeTextField.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/FreeTextField.java	2007-05-21 23:21:56 UTC (rev 616)
+++ phenote/trunk/src/java/phenote/gui/field/FreeTextField.java	2007-05-22 18:48:36 UTC (rev 617)
@@ -105,7 +105,8 @@
   
   protected void setGuiForMultiSelect() {
     setUpdateGuiOnly(true);//updateGuiOnly = true;
-    setText("*"); 
+    setText("*"); // this sets gui text changed to true, but probably shouldnt
+    // guiTextHasChanged = false; // ???
     setUpdateGuiOnly(false);//updateGuiOnly = false;
   }
 
@@ -182,7 +183,12 @@
     public void changedUpdate(DocumentEvent e) { setGuiChanged(); }
     public void insertUpdate(DocumentEvent e) { setGuiChanged(); }
     public void removeUpdate(DocumentEvent e) { setGuiChanged(); }
-    private void setGuiChanged() { guiTextHasChanged = true; }
+    private void setGuiChanged() { 
+      // only note text change if not updating just gui?, * for multi select
+      // fixes bug for * multi select editing model
+      if (!updateGuiOnly())
+        guiTextHasChanged = true;
+    }
   }
 
   private Logger log;


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[Obo-svn-commit] SF.net SVN: obo: [616] phenote/trunk/doc/phenote-website/help

From: <nl...@us...> - 2007-05-21 23:21:59

Revision: 616
          http://svn.sourceforge.net/obo/?rev=616&view=rev
Author:   nlw
Date:     2007-05-21 16:21:56 -0700 (Mon, 21 May 2007)

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


Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/help/Phenote.jhm
    phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak
    phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml
    phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml.bak
    phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html
    phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html.tmp
    phenote/trunk/doc/phenote-website/help/html/Phenote_from_the_Command_Line.htm
    phenote/trunk/doc/phenote-website/help/html/Term_Info.htm
    phenote/trunk/doc/phenote-website/help/html/The__field__Tag.htm
    phenote/trunk/doc/phenote-website/help/html/XML_skeleton.htm

Added Paths:
-----------
    phenote/trunk/doc/phenote-website/help/html/The__master_to_local_config__Tag.htm
    phenote/trunk/doc/phenote-website/help/html/The__phenote_configuration__Tag.htm
    phenote/trunk/doc/phenote-website/help/html/The__tab__Tag.htm
    phenote/trunk/doc/phenote-website/help/html/Writing_a_Data_Adapter.htm
    phenote/trunk/doc/phenote-website/help/images/QueryField.png

Modified: phenote/trunk/doc/phenote-website/help/Phenote.jhm
===================================================================
--- phenote/trunk/doc/phenote-website/help/Phenote.jhm	2007-05-21 22:26:56 UTC (rev 615)
+++ phenote/trunk/doc/phenote-website/help/Phenote.jhm	2007-05-21 23:21:56 UTC (rev 616)
@@ -133,6 +133,8 @@
    <mapID target="The__auto_update_ontologies__Tag115" url="html/The__auto_update_ontologies__Tag.htm"/>
    <mapID target="The__ontology__Tag" url="html/The__ontology__Tag.htm"/>
    <mapID target="The__update_timer__Tag" url="html/The__update_timer__Tag.htm"/>
+   <mapID target="The__master_to_local_config__Tag" url="html/The__master_to_local_config__Tag.htm"/>
+   <mapID target="The__tab__Tag" url="html/The__tab__Tag.htm"/>
    <mapID target="The_Scroller_Tag" url="html/The_Basic_Flat_File_Interface.htm"/>
    <mapID target="The_Box_Tag" url="html/The_Box_Tag.htm"/>
    <mapID target="The_Category_Manager_Plugin" url="html/The_Category_Manager_Plugin.htm"/>
@@ -187,6 +189,8 @@
    <mapID target="Working_with_Selections" url="html/Working_with_Selections.htm"/>
    <mapID target="Working_with_Synonym_Categories" url="html/Working_with_Synonym_Categories.htm"/>
    <mapID target="Working_with_XML_Layouts" url="html/Working_with_XML_Layouts.htm"/>
+   <mapID target="Writing_a_Data_Adapter" url="html/Writing_a_Data_Adapter.htm"/>
+   <mapID target="The__phenote_configuration__Tag" url="html/The__phenote_configuration__Tag.htm"/>
    <mapID target="XML_skeleton" url="html/XML_skeleton.htm"/>
 
 <!-- Index Bookmarks -->

Modified: phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak
===================================================================
--- phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak	2007-05-21 22:26:56 UTC (rev 615)
+++ phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak	2007-05-21 23:21:56 UTC (rev 616)
@@ -133,6 +133,8 @@
    <mapID target="The__auto_update_ontologies__Tag115" url="html/The__auto_update_ontologies__Tag.htm"/>
    <mapID target="The__ontology__Tag" url="html/The__ontology__Tag.htm"/>
    <mapID target="The__update_timer__Tag" url="html/The__update_timer__Tag.htm"/>
+   <mapID target="The__master_to_local_config__Tag" url="html/The__master_to_local_config__Tag.htm"/>
+   <mapID target="The__tab__Tag" url="html/The__tab__Tag.htm"/>
    <mapID target="The_Scroller_Tag" url="html/The_Basic_Flat_File_Interface.htm"/>
    <mapID target="The_Box_Tag" url="html/The_Box_Tag.htm"/>
    <mapID target="The_Category_Manager_Plugin" url="html/The_Category_Manager_Plugin.htm"/>
@@ -187,6 +189,8 @@
    <mapID target="Working_with_Selections" url="html/Working_with_Selections.htm"/>
    <mapID target="Working_with_Synonym_Categories" url="html/Working_with_Synonym_Categories.htm"/>
    <mapID target="Working_with_XML_Layouts" url="html/Working_with_XML_Layouts.htm"/>
+   <mapID target="Writing_a_Data_Adapter" url="html/Writing_a_Data_Adapter.htm"/>
+   <mapID target="The__phenote_configuration__Tag" url="html/The__phenote_configuration__Tag.htm"/>
    <mapID target="XML_skeleton" url="html/XML_skeleton.htm"/>
 
 <!-- Index Bookmarks -->

Modified: phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml	2007-05-21 22:26:56 UTC (rev 615)
+++ phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml	2007-05-21 23:21:56 UTC (rev 616)
@@ -40,7 +40,7 @@
      <tocitem text="Sample Annotations" target="Sample_Annotations"/>
 </tocitem>
 <tocitem text="Information for Developers">
-     <tocitem text="Writing a Data Adapter"/>
+     <tocitem text="Writing a Data Adapter" target="Writing_a_Data_Adapter"/>
      <tocitem text="Connecting to a Database" target="Connecting_to_a_Database"/>
      <tocitem text="Adding configurability" target="Adding_configurability"/>
 </tocitem>
@@ -54,7 +54,10 @@
      <tocitem text="Sample Configuration 1" target="Sample_Configuration_1"/>
      <tocitem text="Sample Configuration 2" target="Sample_Configuration_2"/>
      <tocitem text="XML skeleton" target="XML_skeleton"/>
+     <tocitem text="The &lt;phenote-configuration&gt; Tag" target="The__phenote_configuration__Tag"/>
+     <tocitem text="The &lt;tab&gt; Tag" target="The__tab__Tag"/>
      <tocitem text="The &lt;dataadapter&gt; Tag" target="The__dataadapter__Tag116"/>
+     <tocitem text="The &lt;master-to-local-config&gt; Tag" target="The__master_to_local_config__Tag"/>
      <tocitem text="The &lt;field&gt; Tag" target="The__field__Tag"/>
      <tocitem text="The &lt;ontology&gt; Tag" target="The__ontology__Tag"/>
      <tocitem text="The &lt;auto-update-ontologies&gt; Tag" target="The__auto_update_ontologies__Tag115"/>

Modified: phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml.bak
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml.bak	2007-05-21 22:26:56 UTC (rev 615)
+++ phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml.bak	2007-05-21 23:21:56 UTC (rev 616)
@@ -17,7 +17,7 @@
      <tocitem text="Running Phenote for the First Time" target="Running_Phenote_for_the_First_Time"/>
      <tocitem text="Exiting Phenote" target="Exiting_Phenote"/>
 </tocitem>
-<tocitem text="The Phenote Interface">
+<tocitem text="The Phenote Interface" target="The_Phenote_Interface">
      <tocitem text="Menu Bars" target="Menu_Bars"/>
      <tocitem text="Data Entry" target="Data_Entry"/>
      <tocitem text="Term Info" target="Term_Info"/>
@@ -54,7 +54,10 @@
      <tocitem text="Sample Configuration 1" target="Sample_Configuration_1"/>
      <tocitem text="Sample Configuration 2" target="Sample_Configuration_2"/>
      <tocitem text="XML skeleton" target="XML_skeleton"/>
+     <tocitem text="The &lt;phenote-configuration&gt; Tag" target="The__phenote_configuration__Tag"/>
+     <tocitem text="The &lt;tab&gt; Tag" target="The__tab__Tag"/>
      <tocitem text="The &lt;dataadapter&gt; Tag" target="The__dataadapter__Tag116"/>
+     <tocitem text="The &lt;master-to-local-config&gt; Tag" target="The__master_to_local_config__Tag"/>
      <tocitem text="The &lt;field&gt; Tag" target="The__field__Tag"/>
      <tocitem text="The &lt;ontology&gt; Tag" target="The__ontology__Tag"/>
      <tocitem text="The &lt;auto-update-ontologies&gt; Tag" target="The__auto_update_ontologies__Tag115"/>

Modified: phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html	2007-05-21 22:26:56 UTC (rev 615)
+++ phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html	2007-05-21 23:21:56 UTC (rev 616)
@@ -76,6 +76,9 @@
 ctable(wdt167);
 ctable(wdt168);
 ctable(wdt169);
+ctable(wdt170);
+ctable(wdt171);
+ctable(wdt172);
 }
 
   
@@ -273,7 +276,7 @@
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Information for Developers</font>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt126>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Writing a Data Adapter</face>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Writing_a_Data_Adapter.htm" target=bodyframe>Writing a Data Adapter</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt127>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Connecting_to_a_Database.htm" target=bodyframe>Connecting to a Database</font></a>
@@ -309,110 +312,119 @@
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/XML_skeleton.htm" target=bodyframe>XML skeleton</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt136>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__phenote_configuration__Tag.htm" target=bodyframe>The &amp;lt;phenote-configuration&amp;gt; Tag</font></a>
+</td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt137>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__tab__Tag.htm" target=bodyframe>The &amp;lt;tab&amp;gt; Tag</font></a>
+</td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt138>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__dataadapter__Tag.htm" target=bodyframe>The &amp;lt;dataadapter&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt137>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt139>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__master_to_local_config__Tag.htm" target=bodyframe>The &amp;lt;master-to-local-config&amp;gt; Tag</font></a>
+</td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt140>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__field__Tag.htm" target=bodyframe>The &amp;lt;field&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt138>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt141>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__ontology__Tag.htm" target=bodyframe>The &amp;lt;ontology&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt139>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt142>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__auto_update_ontologies__Tag.htm" target=bodyframe>The &amp;lt;auto-update-ontologies&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt140>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt143>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__update_timer__Tag.htm" target=bodyframe>The &amp;lt;update-timer&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt141>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt144>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__term_history__Tag.htm" target=bodyframe>The &amp;lt;term-history&amp;gt; Tag</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Appendix</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt142>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt145>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/An_Introduction_to_OBO_Ontologies.htm" target=bodyframe>An Introduction to OBO Ontologies</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt143>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt146>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Basic_Concepts_and_Vocabulary.htm" target=bodyframe>Basic Concepts and Vocabulary</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>from OBOedit</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt144>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt147>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing OBO-Edit</face>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt145>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt148>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Configuration_Plugin.htm" target=bodyframe>The Configuration Plugin</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt146>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt149>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing the Interface</face>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt147>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt150>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Working_with_XML_Layouts.htm" target=bodyframe>Working with XML Layouts</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt148>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt151>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Common_Parameters.htm" target=bodyframe>Common Parameters</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt149>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt152>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Glue_Tag.htm" target=bodyframe>The &amp;lt;glue&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt150>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt153>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Spacer_Tag.htm" target=bodyframe>The &amp;lt;spacer&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt151>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt154>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Label_Tag.htm" target=bodyframe>The &amp;lt;label&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt152>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt155>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Box_Tag.htm" target=bodyframe>The &amp;lt;box&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt153>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt156>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Grid_Tag.htm" target=bodyframe>The &amp;lt;grid&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt154>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt157>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Panel_Tag.htm" target=bodyframe>The &amp;lt;panel&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt155>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt158>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Compactgrid_Tag.htm" target=bodyframe>The &amp;lt;compactgrid&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt156>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt159>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Divider_Tag.htm" target=bodyframe>The &amp;lt;divider&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt157>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt160>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Tabs_Tag.htm" target=bodyframe>The &amp;lt;tabs&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt158>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt161>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Window_Tag.htm" target=bodyframe>The &amp;lt;window&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt159>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt162>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_If_Tag.htm" target=bodyframe>The &amp;lt;if&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt160>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt163>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Component_Tag.htm" target=bodyframe>The &amp;lt;component&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt161>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt164>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Example_Layouts.htm" target=bodyframe>Example Layouts</face></a>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt162>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt165>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Introduction.htm" target=bodyframe>The Default Layout</font></a>
 </td></tr></table>
 </td></tr></table>
 </td></tr></table>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt163>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt166>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>New Topic</face>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt164>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt167>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Working with Data Adapters</face>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt165>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt168>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Basic_Flat_File_Interface.htm" target=bodyframe>The Basic Flat File Interface</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt166>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt169>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_OBO_Adapter.htm" target=bodyframe>The OBO Adapter</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt167>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt170>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_GO_Flat_File_Adapter.htm" target=bodyframe>The GO Flat File Adapter</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt168>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt171>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Serial_Adapter.htm" target=bodyframe>The Serial Adapter</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt169>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt172>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Custom_Data_Adapters.htm" target=bodyframe>Custom Data Adapters</font></a>
 </td></tr></table>
 </td></tr></table>

Modified: phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html.tmp
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html.tmp	2007-05-21 22:26:56 UTC (rev 615)
+++ phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html.tmp	2007-05-21 23:21:56 UTC (rev 616)
@@ -96,7 +96,7 @@
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Information for Developers</font>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt126>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Writing a Data Adapter</face>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Writing_a_Data_Adapter.htm" target=bodyframe>Writing a Data Adapter</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt127>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Connecting_to_a_Database.htm" target=bodyframe>Connecting to a Database</font></a>
@@ -132,110 +132,119 @@
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/XML_skeleton.htm" target=bodyframe>XML skeleton</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt136>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__phenote_configuration__Tag.htm" target=bodyframe>The &amp;lt;phenote-configuration&amp;gt; Tag</font></a>
+</td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt137>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__tab__Tag.htm" target=bodyframe>The &amp;lt;tab&amp;gt; Tag</font></a>
+</td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt138>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__dataadapter__Tag.htm" target=bodyframe>The &amp;lt;dataadapter&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt137>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt139>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__master_to_local_config__Tag.htm" target=bodyframe>The &amp;lt;master-to-local-config&amp;gt; Tag</font></a>
+</td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt140>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__field__Tag.htm" target=bodyframe>The &amp;lt;field&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt138>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt141>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__ontology__Tag.htm" target=bodyframe>The &amp;lt;ontology&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt139>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt142>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__auto_update_ontologies__Tag.htm" target=bodyframe>The &amp;lt;auto-update-ontologies&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt140>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt143>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__update_timer__Tag.htm" target=bodyframe>The &amp;lt;update-timer&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt141>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt144>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__term_history__Tag.htm" target=bodyframe>The &amp;lt;term-history&amp;gt; Tag</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Appendix</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt142>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt145>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/An_Introduction_to_OBO_Ontologies.htm" target=bodyframe>An Introduction to OBO Ontologies</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt143>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt146>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Basic_Concepts_and_Vocabulary.htm" target=bodyframe>Basic Concepts and Vocabulary</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>from OBOedit</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt144>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt147>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing OBO-Edit</face>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt145>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt148>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Configuration_Plugin.htm" target=bodyframe>The Configuration Plugin</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt146>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt149>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing the Interface</face>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt147>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt150>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Working_with_XML_Layouts.htm" target=bodyframe>Working with XML Layouts</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt148>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt151>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Common_Parameters.htm" target=bodyframe>Common Parameters</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt149>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt152>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Glue_Tag.htm" target=bodyframe>The &amp;lt;glue&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt150>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt153>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Spacer_Tag.htm" target=bodyframe>The &amp;lt;spacer&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt151>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt154>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Label_Tag.htm" target=bodyframe>The &amp;lt;label&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt152>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt155>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Box_Tag.htm" target=bodyframe>The &amp;lt;box&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt153>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt156>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Grid_Tag.htm" target=bodyframe>The &amp;lt;grid&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt154>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt157>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Panel_Tag.htm" target=bodyframe>The &amp;lt;panel&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt155>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt158>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Compactgrid_Tag.htm" target=bodyframe>The &amp;lt;compactgrid&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt156>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt159>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Divider_Tag.htm" target=bodyframe>The &amp;lt;divider&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt157>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt160>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Tabs_Tag.htm" target=bodyframe>The &amp;lt;tabs&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt158>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt161>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Window_Tag.htm" target=bodyframe>The &amp;lt;window&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt159>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt162>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_If_Tag.htm" target=bodyframe>The &amp;lt;if&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt160>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt163>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Component_Tag.htm" target=bodyframe>The &amp;lt;component&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt161>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt164>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Example_Layouts.htm" target=bodyframe>Example Layouts</face></a>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt162>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt165>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Introduction.htm" target=bodyframe>The Default Layout</font></a>
 </td></tr></table>
 </td></tr></table>
 </td></tr></table>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt163>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt166>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>New Topic</face>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt164>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt167>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Working with Data Adapters</face>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt165>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt168>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Basic_Flat_File_Interface.htm" target=bodyframe>The Basic Flat File Interface</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt166>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt169>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_OBO_Adapter.htm" target=bodyframe>The OBO Adapter</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt167>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt170>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_GO_Flat_File_Adapter.htm" target=bodyframe>The GO Flat File Adapter</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt168>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt171>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Serial_Adapter.htm" target=bodyframe>The Serial Adapter</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt169>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt172>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Custom_Data_Adapters.htm" target=bodyframe>Custom Data Adapters</font></a>
 </td></tr></table>
 </td></tr></table>

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	2007-05-21 22:26:56 UTC (rev 615)
+++ phenote/trunk/doc/phenote-website/help/html/Phenote_from_the_Command_Line.htm	2007-05-21 23:21:56 UTC (rev 616)
@@ -40,11 +40,11 @@
 <h2>2) Get Phenote</h2>
 <p>The latest development version of Phenote can be retrieved 
 from&nbsp;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>&nbsp;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>&nbsp;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.&nbsp; 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>&nbsp;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>&nbsp;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/Term_Info.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Term_Info.htm	2007-05-21 22:26:56 UTC (rev 615)
+++ phenote/trunk/doc/phenote-website/help/html/Term_Info.htm	2007-05-21 23:21:56 UTC (rev 616)
@@ -16,17 +16,17 @@
 <p><strong>Ontology</strong> - the name of the Ontology from which the term 
 comes, in this case the Biological Process ontology from the Gene Ontology.</p>
 <p><strong>Term</strong> - the actual name of the term</p>
-<p><strong>ID</strong> - the official alphanumeric identifier for the 
-term.&nbsp; It is often presented in the id:####### format.&nbsp; The id part 
-before the colon usually reflects the abbreviation for the ontology and should 
-be unique.</p>
-<p><strong>Synonyms</strong> - many 
-terms have synonyms.&nbsp; These synonyms&nbsp;may&nbsp;be defined as having 
-different scope, such as: Exact, Narrow, Broad,&nbsp;or Other.&nbsp; If the 
+<p><strong>ID</strong> - the official alphanumeric identifier 
+for the term.&nbsp; It is often presented in the format&nbsp;of a unique&nbsp;abbreviation 
+for the ontology followed by a numeric identifier, separated with a colon 
+(ie GO:0007605).&nbsp;</p>
+<P><strong>Synonyms</strong> - many terms have 
+synonyms.&nbsp; These synonyms&nbsp;may&nbsp;be defined as having different 
+scope, such as: Exact, Narrow, Broad,&nbsp;or Other.&nbsp; If the 
 synonym&nbsp;is from a particular categorization (such as an abbreviation, a 
-chemical formula, a community standard like IUPAC,&nbsp;etc.), this will be indicated following the synonym 
-in brackets.&nbsp; If no synonyms are present, this section will not 
-appear.</p>
+chemical formula, a community standard like IUPAC,&nbsp;etc.), this will be 
+indicated following the synonym in brackets.&nbsp; If no synonyms are present, 
+this section will not appear.</P>
 <p><strong>Definition</strong> - the definition for the term is displayed</p>
 <p><STRONG>Replacements</STRONG> - If a term is obsoleted, 
 a replacement term is often recommended by the maintainers of the ontology, or 

Modified: phenote/trunk/doc/phenote-website/help/html/The__field__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__field__Tag.htm	2007-05-21 22:26:56 UTC (rev 615)
+++ phenote/trunk/doc/phenote-website/help/html/The__field__Tag.htm	2007-05-21 23:21:56 UTC (rev 616)
@@ -32,6 +32,12 @@
     <td>This is a short abbreviation used by the Pheno-syntax data adapter</td>
     <td><em>any text value</em></td>
     <td></td></tr>
+  <TR>
+    <TD><FONT face=Courier>desc</FONT></TD>
+    <TD>A short description or definition of what a field is for; could be 
+      used to describe contents, proper usage, etc.</TD>
+    <TD><EM>any text value</EM></TD>
+    <TD></TD></TR>
   <tr>
     <td><font face="Courier">enable</font></td>
     <td>A flag that turns this field on or off.</td>

Added: phenote/trunk/doc/phenote-website/help/html/The__master_to_local_config__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__master_to_local_config__Tag.htm	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/help/html/The__master_to_local_config__Tag.htm	2007-05-21 23:21:56 UTC (rev 616)
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<HTML>
+<HEAD>
+<META NAME="GENERATOR" CONTENT="Solutionsoft HelpBreeze JavaHelp Edition">
+<TITLE>The <master-to-local-config> Tag</TITLE>
+<LINK REL="stylesheet" TYPE="text/css" HREF=../javahelp.css>
+</HEAD>
+<BODY BGCOLOR=#ffffff>
+<H1>The 
+&lt;master-to-local-config&gt; <master-to-local-config> Tag</H1>
+<H2>Parameters</H2>
+<H1>
+<TABLE borderColor=#000000 cellPadding=5 width="100%" align=center border=1>
+  
+  <TR>
+    <TD align=middle><STRONG>Name</STRONG></TD>
+    <TD align=middle><STRONG>Description</STRONG></TD>
+    <TD align=middle><STRONG><STRONG></STRONG>Legal Values</STRONG></TD>
+    <TD align=middle><STRONG>Required</STRONG></TD>
+    <TD align=middle><STRONG>Default</STRONG></TD></TR>
+  <TR>
+    <TD>
+      <P><FONT face=Courier>mode</FONT></P></TD>
+    <TD>
+      <P>This designates how to merge files together.</P></TD>
+    <TD>
+      <UL>
+        <LI>
+        <DIV align=left><FONT size=2>UPDATE</FONT></DIV>
+        <LI>
+        <DIV align=left><FONT size=2>WIPEOUT</FONT></DIV></LI></UL></TD>
+    <TD align=middle>no</TD>
+    <TD><FONT size=2>&nbsp;UPDATE</FONT></TD></TR>
+  <TR>
+    <TD><FONT face=Courier>when</FONT></TD>
+    <TD>
+      <P>When and how a configuration merger will take place.&nbsp; </P></TD>
+    <TD align=left>
+      <UL>
+        <LI>
+        <DIV align=left><FONT size=2>ON_VERSION_ CHANGE</FONT></DIV>
+        <LI>
+        <DIV align=left><FONT size=2>ALWAYS</FONT></DIV></LI></UL></TD>
+    <TD align=middle>no</TD>
+    <TD><FONT size=2>ON_VERSION_ 
+      CHANGE</FONT></TD></TR>
+  <TR>
+    <TD><FONT face=Courier>overriding-master-url</FONT></TD>
+    <TD>
+      <P>The config file located at this&nbsp;URL will override the config file 
+      of the same name in webstart jar (or svn/app conf).&nbsp; If the URL 
+      points to the phenote&nbsp;svn checkout for the config, it means one can 
+      just commit updates to a config to subversion and it will become the new 
+      template/master</P></TD>
+    <TD align=left><EM>any valid URL</EM></TD>
+    <TD align=middle>no</TD>
+    <TD></TD></TR></TABLE>
+<H2>&nbsp;</H2>
+<H2>Contents</H2></H1>
+<P>All other tags should be included within the &lt;phenote-configuration&gt; 
+tag, including:</P>
+<UL>
+  <LI>
+  <DIV>data-adapters</DIV>
+  <LI>
+  <DIV>fields (and ontologies)</DIV>
+  <LI>
+  <DIV>settings such as update-timer, auto-update-ontologies, etc.</DIV></LI></UL>
+<H1><FONT color=#000000 size=3></FONT>&nbsp;</H1>
+<H2>Example</H2><PRE>&nbsp; &lt;ns:master-to-local-config mode="UPDATE" when="ON_VERSION_CHANGE" <BR>&nbsp;&nbsp;&nbsp;&nbsp; overriding-master-url="<A href="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/ncbo.cfg">http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/ncbo.cfg</A>" /&gt;<BR></PRE>
+</BODY>
+</HTML>
\ No newline at end of file

Added: phenote/trunk/doc/phenote-website/help/html/The__phenote_configuration__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__phenote_configuration__Tag.htm	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/help/html/The__phenote_configuration__Tag.htm	2007-05-21 23:21:56 UTC (rev 616)
@@ -0,0 +1,105 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<html>
+<head>
+<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
+<title>XML skeleton</title>
+<link rel="stylesheet" type="text/css" href="../javahelp.css">
+</head>
+<body bgcolor="#ffffff">
+<h1>The &lt;phenote-configuration&gt; Tag</h1>
+<p>            
+          
+            
+     The &lt;phenote-configuration&gt; tag ...</p>
+<p>            
+          
+            
+        &nbsp;</p>
+<h2>            
+          
+            
+        Parameters</h2>
+<h1>
+<table bordercolor="#000000" cellpadding="5" width="100%" align="center" border="1">
+  
+  <tr>
+    <td align="middle"><strong>Name</strong></td>
+    <td align="middle"><strong>Description</strong></td>
+    <td align="middle"><strong>Legal Values</strong></td>
+    <td align="middle"><strong>Required</strong></td>
+    <td align="middle"><strong>Default</strong></td></tr>
+  <tr>
+    <td>
+      <p align="left"><font face="Courier">name</font></p></td>
+    <td>
+      <p>This is a short descriptive name given to the 
+      Configuration to be displayed in the "chooser" window.&nbsp; This does not have to be the same as the 
+      filename.&nbsp; In the case that it is unspecified, the filename will be 
+      displayed instead.</p></td>
+    <td><em>any text value</em></td>
+    <td align="middle">no</td>
+    <td>&nbsp;</td></tr>
+  <tr>
+    <td>
+      <p align="left"><font face="Courier">xmlns</font></p></td>
+    <td>
+      <p>This line is required for use by phenote software.&nbsp; Please include 
+      as specified:</p></td>
+    <td align="left"><font face="Courier">"phenote/config/xml"</font></td>
+    <td align="middle">yes</td>
+    <td></td></tr>
+  <tr>
+    <td>
+      <p align="left"><font face="Courier">author</font></p></td>
+    <td>
+      <p>The name of the author of the configuration file.&nbsp; It might be 
+      nice to include an email address incase if there are questions.</p></td>
+    <td align="left"><em>any text value</em></td>
+    <td align="middle">no</td>
+    <td></td></tr>
+  <tr>
+    <td>
+      <p align="left"><font face="Courier">version</font></p></td>
+    <td>A version number for the configuration.&nbsp; This should indicate 
+      which version of phenote it is compatible with, and something about the 
+      revision history itself.&nbsp; Keep the format:&nbsp; 1.3.1 (first two 
+      numbers indicate phenote version, last number is the revision number for 
+      the configuration)</td>
+    <td align="left"><em>any text value</em></td>
+    <td align="middle">yes</td>
+    <td></td></tr>
+  <tr>
+    <td>
+      <p align="left"><font face="Courier">description</font></p></td>
+    <td>This is a general description about the purpose of the 
+      configuration.&nbsp; The author might list the general target community, 
+      the overall use of the data, a repository where the data might be stored, 
+      or other important information.</td>
+    <td align="left"><em>any text value</em></td>
+    <td align="middle">no</td>
+    <td></td></tr></table>
+<h2>&nbsp;</h2>
+<h2>Contents</h2></h1>
+<p>            
+            
+       All other tags should be included within 
+the &lt;phenote-configuration&gt; tag, including:</p>
+<ul>
+  <li>
+<div>            
+            
+              
+   data-adapters</div>
+  <li>
+<div>            
+            
+              
+ fields (and ontologies)</div>
+  <li>
+<div>            
+            
+            settings such 
+as update-timer, auto-update-ontologies, etc.</div></li></ul>
+<h1><font color="#000000" size="3"></font>&nbsp;</h1>
+<h2>Example</h2><pre><pre>&lt;ns:phenote-configuration version="1.3.1" xmlns:ns="phenote/config/xml"&gt;<br>&nbsp;</pre><pre>&lt;!--Enter your configuration options here --&gt;</pre><pre><br>&lt;/ns:phenote-configuration&gt;</pre></pre>
+<p></p></body></html>

Added: phenote/trunk/doc/phenote-website/help/html/The__tab__Tag.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The__tab__Tag.htm	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/help/html/The__tab__Tag.htm	2007-05-21 23:21:56 UTC (rev 616)
@@ -0,0 +1,18 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<html>
+<head>
+<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
+<title>The <tab> Tag</title>
+<link rel="stylesheet" type="text/css" href="../javahelp.css">
+</head>
+<body bgcolor="#ffffff">
+<h1>The &lt;tab&gt; <tab> Tag</h1>
+<p>The &lt;tab&gt; tag will allow the user to specify 
+groupings of fields into separate, paged tabs.&nbsp; This provides a way of 
+organizing fields into groups for ease of data entry.&nbsp;</p>
+<p>Phenote can accomodate approximately 12 fields per 
+tab.&nbsp;</p>
+<p>&nbsp;</p>
+<p>in development...</p>
+</body>
+</html>
\ No newline at end of file

Added: phenote/trunk/doc/phenote-website/help/html/Writing_a_Data_Adapter.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Writing_a_Data_Adapter.htm	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/help/html/Writing_a_Data_Adapter.htm	2007-05-21 23:21:56 UTC (rev 616)
@@ -0,0 +1,154 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<html>
+<head>
+<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
+<title>Writing a Data Adapter</title>
+<link rel="stylesheet" type="text/css" href="../javahelp.css">
+</head>
+<body bgcolor="#ffffff">
+<h1>Writing a Data Adapter</h1>
+
+<p>First off if you've just downloaded phenote from sourceforge obo svn, the (latest) source is located in <font face="Courier">phenote/trunk/src/java</font>. The most important subdirectories under <font face="Courier">src/java</font> for creating a data adapter are: </p>
+<ul>
+  <li><font face="Courier">phenote/dataadapter</font>&nbsp; -and- 
+  <li><font face="Courier">phenote/datamodel</font>. </li>
+</ul>
+<p>
+   For a good example of a data adapter, check out <font face="Courier"> phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter</font> 
+</p>
+<h2>Types of Data Adapters</h2>
+<p>There are two types of Data Adapters used in Phenote.&nbsp; The first is a 
+<strong>File Data Adapter</strong> which...
 
