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[Obo-svn-commit] SF.net SVN: obo: [231] phenote/trunk/src/java/phenote/servlet/PhenoteBean. java

From: <cm...@us...> - 2006-11-30 23:53:23

Revision: 231
          http://svn.sourceforge.net/obo/?rev=231&view=rev
Author:   cmpich
Date:     2006-11-30 15:53:23 -0800 (Thu, 30 Nov 2006)

Log Message:
-----------
Fixed broken code

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/servlet/PhenoteBean.java

Modified: phenote/trunk/src/java/phenote/servlet/PhenoteBean.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/PhenoteBean.java	2006-11-30 23:51:39 UTC (rev 230)
+++ phenote/trunk/src/java/phenote/servlet/PhenoteBean.java	2006-11-30 23:53:23 UTC (rev 231)
@@ -129,7 +129,7 @@
   }
 
   private void removeStages(List<Link> parents) {
-    for()
+    
   }
 
   public List<Link> getChildren(){


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[Obo-svn-commit] SF.net SVN: obo: [230] phenote/trunk/src/web/WEB-INF/jsp/term_completion. jsp

From: <cm...@us...> - 2006-11-30 23:51:38

Revision: 230
          http://svn.sourceforge.net/obo/?rev=230&view=rev
Author:   cmpich
Date:     2006-11-30 15:51:39 -0800 (Thu, 30 Nov 2006)

Log Message:
-----------
Moved ajax html code into jsp pages

Added Paths:
-----------
    phenote/trunk/src/web/WEB-INF/jsp/term_completion.jsp

Added: phenote/trunk/src/web/WEB-INF/jsp/term_completion.jsp
===================================================================
--- phenote/trunk/src/web/WEB-INF/jsp/term_completion.jsp	                        (rev 0)
+++ phenote/trunk/src/web/WEB-INF/jsp/term_completion.jsp	2006-11-30 23:51:39 UTC (rev 230)
@@ -0,0 +1,11 @@
+<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core" %>
+<html>
+<body>
+<ul>
+  <c:forEach var="completionTerm" items="${formBean.completionTermList}">
+    <li onmouseover="getTermInfo('<c:out value="${completionTerm.ID}" />','<c:out value="${completionTerm.name}" />','<c:out value="${completionTerm.ontol}" />','<c:out value="${completionTerm.field}" />')" id='<c:out value="${completionTerm.ID}" />'
+        onclick="selectTerm('<c:out value="${completionTerm.name}" />','<c:out value="${completionTerm.field}" />')"><c:out value="${completionTerm.name}" /></li>
+  </c:forEach>
+</ul>
+</body>
+</html>
\ No newline at end of file


Property changes on: phenote/trunk/src/web/WEB-INF/jsp/term_completion.jsp
___________________________________________________________________
Name: svn:eol-style
   + native


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[Obo-svn-commit] SF.net SVN: obo: [229] phenote/trunk

From: <cm...@us...> - 2006-11-30 23:50:05

Revision: 229
          http://svn.sourceforge.net/obo/?rev=229&view=rev
Author:   cmpich
Date:     2006-11-30 15:49:58 -0800 (Thu, 30 Nov 2006)

Log Message:
-----------
Moved ajax html code into jsp pages

Modified Paths:
--------------
    phenote/trunk/build.xml
    phenote/trunk/jars/oboedit.jar
    phenote/trunk/jars/org.geneontology.jar
    phenote/trunk/obo-files/gene_ontology.obo
    phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
    phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java
    phenote/trunk/src/java/phenote/gui/field/CompletionTerm.java
    phenote/trunk/src/java/phenote/gui/field/FieldPanel.java
    phenote/trunk/src/java/phenote/jobs/OntologyUpdateJob.java
    phenote/trunk/src/java/phenote/servlet/PhenoteBean.java
    phenote/trunk/src/java/phenote/servlet/PhenoteController.java
    phenote/trunk/src/web/WEB-INF/web.xml

Added Paths:
-----------
    phenote/trunk/src/java/phenote/datamodel/RelationshipEnumeration.java
    phenote/trunk/src/java/phenote/presentation/
    phenote/trunk/src/java/phenote/presentation/tags/
    phenote/trunk/src/java/phenote/presentation/tags/RelationshipTag.java
    phenote/trunk/src/java/phenote/util/TermLinkComparator.java
    phenote/trunk/src/java/test/phenote/util/TermLinkComparatorTest.java
    phenote/trunk/src/web/WEB-INF/jsp/term_info.jsp
    phenote/trunk/src/web/WEB-INF/tld/
    phenote/trunk/src/web/WEB-INF/tld/phenote-tags.tld

Removed Paths:
-------------
    phenote/trunk/src/web/WEB-INF/jsp/ajax.jsp

Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml	2006-11-30 17:26:06 UTC (rev 228)
+++ phenote/trunk/build.xml	2006-11-30 23:49:58 UTC (rev 229)
@@ -22,6 +22,7 @@
     <property name="web-html" value="${env.PHENOTE_WEB_HTML}"/>
     <property name="web-jars" value="${env.PHENOTE_WEB_JAR_DIR}"/>
     <property name="web.xml-dir" value="${env.PHENOTE_WEB_XML_DIR}"/>
+    <property name="data_transfer" value="src/web/WEB-INF/data_transfer"/>
 
     <property name="lib" value="jars"/>
     <property name="jarfile" value="jars/phenote.jar"/>
@@ -195,6 +196,13 @@
         </jar>
     </target>
 
+    <target name="jar-web" depends="compile">
+        <jar destfile="${jarfile}">
+            <fileset dir="${classfiles}"/>
+            <fileset file="${conf}/*.cfg"/>
+        </jar>
+    </target>
+
     <!-- file=${obo}/*.obo -->
 
 
@@ -302,8 +310,14 @@
         </copy>
     </target>
 
-    <target name="war-init-dir" depends="jar, war-clean">
+    <target name="war-init-dir" depends="jar-web, war-clean">
         <mkdir dir="war-deployment"/>
+        <delete dir="${data_transfer}" />
+        <mkdir dir="${data_transfer}" />
+      <copy todir="${data_transfer}">
+          <fileset file="${obo}/**" />
+      </copy>
+
         <war destfile="war-deployment/phenote.war" webxml="src/web/WEB-INF/web.xml">
             <fileset dir="src/web">
                 <exclude name="perl/*" />
@@ -312,8 +326,8 @@
                 <exclude name="junit-4.0.jar" />
                 <exclude name="BrowserLauncher2-10rc4.jar" />
                 <exclude name="tomcat-servlet.jar" />
+              <exclude name="jsp-api.jar" />
             </lib>
-            <classes dir="${obo}" />
             <classes dir="${conf}" />
         </war>
     </target>

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

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

Modified: phenote/trunk/obo-files/gene_ontology.obo
===================================================================
--- phenote/trunk/obo-files/gene_ontology.obo	2006-11-30 17:26:06 UTC (rev 228)
+++ phenote/trunk/obo-files/gene_ontology.obo	2006-11-30 23:49:58 UTC (rev 229)
@@ -8,7 +8,9 @@
 subsetdef: goslim_yeast "Yeast GO slim"
 subsetdef: gosubset_prok "Prokaryotic GO subset"
 default-namespace: gene_ontology
-remark: geneontology.org version: Revision: 4.62
+remark: geneontology.org 
+data-version: 4.62
+version: 4.62
 
 [Term]
 id: GO:0000001

Added: phenote/trunk/src/java/phenote/datamodel/RelationshipEnumeration.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/RelationshipEnumeration.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/datamodel/RelationshipEnumeration.java	2006-11-30 23:49:58 UTC (rev 229)
@@ -0,0 +1,55 @@
+package phenote.datamodel;
+
+import org.geneontology.oboedit.datamodel.OBOProperty;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: Christian Pich
+ * Date: Nov 30, 2006
+ * Time: 3:19:18 PM
+ * To change this template use File | Settings | File Templates.
+ */
+
+// Note: The 'name' and 'id' attribute are not consistent with underscores etc.
+//
+public enum RelationshipEnumeration {
+  IS_A(OBOProperty.IS_A.getName(), 1),
+  PART_OF("part of", 2) {
+    boolean matches(String name) {
+      return name.equals("part of") || name.equals("part_of");
+    }
+  },
+  PART_OF_("part_of", 3),
+  DEVELOPS_FROM("develops from", 3),
+  START_STAGE("start stage", 4),
+  END_STAGE("end stage", 5);
+
+  private String name;
+  private int index;
+
+  RelationshipEnumeration(String name, int index) {
+    this.name = name;
+    this.index = index;
+  }
+
+  boolean matches(String name) {
+    return this.name.equals(name);
+  }
+
+  public String getName() {
+    return name;
+  }
+
+  public int getIndex() {
+    return index;
+  }
+
+  static public RelationshipEnumeration getRelationshipEnum(String name) {
+    for (RelationshipEnumeration item : values()) {
+      if (item.matches(name))
+        return item;
+    }
+    return null;
+  }
+
+}

Modified: phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2006-11-30 17:26:06 UTC (rev 228)
+++ phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2006-11-30 23:49:58 UTC (rev 229)
@@ -4,7 +4,6 @@
 import java.awt.Font;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.awt.event.KeyAdapter;
 import java.awt.event.KeyEvent;
 import java.util.Vector;
 import javax.swing.ComboBoxEditor;
@@ -24,19 +23,11 @@
 
 import org.apache.log4j.Logger;
 
-import org.geneontology.oboedit.datamodel.OBOClass;
-import org.geneontology.oboedit.datamodel.OBOProperty;
-
 import phenote.datamodel.CharField;
 import phenote.datamodel.CharacterI;
 //import phenote.datamodel.CharFieldEnum;
 //import phenote.datamodel.CharacterI;
 //import phenote.datamodel.Ontology;
-import phenote.edit.EditManager;
-import phenote.edit.UpdateTransaction;
-import phenote.gui.selection.SelectionManager;
-import phenote.gui.selection.UseTermEvent;
-import phenote.gui.selection.UseTermListener;
 
 /** The jcombobox that does auto completion - i had to do some tricks(hacks) to get it
     working with mouse over which doesnt come naturally to jcombobox */
@@ -107,7 +98,7 @@
   //void setSearchParams(SearchParamsI sp) { searchParams = sp; }
 
   void setCharField(CharField charField) { this.charField = charField; }
-  
+
   protected CharField getCharField() { return charField; }
 
   protected boolean editModelEnabled() { return editModel; }
@@ -194,13 +185,13 @@
       getDocument().addDocumentListener(dl);
     }
   }
-  
 
+
   /** AutoTextField inner class - ignores set text when in
    * changingCompletionList mode - this is the text field for the
    combo box */
   private class AutoTextField extends JTextField {
-    
+
     private AutoTextField() {
       super(25); // width
     }
@@ -210,7 +201,7 @@
         thus wont get completion on user selection, leaving popup hanging */
     public void setText(String text) {
       if (changingCompletionList)
-	return;
+  return;
       // this makes setText(text,true) turn to false (called from TextPhenote)
       // but this is needed from mouse release on selection set text
       // is called and will cause completion list to come up after sel
@@ -218,7 +209,7 @@
       //if (charField!=null)
       //log().debug(charField.getName()+" AutoTextField.setText ["+text+"]"+getCurrentTermRelName());
       //new Throwable().printStackTrace();
-      doCompletion = false; 
+      doCompletion = false;
       //this is problematic for syns & such where string is diff than term name
       // JComboBox sets this text AFTER got event and set to name
       //super.setText(text); 
@@ -232,14 +223,14 @@
         super.setText(getCurrentTermRelName()); // set to term name with syn select
       doCompletion = true;
     }
-    
+
     protected void processKeyEvent(KeyEvent e) {
       //boolean fiddle = KeyboardState.shouldProcess(e);
       super.processKeyEvent(e);
     }
   }
 
-    
+
   /** Return the name of the current term or relation - was gonna call this
       item name but that gets confused with "items" in combo box */
   protected abstract String getCurrentTermRelName();
@@ -328,13 +319,13 @@
 //       previousInput = newInput;
 //     return inputChanged;
 //   }
-  
+
   /** call Ontology to get a Vector of OBOClass's that contain "in"
       in ontology */
 //   private Vector<OBOClass> getTermsOld(String in) {
 //     // or CompletionList.getCompletionList(getOntology()) ??
 //     //CompletionList cl = CompletionList.getCompletionList();
-//     //return cl.getCompletionTerms(getOntology(),in,searchParams);
+//     //return cl.getCompletionTermList(getOntology(),in,searchParams);
 //     return ontology.getSearchTerms(in,searchParams); // vector of OBOClass's
 //   }
 
@@ -389,12 +380,12 @@
 //       super.layoutComboBox(parent,manager);
 //     }    
   }
-  
-  
 
+
+
    /** Listens for actions from combo boxes and edits model/character 
    * actions come from mouse select of term as well as return & tab  */
-  private class ComboBoxActionListener implements ActionListener {
+   private class ComboBoxActionListener implements ActionListener {
     //private OBOClass previousOboClass=null;
 
     private ComboBoxActionListener() {}
@@ -453,8 +444,8 @@
     // it appears to be ok to supress this entirely
     super.configureEditor(anEditor,anItem); // ??? supress
   }
-  
 
+
   protected abstract void editModel();
 
   private Logger log;
@@ -466,7 +457,7 @@
     autoTextField.processKeyEvent(new KeyEvent(this,KeyEvent.KEY_PRESSED,0,0,KeyEvent.VK_L,'l'));
     autoTextField.processKeyEvent(new KeyEvent(this,KeyEvent.KEY_TYPED,0,0,KeyEvent.VK_UNDEFINED,'l'));
   }
-  
+
   public void simulateKeyStroke(int keyCode, char c) {
     KeyEvent k = new KeyEvent(this,KeyEvent.KEY_PRESSED,0,0,keyCode,c);
     autoTextField.processKeyEvent(k);

Modified: phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java	2006-11-30 17:26:06 UTC (rev 228)
+++ phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java	2006-11-30 23:49:58 UTC (rev 229)
@@ -46,6 +46,30 @@
       should input be just part of search params? 
       its a vector as thats what ComboBox requires 
       put in separate class? */
+  public List<CompletionTerm> getStringMatchTermList(String input) {
+   List<CompletionTerm> searchTerms = new ArrayList<CompletionTerm>();
+    if (input == null || input.equals(""))
+      return searchTerms;
+
+    // gets term set for currently selected ontology
+    //Set ontologyTermList = getCurrentOntologyTermSet();
+    List<OBOClass> ontologyTermList = ontology.getSortedTerms(); // non obsolete
+    searchTerms = getSearchTermList(input,ontologyTermList);
+
+    // if obsoletes set then add them in addition to regulars
+    if (searchParams.searchObsoletes()) {
+      ontologyTermList = ontology.getSortedObsoleteTerms();
+      List obsoletes = getSearchTermList(input,ontologyTermList);
+      searchTerms.addAll(obsoletes);
+    }
+    return searchTerms;
+  }
+
+  /** Returns a Vector of OBOClass from ontology that contain input string
+      constrained by compParams. compParams specifies syns,terms,defs,& obs
+      should input be just part of search params?
+      its a vector as thats what ComboBox requires
+      put in separate class? */
   public Vector<CompletionTerm> getStringMatchTerms(String input) {
    Vector<CompletionTerm> searchTerms = new Vector<CompletionTerm>();
     if (input == null || input.equals(""))
@@ -110,6 +134,25 @@
     }
     return searchTermList.getVector();
   }
+
+  /** helper fn for getSearchTerms(String,SearhParamsI) */
+  private List<CompletionTerm> getSearchTermList(String input,
+                                                List<OBOClass> ontologyTermList) {
+    SearchTermList searchTermList = new SearchTermList();
+    if (ontologyTermList == null)
+      return searchTermList.getList();
+
+    for (OBOClass oboClass : ontologyTermList) {
+
+      CompletionTerm ct = new CompletionTerm(oboClass);
+      if (ct.matches(input, searchParams)) {
+        searchTermList.addTerm(ct);
+      }
+
+    }
+    return searchTermList.getList();
+  }
+
   /** User input is already lower cased, this potentially adds oboClass to
    * searchTerms if input & compareTerm match. Puts it first if exact. 
    * for term names comp = obo, for syns comp is the syn. 
@@ -213,6 +256,18 @@
       sortedTerms.addAll(obsoletes);
       return sortedTerms;
     }
+
+    private List<CompletionTerm> getList() {
+      //startsWithTerms.addAll(containTerms); return startsWithTerms;
+      List<CompletionTerm> sortedTerms = new ArrayList<CompletionTerm>();
+      sortedTerms.addAll(startsWithTerms);
+      sortedTerms.addAll(containTerms);
+      sortedTerms.addAll(startsWithSyns);
+      sortedTerms.addAll(containSyns);
+      sortedTerms.addAll(definitions);
+      sortedTerms.addAll(obsoletes);
+      return sortedTerms;
+    }
   }
 }
 

Modified: phenote/trunk/src/java/phenote/gui/field/CompletionTerm.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/CompletionTerm.java	2006-11-30 17:26:06 UTC (rev 228)
+++ phenote/trunk/src/java/phenote/gui/field/CompletionTerm.java	2006-11-30 23:49:58 UTC (rev 229)
@@ -16,6 +16,11 @@
   private boolean exactMatch = false;
   private boolean startsWith = false;
   private boolean contains = false; // do we need this?
+  // These attributes are needed for the web ajax call
+  // because we do not keep a handle to the oboClass for the termInfo.
+  private String ontol;
+  // Need to track the active gui field for use term in termInfo
+  private String field;
 
   CompletionTerm(OBOClass term) {
     this.term = term;
@@ -118,4 +123,19 @@
     return false; // all above failed - no match
   }
 
+  public String getOntol() {
+    return ontol;
+  }
+
+  public void setOntol(String ontol) {
+    this.ontol = ontol;
+  }
+
+  public String getField() {
+    return field;
+  }
+
+  public void setField(String field) {
+    this.field = field;
+  }
 }

Modified: phenote/trunk/src/java/phenote/gui/field/FieldPanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/FieldPanel.java	2006-11-30 17:26:06 UTC (rev 228)
+++ phenote/trunk/src/java/phenote/gui/field/FieldPanel.java	2006-11-30 23:49:58 UTC (rev 229)
@@ -1,17 +1,11 @@
 package phenote.gui.field;
 
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.Container;
 import java.awt.Dimension;
 import java.awt.GridBagConstraints;
 import java.awt.GridBagLayout;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Vector;
 
-import javax.swing.DefaultComboBoxModel;
-import javax.swing.text.Document;
 import javax.swing.JButton;
 import javax.swing.JComboBox;
 import javax.swing.JComponent;
@@ -21,9 +15,7 @@
 import phenote.datamodel.CharField;
 import phenote.datamodel.CharFieldEnum;
 import phenote.datamodel.CharacterI;
-import phenote.datamodel.Ontology;
 import phenote.datamodel.OntologyManager;
-import phenote.config.FieldConfig;
 import phenote.gui.GridBagUtil;
 
 /**
@@ -374,7 +366,7 @@
 //     private void doCompletion() {
 //       String input = (String)comboBox.getEditor().getItem();
 //       CompletionList cl = CompletionList.getCompletionList();
-//       Vector v = cl.getCompletionTerms(ontology,input);
+//       Vector v = cl.getCompletionTermList(ontology,input);
 //       System.out.println(input + v);
 //       comboBox.setModel(new DefaultComboBoxModel(v));
 //     }

Modified: phenote/trunk/src/java/phenote/jobs/OntologyUpdateJob.java
===================================================================
--- phenote/trunk/src/java/phenote/jobs/OntologyUpdateJob.java	2006-11-30 17:26:06 UTC (rev 228)
+++ phenote/trunk/src/java/phenote/jobs/OntologyUpdateJob.java	2006-11-30 23:49:58 UTC (rev 229)
@@ -38,9 +38,11 @@
         OntologyDataAdapter ontReader = OntologyDataAdapter.getInstance();
         ontReader.reloadOntology(ontology);
 
+/*
         File archiveFile = FileUtil.archiveFile(newFile, PhenoteWebConfiguration.getInstance().getWebRoot(), archiveDirectory);
         long purgePeriodInMilliseconds = (long) (purgePeriodInDays * MILLISECONDS_PER_DAY );
         FileUtil.purgeArchiveDirectory(archiveFile.getParentFile(), purgePeriodInMilliseconds);
+*/
       }
     } catch (Exception e) {
       LOG.error(e.getMessage(), e);

Added: phenote/trunk/src/java/phenote/presentation/tags/RelationshipTag.java
===================================================================
--- phenote/trunk/src/java/phenote/presentation/tags/RelationshipTag.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/presentation/tags/RelationshipTag.java	2006-11-30 23:49:58 UTC (rev 229)
@@ -0,0 +1,104 @@
+package phenote.presentation.tags;
+
+import org.apache.commons.lang.StringUtils;
+import org.apache.struts.taglib.TagUtils;
+
+import javax.servlet.jsp.tagext.TagSupport;
+import javax.servlet.jsp.tagext.Tag;
+import javax.servlet.jsp.JspException;
+import java.io.IOException;
+
+import phenote.util.TermLinkComparator;
+import phenote.datamodel.RelationshipEnumeration;
+
+/**
+ * Tag that creates the display name for a relationship of a term to a child or a parent.
+ */
+public class RelationshipTag extends TagSupport {
+
+  private String type;
+  private String beanName;
+  private String property;
+  private String scope;
+
+
+  public int doStartTag() throws JspException {
+
+      // Default scope is 'Page' scope
+      if (StringUtils.isEmpty(scope))
+          scope = "Page";
+      String relationshipString = (String) TagUtils.getInstance().lookup(pageContext, beanName, property, scope);
+
+      StringBuilder sb = new StringBuilder();
+      if (type != null && type.equals("parent")) {
+        if(relationshipString != null && relationshipString.equals(RelationshipEnumeration.IS_A.getName()))
+          sb.append("Is a type of");
+        if(relationshipString != null && relationshipString.equals(RelationshipEnumeration.PART_OF.getName()))
+          sb.append("Is part of");
+        if(relationshipString != null && relationshipString.equals(RelationshipEnumeration.DEVELOPS_FROM.getName()))
+          sb.append("Develops from");
+      } else if (type != null && type.equals("child")) {
+        if(relationshipString != null && relationshipString.equals(RelationshipEnumeration.IS_A.getName()))
+          sb.append("Has subtype");
+        if(relationshipString != null && relationshipString.equals(RelationshipEnumeration.PART_OF.getName()))
+          sb.append("Has parts");
+        if(relationshipString != null && relationshipString.equals(RelationshipEnumeration.DEVELOPS_FROM.getName()))
+          sb.append("Develops into");
+      }
+
+      try {
+          pageContext.getOut().print(sb);
+      } catch (IOException ioe) {
+          throw new JspException("Error: IOException while writing to client" + ioe.getMessage());
+      }
+      release();
+      return Tag.SKIP_BODY;
+  }
+
+  /**
+   * Release all allocated resources.
+   */
+  public void release() {
+      super.release();
+
+      type = null;
+      property = null;
+      beanName =null;
+      id = null;
+      scope = null;
+
+  }
+
+
+
+  public String getType() {
+      return type;
+  }
+
+  public void setType(String type) {
+      this.type = type;
+  }
+
+  public String getBeanName() {
+      return beanName;
+  }
+
+  public void setBeanName(String beanName) {
+      this.beanName = beanName;
+  }
+  public String getScope() {
+      return scope;
+  }
+
+  public void setScope(String scope) {
+      this.scope = scope;
+  }
+
+  public String getProperty() {
+    return property;
+  }
+
+  public void setProperty(String property) {
+    this.property = property;
+  }
+}