[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [615] phenote/trunk/doc/phenote-website/developer-docs/ developer-docs.html

From: <mg...@us...> - 2007-05-21 22:26:54

Revision: 615
          http://svn.sourceforge.net/obo/?rev=615&view=rev
Author:   mgibson
Date:     2007-05-21 15:26:56 -0700 (Mon, 21 May 2007)

Log Message:
-----------
new docs for coding configs with config refactor - nicole, juancarlos - check
it out - its a little easier now taking full advantage of xml beans

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	2007-05-21 20:54:52 UTC (rev 614)
+++ phenote/trunk/doc/phenote-website/developer-docs/developer-docs.html	2007-05-21 22:26:56 UTC (rev 615)
@@ -2,20 +2,27 @@
 <html>
 <head>
 
+
   
+  
   <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
 
+
   
+  
   <title>Developer docs</title>
 </head>
 
 
 <body>
 
+
 <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&nbsp;
 it calls a method on the EditManager. For instance, for updating
 multiple fields at once CharFieldGui makes a bunch of
@@ -28,67 +35,125 @@
 model has been changed, and adds the transaction to its list of
 transactions (for undo).<br>
 
+
 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
 &amp; 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 &amp; 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&nbsp;/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.UvicGraphDocument.UvicGraph;<br>
+import phenote.config.xml.TermHistoryDocument.TermHistory;<br>
 <br>
-b) The simple case is just adding a top level config boolean option - like enabling Uvic graphics - so ill go with that. <br>
-- add a boolean var to Config. <br>
-- modify the &nbsp;parseXmlUrl(URL configUrl) method with something like:<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; UvicGraph gr = pc.getUvicGraph();<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if (gr != null)<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; uvicGraphEnabled = gr.getEnable();<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>
+&nbsp; private TermHistory getHistoryBean() {<br>
+&nbsp;&nbsp;&nbsp; TermHistory history = phenoConfigBean.getTermHistory();<br>
+&nbsp;&nbsp;&nbsp; if (history == null) {<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; history = phenoConfigBean.addNewTermHistory();<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; history.setEnable(false); // default false<br>
+&nbsp;&nbsp;&nbsp; }<br>
+&nbsp;&nbsp;&nbsp; return history;<br>
+&nbsp; }<br>
+&nbsp;<br>
+- add a public getter method like:<br>
+&nbsp; public boolean termHistoryIsEnabled() { <br>
+&nbsp;&nbsp;&nbsp; return getHistoryBean().getEnable();<br>
+&nbsp; }<br>
 <br>
-- add a public getter method like:<br>
-&nbsp; public boolean uvicGraphIsEnabled() { return uvicGraphEnabled; }<br>
+- setters are used by merge code and will be used in future by gui config:<br>
+&nbsp; public void setTermHistory(boolean setter) { <br>
+&nbsp;&nbsp;&nbsp; getHistoryBean().setEnable(setter);<br>
+&nbsp; }<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>
-&nbsp; oldCfg.uvicGraphEnabled = newCfg.uvicGraphEnabled; <br>
+<br>
+&nbsp;&nbsp;&nbsp; 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)<br>
+something) - this example is for auto update.<br>
+
 <br>
+
  
 </body>
 </html>


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[Obo-svn-commit] SF.net SVN: obo: [614] phenote/trunk

From: <mg...@us...> - 2007-05-21 20:54:51

Revision: 614
          http://svn.sourceforge.net/obo/?rev=614&view=rev
Author:   mgibson
Date:     2007-05-21 13:54:52 -0700 (Mon, 21 May 2007)

Log Message:
-----------
so there was a redundancy in config - in that it was using both the xml beans
and its own datamodel - so i scrapped its own datamodel now just using xml
beans - this simplifies adding new config params - it also means you now
modify the actual xml model that gets read & written - a good step for gui
config
and it means you dont have to explicitly dump from config model to xml model
to write out (for config update/merge) which i forgot to put in dev docs and
some new params werent doing - 
nicole just added some newer params - that now need to change to new way
ill update docs as well
also with merge/update now default is just copies from old config - where
before default was it got dropped
also i got rid of queryable-dataapdater - now just dataadapter - with
is-queryable param (only affects worm)
the ConfigWriter now really just adds a version and tells the xml beans to
write out 

Modified Paths:
--------------
    phenote/trunk/conf/phenote-config.rnc
    phenote/trunk/conf/phenote-config.xsd
    phenote/trunk/conf/worm.cfg
    phenote/trunk/jars/phenoteconfigbeans.jar
    phenote/trunk/src/java/phenote/config/Config.java
    phenote/trunk/src/java/phenote/config/ConfigWriter.java
    phenote/trunk/src/java/phenote/config/DataAdapterConfig.java
    phenote/trunk/src/java/phenote/config/FieldConfig.java
    phenote/trunk/src/java/phenote/config/OntologyConfig.java
    phenote/trunk/src/java/phenote/config/QueryableAdapConfig.java
    phenote/trunk/src/java/phenote/dataadapter/DataAdapterI.java
    phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
    phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java
    phenote/trunk/src/java/phenote/datamodel/Ontology.java
    phenote/trunk/src/java/phenote/gui/CharacterTableModel.java
    phenote/trunk/src/java/phenote/gui/field/FieldPanel.java

Modified: phenote/trunk/conf/phenote-config.rnc
===================================================================
--- phenote/trunk/conf/phenote-config.rnc	2007-05-21 18:47:07 UTC (rev 613)
+++ phenote/trunk/conf/phenote-config.rnc	2007-05-21 20:54:52 UTC (rev 614)
@@ -10,7 +10,6 @@
     attribute author { xsd:string },
     master-to-local-config,
     log,
-    queryable-dataadapter*,
     dataadapter*,
     uvic-graph,
     term-history,
@@ -30,13 +29,7 @@
   attribute overriding-master-url { xsd:string }
 }
 
-queryable-dataadapter = element queryable-dataadapter {
-  ## actual class name, eg phenote.dataadapter.worm.WormAdapter
-  attribute name { xsd:string },
-  attribute enable { xsd:boolean }
-} 
 
-
 ## rename/add file-dataadapter - keep dataadapter for backward compatibility?
 dataadapter =
   element dataadapter {
@@ -45,6 +38,7 @@
     ##attribute name {"phenoxml" | "phenosyntax" | "nexus"}
     ## actual class name phenote.dataadapter.phenoxml.PhenoXmlAdapter
     attribute name { xsd:string },
+    attribute is-queryable { xsd:boolean },
     attribute enable { xsd:boolean }
   }
 
@@ -61,7 +55,7 @@
 
 auto-update-ontologies = element auto-update-ontologies { attribute enable { xsd:boolean } }
 
-update-timer = element update-timer { attribute timer {xsd:integer} }
+update-timer = element update-timer { attribute timer {xsd:int} }
 
 obo-repository = element obo-repository { attribute url-dir {xsd:string} }
 
@@ -93,6 +87,7 @@
     ## obo file for ontology
     attribute file { xsd:string },
     attribute namespace { xsd:string },
+    ## filter out replaced by namespace, pase'
     attribute filter-out { xsd:string },
     attribute slim { xsd:string },
     attribute repos-subdir {xsd:string},

Modified: phenote/trunk/conf/phenote-config.xsd
===================================================================
--- phenote/trunk/conf/phenote-config.xsd	2007-05-21 18:47:07 UTC (rev 613)
+++ phenote/trunk/conf/phenote-config.xsd	2007-05-21 20:54:52 UTC (rev 614)
@@ -5,7 +5,6 @@
       <xs:sequence>
         <xs:element ref="x:master-to-local-config"/>
         <xs:element ref="x:log"/>
-        <xs:element minOccurs="0" maxOccurs="unbounded" ref="x:queryable-dataadapter"/>
         <xs:element minOccurs="0" maxOccurs="unbounded" ref="x:dataadapter"/>
         <xs:element ref="x:uvic-graph"/>
         <xs:element ref="x:term-history"/>
@@ -27,19 +26,10 @@
       <xs:attribute name="overriding-master-url" use="required" type="xs:string"/>
     </xs:complexType>
   </xs:element>
-  <xs:element name="queryable-dataadapter">
-    <xs:complexType>
-      <xs:attribute name="name" use="required" type="xs:string">
-        <xs:annotation>
-          <xs:documentation>actual class name, eg phenote.dataadapter.worm.WormAdapter</xs:documentation>
-        </xs:annotation>
-      </xs:attribute>
-      <xs:attribute name="enable" use="required" type="xs:boolean"/>
-    </xs:complexType>
-  </xs:element>
   <xs:element name="dataadapter">
     <xs:complexType>
       <xs:attribute name="name" use="required" type="xs:string"/>
+      <xs:attribute name="is-queryable" use="required" type="xs:boolean"/>
       <xs:attribute name="enable" use="required" type="xs:boolean"/>
     </xs:complexType>
   </xs:element>
@@ -65,7 +55,7 @@
   </xs:element>
   <xs:element name="update-timer">
     <xs:complexType>
-      <xs:attribute name="timer" use="required" type="xs:integer"/>
+      <xs:attribute name="timer" use="required" type="xs:int"/>
     </xs:complexType>
   </xs:element>
   <xs:element name="obo-repository">
@@ -115,7 +105,11 @@
         </xs:annotation>
       </xs:attribute>
       <xs:attribute name="namespace" use="required" type="xs:string"/>
-      <xs:attribute name="filter-out" use="required" type="xs:string"/>
+      <xs:attribute name="filter-out" use="required" type="xs:string">
+        <xs:annotation>
+          <xs:documentation>filter out replaced by namespace, pase'</xs:documentation>
+        </xs:annotation>
+      </xs:attribute>
       <xs:attribute name="slim" use="required" type="xs:string"/>
       <xs:attribute name="repos-subdir" use="required" type="xs:string"/>
       <xs:attribute name="is-postcomp-rel" use="required" type="xs:boolean"/>

Modified: phenote/trunk/conf/worm.cfg
===================================================================
--- phenote/trunk/conf/worm.cfg	2007-05-21 18:47:07 UTC (rev 613)
+++ phenote/trunk/conf/worm.cfg	2007-05-21 20:54:52 UTC (rev 614)
@@ -1,12 +1,16 @@
 <phenote-configuration xmlns="phenote/config/xml" xmlns:xsi="http://www.w3.org/1999/XMLSchema/instance" schemaLocation="phenote-config.xsd">
 
+  <master-to-local-config mode="UPDATE" when="ALWAYS"/>
+   <!--  ??? overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/worm.cfg" / ??? -->
+
   <dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
   <dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter"
                   enable="true"/>
   <dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="false"/>
   <dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/>
 
-  <queryable-dataadapter name="phenote.dataadapter.worm.WormAdapter" enable="true"/>
+  <dataadapter name="phenote.dataadapter.worm.WormAdapter" is-queryable="true"
+               enable="true"/>
 
   <log config-file="conf/log4j-standalone.xml"/>
 

Modified: phenote/trunk/jars/phenoteconfigbeans.jar
===================================================================
(Binary files differ)

Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java	2007-05-21 18:47:07 UTC (rev 613)
+++ phenote/trunk/src/java/phenote/config/Config.java	2007-05-21 20:54:52 UTC (rev 614)
@@ -19,7 +19,7 @@
 import phenote.main.PhenoteVersion;
 import phenote.config.xml.PhenoteConfigurationDocument;
 import phenote.config.xml.DataadapterDocument.Dataadapter;
-import phenote.config.xml.QueryableDataadapterDocument.QueryableDataadapter;
+//import phenote.config.xml.QueryableDataadapterDocument.QueryableDataadapter;
 import phenote.config.xml.FieldDocument.Field;
 import phenote.config.xml.LogDocument.Log;
 import phenote.config.xml.OboRepositoryDocument.OboRepository;
@@ -43,24 +43,25 @@
   private static Config singleton = new Config();
   private String configFile = FLYBASE_DEFAULT_CONFIG_FILE;
   private List<DataAdapterConfig> dataAdapConfList;
-  private List<QueryableAdapConfig> queryAdapConfList;
+  private List<DataAdapterConfig> queryAdapConfList;
   /** only enabled fields */
   private List<FieldConfig> enabledFields = new ArrayList<FieldConfig>();
   /** enabled & disabled */
   private List<FieldConfig> allFields = new ArrayList<FieldConfig>();
-  private String logConfigFile = "conf/log4j.xml"; // default log config file
+  private static final String defaultLogConfigFile = "conf/log4j.xml";
   // maybe should be using xmlbean where possible?
-  private boolean uvicGraphEnabled = false; // default false for now
-  private boolean termHistoryEnabled = false;   //default to false for now
-  private boolean autoUpdateEnabled = true; //default to true if not in config
-  private int updateTimer = 0; //default is to not wait
-  private String reposUrlDir;
+  //private boolean uvicGraphEnabled = false; // default false for now
+  //private boolean termHistoryEnabled = false;   //default to false for now
+  //private boolean autoUpdateEnabled = true; //default to true if not in config
+  //private int updateTimer = 0; //default is to not wait
+  //private String reposUrlDir;
   private String version;
   private String configName;
   private String configDesc;
   private String configAuthor;
   //private String masterToLocalConfigMode;
   //private MasterToLocalConfig masterToLocalBean;
+  private PhenoteConfigurationDocument phenoDocBean;
   private PhenoteConfiguration phenoConfigBean; // cache the xml parse bean??
 
   private boolean configInitialized = false;
@@ -443,20 +444,27 @@
     else
       System.out.println("System config is newer than user, updating user config");
 
-    // Data Adapters
-    for (DataAdapterConfig dac : newCfg.getAdapConfigs()) {
-      if (!oldCfg.hasAdapConfig(dac))
-        oldCfg.addAdapConfig(dac);
+    // File Adapters - preserves enable state of old/local - should it?
+    for (DataAdapterConfig dac : newCfg.getFileAdapConfigs()) {
+      if (!oldCfg.hasFileAdapConfig(dac))
+        oldCfg.addFileAdapConfig(dac);
     }
+    for (DataAdapterConfig dac : newCfg.getQueryAdapCfgs()) {
+      if (!oldCfg.hasQueryAdapCfg(dac))
+        oldCfg.addQueryAdapCfg(dac);
+    }
     // log defaulted and probably wont change - dont worry about?? or check if set?
     // but it is a version change so check if diff? maybe? not sure hmmm
     // but i do think ok to update uvic - version change may go from false to true
-    oldCfg.uvicGraphEnabled = newCfg.uvicGraphEnabled; // hmmmm?
-    oldCfg.termHistoryEnabled = newCfg.termHistoryEnabled;
-    oldCfg.reposUrlDir = newCfg.reposUrlDir; // ??
-    oldCfg.autoUpdateEnabled = newCfg.autoUpdateEnabled;
-    oldCfg.updateTimer = newCfg.updateTimer;
-    for (FieldConfig newFC : newCfg.getFieldConfigList())
+    //oldCfg.uvicGraphEnabled = newCfg.uvicGraphEnabled; // hmmmm?
+    oldCfg.setUvicGraphIsEnabled(newCfg.uvicGraphIsEnabled());
+    oldCfg.setTermHistory(newCfg.termHistoryIsEnabled()); //preserve old user pref?
+    oldCfg.setReposUrlDir(newCfg.getReposUrlDir()); // ?? pase
+    oldCfg.setAutoUpdate(newCfg.autoUpdateIsEnabled());
+    oldCfg.setUpdateTimer(newCfg.getUpdateTimer()); // ??? master shouldnt override???
+    // should it merge just enabled fields or all fields - probably all fields
+    //for (FieldConfig newFC : newCfg.getEnabledFieldCfgs())
+    for (FieldConfig newFC : newCfg.getAllFieldCfgs())
       newFC.mergeWithOldConfig(oldCfg,newCfg);
 
     // write out updated old cfg
@@ -471,20 +479,27 @@
     return getDataAdapters() != null && !getDataAdapters().isEmpty();
   }
   
-  List<DataAdapterConfig> getAdapConfigs() {
+  List<DataAdapterConfig> getFileAdapConfigs() {
     if (dataAdapConfList == null)
       dataAdapConfList = new ArrayList<DataAdapterConfig>(4);
     return dataAdapConfList;
   }
-  /** Check if has data adapter config with same name */
-  private boolean hasAdapConfig(DataAdapterConfig dac) {
-    for (DataAdapterConfig d : getAdapConfigs()) {
-      //if (d.getName().equals(dac.getName()))
+  /** Check if has file adapter config with same name */
+  private boolean hasFileAdapConfig(DataAdapterConfig dac) {
+    for (DataAdapterConfig d : getFileAdapConfigs()) {
       if (d.hasSameAdapter(dac))
         return true;
     }
     return false;
   }
+  /** Check if has file adapter config with same name */
+  private boolean hasQueryAdapCfg(DataAdapterConfig dac) {
+    for (DataAdapterConfig d : getQueryAdapCfgs()) {
+      if (d.hasSameAdapter(dac))
+        return true;
+    }
+    return false;
+  }
 
   /** Returns enabled data adapters - empty list if none enabled */
   public List<DataAdapterI> getDataAdapters() {
@@ -492,7 +507,7 @@
     ArrayList daList = new ArrayList(dataAdapConfList.size());
     for (DataAdapterConfig d : dataAdapConfList) {
       if (d.isEnabled())
-        daList.add(d.getDataAdapter());
+        daList.add(d.getFileAdapter());
     }
     return daList; //new ArrayList(dataAdapConfList);
   }
@@ -508,7 +523,7 @@
     if (!hasDataAdapters()) return null; // ex?
     // if defaultFileAdapter != null retrun defaultFileAdapter - set by config
     for (DataAdapterConfig d : dataAdapConfList)
-      if (d.isEnabled()) return d.getDataAdapter();
+      if (d.isEnabled()) return d.getFileAdapter();
     //return dataAdapConfList.get(0);
     return null; // none enabled - shouldnt happen - ex?
   }
@@ -516,75 +531,155 @@
 
 
   /** config flag for enabling uvic shrimp dag graph */ 
-  public boolean uvicGraphIsEnabled() { return uvicGraphEnabled; }
+  public boolean uvicGraphIsEnabled() {
+    //return uvicGraphEnabled;
+    return getUvicGraphBean().getEnable();
+  }
 
+  private UvicGraph getUvicGraphBean() {
+    UvicGraph g = phenoConfigBean.getUvicGraph();
+    if (g == null) {
+      g = phenoConfigBean.addNewUvicGraph(); // will this default to false?
+    }
+    return g;
+  }
+
+  public void setUvicGraphIsEnabled(boolean enable) {
+    getUvicGraphBean().setEnable(enable);
+  }
+
   public boolean termHistoryIsEnabled() { 
-    return termHistoryEnabled; }
+    return getHistoryBean().getEnable();
+  }
 
+  private TermHistory getHistoryBean() {
+    TermHistory history = phenoConfigBean.getTermHistory();
+    if (history == null) {
+      history = phenoConfigBean.addNewTermHistory();
+      history.setEnable(false); // default false
+    }
+    return history;
+  }
+
   public void setTermHistory(boolean setter) { 
-    termHistoryEnabled = setter;
-    return; }
+    getHistoryBean().setEnable(setter);
+  }
 
   public boolean autoUpdateIsEnabled() {
-    return autoUpdateEnabled; }
+    return getAutoUpdateBean().getEnable();
+  }
 
+  public void setAutoUpdate(boolean enable) {
+    getAutoUpdateBean().setEnable(enable);
+  }
+
+  private AutoUpdateOntologies getAutoUpdateBean() {
+    AutoUpdateOntologies au = phenoConfigBean.getAutoUpdateOntologies();
+    if (au == null) {
+      au = phenoConfigBean.addNewAutoUpdateOntologies();
+      au.setEnable(true); // default true??
+    }
+    return au;
+  }
+
+  // rename getUpdateTimerSeconds?
   public int getUpdateTimer() {
-      return updateTimer; }
+    return getTimerBean().getTimer();
+  }
+
+  public void setUpdateTimer(int seconds) {
+    getTimerBean().setTimer(seconds);
+  }
+
+  private UpdateTimer getTimerBean() {
+    UpdateTimer u = phenoConfigBean.getUpdateTimer();
+    if (u == null) {
+      u = phenoConfigBean.addNewUpdateTimer();
+      u.setTimer(0); // default is not to wait???
+    }
+    return u;
+  }
   
   public URL getLogConfigUrl() throws FileNotFoundException {
-    return FileUtil.findUrl(logConfigFile);
+    return FileUtil.findUrl(getLogConfigFile());
   }
 
-  String getLogConfigFile() { return logConfigFile; }
+  String getLogConfigFile() { 
+    if (phenoConfigBean.getLog() == null) {
+      Log log = phenoConfigBean.addNewLog();
+      log.setConfigFile(defaultLogConfigFile);
+    }
+    return phenoConfigBean.getLog().getConfigFile();
+  }
 
   public int getNumberOfFields() {
-    return getFieldConfigList().size();
+    return getEnbldFieldCfgs().size();
   }
 
   /** Gives name of field at index, 0 based (for table heading) */
   public String getFieldLabel(int index) {
-    return getFieldConfig(index).getLabel();
+    return getEnbldFieldCfg(index).getLabel();
   }
 
 //   public CharFieldEnum getCharFieldEnum(int index) {
 //     return getFieldConfig(index).getCharFieldEnum();
 //   }
-  public CharField getCharField(int index) {
-    return getFieldConfig(index).getCharField();
+  public CharField getEnbldCharField(int index) {
+    return getEnbldFieldCfg(index).getCharField();
   }
 
   /** needed for getFieldLabel for table */
-  private FieldConfig getFieldConfig(int index) {
-    return getFieldConfigList().get(index);
+  private FieldConfig getEnbldFieldCfg(int index) {
+    return getEnbldFieldCfgs().get(index);
   }
 
   /** OntologyDataAdapter calls this to figure which ontologies to load
    This is a list of enabled fields - does not include disabled fields!
   retname getEnabledFieldConfigs? */
-  public List<FieldConfig> getFieldConfigList() {
+  public List<FieldConfig> getEnbldFieldCfgs() {
     return enabledFields;
   }
 
+  private void reconstructEnabledFieldList() {
+    enabledFields.clear();
+    for (FieldConfig fc : getAllFieldCfgs()) {
+      if (fc.isEnabled())
+        enabledFields.add(fc);
+    }
+  }
+
+  public List<FieldConfig> getAllFieldCfgs() { return allFields; }
+
   /** returns true if has field config with same name - contents may differ */
-  boolean hasFieldConfig(FieldConfig newFC) {
-    return getFieldConfig(newFC.getLabel()) != null;
+  boolean hasEnbldFieldCfg(FieldConfig newFC) {
+    return getEnbldFieldCfg(newFC.getLabel()) != null;
   }
+  boolean hasFieldCfgAll(FieldConfig fc) {
+    return getAllFieldCfg(fc.getLabel()) != null;
+  }
 
   /** returns field config with label fieldName */
-  FieldConfig getFieldConfig(String fieldName) {
-    for (FieldConfig fc : getFieldConfigList()) {
+  FieldConfig getEnbldFieldCfg(String fieldName) {
+    for (FieldConfig fc : getEnbldFieldCfgs()) {
       if (fc.getLabel().equals(fieldName))
         return fc;
     }
     return null; // ex?
   }
+  FieldConfig getAllFieldCfg(String fieldName) {
+    for (FieldConfig fc : getAllFieldCfgs()) {
+      if (fc.getLabel().equals(fieldName))
+        return fc;
+    }
+    return null; // ex?
+  }
 
   /** kinda silly to return list?? so there are 2 fields for "Tag" which perhaps is silly
       but thats whats happening so need to deal with it */
   public List<CharField> getCharFieldsForSyntaxAbbrev(String abb) throws ConfigException {
     // cache in hash??
     List<CharField> fields = new ArrayList<CharField>(2);
-    for (FieldConfig fc : getFieldConfigList()) {
+    for (FieldConfig fc : getEnbldFieldCfgs()) {
       if (fc.hasSyntaxAbbrev(abb) || fc.hasLabel(abb)) // abbrev or label
         fields.add(fc.getCharField());
         //return fc.getCharField();
@@ -597,8 +692,8 @@
   public List<CharField> getCharFieldsForDelimited(int colNum) throws ConfigException {
 	    // cache in hash??
 	    List<CharField> fields = new ArrayList<CharField>(2);
-	    for (FieldConfig fc : getFieldConfigList()) {
-	    	fields.add(getCharField(colNum));
+	    for (FieldConfig fc : getEnbldFieldCfgs()) {
+	    	fields.add(getEnbldCharField(colNum));
 	        //return fc.getCharField();
 	    }
 	    if (fields.isEmpty())
@@ -607,7 +702,7 @@
 	  }
   
   public String getLabelForCharField(CharField cf) throws ConfigException {
-	    for (FieldConfig fc : getFieldConfigList()) {
+	    for (FieldConfig fc : getEnbldFieldCfgs()) {
 	      if (fc.hasCharField(cf))
 	        return fc.getLabel();
 	    }
@@ -616,7 +711,7 @@
 	  }
   
   public String getSyntaxAbbrevForCharField(CharField cf) throws ConfigException {
-    for (FieldConfig fc : getFieldConfigList()) {
+    for (FieldConfig fc : getEnbldFieldCfgs()) {
       if (fc.hasCharField(cf))
         return fc.getSyntaxAbbrev();
     }
@@ -624,7 +719,17 @@
     throw new ConfigException("Syn Abbrev for "+cf+" not found");
   }
 
-  String getReposUrlDir() { return reposUrlDir; }
+  // pase - phase out - returns null if doesnt have
+  String getReposUrlDir() {
+    if (phenoConfigBean.getOboRepository() == null) return null;
+    return phenoConfigBean.getOboRepository().getUrlDir();
+  }
+  private void setReposUrlDir(String d) { // phase out
+    if (d==null) return;
+    if (phenoConfigBean.getOboRepository() == null)
+      phenoConfigBean.addNewOboRepository();
+    phenoConfigBean.getOboRepository().setUrlDir(d);
+  }
 
   /** should this just be a part of fieldConfigList? and main window would filter it
       out when making up fields? rel is for post comp gui - or maybe FieldConfig
@@ -642,14 +747,16 @@
     }
     catch (FileNotFoundException e) { throw new ConfigException(e); }
   }
+
+  PhenoteConfigurationDocument getPhenoDocBean() { return phenoDocBean; }
       
   private void parseXmlUrl(URL configUrl) throws ConfigException {
     try {
       System.out.println("config file: "+configUrl);
-      PhenoteConfigurationDocument pcd = 
-        PhenoteConfigurationDocument.Factory.parse(configUrl);//configFile);
-      pcd.validate(); //???
-      phenoConfigBean = pcd.getPhenoteConfiguration();
+      //PhenoteConfigurationDocument pcd = 
+      phenoDocBean = PhenoteConfigurationDocument.Factory.parse(configUrl);
+      phenoDocBean.validate(); //???
+      phenoConfigBean = phenoDocBean.getPhenoteConfiguration();
 
       version = phenoConfigBean.getVersion();
       
@@ -667,52 +774,53 @@
 //         masterToLocalConfigMode = m.getMode();
 
       // LOG CONFIG FILE
-      Log log = phenoConfigBean.getLog();
-      if (log != null && log.getConfigFile() != null) {
-        logConfigFile = log.getConfigFile();
-      }
+//       Log log = phenoConfigBean.getLog();
+//       if (log != null && log.getConfigFile() != null) {
+//         logConfigFile = log.getConfigFile();
+//       }
       
       // DATA ADAPTERS  <dataadapter name="phenoxml" enable="true"/>
 
       Dataadapter[] adapters = phenoConfigBean.getDataadapterArray();
       for (Dataadapter da : adapters) {
         DataAdapterConfig dac = new DataAdapterConfig(da);
-        addAdapConfig(dac);
-        //String name = da.getName().toString();
-        //addDataAdapterFromString(name);
+        if (dac.isQueryable())
+          addQueryAdapCfg(dac);
+        else
+          addFileAdapConfig(dac);
       }
 
-      QueryableDataadapter[] queryAdaps = phenoConfigBean.getQueryableDataadapterArray();
-      for (QueryableDataadapter da : queryAdaps) {
-        QueryableAdapConfig qac = new QueryableAdapConfig(da);
-        addQueryAdapCfg(qac);
-      }
+//       QueryableDataadapter[] queryAdaps = phenoConfigBean.getQueryableDataadapterArray();
+//       for (QueryableDataadapter da : queryAdaps) {
+//         QueryableAdapConfig qac = new QueryableAdapConfig(da);
+//         addQueryAdapCfg(qac);
+//       }
 
 
-      // GRAPH
-      UvicGraph gr = phenoConfigBean.getUvicGraph();
-      if (gr != null)
-        uvicGraphEnabled = gr.getEnable();
+      // GRAPH - now accesses bean directly
+//       UvicGraph gr = phenoConfigBean.getUvicGraph();
+//       if (gr != null)
+//         uvicGraphEnabled = gr.getEnable();
 
       // TERM HISTORY
-      TermHistory history = phenoConfigBean.getTermHistory();
-      if (history != null)
-        termHistoryEnabled = history.getEnable();
+//       TermHistory history = phenoConfigBean.getTermHistory();
+//       if (history != null)
+//         termHistoryEnabled = history.getEnable();
 
       // AUTO UPDATE OF ONTOLOGIES
-      AutoUpdateOntologies autoUpdate = phenoConfigBean.getAutoUpdateOntologies();
-      if (autoUpdate != null)
-        autoUpdateEnabled = autoUpdate.getEnable();
+//       AutoUpdateOntologies autoUpdate = phenoConfigBean.getAutoUpdateOntologies();
+//       if (autoUpdate != null)
+//         autoUpdateEnabled = autoUpdate.getEnable();
 
       // TIMER for UPDATE OF ONTOLOGIES
-      UpdateTimer time = phenoConfigBean.getUpdateTimer();
-      if (time != null)
-	  updateTimer = time.getTimer().intValue();
+//       UpdateTimer time = phenoConfigBean.getUpdateTimer();
+//       if (time != null)
+// 	  updateTimer = time.getTimer().intValue();
 
       // Repos url dir
-      OboRepository or = phenoConfigBean.getOboRepository();
-      if (or != null && or.getUrlDir() != null)
-        reposUrlDir = or.getUrlDir();
+//       OboRepository or = phenoConfigBean.getOboRepository();
+//       if (or != null && or.getUrlDir() != null)
+//         reposUrlDir = or.getUrlDir();
 
       // FIELDS
       Field[] fields = phenoConfigBean.getFieldArray();
@@ -735,9 +843,12 @@
     return FileUtil.findUrl(filename);
   }
 
+  private void addQueryAdapCfg(DataAdapterConfig dac) {
+    getQueryAdapCfgs().add(dac);
+  }
 
-  private void addAdapConfig(DataAdapterConfig dac) {
-    getAdapConfigs().add(dac);
+  private void addFileAdapConfig(DataAdapterConfig dac) {
+    getFileAdapConfigs().add(dac);
   }
 
   public boolean hasQueryableDataAdapter() {
@@ -750,15 +861,16 @@
     if (queryAdapConfList == null) return null;
     //queryAdapConfList.get(0).getQueryableAdapter();
     // return first enabled adap
-    for (QueryableAdapConfig q : getQueryAdapCfgs())
+    //for (QueryableAdapConfig q : getQueryAdapCfgs())
+    for (DataAdapterConfig q : getQueryAdapCfgs())
       if (q.isEnabled()) return q.getQueryableAdapter();
     return null;
   }
 
   /** all configs for query adaps - enabled or not */
-  List<QueryableAdapConfig> getQueryAdapCfgs() {
+  List<DataAdapterConfig> getQueryAdapCfgs() {
     if (queryAdapConfList == null)
-      queryAdapConfList = new ArrayList<QueryableAdapConfig>(1);
+      queryAdapConfList = new ArrayList<DataAdapterConfig>(1);
     return queryAdapConfList;
   }
 
@@ -779,14 +891,23 @@
 
   /** get index of field config in enabled field config list - returns -1 if
       not in there -- ex? */
-  int getEnabledFieldIndex(FieldConfig fc) {
-    return enabledFields.indexOf(fc);
+//   int getEnabledFieldIndex(FieldConfig fc) {
+//     return enabledFields.indexOf(fc);
+//   }
+
+  int getAllFieldIndex(FieldConfig fc) {
+    return allFields.indexOf(fc);
   }
 
+  /** adds to both field config list and xml beans field list */
   void insertFieldConfig(int index, FieldConfig fc) {
+    allFields.add(index,fc); // ??
     if (fc.isEnabled())
-      enabledFields.add(index,fc);
-    allFields.add(index,fc); // ??
+      reconstructEnabledFieldList();//enabledFields.add(index,fc);
+    // make space for new field
+    phenoConfigBean.insertNewField(index);
+    // set bean for that field
+    phenoConfigBean.setFieldArray(index,fc.getFieldBean());
   }
   
   public String getConfigName() {	return configName;  }
@@ -824,100 +945,3 @@
 //   public int getOntologyCheckMinutes() { return newOntologyCheckMinutes; }
 //   private class DataAdapterConfig {
 
-//     /** construct from Dataadapter xml bean */
-//     private DataAdapterConfig(Dataadapter xmlBean) {
-//       String name = da.getName();
-//       addDataAdapterFromString(name);
-//     }
-
-//     boolean enabled=true; // enabled by default
-//     // new -> class name, old -> phenoxml|phenosyntax|nexus 
-//     String configString;
-//     // will be null if enabled = false
-//     DataAdapterI dataAdapter;
-
-//     // do some other way? DataAdapterManager has mapping? DataAdapter has mapping?
-//     // DataAdapterManager.getAdapter(name)???
-//     // just do class string see tracker issue 1649004
-//     private void addDataAdapterFromString(String daString) {
-      
-//       // new way of doing things is class name itself - so 1st try introspect...
-//       try {
-//         Class c = Class.forName(daString);
-//         Object o = c.newInstance();
-//         if ( ! (o instanceof DataAdapterI))
-//           throw new Exception("class not instance of DataAdapterI");
-//         DataAdapterI da = (DataAdapterI)o;
-//         addDataAdapter(da);
-//       }
-//       catch (Exception e) { 
-        
-//         // backward compatibility - have merger replace these with class names eventually
-//         if (daString.equalsIgnoreCase("phenoxml"))
-//           addDataAdapter(new PhenoXmlAdapter());
-//         else if (daString.equalsIgnoreCase("phenosyntax"))
-//           addDataAdapter(new PhenoSyntaxFileAdapter());
-//         else if (daString.equalsIgnoreCase("flybase")) // pase??
-//           addDataAdapter(new FlybaseDataAdapter()); // for now...
-//         else if (daString.equalsIgnoreCase("nexus"))
-//           addDataAdapter(new NEXUSAdapter());
-//         // LOG not set up yet???
-//         else
-//           System.out.println("Data adapter not recognized "+daString);
-//       }
-//     }
-//   }
-
-//}
-
-//     String name = field.getName(); //toString();
-//     // has to be a valid value - no longer true for generic free types
-//     FieldConfig fc;
-//     try { // phase this out!!
-//       CharFieldEnum cfe = CharFieldEnum.getCharFieldEnum(name);
-//       //if (cfe == null) ???
-//       fc = new FieldConfig(cfe,name);
-//     }
-//     catch (Exception e) { // no char field enum for name - new generic!
-//       fc = new FieldConfig(name);
-//     }
-
-//     if (field.getSyntaxAbbrev() != null) {
-//       fc.setSyntaxAbbrev(field.getSyntaxAbbrev());
-//     }
-    
-//     // POST COMP, relationship ontol
-//     if (field.getPostcomp() != null) {
-//       fc.setIsPostComp(true);
-//       String relFile = field.getPostcomp().getRelationshipOntology();
-//       fc.setPostCompRelOntCfg(OntologyConfig.makeRelCfg(relFile));
-//     }
-
-
-//     // ONTOLOGIES if only one ontology file is an attribute... (convenience)
-//     if (field.getFile() != null) {
-//       fc.addOntologyConfig(new OntologyConfig(field));
-//     }
-//     // otherwise its multiple ontologies listed in ontology elements (entity)
-//     else {
-//       Ontology[] ontologies = field.getOntologyArray();
-//       for (Ontology o : ontologies) {
-//         fc.addOntologyConfig(new OntologyConfig(o));
-//       }
-//     }
-
-//   private OntologyConfig makeOntologyConfig(String name, String file) {
-//     OntologyConfig oc = new OntologyConfig(name,file);
-//     return oc;
-//   }
-
-
-//       // CHECK FOR ONTOLOGIES
-//       CheckForNewOntologies cfno = pc.getCheckForNewOntologies();
-//       if (cfno != null) { // ?
-//         checkForNewOntologies = true;
-//         BigInteger bi = cfno.getIntervalMinutes();
-//         if (bi != null)
-//           newOntologyCheckMinutes = bi.intValue();
-//       }
-

Modified: phenote/trunk/src/java/phenote/config/ConfigWriter.java
===================================================================
--- phenote/trunk/src/java/phenote/config/ConfigWriter.java	2007-05-21 18:47:07 UTC (rev 613)
+++ phenote/trunk/src/java/phenote/config/ConfigWriter.java	2007-05-21 20:54:52 UTC (rev 614)
@@ -4,14 +4,14 @@
 import java.io.IOException;
 
 import org.apache.xmlbeans.XmlOptions;
-import phenote.config.xml.DataadapterDocument.Dataadapter;
-import phenote.config.xml.QueryableDataadapterDocument.QueryableDataadapter;
-import phenote.config.xml.LogDocument.Log;
-import phenote.config.xml.OboRepositoryDocument.OboRepository;
-import phenote.config.xml.OntologyDocument.Ontology;
+//import phenote.config.xml.DataadapterDocument.Dataadapter;
+//import phenote.config.xml.QueryableDataadapterDocument.QueryableDataadapter;
+// import phenote.config.xml.LogDocument.Log;
+// import phenote.config.xml.OboRepositoryDocument.OboRepository;
+// import phenote.config.xml.OntologyDocument.Ontology;
 import phenote.config.xml.PhenoteConfigurationDocument;
 import phenote.config.xml.PhenoteConfigurationDocument.PhenoteConfiguration;
-import phenote.config.xml.UvicGraphDocument.UvicGraph;
+// import phenote.config.xml.UvicGraphDocument.UvicGraph;
 
 import phenote.dataadapter.DataAdapterI;
 import phenote.main.PhenoteVersion;
@@ -22,27 +22,29 @@
     hindsight is 20 20 */
 class ConfigWriter {
 
-  private Config config;
-  private PhenoteConfiguration phenCfg;
+  //private Config config;
+  //private PhenoteConfiguration phenCfg;
 
   void writeConfig(Config config, File file) { //throws IOException? {
-    this.config = config; // convenience
-    PhenoteConfigurationDocument doc = PhenoteConfigurationDocument.Factory.newInstance();
-    phenCfg = doc.addNewPhenoteConfiguration();
+    //this.config = config; // convenience
+    PhenoteConfigurationDocument doc = config.getPhenoDocBean();
+    //PhenoteConfigurationDocument.Factory.newInstance();
+    //phenCfg = doc.addNewPhenoteConfiguration();
+    PhenoteConfiguration phenCfg = doc.getPhenoteConfiguration();
     phenCfg.setVersion(PhenoteVersion.versionString());
-    // namespace??? need to get that working - xsd as a check - dont know how
+    //xml namespace? need to get that working - xsd as a check - dont know how
 
-    addDataAdapters();
+    //addDataAdapters();
 
-    addQueryDataAdapters();
+    //addQueryDataAdapters();
 
-    addLog();
+    //addLog();
 
-    addUvicGraph();
+    //addUvicGraph();
 
-    addRepository();
+    //addRepository();
 
-    addFields();
+    //addFields();
 
     try { // xmlOptions? pretty print
     doc.save(file,getXmlOptions()); } 
@@ -50,57 +52,58 @@
       System.out.println("Failed to save config file "+e); }
   }
 
-  private void addDataAdapters() {
-    for (DataAdapterConfig dac : config.getAdapConfigs()) {
-      addDataAdapter(dac);
-    }
+  private XmlOptions getXmlOptions() {
+    XmlOptions options = new XmlOptions();
+    options.setSavePrettyPrint();
+    options.setSavePrettyPrintIndent(2);
+    return options;
   }
-  private void addDataAdapter(DataAdapterConfig dac) {
-    // ideally config string is the class name (unless its an invalid class??)
-    String daClassString = dac.getConfigString(); //getClass().getName();
-    Dataadapter daBean = phenCfg.addNewDataadapter();
-    daBean.setName(daClassString);
-    daBean.setEnable(dac.isEnabled());
-  }
 
-  private void addQueryDataAdapters() {
-    for (QueryableAdapConfig q : config.getQueryAdapCfgs()) {
-      addQueryAdapter(q);
-    }
-  }
+//   private void addDataAdapters() {
+//     for (DataAdapterConfig dac : config.getAdapConfigs()) {
+//       addDataAdapter(dac);
+//     }
+//   }
+//   private void addDataAdapter(DataAdapterConfig dac) {
+//     // ideally config string is the class name (unless its an invalid class??)
+//     String daClassString = dac.getConfigString(); //getClass().getName();
+//     Dataadapter daBean = phenCfg.addNewDataadapter();
+//     daBean.setName(daClassString);
+//     daBean.setEnable(dac.isEnabled());
+//   }
 
-  private void addQueryAdapter(QueryableAdapConfig qac) {
-    String qacClassString = qac.getConfigString();
-    QueryableDataadapter qdBean = phenCfg.addNewQueryableDataadapter();
-    qdBean.setName(qacClassString);
-    qdBean.setEnable(qac.isEnabled());
-  }  
-  private void addLog() {
-    Log log = phenCfg.addNewLog();
-    log.setConfigFile(config.getLogConfigFile());
-  }
+//   private void addQueryDataAdapters() {
+//     for (QueryableAdapConfig q : config.getQueryAdapCfgs()) {
+//       addQueryAdapter(q);
+//     }
+//   }
 
-  private void addUvicGraph() {
-    UvicGraph uvic = phenCfg.addNewUvicGraph();
-    uvic.setEnable(config.uvicGraphIsEnabled());
-  }
+//   private void addQueryAdapter(QueryableAdapConfig qac) {
+//     String qacClassString = qac.getConfigString();
+//     QueryableDataadapter qdBean = phenCfg.addNewQueryableDataadapter();
+//     qdBean.setName(qacClassString);
+//     qdBean.setEnable(qac.isEnabled());
+//   }  
+//   private void addLog() {
+//     Log log = phenCfg.addNewLog();
+//     log.setConfigFile(config.getLogConfigFile());
+//   }
 
-  private void addRepository() {
-    if (config.getReposUrlDir() == null) return; // should there be a default
-    OboRepository rep = phenCfg.addNewOboRepository();
-    rep.setUrlDir(config.getReposUrlDir());
-  }
+//   private void addUvicGraph() {
+//     UvicGraph uvic = phenCfg.addNewUvicGraph();
+//     uvic.setEnable(config.uvicGraphIsEnabled());
+//   }
 
-  private void addFields() {
-    for (FieldConfig fc : config.getFieldConfigList()) {
-      fc.write(phenCfg);
-    }
-  }
+//   private void addRepository() {
+//     if (config.getReposUrlDir() == null) return; // should there be a default
+//     OboRepository rep = phenCfg.addNewOboRepository();
+//     rep.setUrlDir(config.getReposUrlDir());
+//   }
 
-  private XmlOptions getXmlOptions() {
-    XmlOptions options = new XmlOptions();
-    options.setSavePrettyPrint();
-    options.setSavePrettyPrintIndent(2);
-    return options;
-  }
+//   private void addFields() {
+//     for (FieldConfig fc : config.getFieldConfigList()) {
+//       fc.write(phenCfg);
+//     }
+//   }
+
 }

Modified: phenote/trunk/src/java/phenote/config/DataAdapterConfig.java
===================================================================
--- phenote/trunk/src/java/phenote/config/DataAdapterConfig.java	2007-05-21 18:47:07 UTC (rev 613)
+++ phenote/trunk/src/java/phenote/config/DataAdapterConfig.java	2007-05-21 20:54:52 UTC (rev 614)
@@ -6,6 +6,7 @@
 //so that programmers don't have to modify this file?
 
 import phenote.dataadapter.DataAdapterI;
+import phenote.dataadapter.QueryableDataAdapterI;
 import phenote.dataadapter.fly.FlybaseDataAdapter;
 import phenote.dataadapter.nexus.NEXUSAdapter;
 import phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter;
@@ -14,87 +15,132 @@
 
 class DataAdapterConfig {
 
-  String name;
-  boolean enabled=true; // enabled by default
+  //String name;
+  //boolean enabled=true; // enabled by default
   // new -> class name, old -> phenoxml|phenosyntax|nexus 
-  String configString;
-  boolean configStringIsClassName = false;
+  //String configString;
+  //boolean configStringIsClassName = false;
   // will be null if enabled = false
-  DataAdapterI dataAdapter;
+  private DataAdapterI fileAdapter;
+  private QueryableDataAdapterI queryableDataAdapter;
+  private Dataadapter xmlBean;
 
   /** construct from Dataadapter xml bean */
   DataAdapterConfig(Dataadapter xmlBean) {
-    name = xmlBean.getName();
-    configString = xmlBean.getName(); // must be set for setDAFromCfgStr
+    this.xmlBean = xmlBean;
+    //name = xmlBean.getName();
+    //configString = xmlBean.getName(); // must be set for setDAFromCfgStr
     
-    // yes - this is a way of checking if flag actually specified - nice
+    // this is a way of checking if flag actually specified - nice
     // if not specified default is true actually not false
-    if (xmlBean.xgetEnable() != null)
-      enabled = xmlBean.getEnable();
+//     if (xmlBean.xgetEnable() != null)
+//       enabled = xmlBean.getEnable();
     
-    if (enabled)
-      setDataAdapterFromConfigString();
+    if (isEnabled())
+      setDataAdapterFromName();
   }
 
   protected DataAdapterConfig() {}; // for subclass hmmm
 
-  String getName() { return name; }
+  String getName() { return xmlBean.getName(); }
+  private void setName(String name) { xmlBean.setName(name); }
 
-  boolean isEnabled() { return enabled; }
+  boolean isQueryable() { return xmlBean.getIsQueryable(); }
+  /** Either its a file adapter or its a queryable/database adapter */
+  boolean isFileAdapter() { return !isQueryable(); }
+
+  /** default is true */
+  boolean isEnabled() { 
+    if (xmlBean.xgetEnable() == null)
+      xmlBean.setEnable(true);
+    return xmlBean.getEnable();
+  }
   
   /** check if enabled/constructed? */
-  DataAdapterI getDataAdapter() { return dataAdapter; }
+  DataAdapterI getFileAdapter() { return fileAdapter; }
 
   boolean hasSameAdapter(DataAdapterConfig dac) {
-    if (name.equals(dac.getName())) return true;
-    return getConfigString().equals(dac.getConfigString());
+    return getName().equals(dac.getName());
+    //return getConfigString().equals(dac.getConfigString());
   }
 
-  String getConfigString() {
-    // attempt to make class string (even if not enabled) - flag for attempt made?
-    if (!configStringIsClassName) {
-      if (dataAdapter == null)
-        setDataAdapterFromConfigString();
-      if (dataAdapter != null)
-        configString = dataAdapter.getClass().getName();
-    }
-    return configString;
-  }
+   QueryableDataAdapterI getQueryableAdapter() { return queryableDataAdapter; }
 
   // do some other way? DataAdapterManager has mapping? DataAdapter has mapping?
   // DataAdapterManager.getAdapter(name)???
   // just do class string see tracker issue 1649004
-  private void setDataAdapterFromConfigString() {
-      
+  private void setDataAdapterFromName() {
+    try {
+      if (!isQueryable())
+        setFileAdapterFromName(); // throws config ex
+      else
+       setQueryableAdapterFromName();
+    }
+    catch (ConfigException e) {
+      System.out.println(e.getMessage()+" trying queryable");
+      setQueryableAdapterFromName(); // why not
+    }
+     
+  }
+  
+  private void setFileAdapterFromName() throws ConfigException {
     // new way of doing things is class name itself - so 1st try introspect...
     try {
-      Class c = Class.forName(configString);
-      Object o = c.newInstance();
+      Object o = getInstanceForName();
       if ( ! (o instanceof DataAdapterI))
         throw new Exception("class not instance of DataAdapterI");
-      DataAdapterI da = (DataAdapterI)o;
-      //addDataAdapter(da);
-      dataAdapter = da;
-      configStringIsClassName = true;
+      fileAdapter = (DataAdapterI)o;
+      //configStringIsClassName = true;
     }
     catch (Exception e) { 
         
-      // backward compatibility - have merger replace these with class names eventually
-      if (configString.equalsIgnoreCase("phenoxml"))
-        dataAdapter = new PhenoXmlAdapter();
-      else if (configString.equalsIgnoreCase("phenosyntax"))
-        dataAdapter = new PhenoSyntaxFileAdapter();
-      else if (configString.equalsIgnoreCase("flybase")) // pase??
-        dataAdapter = new FlybaseDataAdapter(); // for now...
-      else if (configString.equalsIgnoreCase("nexus"))
-        dataAdapter = new NEXUSAdapter();
-      else if (configString.equalsIgnoreCase("delimited"))
-    	dataAdapter = new DelimitedFileAdapter();
-      // LOG not set up yet???
-      else
-        System.out.println("Data adapter not recognized "+configString);
-      configStringIsClassName = false;
+      // backward compatibility, merge/update replaces these with class names
+      // PLEASE DONT ADD NEW ADAPTERS TO THIS LIST - FORCE THEM TO USE NEW WAY
+      if (getName().equalsIgnoreCase("phenoxml"))
+        fileAdapter = new PhenoXmlAdapter();
+      else if (getName().equalsIgnoreCase("phenosyntax"))
+        fileAdapter = new PhenoSyntaxFileAdapter();
+      else if (getName().equalsIgnoreCase("flybase")) // pase??
+        fileAdapter = new FlybaseDataAdapter(); // for now...
+      else if (getName().equalsIgnoreCase("nexus"))
+        fileAdapter = new NEXUSAdapter();
+      else if (getName().equalsIgnoreCase("delimited"))
+    	fileAdapter = new DelimitedFileAdapter();
+      else // LOG not set up yet???
+        throw new ConfigException("File adapter not recognized "+getName());
+
+      //configStringIsClassName = false;
+      setName(fileAdapter.getClass().getName());
     }
+
   }
+
+  private void setQueryableAdapterFromName() {
+    try {
+      Object o = getInstanceForName();
+      if ( ! (o instanceof QueryableDataAdapterI))
+        throw new Exception("class not instance of QueryableDataAdapterI");
+      queryableDataAdapter = (QueryableDataAdapterI)o;
+    }
+    catch (Exception e) {
+      System.out.println("Queryable data adapter not recognized "+getName());
+    }
+  }
+
+  private Object getInstanceForName() throws Exception {
+    Class c = Class.forName(getName()); //configString);
+    return c.newInstance();
+  }
+
 }
 
+//   String getConfigString() {
+//     // attempt to make class string (even if not enabled) - flag for attempt made?
+//     if (!configStringIsClassName) {
+//       if (fileAdapter == null)
+//         setDataAdapterFromConfigString();
+//       if (fileAdapter != null)
+//         configString = fileAdapter.getClass().getName();
+//     }
+//     return configString;
+//   }

Modified: phenote/trunk/src/java/phenote/config/FieldConfig.java
===================================================================
--- phenote/trunk/src/java/phenote/config/FieldConfig.java	2007-05-21 18:47:07 UTC (rev 613)
+++ phenote/trunk/src/java/phenote/config/FieldConfig.java	2007-05-21 20:54:52 UTC (rev 614)
@@ -15,39 +15,45 @@
 
   //private CharFieldEnum charFieldEnum; // phase out
   private CharField charField;
-  private String label;
+  //private String label;
   private String desc;
   // Entity field can have multiple ontologies
   private List<OntologyConfig> ontologyConfigList;
   //private boolean isPostComp;
   //private OntologyConfig postCompRelOntCfg;
-  private String syntaxAbbrev;
-  private boolean enabled = true; // default if not specified is true
+  //private String syntaxAbbrev;
+  //private boolean enabled = true; // default if not specified is true
   private Config config;
+  private Field fieldBean;
 
 
+  // from gui config
+  // public FieldConfig(Config cfg) ?? { 
+  // fieldBean = cfg.getPhenCfgBean().addNewField()
+
   /** construct from xml bean field - READ */
   FieldConfig(Field fieldBean,Config cfg) {
     this.config = cfg;
-    this.label = fieldBean.getName();
+    this.fieldBean = fieldBean; // test for null - even possible?
+    //this.label = fieldBean.getName();
     this.desc = fieldBean.getDesc();
 //   try{//phase this out!charFieldEnum = CharFieldEnum.getCharFieldEnum(label);}
 //     catch (Exception e) {} // no char field enum for name - new generic!
     //fc = new FieldConfig(name);
     
-    if (fieldBean.xgetEnable() != null)
-      enabled = fieldBean.getEnable();
+//     if (fieldBean.xgetEnable() != null)
+//       enabled = fieldBean.getEnable();
 
-    if (fieldBean.getTab() != null) {
+    if (fieldBean.getTab() != null) { //todo...
     }
 
-    if (fieldBean.getSyntaxAbbrev() != null) {
-      setSyntaxAbbrev(fieldBean.getSyntaxAbbrev());
-    }
+//     if (fieldBean.getSyntaxAbbrev() != null) {
+//       setSyntaxAbbrev(fieldBean.getSyntaxAbbrev());
+//     }
     
     // POST COMP, relationship ontol - OLD WAY - PHASING OUT - now in ont arr below
     if (fieldBean.getPostcomp() != null) {
-      //setIsPostComp(true); - set in OC read by ODA
+      //setIsPostComp(true); - set in OC read by ODAe
       String relFile = fieldBean.getPostcomp().getRelationshipOntology();
       OntologyConfig rel = OntologyConfig.makePostCompRelCfg(relFile,this);
       //setPostCompRelOntCfg(rel); dont need anymore - set in OC
@@ -64,17 +70,24 @@
     else {
       Ontology[] ontologies = fieldBean.getOntologyArray();
       for (Ontology ontBean : ontologies) {
-        addOntologyConfig(new OntologyConfig(ontBean,getLabel(),this)); // label -> default name
+        addOntologyConfig(new OntologyConfig(ontBean,this)); // label -> default name
       }
     }
   }
 
   Config getConfig() { return config; }
 
+  /** return xml bean for field -always non null */
+  Field getFieldBean() { return fieldBean; } 
+
   // --> getName?
-  public String getLabel() { return label; }
+  public String getLabel() { return fieldBean.getName(); } //return label; }
+  boolean hasLabel(String label) { return label.equals(getLabel()); } 
+  // public void setLabel(String label) { fieldBean.setName(label); } // ??
+
+  //public String getLabel() { return label; }
   public String getDesc() { return desc; }
-  boolean hasLabel(String label) { return label.equals(this.label); } 
+  // boolean hasLabel(String label) { return label.equals(this.label); } 
   boolean hasDesc(String desc) { return desc.equals(this.desc); }
 
   //private void setOntologyFile(String f){getOntologyConfig().setOntologyFile(f);}
@@ -93,10 +106,16 @@
 //   }
 
   void addOntologyConfig(OntologyConfig o) {
-    if (o == null)
-      return;
+    if (o == null)  return;
     getOntologyConfigList().add(o);
   }
+  void insertOntologyConfig(int index,OntologyConfig o) {
+    // hmmm funny parallel data structures hmm
+    // hafta make space in array for new bean
+    getFieldBean().insertNewOntology(index);
+    getFieldBean().setOntologyArray(index,o.getOntologyBean());
+    getOntologyConfigList().add(index,o);
+  }
 
   boolean hasOntConfig(OntologyConfig oc) {
     return getOntConfig(oc.getName()) != null;
@@ -121,22 +140,27 @@
     return ontologyConfigList;
   }
 
+  int getOntCfgIndex(OntologyConfig oc) {
+    return ontologyConfigList.indexOf(oc);
+  }
 
+
   void setSyntaxAbbrev(String syn) {
-    this.syntaxAbbrev = syn;
+    //this.syntaxAbbrev = syn;
+    fieldBean.setSyntaxAbbrev(syn);
   }
   /** gets from label if no syntax abbrev explicitly set, replaces spaces with underscores
       as pheno syntax is sensitive to spaces (in theory at least) */
   String getSyntaxAbbrev() {
-    String s =  (syntaxAbbrev == null) ? getLabel() : syntaxAbbrev;
+    String s = fieldBean.getSyntaxAbbrev();
+    if (s == null) s = getLabel(); // setSynAbb?
     s = s.replace(' ','_');
     return s;
   }
   //void String getSyntaxAbbrev() { return syntaxAbbrev; }
   /** Test both syntaxAbbrev & label - also test for replacing spaces with underscores */
   boolean hasSyntaxAbbrev(String abb) {
-    if (equalsWithSpaceUnderscore(abb,syntaxAbbrev)) return true;
-    return equalsWithSpaceUnderscore(abb,label);
+    return equalsWithSpaceUnderscore(abb,getSyntaxAbbrev());
   }
 
   /** returns true if strings equal or if strings equal after replacing space with
@@ -148,8 +172,18 @@
     return abbrev.equalsIgnoreCase(underForSpace);
   }
 
-  public  boolean isEnabled() { return enabled; }
+  public  boolean isEnabled() {
+    //return enabled;
+    if (fieldBean.xgetEnable() == null)
+      fieldBean.setEnable(true); // default true
+    return fieldBean.getEnable();
+  }
 
+  public void setEnabled(boolean e) {
+    fieldBean.setEnable(e);
+  }
+
+
   public void setCharField(CharField cf) { charField = cf; }
 
   /** Actually creates char field if null, as char fields utimately come from field
@@ -161,39 +195,27 @@
   }
   boolean hasCharField(CharField cf) { return charField == cf; }
 
-  /** create xml bean and add it to phenCfg for writeback */
-  void write(PhenoteConfiguration phenCfg) {
-    Field f = phenCfg.addNewField();
-    f.setName(getLabel());
-    f.setSyntaxAbbrev(getSyntaxAbbrev());
-    f.setEnable(isEnabled());
-    // f.setType(getType()); // do we need this - no - maybe in future?
-    // new way is to just write out with other ontol configs - delete this
-//     if (isPostComp()) getPostCompRelOntCfg().writePostComp(f);
-    // everything else is in ontology config
-    // change here - writing out ontology element even for single ontology - phasing
-    // out shoving ontology in field attribs
-    // this also will have post comp rel - new way
-    for (OntologyConfig oc : getOntologyConfigList())
-      oc.writeOntology(f);
-  }
 
   void mergeWithOldConfig(Config oldConfig,Config thisCfg) { // should FC know its Cfg?
     // ADD - 1st see if field is new - if so add it and done
-    if (!oldConfig.hasFieldConfig(this)) {
+    if (!oldConfig.hasFieldCfgAll(this)) {
       // cant just add - need to add in proper place! insert!
       //oldConfig.addFieldConfig(this);
-      int index = thisCfg.getEnabledFieldIndex(this);
+      int index = thisCfg.getAllFieldIndex(this); // enabled??? disabled?
+      System.out.println("index merge "+index+" fc "+this);
       oldConfig.insertFieldConfig(index,this);
       return;
     }
 
     // UPDATE - its not new - need to check contents
-    FieldConfig oldFieldConfig = oldConfig.getFieldConfig(getLabel());
+    FieldConfig oldFieldConfig = oldConfig.getAllFieldCfg(getLabel());
     // replace syntax abbrev or fill in if blank?? - it is a change in version so replace?
     // yea if syn has changed that prob means its a cng in format
-    if (syntaxAbbrev != null)
-      oldFieldConfig.syntaxAbbrev = syntaxAbbrev;
+    //if (syntaxAbbrev != null)
+    // only do if in bean, not getSA which grabs label if bean is null
+    if (fieldBean.getSyntaxAbbrev() != null)
+      oldFieldConfig.setSyntaxAbbrev(fieldBean.getSyntaxAbbrev());
+    oldFieldConfig.setEnabled(isEnabled()); // ??? mode?
     // ONTOLOGIES
     for (OntologyConfig newOC : getOntologyConfigList()) {
       newOC.mergeWithOldConfig(oldFieldConfig);
@@ -202,39 +224,20 @@
 
 }
 
-//   FieldConfig(CharFieldEnum c, String label) {
-//     charFieldEnum = c;
-//     this.label = label;
+  // this should come for free with new bean datamodel
+  /** create xml bean and add it to phenCfg for writeback */
+//   void write(PhenoteConfiguration phenCfg) {
+//     Field f = phenCfg.addNewField();
+//     f.setName(getLabel());
+//     f.setSyntaxAbbrev(getSyntaxAbbrev());
+//     f.setEnable(isEnabled());
+//     // f.setType(getType()); // do we need this - no - maybe in future?
+//     // new way is to just write out with other ontol configs - delete this
+// //     if (isPostComp()) getPostCompRelOntCfg().writePostComp(f);
+//     // everything else is in ontology config
+//     // change here - writing out ontology element even for single ontology - phasing
+//     // out shoving ontology in field attribs
+//     // this also will have post comp rel - new way
+//     for (OntologyConfig oc : getOntologyConfigList())
+//       oc.writeOntology(f);
 //   }
-
-  /** No char field enum - its a generic not in hard wired datamodel! */
-//   FieldConfig(String label) {
-//     this.label = label;
-//     //isGeneric = true;
-//   }
-  /** with generic fields these are going to become pase' */
-  //public CharFieldEnum getCharFieldEnum() { return charFieldEnum; }
-  //public boolean hasCharFieldEnum() { return charFieldEnum != null; }
-  // POST COMP config... 
-//   void setIsPostComp(boolean isPostComp) {
-//     this.isPostComp = isPostComp;
-//   }
-//   public boolean isPostComp() {
-//     return isPostComp;
-//   }
-//   void setPostCompRelOntCfg(OntologyConfig oc) {
-//     setIsPostComp(true);
-//     postCompRelOntCfg = oc;
-//   }
-
-//   /** If isPostComp() return relationship ontology filename */
-//   public OntologyConfig getPostCompRelOntCfg() {
-//     return postCompRelOntCfg;
-//   }
-
-//   FieldConfig(CharFieldEnum c,OntologyConfig o) {
-//     charFieldEnum = c;
-//     if (o == null) return; // shouldnt happen
-//     label = o.getName();
-//     addOntologyConfig(o);
-//   }

Modified: phenote/trunk/src/java/phenote/config/OntologyConfig.java
===================================================================
--- phenote/trunk/src/java/phenote/config/OntologyConfig.java	2007-05-21 18:47:07 UTC (rev 613)
+++ phenote/trunk/src/java/phenote/config/OntologyConfig.java	2007-05-21 20:54:52 UTC (rev 614)
@@ -5,93 +5,92 @@
 
 import phenote.config.xml.FieldDocument.Field;
 import phenote.config.xml.OntologyDocument.Ontology;
-import phenote.config.xml.PostcompDocument.Postcomp;
+//import phenote.config.xml.PostcompDocument.Postcomp;
 
 /** May not even have ontology file (free text eg genotype) rename FieldConfig? */
 public class OntologyConfig {
 
-  public String name;
+  //public String name;
+  //public String namespace; // this should replace filterOut
+  //public String filterOut; // public?
+  //private String slim;
+  //private String reposSubdir; // pase!
+  //private boolean isPostCompRel = false;
+  /** just the filename - no path/url */
   public String ontologyFile;
-  public String namespace; // this should replace filterOut
-  public String filterOut; // public?
-  private String slim;
-  private String reposSubdir;
-  private boolean isPostCompRel = false;
-  /** load url is url where ontol loaded from, repos or local file cache or jar */
+  /** if url given for file then this string gets set (or old backward compatible repos
+      subdir & basedir - phase out) otherwise null */
+  private String reposUrlString;
+  /** load url is url where ontol loaded from, repos or local file cache or jar 
+      this is handy for ontology adapter to record - i forget why */
   private URL loadUrl;
-  private String reposUrlString;
   private FieldConfig fieldConfig;
+  private Ontology ontologyBean; // from xml beans - replaces above fields!
 