Modified: phenote/trunk/src/java/phenote/servlet/PhenoteBean.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/PhenoteBean.java	2006-11-30 17:26:06 UTC (rev 228)
+++ phenote/trunk/src/java/phenote/servlet/PhenoteBean.java	2006-11-30 23:49:58 UTC (rev 229)
@@ -1,7 +1,15 @@
 package phenote.servlet;
 
 import org.apache.commons.lang.StringUtils;
+import org.geneontology.oboedit.datamodel.OBOClass;
+import org.geneontology.oboedit.datamodel.Link;
+import phenote.gui.field.CompletionTerm;
+import phenote.util.TermLinkComparator;
 
+import java.util.List;
+import java.util.Collections;
+import java.util.ArrayList;
+
 /**
  * This is the main form bean that contains all request parameters.
  * Spring populates these attributes automatically and make them available
@@ -16,7 +24,9 @@
   private String termId;
   private String field;
 
-  private String ajaxList;
+  private String ajaxReturn;
+  private List<CompletionTerm> completionTermList;
+  private OBOClass term;
 
   public boolean isTermCompletionRequest() {
     if (!StringUtils.isEmpty(userInput))
@@ -82,12 +92,12 @@
     this.field = field;
   }
 
-  public String getAjaxList() {
-    return ajaxList;
+  public String getAjaxReturnList() {
+    return ajaxReturn;
   }
 
-  public void setAjaxList(String ajaxList) {
-    this.ajaxList = ajaxList;
+  public void setAjaxReturnList(String ajaxReturnList) {
+    this.ajaxReturn = ajaxReturnList;
   }
 
   public String getTermId() {
@@ -98,5 +108,39 @@
     this.termId = termId;
   }
 
+  public List<CompletionTerm> getCompletionTermList() {
+    return completionTermList;
+  }
+
+  public void setCompletionTermList(List<CompletionTerm> completionTermList) {
+    this.completionTermList = completionTermList;
+  }
+
+  public OBOClass getTerm() {
+    return term;
+  }
+
+  public List<Link> getParents(){
+    List<Link> parents = new ArrayList<Link>();
+    parents.addAll(term.getParents());
+    removeStages(parents);
+    Collections.sort(parents, new TermLinkComparator());
+    return parents;
+  }
+
+  private void removeStages(List<Link> parents) {
+    for()
+  }
+
+  public List<Link> getChildren(){
+    List<Link> children = new ArrayList<Link>();
+    children.addAll(term.getChildren());
+    Collections.sort(children, new TermLinkComparator());
+    return children;
+  }
+
+  public void setTerm(OBOClass term) {
+    this.term = term;
+  }
 }
 

Modified: phenote/trunk/src/java/phenote/servlet/PhenoteController.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/PhenoteController.java	2006-11-30 17:26:06 UTC (rev 228)
+++ phenote/trunk/src/java/phenote/servlet/PhenoteController.java	2006-11-30 23:49:58 UTC (rev 229)
@@ -1,5 +1,5 @@
-package phenote.servlet;
-
+package phenote.servlet;
+
 import org.apache.log4j.Logger;
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
@@ -18,6 +18,7 @@
 import phenote.util.HtmlUtil;
 
 import java.util.Vector;
+import java.util.List;
 
 /**
  * The main controller that receives Ajax ontology requests.
@@ -42,27 +43,49 @@
       LOG.info("param entityInput: " + userInput);
       LOG.info("Field entity: " + field);
 
-      form.setAjaxList(getCompletionList(userInput, ontologyName, field));
-      LOG.debug(form.getAjaxList());
+      form.setCompletionTermList(getCompletionList(userInput, ontologyName, field));
+      LOG.debug(form.getAjaxReturnList());
     } else if (form.isTermInfoRequest()) {
       String termId = form.getTermId();
       LOG.debug("doGet term info param: " + termId + " ont " + ontologyName);
       try {
         Ontology ont = getOntology(ontologyName);
+        // ToDo: Put oboClass in the web session, then we do not need to pass in the ontology name in
+        // the html ajax call
         OBOClass oboClass = ont.getOboClass(termId);
-        String termInfo = HtmlUtil.termInfo(oboClass);
-        LOG.debug("term info " + termInfo.substring(0,60));
-        String termInfoObo = HtmlUtil.termInfo(oboClass, ontologyName, field);
-        form.setAjaxList(termInfoObo);
+        form.setTerm(oboClass);
+        return new ModelAndView("term_info", "formBean", form);
       }
       catch (OntologyException e) {
         LOG.error(e.getMessage(), e);
       }
     }
-    return new ModelAndView("ajax", "formBean", form);
+    return new ModelAndView("term_completion", "formBean", form);
   }
 
+  private List<CompletionTerm> getCompletionList(String userInput, String ontologyName, String field) {
+    List<CompletionTerm> termList = null;
+    try {
+      termList = getCompListSearcher(ontologyName).getStringMatchTermList(userInput);
+    } catch (OntologyException e) {
+      // Todo: Add this error as an error completion list
+      LOG.error(e.getMessage(), e);
+    }
+    includeAdditionalAttributes(termList, ontologyName, field);
+    return termList;
+  }
 
+  private void includeAdditionalAttributes(List<CompletionTerm> termList, String ontologyName, String field) {
+    if (termList == null)
+      return;
+
+    for (CompletionTerm term : termList) {
+      term.setField(field);
+      term.setOntol(ontologyName);
+    }
+  }
+
+
   /**
    * ToDo: Need to cleanup this comment.
    * List<String>? String[]? or String htmlLiString?
@@ -76,7 +99,7 @@
    * @param ontologyName
    * @param field
    */
-  private String getCompletionList(String userInput, String ontologyName, String field) {
+  private String getHtmlCompletionList(String userInput, String ontologyName, String field) {
     StringBuffer sb = new StringBuffer("<ul>");
     try {
       Vector<CompletionTerm> v = getCompListSearcher(ontologyName).getStringMatchTerms(userInput);
@@ -95,16 +118,16 @@
     return sb.toString();
   }
 
-  private String makeCompListHtmlItem(CompletionTerm term, String ontol,String field) {
+  private String makeCompListHtmlItem(CompletionTerm term, String ontol, String field) {
     String id = term.getID();
     String display = term.getCompListDisplayString();
     String name = term.getName();
     // pass in id, name & ontology - name for setting field on UseTerm
-    StringBuffer info = dq(fn("getTermInfo",new String[]{id,name,ontol,field}));
-    StringBuffer select = dq(fn("selectTerm",new String[]{name,field}));
+    StringBuffer info = dq(fn("getTermInfo", new String[]{id, name, ontol, field}));
+    StringBuffer select = dq(fn("selectTerm", new String[]{name, field}));
     //String info = "\"getTermInfo("+id +","+q(name)+","+ q(ontol) + ")\"";
     return "<li onmouseover=" + info + " id=" + q(id) + " termTest='dude' " +
-      " onclick=" + select + ">" + display + "</li>\n";
+            " onclick=" + select + ">" + display + "</li>\n";
   }
 
   private CompListSearcher getCompListSearcher(String ontologyName) throws OntologyException {

Added: phenote/trunk/src/java/phenote/util/TermLinkComparator.java
===================================================================
--- phenote/trunk/src/java/phenote/util/TermLinkComparator.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/util/TermLinkComparator.java	2006-11-30 23:49:58 UTC (rev 229)
@@ -0,0 +1,83 @@
+package phenote.util;
+
+import org.geneontology.oboedit.datamodel.Link;
+import org.geneontology.oboedit.datamodel.OBOProperty;
+
+import java.util.Comparator;
+
+/**
+ * Sort term
+ */
+public class TermLinkComparator implements Comparator<Link> {
+
+  // Note: The 'name' and 'id' attribute are not consistent with underscores etc.
+  //
+  public enum RelationshipEnum {
+    IS_A(OBOProperty.IS_A.getName(), 1),
+    PART_OF("part of", 2) {
+      boolean matches(String name) {
+        return name.equals("part of") || name.equals("part_of");
+      }
+    },
+    PART_OF_("part_of", 3),
+    DEVELOPS_FROM("develops from", 3),
+    START_STAGE("start stage", 4),
+    END_STAGE("end stage", 5);
+
+    private String name;
+    private int index;
+
+    RelationshipEnum(String name, int index) {
+      this.name = name;
+      this.index = index;
+    }
+
+    boolean matches(String name) {
+      return this.name.equals(name);
+    }
+
+    public String getName() {
+      return name;
+    }
+
+    public int getIndex() {
+      return index;
+    }
+
+    static public RelationshipEnum getRelationshipEnum(String name) {
+      for (RelationshipEnum item : values()) {
+        if (item.matches(name))
+          return item;
+      }
+      return null;
+    }
+  }
+
+  public int compare(Link link1, Link link2) {
+
+
+    OBOProperty type = link1.getType();
+    if (type.equals(link2.getType()))
+      return 0;
+
+    String name1 = link1.getType().getID();
+    String name2 = link2.getType().getID();
+
+    RelationshipEnum relationship1 = RelationshipEnum.getRelationshipEnum(name1);
+    RelationshipEnum relationship2 = RelationshipEnum.getRelationshipEnum(name2);
+
+    if (relationship1 != null && relationship2 != null) {
+      return relationship1.getIndex() - relationship2.getIndex();
+    }
+
+    if (relationship1 != null && relationship2 == null) {
+      return -1;
+    }
+
+    if (relationship2 != null && relationship1 == null) {
+      return 1;
+    }
+
+    return name1.compareTo(name2);
+  }
+}

Added: phenote/trunk/src/java/test/phenote/util/TermLinkComparatorTest.java
===================================================================
--- phenote/trunk/src/java/test/phenote/util/TermLinkComparatorTest.java	                        (rev 0)
+++ phenote/trunk/src/java/test/phenote/util/TermLinkComparatorTest.java	2006-11-30 23:49:58 UTC (rev 229)
@@ -0,0 +1,90 @@
+package phenote.util;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+import junit.textui.TestRunner;
+import org.geneontology.oboedit.datamodel.Link;
+import org.geneontology.oboedit.datamodel.OBOProperty;
+import org.geneontology.oboedit.datamodel.impl.InstancePropertyValue;
+import org.geneontology.oboedit.datamodel.impl.OBOPropertyImpl;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+/**
+ * Unit test class for FileUtil.
+ */
+public class TermLinkComparatorTest extends TestCase {
+
+  public static void main(String args[]) {
+    TestRunner.run(TermLinkComparatorTest.suite());
+  }
+
+  public static Test suite() {
+    return new TestSuite(TermLinkComparatorTest.class);
+  }
+
+  /**
+   * Create a single file and archive it. Make sure it moved into the archive directory.
+   */
+  public void testIS_A_Before_PART_Of() {
+    List<InstancePropertyValue> links = new ArrayList<InstancePropertyValue>();
+    links.add(getLinkUnknownOne());
+    links.add(getLinkUnknownTwo());
+    links.add(getLinkDevelops_From());
+    links.add(getLinkPart_Of());
+    links.add(getLinkIS_A());
+
+    Collections.sort(links, new TermLinkComparator());
+
+    Link link = (Link) links.get(0);
+    assertEquals("IS a first", "is_a", link.getType().getName());
+    link = (Link) links.get(1);
+    assertEquals("Part of is second", "part of", link.getType().getName());
+    link = (Link) links.get(2);
+    assertEquals("Part of is second", "develops from", link.getType().getName());
+    link = (Link) links.get(3);
+    assertEquals("IS a first", "Unknown A", link.getType().getName());
+    link = (Link) links.get(4);
+    assertEquals("IS a first", "Unknown B", link.getType().getName());
+
+  }
+
+  private InstancePropertyValue getLinkIS_A(){
+    InstancePropertyValue link = new InstancePropertyValue();
+    OBOProperty prop = new OBOPropertyImpl(TermLinkComparator.RelationshipEnum.IS_A.getName());
+    link.setType(prop);
+    return link;
+  }
+
+  private InstancePropertyValue getLinkPart_Of(){
+    InstancePropertyValue link = new InstancePropertyValue();
+    OBOProperty prop = new OBOPropertyImpl(TermLinkComparator.RelationshipEnum.PART_OF.getName());
+    link.setType(prop);
+    return link;
+  }
+
+  private InstancePropertyValue getLinkDevelops_From(){
+    InstancePropertyValue link = new InstancePropertyValue();
+    OBOProperty prop = new OBOPropertyImpl(TermLinkComparator.RelationshipEnum.DEVELOPS_FROM.getName());
+    link.setType(prop);
+    return link;
+  }
+
+  private InstancePropertyValue getLinkUnknownOne(){
+    InstancePropertyValue link = new InstancePropertyValue();
+    OBOProperty prop = new OBOPropertyImpl("Unknown B");
+    link.setType(prop);
+    return link;
+  }
+
+  private InstancePropertyValue getLinkUnknownTwo(){
+    InstancePropertyValue link = new InstancePropertyValue();
+    OBOProperty prop = new OBOPropertyImpl("Unknown A");
+    link.setType(prop);
+    return link;
+  }
+
+}

Deleted: phenote/trunk/src/web/WEB-INF/jsp/ajax.jsp
===================================================================
--- phenote/trunk/src/web/WEB-INF/jsp/ajax.jsp	2006-11-30 17:26:06 UTC (rev 228)
+++ phenote/trunk/src/web/WEB-INF/jsp/ajax.jsp	2006-11-30 23:49:58 UTC (rev 229)
@@ -1,6 +0,0 @@
-<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core" %>
-<html>
-<body>
-<c:out value="${formBean.ajaxList}" escapeXml="false"/>
-</body>
-</html>
\ No newline at end of file

Added: phenote/trunk/src/web/WEB-INF/jsp/term_info.jsp
===================================================================
--- phenote/trunk/src/web/WEB-INF/jsp/term_info.jsp	                        (rev 0)
+++ phenote/trunk/src/web/WEB-INF/jsp/term_info.jsp	2006-11-30 23:49:58 UTC (rev 229)
@@ -0,0 +1,29 @@
+<%@ taglib prefix="phenote"    uri="/WEB-INF/tld/phenote-tags.tld"%>
+<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core" %>
+<html>
+<body>
+
+<b>TERM: </b><c:out value="${formBean.term.name}" />
+<br><b>ID: </b><c:out value="${formBean.term.ID}" />
+<c:forEach var="synonym" items="${formBean.term.synonyms}" >
+  <br><b>Synonym: </b>  <c:out value="${synonym}" />
+</c:forEach>
+<br>
+<br><b>PARENTS: </b>
+<c:forEach var="parent" items="${formBean.parents}" >
+  <br><b> <phenote:relationhipName beanName="parent" property="type.name" type="parent" />
+  : </b><a href="javascript:;" onclick="getTermInfo('<c:out value="${parent.parent.ID}" />','<c:out value="${parent.parent.name}" />','<c:out value="${formBean.ontologyName}" />','<c:out value="${formBean.field}" />')">
+  <c:out value="${parent.parent.name}" /></a>
+</c:forEach>
+<br>
+<br><b>CHILDREN: </b>
+<c:forEach var="parent" items="${formBean.children}" >
+  <br><b>Subclass: </b><a href="javascript:;" onclick="getTermInfo('<c:out value="${parent.child.ID}" />','<c:out value="${parent.child.name}" />','<c:out value="${formBean.ontologyName}" />','<c:out value="${formBean.field}" />')">
+  <c:out value="${parent.child.name}" /></a>
+</c:forEach>
+
+<br>
+<br><b>Definition: </b><c:out value="${formBean.term.definition}" escapeXml="false"/>
+
+</body>
+</html>
\ No newline at end of file

Added: phenote/trunk/src/web/WEB-INF/tld/phenote-tags.tld
===================================================================
--- phenote/trunk/src/web/WEB-INF/tld/phenote-tags.tld	                        (rev 0)
+++ phenote/trunk/src/web/WEB-INF/tld/phenote-tags.tld	2006-11-30 23:49:58 UTC (rev 229)
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="ISO-8859-1" ?>
+<!DOCTYPE taglib PUBLIC "-//Sun Microsystems, Inc.//DTD JSP Tag Library 1.1//EN" "http://java.sun.com/j2ee/dtds/web-jsptaglibrary_1_1.dtd">
+<!-- a tag library descriptor -->
+
+<taglib>
+    <tlibversion>1.0</tlibversion>
+    <jspversion>1.1</jspversion>
+    <shortname>first</shortname>
+    <uri></uri>
+    <info>Tab library for recurring phenote businesses</info>
+
+    <tag>
+        <name>relationhipName</name>
+        <tagclass>phenote.presentation.tags.RelationshipTag</tagclass>
+        <info>Create the proper relationhip name for display</info>
+        <attribute>
+            <name>beanName</name>
+            <required>true</required>
+            <rtexprvalue>false</rtexprvalue>
+        </attribute>
+        <attribute>
+            <name>property</name>
+            <required>true</required>
+            <rtexprvalue>false</rtexprvalue>
+        </attribute>
+<!--
+      child or parent
+-->
+        <attribute>
+            <name>type</name>
+            <required>false</required>
+            <rtexprvalue>false</rtexprvalue>
+        </attribute>
+        <attribute>
+            <name>scope</name>
+            <required>false</required>
+            <rtexprvalue>false</rtexprvalue>
+        </attribute>
+    </tag>
+
+</taglib>
\ No newline at end of file

Modified: phenote/trunk/src/web/WEB-INF/web.xml
===================================================================
--- phenote/trunk/src/web/WEB-INF/web.xml	2006-11-30 17:26:06 UTC (rev 228)
+++ phenote/trunk/src/web/WEB-INF/web.xml	2006-11-30 23:49:58 UTC (rev 229)
@@ -8,7 +8,7 @@
     <servlet-class>phenote.servlet.PhenoteServlet</servlet-class>
     <init-param>
        <param-name>configuration-file</param-name>
-       <param-value>/initial-zfin.cfg</param-value>
+       <param-value>/zfin-web.cfg</param-value>
     </init-param>
     <load-on-startup>1</load-on-startup>
   </servlet>


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[Obo-svn-commit] SF.net SVN: obo: [228] phenote/trunk/conf/zfin-web.cfg

From: <kev...@us...> - 2006-11-30 17:26:13

Revision: 228
          http://svn.sourceforge.net/obo/?rev=228&view=rev
Author:   kevinschaper
Date:     2006-11-30 09:26:06 -0800 (Thu, 30 Nov 2006)

Log Message:
-----------
slimmed down zfin config

Added Paths:
-----------
    phenote/trunk/conf/zfin-web.cfg

Added: phenote/trunk/conf/zfin-web.cfg
===================================================================
--- phenote/trunk/conf/zfin-web.cfg	                        (rev 0)
+++ phenote/trunk/conf/zfin-web.cfg	2006-11-30 17:26:06 UTC (rev 228)
@@ -0,0 +1,10 @@
+<phenote-configuration version="0.8" xmlns="phenote/config/xml">
+
+  <field name="Entity">
+     <ontology name="ZF" file="zebrafish_anatomy.obo" filter-out="ZFS:" />
+     <ontology name="GO" file="gene_ontology.obo"/>
+  </field>
+
+  <field name="Quality" file="quality.obo"/>
+
+</phenote-configuration>


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[Obo-svn-commit] SF.net SVN: obo: [227] phenote/trunk/src/java/phenote/util/HtmlUtil.java

From: <kev...@us...> - 2006-11-28 22:48:59

Revision: 227
          http://svn.sourceforge.net/obo/?rev=227&view=rev
Author:   kevinschaper
Date:     2006-11-28 14:48:59 -0800 (Tue, 28 Nov 2006)

Log Message:
-----------
changed term info link from href="#" to href="javascript:;"

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

Modified: phenote/trunk/src/java/phenote/util/HtmlUtil.java
===================================================================
--- phenote/trunk/src/java/phenote/util/HtmlUtil.java	2006-11-28 00:41:40 UTC (rev 226)
+++ phenote/trunk/src/java/phenote/util/HtmlUtil.java	2006-11-28 22:48:59 UTC (rev 227)
@@ -159,7 +159,7 @@
     if (isStandAlone)
       return "href='"+makePhenoIdLink(id)+"'";
     else // this needs some reworking - causes page refresh and goes to top
-      return "href=# "+onClickJavaScript(id,name);
+      return "href=" + dq("javascript:;") + onClickJavaScript(id,name);
   }
 
   /**<A href='#' onClick='getTermInfo("id","name","ontology")'> - added in name for


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[Obo-svn-commit] SF.net SVN: obo: [226] fma-conversion/trunk/fma_obo.obof1_2.obo

From: <cmu...@us...> - 2006-11-28 00:41:49

Revision: 226
          http://svn.sourceforge.net/obo/?rev=226&view=rev
Author:   cmungall
Date:     2006-11-27 16:41:40 -0800 (Mon, 27 Nov 2006)

Log Message:
-----------
reverted fma_obo.obo back to obof1.0; added new file for obof1.2

Added Paths:
-----------
    fma-conversion/trunk/fma_obo.obof1_2.obo

Added: fma-conversion/trunk/fma_obo.obof1_2.obo
===================================================================
--- fma-conversion/trunk/fma_obo.obof1_2.obo	                        (rev 0)
+++ fma-conversion/trunk/fma_obo.obof1_2.obo	2006-11-28 00:41:40 UTC (rev 226)
@@ -0,0 +1,466388 @@
+format-version: 1.2
+date: 15:09:2006 13:29
+saved-by: dilvan
+auto-generated-by: Protege OBO plugin version 1.0
+version: 0.1
+
+[Term]
+id: FMA:10000
+name: Eighth thoracic vertebral arch
+exact_synonym: "Arch of eighth thoracic vertebra" []
+exact_synonym: "Arch of T8 vertebra" []
+is_a: FMA:9151 ! Thoracic vertebral arch
+relationship: part_of FMA:9991 ! Eighth thoracic vertebra
+relationship: has_part FMA:10005 ! Spinous process of eighth thoracic vertebra
+relationship: has_part FMA:11906 ! Right inferior articular process of eighth thoracic vertebra
+relationship: has_part FMA:12060 ! Left lamina of eighth thoracic vertebra
+relationship: has_part FMA:28729 ! Periosteum of eighth thoracic vertebral arch
+relationship: has_part FMA:11901 ! Left transverse process of eighth thoracic vertebra
+relationship: has_part FMA:11895 ! Left pedicle of eighth thoracic vertebra
+relationship: has_part FMA:11904 ! Right superior articular process of eighth thoracic vertebra
+relationship: has_part FMA:29990 ! Bony part of eighth thoracic vertebral arch
+relationship: has_part FMA:11905 ! Left superior articular process of eighth thoracic vertebra
+relationship: has_part FMA:12059 ! Right lamina of eighth thoracic vertebra
+relationship: has_part FMA:11900 ! Right transverse process of eighth thoracic vertebra
+relationship: has_part FMA:11907 ! Left inferior articular process of eighth thoracic vertebra
+relationship: has_part FMA:11894 ! Right pedicle of eighth thoracic vertebra
+
+[Term]
+id: FMA:10001
+name: Pedicle of eighth thoracic vertebra
+exact_synonym: "Eighth thoracic vertebral pedicle" []
+exact_synonym: "Pedicle of T8 vertebra" []
+is_a: FMA:9152 ! Pedicle of thoracic vertebra
+
+[Term]
+id: FMA:10002
+name: Superior vertebral notch of eighth thoracic vertebra
+exact_synonym: "Superior vertebral incisure of pedicle of eighth thoracic vertebra" []
+is_a: FMA:9157 ! Superior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10003
+name: Inferior vertebral notch of eighth thoracic vertebra
+exact_synonym: "Inferior vertebral incisure of pedicle of eighth thoracic vertebra" []
+is_a: FMA:9158 ! Inferior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10004
+name: Lamina of eighth thoracic vertebra
+exact_synonym: "Eighth thoracic vertebral lamina" []
+is_a: FMA:9153 ! Lamina of thoracic vertebra
+
+[Term]
+id: FMA:10005
+name: Spinous process of eighth thoracic vertebra
+exact_synonym: "Spinous process of T8 vertebra" []
+is_a: FMA:9149 ! Spinous process of thoracic vertebra
+relationship: has_part FMA:30277 ! Bony part of spinous process of eighth thoracic vertebra
+relationship: part_of FMA:10000 ! Eighth thoracic vertebral arch
+relationship: has_part FMA:28957 ! Periosteum of spinous process of eighth thoracic vertebra
+
+[Term]
+id: FMA:10006
+name: Transverse process of eighth thoracic vertebra
+exact_synonym: "Transverse process of T8 vertebra" []
+is_a: FMA:9150 ! Transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10007
+name: Costal facet of transverse process of eighth thoracic vertebra
+exact_synonym: "Articular facet of transverse process of eighth thoracic vertebra" []
+is_a: FMA:10440 ! Costal facet of transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10008
+name: Vasculature of bony part of eighth thoracic vertebra
+is_a: FMA:9154 ! Vasculature of bony part of thoracic vertebra
+
+[Term]
+id: FMA:10009
+name: Superior articular process of eighth thoracic vertebra
+exact_synonym: "Cranial articular process of eighth thoracic vertebra" []
+is_a: FMA:9155 ! Superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10010
+name: Articular facet of superior articular process of eighth thoracic vertebra
+is_a: FMA:10521 ! Articular facet of superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10011
+name: Inferior articular process of eighth thoracic vertebra
+exact_synonym: "Caudal articular process of eighth thoracic vertebra" []
+is_a: FMA:9156 ! Inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10012
+name: Articular facet of inferior articular process of eighth thoracic vertebra
+is_a: FMA:9160 ! Articular facet of inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10013
+name: Intervertebral foramen of eighth thoracic vertebra
+is_a: FMA:9144 ! Intervertebral foramen of thoracic vertebra
+
+[Term]
+id: FMA:10014
+name: Ninth thoracic vertebra
+exact_synonym: "T9 vertebra" []
+exact_synonym: "Ninth dorsal vertebra" []
+is_a: FMA:9139 ! Thoracic vertebra
+relationship: has_part FMA:29784 ! Bony part of ninth thoracic vertebra
+relationship: part_of FMA:9140 ! Thoracic vertebral column
+relationship: has_part FMA:10015 ! Body of ninth thoracic vertebra
+relationship: has_part FMA:26724 ! Cartilage of ninth thoracic vertebra
+relationship: has_part FMA:28188 ! Periosteum of ninth thoracic vertebra
+relationship: part_of FMA:72064 ! Set of thoracic vertebrae
+relationship: has_part FMA:10023 ! Ninth thoracic vertebral arch
+relationship: has_part FMA:26688 ! Bone of ninth thoracic vertebra
+
+[Term]
+id: FMA:10015
+name: Body of ninth thoracic vertebra
+exact_synonym: "Ninth thoracic vertebral body" []
+exact_synonym: "Body of T9 vertebra" []
+is_a: FMA:9141 ! Body of thoracic vertebra
+relationship: has_part FMA:29899 ! Bony part of body of ninth thoracic vertebra
+relationship: has_part FMA:30368 ! Cartilage of body of ninth thoracic vertebra
+relationship: has_part FMA:26605 ! Central part of body of ninth thoracic vertebra
+relationship: part_of FMA:10014 ! Ninth thoracic vertebra
+relationship: has_part FMA:26637 ! Right posterolateral part of body of ninth thoracic vertebra
+relationship: has_part FMA:26247 ! Right neurocentral junction of ninth thoracic vertebra
+relationship: has_part FMA:28670 ! Periosteum of body of ninth thoracic vertebra
+relationship: has_part FMA:26638 ! Left posterolateral part of body of ninth thoracic vertebra
+relationship: has_part FMA:26248 ! Left neurocentral junction of ninth thoracic vertebra
+
+[Term]
+id: FMA:10016
+name: Anterior surface of body of ninth thoracic vertebra
+is_a: FMA:9147 ! Anterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10017
+name: Posterior surface of body of ninth thoracic vertebra
+is_a: FMA:9148 ! Posterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10018
+name: Lateral surface of body of ninth thoracic vertebra
+is_a: FMA:9162 ! Lateral surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10019
+name: Superior costal facet of body of ninth thoracic vertebra
+exact_synonym: "Superior costocapitular demifacet of body of ninth thoracic vertebra" []
+exact_synonym: "Upper costal facet of body of ninth thoracic vertebra" []
+is_a: FMA:9145 ! Superior costal facet of body of thoracic vertebra
+relationship: part_of FMA:8945 ! Joint of head of ninth rib
+
+[Term]
+id: FMA:10021
+name: Superior surface of body of ninth thoracic vertebra
+exact_synonym: "Upper border of body of ninth thoracic vertebra" []
+is_a: FMA:9163 ! Superior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10022
+name: Inferior surface of body of ninth thoracic vertebra
+exact_synonym: "Lower border of body of ninth thoracic vertebra" []
+is_a: FMA:9164 ! Inferior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10023
+name: Ninth thoracic vertebral arch
+exact_synonym: "Arch of T9 vertebra" []
+exact_synonym: "Arch of ninth thoracic vertebra" []
+is_a: FMA:9151 ! Thoracic vertebral arch
+relationship: has_part FMA:12064 ! Right lamina of ninth thoracic vertebra
+relationship: has_part FMA:11914 ! Right pedicle of ninth thoracic vertebra
+relationship: has_part FMA:11924 ! Right superior articular process of ninth thoracic vertebra
+relationship: has_part FMA:11920 ! Right transverse process of ninth thoracic vertebra
+relationship: has_part FMA:11921 ! Left transverse process of ninth thoracic vertebra
+relationship: has_part FMA:11926 ! Right inferior articular process of ninth thoracic vertebra
+relationship: has_part FMA:10028 ! Spinous process of ninth thoracic vertebra
+relationship: has_part FMA:29991 ! Bony part of ninth thoracic vertebral arch
+relationship: has_part FMA:12065 ! Left lamina of ninth thoracic vertebra
+relationship: has_part FMA:11915 ! Left pedicle of ninth thoracic vertebra
+relationship: has_part FMA:11927 ! Left inferior articular process of ninth thoracic vertebra
+relationship: has_part FMA:28730 ! Periosteum of ninth thoracic vertebral arch
+relationship: has_part FMA:11925 ! Left superior articular process of ninth thoracic vertebra
+relationship: part_of FMA:10014 ! Ninth thoracic vertebra
+
+[Term]
+id: FMA:10024
+name: Pedicle of ninth thoracic vertebra
+exact_synonym: "Pedicle of T9 vertebra" []
+exact_synonym: "Ninth thoracic vertebral pedicle" []
+is_a: FMA:9152 ! Pedicle of thoracic vertebra
+
+[Term]
+id: FMA:10025
+name: Superior vertebral notch of ninth thoracic vertebra
+exact_synonym: "Superior vertebral incisure of pedicle of ninth thoracic vertebra" []
+is_a: FMA:9157 ! Superior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10026
+name: Inferior vertebral notch of ninth thoracic vertebra
+exact_synonym: "Inferior vertebral incisure of pedicle of ninth thoracic vertebra" []
+is_a: FMA:9158 ! Inferior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10027
+name: Lamina of ninth thoracic vertebra
+exact_synonym: "Ninth thoracic vertebral lamina" []
+is_a: FMA:9153 ! Lamina of thoracic vertebra
+
+[Term]
+id: FMA:10028
+name: Spinous process of ninth thoracic vertebra
+exact_synonym: "Spinous process of T9 vertebra" []
+is_a: FMA:9149 ! Spinous process of thoracic vertebra
+relationship: has_part FMA:28958 ! Periosteum of spinous process of ninth thoracic vertebra
+relationship: has_part FMA:30278 ! Bony part of spinous process of ninth thoracic vertebra
+relationship: part_of FMA:10023 ! Ninth thoracic vertebral arch
+
+[Term]
+id: FMA:10029
+name: Transverse process of ninth thoracic vertebra
+exact_synonym: "Transverse process of T9 vertebra" []
+is_a: FMA:9150 ! Transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10030
+name: Costal facet of transverse process of ninth thoracic vertebra
+exact_synonym: "Articular facet of transverse process of ninth thoracic vertebra" []
+is_a: FMA:10440 ! Costal facet of transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10031
+name: Vasculature of bony part of ninth thoracic vertebra
+is_a: FMA:9154 ! Vasculature of bony part of thoracic vertebra
+
+[Term]
+id: FMA:10032
+name: Superior articular process of ninth thoracic vertebra
+exact_synonym: "Cranial articular process of ninth thoracic vertebra" []
+is_a: FMA:9155 ! Superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10033
+name: Articular facet of superior articular process of ninth thoracic vertebra
+is_a: FMA:10521 ! Articular facet of superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10034
+name: Inferior articular process of ninth thoracic vertebra
+exact_synonym: "Caudal articular process of ninth thoracic vertebra" []
+is_a: FMA:9156 ! Inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10035
+name: Articular facet of inferior articular process of ninth thoracic vertebra
+is_a: FMA:9160 ! Articular facet of inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10036
+name: Intervertebral foramen of ninth thoracic vertebra
+is_a: FMA:9144 ! Intervertebral foramen of thoracic vertebra
+
+[Term]
+id: FMA:10037
+name: Tenth thoracic vertebra
+exact_synonym: "Tenth dorsal vertebra" []
+exact_synonym: "T10 vertebra" []
+is_a: FMA:9139 ! Thoracic vertebra
+relationship: has_part FMA:10038 ! Body of tenth thoracic vertebra
+relationship: has_part FMA:10045 ! Tenth thoracic vertebral arch
+relationship: has_part FMA:26725 ! Cartilage of tenth thoracic vertebra
+relationship: has_part FMA:29785 ! Bony part of tenth thoracic vertebra
+relationship: has_part FMA:28189 ! Periosteum of tenth thoracic vertebra
+relationship: has_part FMA:26689 ! Bone of tenth thoracic vertebra
+relationship: part_of FMA:72064 ! Set of thoracic vertebrae
+relationship: part_of FMA:9140 ! Thoracic vertebral column
+
+[Term]
+id: FMA:10038
+name: Body of tenth thoracic vertebra
+exact_synonym: "Tenth thoracic vertebral body" []
+exact_synonym: "Body of T10 vertebra" []
+is_a: FMA:9141 ! Body of thoracic vertebra
+relationship: has_part FMA:26606 ! Central part of body of tenth thoracic vertebra
+relationship: part_of FMA:10037 ! Tenth thoracic vertebra
+relationship: has_part FMA:30369 ! Cartilage of body of tenth thoracic vertebra
+relationship: has_part FMA:26639 ! Right posterolateral part of body of tenth thoracic vertebra
+relationship: has_part FMA:26250 ! Left neurocentral junction of tenth thoracic vertebra
+relationship: has_part FMA:26249 ! Right neurocentral junction of tenth thoracic vertebra
+relationship: has_part FMA:29900 ! Bony part of body of tenth thoracic vertebra
+relationship: has_part FMA:28671 ! Periosteum of body of tenth thoracic vertebra
+relationship: has_part FMA:26640 ! Left posterolateral part of body of tenth thoracic vertebra
+
+[Term]
+id: FMA:10039
+name: Anterior surface of body of tenth thoracic vertebra
+is_a: FMA:9147 ! Anterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10040
+name: Posterior surface of body of tenth thoracic vertebra
+is_a: FMA:9148 ! Posterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10041
+name: Lateral surface of body of tenth thoracic vertebra
+is_a: FMA:9162 ! Lateral surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10042
+name: Superior costal facet of body of tenth thoracic vertebra
+exact_synonym: "Upper costal facet of body of tenth thoracic vertebra" []
+exact_synonym: "Superior costocapitular demifacet of body of tenth thoracic vertebra" []
+is_a: FMA:9145 ! Superior costal facet of body of thoracic vertebra
+relationship: part_of FMA:8948 ! Joint of head of tenth rib
+
+[Term]
+id: FMA:10043
+name: Superior surface of body of tenth thoracic vertebra
+exact_synonym: "Upper border of body of tenth thoracic vertebra" []
+is_a: FMA:9163 ! Superior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10044
+name: Inferior surface of body of tenth thoracic vertebra
+exact_synonym: "Lower border of body of tenth thoracic vertebra" []
+is_a: FMA:9164 ! Inferior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10045
+name: Tenth thoracic vertebral arch
+exact_synonym: "Arch of T10 vertebra" []
+exact_synonym: "Arch of tenth thoracic vertebra" []
+is_a: FMA:9151 ! Thoracic vertebral arch
+relationship: has_part FMA:12076 ! Right inferior articular process of tenth thoracic vertebra
+relationship: has_part FMA:29992 ! Bony part of tenth thoracic vertebral arch
+relationship: has_part FMA:11942 ! Left transverse process of tenth thoracic vertebra
+relationship: has_part FMA:10050 ! Spinous process of tenth thoracic vertebra
+relationship: has_part FMA:11935 ! Right pedicle of tenth thoracic vertebra
+relationship: has_part FMA:12077 ! Left inferior articular process of tenth thoracic vertebra
+relationship: has_part FMA:11936 ! Left pedicle of tenth thoracic vertebra
+relationship: has_part FMA:11941 ! Right transverse process of tenth thoracic vertebra
+relationship: has_part FMA:12069 ! Right lamina of tenth thoracic vertebra
+relationship: has_part FMA:28731 ! Periosteum of tenth thoracic vertebral arch
+relationship: has_part FMA:12070 ! Left lamina of tenth thoracic vertebra
+relationship: has_part FMA:12075 ! Left superior articular process of tenth thoracic vertebra
+relationship: has_part FMA:12074 ! Right superior articular process of tenth thoracic vertebra
+relationship: part_of FMA:10037 ! Tenth thoracic vertebra
+
+[Term]
+id: FMA:10046
+name: Pedicle of tenth thoracic vertebra
+exact_synonym: "Pedicle of T10 vertebra" []
+exact_synonym: "Tenth thoracic vertebral pedicle" []
+is_a: FMA:9152 ! Pedicle of thoracic vertebra
+
+[Term]
+id: FMA:10047
+name: Superior vertebral notch of tenth thoracic vertebra
+exact_synonym: "Superior vertebral incisure of pedicle of tenth thoracic vertebra" []
+is_a: FMA:9157 ! Superior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10048
+name: Inferior vertebral notch of tenth thoracic vertebra
+exact_synonym: "Inferior vertebral incisure of pedicle of tenth thoracic vertebra" []
+is_a: FMA:9158 ! Inferior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10049
+name: Lamina of tenth thoracic vertebra
+exact_synonym: "Tenth thoracic vertebral lamina" []
+is_a: FMA:9153 ! Lamina of thoracic vertebra
+
+[Term]
+id: FMA:10050
+name: Spinous process of tenth thoracic vertebra
+exact_synonym: "Spinous process of T10 vertebra" []
+is_a: FMA:9149 ! Spinous process of thoracic vertebra
+relationship: has_part FMA:30279 ! Bony part of spinous process of tenth thoracic vertebra
+relationship: has_part FMA:28959 ! Periosteum of spinous process of tenth thoracic vertebra
+relationship: part_of FMA:10045 ! Tenth thoracic vertebral arch
+
+[Term]
+id: FMA:10051
+name: Transverse process of tenth thoracic vertebra
+exact_synonym: "Transverse process of T10 vertebra" []
+is_a: FMA:9150 ! Transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10052
+name: Costal facet of transverse process of tenth thoracic vertebra
+exact_synonym: "Articular facet of transverse process of tenth thoracic vertebra" []
+is_a: FMA:10440 ! Costal facet of transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10053
+name: Vasculature of bony part of tenth thoracic vertebra
+is_a: FMA:9154 ! Vasculature of bony part of thoracic vertebra
+
+[Term]
+id: FMA:10054
+name: Superior articular process of tenth thoracic vertebra
+exact_synonym: "Cranial articular process of tenth thoracic vertebra" []
+is_a: FMA:9155 ! Superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10055
+name: Articular facet of superior articular process of tenth thoracic vertebra
+is_a: FMA:10521 ! Articular facet of superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10056
+name: Inferior articular process of tenth thoracic vertebra
+exact_synonym: "Caudal articular process of tenth thoracic vertebra" []
+is_a: FMA:9156 ! Inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10057
+name: Articular facet of inferior articular process of tenth thoracic vertebra
+is_a: FMA:9160 ! Articular facet of inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10058
+name: Intervertebral foramen of tenth thoracic vertebra
+is_a: FMA:9144 ! Intervertebral foramen of thoracic vertebra
+
+[Term]
+id: FMA:10059
+name: Eleventh thoracic vertebra
+exact_synonym: "T11 vertebra" []
+exact_synonym: "Eleventh dorsal vertebra" []
+is_a: FMA:9139 ! Thoracic vertebra
+relationship: part_of FMA:72064 ! Set of thoracic vertebrae
+relationship: has_part FMA:26726 ! Cartilage of eleventh thoracic vertebra
+relationship: has_part FMA:29786 ! Bony part of eleventh thoracic vertebra
+relationship: has_part FMA:26690 ! Bone of eleventh thoracic vertebra
+relationship: has_part FMA:10060 ! Body of eleventh thoracic vertebra
+relationship: part_of FMA:9140 ! Thoracic vertebral column
+relationship: has_part FMA:10067 ! Eleventh thoracic vertebral arch
+relationship: has_part FMA:28190 ! Periosteum of eleventh thoracic vertebra
+
+[Term]
+id: FMA:10060
+name: Body of eleventh thoracic vertebra
+exact_synonym: "Body of T11 vertebra" []
+exact_synonym: "Eleventh thoracic vertebral body" []
+is_a: FMA:9141 ! Body of thoracic vertebra
+relationship: has_part FMA:26607 ! Central part of body of eleventh thoracic vertebra
+relationship: has_part FMA:26252 ! Left neurocentral junction of eleventh thoracic vertebra
+relationship: has_part FMA:30370 ! Cartilage of body of eleventh thoracic vertebra
+relationship: has_part FMA:26642 ! Left posterolateral part of body of eleventh thoracic vertebra
+relationship: has_part FMA:26251 ! Right neurocentral junction of eleventh thoracic vertebra
+relationship: has_part FMA:29901 ! Bony part of body of eleventh thoracic vertebra
+relationship: has_part FMA:28672 ! Periosteum of body of eleventh thoracic vertebra
+relationship: part_of FMA:10059 ! Eleventh thoracic vertebra
+relationship: has_part FMA:26641 ! Right posterolateral part of body of eleventh thoracic vertebra
+
+[Term]
+id: FMA:10061
+name: Anterior surface of body of eleventh thoracic vertebra
+is_a: FMA:9147 ! Anterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10062
+name: Posterior surface of body of eleventh thoracic vertebra
+is_a: FMA:9148 ! Posterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10063
+name: Lateral surface of body of eleventh thoracic vertebra
+is_a: FMA:9162 ! Lateral surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10064
+name: Costal facet of body of eleventh thoracic vertebra
+exact_synonym: "Costocapitular demifacet of body of eleventh thoracic vertebra" []
+is_a: FMA:13577 ! Costal facet of body of thoracic vertebra
+relationship: part_of FMA:8951 ! Joint of head of eleventh rib
+
+[Term]
+id: FMA:10065
+name: Superior surface of body of eleventh thoracic vertebra
+exact_synonym: "Upper border of body of eleventh thoracic vertebra" []
+is_a: FMA:9163 ! Superior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10066
+name: Inferior surface of body of eleventh thoracic vertebra
+exact_synonym: "Lower border of body of eleventh thoracic vertebra" []
+is_a: FMA:9164 ! Inferior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10067
+name: Eleventh thoracic vertebral arch
+exact_synonym: "Arch of T11 vertebra" []
+exact_synonym: "Arch of eleventh thoracic vertebra" []
+is_a: FMA:9151 ! Thoracic vertebral arch
+relationship: has_part FMA:12086 ! Left pedicle of eleventh thoracic vertebra
+relationship: has_part FMA:12093 ! Right transverse process of eleventh thoracic vertebra
+relationship: has_part FMA:12088 ! Left lamina of eleventh thoracic vertebra
+relationship: has_part FMA:12085 ! Right pedicle of eleventh thoracic vertebra
+relationship: has_part FMA:12097 ! Right superior articular process of eleventh thoracic vertebra
+relationship: has_part FMA:12100 ! Left inferior articular process of eleventh thoracic vertebra
+relationship: has_part FMA:12094 ! Left transverse process of eleventh thoracic vertebra
+relationship: has_part FMA:29993 ! Bony part of eleventh thoracic vertebral arch
+relationship: has_part FMA:12099 ! Right inferior articular process of eleventh thoracic vertebra
+relationship: has_part FMA:28732 ! Periosteum of eleventh thoracic vertebral arch
+relationship: part_of FMA:10059 ! Eleventh thoracic vertebra
+relationship: has_part FMA:12098 ! Left superior articular process of eleventh thoracic vertebra
+relationship: has_part FMA:12087 ! Right lamina of eleventh thoracic vertebra
+relationship: has_part FMA:10072 ! Spinous process of eleventh thoracic vertebra
+
+[Term]
+id: FMA:10068
+name: Pedicle of eleventh thoracic vertebra
+exact_synonym: "Pedicle of T11 vertebra" []
+exact_synonym: "Eleventh thoracic vertebral pedicle" []
+is_a: FMA:9152 ! Pedicle of thoracic vertebra
+
+[Term]
+id: FMA:10069
+name: Superior vertebral notch of eleventh thoracic vertebra
+exact_synonym: "Superior vertebral incisure of pedicle of eleventh thoracic vertebra" []
+is_a: FMA:9157 ! Superior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10070
+name: Inferior vertebral notch of eleventh thoracic vertebra
+exact_synonym: "Inferior vertebral incisure of pedicle of eleventh thoracic vertebra" []
+is_a: FMA:9158 ! Inferior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10071
+name: Lamina of eleventh thoracic vertebra
+exact_synonym: "Eleventh thoracic vertebral lamina" []
+is_a: FMA:9153 ! Lamina of thoracic vertebra
+
+[Term]
+id: FMA:10072
+name: Spinous process of eleventh thoracic vertebra
+exact_synonym: "Spinous process of T11 vertebra" []
+is_a: FMA:9149 ! Spinous process of thoracic vertebra
+relationship: has_part FMA:30280 ! Bony part of spinous process of eleventh thoracic vertebra
+relationship: part_of FMA:10067 ! Eleventh thoracic vertebral arch
+relationship: has_part FMA:28960 ! Periosteum of spinous process of eleventh thoracic vertebra
+
+[Term]
+id: FMA:10073
+name: Transverse process of eleventh thoracic vertebra
+exact_synonym: "Transverse process of T11 vertebra" []
+is_a: FMA:9150 ! Transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10075
+name: Vasculature of bony part of eleventh thoracic vertebra
+is_a: FMA:9154 ! Vasculature of bony part of thoracic vertebra
+
+[Term]
+id: FMA:10076
+name: Superior articular process of eleventh thoracic vertebra
+exact_synonym: "Cranial articular process of eleventh thoracic vertebra" []
+is_a: FMA:9155 ! Superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10077
+name: Articular facet of superior articular process of eleventh thoracic vertebra
+is_a: FMA:10521 ! Articular facet of superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10078
+name: Inferior articular process of eleventh thoracic vertebra
+exact_synonym: "Caudal articular process of eleventh thoracic vertebra" []
+is_a: FMA:9156 ! Inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10079
+name: Articular facet of inferior articular process of eleventh thoracic vertebra
+is_a: FMA:9160 ! Articular facet of inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10080
+name: Intervertebral foramen of eleventh thoracic vertebra
+is_a: FMA:9144 ! Intervertebral foramen of thoracic vertebra
+
+[Term]
+id: FMA:10081
+name: Twelfth thoracic vertebra
+exact_synonym: "Twelfth dorsal vertebra" []
+exact_synonym: "T12 vertebra" []
+is_a: FMA:9139 ! Thoracic vertebra
+relationship: part_of FMA:72064 ! Set of thoracic vertebrae
+relationship: has_part FMA:29787 ! Bony part of twelfth thoracic vertebra
+relationship: part_of FMA:9140 ! Thoracic vertebral column
+relationship: has_part FMA:10089 ! Twelfth thoracic vertebral arch
+relationship: has_part FMA:10082 ! Body of twelfth thoracic vertebra
+relationship: has_part FMA:28191 ! Periosteum of twelfth thoracic vertebra
+relationship: has_part FMA:26691 ! Bone of twelfth thoracic vertebra
+relationship: has_part FMA:26727 ! Cartilage of twelfth thoracic vertebra
+
+[Term]
+id: FMA:10082
+name: Body of twelfth thoracic vertebra
+exact_synonym: "Twelfth thoracic vertebral body" []
+exact_synonym: "Body of T12 vertebra" []
+is_a: FMA:9141 ! Body of thoracic vertebra
+relationship: part_of FMA:10081 ! Twelfth thoracic vertebra
+relationship: has_part FMA:28673 ! Periosteum of body of twelfth thoracic vertebra
+relationship: has_part FMA:26253 ! Right neurocentral junction of twelfth thoracic vertebra
+relationship: has_part FMA:29902 ! Bony part of body of twelfth thoracic vertebra
+relationship: has_part FMA:26254 ! Left neurocentral junction of twelfth thoracic vertebra
+relationship: has_part FMA:26643 ! Right posterolateral part of body of twelfth thoracic vertebra
+relationship: has_part FMA:26608 ! Central part of body of twelfth thoracic vertebra
+relationship: has_part FMA:30371 ! Cartilage of body of twelfth thoracic vertebra
+relationship: has_part FMA:26644 ! Left posterolateral part of body of twelfth thoracic vertebra
+
+[Term]
+id: FMA:10083
+name: Anterior surface of body of twelfth thoracic vertebra
+is_a: FMA:9147 ! Anterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10084
+name: Posterior surface of body of twelfth thoracic vertebra
+is_a: FMA:9148 ! Posterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10085
+name: Lateral surface of body of twelfth thoracic vertebra
+is_a: FMA:9162 ! Lateral surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10087
+name: Superior surface of body of twelfth thoracic vertebra
+exact_synonym: "Upper border of body of twelfth thoracic vertebra" []
+is_a: FMA:9163 ! Superior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10088
+name: Inferior surface of body of twelfth thoracic vertebra
+exact_synonym: "Lower border of body of twelfth thoracic vertebra" []
+is_a: FMA:9164 ! Inferior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10089
+name: Twelfth thoracic vertebral arch
+exact_synonym: "Arch of T12 vertebra" []
+exact_synonym: "Arch of twelfth thoracic vertebra" []
+is_a: FMA:9151 ! Thoracic vertebral arch
+relationship: part_of FMA:10081 ! Twelfth thoracic vertebra
+relationship: has_part FMA:12111 ! Left lamina of twelfth thoracic vertebra
+relationship: has_part FMA:12108 ! Right pedicle of twelfth thoracic vertebra
+relationship: has_part FMA:28733 ! Periosteum of twelfth thoracic vertebral arch
+relationship: has_part FMA:12121 ! Left superior articular process of twelfth thoracic vertebra
+relationship: has_part FMA:12117 ! Left transverse process of twelfth thoracic vertebra
+relationship: has_part FMA:12122 ! Right inferior articular process of twelfth thoracic vertebra
+relationship: has_part FMA:29994 ! Bony part of twelfth thoracic vertebral arch
+relationship: has_part FMA:12109 ! Left pedicle of twelfth thoracic vertebra
+relationship: has_part FMA:12123 ! Left inferior articular process of twelfth thoracic vertebra
+relationship: has_part FMA:12110 ! Right lamina of twelfth thoracic vertebra
+relationship: has_part FMA:10094 ! Spinous process of twelfth thoracic vertebra