-  //static OntologyConfig defaultPato = new OntologyConfig("Pato","attribute_and_value.obo");
 
-  //OntologyConfig() {} // not sure this is actually needed/used
-  private OntologyConfig(String name,FieldConfig fc) {
-    this.name = name;
-    fieldConfig = fc;
-  }
-
-
-
-  /** Ontology stuff in field itself (field only has one ontology) - this is getting phased 
-      out replaced by field with single ontology element */
-  OntologyConfig(Field field,FieldConfig fc) {
-    fieldConfig = fc;
-    name = field.getName();
-    ontologyFile = field.getFile();
-    // downside of strongly types xml beans is filterOut has to be dealt with 
-    // separately for field & ontology - annoying - & all other attribs
-    filterOut = field.getFilterOut()!=null ? field.getFilterOut() : null;
-    slim = field.getSlim()!=null ? field.getSlim() : null;
-    reposSubdir = field.getReposSubdir()!=null ?
-      field.getReposSubdir() : null;
-  }
-
   /** confusing - this is xml bean Ontology NOT datamodel Ontology - this is reading
    in from xml config - if ontology doesnt have name use fieldName (single ontols
    just use field name) */
-  OntologyConfig(phenote.config.xml.OntologyDocument.Ontology o, String fieldName,
-                 FieldConfig fc) {
+  OntologyConfig(phenote.config.xml.OntologyDocument.Ontology o,FieldConfig fc) {
+    ontologyBean = o;
     fieldConfig = fc;
-    name = o.getName()!=null ? o.getName() : fieldName;
+    //name = o.getName()!=null ? o.getName() : fieldName;
     setFile(o.getFile());
-    if (o.getNamespace() != null)
-      namespace = o.getNamespace();
-    if (o.getFilterOut() != null)
-      filterOut = o.getFilterOut();
-    slim = o.getSlim()!=null ? o.getSlim() : null;
-    if (o.getReposSubdir()!=null)
-      reposSubdir = o.getReposSubdir();
+    //if (o.getNamespace() != null) namespace = o.getNamespace();
+//    if (o.getFilterOut() != null) filterOut = o.getFilterOut();
+    //slim = o.getSlim()!=null ? o.getSlim() : null;
+    //if (o.getReposSubdir()!=null) reposSubdir = o.getReposSubdir();
     // if xgetIsPostCompRel != null
-    isPostCompRel = o.getIsPostcompRel(); // hmm what will return when not set??
+    //isPostCompRel = o.getIsPostcompRel(); // hmm what will return when not set??
     
     // for now ignoring if name set as there was a bug where name was getting set
     // to "Entity" in the -u .phenote/conf file - woops
-    if (isPostCompRel /*&& o.getName()==null*/) // default Relationship name
-      name = "Relationship";
-    //if (isPostCompRel)  fc.setPostCompRelOntCfg(this);
+    if (isPostCompRel()) //&& o.getName()==null // default Relationship name
+      setName("Relationship");
   }
 
-  // for makePostCompRelCfg
+  Ontology getOntologyBean() {
+    // if ontologyBean == null ontologyBean = new Ontology(); ???
+    if (ontologyBean == null) // this is for backward compatible to old ontol ways
+      ontologyBean = fieldConfig.getFieldBean().addNewOntology();
+    return ontologyBean;
+  }
+
+  /** PASE! Ontology stuff in field itself (field only has one ontology) - this is
+      getting phased out replaced by field with single ontology element 
+      this also doesnt have Ontology xml bean - phase out now??*/
+  OntologyConfig(Field field,FieldConfig fc) {
+    fieldConfig = fc;
+    //name = field.getName();
+    setName(field.getName());...
 
[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [613] phenote/trunk/obo-files/ro.obo

From: <nl...@us...> - 2007-05-21 18:47:09

Revision: 613
          http://svn.sourceforge.net/obo/?rev=613&view=rev
Author:   nlw
Date:     2007-05-21 11:47:07 -0700 (Mon, 21 May 2007)

Log Message:
-----------
adding in the official relationship obo file.  its ro.obo, and should be found at http://obo.cvs.sourceforge.net/obo/obo/ontology/OBO_REL/ro.obo

Added Paths:
-----------
    phenote/trunk/obo-files/ro.obo

Added: phenote/trunk/obo-files/ro.obo
===================================================================
--- phenote/trunk/obo-files/ro.obo	                        (rev 0)
+++ phenote/trunk/obo-files/ro.obo	2007-05-21 18:47:07 UTC (rev 613)
@@ -0,0 +1,399 @@
+
+
+
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<!-- ViewVC - http://viewvc.org/
+by Greg Stein - mailto:gs...@ly... -->
+<head>
+<title>SourceForge.net Repository - [obo] Log of /obo/ontology/OBO_REL/ro.obo</title>
+<meta name="generator" content="ViewVC 1.0.3" />
+<link rel="stylesheet" href="/*docroot*/styles.css" type="text/css" />
+</head>
+<body>
+<table style="padding:0.1em;">
+<tr>
+<td>
+<strong>
+
+<a href="/obo/">
+
+[obo]</a>
+/
+
+<a href="/obo/obo/">
+
+obo</a>
+/
+
+<a href="/obo/obo/ontology/">
+
+ontology</a>
+/
+
+<a href="/obo/obo/ontology/OBO_REL/">
+
+OBO_REL</a>
+/
+
+
+
+ro.obo
+
+
+</strong>
+
+</td>
+</tr>
+</table>
+
+
+<div style="float: right; padding: 5px;"><a href="http://sourceforge.net"><img src="/*docroot*/images/sourceforge_whitebg.gif" alt="(logo)" border=0 width=136 height=79></a></div>
+<h1>Log of /obo/ontology/OBO_REL/ro.obo</h1>
+
+<p style="margin:0;">
+
+<a href="/obo/obo/ontology/OBO_REL/"><img src="/*docroot*/images/back_small.png" width="16" height="16" alt="Parent Directory" /> Parent Directory</a>
+
+
+
+
+</p>
+
+<hr />
+<table class="auto">
+
+
+
+<tr>
+<td>Links to HEAD:</td>
+<td>
+(<a href="/obo/obo/ontology/OBO_REL/ro.obo?view=markup">view</a>)
+(<a href="/*checkout*/obo/obo/ontology/OBO_REL/ro.obo">download</a>)
+
+(<a href="/obo/obo/ontology/OBO_REL/ro.obo?view=annotate">annotate</a>)
+</td>
+</tr>
+
+
+
+<tr>
+<td>Sticky Tag:</td>
+<td><form method="get" action="/obo/obo/ontology/OBO_REL/ro.obo" style="display: inline">
+<input type="hidden" name="view" value="log" />
+
+
+<select name="pathrev" onchange="submit()">
+<option value=""></option>
+
+<optgroup label="Branches">
+
+
+<option>MAIN</option>
+
+
+</optgroup>
+
+<optgroup label="Non-branch tags">
+
+
+<option>HEAD</option>
+
+
+</optgroup>
+
+</select>
+
+<input type="submit" value="Set" />
+</form>
+
+</td>
+</tr>
+</table>
+ 
+
+
+
+
+
+
+
+
+<div>
+<hr />
+
+<a name="rev1.3"></a>
+<a name="HEAD"></a>
+
+
+Revision <strong>1.3</strong> -
+
+(<a href="/obo/obo/ontology/OBO_REL/ro.obo?revision=1.3&amp;view=markup">view</a>)
+
+(<a href="/*checkout*/obo/obo/ontology/OBO_REL/ro.obo?revision=1.3">download</a>)
+
+(<a href="/obo/obo/ontology/OBO_REL/ro.obo?annotate=1.3">annotate</a>)
+
+
+
+- <a href="/obo/obo/ontology/OBO_REL/ro.obo?r1=1.3&amp;view=log">[select for diffs]</a>
+
+
+
+
+<br />
+
+<em>Thu May 17 05:17:37 2007 UTC</em> (4 days, 13 hours ago) by <em>cmungall</em>
+
+
+<br />Branch:
+
+<a href="/obo/obo/ontology/OBO_REL/ro.obo?view=log&amp;pathrev=MAIN"><strong>MAIN</strong></a>
+
+
+
+<br />CVS Tags:
+
+<a href="/obo/obo/ontology/OBO_REL/ro.obo?view=log&amp;pathrev=HEAD"><strong>HEAD</strong></a>
+
+
+
+
+
+
+<br />Changes since <strong>1.2: +21 -21 lines</strong>
+
+
+
+
+
+
+
+<br />Diff to <a href="/obo/obo/ontology/OBO_REL/ro.obo?r1=1.2&amp;r2=1.3">previous 1.2</a>
+
+
+
+
+
+
+
+
+
+
+<pre class="vc_log">*** empty log message ***
+</pre>
+</div>
+
+
+
+<div>
+<hr />
+
+<a name="rev1.2"></a>
+
+
+Revision <strong>1.2</strong> -
+
+(<a href="/obo/obo/ontology/OBO_REL/ro.obo?revision=1.2&amp;view=markup">view</a>)
+
+(<a href="/*checkout*/obo/obo/ontology/OBO_REL/ro.obo?revision=1.2">download</a>)
+
+(<a href="/obo/obo/ontology/OBO_REL/ro.obo?annotate=1.2">annotate</a>)
+
+
+
+- <a href="/obo/obo/ontology/OBO_REL/ro.obo?r1=1.2&amp;view=log">[select for diffs]</a>
+
+
+
+
+<br />
+
+<em>Sat Apr 21 18:57:19 2007 UTC</em> (4 weeks, 1 day ago) by <em>cmungall</em>
+
+
+<br />Branch:
+
+<a href="/obo/obo/ontology/OBO_REL/ro.obo?view=log&amp;pathrev=MAIN"><strong>MAIN</strong></a>
+
+
+
+
+
+
+
+<br />Changes since <strong>1.1: +6 -6 lines</strong>
+
+
+
+
+
+
+
+<br />Diff to <a href="/obo/obo/ontology/OBO_REL/ro.obo?r1=1.1&amp;r2=1.2">previous 1.1</a>
+
+
+
+
+
+
+
+
+
+
+<pre class="vc_log">ifixed snap/span Continuant error
+</pre>
+</div>
+
+
+
+<div>
+<hr />
+
+<a name="rev1.1"></a>
+
+
+Revision <strong>1.1</strong> -
+
+(<a href="/obo/obo/ontology/OBO_REL/ro.obo?revision=1.1&amp;view=markup">view</a>)
+
+(<a href="/*checkout*/obo/obo/ontology/OBO_REL/ro.obo?revision=1.1">download</a>)
+
+(<a href="/obo/obo/ontology/OBO_REL/ro.obo?annotate=1.1">annotate</a>)
+
+
+
+- <a href="/obo/obo/ontology/OBO_REL/ro.obo?r1=1.1&amp;view=log">[select for diffs]</a>
+
+
+
+
+<br />
+
+<em>Wed Jan 24 20:16:34 2007 UTC</em> (3 months, 3 weeks ago) by <em>cmungall</em>
+
+
+<br />Branch:
+
+<a href="/obo/obo/ontology/OBO_REL/ro.obo?view=log&amp;pathrev=MAIN"><strong>MAIN</strong></a>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+<pre class="vc_log">*** empty log message ***
+</pre>
+</div>
+
+ 
+
+
+
+ <hr />
+<p><a name="diff"></a>
+This form allows you to request diffs between any two revisions of this file.
+For each of the two "sides" of the diff,
+
+select a symbolic revision name using the selection box, or choose
+'Use Text Field' and enter a numeric revision.
+
+</p>
+<form method="get" action="/obo/obo/ontology/OBO_REL/ro.obo" name="diff_select">
+<table cellpadding="2" cellspacing="0" class="auto">
+<tr>
+<td>&nbsp;</td>
+<td>
+<input type="hidden" name="view" value="diff" />
+Diffs between
+
+<select name="r1">
+<option value="text" selected="selected">Use Text Field</option>
+
+<option value="1.3:MAIN">MAIN</option>
+
+<option value="1.3:HEAD">HEAD</option>
+
+</select>
+<input type="text" size="12" name="tr1"
+value="1.3"
+onchange="document.diff_select.r1.selectedIndex=0" />
+
+and
+
+<select name="r2">
+<option value="text" selected="selected">Use Text Field</option>
+
+<option value="1.3:MAIN">MAIN</option>
+
+<option value="1.3:HEAD">HEAD</option>
+
+</select>
+<input type="text" size="12" name="tr2"
+value="1.1"
+onchange="document.diff_select.r1.selectedIndex=0" />
+
+</td>
+</tr>
+<tr>
+<td>&nbsp;</td>
+<td>
+Type of Diff should be a
+<select name="diff_format" onchange="submit()">
+<option value="h" selected="selected">Colored Diff</option>
+<option value="l" >Long Colored Diff</option>
+<option value="u" >Unidiff</option>
+<option value="c" >Context Diff</option>
+<option value="s" >Side by Side</option>
+</select>
+<input type="submit" value=" Get Diffs " />
+</td>
+</tr>
+</table>
+</form>
+
+
+<form method="get" action="/obo/obo/ontology/OBO_REL/ro.obo">
+<div>
+<hr />
+<a name="logsort"></a>
+<input type="hidden" name="view" value="log" />
+Sort log by:
+<select name="logsort" onchange="submit()">
+<option value="cvs" >Not sorted</option>
+<option value="date" selected="selected">Commit date</option>
+<option value="rev" >Revision</option>
+</select>
+<input type="submit" value=" Sort " />
+</div>
+</form>
+
+
+<hr />
+<table>
+<tr>
+<td>
+<address><a href="http://sourceforge.net/">Back to SourceForge.net</a></address><br />
+Powered by <a href="http://viewvc.tigris.org/">ViewVC 1.0.3</a>
+</td>
+<td style="text-align:right;">
+<h3><a href="/*docroot*/help_log.html">ViewVC and Help</a></h3>
+</td>
+</tr>
+</table>
+</body>
+</html>
+
+


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[Obo-svn-commit] SF.net SVN: obo: [612] phenote/trunk/conf/ncbo.cfg

From: <nl...@us...> - 2007-05-21 18:45:53

Revision: 612
          http://svn.sourceforge.net/obo/?rev=612&view=rev
Author:   nlw
Date:     2007-05-21 11:45:46 -0700 (Mon, 21 May 2007)

Log Message:
-----------
changes to ncbo config - added in proper repository locations, updated look&feel of config...added descriptions for some of the fields.

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

Modified: phenote/trunk/conf/ncbo.cfg
===================================================================
--- phenote/trunk/conf/ncbo.cfg	2007-05-21 18:27:13 UTC (rev 611)
+++ phenote/trunk/conf/ncbo.cfg	2007-05-21 18:45:46 UTC (rev 612)
@@ -1,63 +1,78 @@
-<?xml version="1.3.1" encoding="UTF-8"?>
+<?xml version="1.3.2" encoding="UTF-8"?>
+<!-- *********************** CONFIG INFO ************************** -->
+<ns:phenote-configuration xmlns:ns="phenote/config/xml"
+			  name="NCBO-OMIM Configuration"
+			  author="Nicole Washington"
+			  description="This configuration is for the curators working with the NCBO on OMIM curation.">
 
-<ns:phenote-configuration xmlns:ns="phenote/config/xml">
-
+  <!-- *********************** 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/ncbo.cfg" />
 
   <ns:log config-file="conf/log4j-standalone.xml"/>
 
-  <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
-  <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>
-  <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="false"/>
-  <ns:dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/>
-
   <ns:uvic-graph enable="false"/>
   <ns:term-history enable="false"/>
   <ns:auto-update-ontologies enable="true"/>  <!--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:obo-repository url-dir="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/>
 
-  <ns:field name="Pub" syntax-abbrev="PUB" enable="true"/>
 
-  <ns:field name="Genotype" syntax-abbrev="GT" enable="true"/>
+  <!-- ********************* FILE ADAPTERS ************************** -->
+  <!-- be sure to include at least one enabled file adapter -->
+  <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
+  <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>
+  <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="false"/>
 
+  <!-- ******************** FIELD DEFINITIONS *********************** --> 
+  <!--The order of the fields is important, and will display in the order 
+  listed here.  If a repository location is given as the filename (ie 
+  "http://www.your-repository.com/your_obo_file.obo"), then this site 
+  will be checked for updates -->
+
+  <ns:field name="Pub" syntax-abbrev="PUB" enable="true" desc="For publication references.  Format ID:1234567; Typically PMID:1234567."/>
+
+  <ns:field name="Genotype" syntax-abbrev="GT" enable="true" desc="Genotype or genotype ID"/>
+
   <ns:field name="Genetic Context" syntax-abbrev="GC" enable="true">
     <ns:ontology name="Genetic Context" file="context.obo"/>
   </ns:field>
 
   <ns:field name="Entity" syntax-abbrev="E" enable="true">
-    <ns:ontology name="Relationship" file="relationship.obo" is-postcomp-rel="true"/>
+    <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" is-postcomp-rel="true"/>
     <ns:ontology name="FMA" file="fma_obo.obo"/>
-    <ns:ontology name="EHDAA" file="human-dev-anat-abstract.obo"/>
+    <ns:ontology name="EHDAA" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo"/>
     <ns:ontology name="GO"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
     <ns:ontology name="CL"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo"/>
-    <ns:ontology name="CHEBI" file="chebi.obo" repos-subdir="chemical"/>
+    <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
   </ns:field>
 
   <ns:field name="Quality" syntax-abbrev="Q" enable="true">
-    <ns:ontology name="PATO" file="quality.obo" repos-subdir="phenotype"/>
-    <ns:ontology name="MP" file="mammalian_phenotype.obo" repos-subdir="phenotype"/>
+    <ns:ontology name="PATO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
+    <ns:ontology name="MP" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mammalian_phenotype.obo"/>
   </ns:field>
 
-  <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true">
-    <ns:ontology name="Relationship" file="relationship.obo" is-postcomp-rel="true"/>
+  <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true" desc="To be used when using relational qualities">
+    <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" is-postcomp-rel="true"/>
     <ns:ontology name="FMA" file="fma_obo.obo"/>
-    <ns:ontology name="EHDAA" file="human-dev-anat-abstract.obo"/>
+    <ns:ontology name="EHDAA" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo"/>
     <ns:ontology name="GO"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
-    <ns:ontology name="CHEBI" file="chebi.obo" repos-subdir="chemical"/>
+    <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
     <ns:ontology name="CL"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo"/>
   </ns:field>
 
-  <ns:field name="Abnormal" syntax-abbrev="Tag" enable="true">
+  <ns:field name="Abnormal" syntax-abbrev="Tag" enable="true" desc="To specify if the phenotype statement is reflecting an abnormal/normal phenotype; most likely a mutant phenotype will be abnormal, except for exceptional cases of normality">
     <ns:ontology name="Abnormal" file="quality.obo" slim="abnormal_slim"/>
   </ns:field>
 
-  <ns:field name="Description" syntax-abbrev="Desc" enable="true"/>
+  <ns:field name="Description" syntax-abbrev="Desc" enable="true" desc="Some kind of free text description, actual sentence, note to yourself, etc."/>
 
+  <!-- ******************** REVISION HISTORY *********************** --> 
+  <!-- 05.20.2007 - Latest update changes relationship.obo to ro.obo; included ehdaa repository; 
+       removed obo-repository url-dir and incorporated into each filename; added in comments; 
+       removed the nexus adapter...it won't ever be used by this group.-->
+
 </ns:phenote-configuration>
\ No newline at end of file


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[Obo-svn-commit] SF.net SVN: obo: [610] phenote/trunk/doc/phenote-website/ phenote-release-notes.html

From: <nl...@us...> - 2007-05-19 00:21:34

Revision: 610
          http://svn.sourceforge.net/obo/?rev=610&view=rev
Author:   nlw
Date:     2007-05-18 17:21:36 -0700 (Fri, 18 May 2007)

Log Message:
-----------
added new feature for configuration options desc,author, name into docs

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	2007-05-19 00:18:06 UTC (rev 609)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.html	2007-05-19 00:21:36 UTC (rev 610)
@@ -13,7 +13,9 @@
 
 in development, 1.3-beta2 <br>
 <ul>
-  <li>feature:  Web-based documentation and Help features<br>
+  <li>feature:  Web-based documentation and Help features</li>
+  <li>feature:  Metadata fields added to configuration.  User can name their configuration, add a description, and author</li>
+<li>feature:  Descriptions can be added for fields</li>
   <li>change:  File-&gt;New is disabled until next version</li>
 </ul>
 


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[Obo-svn-commit] SF.net SVN: obo: [609] phenote/trunk/src/java/phenote/config

From: <nl...@us...> - 2007-05-19 00:18:04

Revision: 609
          http://svn.sourceforge.net/obo/?rev=609&view=rev
Author:   nlw
Date:     2007-05-18 17:18:06 -0700 (Fri, 18 May 2007)

Log Message:
-----------
Added public getters to config and fieldconfig to get the desc, name, etc.

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/config/Config.java
    phenote/trunk/src/java/phenote/config/FieldConfig.java

Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java	2007-05-19 00:06:57 UTC (rev 608)
+++ phenote/trunk/src/java/phenote/config/Config.java	2007-05-19 00:18:06 UTC (rev 609)
@@ -789,6 +789,10 @@
     allFields.add(index,fc); // ??
   }
   
+  public String getConfigName() {	return configName;  }
+  public String getConfigDesc() { return configDesc; }
+  public String getConfigAuthor() { return configAuthor; }
+  
 }
 
 //       if (overwrite || mode.equals("WIPEOUT_ALWAYS"))

Modified: phenote/trunk/src/java/phenote/config/FieldConfig.java
===================================================================
--- phenote/trunk/src/java/phenote/config/FieldConfig.java	2007-05-19 00:06:57 UTC (rev 608)
+++ phenote/trunk/src/java/phenote/config/FieldConfig.java	2007-05-19 00:18:06 UTC (rev 609)
@@ -73,7 +73,9 @@
 
   // --> getName?
   public String getLabel() { return label; }
+  public String getDesc() { return desc; }
   boolean hasLabel(String label) { return label.equals(this.label); } 
+  boolean hasDesc(String desc) { return desc.equals(this.desc); }
 
   //private void setOntologyFile(String f){getOntologyConfig().setOntologyFile(f);}
   public boolean hasOntologies() {


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[Obo-svn-commit] SF.net SVN: obo: [608] phenote/trunk/src/java/phenote

From: <nl...@us...> - 2007-05-19 00:06:55

Revision: 608
          http://svn.sourceforge.net/obo/?rev=608&view=rev
Author:   nlw
Date:     2007-05-18 17:06:57 -0700 (Fri, 18 May 2007)

Log Message:
-----------
Added setting of phenote-configuration attributes of description, name, author; field attribute desc.

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/config/Config.java
    phenote/trunk/src/java/phenote/config/FieldConfig.java
    phenote/trunk/src/java/phenote/util/HtmlUtil.java

Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java	2007-05-18 23:51:11 UTC (rev 607)
+++ phenote/trunk/src/java/phenote/config/Config.java	2007-05-19 00:06:57 UTC (rev 608)
@@ -56,6 +56,9 @@
   private int updateTimer = 0; //default is to not wait
   private String reposUrlDir;
   private String version;
+  private String configName;
+  private String configDesc;
+  private String configAuthor;
   //private String masterToLocalConfigMode;
   //private MasterToLocalConfig masterToLocalBean;
   private PhenoteConfiguration phenoConfigBean; // cache the xml parse bean??
@@ -649,7 +652,15 @@
       phenoConfigBean = pcd.getPhenoteConfiguration();
 
       version = phenoConfigBean.getVersion();
+      
+      configName = phenoConfigBean.getName();
+      
+      configDesc = phenoConfigBean.getDescription();
+      
+      configAuthor = phenoConfigBean.getAuthor();
 
+      System.out.println("version:  "+version+"\nname:  "+configName+"\nDesc:  "+
+      		configDesc+"\nAuthor:  "+configAuthor);
       //MasterToLocalConfig m 
 //         = phenoConfigBean.getMasterToLocalConfig();
 //       if (m != null && m.getMode() != null)

Modified: phenote/trunk/src/java/phenote/config/FieldConfig.java
===================================================================
--- phenote/trunk/src/java/phenote/config/FieldConfig.java	2007-05-18 23:51:11 UTC (rev 607)
+++ phenote/trunk/src/java/phenote/config/FieldConfig.java	2007-05-19 00:06:57 UTC (rev 608)
@@ -16,6 +16,7 @@
   //private CharFieldEnum charFieldEnum; // phase out
   private CharField charField;
   private String label;
+  private String desc;
   // Entity field can have multiple ontologies
   private List<OntologyConfig> ontologyConfigList;
   //private boolean isPostComp;
@@ -29,7 +30,7 @@
   FieldConfig(Field fieldBean,Config cfg) {
     this.config = cfg;
     this.label = fieldBean.getName();
-    
+    this.desc = fieldBean.getDesc();
 //   try{//phase this out!charFieldEnum = CharFieldEnum.getCharFieldEnum(label);}
 //     catch (Exception e) {} // no char field enum for name - new generic!
     //fc = new FieldConfig(name);

Modified: phenote/trunk/src/java/phenote/util/HtmlUtil.java
===================================================================
--- phenote/trunk/src/java/phenote/util/HtmlUtil.java	2007-05-18 23:51:11 UTC (rev 607)
+++ phenote/trunk/src/java/phenote/util/HtmlUtil.java	2007-05-19 00:06:57 UTC (rev 608)
@@ -46,7 +46,7 @@
 		if (oboClass.isObsolete()) {
 			sb.append("This term is OBSOLETE").append(newLine());
 
-			
+
 		}		
 		sb.append(nl()).append(bold("ID: ")).append(colorFont(oboClass.getID(), "red"));
 
@@ -203,7 +203,7 @@
 //			int totSyns = 0;
 //			totSyns=broadSynCount+exactSynCount+narrowSynCount+relatedSynCount+unknownScopeCount;
 //			if (totSyns>0) {
-//				sb.append(makeRow(makeLeftCol(bold("Synonyms:"))+makeRightCol(temp.toString())));
+//			sb.append(makeRow(makeLeftCol(bold("Synonyms:"))+makeRightCol(temp.toString())));
 //			}
 			if (exactSynCount>0)
 				sb.append(makeRow(makeLeftCol(bold("Exact Synonyms:"))+makeRightCol(exactBuf.toString())));
@@ -218,7 +218,7 @@
 		}
 		return sb.toString();
 	}
-	
+
 	public static String termInfo(OBOClass oboClass, String ontology,String field) {
 		// funny - revisit for sure - either should pass through all methods
 		// or util should actually be an object - singleton? i think maybe its


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[Obo-svn-commit] SF.net SVN: obo: [607] phenote/trunk

From: <nl...@us...> - 2007-05-18 23:51:09

Revision: 607
          http://svn.sourceforge.net/obo/?rev=607&view=rev
Author:   nlw
Date:     2007-05-18 16:51:11 -0700 (Fri, 18 May 2007)

Log Message:
-----------
added new items for configuration to rnc...  description, name, autor for phenote-configuration; field desc

Modified Paths:
--------------
    phenote/trunk/conf/phenote-config.rnc
    phenote/trunk/conf/phenote-config.xsd
    phenote/trunk/doc/phenote-website/phenote-release-notes.html
    phenote/trunk/doc/phenote-website/sample_data.xls
    phenote/trunk/jars/phenoteconfigbeans.jar

Modified: phenote/trunk/conf/phenote-config.rnc
===================================================================
--- phenote/trunk/conf/phenote-config.rnc	2007-05-18 23:12:39 UTC (rev 606)
+++ phenote/trunk/conf/phenote-config.rnc	2007-05-18 23:51:11 UTC (rev 607)
@@ -5,6 +5,9 @@
 start =
   element phenote-configuration {
     attribute version { xsd:string },
+    attribute description { xsd:string },
+    attribute name { xsd:string },
+    attribute author { xsd:string },
     master-to-local-config,
     log,
     queryable-dataadapter*,
@@ -67,6 +70,7 @@
     attribute enable { xsd:boolean },
     ##attribute name { "Pub" | "Genotype" | "Genetic Context" | "Entity" | "Quality" },
     attribute name { xsd:string },
+    attribute desc { xsd:string },
     ## tag for field for pheno-syntax adapter
     attribute syntax-abbrev { xsd:string },
     ## whether field is free text or constrained by ontology - take out?

Modified: phenote/trunk/conf/phenote-config.xsd
===================================================================
--- phenote/trunk/conf/phenote-config.xsd	2007-05-18 23:12:39 UTC (rev 606)
+++ phenote/trunk/conf/phenote-config.xsd	2007-05-18 23:51:11 UTC (rev 607)
@@ -15,6 +15,9 @@
         <xs:element minOccurs="0" maxOccurs="unbounded" ref="x:field"/>
       </xs:sequence>
       <xs:attribute name="version" use="required" type="xs:string"/>
+      <xs:attribute name="description" use="required" type="xs:string"/>
+      <xs:attribute name="name" use="required" type="xs:string"/>
+      <xs:attribute name="author" use="required" type="xs:string"/>
     </xs:complexType>
   </xs:element>
   <xs:element name="master-to-local-config">
@@ -82,6 +85,7 @@
           <xs:documentation>attribute name { "Pub" | "Genotype" | "Genetic Context" | "Entity" | "Quality" },</xs:documentation>
         </xs:annotation>
       </xs:attribute>
+      <xs:attribute name="desc" use="required" type="xs:string"/>
       <xs:attribute name="syntax-abbrev" use="required" type="xs:string">
         <xs:annotation>
           <xs:documentation>tag for field for pheno-syntax adapter</xs:documentation>

Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.html	2007-05-18 23:12:39 UTC (rev 606)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.html	2007-05-18 23:51:11 UTC (rev 607)
@@ -26,6 +26,7 @@
   <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>
 

Modified: phenote/trunk/doc/phenote-website/sample_data.xls
===================================================================
--- phenote/trunk/doc/phenote-website/sample_data.xls	2007-05-18 23:12:39 UTC (rev 606)
+++ phenote/trunk/doc/phenote-website/sample_data.xls	2007-05-18 23:51:11 UTC (rev 607)
@@ -18,7 +18,7 @@
 PMID:9462749 	OMIM602229.0002 			SO:1000062	nonsense_codon_change_in_transcript	PATO:0001632	anterior to	SO:0000330	conserved_region							Y83X stop codon mutation before HMG domain 	
 PMID:9722528 	OMIM602229.0002 			GO:0065004	protein-DNA complex assembly	PATO:0001511	non-functional									***SOX10mut failed to form protein-DNA complexes 	
 PMID:9722528 	OMIM602229.0002 			GO:0008104	protein localization	PATO:0000628	mislocalised	GO:0005829	cytosol					PATO:0000460	abnormal	protein mislocalization to the cytosol 	
-PMID:9462749 	OMIM602229.0003 			SO:1000034^located_in(SO:0000330)	nucleotide_insertion^located_in(conserved_region)	PATO:0000467	present									6-bp insertion in middle of HMG domain 	
+PMID:9462749 	OMIM602229.0003 			SO:1000034^OBO_REL:located_in(SO:0000330)	nucleotide_insertion^located_in(conserved_region)	PATO:0000467	present									6-bp insertion in middle of HMG domain 	
 PMID:9722528 	OMIM602229.0003 			GO:0065004	protein-DNA complex assembly	PATO:0001511	non-functional									***SOX10mut failed to form protein-DNA complexes 	
 PMID:9722528 	OMIM602229.0003 			GO:0008104	protein localization	PATO:0001032	position	GO:0005634	nucleus					PATO:0000461	normal	protein localization to the nucleus 	
 PMID:12668617 	OMIM602229.0003 			GO:0016563	transcriptional activator activity	PATO:0001508	abolished									***Sox10 ability to activate transcription eliminated 	
@@ -33,11 +33,11 @@
 PMID:9722528 	OMIM602229.? 			GO:0016563	transcriptional activator activity	PATO:0001511	non-functional			 	 					deficient in activity as a transcriptional activator 	
 PMID:11734543 	OMIM602229.? 			FMA:62983	Myelin sheath	PATO:0001617	deformed									myelin defects 	
 PMID:11734543 	OMIM602229.? 			GO:0016563	transcriptional activator activity	PATO:0000462	absent									***SOX10 failed to transactivate the CX32 promoter 	
-PMID:11734543 	OMIM602229.? 			GO:0008134^located_in(SO:0000167)	transcription factor binding^located_in(promoter)	PATO:0000462	absent									***SOX10 failed to transactivate the CX32 promoter 	
+PMID:11734543 	OMIM602229.? 			GO:0008134^OBO_REL:located_in(SO:0000167)	transcription factor binding^located_in(promoter)	PATO:0000462	absent									***SOX10 failed to transactivate the CX32 promoter 	
 PMID:9462749 	[OMIM602229.0001/+] 			GO:0007605	sensory perception of sound	PATO:0000468	decreased									bilateral profound hearing loss 	
 PMID:9462749 	[OMIM602229.0001/+] 			FMA:53667	Hair	PATO:0000323	white									white hair color 	
 PMID:9462749 	[OMIM602229.0001/+] 			FMA:58611	Iridial part of retina	PATO:0000318	blue									blue irides with grey speckles 	
-PMID:9462749 	[OMIM602229.0001/+] 			FMA:63846^located_in(FMA:7163)	Cell pigment^located_in(Skin)	PATO:0001608	patchy									depigmented skin patches 	
+PMID:9462749 	[OMIM602229.0001/+] 			FMA:63846^OBO_REL:located_in(FMA:7163)	Cell pigment^located_in(Skin)	PATO:0001608	patchy									depigmented skin patches 	
 PMID:9462749 	[OMIM602229.0001/+] 			FMA:63846	Cell pigment	PATO:0000460	abnormal									pigmentary abnormalities (detailed with other entries) 	
 PMID:9462749 	[OMIM602229.0001/+] 			FMA:7199	Intestine	PATO:0000648	obstructed									intestinal obstruction in neonates 	
 PMID:9462749 	[OMIM602229.0001/+] 			GO:0007588	excretion	PATO:0000911	decreased rate									constipation in adults 	
@@ -49,37 +49,37 @@
 PMID:9462749 	[OMIM602229.0002/+] 			FMA:53667	Hair	PATO:0000665	light									fair hair color 	
 PMID:9462749 	[OMIM602229.0002/+] 			FMA:58611	Iridial part of retina	PATO:0001265	bright blue									vivid blue eyes 	
 PMID:9462749 	[OMIM602229.0002/+] 			FMA:7199	Intestine	PATO:0001624	decreased functionality									bowel problems 	
-PMID:9462749 	[OMIM602229.0002/+] 			FMA:5884^located_in(FMA:14544)	Ganglion^located_in(Rectum)	PATO:0000419	decreased number									number of ganglia was dramatically reduced 	
+PMID:9462749 	[OMIM602229.0002/+] 			FMA:5884^OBO_REL:located_in(FMA:14544)	Ganglion^located_in(Rectum)	PATO:0000419	decreased number									number of ganglia was dramatically reduced 	
 PMID:9462749 	[OMIM602229.0003/+] 			GO:0007605	sensory perception of sound	PATO:0000468	decreased									deafness 	
 PMID:9462749 	[OMIM602229.0003/+] 			FMA:14544	Rectum	PATO:0001557	lacking physical part	FMA:5884	Ganglion							short segment HSCR - aganglionic tract in rectum+sigmoid colon 	
 PMID:9462749 	[OMIM602229.0003/+] 			FMA:14548	Sigmoid colon	PATO:0001557	lacking physical part	FMA:5884	Ganglion							short segment HSCR - aganglionic tract in rectum+sigmoid colon 	
 PMID:9462749 	[OMIM602229.0004/+] 	PM:0000019	penetrance_incomplete	GO:0007605	sensory perception of sound	PATO:0000468	decreased									deafness 	
-PMID:9462749 	[OMIM602229.0004/+] 	PM:0000023	expressivity_incomplete	FMA:63846^contained_in(FMA:61695)	Cell pigment^contained_in(Body surface)	PATO:0000468	decreased									hypopigmentation 	
+PMID:9462749 	[OMIM602229.0004/+] 	PM:0000023	expressivity_incomplete	FMA:63846^OBO_REL:contained_in(FMA:61695)	Cell pigment^contained_in(Body surface)	PATO:0000468	decreased									hypopigmentation 	
 PMID:9462749 	[OMIM602229.0004/+] 			FMA:7199	Intestine	PATO:0001557	lacking physical part	FMA:84048	Ganglion cell							HSCR 	
 PMID:9462749 	[OMIM602229.0004/+] 	PM:0000023	expressivity_incomplete	FMA:53667	Hair	PATO:0000323	white									white hair color 	
 PMID:9462749 	[OMIM602229.0004/+] 	PM:0000019	penetrance_incomplete	FMA:7199	Intestine	PATO:0001571	dilated									megacolon 	
 PMID:10441344 	OMIM602229.0005 			SO:1000061	nonconservative_missense_codon_change_in_transcript	PATO:0000467	present									SER135THR mutation 	
 PMID:10441344 	OMIM602229.0005 			SO:1000061	nonconservative_missense_codon_change_in_transcript	PATO:0000467	present									SER135THR mutation 	
-PMID:2280978 	Yemenite deaf-blind hypopigmentation syndrome 			FMA:63846^located_in(FMA:7163)	Cell pigment^located_in(Skin)	PATO:0001608	patchy									hypo and hyperpigmented skin 	
+PMID:2280978 	Yemenite deaf-blind hypopigmentation syndrome 			FMA:63846^OBO_REL:located_in(FMA:7163)	Cell pigment^located_in(Skin)	PATO:0001608	patchy									hypo and hyperpigmented skin 	
 PMID:2280978 	Yemenite deaf-blind hypopigmentation syndrome 			FMA:58238	Cornea	PATO:0000587	decreased size									microcornea 	
 PMID:2280978 	Yemenite deaf-blind hypopigmentation syndrome 			FMA:54448	Eye	MP:0005262	coloboma									coloboma 	
 PMID:2280978 	Yemenite deaf-blind hypopigmentation syndrome 	PM:0000019	penetrance_incomplete	GO:0007605	sensory perception of sound	PATO:0000468	decreased									severe hearing loss 	
-PMID:10441344 	OMIM602229.0005 			FMA:63846^located_in(FMA:7163)	Cell pigment^located_in(Skin)	PATO:0001608	patchy									hypo and hyperpigmented skin 	
+PMID:10441344 	OMIM602229.0005 			FMA:63846^OBO_REL:located_in(FMA:7163)	Cell pigment^located_in(Skin)	PATO:0001608	patchy									hypo and hyperpigmented skin 	
 PMID:10441344 	OMIM602229.0005 	PM:0000019	penetrance_incomplete	GO:0007605	sensory perception of sound	PATO:0000468	decreased									severe hearing loss 	
 PMID:10482261 	OMIM602229.0008 			FMA:62983	Myelin sheath	PATO:0001617	deformed			 	 					leukodystrophy - progressive degeneration development of the myelin sheath 	
 PMID:10482261 	OMIM602229.0008 			FMA:7199	Intestine	PATO:0000648	obstructed									intestinal obstruction in neonates 	
 PMID:10482261 	OMIM602229.0008 			FMA:7199	Intestine	PATO:0001557	lacking physical part	FMA:5884	Ganglion							long segment HSCR - aganglionic tract in entire colon 	
-PMID:10482261 	OMIM602229.0008 			FMA:63846^located_in(FMA:58237)	Cell pigment^located_in(Left iris)	PATO:0000616	asymmetrical	FMA:63846^located_in(FMA:58236)	Cell pigment^located_in(Right iris)							heterochromia iridis - one eye is different color (intensity) than the other 	
+PMID:10482261 	OMIM602229.0008 			FMA:63846^OBO_REL:located_in(FMA:58237)	Cell pigment^located_in(Left iris)	PATO:0000616	asymmetrical	FMA:63846^OBO_REL:located_in(FMA:58236)	Cell pigment^located_in(Right iris)							heterochromia iridis - one eye is different color (intensity) than the other 	
 PMID:10482261 	OMIM602229.0008 	PM:0000022	expressivity_complete	GO:0007605	sensory perception of sound	PATO:0000468	decreased									profound hearing loss 	
 PMID:10482261 	OMIM602229.0008 			FMA:59516	Root of nose	PATO:0000600	increased width									broad nasal root 	
 PMID:10482261 	OMIM602229.0008 			FMA:59324	Medial angle of left eye	PATO:0000374	increased distance	FMA:59323	Medial angle of right eye	 	 					dystopia canthorum - inner corners of the eyes (canthi) are spaced farther apart than normal 	
-PMID:10482261 	OMIM602229.0008 			GO:0048589^has_participant(FMA:20394)	developmental growth^has_participant(Body)	PATO:0000911	decreased rate									developmental delay 	
+PMID:10482261 	OMIM602229.0008 			GO:0048589^OBO_REL:has_participant(FMA:20394)	developmental growth^has_participant(Body)	PATO:0000911	decreased rate									developmental delay 	
 PMID:10482261 	OMIM602229.0008 			FMA:20394	Body	MP:0000754	partial paralysis									spastic quadraplegia 	
 PMID:10482261 	OMIM602229.0008 			FMA:9721	Tendon	PATO:0001568	having decreased function	GO:0060004	reflex							loss of deep tendon reflexes 	
 PMID:10482261 	OMIM602229.0008 	PM:0000022	expressivity_complete	GO:0007600	sensory perception	PATO:0000468	decreased									sensory dullness 	
 PMID:10482261 	OMIM602229.0008 			FMA:9903	Peripheral nervous system	PATO:0001624	decreased functionality									peripheral neuropathy 	
 PMID:10482261 	OMIM602229.0008 			FMA:5867	Motor nerve	PATO:0001585	conduction									***decreased conductive velocity 	
-PMID:10482261 	OMIM602229.0008 			FMA:30316^contained_in(FMA:7182)	Muscle^contained_in(Limb)	PATO:0001623	atrophied									muscles in all limbs were severely atrophic 	
-PMID:10482261 	OMIM602229.0008 			FMA:67257^contained_in(FMA:20935)	Protein^contained_in(Cerebrospinal fluid)	PATO:0001162	increased concentration									Protein in the cerebrospinal fluid was elevated  	
-PMID:10482261 	OMIM602229.0008 			GO:0008038^contained_in(FMA:79876)	neuron recognition^contained_in(Brainstem)	PATO:0000468	decreased	GO:0007605	sensory perception of sound							no auditory brainstem response bilaterally 	
-PMID:10482261 	OMIM602229.0008 			FMA:62983^located_in(FMA:50801)	Myelin sheath^located_in(Brain)	PATO:0000468	decreased			 	 					prominent deficiency of myelination in the entire brain 	
+PMID:10482261 	OMIM602229.0008 			FMA:30316^OBO_REL:contained_in(FMA:7182)	Muscle^contained_in(Limb)	PATO:0001623	atrophied									muscles in all limbs were severely atrophic 	
+PMID:10482261 	OMIM602229.0008 			FMA:67257^OBO_REL:contained_in(FMA:20935)	Protein^contained_in(Cerebrospinal fluid)	PATO:0001162	increased concentration									Protein in the cerebrospinal fluid was elevated  	
+PMID:10482261 	OMIM602229.0008 			GO:0008038^OBO_REL:contained_in(FMA:79876)	neuron recognition^contained_in(Brainstem)	PATO:0000468	decreased	GO:0007605	sensory perception of sound							no auditory brainstem response bilaterally 	
+PMID:10482261 	OMIM602229.0008 			FMA:62983^OBO_REL:located_in(FMA:50801)	Myelin sheath^located_in(Brain)	PATO:0000468	decreased			 	 					prominent deficiency of myelination in the entire brain 	

Modified: phenote/trunk/jars/phenoteconfigbeans.jar
===================================================================
(Binary files differ)


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[Obo-svn-commit] SF.net SVN: obo: [606] phenote/trunk/doc/phenote-website/help

From: <nl...@us...> - 2007-05-18 23:12:37

Revision: 606
          http://svn.sourceforge.net/obo/?rev=606&view=rev
Author:   nlw
Date:     2007-05-18 16:12:39 -0700 (Fri, 18 May 2007)

Log Message:
-----------
Help docs:  added general interface screenshot to phenote interface main page, added info to editing functions.

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/help/Phenote.jhm
    phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak
    phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml
    phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml.bak
    phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html
    phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html.tmp
    phenote/trunk/doc/phenote-website/help/html/Editing_Functions.htm
    phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Ontology_Fields.htm
    phenote/trunk/doc/phenote-website/help/html/Menu_Bars.htm
    phenote/trunk/doc/phenote-website/help/html/The_Phenote_Interface.htm
    phenote/trunk/doc/phenote-website/help/javahelp.css

Added Paths:
-----------
    phenote/trunk/doc/phenote-website/help/images/phenote-data-markup.png

Modified: phenote/trunk/doc/phenote-website/help/Phenote.jhm
===================================================================
--- phenote/trunk/doc/phenote-website/help/Phenote.jhm	2007-05-18 22:13:16 UTC (rev 605)
+++ phenote/trunk/doc/phenote-website/help/Phenote.jhm	2007-05-18 23:12:39 UTC (rev 606)
@@ -24,6 +24,7 @@
    <mapID target="Building_a_Filter" url="html/Building_a_Filter.htm"/>
    <mapID target="Building_Filters" url="html/Building_Filters.htm"/>
    <mapID target="Changing_Link_Attributes" url="html/Changing_Link_Attributes.htm"/>
+   <mapID target="The_Phenote_Interface" url="html/The_Phenote_Interface.htm"/>
    <mapID target="Changing_Relationship_Types" url="html/Changing_Relationship_Types.htm"/>
    <mapID target="Changing_your_Autocompletion_Settings" url="html/Changing_your_Autocompletion_Settings.htm"/>
    <mapID target="Changing_your_Configuration" url="html/Changing_your_Configuration.htm"/>

Modified: phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak
===================================================================
--- phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak	2007-05-18 22:13:16 UTC (rev 605)
+++ phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak	2007-05-18 23:12:39 UTC (rev 606)
@@ -24,6 +24,7 @@
    <mapID target="Building_a_Filter" url="html/Building_a_Filter.htm"/>
    <mapID target="Building_Filters" url="html/Building_Filters.htm"/>
    <mapID target="Changing_Link_Attributes" url="html/Changing_Link_Attributes.htm"/>
+   <mapID target="The_Phenote_Interface" url="html/The_Phenote_Interface.htm"/>
    <mapID target="Changing_Relationship_Types" url="html/Changing_Relationship_Types.htm"/>
    <mapID target="Changing_your_Autocompletion_Settings" url="html/Changing_your_Autocompletion_Settings.htm"/>
    <mapID target="Changing_your_Configuration" url="html/Changing_your_Configuration.htm"/>

Modified: phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml	2007-05-18 22:13:16 UTC (rev 605)
+++ phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml	2007-05-18 23:12:39 UTC (rev 606)
@@ -17,7 +17,7 @@
      <tocitem text="Running Phenote for the First Time" target="Running_Phenote_for_the_First_Time"/>
      <tocitem text="Exiting Phenote" target="Exiting_Phenote"/>
 </tocitem>
-<tocitem text="The Phenote Interface">
+<tocitem text="The Phenote Interface" target="The_Phenote_Interface">
      <tocitem text="Menu Bars" target="Menu_Bars"/>
      <tocitem text="Data Entry" target="Data_Entry"/>
      <tocitem text="Term Info" target="Term_Info"/>

Modified: phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml.bak
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml.bak	2007-05-18 22:13:16 UTC (rev 605)
+++ phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml.bak	2007-05-18 23:12:39 UTC (rev 606)
@@ -34,6 +34,7 @@
 </tocitem>
 <tocitem text="Creating Annotations">
      <tocitem text="Editing Functions" target="Editing_Functions"/>
+     <tocitem text="Changing your Autocompletion Settings" target="Changing_your_Autocompletion_Settings"/>
      <tocitem text="Entering data into Free-Text fields" target="Entering_data_into_Free_Text_fields"/>
      <tocitem text="Entering data into Ontology Fields" target="Entering_data_into_Ontology_Fields"/>
      <tocitem text="Sample Annotations" target="Sample_Annotations"/>

Modified: phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html	2007-05-18 22:13:16 UTC (rev 605)
+++ phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html	2007-05-18 23:12:39 UTC (rev 606)
@@ -214,7 +214,7 @@
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
-<tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>The Phenote Interface</font>
+<tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Phenote_Interface.htm" target=bodyframe>The Phenote Interface</font></a>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt110>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Menu_Bars.htm" target=bodyframe>Menu Bars</font></a>
 </td></tr></table>

Modified: phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html.tmp
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html.tmp	2007-05-18 22:13:16 UTC (rev 605)
+++ phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html.tmp	2007-05-18 23:12:39 UTC (rev 606)
@@ -37,7 +37,7 @@
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
-<tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>The Phenote Interface</font>
+<tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Phenote_Interface.htm" target=bodyframe>The Phenote Interface</font></a>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt110>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Menu_Bars.htm" target=bodyframe>Menu Bars</font></a>
 </td></tr></table>

Modified: phenote/trunk/doc/phenote-website/help/html/Editing_Functions.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Editing_Functions.htm	2007-05-18 22:13:16 UTC (rev 605)
+++ phenote/trunk/doc/phenote-website/help/html/Editing_Functions.htm	2007-05-18 23:12:39 UTC (rev 606)
@@ -7,9 +7,9 @@
 </HEAD>
 <BODY BGCOLOR=#ffffff>
 <H1>Editing Functions</H1>
-<P><STRONG>New Annotation</STRONG> - creates a new row in 
-the table for data entry.&nbsp; when creating a new annotation row, the cursor 
-will be placed in the first field ready for data entry.</P>
+<P><STRONG>New Annotation</STRONG>    - creates a 
+new row in the spreadsheet for an annotation.&nbsp; When creating a new annotation 
+row, the cursor will be placed in the first data entry&nbsp;field.</P>
 <P><STRONG>Copy Annotation</STRONG> - the currently selected 
 row(s) will be duplicated and placed at the end of the spreadsheet.&nbsp; This 
 action can be reversed with the 'undo' command.</P>

Modified: phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Ontology_Fields.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Ontology_Fields.htm	2007-05-18 22:13:16 UTC (rev 605)
+++ phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Ontology_Fields.htm	2007-05-18 23:12:39 UTC (rev 606)
@@ -38,10 +38,10 @@
     <LI>synonyms - indicated with "[syn]"
     <LI>definitions - indicated with "[def]"
     <LI>obsoletes - indicated with "[obs]"</LI></UL></UL>    
-    <P designtimesp="32337">If you have selected to search in 
+    <p >If you have selected to search in 
 ALL ontologies, then the matches are listed in this order, in the order of the 
 ontologies.&nbsp; For example, you will find a matches to "kidney" in FMA before 
-you will find them in GO.</P>
+you will find them in GO.</p>
 <H3>        &nbsp;</H3>
 <H3>Step 3: scroll down to find your matching term</H3>
 <P>You can navigate through these matches with the 

Modified: phenote/trunk/doc/phenote-website/help/html/Menu_Bars.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Menu_Bars.htm	2007-05-18 22:13:16 UTC (rev 605)
+++ phenote/trunk/doc/phenote-website/help/html/Menu_Bars.htm	2007-05-18 23:12:39 UTC (rev 606)
@@ -1,48 +1,48 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
-<HTML>
-<HEAD>
-<META NAME="GENERATOR" CONTENT="Solutionsoft HelpBreeze JavaHelp Edition">
-<TITLE>Menu Bars</TITLE>
-<LINK REL="stylesheet" TYPE="text/css" HREF=../javahelp.css>
-</HEAD>
-<BODY BGCOLOR=#ffffff>
-<H1>Menu Bars</H1>
-<P>Phenote contains&nbsp;four menus with the following 
-functions:</P>
-<UL>
-  <LI><STRONG>File</STRONG>
-  <UL>
-    <LI>New - clears any currently loaded annotations and lets 
+<html>
+<head>
+<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
+<title>Menu Bars</title>
+<link rel="stylesheet" type="text/css" href="../javahelp.css">
+</head>
+<body bgcolor="#ffffff">
+<h1>Menu Bars</h1>
+<p>Phenote contains&nbsp;four menus with the following 
+functions:</p>
+<ul>
+  <li><strong>File</strong>
+  <ul>
+    <li>New - clears any currently loaded annotations and lets 
     the user start over (disabled) 
-    <LI>Open&nbsp;- prompts the user to load a set of 
+    <li>Open&nbsp;- prompts the user to load a set of 
     annotations saved to their computer.&nbsp; 
-    <LI>Save - prompts the user to save the current 
+    <li>Save - prompts the user to save the current 
     annotations to a file. 
-    <LI>Exit - close the Phenote Application.</LI></UL>
-  <LI><STRONG>Edit (disabled)</STRONG>
-  <LI><STRONG>Settings</STRONG>
-  <UL>
-    <LI>Search Filters - users can select the filters to be 
+    <li>Exit - close the Phenote Application.</li></ul>
+  <li><strong>Edit (disabled)</strong>
+  <li><strong>Settings</strong>
+  <ul>
+    <li>Search Filters - users can select the filters to be 
     used during autocompletion on ontology fields. 
-    <UL>
-      <LI>Term Name 
-      <LI>Synonyms 
-      <LI>Definitions 
-      <LI>Obsoletes</LI></UL>
-    <LI>Configuration - allows the user to choose a 
+    <ul>
+      <li>Term Name 
+      <li>Synonyms 
+      <li>Definitions 
+      <li>Obsoletes</li></ul>
+    <li>Configuration - allows the user to choose a 
     different Phenote configuration 
-    <LI>Show History - displays recently selected ontology terms in a list 
-    (under development)</LI></UL>
-  <LI><STRONG>Help</STRONG>
-  <UL>
-    <LI>Phenote Help - brings up this help documentation 
+    <li>Show History - displays recently selected ontology terms in a list 
+    (under development)</li></ul>
+  <li><strong>Help</strong>
+  <ul>
+    <li>Phenote Help - brings up this help documentation 
     within the Phenote Application.&nbsp; 
-    <LI>About - a splash screen about Phenote, including 
+    <li>About - a splash screen about Phenote, including 
     its current version number.
-    <LI>Release Notes - information regarding the updates in the current 
-    release.</LI></UL></LI></UL>
-<P>&nbsp;</P>
-<P>You can find out more information on each of these topics by looking through 
-this documentation.</P>
-</BODY>
-</HTML>
\ No newline at end of file
+    <li>Release Notes - information regarding the updates in the current 
+    release.</li></ul></li></ul>
+<p>&nbsp;</p>
+<p>You can find out more information on each of these topics by looking through 
+this documentation.</p>
+</body>
+</html>
\ No newline at end of file

Modified: phenote/trunk/doc/phenote-website/help/html/The_Phenote_Interface.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The_Phenote_Interface.htm	2007-05-18 22:13:16 UTC (rev 605)
+++ phenote/trunk/doc/phenote-website/help/html/The_Phenote_Interface.htm	2007-05-18 23:12:39 UTC (rev 606)
@@ -1,27 +1,25 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD html 3.2//EN">
 <html>
-<HEAD>
-<META NAME="GENERATOR" CONTENT="Solutionsoft HelpBreeze JavaHelp Edition">
-<TITLE>Changing Link Attributes</TITLE>
-<LINK REL="stylesheet" TYPE="text/css" HREF=../javahelp.css>
-</HEAD>
-<BODY bgColor=#ffffff>
-<H1>The Phenote Interface  </H1>
-<P>This screenshot is of Phenote when configured with the 
-"demo" configuration.&nbsp; It is a typical interface for phenotype 
-annotation.  </P>
-<P>  </P>
-<H1>  <IMG hspace=0 
-src="../Images/phenote-startup.png" width="100%" border=0>  </H1>
-<P>  The Phenote application window is comprised of three main 
-  areas:</P>
-<UL>
-  <LI>The Data Entry frame located in the&nbsp;upper left. 
-  <LI>The Term Info frame located in the&nbsp;upper right. 
-  <LI>The Annotation Spreadsheet located in the lower half.</LI></UL>
-<P>The Phenote application runs best in 1024x768, but&nbsp;the window is easily 
-adjusted to meet your specific size needs.</P>
+<head>
+<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
+<title>Changing Link Attributes</title>
+<link rel="stylesheet" type="text/css" href="../javahelp.css">
+</head>
+<BODY BGCOLOR=#ffffff>
+<h1>The Phenote Interface  </h1>
+<p>This screenshot is of Phenote when configured with the "demo" configuration and loaded 
+with data.&nbsp; It is a typical interface for phenotype 
+annotation.  </p>
+<p><IMG hspace=0 src="../images/phenote-data-markup.png" width="100%" border=0>  The Phenote application window is comprised of three main 
+
+  areas:</p>
+<ul>
+  <li>The Data Entry frame located in the&nbsp;upper left. 
+  <li>The Term Info frame located in the&nbsp;upper right. 
+  <li>The Annotation Spreadsheet located in the lower half.</li></ul>
+<p>The Phenote application runs best in 1024x768, but&nbsp;the window is easily 
+adjusted to meet your specific size needs.</p>
 <div class="tabbed">
 </div>
 </BODY>
-</html>
\ No newline at end of file
+</html>

Added: phenote/trunk/doc/phenote-website/help/images/phenote-data-markup.png
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/doc/phenote-website/help/images/phenote-data-markup.png
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Modified: phenote/trunk/doc/phenote-website/help/javahelp.css
===================================================================
--- phenote/trunk/doc/phenote-website/help/javahelp.css	2007-05-18 22:13:16 UTC (rev 605)
+++ phenote/trunk/doc/phenote-website/help/javahelp.css	2007-05-18 23:12:39 UTC (rev 606)
@@ -119,6 +119,7 @@
 
 [border] {border: solid thin;
        border-color: silver}
+img {border: none }
 
 table {border: none;
        border-color: white;


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [605] phenote/trunk/doc/phenote-website/ phenote-release-notes.html

From: <nl...@us...> - 2007-05-18 22:13:17

Revision: 605
          http://svn.sourceforge.net/obo/?rev=605&view=rev
Author:   nlw
Date:     2007-05-18 15:13:16 -0700 (Fri, 18 May 2007)

Log Message:
-----------
modified release notes; new format - delineate features, changes, bugfixes, etc.  added in sourceforge bug/feature request links if available.  

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	2007-05-18 20:50:13 UTC (rev 604)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.html	2007-05-18 22:13:16 UTC (rev 605)
@@ -2,859 +2,242 @@
 <html>
 <head>
   
-  <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
+<meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
 
-  <title>Phenote Release Notes</title>
+<title>Phenote Release Notes</title>
 </head>
 
 <body>
 <h1>Phenote Release Notes</h1>
+<h2>1.3<hr></h2>
 
-1.3
-will probably come out in June<br>
+in development, 1.3-beta2 <br>
+<ul>
+  <li>feature:  Web-based documentation and Help features<br>
+  <li>change:  File-&gt;New is disabled until next version</li>
+</ul>
 
-<h2><span style="text-decoration: underline;">1.3-beta2</span></h2>
-under development, not yet released.
-<br>
-File-&gt;New is disabled until next version<br>
-Web-based documentation and Help features<br>
+05.09.2007, version <a href="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>
 
-<h2><span style="text-decoration: underline;">1.3-beta1</span></h2>
+</ul>
 
-<a href="1.3-beta1/phenote.jnlp">Phenote 1.3-beta1</a><br>
-<br>
-Added config for birn<br>
-Added SAO.obo for birn<br>
-Namespace config writes back<br>
-Config update/merge bug where fields in wrong order fixed.<br>
-Can specify more than one website for ontology update<br>
-Empty field shows all terms in ontology rather than none<br>
-Can add more differentia to post comp<br>
-<h2><span style="text-decoration: underline;">1.2</span></h2>
+<h2>1.2<hr></h2>
+05.02.2007, version <a href="1.2/phenote.jnlp">1.2</a><br>
 
-<a href="1.2/phenote.jnlp">Phenote 1.2</a><br>
+<ul>
+  <li>feature:  Can post-compose with &gt;2 terms </li>
+  <li>feature:  Term history display can be toggled on/off (Settings-&gt;Term History menu)</li>
+<li>feature:  Synonyms delineated by scope in Term Info:  Exact, Narrow, Broad, General, Related.  If the synonym category is given, it is displayed.  For example,  the term 'water' has the <i>related</i> synonym H2O, which has the category of a chemical <i>formula</i>.</li>
+<li>feature:  Obsolete replacements or consideration terms are displayed in term info with links</li>
+<li>feature:  Loading splash screen </li>
+<li>feature:  Can configure by namespace for ontologies</li>
+<li>feature:  Can automatically update ontologies during startup (configurable)</li>
+<li>feature:  Timer added to configuration during ontology update check (configurable)</li>
+<li>feature:  Can check which version of phenote is running by selecting Help-&gt;About.</li>
+<li>feature:  Added common configuration for OMIM curation for use by NCBO (ncbo.cfg).</li>
+<li>feature:  can forward and reverse sort columns by repeatedly clicking on column header [<a href="https://sourceforge.net/tracker/index.php?func=detail&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>
 
-<br>
-
-
-
-Features:
-Can post-compose with &gt;2 terms <br>
-
-
-Term history display can be toggled on/off (Settings-&gt;Term History menu)<br>
-
-
-Synonyms are delineated by their scope in Term Info:  Exact, Narrow, Broad, General, Related.  If the synonym category is given, it is displayed next to the synonym.  For example:  the term 'water' has the <i>related</i> synonym H2O, which has the category of a chemical <i>formula</i>.<br>
-<br>
-
-
-Obsolete replacements or consideration terms are displayed in term info with links<br>
-
-Search filters moved into menu <br>
-
-Loading splash screen <br>
-
-Can configure by namespace for ontologies<br>
-
-Can automatically update ontologies during startup (configurable)<br>
-
-Timer added to configuration during ontology update check (configurable)<br>
-
-Can check which version of phenote is running by selecting Help-&gt;About.<br>
-
-Common configuration for OMIM curation for use by NCBO included (ncbo.cfg).
-
-Updates to the zfin-standalone.cfg for the zebrafish community annotation.  Only includes GO and ZFanatomy ontologies.
-
-Bug Fixes: Free text field text not "sticking"
-
-<h2><span style="text-decoration: underline;">1.1</span></h2>
-
-
-<a href="1.1/phenote.jnlp">Phenote 1.1</a><br>
-
-
-<br>
-
-
-March 28, 2007<br>
-
-
-<br>
-
-
-Phenote will merge its default configuration with users configuration,
-preserving users changes as well as adding anything new from phenote
-upgrade.<br>
-
-
-User can select configuration they want to use at initialization or
-subsequently from file menu &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;
-&nbsp;&nbsp;&nbsp; (currently requires phenote restart).<br>
-
-
-Tab delimited data adapter - thank you nicole!<br>
-
-
-Beginnings of term history - thank you nicole!<br>
-
-
-Tabbed main field panel if more than 12 fields.<br>
-
-
-QueryableDataAdapter interface for adding a database data adapter that
-can be queried. The data adapter specifies queryable fields, which get
-a retrieve button.<br>
-
-
-Layout improved<br>
-
-
-Can now search ALL ontologies of a field<br>
-
-
-Retrieve obo from web if more up to date or no local found<br>
-
-
-Refactored code for field guis<br>
-
-
-Ontology chooser reflects current term (bug fix)
-<h2><span style="text-decoration: underline;">1.0</span></h2>
-
-
-
-<a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br>
-
-
-
-
-<a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br>
-
-
-
-<a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DichtyBase
-webby phenote</a><br>
-
-
-
+<h2>1.1<hr></h2>
+04.06.2007, version <a href="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 &gt;12 fields included</li>
+<li>feature:  Tab delimited data adapter; data in/output format compatible with excel and other spreadsheet software [<a href="https://sourceforge.net/tracker/index.php?func=detail&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="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>
-
-
-
-<br>
-
-
-
-January 12, 2007<br>
-
-
-
-<br>
-
-
-
-The main improvement here is the ability to add any field you like, not
-just E,Q,GC,GT,Pub. In the configured webstarts Stage, Evidence,
-Description, Abnormal, and Absent have been added through this new
-mechanism. This entailed a refactoring of the datamodel.<br>
-
-
-
-<br>
-
-
-
-Webby phenote is now using JSP and Spring.<br>
-
-
-
-<br>
-
-
-
-There has been some recent work with UVictoria for ontology graph
+<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.
-<h2><span style="text-decoration: underline;">0.9</span></h2>
-
-
-
-
-<a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br>
-
-
-
-
-<a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br>
-
-
-
-
-<a href="http://165.124.152.194/web/html/interface.html">DichtyBase
+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="0.9/phenote-flybase.jnlp">0.9-fly</a>, 
+<a href="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>
-
-
-
-
-<br>
-
-
-
-
-mid November 2006<br>
-
-
-
-
-<br>
-
-
-
-
-Undo<br>
-
-
-
-
-Christian Pich(Zfin) has added a Quartz scheduler to phenote, which
-zfin takes advantage of, to schedule when to check for new obo files.<br>
-
-
-
-
-Also Christian Pich upgraded the PhenoteServlet to the Spring framework
-- much nicer!<br>
-
-
-
-
-Synonyms are now returned from auto complete with [syn] and when
-selected the term goes in the field (webby &amp; standalone), obsoletes
-hits with [obs]<br>
-
-
-
-
-Bulk update &amp; copy in standalone.<br>
-
-
-
-
-Jim Balhoff(Nescent) changed radio buttons to checkboxes, and file
-saver says save not load and recognizes adapter by file extensions,
-psx-&gt;phenosyntax, .xml -&gt; phenoxml <br>
-
-
-
-
-Single quotes escaped for javascript fns.<br>
-
-
-
-
-<h2><span style="text-decoration: underline;">0.8</span></h2>
-
-
-
-
-<a href="0.8/phenote-flybase.jnlp">Phenote 0.8 for fly.</a><br>
-
-
-
-
-<a href="0.8/phenote-zfin.jnlp">Phenote (standalone) 0.8 for zfin</a><br>
-
-
-
-
-<a href="http://165.124.152.194/web/html/interface.html">DichtyBase
+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 &amp; standalone)</li>
+<li>feature:  obsoletes are displayed from autocomplete with [obs]</li>
+<li>feature:  Bulk update &amp; copy in standalone. [<a href="https://sourceforge.net/tracker/index.php?func=detail&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>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="0.8/phenote-flybase.jnlp">0.8-fly</a>, 
+<a href="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 &amp; standalone.</li>
+  <li>feature:  Pheno-xml reader (thanks to Jim Balhoff) and improvements to pheno-xml
+writer (does pub &amp; genetic context)</li>
+<li> feature:  Command line reading &amp; writing of phenoxml &amp; phenosyntax.</li>
+<li>feature:  Application exits on window exit (unless servlet)</li>
+<li>feature:  Can filter out stage terms from zfin anatomy</li>
+</ul>
 