+relationship: has_part FMA:12116 ! Right transverse process of twelfth thoracic vertebra
+relationship: has_part FMA:12120 ! Right superior articular process of twelfth thoracic vertebra
+
+[Term]
+id: FMA:10090
+name: Pedicle of twelfth thoracic vertebra
+exact_synonym: "Twelfth thoracic vertebral pedicle" []
+exact_synonym: "Pedicle of T12 vertebra" []
+is_a: FMA:9152 ! Pedicle of thoracic vertebra
+
+[Term]
+id: FMA:10091
+name: Superior vertebral notch of twelfth thoracic vertebra
+exact_synonym: "Superior vertebral incisure of pedicle of twelfth thoracic vertebra" []
+is_a: FMA:9157 ! Superior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10092
+name: Inferior vertebral notch of twelfth thoracic vertebra
+exact_synonym: "Inferior vertebral incisure of pedicle of twelfth thoracic vertebra" []
+is_a: FMA:9158 ! Inferior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10093
+name: Lamina of twelfth thoracic vertebra
+exact_synonym: "Twelfth thoracic vertebral lamina" []
+is_a: FMA:9153 ! Lamina of thoracic vertebra
+
+[Term]
+id: FMA:10094
+name: Spinous process of twelfth thoracic vertebra
+exact_synonym: "Spinous process of T12 vertebra" []
+is_a: FMA:9149 ! Spinous process of thoracic vertebra
+relationship: part_of FMA:10089 ! Twelfth thoracic vertebral arch
+relationship: has_part FMA:28961 ! Periosteum of spinous process of twelfth thoracic vertebra
+relationship: has_part FMA:30281 ! Bony part of spinous process of twelfth thoracic vertebra
+
+[Term]
+id: FMA:10095
+name: Transverse process of twelfth thoracic vertebra
+exact_synonym: "Transverse process of T12 vertebra" []
+is_a: FMA:9150 ! Transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10096
+name: Vasculature of bony part of twelfth thoracic vertebra
+is_a: FMA:9154 ! Vasculature of bony part of thoracic vertebra
+
+[Term]
+id: FMA:10097
+name: Superior articular process of twelfth thoracic vertebra
+exact_synonym: "Cranial articular process of twelfth thoracic vertebra" []
+is_a: FMA:9155 ! Superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10098
+name: Articular facet of superior articular process of twelfth thoracic vertebra
+is_a: FMA:10521 ! Articular facet of superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10099
+name: Inferior articular process of twelfth thoracic vertebra
+exact_synonym: "Caudal articular process of twelfth thoracic vertebra" []
+is_a: FMA:9156 ! Inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10100
+name: Articular facet of inferior articular process of twelfth thoracic vertebra
+is_a: FMA:9160 ! Articular facet of inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10101
+name: Intervertebral foramen of twelfth thoracic vertebra
+is_a: FMA:9144 ! Intervertebral foramen of thoracic vertebra
+
+[Term]
+id: FMA:10102
+name: First costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10103
+name: Right first costochondral joint
+is_a: FMA:10102 ! First costochondral joint
+relationship: part_of FMA:7857 ! Right first rib
+
+[Term]
+id: FMA:10104
+name: Left first costochondral joint
+is_a: FMA:10102 ! First costochondral joint
+relationship: part_of FMA:7987 ! Left first rib
+
+[Term]
+id: FMA:10105
+name: Second costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10106
+name: Right second costochondral joint
+is_a: FMA:10105 ! Second costochondral joint
+relationship: part_of FMA:7882 ! Right second rib
+
+[Term]
+id: FMA:10107
+name: Left second costochondral joint
+is_a: FMA:10105 ! Second costochondral joint
+relationship: part_of FMA:8012 ! Left second rib
+
+[Term]
+id: FMA:10108
+name: Third costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10109
+name: Right third costochondral joint
+is_a: FMA:10108 ! Third costochondral joint
+relationship: part_of FMA:7909 ! Right third rib
+
+[Term]
+id: FMA:10110
+name: Left third costochondral joint
+is_a: FMA:10108 ! Third costochondral joint
+relationship: part_of FMA:8039 ! Left third rib
+
+[Term]
+id: FMA:10111
+name: Fourth costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10112
+name: Right fourth costochondral joint
+is_a: FMA:10111 ! Fourth costochondral joint
+relationship: part_of FMA:7957 ! Right fourth rib
+
+[Term]
+id: FMA:10113
+name: Left fourth costochondral joint
+is_a: FMA:10111 ! Fourth costochondral joint
+relationship: part_of FMA:8148 ! Left fourth rib
+
+[Term]
+id: FMA:10114
+name: Fifth costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10115
+name: Right fifth costochondral joint
+is_a: FMA:10114 ! Fifth costochondral joint
+relationship: part_of FMA:8066 ! Right fifth rib
+
+[Term]
+id: FMA:10116
+name: Left fifth costochondral joint
+is_a: FMA:10114 ! Fifth costochondral joint
+relationship: part_of FMA:8093 ! Left fifth rib
+
+[Term]
+id: FMA:10117
+name: Sixth costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10118
+name: Right sixth costochondral joint
+is_a: FMA:10117 ! Sixth costochondral joint
+relationship: part_of FMA:8175 ! Right sixth rib
+
+[Term]
+id: FMA:10119
+name: Left sixth costochondral joint
+is_a: FMA:10117 ! Sixth costochondral joint
+relationship: part_of FMA:8202 ! Left sixth rib
+
+[Term]
+id: FMA:10120
+name: Seventh costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10121
+name: Right seventh costochondral joint
+is_a: FMA:10120 ! Seventh costochondral joint
+relationship: part_of FMA:8229 ! Right seventh rib
+
+[Term]
+id: FMA:10122
+name: Left seventh costochondral joint
+is_a: FMA:10120 ! Seventh costochondral joint
+relationship: part_of FMA:8256 ! Left seventh rib
+
+[Term]
+id: FMA:10123
+name: Eighth costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10124
+name: Right eighth costochondral joint
+is_a: FMA:10123 ! Eighth costochondral joint
+relationship: part_of FMA:8283 ! Right eighth rib
+
+[Term]
+id: FMA:10125
+name: Left eighth costochondral joint
+is_a: FMA:10123 ! Eighth costochondral joint
+relationship: part_of FMA:8310 ! Left eighth rib
+
+[Term]
+id: FMA:10126
+name: Ninth costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10127
+name: Right ninth costochondral joint
+is_a: FMA:10126 ! Ninth costochondral joint
+relationship: part_of FMA:8364 ! Right ninth rib
+
+[Term]
+id: FMA:10128
+name: Left ninth costochondral joint
+is_a: FMA:10126 ! Ninth costochondral joint
+relationship: part_of FMA:8391 ! Left ninth rib
+
+[Term]
+id: FMA:10129
+name: Tenth costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10130
+name: Right tenth costochondral joint
+is_a: FMA:10129 ! Tenth costochondral joint
+relationship: part_of FMA:8445 ! Right tenth rib
+
+[Term]
+id: FMA:10131
+name: Left tenth costochondral joint
+is_a: FMA:10129 ! Tenth costochondral joint
+relationship: part_of FMA:8472 ! Left tenth rib
+
+[Term]
+id: FMA:10132
+name: Eleventh costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10133
+name: Right eleventh costochondral joint
+is_a: FMA:10132 ! Eleventh costochondral joint
+relationship: part_of FMA:8531 ! Right eleventh rib
+
+[Term]
+id: FMA:10134
+name: Left eleventh costochondral joint
+is_a: FMA:10132 ! Eleventh costochondral joint
+relationship: part_of FMA:8532 ! Left eleventh rib
+
+[Term]
+id: FMA:10135
+name: Twelfth costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10136
+name: Right twelfth costochondral joint
+is_a: FMA:10135 ! Twelfth costochondral joint
+relationship: part_of FMA:8533 ! Right twelfth rib
+
+[Term]
+id: FMA:10137
+name: Left twelfth costochondral joint
+is_a: FMA:10135 ! Twelfth costochondral joint
+relationship: part_of FMA:8534 ! Left twelfth rib
+
+[Term]
+id: FMA:10138
+name: Accessory ligament
+is_a: FMA:11106 ! Ligament of costotransverse joint
+relationship: part_of FMA:7952 ! Costotransverse joint
+
+[Term]
+id: FMA:10139
+name: First costotransverse joint
+is_a: FMA:7952 ! Costotransverse joint
+relationship: has_part FMA:10145 ! Lateral costotransverse ligament of first costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10142 ! Capsule of first costotransverse joint
+relationship: has_part FMA:10144 ! Costotransverse ligament of first costotransverse joint
+
+[Term]
+id: FMA:10140
+name: Capsule of costotransverse joint
+exact_synonym: "Costotransverse joint capsule" []
+exact_synonym: "Fibrous capsule of costotransverse joint" []
+is_a: FMA:34836 ! Articular capsule
+relationship: part_of FMA:7952 ! Costotransverse joint
+
+[Term]
+id: FMA:10141
+name: Second costotransverse joint
+is_a: FMA:7952 ! Costotransverse joint
+relationship: has_part FMA:10161 ! Accessory ligament of second costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10157 ! Capsule of second costotransverse joint
+relationship: has_part FMA:10158 ! Superior costotransverse ligament of second costotransverse joint
+relationship: has_part FMA:10159 ! Costotransverse ligament of second costotransverse joint
+relationship: has_part FMA:10160 ! Lateral costotransverse ligament of second costotransverse joint
+
+[Term]
+id: FMA:10142
+name: Capsule of first costotransverse joint
+exact_synonym: "First costotransverse joint capsule" []
+is_a: FMA:10140 ! Capsule of costotransverse joint
+relationship: part_of FMA:10139 ! First costotransverse joint
+
+[Term]
+id: FMA:10143
+name: Costotransverse foramen
+is_a: FMA:9338 ! Anatomical conduit
+
+[Term]
+id: FMA:10144
+name: Costotransverse ligament of first costotransverse joint
+is_a: FMA:12163 ! Costotransverse ligament
+relationship: part_of FMA:10139 ! First costotransverse joint
+
+[Term]
+id: FMA:10145
+name: Lateral costotransverse ligament of first costotransverse joint
+is_a: FMA:12162 ! Lateral costotransverse ligament
+relationship: part_of FMA:10139 ! First costotransverse joint
+
+[Term]
+id: FMA:10146
+name: First costotransverse foramen
+is_a: FMA:10143 ! Costotransverse foramen
+
+[Term]
+id: FMA:10147
+name: Right first costotransverse joint
+is_a: FMA:10139 ! First costotransverse joint
+relationship: has_part FMA:10148 ! Capsule of right first costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10150 ! Lateral costotransverse ligament of right first costotransverse joint
+relationship: has_part FMA:10149 ! Costotransverse ligament of right first costotransverse joint
+
+[Term]
+id: FMA:10148
+name: Capsule of right first costotransverse joint
+exact_synonym: "Right first costotransverse joint capsule" []
+is_a: FMA:10142 ! Capsule of first costotransverse joint
+relationship: part_of FMA:10147 ! Right first costotransverse joint
+
+[Term]
+id: FMA:10149
+name: Costotransverse ligament of right first costotransverse joint
+is_a: FMA:10144 ! Costotransverse ligament of first costotransverse joint
+relationship: part_of FMA:10147 ! Right first costotransverse joint
+
+[Term]
+id: FMA:10150
+name: Lateral costotransverse ligament of right first costotransverse joint
+is_a: FMA:10145 ! Lateral costotransverse ligament of first costotransverse joint
+relationship: part_of FMA:10147 ! Right first costotransverse joint
+
+[Term]
+id: FMA:10151
+name: Right first costotransverse foramen
+is_a: FMA:10146 ! First costotransverse foramen
+
+[Term]
+id: FMA:10152
+name: Left first costotransverse joint
+is_a: FMA:10139 ! First costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10153 ! Capsule of left first costotransverse joint
+relationship: has_part FMA:10154 ! Costotransverse ligament of left first costotransverse joint
+relationship: has_part FMA:10155 ! Lateral costotransverse ligament of left first costotransverse joint
+
+[Term]
+id: FMA:10153
+name: Capsule of left first costotransverse joint
+exact_synonym: "Left first costotransverse joint capsule" []
+is_a: FMA:10142 ! Capsule of first costotransverse joint
+relationship: part_of FMA:10152 ! Left first costotransverse joint
+
+[Term]
+id: FMA:10154
+name: Costotransverse ligament of left first costotransverse joint
+is_a: FMA:10144 ! Costotransverse ligament of first costotransverse joint
+relationship: part_of FMA:10152 ! Left first costotransverse joint
+
+[Term]
+id: FMA:10155
+name: Lateral costotransverse ligament of left first costotransverse joint
+is_a: FMA:10145 ! Lateral costotransverse ligament of first costotransverse joint
+relationship: part_of FMA:10152 ! Left first costotransverse joint
+
+[Term]
+id: FMA:10156
+name: Left first costotransverse foramen
+is_a: FMA:10146 ! First costotransverse foramen
+
+[Term]
+id: FMA:10157
+name: Capsule of second costotransverse joint
+exact_synonym: "Second costotransverse joint capsule" []
+is_a: FMA:10140 ! Capsule of costotransverse joint
+relationship: part_of FMA:10141 ! Second costotransverse joint
+
+[Term]
+id: FMA:10158
+name: Superior costotransverse ligament of second costotransverse joint
+is_a: FMA:8958 ! Superior costotransverse ligament
+relationship: part_of FMA:10141 ! Second costotransverse joint
+
+[Term]
+id: FMA:10159
+name: Costotransverse ligament of second costotransverse joint
+is_a: FMA:12163 ! Costotransverse ligament
+relationship: part_of FMA:10141 ! Second costotransverse joint
+
+[Term]
+id: FMA:10160
+name: Lateral costotransverse ligament of second costotransverse joint
+is_a: FMA:12162 ! Lateral costotransverse ligament
+relationship: part_of FMA:10141 ! Second costotransverse joint
+
+[Term]
+id: FMA:10161
+name: Accessory ligament of second costotransverse joint
+is_a: FMA:10138 ! Accessory ligament
+relationship: part_of FMA:10141 ! Second costotransverse joint
+
+[Term]
+id: FMA:10162
+name: Second costotransverse foramen
+is_a: FMA:10143 ! Costotransverse foramen
+
+[Term]
+id: FMA:10163
+name: Right second costotransverse joint
+is_a: FMA:10141 ! Second costotransverse joint
+relationship: has_part FMA:10167 ! Lateral costotransverse ligament of right second costotransverse joint
+relationship: has_part FMA:10168 ! Accessory ligament of right second costotransverse joint
+relationship: has_part FMA:10165 ! Superior costotransverse ligament of right second costotransverse joint
+relationship: has_part FMA:10164 ! Capsule of right second costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10166 ! Costotransverse ligament of right second costotransverse joint
+
+[Term]
+id: FMA:10164
+name: Capsule of right second costotransverse joint
+exact_synonym: "Right second costotransverse joint capsule" []
+is_a: FMA:10157 ! Capsule of second costotransverse joint
+relationship: part_of FMA:10163 ! Right second costotransverse joint
+
+[Term]
+id: FMA:10165
+name: Superior costotransverse ligament of right second costotransverse joint
+is_a: FMA:10158 ! Superior costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10163 ! Right second costotransverse joint
+
+[Term]
+id: FMA:10166
+name: Costotransverse ligament of right second costotransverse joint
+is_a: FMA:10159 ! Costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10163 ! Right second costotransverse joint
+
+[Term]
+id: FMA:10167
+name: Lateral costotransverse ligament of right second costotransverse joint
+is_a: FMA:10160 ! Lateral costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10163 ! Right second costotransverse joint
+
+[Term]
+id: FMA:10168
+name: Accessory ligament of right second costotransverse joint
+is_a: FMA:10161 ! Accessory ligament of second costotransverse joint
+relationship: part_of FMA:10163 ! Right second costotransverse joint
+
+[Term]
+id: FMA:10169
+name: Right second costotransverse foramen
+is_a: FMA:10162 ! Second costotransverse foramen
+
+[Term]
+id: FMA:10170
+name: Left second costotransverse joint
+is_a: FMA:10141 ! Second costotransverse joint
+relationship: has_part FMA:10171 ! Capsule of left second costotransverse joint
+relationship: has_part FMA:10174 ! Lateral costotransverse ligament of left second costotransverse joint
+relationship: has_part FMA:10173 ! Costotransverse ligament of left second costotransverse joint
+relationship: has_part FMA:10175 ! Accessory ligament of left second costotransverse joint
+relationship: has_part FMA:10172 ! Superior costotransverse ligament of left second costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10171
+name: Capsule of left second costotransverse joint
+exact_synonym: "Left second costotransverse joint capsule" []
+is_a: FMA:10157 ! Capsule of second costotransverse joint
+relationship: part_of FMA:10170 ! Left second costotransverse joint
+
+[Term]
+id: FMA:10172
+name: Superior costotransverse ligament of left second costotransverse joint
+is_a: FMA:10158 ! Superior costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10170 ! Left second costotransverse joint
+
+[Term]
+id: FMA:10173
+name: Costotransverse ligament of left second costotransverse joint
+is_a: FMA:10159 ! Costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10170 ! Left second costotransverse joint
+
+[Term]
+id: FMA:10174
+name: Lateral costotransverse ligament of left second costotransverse joint
+is_a: FMA:10160 ! Lateral costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10170 ! Left second costotransverse joint
+
+[Term]
+id: FMA:10175
+name: Accessory ligament of left second costotransverse joint
+is_a: FMA:10161 ! Accessory ligament of second costotransverse joint
+relationship: part_of FMA:10170 ! Left second costotransverse joint
+
+[Term]
+id: FMA:10176
+name: Left second costotransverse foramen
+is_a: FMA:10162 ! Second costotransverse foramen
+
+[Term]
+id: FMA:10177
+name: Third costotransverse joint
+is_a: FMA:7952 ! Costotransverse joint
+relationship: has_part FMA:10181 ! Lateral costotransverse ligament of third costotransverse joint
+relationship: has_part FMA:10182 ! Accessory ligament of third costotransverse joint
+relationship: has_part FMA:10179 ! Superior costotransverse ligament of third costotransverse joint
+relationship: has_part FMA:10178 ! Capsule of third costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10180 ! Costotransverse ligament of third costotransverse joint
+
+[Term]
+id: FMA:10178
+name: Capsule of third costotransverse joint
+exact_synonym: "Third costotransverse joint capsule" []
+is_a: FMA:10140 ! Capsule of costotransverse joint
+relationship: part_of FMA:10177 ! Third costotransverse joint
+
+[Term]
+id: FMA:10179
+name: Superior costotransverse ligament of third costotransverse joint
+is_a: FMA:8958 ! Superior costotransverse ligament
+relationship: part_of FMA:10177 ! Third costotransverse joint
+
+[Term]
+id: FMA:10180
+name: Costotransverse ligament of third costotransverse joint
+is_a: FMA:12163 ! Costotransverse ligament
+relationship: part_of FMA:10177 ! Third costotransverse joint
+
+[Term]
+id: FMA:10181
+name: Lateral costotransverse ligament of third costotransverse joint
+is_a: FMA:12162 ! Lateral costotransverse ligament
+relationship: part_of FMA:10177 ! Third costotransverse joint
+
+[Term]
+id: FMA:10182
+name: Accessory ligament of third costotransverse joint
+is_a: FMA:10138 ! Accessory ligament
+relationship: part_of FMA:10177 ! Third costotransverse joint
+
+[Term]
+id: FMA:10183
+name: Third costotransverse foramen
+is_a: FMA:10143 ! Costotransverse foramen
+
+[Term]
+id: FMA:10184
+name: Right third costotransverse joint
+is_a: FMA:10177 ! Third costotransverse joint
+relationship: has_part FMA:10186 ! Superior costotransverse ligament of right third costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10188 ! Lateral costotransverse ligament of right third costotransverse joint
+relationship: has_part FMA:10185 ! Capsule of right third costotransverse joint
+relationship: has_part FMA:10189 ! Accessory ligament of right third costotransverse joint
+
+[Term]
+id: FMA:10185
+name: Capsule of right third costotransverse joint
+exact_synonym: "Right third costotransverse joint capsule" []
+is_a: FMA:10178 ! Capsule of third costotransverse joint
+relationship: part_of FMA:10184 ! Right third costotransverse joint
+
+[Term]
+id: FMA:10186
+name: Superior costotransverse ligament of right third costotransverse joint
+is_a: FMA:10179 ! Superior costotransverse ligament of third costotransverse joint
+relationship: part_of FMA:10184 ! Right third costotransverse joint
+
+[Term]
+id: FMA:10187
+name: Costotransverse ligament of right third costotransverse joint
+is_a: FMA:10180 ! Costotransverse ligament of third costotransverse joint
+
+[Term]
+id: FMA:10188
+name: Lateral costotransverse ligament of right third costotransverse joint
+is_a: FMA:10181 ! Lateral costotransverse ligament of third costotransverse joint
+relationship: part_of FMA:10184 ! Right third costotransverse joint
+
+[Term]
+id: FMA:10189
+name: Accessory ligament of right third costotransverse joint
+is_a: FMA:10182 ! Accessory ligament of third costotransverse joint
+relationship: part_of FMA:10184 ! Right third costotransverse joint
+
+[Term]
+id: FMA:10190
+name: Right third costotransverse foramen
+is_a: FMA:10183 ! Third costotransverse foramen
+
+[Term]
+id: FMA:10191
+name: Left third costotransverse joint
+is_a: FMA:10177 ! Third costotransverse joint
+relationship: has_part FMA:10196 ! Accessory ligament of left third costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10193 ! Superior costotransverse ligament of left third costotransverse joint
+relationship: has_part FMA:10194 ! Costotransverse ligament of left third costotransverse joint
+relationship: has_part FMA:10192 ! Capsule of left third costotransverse joint
+relationship: has_part FMA:10195 ! Lateral costotransverse ligament of left third costotransverse joint
+
+[Term]
+id: FMA:10192
+name: Capsule of left third costotransverse joint
+exact_synonym: "Left third costotransverse joint capsule" []
+is_a: FMA:10178 ! Capsule of third costotransverse joint
+relationship: part_of FMA:10191 ! Left third costotransverse joint
+
+[Term]
+id: FMA:10193
+name: Superior costotransverse ligament of left third costotransverse joint
+is_a: FMA:10179 ! Superior costotransverse ligament of third costotransverse joint
+relationship: part_of FMA:10191 ! Left third costotransverse joint
+
+[Term]
+id: FMA:10194
+name: Costotransverse ligament of left third costotransverse joint
+is_a: FMA:10180 ! Costotransverse ligament of third costotransverse joint
+relationship: part_of FMA:10191 ! Left third costotransverse joint
+
+[Term]
+id: FMA:10195
+name: Lateral costotransverse ligament of left third costotransverse joint
+is_a: FMA:10181 ! Lateral costotransverse ligament of third costotransverse joint
+relationship: part_of FMA:10191 ! Left third costotransverse joint
+
+[Term]
+id: FMA:10196
+name: Accessory ligament of left third costotransverse joint
+is_a: FMA:10182 ! Accessory ligament of third costotransverse joint
+relationship: part_of FMA:10191 ! Left third costotransverse joint
+
+[Term]
+id: FMA:10197
+name: Left third costotransverse foramen
+is_a: FMA:10183 ! Third costotransverse foramen
+
+[Term]
+id: FMA:10198
+name: Fourth costotransverse joint
+is_a: FMA:7952 ! Costotransverse joint
+relationship: has_part FMA:10201 ! Lateral costotransverse ligament of fourth costotransverse joint
+relationship: has_part FMA:10202 ! Costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10199 ! Capsule of fourth costotransverse joint
+relationship: has_part FMA:10200 ! Superior costotransverse ligament of fourth costotransverse joint
+relationship: has_part FMA:10203 ! Accessory ligament of fourth costotransverse joint
+
+[Term]
+id: FMA:10199
+name: Capsule of fourth costotransverse joint
+exact_synonym: "Fourth costotransverse joint capsule" []
+is_a: FMA:10140 ! Capsule of costotransverse joint
+relationship: part_of FMA:10198 ! Fourth costotransverse joint
+
+[Term]
+id: FMA:10200
+name: Superior costotransverse ligament of fourth costotransverse joint
+is_a: FMA:8958 ! Superior costotransverse ligament
+relationship: part_of FMA:10198 ! Fourth costotransverse joint
+
+[Term]
+id: FMA:10201
+name: Lateral costotransverse ligament of fourth costotransverse joint
+is_a: FMA:12162 ! Lateral costotransverse ligament
+relationship: part_of FMA:10198 ! Fourth costotransverse joint
+
+[Term]
+id: FMA:10202
+name: Costotransverse ligament of fourth costotransverse joint
+is_a: FMA:12163 ! Costotransverse ligament
+relationship: part_of FMA:10198 ! Fourth costotransverse joint
+
+[Term]
+id: FMA:10203
+name: Accessory ligament of fourth costotransverse joint
+is_a: FMA:10138 ! Accessory ligament
+relationship: part_of FMA:10198 ! Fourth costotransverse joint
+
+[Term]
+id: FMA:10204
+name: Fourth costotransverse foramen
+is_a: FMA:10143 ! Costotransverse foramen
+
+[Term]
+id: FMA:10205
+name: Right fourth costotransverse joint
+is_a: FMA:10198 ! Fourth costotransverse joint
+relationship: has_part FMA:10209 ! Lateral costotransverse ligament of right fourth costotransverse joint
+relationship: has_part FMA:10207 ! Superior costotransverse ligament of right fourth costotransverse joint
+relationship: has_part FMA:10210 ! Accessory ligament of right fourth costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10206 ! Capsule of right fourth costotransverse joint
+relationship: has_part FMA:10208 ! Costotransverse ligament of right fourth costotransverse joint
+
+[Term]
+id: FMA:10206
+name: Capsule of right fourth costotransverse joint
+exact_synonym: "Right fourth costotransverse joint capsule" []
+is_a: FMA:10199 ! Capsule of fourth costotransverse joint
+relationship: part_of FMA:10205 ! Right fourth costotransverse joint
+
+[Term]
+id: FMA:10207
+name: Superior costotransverse ligament of right fourth costotransverse joint
+is_a: FMA:10200 ! Superior costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10205 ! Right fourth costotransverse joint
+
+[Term]
+id: FMA:10208
+name: Costotransverse ligament of right fourth costotransverse joint
+is_a: FMA:10202 ! Costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10205 ! Right fourth costotransverse joint
+
+[Term]
+id: FMA:10209
+name: Lateral costotransverse ligament of right fourth costotransverse joint
+is_a: FMA:10201 ! Lateral costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10205 ! Right fourth costotransverse joint
+
+[Term]
+id: FMA:10210
+name: Accessory ligament of right fourth costotransverse joint
+is_a: FMA:10203 ! Accessory ligament of fourth costotransverse joint
+relationship: part_of FMA:10205 ! Right fourth costotransverse joint
+
+[Term]
+id: FMA:10211
+name: Right fourth costotransverse foramen
+is_a: FMA:10204 ! Fourth costotransverse foramen
+
+[Term]
+id: FMA:10212
+name: Left fourth costotransverse joint
+is_a: FMA:10198 ! Fourth costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10215 ! Costotransverse ligament of left fourth costotransverse joint
+relationship: has_part FMA:10217 ! Accessory ligament of left fourth costotransverse joint
+relationship: has_part FMA:10213 ! Capsule of left fourth costotransverse joint
+relationship: has_part FMA:10216 ! Lateral costotransverse ligament of left fourth costotransverse joint
+relationship: has_part FMA:10214 ! Superior costotransverse ligament of left fourth costotransverse joint
+
+[Term]
+id: FMA:10213
+name: Capsule of left fourth costotransverse joint
+exact_synonym: "Left fourth costotransverse joint capsule" []
+is_a: FMA:10199 ! Capsule of fourth costotransverse joint
+relationship: part_of FMA:10212 ! Left fourth costotransverse joint
+
+[Term]
+id: FMA:10214
+name: Superior costotransverse ligament of left fourth costotransverse joint
+is_a: FMA:10200 ! Superior costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10212 ! Left fourth costotransverse joint
+
+[Term]
+id: FMA:10215
+name: Costotransverse ligament of left fourth costotransverse joint
+is_a: FMA:10202 ! Costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10212 ! Left fourth costotransverse joint
+
+[Term]
+id: FMA:10216
+name: Lateral costotransverse ligament of left fourth costotransverse joint
+is_a: FMA:10201 ! Lateral costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10212 ! Left fourth costotransverse joint
+
+[Term]
+id: FMA:10217
+name: Accessory ligament of left fourth costotransverse joint
+is_a: FMA:10203 ! Accessory ligament of fourth costotransverse joint
+relationship: part_of FMA:10212 ! Left fourth costotransverse joint
+
+[Term]
+id: FMA:10218
+name: Left fourth costotransverse foramen
+is_a: FMA:10204 ! Fourth costotransverse foramen
+
+[Term]
+id: FMA:10219
+name: Fifth costotransverse joint
+is_a: FMA:7952 ! Costotransverse joint
+relationship: has_part FMA:10223 ! Lateral costotransverse ligament of fifth costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10221 ! Superior costotransverse ligament of fifth costotransverse joint
+relationship: has_part FMA:10224 ! Accessory ligament of fifth costotransverse joint
+relationship: has_part FMA:10222 ! Costotransverse ligament of fifth costotransverse joint
+relationship: has_part FMA:10220 ! Capsule of fifth costotransverse joint
+
+[Term]
+id: FMA:10220
+name: Capsule of fifth costotransverse joint
+exact_synonym: "Fifth costotransverse joint capsule" []
+is_a: FMA:10140 ! Capsule of costotransverse joint
+relationship: part_of FMA:10219 ! Fifth costotransverse joint
+
+[Term]
+id: FMA:10221
+name: Superior costotransverse ligament of fifth costotransverse joint
+is_a: FMA:8958 ! Superior costotransverse ligament
+relationship: part_of FMA:10219 ! Fifth costotransverse joint
+
+[Term]
+id: FMA:10222
+name: Costotransverse ligament of fifth costotransverse joint
+is_a: FMA:12163 ! Costotransverse ligament
+relationship: part_of FMA:10219 ! Fifth costotransverse joint
+
+[Term]
+id: FMA:10223
+name: Lateral costotransverse ligament of fifth costotransverse joint
+is_a: FMA:12162 ! Lateral costotra...
 
[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [225] fma-conversion

From: <cmu...@us...> - 2006-11-27 22:53:10

Revision: 225
          http://svn.sourceforge.net/obo/?rev=225&view=rev
Author:   cmungall
Date:     2006-11-27 14:52:56 -0800 (Mon, 27 Nov 2006)

Log Message:
-----------
initial import, from Nigam

Added Paths:
-----------
    fma-conversion/
    fma-conversion/branches/
    fma-conversion/tags/
    fma-conversion/trunk/
    fma-conversion/trunk/fma_obo.obo

Added: fma-conversion/trunk/fma_obo.obo
===================================================================
--- fma-conversion/trunk/fma_obo.obo	                        (rev 0)
+++ fma-conversion/trunk/fma_obo.obo	2006-11-27 22:52:56 UTC (rev 225)
@@ -0,0 +1,466385 @@
+format-version: 1.0
+date: 15:09:2006 13:29
+saved-by: dilvan
+auto-generated-by: Protege OBO plugin version 1.0
+version: 0.1
+
+[Term]
+id: FMA:10000
+name: Eighth thoracic vertebral arch
+exact_synonym: "Arch of eighth thoracic vertebra" []
+exact_synonym: "Arch of T8 vertebra" []
+is_a: FMA:9151 ! Thoracic vertebral arch
+relationship: part_of FMA:9991 ! Eighth thoracic vertebra
+relationship: has_part FMA:10005 ! Spinous process of eighth thoracic vertebra
+relationship: has_part FMA:11906 ! Right inferior articular process of eighth thoracic vertebra
+relationship: has_part FMA:12060 ! Left lamina of eighth thoracic vertebra
+relationship: has_part FMA:28729 ! Periosteum of eighth thoracic vertebral arch
+relationship: has_part FMA:11901 ! Left transverse process of eighth thoracic vertebra
+relationship: has_part FMA:11895 ! Left pedicle of eighth thoracic vertebra
+relationship: has_part FMA:11904 ! Right superior articular process of eighth thoracic vertebra
+relationship: has_part FMA:29990 ! Bony part of eighth thoracic vertebral arch
+relationship: has_part FMA:11905 ! Left superior articular process of eighth thoracic vertebra
+relationship: has_part FMA:12059 ! Right lamina of eighth thoracic vertebra
+relationship: has_part FMA:11900 ! Right transverse process of eighth thoracic vertebra
+relationship: has_part FMA:11907 ! Left inferior articular process of eighth thoracic vertebra
+relationship: has_part FMA:11894 ! Right pedicle of eighth thoracic vertebra
+
+[Term]
+id: FMA:10001
+name: Pedicle of eighth thoracic vertebra
+exact_synonym: "Eighth thoracic vertebral pedicle" []
+exact_synonym: "Pedicle of T8 vertebra" []
+is_a: FMA:9152 ! Pedicle of thoracic vertebra
+
+[Term]
+id: FMA:10002
+name: Superior vertebral notch of eighth thoracic vertebra
+exact_synonym: "Superior vertebral incisure of pedicle of eighth thoracic vertebra" []
+is_a: FMA:9157 ! Superior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10003
+name: Inferior vertebral notch of eighth thoracic vertebra
+exact_synonym: "Inferior vertebral incisure of pedicle of eighth thoracic vertebra" []
+is_a: FMA:9158 ! Inferior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10004
+name: Lamina of eighth thoracic vertebra
+exact_synonym: "Eighth thoracic vertebral lamina" []
+is_a: FMA:9153 ! Lamina of thoracic vertebra
+
+[Term]
+id: FMA:10005
+name: Spinous process of eighth thoracic vertebra
+exact_synonym: "Spinous process of T8 vertebra" []
+is_a: FMA:9149 ! Spinous process of thoracic vertebra
+relationship: has_part FMA:30277 ! Bony part of spinous process of eighth thoracic vertebra
+relationship: part_of FMA:10000 ! Eighth thoracic vertebral arch
+relationship: has_part FMA:28957 ! Periosteum of spinous process of eighth thoracic vertebra
+
+[Term]
+id: FMA:10006
+name: Transverse process of eighth thoracic vertebra
+exact_synonym: "Transverse process of T8 vertebra" []
+is_a: FMA:9150 ! Transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10007
+name: Costal facet of transverse process of eighth thoracic vertebra
+exact_synonym: "Articular facet of transverse process of eighth thoracic vertebra" []
+is_a: FMA:10440 ! Costal facet of transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10008
+name: Vasculature of bony part of eighth thoracic vertebra
+is_a: FMA:9154 ! Vasculature of bony part of thoracic vertebra
+
+[Term]
+id: FMA:10009
+name: Superior articular process of eighth thoracic vertebra
+exact_synonym: "Cranial articular process of eighth thoracic vertebra" []
+is_a: FMA:9155 ! Superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10010
+name: Articular facet of superior articular process of eighth thoracic vertebra
+is_a: FMA:10521 ! Articular facet of superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10011
+name: Inferior articular process of eighth thoracic vertebra
+exact_synonym: "Caudal articular process of eighth thoracic vertebra" []
+is_a: FMA:9156 ! Inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10012
+name: Articular facet of inferior articular process of eighth thoracic vertebra
+is_a: FMA:9160 ! Articular facet of inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10013
+name: Intervertebral foramen of eighth thoracic vertebra
+is_a: FMA:9144 ! Intervertebral foramen of thoracic vertebra
+
+[Term]
+id: FMA:10014
+name: Ninth thoracic vertebra
+exact_synonym: "T9 vertebra" []
+exact_synonym: "Ninth dorsal vertebra" []
+is_a: FMA:9139 ! Thoracic vertebra
+relationship: has_part FMA:29784 ! Bony part of ninth thoracic vertebra
+relationship: part_of FMA:9140 ! Thoracic vertebral column
+relationship: has_part FMA:10015 ! Body of ninth thoracic vertebra
+relationship: has_part FMA:26724 ! Cartilage of ninth thoracic vertebra
+relationship: has_part FMA:28188 ! Periosteum of ninth thoracic vertebra
+relationship: part_of FMA:72064 ! Set of thoracic vertebrae
+relationship: has_part FMA:10023 ! Ninth thoracic vertebral arch
+relationship: has_part FMA:26688 ! Bone of ninth thoracic vertebra
+
+[Term]
+id: FMA:10015
+name: Body of ninth thoracic vertebra
+exact_synonym: "Ninth thoracic vertebral body" []
+exact_synonym: "Body of T9 vertebra" []
+is_a: FMA:9141 ! Body of thoracic vertebra
+relationship: has_part FMA:29899 ! Bony part of body of ninth thoracic vertebra
+relationship: has_part FMA:30368 ! Cartilage of body of ninth thoracic vertebra
+relationship: has_part FMA:26605 ! Central part of body of ninth thoracic vertebra
+relationship: part_of FMA:10014 ! Ninth thoracic vertebra
+relationship: has_part FMA:26637 ! Right posterolateral part of body of ninth thoracic vertebra
+relationship: has_part FMA:26247 ! Right neurocentral junction of ninth thoracic vertebra
+relationship: has_part FMA:28670 ! Periosteum of body of ninth thoracic vertebra
+relationship: has_part FMA:26638 ! Left posterolateral part of body of ninth thoracic vertebra
+relationship: has_part FMA:26248 ! Left neurocentral junction of ninth thoracic vertebra
+
+[Term]
+id: FMA:10016
+name: Anterior surface of body of ninth thoracic vertebra
+is_a: FMA:9147 ! Anterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10017
+name: Posterior surface of body of ninth thoracic vertebra
+is_a: FMA:9148 ! Posterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10018
+name: Lateral surface of body of ninth thoracic vertebra
+is_a: FMA:9162 ! Lateral surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10019
+name: Superior costal facet of body of ninth thoracic vertebra
+exact_synonym: "Superior costocapitular demifacet of body of ninth thoracic vertebra" []
+exact_synonym: "Upper costal facet of body of ninth thoracic vertebra" []
+is_a: FMA:9145 ! Superior costal facet of body of thoracic vertebra
+relationship: part_of FMA:8945 ! Joint of head of ninth rib
+
+[Term]
+id: FMA:10021
+name: Superior surface of body of ninth thoracic vertebra
+exact_synonym: "Upper border of body of ninth thoracic vertebra" []
+is_a: FMA:9163 ! Superior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10022
+name: Inferior surface of body of ninth thoracic vertebra
+exact_synonym: "Lower border of body of ninth thoracic vertebra" []
+is_a: FMA:9164 ! Inferior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10023
+name: Ninth thoracic vertebral arch
+exact_synonym: "Arch of T9 vertebra" []
+exact_synonym: "Arch of ninth thoracic vertebra" []
+is_a: FMA:9151 ! Thoracic vertebral arch
+relationship: has_part FMA:12064 ! Right lamina of ninth thoracic vertebra
+relationship: has_part FMA:11914 ! Right pedicle of ninth thoracic vertebra
+relationship: has_part FMA:11924 ! Right superior articular process of ninth thoracic vertebra
+relationship: has_part FMA:11920 ! Right transverse process of ninth thoracic vertebra
+relationship: has_part FMA:11921 ! Left transverse process of ninth thoracic vertebra
+relationship: has_part FMA:11926 ! Right inferior articular process of ninth thoracic vertebra
+relationship: has_part FMA:10028 ! Spinous process of ninth thoracic vertebra
+relationship: has_part FMA:29991 ! Bony part of ninth thoracic vertebral arch
+relationship: has_part FMA:12065 ! Left lamina of ninth thoracic vertebra
+relationship: has_part FMA:11915 ! Left pedicle of ninth thoracic vertebra
+relationship: has_part FMA:11927 ! Left inferior articular process of ninth thoracic vertebra
+relationship: has_part FMA:28730 ! Periosteum of ninth thoracic vertebral arch
+relationship: has_part FMA:11925 ! Left superior articular process of ninth thoracic vertebra
+relationship: part_of FMA:10014 ! Ninth thoracic vertebra
+
+[Term]
+id: FMA:10024
+name: Pedicle of ninth thoracic vertebra
+exact_synonym: "Pedicle of T9 vertebra" []
+exact_synonym: "Ninth thoracic vertebral pedicle" []
+is_a: FMA:9152 ! Pedicle of thoracic vertebra
+
+[Term]
+id: FMA:10025
+name: Superior vertebral notch of ninth thoracic vertebra
+exact_synonym: "Superior vertebral incisure of pedicle of ninth thoracic vertebra" []
+is_a: FMA:9157 ! Superior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10026
+name: Inferior vertebral notch of ninth thoracic vertebra
+exact_synonym: "Inferior vertebral incisure of pedicle of ninth thoracic vertebra" []
+is_a: FMA:9158 ! Inferior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10027
+name: Lamina of ninth thoracic vertebra
+exact_synonym: "Ninth thoracic vertebral lamina" []
+is_a: FMA:9153 ! Lamina of thoracic vertebra
+
+[Term]
+id: FMA:10028
+name: Spinous process of ninth thoracic vertebra
+exact_synonym: "Spinous process of T9 vertebra" []
+is_a: FMA:9149 ! Spinous process of thoracic vertebra
+relationship: has_part FMA:28958 ! Periosteum of spinous process of ninth thoracic vertebra
+relationship: has_part FMA:30278 ! Bony part of spinous process of ninth thoracic vertebra
+relationship: part_of FMA:10023 ! Ninth thoracic vertebral arch
+
+[Term]
+id: FMA:10029
+name: Transverse process of ninth thoracic vertebra
+exact_synonym: "Transverse process of T9 vertebra" []
+is_a: FMA:9150 ! Transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10030
+name: Costal facet of transverse process of ninth thoracic vertebra
+exact_synonym: "Articular facet of transverse process of ninth thoracic vertebra" []
+is_a: FMA:10440 ! Costal facet of transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10031
+name: Vasculature of bony part of ninth thoracic vertebra
+is_a: FMA:9154 ! Vasculature of bony part of thoracic vertebra
+
+[Term]
+id: FMA:10032
+name: Superior articular process of ninth thoracic vertebra
+exact_synonym: "Cranial articular process of ninth thoracic vertebra" []
+is_a: FMA:9155 ! Superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10033
+name: Articular facet of superior articular process of ninth thoracic vertebra
+is_a: FMA:10521 ! Articular facet of superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10034
+name: Inferior articular process of ninth thoracic vertebra
+exact_synonym: "Caudal articular process of ninth thoracic vertebra" []
+is_a: FMA:9156 ! Inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10035
+name: Articular facet of inferior articular process of ninth thoracic vertebra
+is_a: FMA:9160 ! Articular facet of inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10036
+name: Intervertebral foramen of ninth thoracic vertebra
+is_a: FMA:9144 ! Intervertebral foramen of thoracic vertebra
+
+[Term]
+id: FMA:10037
+name: Tenth thoracic vertebra
+exact_synonym: "Tenth dorsal vertebra" []
+exact_synonym: "T10 vertebra" []
+is_a: FMA:9139 ! Thoracic vertebra
+relationship: has_part FMA:10038 ! Body of tenth thoracic vertebra
+relationship: has_part FMA:10045 ! Tenth thoracic vertebral arch
+relationship: has_part FMA:26725 ! Cartilage of tenth thoracic vertebra
+relationship: has_part FMA:29785 ! Bony part of tenth thoracic vertebra
+relationship: has_part FMA:28189 ! Periosteum of tenth thoracic vertebra
+relationship: has_part FMA:26689 ! Bone of tenth thoracic vertebra
+relationship: part_of FMA:72064 ! Set of thoracic vertebrae
+relationship: part_of FMA:9140 ! Thoracic vertebral column
+
+[Term]
+id: FMA:10038
+name: Body of tenth thoracic vertebra
+exact_synonym: "Tenth thoracic vertebral body" []
+exact_synonym: "Body of T10 vertebra" []
+is_a: FMA:9141 ! Body of thoracic vertebra
+relationship: has_part FMA:26606 ! Central part of body of tenth thoracic vertebra
+relationship: part_of FMA:10037 ! Tenth thoracic vertebra
+relationship: has_part FMA:30369 ! Cartilage of body of tenth thoracic vertebra
+relationship: has_part FMA:26639 ! Right posterolateral part of body of tenth thoracic vertebra
+relationship: has_part FMA:26250 ! Left neurocentral junction of tenth thoracic vertebra
+relationship: has_part FMA:26249 ! Right neurocentral junction of tenth thoracic vertebra
+relationship: has_part FMA:29900 ! Bony part of body of tenth thoracic vertebra
+relationship: has_part FMA:28671 ! Periosteum of body of tenth thoracic vertebra
+relationship: has_part FMA:26640 ! Left posterolateral part of body of tenth thoracic vertebra
+
+[Term]
+id: FMA:10039
+name: Anterior surface of body of tenth thoracic vertebra
+is_a: FMA:9147 ! Anterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10040
+name: Posterior surface of body of tenth thoracic vertebra
+is_a: FMA:9148 ! Posterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10041
+name: Lateral surface of body of tenth thoracic vertebra
+is_a: FMA:9162 ! Lateral surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10042
+name: Superior costal facet of body of tenth thoracic vertebra
+exact_synonym: "Upper costal facet of body of tenth thoracic vertebra" []
+exact_synonym: "Superior costocapitular demifacet of body of tenth thoracic vertebra" []
+is_a: FMA:9145 ! Superior costal facet of body of thoracic vertebra
+relationship: part_of FMA:8948 ! Joint of head of tenth rib
+
+[Term]
+id: FMA:10043
+name: Superior surface of body of tenth thoracic vertebra
+exact_synonym: "Upper border of body of tenth thoracic vertebra" []
+is_a: FMA:9163 ! Superior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10044
+name: Inferior surface of body of tenth thoracic vertebra
+exact_synonym: "Lower border of body of tenth thoracic vertebra" []
+is_a: FMA:9164 ! Inferior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10045
+name: Tenth thoracic vertebral arch
+exact_synonym: "Arch of T10 vertebra" []
+exact_synonym: "Arch of tenth thoracic vertebra" []
+is_a: FMA:9151 ! Thoracic vertebral arch
+relationship: has_part FMA:12076 ! Right inferior articular process of tenth thoracic vertebra
+relationship: has_part FMA:29992 ! Bony part of tenth thoracic vertebral arch
+relationship: has_part FMA:11942 ! Left transverse process of tenth thoracic vertebra
+relationship: has_part FMA:10050 ! Spinous process of tenth thoracic vertebra
+relationship: has_part FMA:11935 ! Right pedicle of tenth thoracic vertebra
+relationship: has_part FMA:12077 ! Left inferior articular process of tenth thoracic vertebra
+relationship: has_part FMA:11936 ! Left pedicle of tenth thoracic vertebra
+relationship: has_part FMA:11941 ! Right transverse process of tenth thoracic vertebra
+relationship: has_part FMA:12069 ! Right lamina of tenth thoracic vertebra
+relationship: has_part FMA:28731 ! Periosteum of tenth thoracic vertebral arch
+relationship: has_part FMA:12070 ! Left lamina of tenth thoracic vertebra
+relationship: has_part FMA:12075 ! Left superior articular process of tenth thoracic vertebra
+relationship: has_part FMA:12074 ! Right superior articular process of tenth thoracic vertebra
+relationship: part_of FMA:10037 ! Tenth thoracic vertebra
+
+[Term]
+id: FMA:10046
+name: Pedicle of tenth thoracic vertebra
+exact_synonym: "Pedicle of T10 vertebra" []
+exact_synonym: "Tenth thoracic vertebral pedicle" []
+is_a: FMA:9152 ! Pedicle of thoracic vertebra
+
+[Term]
+id: FMA:10047
+name: Superior vertebral notch of tenth thoracic vertebra
+exact_synonym: "Superior vertebral incisure of pedicle of tenth thoracic vertebra" []
+is_a: FMA:9157 ! Superior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10048
+name: Inferior vertebral notch of tenth thoracic vertebra
+exact_synonym: "Inferior vertebral incisure of pedicle of tenth thoracic vertebra" []
+is_a: FMA:9158 ! Inferior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10049
+name: Lamina of tenth thoracic vertebra
+exact_synonym: "Tenth thoracic vertebral lamina" []
+is_a: FMA:9153 ! Lamina of thoracic vertebra
+
+[Term]
+id: FMA:10050
+name: Spinous process of tenth thoracic vertebra
+exact_synonym: "Spinous process of T10 vertebra" []
+is_a: FMA:9149 ! Spinous process of thoracic vertebra
+relationship: has_part FMA:30279 ! Bony part of spinous process of tenth thoracic vertebra
+relationship: has_part FMA:28959 ! Periosteum of spinous process of tenth thoracic vertebra
+relationship: part_of FMA:10045 ! Tenth thoracic vertebral arch
+
+[Term]
+id: FMA:10051
+name: Transverse process of tenth thoracic vertebra
+exact_synonym: "Transverse process of T10 vertebra" []
+is_a: FMA:9150 ! Transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10052
+name: Costal facet of transverse process of tenth thoracic vertebra
+exact_synonym: "Articular facet of transverse process of tenth thoracic vertebra" []
+is_a: FMA:10440 ! Costal facet of transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10053
+name: Vasculature of bony part of tenth thoracic vertebra
+is_a: FMA:9154 ! Vasculature of bony part of thoracic vertebra
+
+[Term]
+id: FMA:10054
+name: Superior articular process of tenth thoracic vertebra
+exact_synonym: "Cranial articular process of tenth thoracic vertebra" []
+is_a: FMA:9155 ! Superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10055
+name: Articular facet of superior articular process of tenth thoracic vertebra
+is_a: FMA:10521 ! Articular facet of superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10056
+name: Inferior articular process of tenth thoracic vertebra
+exact_synonym: "Caudal articular process of tenth thoracic vertebra" []
+is_a: FMA:9156 ! Inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10057
+name: Articular facet of inferior articular process of tenth thoracic vertebra
+is_a: FMA:9160 ! Articular facet of inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10058
+name: Intervertebral foramen of tenth thoracic vertebra
+is_a: FMA:9144 ! Intervertebral foramen of thoracic vertebra
+
+[Term]
+id: FMA:10059
+name: Eleventh thoracic vertebra
+exact_synonym: "T11 vertebra" []
+exact_synonym: "Eleventh dorsal vertebra" []
+is_a: FMA:9139 ! Thoracic vertebra
+relationship: part_of FMA:72064 ! Set of thoracic vertebrae
+relationship: has_part FMA:26726 ! Cartilage of eleventh thoracic vertebra
+relationship: has_part FMA:29786 ! Bony part of eleventh thoracic vertebra
+relationship: has_part FMA:26690 ! Bone of eleventh thoracic vertebra
+relationship: has_part FMA:10060 ! Body of eleventh thoracic vertebra
+relationship: part_of FMA:9140 ! Thoracic vertebral column
+relationship: has_part FMA:10067 ! Eleventh thoracic vertebral arch