-
-
-
-<br>
-
-
-
-
-10/2/06<br>
-
-
-
-
-Added post composition to standalone phenote. Logging for both
-webby/servlet &amp; standalone.<br>
-
-
-
-
-Pheno-xml reader (thanks to Jim Balhoff) and improvements to pheno-xml
-writer (does pub &amp; genetic context)<br>
-
-
-
-
-Command line reading &amp; writing of phenoxml &amp; phenosyntax.<br>
-
-
-
-
-Application exits on window exit (unless servlet)<br>
-
-
-
-
-Can filter out stage terms from zfin anatomy<br>
-
-
-
-
-<h2><span style="text-decoration: underline;">0.7</span></h2>
-
-
-
-
-<a href="0.7/phenote-flybase.jnlp">Phenote 0.7 for fly.</a><br>
-
-
-
-
-<a href="0.7/phenote-zfin.jnlp">Phenote (standalone) 0.7 for zfin</a><br>
-
-
-
-
-<a href="http://165.124.152.194/web/html/interface.html">DichtyBase
-webby phenote</a><br>
-
-
-
-
-<br>
-
-
-
-
-Web: entity chooser, can configure to check for new obo files and load
+<h2>0.7<hr></h2>
+08.23.2007, version <a href="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). Entity field and term info installed into zfin
-phenotype site. term info &amp; completion are scrollable.<br>
-
-
-
-
-Standalone: can read &amp; write pheno-syntax with ids &amp; term names
-in comments, entity chooser, pub field, use button in term info, sort
-table by clicking on headers, personal config file gets copied out of
-jar, paste mac bug fixed, file load/save remembered,layout fixed<br>
-
-
-
-
-<br>
-
-
-
-
-<h2><span style="font-weight: bold;"><span style="text-decoration: underline;">0.6</span></span></h2>
-
-
-
-
+publicly let me know).</li>
+<li>feature:  entity field and term info installed into zfin (web)
+phenotype site. Term info &amp; completion are scrollable.</li>
+<li>feature: standalone version can read &amp; write pheno-syntax with ids &amp; term names in comments</li>
+<li>feature:  standalone entity chooser</li>
+<li>feature:  added pub field</li>
+<li>feature:  added 'use term' button in term info</li>
+<li>feature:  can sort table by any field in forward order by clicking on headers</li>
+<li>change:  personal config file gets copied out of jar
+<li>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="0.6/phenote-flybase.jnlp">0.6-fly</a>, <a href="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>
-
-
-
-
-<a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br>
-
-
-
-
-<a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br>
-
-
-
-
-<br>
-
-
-
-
-The main feature of release 0.6 is a webby phenote. This is in its
-extremely early stages (very little functionality and buggy). At this
-point it only does Entity and Quality fields and term info and thats
-it, and even thats buggy, but more coming soon! <br>
-
-
-
-
-<br>
-
-
-
-
-Not much new in the stand alone phenote (as Ive been working on the
-webby phenote). Mainly it can write pheno-xml, and it uses the latest
-pato (as of July 28, 2006).<br>
-
-
-
-
-<h2><span style="font-weight: bold;"><span style="text-decoration: underline;">0.5</span></span></h2>
-
-
-
-
-<br>
-
-
-
-
-<a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br>
-
-
-
-
-<a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br>
-
-
-
-
-<br>
-
-
-
-
-5/12/06<br>
-
-
-
-
-No&nbsp; new additions to the gui here. In preparation for my visit to
+<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="0.5/phenote-flybase.jnlp">0.5-FlyBase</a>, <a href="0.5/phenote-zfin.jnlp">0.5-ZFIN</a><br>
+<p>
+No new additions to the gui here. In preparation for my visit to
 Cambridge/FlyBase, I worked on a FlyBase dataadapter. This is phenote
 first data adapter so I also laid down the foundations for data
 adapters. The FlyBase data adapter simply cuts and pastes phenotype
 character objects to the system clipboard. The idea is that FlyBase's
 Proforma java application will also cut and paste to the clipboard.
 This is a simple way to pass objects between applications, to get us
-off the ground.&nbsp; Proforma is not there yet so this has not been
+off the ground. Proforma is not there yet so this has not been
 tested yet with Proforma, but it works in the test suite. Added special
 FlyBase character wrappers that do the parsing and creating of Proforma
-character strings.<br>
+character strings.</p>
 
-
-
-
-<h2><span style="text-decoration: underline;">0.4</span></h2>
-
-
-
-
-<a href="0.4/phenote-flybase.jnlp">0.4 flybase webstart</a><br>
-
-
-
-
-<a href="0.4/phenote-zfin.jnlp">0.4 zfin webstart</a><br>
-
-
-
-
-<br>
-
-
-
-
-4/26/06<br>
-
-
-
-
-Added Genetic Context field.<br>
-
-
-
-
-Parent &amp; child terms in term info are now clickable/navigable.<br>
-
-
-
-
-Links in descriptions are clickable (should bring up default browser)<br>
-
-
-
-
-Added configuration to configure ontologies &amp; fields. This is
+<h2>0.4<hr></h2>
+04.26.2006, version <a href="0.4/phenote-flybase.jnlp">0.4-flybase</a>, <a href="0.4/phenote-zfin.jnlp">0.4-zfin</a><br>
+<ul>
+  <li>feature:  Added Genetic Context field.</li>
+  <li>feature:  Parent &amp; child terms in term info are now clickable/navigable.</li>
+  <li>feature:  HTML Links in descriptions are clickable (should bring up default browser)</li>
+<li>feature:  configuration files to configure ontologies &amp; fields. This is
 currently at a devloper level (xml file) not a user level(gui - todo).
 There is a command line argument for which configuration file to use.
 This allows for having separate zf &amp; fb releases without having to
 change the code to do it (like was done for the ctol release). The
 configuration for now is for developers (internal xml file), on the
-todo is to have a gui configuration for users.<br>
+todo is to have a gui configuration for users.</li>
+<li>bugfix: can't delete to 0 rows</li>
+<li>bugfix: synonym search duplicates removed</li>
+<li>Development:  Refactored for configuration &amp; adding field. Made the internal code much more generic for adding new fields from configuration, got rid of a lot of hard wiring.&nbsp; Part of this was instituring model-view-controller in some places where views were improperly talking to other views. In theory this should also make it easier to plop a web gui on top of the current phenote model &amp; controller.</li>
+<li>Development:  Renamed Phenotype to Character. Added Character interface CharacterI.</li>
+<li>Development: Added tests to test suite.</li>
 
+</ul>
 
-
-
-Minor bugs:&nbsp; cant delete to 0 rows anymore, synonym search
-duplicates taken out<br>
-
-
-
-
-<br>
-
-
-
-
-Dev stuff:<br>
-
-
-
-
-Refactored for configuration &amp; adding field. Made the internal code
-much more generic for adding new fields from configuration, got rid of
-a lot of hard wiring.&nbsp; Part of this was instituring
-model-view-controller in some places where views were improperly
-talking to other views. In theory this should also make it easier to
-plop a web gui on top of the current phenote model &amp; controller.<br>
-
-
-
-
-Renamed Phenotype to Character. Added Character interface CharacterI.<br>
-
-
-
-
-Added tests to test suite.<br>
-
-
-
-
-<br>
-
-
-
-
-<h2><span style="text-decoration: underline;">0.3.1 (CToL)<br>
-
-
-
-
-</span></h2>
-
-
-
-
-<a href="0.3.1/phenote-webstart.jnlp">0.3.1 phenote webstart (for CToL)</a><br>
-
-
-
-
-<br>
-
-
-
-
-4/7/06<br>
-
-
-
-
-0.3.1 is identical to 0.3 except that it has ontologies for CToL
+<h2>0.3<hr></h2>
+04.07.2006, version <a href="0.3/phenote-webstart.jnlp">0.3</a>, <a href="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.<br>
-
-
-
-
-<h2><span style="text-decoration: underline;">0.3</span></h2>
-
-
-
-
-<a href="0.3/phenote-webstart.jnlp">0.3 phenote webstart</a><br>
-
-
-
-
-<br>
-
-
-
-
-4/7/06<br>
-
-
-
-
-Release for NESCent fish eveolution meeting. No major new functionality
+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.<br>
+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>
 
-
-
-
-<br>
-
-
-
-
-Completion terms now sorted alphabeitcally.<br>
-
-
-
-
-Obsolete is now in addition to regular terms, not in lieu of.<br>
-
-
-
-
-Filtering out attribute values (todo: change to actually filter in
-values)<br>
-
-
-
-
-Html formatting of term info (todo: make terms selectable)<br>
-
-
-
-
-Children relations are in term info<br>
-
-
-
-
-Term info layout greatly improved<br>
-
-
-
-
-Term info in scroller<br>
-
-
-
-
-Border with label around term info<br>
-
-
-
-
-Put definition at end of term info<br>
-
-
-
-
-<br>
-
-
-
-
-Fixed bugs:<br>
-
-
-
-
-Backspace in ontology combo box<br>
-
-
-
-
-Selection of item in comp list causing exception, not going in term box<br>
-
-
-
-
-No terms with just 1 char<br>
-
-
-
-
-Popup was staying up after selection<br>
-
-
-
-
-<br>
-
-
-
-
-Dev stuff:<br>
-
-
-
-
-Test suite added! (todo: add more tests)<br>
-
-
-
-
-Migrated to jdk 1.5 (which caused some of the bugs above)<br>
-
-
-
-
-Ant file made build.xml.<br>
-
-
-
-
-CompletionList refactored into Ontology (prompted by sorting)<br>
-
-
-
-
-<br>
-
-
-
-
-<br>
-
-
-
-
-<h2><span style="text-decoration: underline;">0.2</span></h2>
-
-
-
-
-<a href="0.2/phenote-webstart.jnlp">0.2 phenote webstart</a><br>
-
-
-
-
-<br>
-
-
-
-
-3/27/06<br>
-
-
-
-
-Added the ability to do term completion on Synonyms, Definitions, and
-Obsoletes. Also can mouse over a term in a completion list and get
-information about it in the term info text area. <br>
-
-
-
-
-<br>
-
-
-
-
-The term info area needs a lot of work.<br>
-
-
-
-
-TODO:<br>
-
-
-
-
-&nbsp;layout, scrollbar, border w title, ordering &amp; lumping parents
-&amp; children, formatting. <br>
-
-
-
-
-Also perhaps have children &amp; parents be clickable in some fashion
-either html-like clickable text or as buttons.<br>
-
-
-
-
-Theres also bugs in term completion boxes. If you start backspacing it
-gets wacky for instance.<br>
-
-
-
-
-<br>
-
-
-
-
-<a href="0.2/phenote-webstart.jnlp"><br>
-
-
-
-
-</a>
-<h2><span style="text-decoration: underline;">0.1</span></h2>
-
-
-
-
-<a href="0.1/phenote-webstart.jnlp">0.1 phenote webstart</a><br>
-
-
-
-
-<br>
-
-
-
-
-&nbsp;3/1/06<br>
-
-
-
-
-0.1 was the initial phenote release (known briefly as the plumper at
-the time).&nbsp; It just had a genotype, anatomy and pato fields, where
+<h2>0.2<hr></h2>
+03.27.2006, version <a href="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 &amp; lumping parents
+&amp; children, formatting.  Also perhaps have children &amp; parents be clickable in some fashion  either html-like clickable text or as buttons.</li>
+<li>known bugs:  If you hit backspace in term completion fields it gets wacky </li>
+</ul>
+<h2>0.1<hr></h2>
+03.01.2006, version <a href="0.1/phenote-webstart.jnlp">0.1</a><br>
+<p> 0.1 was the initial phenote release (known briefly as the plumper at
+the time).  It just had a genotype, anatomy and pato fields, where
 anatomy and pato did term completion (just on term names) with there
 ontologies in a drop down list. There was also the phenotype table that
 tracked phenotype instances being edited in the above fields. This very
-limited functionality was demo'd at the cbio meeting 3/3/06 at Stanford.<br>
+limited functionality was demo'd at the cbio meeting 3/3/06 at Stanford.</p>
 
-
-
-
-<br>
-
-
-
-
-<a href="0.2/phenote-webstart.jnlp"></a><br>
-
-
-
-
-<br>
-
-
-
-
-<br>
-
-
-
-
-<a href="phenote.html">Phenote main page</a><br>
-
-
-
-
 </body>
 </html>


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[Obo-svn-commit] SF.net SVN: obo: [604] phenote/trunk/data/sample_data.xls

From: <mg...@us...> - 2007-05-18 20:50:17

Revision: 604
          http://svn.sourceforge.net/obo/?rev=604&view=rev
Author:   mgibson
Date:     2007-05-18 13:50:13 -0700 (Fri, 18 May 2007)

Log Message:
-----------
changed sample_data.xls to have proper post comp rel id otherwise phenote
tosses it 
on thing i noticed - the post comp parser is a bit slow
i think it might bog down with a lot of post comp terms

Modified Paths:
--------------
    phenote/trunk/data/sample_data.xls

Modified: phenote/trunk/data/sample_data.xls
===================================================================
--- phenote/trunk/data/sample_data.xls	2007-05-18 19:12:32 UTC (rev 603)
+++ phenote/trunk/data/sample_data.xls	2007-05-18 20:50:13 UTC (rev 604)
@@ -18,7 +18,7 @@
 PMID:9462749 	OMIM602229.0002 			SO:1000062	nonsense_codon_change_in_transcript	PATO:0001632	anterior to	SO:0000330	conserved_region							Y83X stop codon mutation before HMG domain 	
 PMID:9722528 	OMIM602229.0002 			GO:0065004	protein-DNA complex assembly	PATO:0001511	non-functional									***SOX10mut failed to form protein-DNA complexes 	
 PMID:9722528 	OMIM602229.0002 			GO:0008104	protein localization	PATO:0000628	mislocalised	GO:0005829	cytosol					PATO:0000460	abnormal	protein mislocalization to the cytosol 	
-PMID:9462749 	OMIM602229.0003 			SO:1000034^located_in(SO:0000330)	nucleotide_insertion^located_in(conserved_region)	PATO:0000467	present									6-bp insertion in middle of HMG domain 	
+PMID:9462749 	OMIM602229.0003 			SO:1000034^OBO_REL:located_in(SO:0000330)	nucleotide_insertion^located_in(conserved_region)	PATO:0000467	present									6-bp insertion in middle of HMG domain 	
 PMID:9722528 	OMIM602229.0003 			GO:0065004	protein-DNA complex assembly	PATO:0001511	non-functional									***SOX10mut failed to form protein-DNA complexes 	
 PMID:9722528 	OMIM602229.0003 			GO:0008104	protein localization	PATO:0001032	position	GO:0005634	nucleus					PATO:0000461	normal	protein localization to the nucleus 	
 PMID:12668617 	OMIM602229.0003 			GO:0016563	transcriptional activator activity	PATO:0001508	abolished									***Sox10 ability to activate transcription eliminated 	
@@ -33,11 +33,11 @@
 PMID:9722528 	OMIM602229.? 			GO:0016563	transcriptional activator activity	PATO:0001511	non-functional			 	 					deficient in activity as a transcriptional activator 	
 PMID:11734543 	OMIM602229.? 			FMA:62983	Myelin sheath	PATO:0001617	deformed									myelin defects 	
 PMID:11734543 	OMIM602229.? 			GO:0016563	transcriptional activator activity	PATO:0000462	absent									***SOX10 failed to transactivate the CX32 promoter 	
-PMID:11734543 	OMIM602229.? 			GO:0008134^located_in(SO:0000167)	transcription factor binding^located_in(promoter)	PATO:0000462	absent									***SOX10 failed to transactivate the CX32 promoter 	
+PMID:11734543 	OMIM602229.? 			GO:0008134^OBO_REL:located_in(SO:0000167)	transcription factor binding^located_in(promoter)	PATO:0000462	absent									***SOX10 failed to transactivate the CX32 promoter 	
 PMID:9462749 	[OMIM602229.0001/+] 			GO:0007605	sensory perception of sound	PATO:0000468	decreased									bilateral profound hearing loss 	
 PMID:9462749 	[OMIM602229.0001/+] 			FMA:53667	Hair	PATO:0000323	white									white hair color 	
 PMID:9462749 	[OMIM602229.0001/+] 			FMA:58611	Iridial part of retina	PATO:0000318	blue									blue irides with grey speckles 	
-PMID:9462749 	[OMIM602229.0001/+] 			FMA:63846^located_in(FMA:7163)	Cell pigment^located_in(Skin)	PATO:0001608	patchy									depigmented skin patches 	
+PMID:9462749 	[OMIM602229.0001/+] 			FMA:63846^OBO_REL:located_in(FMA:7163)	Cell pigment^located_in(Skin)	PATO:0001608	patchy									depigmented skin patches 	
 PMID:9462749 	[OMIM602229.0001/+] 			FMA:63846	Cell pigment	PATO:0000460	abnormal									pigmentary abnormalities (detailed with other entries) 	
 PMID:9462749 	[OMIM602229.0001/+] 			FMA:7199	Intestine	PATO:0000648	obstructed									intestinal obstruction in neonates 	
 PMID:9462749 	[OMIM602229.0001/+] 			GO:0007588	excretion	PATO:0000911	decreased rate									constipation in adults 	
@@ -49,37 +49,37 @@
 PMID:9462749 	[OMIM602229.0002/+] 			FMA:53667	Hair	PATO:0000665	light									fair hair color 	
 PMID:9462749 	[OMIM602229.0002/+] 			FMA:58611	Iridial part of retina	PATO:0001265	bright blue									vivid blue eyes 	
 PMID:9462749 	[OMIM602229.0002/+] 			FMA:7199	Intestine	PATO:0001624	decreased functionality									bowel problems 	
-PMID:9462749 	[OMIM602229.0002/+] 			FMA:5884^located_in(FMA:14544)	Ganglion^located_in(Rectum)	PATO:0000419	decreased number									number of ganglia was dramatically reduced 	
+PMID:9462749 	[OMIM602229.0002/+] 			FMA:5884^OBO_REL:located_in(FMA:14544)	Ganglion^located_in(Rectum)	PATO:0000419	decreased number									number of ganglia was dramatically reduced 	
 PMID:9462749 	[OMIM602229.0003/+] 			GO:0007605	sensory perception of sound	PATO:0000468	decreased									deafness 	
 PMID:9462749 	[OMIM602229.0003/+] 			FMA:14544	Rectum	PATO:0001557	lacking physical part	FMA:5884	Ganglion							short segment HSCR - aganglionic tract in rectum+sigmoid colon 	
 PMID:9462749 	[OMIM602229.0003/+] 			FMA:14548	Sigmoid colon	PATO:0001557	lacking physical part	FMA:5884	Ganglion							short segment HSCR - aganglionic tract in rectum+sigmoid colon 	
 PMID:9462749 	[OMIM602229.0004/+] 	PM:0000019	penetrance_incomplete	GO:0007605	sensory perception of sound	PATO:0000468	decreased									deafness 	
-PMID:9462749 	[OMIM602229.0004/+] 	PM:0000023	expressivity_incomplete	FMA:63846^contained_in(FMA:61695)	Cell pigment^contained_in(Body surface)	PATO:0000468	decreased									hypopigmentation 	
+PMID:9462749 	[OMIM602229.0004/+] 	PM:0000023	expressivity_incomplete	FMA:63846^OBO_REL:contained_in(FMA:61695)	Cell pigment^contained_in(Body surface)	PATO:0000468	decreased									hypopigmentation 	
 PMID:9462749 	[OMIM602229.0004/+] 			FMA:7199	Intestine	PATO:0001557	lacking physical part	FMA:84048	Ganglion cell							HSCR 	
 PMID:9462749 	[OMIM602229.0004/+] 	PM:0000023	expressivity_incomplete	FMA:53667	Hair	PATO:0000323	white									white hair color 	
 PMID:9462749 	[OMIM602229.0004/+] 	PM:0000019	penetrance_incomplete	FMA:7199	Intestine	PATO:0001571	dilated									megacolon 	
 PMID:10441344 	OMIM602229.0005 			SO:1000061	nonconservative_missense_codon_change_in_transcript	PATO:0000467	present									SER135THR mutation 	
 PMID:10441344 	OMIM602229.0005 			SO:1000061	nonconservative_missense_codon_change_in_transcript	PATO:0000467	present									SER135THR mutation 	
-PMID:2280978 	Yemenite deaf-blind hypopigmentation syndrome 			FMA:63846^located_in(FMA:7163)	Cell pigment^located_in(Skin)	PATO:0001608	patchy									hypo and hyperpigmented skin 	
+PMID:2280978 	Yemenite deaf-blind hypopigmentation syndrome 			FMA:63846^OBO_REL:located_in(FMA:7163)	Cell pigment^located_in(Skin)	PATO:0001608	patchy									hypo and hyperpigmented skin 	
 PMID:2280978 	Yemenite deaf-blind hypopigmentation syndrome 			FMA:58238	Cornea	PATO:0000587	decreased size									microcornea 	
 PMID:2280978 	Yemenite deaf-blind hypopigmentation syndrome 			FMA:54448	Eye	MP:0005262	coloboma									coloboma 	
 PMID:2280978 	Yemenite deaf-blind hypopigmentation syndrome 	PM:0000019	penetrance_incomplete	GO:0007605	sensory perception of sound	PATO:0000468	decreased									severe hearing loss 	
-PMID:10441344 	OMIM602229.0005 			FMA:63846^located_in(FMA:7163)	Cell pigment^located_in(Skin)	PATO:0001608	patchy									hypo and hyperpigmented skin 	
+PMID:10441344 	OMIM602229.0005 			FMA:63846^OBO_REL:located_in(FMA:7163)	Cell pigment^located_in(Skin)	PATO:0001608	patchy									hypo and hyperpigmented skin 	
 PMID:10441344 	OMIM602229.0005 	PM:0000019	penetrance_incomplete	GO:0007605	sensory perception of sound	PATO:0000468	decreased									severe hearing loss 	
 PMID:10482261 	OMIM602229.0008 			FMA:62983	Myelin sheath	PATO:0001617	deformed			 	 					leukodystrophy - progressive degeneration development of the myelin sheath 	
 PMID:10482261 	OMIM602229.0008 			FMA:7199	Intestine	PATO:0000648	obstructed									intestinal obstruction in neonates 	
 PMID:10482261 	OMIM602229.0008 			FMA:7199	Intestine	PATO:0001557	lacking physical part	FMA:5884	Ganglion							long segment HSCR - aganglionic tract in entire colon 	
-PMID:10482261 	OMIM602229.0008 			FMA:63846^located_in(FMA:58237)	Cell pigment^located_in(Left iris)	PATO:0000616	asymmetrical	FMA:63846^located_in(FMA:58236)	Cell pigment^located_in(Right iris)							heterochromia iridis - one eye is different color (intensity) than the other 	
+PMID:10482261 	OMIM602229.0008 			FMA:63846^OBO_REL:located_in(FMA:58237)	Cell pigment^located_in(Left iris)	PATO:0000616	asymmetrical	FMA:63846^OBO_REL:located_in(FMA:58236)	Cell pigment^located_in(Right iris)							heterochromia iridis - one eye is different color (intensity) than the other 	
 PMID:10482261 	OMIM602229.0008 	PM:0000022	expressivity_complete	GO:0007605	sensory perception of sound	PATO:0000468	decreased									profound hearing loss 	
 PMID:10482261 	OMIM602229.0008 			FMA:59516	Root of nose	PATO:0000600	increased width									broad nasal root 	
 PMID:10482261 	OMIM602229.0008 			FMA:59324	Medial angle of left eye	PATO:0000374	increased distance	FMA:59323	Medial angle of right eye	 	 					dystopia canthorum - inner corners of the eyes (canthi) are spaced farther apart than normal 	
-PMID:10482261 	OMIM602229.0008 			GO:0048589^has_participant(FMA:20394)	developmental growth^has_participant(Body)	PATO:0000911	decreased rate									developmental delay 	
+PMID:10482261 	OMIM602229.0008 			GO:0048589^OBO_REL:has_participant(FMA:20394)	developmental growth^has_participant(Body)	PATO:0000911	decreased rate									developmental delay 	
 PMID:10482261 	OMIM602229.0008 			FMA:20394	Body	MP:0000754	partial paralysis									spastic quadraplegia 	
 PMID:10482261 	OMIM602229.0008 			FMA:9721	Tendon	PATO:0001568	having decreased function	GO:0060004	reflex							loss of deep tendon reflexes 	
 PMID:10482261 	OMIM602229.0008 	PM:0000022	expressivity_complete	GO:0007600	sensory perception	PATO:0000468	decreased									sensory dullness 	
 PMID:10482261 	OMIM602229.0008 			FMA:9903	Peripheral nervous system	PATO:0001624	decreased functionality									peripheral neuropathy 	
 PMID:10482261 	OMIM602229.0008 			FMA:5867	Motor nerve	PATO:0001585	conduction									***decreased conductive velocity 	
-PMID:10482261 	OMIM602229.0008 			FMA:30316^contained_in(FMA:7182)	Muscle^contained_in(Limb)	PATO:0001623	atrophied									muscles in all limbs were severely atrophic 	
-PMID:10482261 	OMIM602229.0008 			FMA:67257^contained_in(FMA:20935)	Protein^contained_in(Cerebrospinal fluid)	PATO:0001162	increased concentration									Protein in the cerebrospinal fluid was elevated  	
-PMID:10482261 	OMIM602229.0008 			GO:0008038^contained_in(FMA:79876)	neuron recognition^contained_in(Brainstem)	PATO:0000468	decreased	GO:0007605	sensory perception of sound							no auditory brainstem response bilaterally 	
-PMID:10482261 	OMIM602229.0008 			FMA:62983^located_in(FMA:50801)	Myelin sheath^located_in(Brain)	PATO:0000468	decreased			 	 					prominent deficiency of myelination in the entire brain 	
+PMID:10482261 	OMIM602229.0008 			FMA:30316^OBO_REL:contained_in(FMA:7182)	Muscle^contained_in(Limb)	PATO:0001623	atrophied									muscles in all limbs were severely atrophic 	
+PMID:10482261 	OMIM602229.0008 			FMA:67257^OBO_REL:contained_in(FMA:20935)	Protein^contained_in(Cerebrospinal fluid)	PATO:0001162	increased concentration									Protein in the cerebrospinal fluid was elevated  	
+PMID:10482261 	OMIM602229.0008 			GO:0008038^OBO_REL:contained_in(FMA:79876)	neuron recognition^contained_in(Brainstem)	PATO:0000468	decreased	GO:0007605	sensory perception of sound							no auditory brainstem response bilaterally 	
+PMID:10482261 	OMIM602229.0008 			FMA:62983^OBO_REL:located_in(FMA:50801)	Myelin sheath^located_in(Brain)	PATO:0000468	decreased			 	 					prominent deficiency of myelination in the entire brain 	


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[Obo-svn-commit] SF.net SVN: obo: [603] phenote/trunk/data/sample_data.xls

From: <nl...@us...> - 2007-05-18 19:12:47

Revision: 603
          http://svn.sourceforge.net/obo/?rev=603&view=rev
Author:   nlw
Date:     2007-05-18 12:12:32 -0700 (Fri, 18 May 2007)

Log Message:
-----------
adding the sample data to this dir.  sample data uses the demo.cfg configuration