+relationship: has_part FMA:28190 ! Periosteum of eleventh thoracic vertebra
+
+[Term]
+id: FMA:10060
+name: Body of eleventh thoracic vertebra
+exact_synonym: "Body of T11 vertebra" []
+exact_synonym: "Eleventh thoracic vertebral body" []
+is_a: FMA:9141 ! Body of thoracic vertebra
+relationship: has_part FMA:26607 ! Central part of body of eleventh thoracic vertebra
+relationship: has_part FMA:26252 ! Left neurocentral junction of eleventh thoracic vertebra
+relationship: has_part FMA:30370 ! Cartilage of body of eleventh thoracic vertebra
+relationship: has_part FMA:26642 ! Left posterolateral part of body of eleventh thoracic vertebra
+relationship: has_part FMA:26251 ! Right neurocentral junction of eleventh thoracic vertebra
+relationship: has_part FMA:29901 ! Bony part of body of eleventh thoracic vertebra
+relationship: has_part FMA:28672 ! Periosteum of body of eleventh thoracic vertebra
+relationship: part_of FMA:10059 ! Eleventh thoracic vertebra
+relationship: has_part FMA:26641 ! Right posterolateral part of body of eleventh thoracic vertebra
+
+[Term]
+id: FMA:10061
+name: Anterior surface of body of eleventh thoracic vertebra
+is_a: FMA:9147 ! Anterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10062
+name: Posterior surface of body of eleventh thoracic vertebra
+is_a: FMA:9148 ! Posterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10063
+name: Lateral surface of body of eleventh thoracic vertebra
+is_a: FMA:9162 ! Lateral surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10064
+name: Costal facet of body of eleventh thoracic vertebra
+exact_synonym: "Costocapitular demifacet of body of eleventh thoracic vertebra" []
+is_a: FMA:13577 ! Costal facet of body of thoracic vertebra
+relationship: part_of FMA:8951 ! Joint of head of eleventh rib
+
+[Term]
+id: FMA:10065
+name: Superior surface of body of eleventh thoracic vertebra
+exact_synonym: "Upper border of body of eleventh thoracic vertebra" []
+is_a: FMA:9163 ! Superior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10066
+name: Inferior surface of body of eleventh thoracic vertebra
+exact_synonym: "Lower border of body of eleventh thoracic vertebra" []
+is_a: FMA:9164 ! Inferior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10067
+name: Eleventh thoracic vertebral arch
+exact_synonym: "Arch of T11 vertebra" []
+exact_synonym: "Arch of eleventh thoracic vertebra" []
+is_a: FMA:9151 ! Thoracic vertebral arch
+relationship: has_part FMA:12086 ! Left pedicle of eleventh thoracic vertebra
+relationship: has_part FMA:12093 ! Right transverse process of eleventh thoracic vertebra
+relationship: has_part FMA:12088 ! Left lamina of eleventh thoracic vertebra
+relationship: has_part FMA:12085 ! Right pedicle of eleventh thoracic vertebra
+relationship: has_part FMA:12097 ! Right superior articular process of eleventh thoracic vertebra
+relationship: has_part FMA:12100 ! Left inferior articular process of eleventh thoracic vertebra
+relationship: has_part FMA:12094 ! Left transverse process of eleventh thoracic vertebra
+relationship: has_part FMA:29993 ! Bony part of eleventh thoracic vertebral arch
+relationship: has_part FMA:12099 ! Right inferior articular process of eleventh thoracic vertebra
+relationship: has_part FMA:28732 ! Periosteum of eleventh thoracic vertebral arch
+relationship: part_of FMA:10059 ! Eleventh thoracic vertebra
+relationship: has_part FMA:12098 ! Left superior articular process of eleventh thoracic vertebra
+relationship: has_part FMA:12087 ! Right lamina of eleventh thoracic vertebra
+relationship: has_part FMA:10072 ! Spinous process of eleventh thoracic vertebra
+
+[Term]
+id: FMA:10068
+name: Pedicle of eleventh thoracic vertebra
+exact_synonym: "Pedicle of T11 vertebra" []
+exact_synonym: "Eleventh thoracic vertebral pedicle" []
+is_a: FMA:9152 ! Pedicle of thoracic vertebra
+
+[Term]
+id: FMA:10069
+name: Superior vertebral notch of eleventh thoracic vertebra
+exact_synonym: "Superior vertebral incisure of pedicle of eleventh thoracic vertebra" []
+is_a: FMA:9157 ! Superior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10070
+name: Inferior vertebral notch of eleventh thoracic vertebra
+exact_synonym: "Inferior vertebral incisure of pedicle of eleventh thoracic vertebra" []
+is_a: FMA:9158 ! Inferior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10071
+name: Lamina of eleventh thoracic vertebra
+exact_synonym: "Eleventh thoracic vertebral lamina" []
+is_a: FMA:9153 ! Lamina of thoracic vertebra
+
+[Term]
+id: FMA:10072
+name: Spinous process of eleventh thoracic vertebra
+exact_synonym: "Spinous process of T11 vertebra" []
+is_a: FMA:9149 ! Spinous process of thoracic vertebra
+relationship: has_part FMA:30280 ! Bony part of spinous process of eleventh thoracic vertebra
+relationship: part_of FMA:10067 ! Eleventh thoracic vertebral arch
+relationship: has_part FMA:28960 ! Periosteum of spinous process of eleventh thoracic vertebra
+
+[Term]
+id: FMA:10073
+name: Transverse process of eleventh thoracic vertebra
+exact_synonym: "Transverse process of T11 vertebra" []
+is_a: FMA:9150 ! Transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10075
+name: Vasculature of bony part of eleventh thoracic vertebra
+is_a: FMA:9154 ! Vasculature of bony part of thoracic vertebra
+
+[Term]
+id: FMA:10076
+name: Superior articular process of eleventh thoracic vertebra
+exact_synonym: "Cranial articular process of eleventh thoracic vertebra" []
+is_a: FMA:9155 ! Superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10077
+name: Articular facet of superior articular process of eleventh thoracic vertebra
+is_a: FMA:10521 ! Articular facet of superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10078
+name: Inferior articular process of eleventh thoracic vertebra
+exact_synonym: "Caudal articular process of eleventh thoracic vertebra" []
+is_a: FMA:9156 ! Inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10079
+name: Articular facet of inferior articular process of eleventh thoracic vertebra
+is_a: FMA:9160 ! Articular facet of inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10080
+name: Intervertebral foramen of eleventh thoracic vertebra
+is_a: FMA:9144 ! Intervertebral foramen of thoracic vertebra
+
+[Term]
+id: FMA:10081
+name: Twelfth thoracic vertebra
+exact_synonym: "Twelfth dorsal vertebra" []
+exact_synonym: "T12 vertebra" []
+is_a: FMA:9139 ! Thoracic vertebra
+relationship: part_of FMA:72064 ! Set of thoracic vertebrae
+relationship: has_part FMA:29787 ! Bony part of twelfth thoracic vertebra
+relationship: part_of FMA:9140 ! Thoracic vertebral column
+relationship: has_part FMA:10089 ! Twelfth thoracic vertebral arch
+relationship: has_part FMA:10082 ! Body of twelfth thoracic vertebra
+relationship: has_part FMA:28191 ! Periosteum of twelfth thoracic vertebra
+relationship: has_part FMA:26691 ! Bone of twelfth thoracic vertebra
+relationship: has_part FMA:26727 ! Cartilage of twelfth thoracic vertebra
+
+[Term]
+id: FMA:10082
+name: Body of twelfth thoracic vertebra
+exact_synonym: "Twelfth thoracic vertebral body" []
+exact_synonym: "Body of T12 vertebra" []
+is_a: FMA:9141 ! Body of thoracic vertebra
+relationship: part_of FMA:10081 ! Twelfth thoracic vertebra
+relationship: has_part FMA:28673 ! Periosteum of body of twelfth thoracic vertebra
+relationship: has_part FMA:26253 ! Right neurocentral junction of twelfth thoracic vertebra
+relationship: has_part FMA:29902 ! Bony part of body of twelfth thoracic vertebra
+relationship: has_part FMA:26254 ! Left neurocentral junction of twelfth thoracic vertebra
+relationship: has_part FMA:26643 ! Right posterolateral part of body of twelfth thoracic vertebra
+relationship: has_part FMA:26608 ! Central part of body of twelfth thoracic vertebra
+relationship: has_part FMA:30371 ! Cartilage of body of twelfth thoracic vertebra
+relationship: has_part FMA:26644 ! Left posterolateral part of body of twelfth thoracic vertebra
+
+[Term]
+id: FMA:10083
+name: Anterior surface of body of twelfth thoracic vertebra
+is_a: FMA:9147 ! Anterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10084
+name: Posterior surface of body of twelfth thoracic vertebra
+is_a: FMA:9148 ! Posterior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10085
+name: Lateral surface of body of twelfth thoracic vertebra
+is_a: FMA:9162 ! Lateral surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10087
+name: Superior surface of body of twelfth thoracic vertebra
+exact_synonym: "Upper border of body of twelfth thoracic vertebra" []
+is_a: FMA:9163 ! Superior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10088
+name: Inferior surface of body of twelfth thoracic vertebra
+exact_synonym: "Lower border of body of twelfth thoracic vertebra" []
+is_a: FMA:9164 ! Inferior surface of body of thoracic vertebra
+
+[Term]
+id: FMA:10089
+name: Twelfth thoracic vertebral arch
+exact_synonym: "Arch of T12 vertebra" []
+exact_synonym: "Arch of twelfth thoracic vertebra" []
+is_a: FMA:9151 ! Thoracic vertebral arch
+relationship: part_of FMA:10081 ! Twelfth thoracic vertebra
+relationship: has_part FMA:12111 ! Left lamina of twelfth thoracic vertebra
+relationship: has_part FMA:12108 ! Right pedicle of twelfth thoracic vertebra
+relationship: has_part FMA:28733 ! Periosteum of twelfth thoracic vertebral arch
+relationship: has_part FMA:12121 ! Left superior articular process of twelfth thoracic vertebra
+relationship: has_part FMA:12117 ! Left transverse process of twelfth thoracic vertebra
+relationship: has_part FMA:12122 ! Right inferior articular process of twelfth thoracic vertebra
+relationship: has_part FMA:29994 ! Bony part of twelfth thoracic vertebral arch
+relationship: has_part FMA:12109 ! Left pedicle of twelfth thoracic vertebra
+relationship: has_part FMA:12123 ! Left inferior articular process of twelfth thoracic vertebra
+relationship: has_part FMA:12110 ! Right lamina of twelfth thoracic vertebra
+relationship: has_part FMA:10094 ! Spinous process of twelfth thoracic vertebra
+relationship: has_part FMA:12116 ! Right transverse process of twelfth thoracic vertebra
+relationship: has_part FMA:12120 ! Right superior articular process of twelfth thoracic vertebra
+
+[Term]
+id: FMA:10090
+name: Pedicle of twelfth thoracic vertebra
+exact_synonym: "Twelfth thoracic vertebral pedicle" []
+exact_synonym: "Pedicle of T12 vertebra" []
+is_a: FMA:9152 ! Pedicle of thoracic vertebra
+
+[Term]
+id: FMA:10091
+name: Superior vertebral notch of twelfth thoracic vertebra
+exact_synonym: "Superior vertebral incisure of pedicle of twelfth thoracic vertebra" []
+is_a: FMA:9157 ! Superior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10092
+name: Inferior vertebral notch of twelfth thoracic vertebra
+exact_synonym: "Inferior vertebral incisure of pedicle of twelfth thoracic vertebra" []
+is_a: FMA:9158 ! Inferior vertebral notch of thoracic vertebra
+
+[Term]
+id: FMA:10093
+name: Lamina of twelfth thoracic vertebra
+exact_synonym: "Twelfth thoracic vertebral lamina" []
+is_a: FMA:9153 ! Lamina of thoracic vertebra
+
+[Term]
+id: FMA:10094
+name: Spinous process of twelfth thoracic vertebra
+exact_synonym: "Spinous process of T12 vertebra" []
+is_a: FMA:9149 ! Spinous process of thoracic vertebra
+relationship: part_of FMA:10089 ! Twelfth thoracic vertebral arch
+relationship: has_part FMA:28961 ! Periosteum of spinous process of twelfth thoracic vertebra
+relationship: has_part FMA:30281 ! Bony part of spinous process of twelfth thoracic vertebra
+
+[Term]
+id: FMA:10095
+name: Transverse process of twelfth thoracic vertebra
+exact_synonym: "Transverse process of T12 vertebra" []
+is_a: FMA:9150 ! Transverse process of thoracic vertebra
+
+[Term]
+id: FMA:10096
+name: Vasculature of bony part of twelfth thoracic vertebra
+is_a: FMA:9154 ! Vasculature of bony part of thoracic vertebra
+
+[Term]
+id: FMA:10097
+name: Superior articular process of twelfth thoracic vertebra
+exact_synonym: "Cranial articular process of twelfth thoracic vertebra" []
+is_a: FMA:9155 ! Superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10098
+name: Articular facet of superior articular process of twelfth thoracic vertebra
+is_a: FMA:10521 ! Articular facet of superior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10099
+name: Inferior articular process of twelfth thoracic vertebra
+exact_synonym: "Caudal articular process of twelfth thoracic vertebra" []
+is_a: FMA:9156 ! Inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10100
+name: Articular facet of inferior articular process of twelfth thoracic vertebra
+is_a: FMA:9160 ! Articular facet of inferior articular process of thoracic vertebra
+
+[Term]
+id: FMA:10101
+name: Intervertebral foramen of twelfth thoracic vertebra
+is_a: FMA:9144 ! Intervertebral foramen of thoracic vertebra
+
+[Term]
+id: FMA:10102
+name: First costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10103
+name: Right first costochondral joint
+is_a: FMA:10102 ! First costochondral joint
+relationship: part_of FMA:7857 ! Right first rib
+
+[Term]
+id: FMA:10104
+name: Left first costochondral joint
+is_a: FMA:10102 ! First costochondral joint
+relationship: part_of FMA:7987 ! Left first rib
+
+[Term]
+id: FMA:10105
+name: Second costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10106
+name: Right second costochondral joint
+is_a: FMA:10105 ! Second costochondral joint
+relationship: part_of FMA:7882 ! Right second rib
+
+[Term]
+id: FMA:10107
+name: Left second costochondral joint
+is_a: FMA:10105 ! Second costochondral joint
+relationship: part_of FMA:8012 ! Left second rib
+
+[Term]
+id: FMA:10108
+name: Third costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10109
+name: Right third costochondral joint
+is_a: FMA:10108 ! Third costochondral joint
+relationship: part_of FMA:7909 ! Right third rib
+
+[Term]
+id: FMA:10110
+name: Left third costochondral joint
+is_a: FMA:10108 ! Third costochondral joint
+relationship: part_of FMA:8039 ! Left third rib
+
+[Term]
+id: FMA:10111
+name: Fourth costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10112
+name: Right fourth costochondral joint
+is_a: FMA:10111 ! Fourth costochondral joint
+relationship: part_of FMA:7957 ! Right fourth rib
+
+[Term]
+id: FMA:10113
+name: Left fourth costochondral joint
+is_a: FMA:10111 ! Fourth costochondral joint
+relationship: part_of FMA:8148 ! Left fourth rib
+
+[Term]
+id: FMA:10114
+name: Fifth costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10115
+name: Right fifth costochondral joint
+is_a: FMA:10114 ! Fifth costochondral joint
+relationship: part_of FMA:8066 ! Right fifth rib
+
+[Term]
+id: FMA:10116
+name: Left fifth costochondral joint
+is_a: FMA:10114 ! Fifth costochondral joint
+relationship: part_of FMA:8093 ! Left fifth rib
+
+[Term]
+id: FMA:10117
+name: Sixth costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10118
+name: Right sixth costochondral joint
+is_a: FMA:10117 ! Sixth costochondral joint
+relationship: part_of FMA:8175 ! Right sixth rib
+
+[Term]
+id: FMA:10119
+name: Left sixth costochondral joint
+is_a: FMA:10117 ! Sixth costochondral joint
+relationship: part_of FMA:8202 ! Left sixth rib
+
+[Term]
+id: FMA:10120
+name: Seventh costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10121
+name: Right seventh costochondral joint
+is_a: FMA:10120 ! Seventh costochondral joint
+relationship: part_of FMA:8229 ! Right seventh rib
+
+[Term]
+id: FMA:10122
+name: Left seventh costochondral joint
+is_a: FMA:10120 ! Seventh costochondral joint
+relationship: part_of FMA:8256 ! Left seventh rib
+
+[Term]
+id: FMA:10123
+name: Eighth costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10124
+name: Right eighth costochondral joint
+is_a: FMA:10123 ! Eighth costochondral joint
+relationship: part_of FMA:8283 ! Right eighth rib
+
+[Term]
+id: FMA:10125
+name: Left eighth costochondral joint
+is_a: FMA:10123 ! Eighth costochondral joint
+relationship: part_of FMA:8310 ! Left eighth rib
+
+[Term]
+id: FMA:10126
+name: Ninth costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10127
+name: Right ninth costochondral joint
+is_a: FMA:10126 ! Ninth costochondral joint
+relationship: part_of FMA:8364 ! Right ninth rib
+
+[Term]
+id: FMA:10128
+name: Left ninth costochondral joint
+is_a: FMA:10126 ! Ninth costochondral joint
+relationship: part_of FMA:8391 ! Left ninth rib
+
+[Term]
+id: FMA:10129
+name: Tenth costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10130
+name: Right tenth costochondral joint
+is_a: FMA:10129 ! Tenth costochondral joint
+relationship: part_of FMA:8445 ! Right tenth rib
+
+[Term]
+id: FMA:10131
+name: Left tenth costochondral joint
+is_a: FMA:10129 ! Tenth costochondral joint
+relationship: part_of FMA:8472 ! Left tenth rib
+
+[Term]
+id: FMA:10132
+name: Eleventh costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10133
+name: Right eleventh costochondral joint
+is_a: FMA:10132 ! Eleventh costochondral joint
+relationship: part_of FMA:8531 ! Right eleventh rib
+
+[Term]
+id: FMA:10134
+name: Left eleventh costochondral joint
+is_a: FMA:10132 ! Eleventh costochondral joint
+relationship: part_of FMA:8532 ! Left eleventh rib
+
+[Term]
+id: FMA:10135
+name: Twelfth costochondral joint
+is_a: FMA:7956 ! Costochondral joint
+
+[Term]
+id: FMA:10136
+name: Right twelfth costochondral joint
+is_a: FMA:10135 ! Twelfth costochondral joint
+relationship: part_of FMA:8533 ! Right twelfth rib
+
+[Term]
+id: FMA:10137
+name: Left twelfth costochondral joint
+is_a: FMA:10135 ! Twelfth costochondral joint
+relationship: part_of FMA:8534 ! Left twelfth rib
+
+[Term]
+id: FMA:10138
+name: Accessory ligament
+is_a: FMA:11106 ! Ligament of costotransverse joint
+relationship: part_of FMA:7952 ! Costotransverse joint
+
+[Term]
+id: FMA:10139
+name: First costotransverse joint
+is_a: FMA:7952 ! Costotransverse joint
+relationship: has_part FMA:10145 ! Lateral costotransverse ligament of first costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10142 ! Capsule of first costotransverse joint
+relationship: has_part FMA:10144 ! Costotransverse ligament of first costotransverse joint
+
+[Term]
+id: FMA:10140
+name: Capsule of costotransverse joint
+exact_synonym: "Costotransverse joint capsule" []
+exact_synonym: "Fibrous capsule of costotransverse joint" []
+is_a: FMA:34836 ! Articular capsule
+relationship: part_of FMA:7952 ! Costotransverse joint
+
+[Term]
+id: FMA:10141
+name: Second costotransverse joint
+is_a: FMA:7952 ! Costotransverse joint
+relationship: has_part FMA:10161 ! Accessory ligament of second costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10157 ! Capsule of second costotransverse joint
+relationship: has_part FMA:10158 ! Superior costotransverse ligament of second costotransverse joint
+relationship: has_part FMA:10159 ! Costotransverse ligament of second costotransverse joint
+relationship: has_part FMA:10160 ! Lateral costotransverse ligament of second costotransverse joint
+
+[Term]
+id: FMA:10142
+name: Capsule of first costotransverse joint
+exact_synonym: "First costotransverse joint capsule" []
+is_a: FMA:10140 ! Capsule of costotransverse joint
+relationship: part_of FMA:10139 ! First costotransverse joint
+
+[Term]
+id: FMA:10143
+name: Costotransverse foramen
+is_a: FMA:9338 ! Anatomical conduit
+
+[Term]
+id: FMA:10144
+name: Costotransverse ligament of first costotransverse joint
+is_a: FMA:12163 ! Costotransverse ligament
+relationship: part_of FMA:10139 ! First costotransverse joint
+
+[Term]
+id: FMA:10145
+name: Lateral costotransverse ligament of first costotransverse joint
+is_a: FMA:12162 ! Lateral costotransverse ligament
+relationship: part_of FMA:10139 ! First costotransverse joint
+
+[Term]
+id: FMA:10146
+name: First costotransverse foramen
+is_a: FMA:10143 ! Costotransverse foramen
+
+[Term]
+id: FMA:10147
+name: Right first costotransverse joint
+is_a: FMA:10139 ! First costotransverse joint
+relationship: has_part FMA:10148 ! Capsule of right first costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10150 ! Lateral costotransverse ligament of right first costotransverse joint
+relationship: has_part FMA:10149 ! Costotransverse ligament of right first costotransverse joint
+
+[Term]
+id: FMA:10148
+name: Capsule of right first costotransverse joint
+exact_synonym: "Right first costotransverse joint capsule" []
+is_a: FMA:10142 ! Capsule of first costotransverse joint
+relationship: part_of FMA:10147 ! Right first costotransverse joint
+
+[Term]
+id: FMA:10149
+name: Costotransverse ligament of right first costotransverse joint
+is_a: FMA:10144 ! Costotransverse ligament of first costotransverse joint
+relationship: part_of FMA:10147 ! Right first costotransverse joint
+
+[Term]
+id: FMA:10150
+name: Lateral costotransverse ligament of right first costotransverse joint
+is_a: FMA:10145 ! Lateral costotransverse ligament of first costotransverse joint
+relationship: part_of FMA:10147 ! Right first costotransverse joint
+
+[Term]
+id: FMA:10151
+name: Right first costotransverse foramen
+is_a: FMA:10146 ! First costotransverse foramen
+
+[Term]
+id: FMA:10152
+name: Left first costotransverse joint
+is_a: FMA:10139 ! First costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10153 ! Capsule of left first costotransverse joint
+relationship: has_part FMA:10154 ! Costotransverse ligament of left first costotransverse joint
+relationship: has_part FMA:10155 ! Lateral costotransverse ligament of left first costotransverse joint
+
+[Term]
+id: FMA:10153
+name: Capsule of left first costotransverse joint
+exact_synonym: "Left first costotransverse joint capsule" []
+is_a: FMA:10142 ! Capsule of first costotransverse joint
+relationship: part_of FMA:10152 ! Left first costotransverse joint
+
+[Term]
+id: FMA:10154
+name: Costotransverse ligament of left first costotransverse joint
+is_a: FMA:10144 ! Costotransverse ligament of first costotransverse joint
+relationship: part_of FMA:10152 ! Left first costotransverse joint
+
+[Term]
+id: FMA:10155
+name: Lateral costotransverse ligament of left first costotransverse joint
+is_a: FMA:10145 ! Lateral costotransverse ligament of first costotransverse joint
+relationship: part_of FMA:10152 ! Left first costotransverse joint
+
+[Term]
+id: FMA:10156
+name: Left first costotransverse foramen
+is_a: FMA:10146 ! First costotransverse foramen
+
+[Term]
+id: FMA:10157
+name: Capsule of second costotransverse joint
+exact_synonym: "Second costotransverse joint capsule" []
+is_a: FMA:10140 ! Capsule of costotransverse joint
+relationship: part_of FMA:10141 ! Second costotransverse joint
+
+[Term]
+id: FMA:10158
+name: Superior costotransverse ligament of second costotransverse joint
+is_a: FMA:8958 ! Superior costotransverse ligament
+relationship: part_of FMA:10141 ! Second costotransverse joint
+
+[Term]
+id: FMA:10159
+name: Costotransverse ligament of second costotransverse joint
+is_a: FMA:12163 ! Costotransverse ligament
+relationship: part_of FMA:10141 ! Second costotransverse joint
+
+[Term]
+id: FMA:10160
+name: Lateral costotransverse ligament of second costotransverse joint
+is_a: FMA:12162 ! Lateral costotransverse ligament
+relationship: part_of FMA:10141 ! Second costotransverse joint
+
+[Term]
+id: FMA:10161
+name: Accessory ligament of second costotransverse joint
+is_a: FMA:10138 ! Accessory ligament
+relationship: part_of FMA:10141 ! Second costotransverse joint
+
+[Term]
+id: FMA:10162
+name: Second costotransverse foramen
+is_a: FMA:10143 ! Costotransverse foramen
+
+[Term]
+id: FMA:10163
+name: Right second costotransverse joint
+is_a: FMA:10141 ! Second costotransverse joint
+relationship: has_part FMA:10167 ! Lateral costotransverse ligament of right second costotransverse joint
+relationship: has_part FMA:10168 ! Accessory ligament of right second costotransverse joint
+relationship: has_part FMA:10165 ! Superior costotransverse ligament of right second costotransverse joint
+relationship: has_part FMA:10164 ! Capsule of right second costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10166 ! Costotransverse ligament of right second costotransverse joint
+
+[Term]
+id: FMA:10164
+name: Capsule of right second costotransverse joint
+exact_synonym: "Right second costotransverse joint capsule" []
+is_a: FMA:10157 ! Capsule of second costotransverse joint
+relationship: part_of FMA:10163 ! Right second costotransverse joint
+
+[Term]
+id: FMA:10165
+name: Superior costotransverse ligament of right second costotransverse joint
+is_a: FMA:10158 ! Superior costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10163 ! Right second costotransverse joint
+
+[Term]
+id: FMA:10166
+name: Costotransverse ligament of right second costotransverse joint
+is_a: FMA:10159 ! Costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10163 ! Right second costotransverse joint
+
+[Term]
+id: FMA:10167
+name: Lateral costotransverse ligament of right second costotransverse joint
+is_a: FMA:10160 ! Lateral costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10163 ! Right second costotransverse joint
+
+[Term]
+id: FMA:10168
+name: Accessory ligament of right second costotransverse joint
+is_a: FMA:10161 ! Accessory ligament of second costotransverse joint
+relationship: part_of FMA:10163 ! Right second costotransverse joint
+
+[Term]
+id: FMA:10169
+name: Right second costotransverse foramen
+is_a: FMA:10162 ! Second costotransverse foramen
+
+[Term]
+id: FMA:10170
+name: Left second costotransverse joint
+is_a: FMA:10141 ! Second costotransverse joint
+relationship: has_part FMA:10171 ! Capsule of left second costotransverse joint
+relationship: has_part FMA:10174 ! Lateral costotransverse ligament of left second costotransverse joint
+relationship: has_part FMA:10173 ! Costotransverse ligament of left second costotransverse joint
+relationship: has_part FMA:10175 ! Accessory ligament of left second costotransverse joint
+relationship: has_part FMA:10172 ! Superior costotransverse ligament of left second costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+
+[Term]
+id: FMA:10171
+name: Capsule of left second costotransverse joint
+exact_synonym: "Left second costotransverse joint capsule" []
+is_a: FMA:10157 ! Capsule of second costotransverse joint
+relationship: part_of FMA:10170 ! Left second costotransverse joint
+
+[Term]
+id: FMA:10172
+name: Superior costotransverse ligament of left second costotransverse joint
+is_a: FMA:10158 ! Superior costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10170 ! Left second costotransverse joint
+
+[Term]
+id: FMA:10173
+name: Costotransverse ligament of left second costotransverse joint
+is_a: FMA:10159 ! Costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10170 ! Left second costotransverse joint
+
+[Term]
+id: FMA:10174
+name: Lateral costotransverse ligament of left second costotransverse joint
+is_a: FMA:10160 ! Lateral costotransverse ligament of second costotransverse joint
+relationship: part_of FMA:10170 ! Left second costotransverse joint
+
+[Term]
+id: FMA:10175
+name: Accessory ligament of left second costotransverse joint
+is_a: FMA:10161 ! Accessory ligament of second costotransverse joint
+relationship: part_of FMA:10170 ! Left second costotransverse joint
+
+[Term]
+id: FMA:10176
+name: Left second costotransverse foramen
+is_a: FMA:10162 ! Second costotransverse foramen
+
+[Term]
+id: FMA:10177
+name: Third costotransverse joint
+is_a: FMA:7952 ! Costotransverse joint
+relationship: has_part FMA:10181 ! Lateral costotransverse ligament of third costotransverse joint
+relationship: has_part FMA:10182 ! Accessory ligament of third costotransverse joint
+relationship: has_part FMA:10179 ! Superior costotransverse ligament of third costotransverse joint
+relationship: has_part FMA:10178 ! Capsule of third costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10180 ! Costotransverse ligament of third costotransverse joint
+
+[Term]
+id: FMA:10178
+name: Capsule of third costotransverse joint
+exact_synonym: "Third costotransverse joint capsule" []
+is_a: FMA:10140 ! Capsule of costotransverse joint
+relationship: part_of FMA:10177 ! Third costotransverse joint
+
+[Term]
+id: FMA:10179
+name: Superior costotransverse ligament of third costotransverse joint
+is_a: FMA:8958 ! Superior costotransverse ligament
+relationship: part_of FMA:10177 ! Third costotransverse joint
+
+[Term]
+id: FMA:10180
+name: Costotransverse ligament of third costotransverse joint
+is_a: FMA:12163 ! Costotransverse ligament
+relationship: part_of FMA:10177 ! Third costotransverse joint
+
+[Term]
+id: FMA:10181
+name: Lateral costotransverse ligament of third costotransverse joint
+is_a: FMA:12162 ! Lateral costotransverse ligament
+relationship: part_of FMA:10177 ! Third costotransverse joint
+
+[Term]
+id: FMA:10182
+name: Accessory ligament of third costotransverse joint
+is_a: FMA:10138 ! Accessory ligament
+relationship: part_of FMA:10177 ! Third costotransverse joint
+
+[Term]
+id: FMA:10183
+name: Third costotransverse foramen
+is_a: FMA:10143 ! Costotransverse foramen
+
+[Term]
+id: FMA:10184
+name: Right third costotransverse joint
+is_a: FMA:10177 ! Third costotransverse joint
+relationship: has_part FMA:10186 ! Superior costotransverse ligament of right third costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10188 ! Lateral costotransverse ligament of right third costotransverse joint
+relationship: has_part FMA:10185 ! Capsule of right third costotransverse joint
+relationship: has_part FMA:10189 ! Accessory ligament of right third costotransverse joint
+
+[Term]
+id: FMA:10185
+name: Capsule of right third costotransverse joint
+exact_synonym: "Right third costotransverse joint capsule" []
+is_a: FMA:10178 ! Capsule of third costotransverse joint
+relationship: part_of FMA:10184 ! Right third costotransverse joint
+
+[Term]
+id: FMA:10186
+name: Superior costotransverse ligament of right third costotransverse joint
+is_a: FMA:10179 ! Superior costotransverse ligament of third costotransverse joint
+relationship: part_of FMA:10184 ! Right third costotransverse joint
+
+[Term]
+id: FMA:10187
+name: Costotransverse ligament of right third costotransverse joint
+is_a: FMA:10180 ! Costotransverse ligament of third costotransverse joint
+
+[Term]
+id: FMA:10188
+name: Lateral costotransverse ligament of right third costotransverse joint
+is_a: FMA:10181 ! Lateral costotransverse ligament of third costotransverse joint
+relationship: part_of FMA:10184 ! Right third costotransverse joint
+
+[Term]
+id: FMA:10189
+name: Accessory ligament of right third costotransverse joint
+is_a: FMA:10182 ! Accessory ligament of third costotransverse joint
+relationship: part_of FMA:10184 ! Right third costotransverse joint
+
+[Term]
+id: FMA:10190
+name: Right third costotransverse foramen
+is_a: FMA:10183 ! Third costotransverse foramen
+
+[Term]
+id: FMA:10191
+name: Left third costotransverse joint
+is_a: FMA:10177 ! Third costotransverse joint
+relationship: has_part FMA:10196 ! Accessory ligament of left third costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10193 ! Superior costotransverse ligament of left third costotransverse joint
+relationship: has_part FMA:10194 ! Costotransverse ligament of left third costotransverse joint
+relationship: has_part FMA:10192 ! Capsule of left third costotransverse joint
+relationship: has_part FMA:10195 ! Lateral costotransverse ligament of left third costotransverse joint
+
+[Term]
+id: FMA:10192
+name: Capsule of left third costotransverse joint
+exact_synonym: "Left third costotransverse joint capsule" []
+is_a: FMA:10178 ! Capsule of third costotransverse joint
+relationship: part_of FMA:10191 ! Left third costotransverse joint
+
+[Term]
+id: FMA:10193
+name: Superior costotransverse ligament of left third costotransverse joint
+is_a: FMA:10179 ! Superior costotransverse ligament of third costotransverse joint
+relationship: part_of FMA:10191 ! Left third costotransverse joint
+
+[Term]
+id: FMA:10194
+name: Costotransverse ligament of left third costotransverse joint
+is_a: FMA:10180 ! Costotransverse ligament of third costotransverse joint
+relationship: part_of FMA:10191 ! Left third costotransverse joint
+
+[Term]
+id: FMA:10195
+name: Lateral costotransverse ligament of left third costotransverse joint
+is_a: FMA:10181 ! Lateral costotransverse ligament of third costotransverse joint
+relationship: part_of FMA:10191 ! Left third costotransverse joint
+
+[Term]
+id: FMA:10196
+name: Accessory ligament of left third costotransverse joint
+is_a: FMA:10182 ! Accessory ligament of third costotransverse joint
+relationship: part_of FMA:10191 ! Left third costotransverse joint
+
+[Term]
+id: FMA:10197
+name: Left third costotransverse foramen
+is_a: FMA:10183 ! Third costotransverse foramen
+
+[Term]
+id: FMA:10198
+name: Fourth costotransverse joint
+is_a: FMA:7952 ! Costotransverse joint
+relationship: has_part FMA:10201 ! Lateral costotransverse ligament of fourth costotransverse joint
+relationship: has_part FMA:10202 ! Costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10199 ! Capsule of fourth costotransverse joint
+relationship: has_part FMA:10200 ! Superior costotransverse ligament of fourth costotransverse joint
+relationship: has_part FMA:10203 ! Accessory ligament of fourth costotransverse joint
+
+[Term]
+id: FMA:10199
+name: Capsule of fourth costotransverse joint
+exact_synonym: "Fourth costotransverse joint capsule" []
+is_a: FMA:10140 ! Capsule of costotransverse joint
+relationship: part_of FMA:10198 ! Fourth costotransverse joint
+
+[Term]
+id: FMA:10200
+name: Superior costotransverse ligament of fourth costotransverse joint
+is_a: FMA:8958 ! Superior costotransverse ligament
+relationship: part_of FMA:10198 ! Fourth costotransverse joint
+
+[Term]
+id: FMA:10201
+name: Lateral costotransverse ligament of fourth costotransverse joint
+is_a: FMA:12162 ! Lateral costotransverse ligament
+relationship: part_of FMA:10198 ! Fourth costotransverse joint
+
+[Term]
+id: FMA:10202
+name: Costotransverse ligament of fourth costotransverse joint
+is_a: FMA:12163 ! Costotransverse ligament
+relationship: part_of FMA:10198 ! Fourth costotransverse joint
+
+[Term]
+id: FMA:10203
+name: Accessory ligament of fourth costotransverse joint
+is_a: FMA:10138 ! Accessory ligament
+relationship: part_of FMA:10198 ! Fourth costotransverse joint
+
+[Term]
+id: FMA:10204
+name: Fourth costotransverse foramen
+is_a: FMA:10143 ! Costotransverse foramen
+
+[Term]
+id: FMA:10205
+name: Right fourth costotransverse joint
+is_a: FMA:10198 ! Fourth costotransverse joint
+relationship: has_part FMA:10209 ! Lateral costotransverse ligament of right fourth costotransverse joint
+relationship: has_part FMA:10207 ! Superior costotransverse ligament of right fourth costotransverse joint
+relationship: has_part FMA:10210 ! Accessory ligament of right fourth costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10206 ! Capsule of right fourth costotransverse joint
+relationship: has_part FMA:10208 ! Costotransverse ligament of right fourth costotransverse joint
+
+[Term]
+id: FMA:10206
+name: Capsule of right fourth costotransverse joint
+exact_synonym: "Right fourth costotransverse joint capsule" []
+is_a: FMA:10199 ! Capsule of fourth costotransverse joint
+relationship: part_of FMA:10205 ! Right fourth costotransverse joint
+
+[Term]
+id: FMA:10207
+name: Superior costotransverse ligament of right fourth costotransverse joint
+is_a: FMA:10200 ! Superior costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10205 ! Right fourth costotransverse joint
+
+[Term]
+id: FMA:10208
+name: Costotransverse ligament of right fourth costotransverse joint
+is_a: FMA:10202 ! Costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10205 ! Right fourth costotransverse joint
+
+[Term]
+id: FMA:10209
+name: Lateral costotransverse ligament of right fourth costotransverse joint
+is_a: FMA:10201 ! Lateral costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10205 ! Right fourth costotransverse joint
+
+[Term]
+id: FMA:10210
+name: Accessory ligament of right fourth costotransverse joint
+is_a: FMA:10203 ! Accessory ligament of fourth costotransverse joint
+relationship: part_of FMA:10205 ! Right fourth costotransverse joint
+
+[Term]
+id: FMA:10211
+name: Right fourth costotransverse foramen
+is_a: FMA:10204 ! Fourth costotransverse foramen
+
+[Term]
+id: FMA:10212
+name: Left fourth costotransverse joint
+is_a: FMA:10198 ! Fourth costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10215 ! Costotransverse ligament of left fourth costotransverse joint
+relationship: has_part FMA:10217 ! Accessory ligament of left fourth costotransverse joint
+relationship: has_part FMA:10213 ! Capsule of left fourth costotransverse joint
+relationship: has_part FMA:10216 ! Lateral costotransverse ligament of left fourth costotransverse joint
+relationship: has_part FMA:10214 ! Superior costotransverse ligament of left fourth costotransverse joint
+
+[Term]
+id: FMA:10213
+name: Capsule of left fourth costotransverse joint
+exact_synonym: "Left fourth costotransverse joint capsule" []
+is_a: FMA:10199 ! Capsule of fourth costotransverse joint
+relationship: part_of FMA:10212 ! Left fourth costotransverse joint
+
+[Term]
+id: FMA:10214
+name: Superior costotransverse ligament of left fourth costotransverse joint
+is_a: FMA:10200 ! Superior costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10212 ! Left fourth costotransverse joint
+
+[Term]
+id: FMA:10215
+name: Costotransverse ligament of left fourth costotransverse joint
+is_a: FMA:10202 ! Costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10212 ! Left fourth costotransverse joint
+
+[Term]
+id: FMA:10216
+name: Lateral costotransverse ligament of left fourth costotransverse joint
+is_a: FMA:10201 ! Lateral costotransverse ligament of fourth costotransverse joint
+relationship: part_of FMA:10212 ! Left fourth costotransverse joint
+
+[Term]
+id: FMA:10217
+name: Accessory ligament of left fourth costotransverse joint
+is_a: FMA:10203 ! Accessory ligament of fourth costotransverse joint
+relationship: part_of FMA:10212 ! Left fourth costotransverse joint
+
+[Term]
+id: FMA:10218
+name: Left fourth costotransverse foramen
+is_a: FMA:10204 ! Fourth costotransverse foramen
+
+[Term]
+id: FMA:10219
+name: Fifth costotransverse joint
+is_a: FMA:7952 ! Costotransverse joint
+relationship: has_part FMA:10223 ! Lateral costotransverse ligament of fifth costotransverse joint
+relationship: part_of FMA:7480 ! Rib cage
+relationship: has_part FMA:10221 ! Superior costotransverse ligament of fifth costotransverse joint
+relationship: has_part FMA:10224 ! Accessory ligament of fifth costotransverse joint
+relationship: has_part FMA:10222 ! Costotransverse ligament of fifth costotransverse joint
+relationship: has_part FMA:10220 ! Capsule of fifth costotransverse joint
+
+[Term]
+id: FMA:10220
+name: Capsule of fifth costotransverse joint
+exact_synonym: "Fifth costotransverse joint capsule" []
+is_a: FMA:10140 ! Capsule of costotransverse joint
+relationship: part_of FMA:10219 ! Fifth costotransverse joint
+
+[Term]
+id: FMA:10221
+name: Superior costotransverse ligament of fifth costotransverse joint
+is_a: FMA:8958 ! Superior costotransverse ligament
+relationship: part_of FMA:10219 ! Fifth costotransverse joint
+
+[Term]
+id: FMA:10222
+name: Costotransverse ligament of fifth costotransverse joint
+is_a: FMA:12163 ! Costotransverse ligament
+relationship: part_of FMA:10219 ! Fifth costotransverse joint
+
+[Term]
+id: FMA:10223
+name: Lateral costotransverse ligament of fifth costotransverse joint
+is_a...
 