Added Paths:
-----------
    phenote/trunk/data/sample_data.xls

Added: phenote/trunk/data/sample_data.xls
===================================================================
--- phenote/trunk/data/sample_data.xls	                        (rev 0)
+++ phenote/trunk/data/sample_data.xls	2007-05-18 19:12:32 UTC (rev 603)
@@ -0,0 +1,85 @@
+Pub	Genotype	Genetic Context ID	Genetic Context Name	Entity ID	Entity Name	Quality ID	Quality Name	Add'l Entity ID	Add'l Entity Name	Time	Count	Unit ID	Unit Name	Abnormal ID	Abnormal Name	Description	
+	OMIM602229 - HSCR 			FMA:7199	Intestine	PATO:0000648	obstructed									intestinal obstruction in neonates 	
+	OMIM602229 - HSCR 			GO:0007588	excretion	PATO:0000911	decreased rate									constipation in adults 	
+	OMIM602229 - HSCR 			FMA:14544	Rectum	PATO:0001557	lacking physical part	FMA:5884	Ganglion							short segment HSCR - aganglionic tract in rectum+sigmoid colon 	
+	OMIM602229 - HSCR 			FMA:14548	Sigmoid colon	PATO:0001557	lacking physical part	FMA:5884	Ganglion							short segment HSCR - aganglionic tract in rectum+sigmoid colon 	
+ 	OMIM602229 - WS 			GO:0007605	sensory perception of sound	PATO:0000762	impaired									hearng loss (sensorineural deafness) 	
+ 	OMIM602229 - WS 			FMA:77832	Stria vascularis of cochlear duct	PATO:0001557	lacking physical part	CL:0000148	melanocyte							absence of melanocytes from stria vascularis of the inner ear 	
+ 	OMIM602229 - WS 			GO:0043473	pigmentation	PATO:0000460	abnormal									pigmentary abnormalities 	
+ 	OMIM602229 - WS 			FMA:45618	Hindgut	PATO:0001557	lacking physical part	FMA:84048	Ganglion cell							absence of intrinsic ganglion cells of the terminal hindgut 	
+PMID:10973953 	OMIM602229.0001 			GO:0016563	transcriptional activator activity	PATO:0001624	decreased functionality									dominant-negative repression of MITF expression 	
+PMID:10973953 	OMIM602229.0001 			FMA:67257	Protein	PATO:0000468	decreased									***endogenous MITF protein levels reduced 	
+PMID:10973953 	OMIM602229.0001 	PM:0000003	dominant	GO:0016566	specific transcriptional repressor activity	PATO:0001559	having extra function									acts as a dominant-negative repressor of MITF expression 	
+PMID:9462749 	OMIM602229.0001 			SO:1000062	nonsense_codon_change_in_transcript	PATO:0000467	present									E189X stop codon mutation 	
+PMID:9722528 	OMIM602229.0001 			GO:0065004	protein-DNA complex assembly	PATO:0000461	normal									***SOX10mut formed protein-DNA complexes despite mutation 	
+PMID:9722528 	OMIM602229.0001 			GO:0008104	protein localization	PATO:0001032	position	GO:0005634	nucleus					PATO:0000461	normal	protein localization to the nucleus 	
+PMID:12668617 	OMIM602229.0001 			GO:0016563	transcriptional activator activity	PATO:0001508	abolished									***Sox10 ability to activate transcription eliminated 	
+PMID:12668617 	OMIM602229.0001 			GO:0016563	transcriptional activator activity	PATO:0001508	abolished									***Pax3 ability to enhance transcription activity eliminated 	
+PMID:9462749 	OMIM602229.0002 			SO:1000062	nonsense_codon_change_in_transcript	PATO:0001632	anterior to	SO:0000330	conserved_region							Y83X stop codon mutation before HMG domain 	
+PMID:9722528 	OMIM602229.0002 			GO:0065004	protein-DNA complex assembly	PATO:0001511	non-functional									***SOX10mut failed to form protein-DNA complexes 	
+PMID:9722528 	OMIM602229.0002 			GO:0008104	protein localization	PATO:0000628	mislocalised	GO:0005829	cytosol					PATO:0000460	abnormal	protein mislocalization to the cytosol 	
+PMID:9462749 	OMIM602229.0003 			SO:1000034^located_in(SO:0000330)	nucleotide_insertion^located_in(conserved_region)	PATO:0000467	present									6-bp insertion in middle of HMG domain 	
+PMID:9722528 	OMIM602229.0003 			GO:0065004	protein-DNA complex assembly	PATO:0001511	non-functional									***SOX10mut failed to form protein-DNA complexes 	
+PMID:9722528 	OMIM602229.0003 			GO:0008104	protein localization	PATO:0001032	position	GO:0005634	nucleus					PATO:0000461	normal	protein localization to the nucleus 	
+PMID:12668617 	OMIM602229.0003 			GO:0016563	transcriptional activator activity	PATO:0001508	abolished									***Sox10 ability to activate transcription eliminated 	
+PMID:12668617 	OMIM602229.0003 			GO:0016563	transcriptional activator activity	PATO:0001508	abolished									***Pax3 ability to enhance transcription activity eliminated 	
+PMID:9462749 	OMIM602229.0004 			SO:1000065	frameshift_mutation	PATO:0000467	present									2-bp deletion causes frameshift, introduces premature termination codon 	
+PMID:9462749 	OMIM602229.0004 			SO:1000033	nucleotide_deletion	PATO:0000467	present									2-bp deletion causes frameshift, introduces premature termination codon 	
+PMID:9462749 	OMIM602229.0004 			SO:0000319	stop_codon	PATO:0001476	decreased position									2-bp deletion causes frameshift, introduces premature termination codon 	
+PMID:9722528 	OMIM602229.0004 			GO:0065004	protein-DNA complex assembly	PATO:0000461	normal									***SOX10mut formed protein-DNA complexes despite mutation 	
+PMID:9722528 	OMIM602229.0004 			GO:0008104	protein localization	PATO:0001032	position	GO:0005634	nucleus					PATO:0000461	normal	protein localization to the nucleus 	
+PMID:12668617 	OMIM602229.0005 			GO:0016563	transcriptional activator activity	PATO:0001508	abolished									***Sox10 ability to activate transcription eliminated 	
+PMID:12668617 	OMIM602229.0005 			GO:0003713	transcription coactivator activity	PATO:0000467	present									***Sox10 ability to coactivate transcription (with Pax3) present 	
+PMID:9722528 	OMIM602229.? 			GO:0016563	transcriptional activator activity	PATO:0001511	non-functional			 	 					deficient in activity as a transcriptional activator 	
+PMID:11734543 	OMIM602229.? 			FMA:62983	Myelin sheath	PATO:0001617	deformed									myelin defects 	
+PMID:11734543 	OMIM602229.? 			GO:0016563	transcriptional activator activity	PATO:0000462	absent									***SOX10 failed to transactivate the CX32 promoter 	
+PMID:11734543 	OMIM602229.? 			GO:0008134^located_in(SO:0000167)	transcription factor binding^located_in(promoter)	PATO:0000462	absent									***SOX10 failed to transactivate the CX32 promoter 	
+PMID:9462749 	[OMIM602229.0001/+] 			GO:0007605	sensory perception of sound	PATO:0000468	decreased									bilateral profound hearing loss 	
+PMID:9462749 	[OMIM602229.0001/+] 			FMA:53667	Hair	PATO:0000323	white									white hair color 	
+PMID:9462749 	[OMIM602229.0001/+] 			FMA:58611	Iridial part of retina	PATO:0000318	blue									blue irides with grey speckles 	
+PMID:9462749 	[OMIM602229.0001/+] 			FMA:63846^located_in(FMA:7163)	Cell pigment^located_in(Skin)	PATO:0001608	patchy									depigmented skin patches 	
+PMID:9462749 	[OMIM602229.0001/+] 			FMA:63846	Cell pigment	PATO:0000460	abnormal									pigmentary abnormalities (detailed with other entries) 	
+PMID:9462749 	[OMIM602229.0001/+] 			FMA:7199	Intestine	PATO:0000648	obstructed									intestinal obstruction in neonates 	
+PMID:9462749 	[OMIM602229.0001/+] 			GO:0007588	excretion	PATO:0000911	decreased rate									constipation in adults 	
+PMID:9462749 	[OMIM602229.0001/+] 			FMA:14544	Rectum	PATO:0001557	lacking physical part	FMA:5884	Ganglion							short segment HSCR - aganglionic tract in rectum+sigmoid colon 	
+PMID:9462749 	[OMIM602229.0001/+] 			FMA:14548	Sigmoid colon	PATO:0001557	lacking physical part	FMA:5884	Ganglion							short segment HSCR - aganglionic tract in rectum+sigmoid colon 	
+PMID:9462749 	[OMIM602229.0001/+] 			FMA:58611	Iridial part of retina	PATO:0001533	multi-colored									blue irides with grey speckles 	
+PMID:9462749 	[OMIM602229.0001/+] 			FMA:58611	Iridial part of retina	PATO:0000950	grey									blue irides with grey speckles 	
+PMID:9462749 	[OMIM602229.0002/+] 			GO:0007605	sensory perception of sound	PATO:0000468	decreased									bilateral profound hearing loss 	
+PMID:9462749 	[OMIM602229.0002/+] 			FMA:53667	Hair	PATO:0000665	light									fair hair color 	
+PMID:9462749 	[OMIM602229.0002/+] 			FMA:58611	Iridial part of retina	PATO:0001265	bright blue									vivid blue eyes 	
+PMID:9462749 	[OMIM602229.0002/+] 			FMA:7199	Intestine	PATO:0001624	decreased functionality									bowel problems 	
+PMID:9462749 	[OMIM602229.0002/+] 			FMA:5884^located_in(FMA:14544)	Ganglion^located_in(Rectum)	PATO:0000419	decreased number									number of ganglia was dramatically reduced 	
+PMID:9462749 	[OMIM602229.0003/+] 			GO:0007605	sensory perception of sound	PATO:0000468	decreased									deafness 	
+PMID:9462749 	[OMIM602229.0003/+] 			FMA:14544	Rectum	PATO:0001557	lacking physical part	FMA:5884	Ganglion							short segment HSCR - aganglionic tract in rectum+sigmoid colon 	
+PMID:9462749 	[OMIM602229.0003/+] 			FMA:14548	Sigmoid colon	PATO:0001557	lacking physical part	FMA:5884	Ganglion							short segment HSCR - aganglionic tract in rectum+sigmoid colon 	
+PMID:9462749 	[OMIM602229.0004/+] 	PM:0000019	penetrance_incomplete	GO:0007605	sensory perception of sound	PATO:0000468	decreased									deafness 	
+PMID:9462749 	[OMIM602229.0004/+] 	PM:0000023	expressivity_incomplete	FMA:63846^contained_in(FMA:61695)	Cell pigment^contained_in(Body surface)	PATO:0000468	decreased									hypopigmentation 	
+PMID:9462749 	[OMIM602229.0004/+] 			FMA:7199	Intestine	PATO:0001557	lacking physical part	FMA:84048	Ganglion cell							HSCR 	
+PMID:9462749 	[OMIM602229.0004/+] 	PM:0000023	expressivity_incomplete	FMA:53667	Hair	PATO:0000323	white									white hair color 	
+PMID:9462749 	[OMIM602229.0004/+] 	PM:0000019	penetrance_incomplete	FMA:7199	Intestine	PATO:0001571	dilated									megacolon 	
+PMID:10441344 	OMIM602229.0005 			SO:1000061	nonconservative_missense_codon_change_in_transcript	PATO:0000467	present									SER135THR mutation 	
+PMID:10441344 	OMIM602229.0005 			SO:1000061	nonconservative_missense_codon_change_in_transcript	PATO:0000467	present									SER135THR mutation 	
+PMID:2280978 	Yemenite deaf-blind hypopigmentation syndrome 			FMA:63846^located_in(FMA:7163)	Cell pigment^located_in(Skin)	PATO:0001608	patchy									hypo and hyperpigmented skin 	
+PMID:2280978 	Yemenite deaf-blind hypopigmentation syndrome 			FMA:58238	Cornea	PATO:0000587	decreased size									microcornea 	
+PMID:2280978 	Yemenite deaf-blind hypopigmentation syndrome 			FMA:54448	Eye	MP:0005262	coloboma									coloboma 	
+PMID:2280978 	Yemenite deaf-blind hypopigmentation syndrome 	PM:0000019	penetrance_incomplete	GO:0007605	sensory perception of sound	PATO:0000468	decreased									severe hearing loss 	
+PMID:10441344 	OMIM602229.0005 			FMA:63846^located_in(FMA:7163)	Cell pigment^located_in(Skin)	PATO:0001608	patchy									hypo and hyperpigmented skin 	
+PMID:10441344 	OMIM602229.0005 	PM:0000019	penetrance_incomplete	GO:0007605	sensory perception of sound	PATO:0000468	decreased									severe hearing loss 	
+PMID:10482261 	OMIM602229.0008 			FMA:62983	Myelin sheath	PATO:0001617	deformed			 	 					leukodystrophy - progressive degeneration development of the myelin sheath 	
+PMID:10482261 	OMIM602229.0008 			FMA:7199	Intestine	PATO:0000648	obstructed									intestinal obstruction in neonates 	
+PMID:10482261 	OMIM602229.0008 			FMA:7199	Intestine	PATO:0001557	lacking physical part	FMA:5884	Ganglion							long segment HSCR - aganglionic tract in entire colon 	
+PMID:10482261 	OMIM602229.0008 			FMA:63846^located_in(FMA:58237)	Cell pigment^located_in(Left iris)	PATO:0000616	asymmetrical	FMA:63846^located_in(FMA:58236)	Cell pigment^located_in(Right iris)							heterochromia iridis - one eye is different color (intensity) than the other 	
+PMID:10482261 	OMIM602229.0008 	PM:0000022	expressivity_complete	GO:0007605	sensory perception of sound	PATO:0000468	decreased									profound hearing loss 	
+PMID:10482261 	OMIM602229.0008 			FMA:59516	Root of nose	PATO:0000600	increased width									broad nasal root 	
+PMID:10482261 	OMIM602229.0008 			FMA:59324	Medial angle of left eye	PATO:0000374	increased distance	FMA:59323	Medial angle of right eye	 	 					dystopia canthorum - inner corners of the eyes (canthi) are spaced farther apart than normal 	
+PMID:10482261 	OMIM602229.0008 			GO:0048589^has_participant(FMA:20394)	developmental growth^has_participant(Body)	PATO:0000911	decreased rate									developmental delay 	
+PMID:10482261 	OMIM602229.0008 			FMA:20394	Body	MP:0000754	partial paralysis									spastic quadraplegia 	
+PMID:10482261 	OMIM602229.0008 			FMA:9721	Tendon	PATO:0001568	having decreased function	GO:0060004	reflex							loss of deep tendon reflexes 	
+PMID:10482261 	OMIM602229.0008 	PM:0000022	expressivity_complete	GO:0007600	sensory perception	PATO:0000468	decreased									sensory dullness 	
+PMID:10482261 	OMIM602229.0008 			FMA:9903	Peripheral nervous system	PATO:0001624	decreased functionality									peripheral neuropathy 	
+PMID:10482261 	OMIM602229.0008 			FMA:5867	Motor nerve	PATO:0001585	conduction									***decreased conductive velocity 	
+PMID:10482261 	OMIM602229.0008 			FMA:30316^contained_in(FMA:7182)	Muscle^contained_in(Limb)	PATO:0001623	atrophied									muscles in all limbs were severely atrophic 	
+PMID:10482261 	OMIM602229.0008 			FMA:67257^contained_in(FMA:20935)	Protein^contained_in(Cerebrospinal fluid)	PATO:0001162	increased concentration									Protein in the cerebrospinal fluid was elevated  	
+PMID:10482261 	OMIM602229.0008 			GO:0008038^contained_in(FMA:79876)	neuron recognition^contained_in(Brainstem)	PATO:0000468	decreased	GO:0007605	sensory perception of sound							no auditory brainstem response bilaterally 	
+PMID:10482261 	OMIM602229.0008 			FMA:62983^located_in(FMA:50801)	Myelin sheath^located_in(Brain)	PATO:0000468	decreased			 	 					prominent deficiency of myelination in the entire brain 	


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[Obo-svn-commit] SF.net SVN: obo: [602] phenote/trunk/doc/phenote-website/help

From: <nl...@us...> - 2007-05-17 23:31:21

Revision: 602
          http://svn.sourceforge.net/obo/?rev=602&view=rev
Author:   nlw
Date:     2007-05-17 16:31:04 -0700 (Thu, 17 May 2007)

Log Message:
-----------
Help docs:  Added basic editing instructions.  Added comments from Mark.  Corrected instructions for running.

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/help/Phenote.jhm
    phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak
    phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml
    phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml.bak
    phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html
    phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html.tmp
    phenote/trunk/doc/phenote-website/help/html/Advantages_to_Annotation_with_Ontolgies.htm
    phenote/trunk/doc/phenote-website/help/html/Bugs_and_Troubleshooting.htm
    phenote/trunk/doc/phenote-website/help/html/Changing_your_Configuration.htm
    phenote/trunk/doc/phenote-website/help/html/Data_Formats.htm
    phenote/trunk/doc/phenote-website/help/html/Menu_Bars.htm
    phenote/trunk/doc/phenote-website/help/html/Ontologies_included_with_Phenote.htm
    phenote/trunk/doc/phenote-website/help/html/Phenote_Webstart.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/Term_Info.htm
    phenote/trunk/doc/phenote-website/help/html/The_PhenoSyntax_Adapter.htm
    phenote/trunk/doc/phenote-website/help/report/report.htm
    phenote/trunk/doc/phenote-website/help/report/report.txt

Added Paths:
-----------
    phenote/trunk/doc/phenote-website/help/html/Changing_your_Autocompletion_Settings.htm
    phenote/trunk/doc/phenote-website/help/html/Editing_Functions.htm
    phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Free_Text_fields.htm
    phenote/trunk/doc/phenote-website/help/html/Entering_data_into_Ontology_Fields.htm
    phenote/trunk/doc/phenote-website/help/images/Settings-menu.png
    phenote/trunk/doc/phenote-website/help/images/prot-autocomple-table.png
    phenote/trunk/doc/phenote-website/help/images/prot-autocomplete-entry.png
    phenote/trunk/doc/phenote-website/help/images/prot-autocomplete-ex.png
    phenote/trunk/doc/phenote-website/help/images/prot-autocomplete-ont.png
    phenote/trunk/doc/phenote-website/help/images/prot-autocomplete-terminfo.png

Modified: phenote/trunk/doc/phenote-website/help/Phenote.jhm
===================================================================
--- phenote/trunk/doc/phenote-website/help/Phenote.jhm	2007-05-17 20:41:31 UTC (rev 601)
+++ phenote/trunk/doc/phenote-website/help/Phenote.jhm	2007-05-17 23:31:04 UTC (rev 602)
@@ -25,6 +25,7 @@
    <mapID target="Building_Filters" url="html/Building_Filters.htm"/>
    <mapID target="Changing_Link_Attributes" url="html/Changing_Link_Attributes.htm"/>
    <mapID target="Changing_Relationship_Types" url="html/Changing_Relationship_Types.htm"/>
+   <mapID target="Changing_your_Autocompletion_Settings" url="html/Changing_your_Autocompletion_Settings.htm"/>
    <mapID target="Changing_your_Configuration" url="html/Changing_your_Configuration.htm"/>
    <mapID target="Classes" url="html/Classes.htm"/>
    <mapID target="Cloning" url="html/Cloning.htm"/>
@@ -45,7 +46,10 @@
    <mapID target="Destroying" url="html/Destroying.htm"/>
    <mapID target="Disjointedness_Check" url="html/Disjointedness_Check.htm"/>
    <mapID target="Editing" url="html/Editing.htm"/>
+   <mapID target="Editing_Functions" url="html/Editing_Functions.htm"/>
    <mapID target="Editing_Obsoletes" url="html/Editing_Obsoletes.htm"/>
+   <mapID target="Entering_data_into_Free_Text_fields" url="html/Entering_data_into_Free_Text_fields.htm"/>
+   <mapID target="Entering_data_into_Ontology_Fields" url="html/Entering_data_into_Ontology_Fields.htm"/>
    <mapID target="Example_Layouts" url="html/Example_Layouts.htm"/>
    <mapID target="Example_Scripts" url="html/Example_Scripts.htm"/>
    <mapID target="Exiting_Phenote" url="html/Exiting_Phenote.htm"/>

Modified: phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak
===================================================================
--- phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak	2007-05-17 20:41:31 UTC (rev 601)
+++ phenote/trunk/doc/phenote-website/help/Phenote.jhm.bak	2007-05-17 23:31:04 UTC (rev 602)
@@ -25,6 +25,7 @@
    <mapID target="Building_Filters" url="html/Building_Filters.htm"/>
    <mapID target="Changing_Link_Attributes" url="html/Changing_Link_Attributes.htm"/>
    <mapID target="Changing_Relationship_Types" url="html/Changing_Relationship_Types.htm"/>
+   <mapID target="Changing_your_Autocompletion_Settings" url="html/Changing_your_Autocompletion_Settings.htm"/>
    <mapID target="Changing_your_Configuration" url="html/Changing_your_Configuration.htm"/>
    <mapID target="Classes" url="html/Classes.htm"/>
    <mapID target="Cloning" url="html/Cloning.htm"/>
@@ -45,7 +46,10 @@
    <mapID target="Destroying" url="html/Destroying.htm"/>
    <mapID target="Disjointedness_Check" url="html/Disjointedness_Check.htm"/>
    <mapID target="Editing" url="html/Editing.htm"/>
+   <mapID target="Editing_Functions" url="html/Editing_Functions.htm"/>
    <mapID target="Editing_Obsoletes" url="html/Editing_Obsoletes.htm"/>
+   <mapID target="Entering_data_into_Free_Text_fields" url="html/Entering_data_into_Free_Text_fields.htm"/>
+   <mapID target="Entering_data_into_Ontology_Fields" url="html/Entering_data_into_Ontology_Fields.htm"/>
    <mapID target="Example_Layouts" url="html/Example_Layouts.htm"/>
    <mapID target="Example_Scripts" url="html/Example_Scripts.htm"/>
    <mapID target="Exiting_Phenote" url="html/Exiting_Phenote.htm"/>

Modified: phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml	2007-05-17 20:41:31 UTC (rev 601)
+++ phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml	2007-05-17 23:31:04 UTC (rev 602)
@@ -33,7 +33,10 @@
      <tocitem text="The Tab-Delimited Adapter" target="The_Tab_Delimited_Adapter"/>
 </tocitem>
 <tocitem text="Creating Annotations">
-     <tocitem text="Editing Functions"/>
+     <tocitem text="Editing Functions" target="Editing_Functions"/>
+     <tocitem text="Changing your Autocompletion Settings" target="Changing_your_Autocompletion_Settings"/>
+     <tocitem text="Entering data into Free-Text fields" target="Entering_data_into_Free_Text_fields"/>
+     <tocitem text="Entering data into Ontology Fields" target="Entering_data_into_Ontology_Fields"/>
      <tocitem text="Sample Annotations" target="Sample_Annotations"/>
 </tocitem>
 <tocitem text="Information for Developers">

Modified: phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml.bak
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml.bak	2007-05-17 20:41:31 UTC (rev 601)
+++ phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml.bak	2007-05-17 23:31:04 UTC (rev 602)
@@ -33,7 +33,9 @@
      <tocitem text="The Tab-Delimited Adapter" target="The_Tab_Delimited_Adapter"/>
 </tocitem>
 <tocitem text="Creating Annotations">
-     <tocitem text="Editing Functions"/>
+     <tocitem text="Editing Functions" target="Editing_Functions"/>
+     <tocitem text="Entering data into Free-Text fields" target="Entering_data_into_Free_Text_fields"/>
+     <tocitem text="Entering data into Ontology Fields" target="Entering_data_into_Ontology_Fields"/>
      <tocitem text="Sample Annotations" target="Sample_Annotations"/>
 </tocitem>
 <tocitem text="Information for Developers">
@@ -55,7 +57,7 @@
      <tocitem text="The &lt;field&gt; Tag" target="The__field__Tag"/>
      <tocitem text="The &lt;ontology&gt; Tag" target="The__ontology__Tag"/>
      <tocitem text="The &lt;auto-update-ontologies&gt; Tag" target="The__auto_update_ontologies__Tag115"/>
-     <tocitem text="The &lt;update-timer&gt; Tag"/>
+     <tocitem text="The &lt;update-timer&gt; Tag" target="The__update_timer__Tag"/>
      <tocitem text="The &lt;term-history&gt; Tag" target="The__term_history__Tag118"/>
 </tocitem>
 <tocitem text="Appendix">

Modified: phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html	2007-05-17 20:41:31 UTC (rev 601)
+++ phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html	2007-05-17 23:31:04 UTC (rev 602)
@@ -73,6 +73,9 @@
 ctable(wdt164);
 ctable(wdt165);
 ctable(wdt166);
+ctable(wdt167);
+ctable(wdt168);
+ctable(wdt169);
 }
 
   
@@ -252,155 +255,164 @@
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Creating Annotations</font>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt121>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Editing Functions</face>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Editing_Functions.htm" target=bodyframe>Editing Functions</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt122>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Changing_your_Autocompletion_Settings.htm" target=bodyframe>Changing your Autocompletion Settings</font></a>
+</td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt123>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Entering_data_into_Free_Text_fields.htm" target=bodyframe>Entering data into Free-Text fields</font></a>
+</td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt124>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Entering_data_into_Ontology_Fields.htm" target=bodyframe>Entering data into Ontology Fields</font></a>
+</td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt125>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Sample_Annotations.htm" target=bodyframe>Sample Annotations</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Information for Developers</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt123>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt126>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Writing a Data Adapter</face>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt124>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt127>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Connecting_to_a_Database.htm" target=bodyframe>Connecting to a Database</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt125>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt128>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Adding_configurability.htm" target=bodyframe>Adding configurability</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>What to do after Phenote</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt126>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt129>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>I've entered my data, now what?</face>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt127>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt130>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Other_Uses_for_Phenote.htm" target=bodyframe>Other Uses for Phenote</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing Phenote</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt128>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt131>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/What_is_a_Configuration_.htm" target=bodyframe>What is a Configuration?</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt129>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt132>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/How_To_Edit_a_Configuration_File.htm" target=bodyframe>How To Edit a Configuration File</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt130>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt133>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Sample_Configuration_1.htm" target=bodyframe>Sample Configuration 1</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt131>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt134>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Sample_Configuration_2.htm" target=bodyframe>Sample Configuration 2</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt132>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt135>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/XML_skeleton.htm" target=bodyframe>XML skeleton</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt133>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__dataadapter__Tag.htm" target=bodyframe>The &lt;dataadapter&gt; Tag</font></a>
-</td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt134>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=topwidth=100%><font face=Arial size=2><a href="html/The__field__Tag.htm" target=bodyframe>The &lt;field&gt; Tag</font></a>
-</td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt135>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__ontology__Tag.htm" target=bodyframe>The &lt;ontology&gt; Tag</font></a>
-</td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt136>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__auto_update_ontologies__Tag.htm" target=bodyframe>The &lt;auto-update-ontologies&gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__dataadapter__Tag.htm" target=bodyframe>The &amp;lt;dataadapter&amp;gt; Tag</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt137>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__update_timer__Tag.htm" target=bodyframe>The &lt;update-timer&gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__field__Tag.htm" target=bodyframe>The &amp;lt;field&amp;gt; Tag</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt138>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__term_history__Tag.htm" target=bodyframe>The &lt;term-history&gt; Tag</font></a>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__ontology__Tag.htm" target=bodyframe>The &amp;lt;ontology&amp;gt; Tag</font></a>
 </td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt139>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__auto_update_ontologies__Tag.htm" target=bodyframe>The &amp;lt;auto-update-ontologies&amp;gt; Tag</font></a>
 </td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt140>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__update_timer__Tag.htm" target=bodyframe>The &amp;lt;update-timer&amp;gt; Tag</font></a>
+</td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt141>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__term_history__Tag.htm" target=bodyframe>The &amp;lt;term-history&amp;gt; Tag</font></a>
+</td></tr></table>
+</td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Appendix</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt139>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt142>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/An_Introduction_to_OBO_Ontologies.htm" target=bodyframe>An Introduction to OBO Ontologies</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt140>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt143>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Basic_Concepts_and_Vocabulary.htm" target=bodyframe>Basic Concepts and Vocabulary</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>from OBOedit</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt141>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt144>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing OBO-Edit</face>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt142>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt145>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Configuration_Plugin.htm" target=bodyframe>The Configuration Plugin</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt143>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt146>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing the Interface</face>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt144>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt147>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Working_with_XML_Layouts.htm" target=bodyframe>Working with XML Layouts</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt145>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt148>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Common_Parameters.htm" target=bodyframe>Common Parameters</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt146>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt149>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Glue_Tag.htm" target=bodyframe>The &amp;lt;glue&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt147>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt150>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Spacer_Tag.htm" target=bodyframe>The &amp;lt;spacer&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt148>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt151>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Label_Tag.htm" target=bodyframe>The &amp;lt;label&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt149>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt152>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Box_Tag.htm" target=bodyframe>The &amp;lt;box&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt150>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt153>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Grid_Tag.htm" target=bodyframe>The &amp;lt;grid&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt151>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt154>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Panel_Tag.htm" target=bodyframe>The &amp;lt;panel&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt152>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt155>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Compactgrid_Tag.htm" target=bodyframe>The &amp;lt;compactgrid&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt153>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt156>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Divider_Tag.htm" target=bodyframe>The &amp;lt;divider&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt154>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt157>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Tabs_Tag.htm" target=bodyframe>The &amp;lt;tabs&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt155>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt158>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Window_Tag.htm" target=bodyframe>The &amp;lt;window&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt156>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt159>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_If_Tag.htm" target=bodyframe>The &amp;lt;if&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt157>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt160>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Component_Tag.htm" target=bodyframe>The &amp;lt;component&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt158>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt161>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Example_Layouts.htm" target=bodyframe>Example Layouts</face></a>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt159>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt162>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Introduction.htm" target=bodyframe>The Default Layout</font></a>
 </td></tr></table>
 </td></tr></table>
 </td></tr></table>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt160>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt163>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>New Topic</face>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt161>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt164>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Working with Data Adapters</face>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt162>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt165>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Basic_Flat_File_Interface.htm" target=bodyframe>The Basic Flat File Interface</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt163>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt166>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_OBO_Adapter.htm" target=bodyframe>The OBO Adapter</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt164>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt167>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_GO_Flat_File_Adapter.htm" target=bodyframe>The GO Flat File Adapter</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt165>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt168>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Serial_Adapter.htm" target=bodyframe>The Serial Adapter</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt166>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt169>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Custom_Data_Adapters.htm" target=bodyframe>Custom Data Adapters</font></a>
 </td></tr></table>
 </td></tr></table>

Modified: phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html.tmp
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html.tmp	2007-05-17 20:41:31 UTC (rev 601)
+++ phenote/trunk/doc/phenote-website/help/PhenoteWebTOC.html.tmp	2007-05-17 23:31:04 UTC (rev 602)
@@ -78,155 +78,164 @@
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Creating Annotations</font>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt121>
-<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Editing Functions</face>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Editing_Functions.htm" target=bodyframe>Editing Functions</font></a>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt122>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Changing_your_Autocompletion_Settings.htm" target=bodyframe>Changing your Autocompletion Settings</font></a>
+</td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt123>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Entering_data_into_Free_Text_fields.htm" target=bodyframe>Entering data into Free-Text fields</font></a>
+</td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt124>
+<tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Entering_data_into_Ontology_Fields.htm" target=bodyframe>Entering data into Ontology Fields</font></a>
+</td></tr></table>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt125>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Sample_Annotations.htm" target=bodyframe>Sample Annotations</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Information for Developers</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt123>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt126>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Writing a Data Adapter</face>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt124>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt127>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Connecting_to_a_Database.htm" target=bodyframe>Connecting to a Database</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt125>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt128>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Adding_configurability.htm" target=bodyframe>Adding configurability</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>What to do after Phenote</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt126>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt129>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>I've entered my data, now what?</face>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt127>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt130>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Other_Uses_for_Phenote.htm" target=bodyframe>Other Uses for Phenote</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing Phenote</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt128>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt131>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/What_is_a_Configuration_.htm" target=bodyframe>What is a Configuration?</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt129>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt132>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/How_To_Edit_a_Configuration_File.htm" target=bodyframe>How To Edit a Configuration File</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt130>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt133>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Sample_Configuration_1.htm" target=bodyframe>Sample Configuration 1</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt131>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt134>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Sample_Configuration_2.htm" target=bodyframe>Sample Configuration 2</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt132>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt135>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/XML_skeleton.htm" target=bodyframe>XML skeleton</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt133>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt136>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__dataadapter__Tag.htm" target=bodyframe>The &amp;lt;dataadapter&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt134>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt137>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__field__Tag.htm" target=bodyframe>The &amp;lt;field&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt135>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt138>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__ontology__Tag.htm" target=bodyframe>The &amp;lt;ontology&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt136>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt139>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__auto_update_ontologies__Tag.htm" target=bodyframe>The &amp;lt;auto-update-ontologies&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt137>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt140>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__update_timer__Tag.htm" target=bodyframe>The &amp;lt;update-timer&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt138>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt141>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The__term_history__Tag.htm" target=bodyframe>The &amp;lt;term-history&amp;gt; Tag</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Appendix</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt139>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt142>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/An_Introduction_to_OBO_Ontologies.htm" target=bodyframe>An Introduction to OBO Ontologies</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt140>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt143>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Basic_Concepts_and_Vocabulary.htm" target=bodyframe>Basic Concepts and Vocabulary</font></a>
 </td></tr></table>
 </td></tr></table>
 <table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt0>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>from OBOedit</font>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt141>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt144>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing OBO-Edit</face>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt142>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt145>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Configuration_Plugin.htm" target=bodyframe>The Configuration Plugin</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt143>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt146>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Customizing the Interface</face>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt144>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt147>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Working_with_XML_Layouts.htm" target=bodyframe>Working with XML Layouts</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt145>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt148>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Common_Parameters.htm" target=bodyframe>Common Parameters</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt146>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt149>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Glue_Tag.htm" target=bodyframe>The &amp;lt;glue&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt147>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt150>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Spacer_Tag.htm" target=bodyframe>The &amp;lt;spacer&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt148>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt151>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Label_Tag.htm" target=bodyframe>The &amp;lt;label&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt149>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt152>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Box_Tag.htm" target=bodyframe>The &amp;lt;box&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt150>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt153>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Grid_Tag.htm" target=bodyframe>The &amp;lt;grid&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt151>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt154>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Panel_Tag.htm" target=bodyframe>The &amp;lt;panel&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt152>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt155>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Compactgrid_Tag.htm" target=bodyframe>The &amp;lt;compactgrid&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt153>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt156>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Divider_Tag.htm" target=bodyframe>The &amp;lt;divider&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt154>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt157>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Tabs_Tag.htm" target=bodyframe>The &amp;lt;tabs&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt155>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt158>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Window_Tag.htm" target=bodyframe>The &amp;lt;window&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt156>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt159>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_If_Tag.htm" target=bodyframe>The &amp;lt;if&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt157>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt160>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Component_Tag.htm" target=bodyframe>The &amp;lt;component&amp;gt; Tag</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt158>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt161>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Example_Layouts.htm" target=bodyframe>Example Layouts</face></a>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt159>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt162>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Introduction.htm" target=bodyframe>The Default Layout</font></a>
 </td></tr></table>
 </td></tr></table>
 </td></tr></table>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt160>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt163>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>New Topic</face>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt161>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt164>
 <tr><td valign=baseline width=15><img src=plus.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2>Working with Data Adapters</face>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt162>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt165>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Basic_Flat_File_Interface.htm" target=bodyframe>The Basic Flat File Interface</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt163>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt166>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_OBO_Adapter.htm" target=bodyframe>The OBO Adapter</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt164>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt167>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_GO_Flat_File_Adapter.htm" target=bodyframe>The GO Flat File Adapter</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt165>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt168>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/The_Serial_Adapter.htm" target=bodyframe>The Serial Adapter</font></a>
 </td></tr></table>
-<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt166>
+<table w2wdynamicoutline border=0 cellpadding=0 cellspacing=0 width=100% class=mytable id=wdt169>
 <tr><td valign=baseline width=15><img src=page.gif width=11 height=11 hspace=3 style=cursor:hand></td><td valign=top width=100%><font face=Arial size=2><a href="html/Custom_Data_Adapters.htm" target=bodyframe>Custom Data Adapters</font></a>
 </td></tr></table>
 </td></tr></table>

Modified: phenote/trunk/doc/phenote-website/help/html/Advantages_to_Annotation_with_Ontolgies.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Advantages_to_Annotation_with_Ontolgies.htm	2007-05-17 20:41:31 UTC (rev 601)
+++ phenote/trunk/doc/phenote-website/help/html/Advantages_to_Annotation_with_Ontolgies.htm	2007-05-17 23:31:04 UTC (rev 602)
@@ -24,7 +24,7 @@
   <LI>Because each term in an ontology is defined, exact 
   concepts are used and recorded, rather than "fuzzy" human language, 
   where&nbsp;phrases can&nbsp;have more than one meaning 
-  <LI>Given the proper analysis tools, the resutling data can be mined in the 
+  <LI>Given the proper analysis tools, the resulting data can be mined in the 
   context of the broader knowledge contained within the ontologies.&nbsp; 
 </LI></UL>
 </body>

Modified: phenote/trunk/doc/phenote-website/help/html/Bugs_and_Troubleshooting.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Bugs_and_Troubleshooting.htm	2007-05-17 20:41:31 UTC (rev 601)
+++ phenote/trunk/doc/phenote-website/help/html/Bugs_and_Troubleshooting.htm	2007-05-17 23:31:04 UTC (rev 602)
@@ -7,14 +7,20 @@
 </HEAD>
 <BODY BGCOLOR=#ffffff>
 <H1>Bugs and Troubleshooting</H1>
-<P>When installing a new version of Phenote, check the README 
-file for&nbsp;a summary of changes in the new version, any known issues, and any 
-last-minute release notes or documentation.</P>
+<P>When installing a new version of Phenote, check the 
+release notes for&nbsp;a summary of changes in the new version, any known 
+issues, and any last-minute release notes or documentation.&nbsp; These can be 
+found at:&nbsp; <A 
+href="http://www.phenote.org/phenote-release-notes.html">http://www.phenote.org/phenote-release-notes.html</A>          
+           or in the 
+Help-&gt;Release Notes menu within Phenote.</P>
 <H2>Bug Reports</H2>
-<P>Phenote is a work in progress. Bugs can and will creep in. Please report any 
-odd behavior or bugs immediately. The Phenote Working Group is very responsive 
-to bug reports, and your bugs will be addressed within a few days (or sometimes 
-hours).</P>
+<P>Phenote is a work in progress. Bugs can and will creep 
+in. Please report any odd behavior or bugs immediately. The Phenote Working 
+Group is very responsive to bug reports, and your bugs w...
 
[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [601] phenote/trunk/src/java/phenote/gui/FileMenu.java

From: <nl...@us...> - 2007-05-17 20:41:54

Revision: 601
          http://svn.sourceforge.net/obo/?rev=601&view=rev
Author:   nlw
Date:     2007-05-17 13:41:31 -0700 (Thu, 17 May 2007)

Log Message:
-----------
disabled the File->New menu item.

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

Modified: phenote/trunk/src/java/phenote/gui/FileMenu.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/FileMenu.java	2007-05-17 20:12:36 UTC (rev 600)
+++ phenote/trunk/src/java/phenote/gui/FileMenu.java	2007-05-17 20:41:31 UTC (rev 601)
@@ -29,7 +29,7 @@
     LoadSaveActionListener actionListener = new LoadSaveActionListener();
 
     JMenuItem newData = new JMenuItem("New");
-    newData.setEnabled(Config.inst().hasDataAdapters());
+    newData.setEnabled(false);
     newData.setActionCommand("new");
     newData.addActionListener(actionListener);
     add(newData);


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[Obo-svn-commit] SF.net SVN: obo: [600] phenote/trunk/doc/phenote-website/ phenote-release-notes.html

From: <nl...@us...> - 2007-05-17 20:13:07

Revision: 600
          http://svn.sourceforge.net/obo/?rev=600&view=rev
Author:   nlw
Date:     2007-05-17 13:12:36 -0700 (Thu, 17 May 2007)

Log Message:
-----------
added more detail to release notes for 1.2 and 1.3beta

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	2007-05-17 18:17:41 UTC (rev 599)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.html	2007-05-17 20:12:36 UTC (rev 600)
@@ -1,40 +1,24 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <html>
 <head>
-
-
-
-
   
-  
-  
-  
   <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
 
-
-
-
-  
-  
-  
-  
   <title>Phenote Release Notes</title>
 </head>
 
-
 <body>
-
-
-
-
 <h1>Phenote Release Notes</h1>
 
-
-
-
 1.3
 will probably come out in June<br>
 
+<h2><span style="text-decoration: underline;">1.3-beta2</span></h2>
+under development, not yet released.
+<br>
+File-&gt;New is disabled until next version<br>
+Web-based documentation and Help features<br>
+
 <h2><span style="text-decoration: underline;">1.3-beta1</span></h2>
 
 <a href="1.3-beta1/phenote.jnlp">Phenote 1.3-beta1</a><br>
@@ -43,10 +27,9 @@
 Added SAO.obo for birn<br>
 Namespace config writes back<br>
 Config update/merge bug where fields in wrong order fixed.<br>
-Can specify more than one website for ontologies<br>
+Can specify more than one website for ontology update<br>
 Empty field shows all terms in ontology rather than none<br>
 Can add more differentia to post comp<br>
-
 <h2><span style="text-decoration: underline;">1.2</span></h2>
 
 <a href="1.2/phenote.jnlp">Phenote 1.2</a><br>
@@ -59,24 +42,31 @@
 Can post-compose with &gt;2 terms <br>
 
 
-Term history display can be toggled on/off <br>
+Term history display can be toggled on/off (Settings-&gt;Term History menu)<br>
 
 
-Synonym types display in term info<br>
+Synonyms are delineated by their scope in Term Info:  Exact, Narrow, Broad, General, Related.  If the synonym category is given, it is displayed next to the synonym.  For example:  the term 'water' has the <i>related</i> synonym H2O, which has the category of a chemical <i>formula</i>.<br>
+<br>
 
 
-Obsolete replacements displayed in term info<br>
+Obsolete replacements or consideration terms are displayed in term info with links<br>
 
-
 Search filters moved into menu <br>
 
-
 Loading splash screen <br>
 
 Can configure by namespace for ontologies<br>
 
+Can automatically update ontologies during startup (configurable)<br>
 
+Timer added to configuration during ontology update check (configurable)<br>
 
+Can check which version of phenote is running by selecting Help-&gt;About.<br>
+
+Common configuration for OMIM curation for use by NCBO included (ncbo.cfg).
+
+Updates to the zfin-standalone.cfg for the zebrafish community annotation.  Only includes GO and ZFanatomy ontologies.
+
 Bug Fixes: Free text field text not "sticking"
 
 <h2><span style="text-decoration: underline;">1.1</span></h2>


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[Obo-svn-commit] SF.net SVN: obo: [599] phenote/trunk/doc/phenote-website/pheno-xml.rnc

From: <nl...@us...> - 2007-05-17 18:18:14

Revision: 599
          http://svn.sourceforge.net/obo/?rev=599&view=rev
Author:   nlw
Date:     2007-05-17 11:17:41 -0700 (Thu, 17 May 2007)

Log Message:
-----------
adding xml spec so it can be accessable on website

Added Paths:
-----------
    phenote/trunk/doc/phenote-website/pheno-xml.rnc

Added: phenote/trunk/doc/phenote-website/pheno-xml.rnc
===================================================================
--- phenote/trunk/doc/phenote-website/pheno-xml.rnc	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/pheno-xml.rnc	2007-05-17 18:17:41 UTC (rev 599)
@@ -0,0 +1,452 @@
+default namespace = "http://www.bioontologies.org/obd/schema/pheno"
+## Pheno-XML
+## Chris Mungall 2006
+##
+## The RNC is the master version -
+##   RNG and XSD is autogenerated from RNC
+
+#default namespace = ""
+#namespace geno = "http://www.gmod.org/schema/genotype"
+
+
+# Changes: 
+#
+# Version: 0.11
+#
+#     genetic_feature_set -> genotype_feature_link
+#
+# Version: 0.10
+#
+#     complete revamp from 0_06
+
+start =
+## A document consists of some combination of genotypes and
+## phenotypes, manifestations of phenotypes via genotypes, and
+## genetic features
+   element phenoset {
+
+      ## : File format version :
+      ##   should match this schema version (eg 0.01)
+      attribute version { xsd:string }?,
+
+      genotype*,
+      genetic_feature*,
+      phenotype*,
+      phenotype_manifestation*
+   }
+
+genotype =
+   ## Each genotype record represents a single individual or group of genetically similar individuals
+   element genotype {
+      attribute id { identifier_Type }?,
+
+      ## NCBI TAxon ID
+      attribute organism { identifier_Type }?,
+
+      ## another genotype
+      attribute background { identifier_Type }?,   
+      
+      element name { name_Type }?,
+
+      ## A genotype is a collection of alleles
+      ## In general, only the mutant alleles are specified.
+      ## sequence variants can also be specified
+      element genotype_feature_link {
+         attribute copy_count {xsd:int}?,
+
+         ## a reference to a genetic feature
+         attribute feature { identifier_Type }?
+      }*
+   }
+
+genetic_feature =
+## A genetic feature may be a gene (allele), transcript, SNP, etc
+## typed by SO
+## This is a partial model of genetic features - a full
+## model can be found in Chado
+   element genetic_feature {
+
+      ## unique stable global identifier - this can be used to
+      ## reference more detailed info in a sequence/genetics db
+      attribute id { identifier_Type },
+      
+      ## optional: same as genotype.organism_id if not specified
+      attribute organism { identifier_Type }?,
+      
+      ## SO type. "gene" for mutant allele. May also be some
+      ## kind of sequence_variant (eg deletion, P_insertion, SNP)
+      ## defaults to SO:gene (ie an allele)
+      typeref?,
+      
+      element name { name_Type }?
+   }
+
+manifest_in =
+## a single genotype can be associated with multiple phenotypes
+## in different experiments and different environments
+   element manifest_in {
+
+      attribute penetrance_percentage { xsd:float }?,
+      attribute genotype { identifier_Type }?,
+      
+      ## may be from genetic context ontology
+      typeref*
+   }
+
+phenotype_manifestation =
+## A phenotype record consists of a collection of phenotype characters
+## (present in a particular organism or collection of organisms)
+## Phenotype characters use the extended-EA model
+##  the core is simply the specification of an bearer type and an
+##  an attribute-state type
+   element phenotype_manifestation {
+      
+      ## Each manifestation can be identified, but this is optional.
+      ## Note that the ID is for the manifestation of the phenotype
+      ## in either a single individual organism, or in a population of
+      ## indistinguishable individuals in an experiment or trial
+      attribute id { identifier_Type }?,
+
+      ## free text summary of the entire phenotype manifestation;
+      description?,
+      
+      ## phenotypes exist by virtue of being manifest in some
+      ## individual or group of individuals
+      manifest_in,
+
+      ## The collection of characteristics exhibited in this
+      ## manifestation
+      phenotype,
+
+      ## support or evidence; experimental details
+      provenance*,
+
+      ## there is an implicit 'normal' environment
+      ## if multiple environments are specified, the association
+      ## holds for ALL of them
+      envirotype*
+   }
+
+phenotype =
+## a phenotype is a collection of phenotype characters
+   element phenotype {
+
+      ## An identifier for a phenotype term. If supplied, this would
+      ## come from a full
+      ## ontology of pre-coordinated phenotype terms such as MPO or
+      ## the plant_trait ontology
+      typeref?,
+      
+      phenotype_character*
+   }
+
+phenotype_character =
+## A phenotype character is one or more quality types inhering in a single
+## "bearer" entity type.
+##
+## examples of phenotype characters:
+##    red hair, low bone mass, square jaw, long thick bristle,
+##    2cm long tail, spermatocyte devoid of asters, elevated blood pressure,
+##    lacking wings, having an additional digit relative to a wild type individual,
+##    having a brain size during embryonic development that is larger than
+##    a typical individual of the same genus/order, short attention span, having
+##    an abnormal shape, abnormal fusion between digits, lacking red spots, 
+##    abnormally low numbers of B-cells after infection, lacking circularity in
+##    the cross-section of an arista lateral
+##
+## A phenotype character represents a type rather than an instance - eg the
+## type "red hair" is instantiated by multiple individuals
+   element phenotype_character {
+      attribute expressivity_percentage { xsd:float }?,
+
+      ## free text summary of the phenotype character
+      description?,
+
+      ## the type of entity in which the qualities inhere
+      ## can be a process type or continuant type
+      bearer,
+
+      ## the quality types (attributes, properties) that are the
+      ## hallmarks of this character
+      quality*
+   }
+
+bearer =
+##   each 'bearer' record represents a particular bearer of some
+##   general bearer type: for example, a particular wing of a
+##   particular fly
+##
+##   entities can be spatial objects (3D e.g. anatomical parts)
+##   or spatiotemporal entities (4D e.g. processes)
+   element bearer {
+
+      ## qualities can be borne by processes or continuants;
+      ## the bearer can thus be drawn from GO process, component,
+      ## or from an ontology of cells or larger anatomical entities.
+      typeref
+   }
+
+quality =
+## aka attribute aka property
+## any one particular bearer can have multiple qualities inhering
+## in it. For example, a particular tail can have qualities such
+## as shape, length, etc
+##
+## each quality inheres in a single bearer throughout the duration
+## of that entities existence. For example, my height is a single
+## quality that inheres in my body throughout my life. This
+## quality can take on different states throughout the lifetime
+## of the bearer.
+##
+   element quality {
+
+      ## not required: it can be deduced from the quality type.
+      ## if provided, the value of this field is always an OBO-style identifier from PATO
+      ## may be useful for report purposes; eg the color of this entity is red
+      ## (where 'color' is the determinable)
+      attribute determinable { classId_Type}?,
+         
+      ## quality type. comes from PATO
+      typeref,
+
+      ## certain kinds of quality implicitly or explicitly refer to
+      ## numbers. Examples of these are the qualities of "having 
+      ## supernumery parts" or the qualities of "lacking parts". It
+      ## can be useful to state the exact number here, rather than
+      ## overloading the ontology of qualities.
+      ##
+      ## the number will refer to either the relative or absolute
+      ## quantity....?
+      ##
+      ## This is purely optional, as it is usually sufficient to
+      ## state that a particular hand has supernumery fingers,
+      ## without saying how many extra
+      
+      attribute count { xsd:integer }?,
+
+      ## optional free text
+      description?,
+
+      ## Relational qualities inhere in additional entities.
+      ## This should be used for relational qualities
+      ## (e.g. sensitivity, distance_from)
+      ## and not for monadic entities.
+      ##
+      ## other examples include:
+      ## "spermatocytes *devoid_of* asters", "thorax *lacks* wing",
+      ## hand *has-supernumerary-parts* finger
+      ## in these cases, the related_entity records the _type_ of part
+      ## that is lacking or present in lower or higher numbers
+      element related_entity {
+         typeref
+      }*,
+
+      ## sometimes a state is only instantiated if a certain condition holds
+      element on_condition { 
+         typeref
+      }*,
+
+      ## for relative qualities we may want an explicit "yardstick"
+      in_comparison_to?,
+
+      ## not all phenotype characters can be specified in
+      ## qualitative terms using classes from an ontology of
+      ## quality states. Sometimes unit-based quantitative measurements
+      ## must be used - for example, weight in kg
+      ## rather than overloading the 'type' field we treat measurements
+      ## separately. Measurements complement quality space annotations;
+      ## a phenotype character can be both "shorter_than" wild-type
+      ## and also 2cm in length. Either or both of these can be
+      ## specified in the annotation
+      measurement*,
+
+      ##  Qualities can change over time: a quality may instantiate 'hot' at one time and 'cold' at a later time.
+      ##  we may know the exact time stage (eg larval to pupal), or we may have an open range (eg post-larval), repeated
+      ##  ranges..
+      ##  multiple qualifiers can be specified (eg before t2 and after t1)
+      ##  if no qualifiers are specified then there is no implied time - it is assumed to happen at some point
+      ##  in the organisms life time, UNLESS it is constrained by the bearer bearer type.
+      ##  for example, if the bearer is "larva" then the attached state occurs during the larval stage. for this
+      ##  to be infered, the appropriate relations must be specified in the anatomical ontology
+      temporal_qualifier*,
+
+      modifier*
+   }
+
+in_comparison_to =
+## quality types can be absolutist (square, red) or
+## relative (high pressure, short height). relative
+## always implies a context. The default context is
+## always an equivalent phenotype character in a
+## typical individual of the same species. We can be
+## more explicit if we like by specifying in_comparison_to
+##
+## Examples:
+##   an allele which has more or less pronounced effects
+##   in different genetic backgrounds;
+##   A yellow eye which is red in wildtype;
+   element in_comparison_to { 
+
+      ## if left blank, this is inferred from the quality type;
+      ## for example, if Q="high pressure", then the relation is
+         ## higher-than or increased-with-respect-to
+      attribute relation { classId_Type }?,
+      
+      ## Can be an ID of a particular phenotype manifestation, or
+      ## an ID for a whole taxon
+      attribute about { identifier_Type }?,
+      
+      ## What the quality type would be in wild-type, or
+      ## whatever the comparison target is. Can specify multiple
+      ## values if these are exhibited by the target.
+      ## for example, if color is red or pink in wildtype, then
+      ## we can specify these two here.
+      ## specifying target types can lead to redundancy, this
+      ## is only required when for example our canonical
+      ## anatomical ontologies are not specific w.r.t quality types
+      typeref*,
+
+      ## What typical measurements would be in wild-type, or
+      ## whatever the comparison target is. Can specify multiple
+      ## values if these are exhibited by the target
+      measurement*
+   }
+
+modifier =
+## for abnormal/normal
+## these should come from the PATO modifier terminology
+   element modifier {
+      attribute about { classId_Type }
+   }
+      
+
+measurement =
+## : measurement :
+##
+## examples: 
+##   length measurement (with ruler, in cm)
+##   spot intensity
+## real-world measurements (exlcuding count measurements) are inexact
+## and hence ranges.
+  element measurement {
+
+    ## the unit should be a reference to an SI unit
+    ## Q: do SI units have an identifier system,
+    ##    or do we just use eg "mm"
+    ## Q: do we need the ability to specify composite units,
+    ##    eg lb/kg - or is this handled by SI?
+    attribute unit { xsd:NMTOKEN },
+
+    ##   the only time this would be omitted is if we only have a range
+    attribute value { xsd:float }?,
+
+    ## Q: does the range reflect our lack of knowledge (eg accuracy
+    ##    of measuring instrument) or an actual range of values?
+    ##    or should we represent an actual range as multiple measurements?
+    attribute min_value { xsd:float }?,
+    attribute max_value { xsd:float }?,
+
+    attribute standard_deviation { xsd:float }?,
+    attribute standard_error { xsd:float }?,
+
+    ## TODO: reference to a particular experiment
+    attribute assay { identifier_Type }?
+  }
+
+provenance =
+## evidence: could refer to papers, figures in papers, raw images, etc
+  element provenance {
+    attribute id { identifier_Type },
+    attribute type { classId_Type }?
+  }
+
+envirotype =
+## The type of environment.
+## For now this is just a pre or post coordinated type reference. In future
+## We may want to add more under here
+   element envirotype {
+      typeref
+   }
+
+typeref =
+## A reference to a type. Here type is used in the ontology sense of
+## a "kind" or "universal". A type can be referenced simply by giving a
+## term ID from an ontology. More complex types can be "post-coordinated"
+   element typeref {
+      ## Base/generic type. This is often all that is required.
+      ## the ID is OBO-compliant and can be from any ontology
+      attribute about { classId_Type },
+
+      ## We can post-compose references to more detailed types
+      ## for which no defined term exists
+      qualifier*
+   }
+
+qualifier =
+## for cross-products
+## these are the characteristics that distinguish a specific type
+## from a general type
+##  e.g. if we want to annotate to an bearer "scutum bristle" and the
+## anatomical ontology does not contain this term, only "scutum" and
+## "bristle". In this case the bearer type_id (ie the primary term) would
+## be the ID for "bristle". We would have one differentium "part_of scutum"
+   element qualifier {
+      attribute relation { classId_Type },
+      element holds_in_relation_to { 
+         typeref
+      }
+   }
+
+
+temporal_qualifier =
+## temporal_qualifier
+##   examples:
+##      during larval stage;
+##      after pupal stage;
+##      at 7pm on 2000/01/01;
+##      overlapping M1-phase;
+##  we do not tie ourself to any one theory of time - time ranges and points are represented using time_range
+   element temporal_qualifier {
+      ## e.g. before, after, during - would come from an ontology of temporal relations
+      ## this is optional. If not specified, treated as *overlap* relation
+      attribute relation { classId_Type }?,
+      time_range?
+   }
+
+time_range =
+## represents an interval or point in time 
+## (we are neutral w.r.t points vs intervals)
+   element time_range {
+    ## : id : OPTIONAL
+    ## this is typically not used. You would use it if you wish to grant an identifier to
+    ## a particular time point or range. This would allow you to make partial-order statements;
+    ## e.g. t1 before t2
+    attribute id { identifier_Type }?,
+
+    ## The interval may be typed by a term/class from an ontology of
+    ## developmental stages, processes or life cycles. 
+    typeref?,
+
+    ## an OPTIONAL measurement of the time; eg in seconds, hours,
+    ## years, etc. Measured either from when the particular attribute
+    ## (and hence bearer) came into existence, or in absolute time.
+    measurement?
+   }          
+
+description =
+## an optionally-attributed textual description
+element description {
+   attribute id {xsd:NMTOKEN }?,
+
+   ## e.g pubmed ID
+   attribute attribution { identifier_Type }?,   
+   xsd:string
+}
+
+# ++ basic types ++
+ 
+identifier_Type = xsd:string
+name_Type = xsd:string
+classId_Type = xsd:NMTOKEN
+
+  


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[Obo-svn-commit] SF.net SVN: obo: [598] phenote/trunk/conf

From: <mg...@us...> - 2007-05-16 17:29:59

Revision: 598
          http://svn.sourceforge.net/obo/?rev=598&view=rev
Author:   mgibson
Date:     2007-05-16 10:29:59 -0700 (Wed, 16 May 2007)

Log Message:
-----------
updated a little with new styles - daunting to do it all

Modified Paths:
--------------
    phenote/trunk/conf/ncbo.cfg
    phenote/trunk/conf/zfin-standalone.cfg

Modified: phenote/trunk/conf/ncbo.cfg
===================================================================
--- phenote/trunk/conf/ncbo.cfg	2007-05-16 17:13:05 UTC (rev 597)
+++ phenote/trunk/conf/ncbo.cfg	2007-05-16 17:29:59 UTC (rev 598)
@@ -31,8 +31,10 @@
     <ns:ontology name="Relationship" file="relationship.obo" is-postcomp-rel="true"/>
     <ns:ontology name="FMA" file="fma_obo.obo"/>
     <ns:ontology name="EHDAA" file="human-dev-anat-abstract.obo"/>
-    <ns:ontology name="GO" file="gene_ontology.obo" repos-subdir="genomic-proteomic"/>
-    <ns:ontology name="CL" file="cell.obo" repos-subdir="anatomy/cell_type"/>
+    <ns:ontology name="GO"
+      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
+    <ns:ontology name="CL"
+      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo"/>
     <ns:ontology name="CHEBI" file="chebi.obo" repos-subdir="chemical"/>
   </ns:field>
 
@@ -45,9 +47,11 @@
     <ns:ontology name="Relationship" file="relationship.obo" is-postcomp-rel="true"/>
     <ns:ontology name="FMA" file="fma_obo.obo"/>
     <ns:ontology name="EHDAA" file="human-dev-anat-abstract.obo"/>
-    <ns:ontology name="GO" file="gene_ontology.obo" repos-subdir="genomic-proteomic"/>
+    <ns:ontology name="GO"
+      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
     <ns:ontology name="CHEBI" file="chebi.obo" repos-subdir="chemical"/>
-    <ns:ontology name="CL" file="cell.obo" repos-subdir="anatomy/cell_type"/>
+    <ns:ontology name="CL"
+      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo"/>
   </ns:field>
 
   <ns:field name="Abnormal" syntax-abbrev="Tag" enable="true">

Modified: phenote/trunk/conf/zfin-standalone.cfg
===================================================================
--- phenote/trunk/conf/zfin-standalone.cfg	2007-05-16 17:13:05 UTC (rev 597)
+++ phenote/trunk/conf/zfin-standalone.cfg	2007-05-16 17:29:59 UTC (rev 598)
@@ -41,7 +41,8 @@
   </ns:field>
 
   <ns:field name="Stage" syntax-abbrev="T" enable="true">
-    <ns:ontology name="Stage" file="zebrafish_anatomy.obo" namespace="zebrafish_stages"/>
+    <ns:ontology name="Stage"  namespace="zebrafish_stages" 
+      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/zebrafish_anatomy.obo"/>
   </ns:field>
 
   <ns:field name="Quality" syntax-abbrev="Q" enable="true">
@@ -50,11 +51,10 @@
   </ns:field>
 
   <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true">
-    <ns:ontology name="Relationship" file="relationship.obo"
-                 repos-subdir="OBO_REL" is-postcomp-rel="true"/>
-    <ns:ontology name="ZF" file="zebrafish_anatomy.obo"
-                 repos-subdir="anatomy/gross_anatomy/animal_gross_anatomy/fish" 
-                 namespace="zebrafish_anatomy"/>
+    <ns:ontology name="Relationship" is-postcomp-rel="true"
+      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/relationship.obo"/>
+    <ns:ontology name="ZF" namespace="zebrafish_anatomy"
+      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/zebrafish_anatomy.obo"/>
     <ns:ontology name="GO" file="gene_ontology.obo"/>
   </ns:field>
 


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[Obo-svn-commit] SF.net SVN: obo: [597] phenote/trunk/conf/so-xp.cfg

From: <mg...@us...> - 2007-05-16 17:13:07

Revision: 597
          http://svn.sourceforge.net/obo/?rev=597&view=rev
Author:   mgibson
Date:     2007-05-16 10:13:05 -0700 (Wed, 16 May 2007)

Log Message:
-----------
changed to new config style

Modified Paths:
--------------
    phenote/trunk/conf/so-xp.cfg

Modified: phenote/trunk/conf/so-xp.cfg
===================================================================
--- phenote/trunk/conf/so-xp.cfg	2007-05-16 16:28:29 UTC (rev 596)
+++ phenote/trunk/conf/so-xp.cfg	2007-05-16 17:13:05 UTC (rev 597)
@@ -8,14 +8,14 @@
 
   <uvic-graph enable="false"/>
 
-  <obo-repository url-dir="http://purl.org/obo/obo-all/"/>
-
   <field name="Term"  syntax-abbrev="Term">
-    <ontology name="SO" file="sequence.obo" repos-subdir="sequence" />
+    <ontology name="SO" file="http://purl.org/obo/obo-all/sequence/sequence.obo"/>
   </field>
+
   <field name="EquivalentTo"  syntax-abbrev="EquivalentTo">
-    <postcomp relationship-ontology="relationship.obo" repos-subdir="OBO_REL"/>
-    <ontology name="SO" file="sequence.obo" repos-subdir="sequence" />
+    <ontology name="Relationship" is-postcomp-rel="true" 
+       file="http://purl.org/obo/obo-all/OBO_REL/relationship.obo"/>
+    <ontology name="SO" file="http://purl.org/obo/obo-all/sequence/sequence.obo"/>
   </field>
 
 </phenote-configuration>


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[Obo-svn-commit] SF.net SVN: obo: [596] phenote/trunk/conf

From: <mg...@us...> - 2007-05-16 16:28:30

Revision: 596
          http://svn.sourceforge.net/obo/?rev=596&view=rev
Author:   mgibson
Date:     2007-05-16 09:28:29 -0700 (Wed, 16 May 2007)

Log Message:
-----------
zfin-web new style of ontology files, formatting

Modified Paths:
--------------
    phenote/trunk/conf/ncbo.cfg
    phenote/trunk/conf/zfin-standalone.cfg
    phenote/trunk/conf/zfin-web.cfg

Modified: phenote/trunk/conf/ncbo.cfg
===================================================================
--- phenote/trunk/conf/ncbo.cfg	2007-05-15 19:00:03 UTC (rev 595)
+++ phenote/trunk/conf/ncbo.cfg	2007-05-16 16:28:29 UTC (rev 596)
@@ -7,7 +7,8 @@
 
   <ns:log config-file="conf/log4j-standalone.xml"/>
 
-  <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>  <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>
+  <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
+  <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>
   <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="false"/>
   <ns:dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/>
 
@@ -17,11 +18,15 @@
   <ns:update-timer timer="0"/><!--set to 0 if you want to bypass the check; time in seconds-->
   
   <ns:obo-repository url-dir="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/>
+
   <ns:field name="Pub" syntax-abbrev="PUB" enable="true"/>
+
   <ns:field name="Genotype" syntax-abbrev="GT" enable="true"/>
+
   <ns:field name="Genetic Context" syntax-abbrev="GC" enable="true">
     <ns:ontology name="Genetic Context" file="context.obo"/>
   </ns:field>
+
   <ns:field name="Entity" syntax-abbrev="E" enable="true">
     <ns:ontology name="Relationship" file="relationship.obo" is-postcomp-rel="true"/>
     <ns:ontology name="FMA" file="fma_obo.obo"/>
@@ -30,10 +35,12 @@
     <ns:ontology name="CL" file="cell.obo" repos-subdir="anatomy/cell_type"/>
     <ns:ontology name="CHEBI" file="chebi.obo" repos-subdir="chemical"/>
   </ns:field>
+
   <ns:field name="Quality" syntax-abbrev="Q" enable="true">
     <ns:ontology name="PATO" file="quality.obo" repos-subdir="phenotype"/>
     <ns:ontology name="MP" file="mammalian_phenotype.obo" repos-subdir="phenotype"/>
   </ns:field>
+
   <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true">
     <ns:ontology name="Relationship" file="relationship.obo" is-postcomp-rel="true"/>
     <ns:ontology name="FMA" file="fma_obo.obo"/>
@@ -42,8 +49,11 @@
     <ns:ontology name="CHEBI" file="chebi.obo" repos-subdir="chemical"/>
     <ns:ontology name="CL" file="cell.obo" repos-subdir="anatomy/cell_type"/>
   </ns:field>
+
   <ns:field name="Abnormal" syntax-abbrev="Tag" enable="true">
     <ns:ontology name="Abnormal" file="quality.obo" slim="abnormal_slim"/>
   </ns:field>
+
   <ns:field name="Description" syntax-abbrev="Desc" enable="true"/>
+
 </ns:phenote-configuration>
\ No newline at end of file

Modified: phenote/trunk/conf/zfin-standalone.cfg
===================================================================
--- phenote/trunk/conf/zfin-standalone.cfg	2007-05-15 19:00:03 UTC (rev 595)
+++ phenote/trunk/conf/zfin-standalone.cfg	2007-05-16 16:28:29 UTC (rev 596)
@@ -23,7 +23,9 @@
   <ns:obo-repository url-dir="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/>
 
   <ns:field name="Pub" syntax-abbrev="PUB" enable="true"/>
+
   <ns:field name="Genotype" syntax-abbrev="GT" enable="true"/>
+
   <ns:field name="Genetic Context" syntax-abbrev="GC" enable="true">
     <ns:ontology name="Genetic Context" file="context.obo"/>
   </ns:field>

Modified: phenote/trunk/conf/zfin-web.cfg
===================================================================
--- phenote/trunk/conf/zfin-web.cfg	2007-05-15 19:00:03 UTC (rev 595)
+++ phenote/trunk/conf/zfin-web.cfg	2007-05-16 16:28:29 UTC (rev 596)
@@ -6,6 +6,9 @@
      <ontology name="GO" file="../data_transfer/gene_ontology.obo"/>
   </field>
 
-  <field name="Quality" file="../data_transfer/quality.obo"/>
+  <field name="Quality" syntax-abbrev="Q" enable="true">
+    <ontology name="PATO" file="../data_transfer/quality.obo"/>
+  </field>
 
+
 </phenote-configuration>


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