[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [224] phenote/trunk/conf/human.cfg

From: <nl...@us...> - 2006-11-27 21:45:05

Revision: 224
          http://svn.sourceforge.net/obo/?rev=224&view=rev
Author:   nlw
Date:     2006-11-27 13:41:43 -0800 (Mon, 27 Nov 2006)

Log Message:
-----------
added human config file

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

Added: phenote/trunk/conf/human.cfg
===================================================================
--- phenote/trunk/conf/human.cfg	                        (rev 0)
+++ phenote/trunk/conf/human.cfg	2006-11-27 21:41:43 UTC (rev 224)
@@ -0,0 +1,29 @@
+
+<phenote-configuration version="0.9" xmlns="phenote/config/xml">
+
+  <dataadapter name="phenosyntax"/>
+  <dataadapter name="phenoxml"/>
+
+  <log config-file="conf/log4j-standalone.xml" />
+
+  <field name="Pub" />                      
+
+  <field name="Genotype" type="free_text"/>
+
+  <field name="Genetic Context" file="context.obo"/>
+
+  <field name="Entity">
+     <postcomp relationship-ontology="relationship.obo"/>
+     <ontology name="Human Anatomy" file="fma_obo.obo"/>	
+     <ontology name="Gene Ontology" file="gene_ontology.obo"/>
+     <ontology name="Chemical" file="chebi.obo"/>	
+     <ontology name="Cell Type" file="cell.obo"/>
+     <ontology name="Spatial" file="spatial.obo"/>
+  </field>
+
+  <field name="Quality">
+	<ontology name="Quality" file="quality.obo"/>
+	<ontology name="MamPheno" file="mammalian_phenotype.obo"/>
+  </field>	
+
+</phenote-configuration>


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[Obo-svn-commit] SF.net SVN: obo: [223] phenote/trunk/src/java/phenote

From: <mg...@us...> - 2006-11-23 00:41:24

Revision: 223
          http://svn.sourceforge.net/obo/?rev=223&view=rev
Author:   mgibson
Date:     2006-11-22 16:41:22 -0800 (Wed, 22 Nov 2006)

Log Message:
-----------
ammended pheno syntax adapter a little - still problems
pheno xml is still broken with new paradigm

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java
    phenote/trunk/src/java/phenote/datamodel/Character.java
    phenote/trunk/src/java/phenote/datamodel/CharacterI.java

Modified: phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java	2006-11-22 23:40:05 UTC (rev 222)
+++ phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java	2006-11-23 00:41:22 UTC (rev 223)
@@ -46,22 +46,31 @@
     }
     StringBuffer sb = new StringBuffer();
 
-    if (character.hasPub())
-      sb.append("PUB=").append(character.getPub());
-    // Genotype - not strictly part of pheno syntax but lets face it we need it
-    // i would say its an omission from syntax
-    sb.append(" GT=").append(character.getGenotype());
-    if (character.hasGeneticContext())
-      sb.append(" GC=").append(makeValue(character.getGeneticContext()));
+    try {
 
-    if (character.getEntity() == null)
-      throw new BadCharException("Error: character has no entity, ignoring");
-    sb.append(" E=").append(makeValue(character.getEntity()));
-
-    if (character.getQuality() == null)
-      throw new BadCharException("Error: character has no quality, ignoring");
-    sb.append(" Q=").append(makeValue(character.getQuality()));
-
+      if (character.hasValue("Pub")) // hasPub
+        sb.append("PUB=").append(character.getValueString("Pub")); //Pub());
+      // Genotype - not strictly part of pheno syntax but lets face it we need it
+      // i would say its an omission from syntax
+      //sb.append(" GT=").append(character.getGenotype());
+      sb.append(" GT=").append(character.getValueString("Genotype"));
+      if (character.hasValue("Genetic Context"))
+        sb.append(" GC=").append(makeValue(character.getTerm("Genetic Context")));
+      
+      if (!character.hasValue("Entity"))
+        throw new BadCharException("Error: character has no entity, ignoring");
+      //sb.append(" E=").append(makeValue(character.getEntity()));
+      sb.append(" E=").append(makeValue(character.getTerm("Entity")));
+      
+      //if (character.getQuality() == null)
+      if (!character.hasValue("Quality"))
+        throw new BadCharException("Error: character has no quality, ignoring");
+      sb.append(" Q=").append(makeValue(character.getTerm("Quality")));
+      
+    }
+    catch (Exception e) {
+      throw new BadCharException(e.getMessage());
+    }
     return sb.toString();
   }
 
@@ -77,20 +86,20 @@
     return term.getID() + " /*" + term.getName() + "*/";
   }
 
-  /** Merges id prefix and name, so for id GO:1234 with name "growth" returns
-      "GO:growth", which is readable and computable & syn acceptable - pase - doing ids*/
-  private String idPrefixAndName(OBOClass term) {
-    return getIdPrefix(term)+term.getName();
-  }
+//   /** Merges id prefix and name, so for id GO:1234 with name "growth" returns
+//       "GO:growth", which is readable and computable & syn acceptable - pase - doing ids*/
+//   private String idPrefixAndName(OBOClass term) {
+//     return getIdPrefix(term)+term.getName();
+//   }
     
 
-  /** for GO:12345 returns GO: - with colon! - pase - doing ids */
-  private String getIdPrefix(OBOClass term) {
-    if (term == null) return ""; // shouldnt happen
-    String id = term.getID();
-    int colonIndex = id.indexOf(":");
-    return id.substring(0,colonIndex+1); // +1 retain colon
-  }
+//   /** for GO:12345 returns GO: - with colon! - pase - doing ids */
+//   private String getIdPrefix(OBOClass term) {
+//     if (term == null) return ""; // shouldnt happen
+//     String id = term.getID();
+//     int colonIndex = id.indexOf(":");
+//     return id.substring(0,colonIndex+1); // +1 retain colon
+//   }
 
 
 

Modified: phenote/trunk/src/java/phenote/datamodel/Character.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/Character.java	2006-11-22 23:40:05 UTC (rev 222)
+++ phenote/trunk/src/java/phenote/datamodel/Character.java	2006-11-23 00:41:22 UTC (rev 223)
@@ -42,13 +42,37 @@
 //       cfv = cf.getCharFieldEnum().getValue(this);
     return cfv;
   }
+
+  public String getValueString(String field) throws Exception {
+    CharField cf = getCharFieldForName(field); // throws ex
+    if (!hasValue(cf)) return null; // ?? exception?
+    return getValue(cf).getName();
+  }
+
+  public OBOClass getTerm(String field) throws Exception {
+    CharField cf = getCharFieldForName(field); // throws ex
+    if (!hasValue(cf)) return null; // ?? exception?
+    return getValue(cf).getOboClass();
+  }
+
   // should this be isNull?
   public boolean hasValue(CharField cf) {
     // empty string is a valid value for non-required field - or should there
     // be some sort of somthing to indicate "empty" value?
     return getValue(cf) != null; // && !getValue(cf).equals("");
   }
+  public boolean hasValue(String fieldName) throws Exception {
+    return hasValue(getCharFieldForName(fieldName));
+  }
 
+  private CharField getCharFieldForName(String fieldName) throws Exception {
+    for (CharField cf : charFieldToValue.keySet()) {
+      if (cf.getName().equalsIgnoreCase(fieldName))
+        return cf;
+    }
+    throw new Exception("No field for "+fieldName);
+  }
+
   public String getPub() { return pub; }
   public boolean hasPub() { return pub!=null && !pub.equals(""); }
   public String getGenotype() { return genotype; }

Modified: phenote/trunk/src/java/phenote/datamodel/CharacterI.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharacterI.java	2006-11-22 23:40:05 UTC (rev 222)
+++ phenote/trunk/src/java/phenote/datamodel/CharacterI.java	2006-11-23 00:41:22 UTC (rev 223)
@@ -34,7 +34,11 @@
   /** generic fields!!! */
   public void setValue(CharField cf, CharFieldValue cfv); // ??
   public CharFieldValue getValue(CharField cf);
+  // should make an exception for this
+  public String getValueString(String fieldName) throws Exception; // yuck
+  public OBOClass getTerm(String field) throws Exception;
   public boolean hasValue(CharField cf);
+  public boolean hasValue(String fieldName) throws Exception;
   
   public CharacterI cloneCharacter();
   public boolean equals(CharacterI c);


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[Obo-svn-commit] SF.net SVN: obo: [222] phenote/trunk/build.xml

From: <mg...@us...> - 2006-11-22 23:40:06

Revision: 222
          http://svn.sourceforge.net/obo/?rev=222&view=rev
Author:   mgibson
Date:     2006-11-22 15:40:05 -0800 (Wed, 22 Nov 2006)

Log Message:
-----------
ant for sneaking phenote jar into webstart

Modified Paths:
--------------
    phenote/trunk/build.xml

Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml	2006-11-22 23:38:29 UTC (rev 221)
+++ phenote/trunk/build.xml	2006-11-22 23:40:05 UTC (rev 222)
@@ -403,7 +403,7 @@
       </copy>
     </target>
 
-    <target name="webstart-just-phenote-jar">
+    <target name="webstart-just-phenote-jar" depends="build-all,jar">
        <signjar jar="${lib}/phenote.jar" keystore="plumpkey" alias="signFiles"
                 storepass="plumper" keypass="plumper"/>
        <copy file="${lib}/phenote.jar"


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[Obo-svn-commit] SF.net SVN: obo: [221] phenote/trunk

From: <mg...@us...> - 2006-11-22 23:38:33

Revision: 221
          http://svn.sourceforge.net/obo/?rev=221&view=rev
Author:   mgibson
Date:     2006-11-22 15:38:29 -0800 (Wed, 22 Nov 2006)

Log Message:
-----------
redid layout & tweeked for all the new fields

Modified Paths:
--------------
    phenote/trunk/build.xml
    phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java
    phenote/trunk/src/java/phenote/gui/TermInfo.java
    phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
    phenote/trunk/src/java/phenote/gui/field/FieldPanel.java
    phenote/trunk/src/java/phenote/main/Phenote.java

Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml	2006-11-22 20:43:59 UTC (rev 220)
+++ phenote/trunk/build.xml	2006-11-22 23:38:29 UTC (rev 221)
@@ -389,7 +389,7 @@
     </target>
 
     
-
+<!-- need to test if PHENOTE_VERSION is defined - possible?? -->
     <target name="webstart">
       <copy todir="phenote-webstart">
          <fileset file="doc/phenote-website/*.html"/>
@@ -403,6 +403,12 @@
       </copy>
     </target>
 
+    <target name="webstart-just-phenote-jar">
+       <signjar jar="${lib}/phenote.jar" keystore="plumpkey" alias="signFiles"
+                storepass="plumper" keypass="plumper"/>
+       <copy file="${lib}/phenote.jar"
+             todir="phenote-webstart/${env.PHENOTE_VERSION}/jars"/>
+    </target>
 
 </project>
 

Modified: phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java	2006-11-22 20:43:59 UTC (rev 220)
+++ phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java	2006-11-22 23:38:29 UTC (rev 221)
@@ -67,8 +67,8 @@
 
   private void init() {
     setLayout(new GridLayout(2,1)); // row,col
-    setPreferredSize(new Dimension(400,800));
-    setMinimumSize(new Dimension(400,500));    
+    setPreferredSize(new Dimension(1800,800));
+    setMinimumSize(new Dimension(1400,630));    
 
     characterTableModel = new CharacterTableModel();
     charJTable = new JTable(characterTableModel);

Modified: phenote/trunk/src/java/phenote/gui/TermInfo.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/TermInfo.java	2006-11-22 20:43:59 UTC (rev 220)
+++ phenote/trunk/src/java/phenote/gui/TermInfo.java	2006-11-22 23:38:29 UTC (rev 221)
@@ -58,8 +58,9 @@
 
   public JComponent getComponent() {
     JPanel termInfoPanel = new JPanel(new BorderLayout(0,0)); // hgap,vgap
-    termInfoPanel.setPreferredSize(new Dimension(600,700));
-    termInfoPanel.setMinimumSize(new Dimension(350,500));
+    termInfoPanel.setPreferredSize(new Dimension(700,100));
+    termInfoPanel.setMinimumSize(new Dimension(380,100));
+    //termInfoPanel.setMaximumSize(new Dimension(380,400));
     if (DO_HTML) {
       JEditorPane editorPane = new JEditorPane(); 
       editorPane.setContentType("text/html"); // sets up HTMLEditorKit

Modified: phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2006-11-22 20:43:59 UTC (rev 220)
+++ phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2006-11-22 23:38:29 UTC (rev 221)
@@ -73,11 +73,11 @@
     // this will probably throw errors if non metal look & feel is used
     setUI(new MetalListComboUI());
     setEditable(true);
-    setPreferredSize(new Dimension(390,22));
-    setMaximumSize(new Dimension(390,22));
+    setPreferredSize(new Dimension(390,20));
+    setMaximumSize(new Dimension(390,20));
     // this is super critical - fixes bug where layout goes to hell if string are long
     // in completion - dont ask me why????
-    setMinimumSize(new Dimension(390,22));
+    setMinimumSize(new Dimension(390,20));
     AutoTextFieldEditor autoTextFieldEditor = new AutoTextFieldEditor();
     this.setEditor(autoTextFieldEditor);
     // dont know why by setting fonts this seem to get worse not better in terms of

Modified: phenote/trunk/src/java/phenote/gui/field/FieldPanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/FieldPanel.java	2006-11-22 20:43:59 UTC (rev 220)
+++ phenote/trunk/src/java/phenote/gui/field/FieldPanel.java	2006-11-22 23:38:29 UTC (rev 221)
@@ -3,6 +3,7 @@
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.Container;
+import java.awt.Dimension;
 import java.awt.GridBagConstraints;
 import java.awt.GridBagLayout;
 import java.util.ArrayList;
@@ -29,7 +30,7 @@
  * TermPanel holds all the fields for the terms - Genotype, Entity/Anatomy, QUALITY.
  * Can be populated by hand (Genotype), or  selection of instance in completion list. 
  rename FieldPanel or CharFieldPanel?
- also has SearchParamPanel.
+ also has SearchParamPanel(?).
  */
 
 public class FieldPanel extends JPanel {
@@ -46,7 +47,11 @@
   }
   // false for post comp panel
   public FieldPanel(boolean doAllOntologies) {
+    //this.setPreferredSize(new Dimension(800,750));
+    // should figure depth from # of fields really
+    this.setMinimumSize(new Dimension(690,490));
     fieldPanel = new JPanel(new GridBagLayout());
+    // panel inside of panel - i think is a leftover no reason now
     add(fieldPanel); // default flow layout?
     if (doAllOntologies)
       initAllOntologies();
@@ -128,7 +133,7 @@
   private GridBagConstraints makeFieldConstraint() {
     int x = 2;//ontologyChooserPresent ? 2 : 1;
     int width = 1;//ontologyChooserPresent ? 1 : 2; // ???
-    return GridBagUtil.makeWidthConstraint(x,gridbagRow++,1,3,width);
+    return GridBagUtil.makeWidthConstraint(x,gridbagRow++,1,2,width);
   }
 
   // put button at end of regular row? or beginning of pc row?

Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java	2006-11-22 20:43:59 UTC (rev 220)
+++ phenote/trunk/src/java/phenote/main/Phenote.java	2006-11-22 23:38:29 UTC (rev 221)
@@ -165,7 +165,7 @@
     frame = new JFrame("Phenote "+PhenoteVersion.versionString()); 
     frame.getContentPane().add(makeMainPanel());
     MenuManager.createMenuManager(frame);
-    frame.setPreferredSize(new Dimension(1100,650));
+    frame.setPreferredSize(new Dimension(1100,700));
     if (standalone) // if stand alone exit java on window close
       frame.addWindowListener(new WindowExit());
     frame.pack();
@@ -186,27 +186,32 @@
   private JPanel makeMainPanel() {
     JPanel mainPanel = new JPanel(new GridBagLayout()); // ??
     
-    JPanel termAndTablePanel = new JPanel();
-    BoxLayout bl = new BoxLayout(termAndTablePanel,BoxLayout.Y_AXIS);
-    termAndTablePanel.setLayout(bl);
+    //JPanel termAndTablePanel = new JPanel();
+    JPanel upperPanel = new JPanel();
+    //BoxLayout bl = new BoxLayout(termAndTablePanel,BoxLayout.Y_AXIS);
+    BoxLayout bl = new BoxLayout(upperPanel,BoxLayout.X_AXIS);
+    upperPanel.setLayout(bl);
 
-    //termAndInstancePanel.add(makeTermPanel());
     fieldPanel = new FieldPanel();
-    termAndTablePanel.add(fieldPanel);
+    upperPanel.add(fieldPanel);
 
-    characterTablePanel = new CharacterTablePanel(); //fieldPanel);
-    // eventually switch to event listener - no explicit connection...
-    //fieldPanel.setCharacterTablePanel(characterTablePanel);
-    termAndTablePanel.add(characterTablePanel);
 
-    GridBagConstraints gbc = GridBagUtil.makeConstraint(0,0,5,5);
-    mainPanel.add(termAndTablePanel,gbc);
 
     termInfo = new TermInfo(); //fieldPanel);
-    ++gbc.gridx;  // ??
-    gbc.anchor = GridBagConstraints.NORTHWEST;
-    mainPanel.add(termInfo.getComponent(),gbc);
+    upperPanel.add(termInfo.getComponent());
+    //++gbc.gridx;  // ??
+    //gbc.anchor = GridBagConstraints.NORTHWEST; // ??
+    //mainPanel.add(termInfo.getComponent(),gbc);
+    
 
+    GridBagConstraints gbc = GridBagUtil.makeConstraint(0,0,5,5);
+    mainPanel.add(upperPanel,gbc);
+
+    characterTablePanel = new CharacterTablePanel();
+    //termAndTablePanel.add(characterTablePanel);
+    ++gbc.gridy; // ?
+    mainPanel.add(characterTablePanel,gbc);
+
     return mainPanel;
   }
 


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[Obo-svn-commit] SF.net SVN: obo: [220] phenote/trunk/build.xml

From: <mg...@us...> - 2006-11-22 20:44:02

Revision: 220
          http://svn.sourceforge.net/obo/?rev=220&view=rev
Author:   mgibson
Date:     2006-11-22 12:43:59 -0800 (Wed, 22 Nov 2006)

Log Message:
-----------
ant webstart

Modified Paths:
--------------
    phenote/trunk/build.xml

Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml	2006-11-22 20:26:15 UTC (rev 219)
+++ phenote/trunk/build.xml	2006-11-22 20:43:59 UTC (rev 220)
@@ -375,7 +375,22 @@
 
 <!-- todo do all jars not just phenote - take out -signed -->
 <!-- depends on sym link phenote-webstart and env var PHENOTE_VERSION -->
-    <target name="webstart-website" depends="sign-jars">
+    <target name="build-webstart" depends="build-sign-jars,webstart"/>
+
+    <target name="build-sign-jars" depends="build-all,jar,sign-jars"/>
+
+    <target name="sign-jars">
+       <signjar keystore="plumpkey" alias="signFiles"
+                storepass="plumper" keypass="plumper">
+         <fileset dir="${lib}">
+            <include name="*.jar"/>
+         </fileset>
+       </signjar>
+    </target>
+
+    
+
+    <target name="webstart">
       <copy todir="phenote-webstart">
          <fileset file="doc/phenote-website/*.html"/>
        </copy>
@@ -388,16 +403,7 @@
       </copy>
     </target>
 
-    <target name="sign-jars" depends="build-all,jar">
-       <signjar keystore="plumpkey" alias="signFiles"
-                storepass="plumper" keypass="plumper">
-         <fileset dir="${lib}">
-            <include name="*.jar"/>
-         </fileset>
-       </signjar>
-    </target>
 
-
 </project>
 
 


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[Obo-svn-commit] SF.net SVN: obo: [219] phenote/trunk

From: <mg...@us...> - 2006-11-22 20:26:16

Revision: 219
          http://svn.sourceforge.net/obo/?rev=219&view=rev
Author:   mgibson
Date:     2006-11-22 12:26:15 -0800 (Wed, 22 Nov 2006)

Log Message:
-----------
so ive added the ability to get generic - that is you can now specify
any field you want in the config file - you are no longer restricted
to just the limited set that phenote knows about - however the data
adapter is another matter - the data adapter has to know what you are
setting up - and currently the data adapters are broken - will fix
soon

the datamodel is now basically a hash of char fields to char field
values. no longer a hardwired datamodel - which is wierd to me - but
given the need for a configuration driven data there was no other way
to go.

char field enum and the hard wired datamdoel need to be phased out - i
dont think they are actually being used anywhere - need to clean that
up - 

the big methods are no Character.setValue(CharField,CharFieldValue)
and CharFieldValue Char.getValue(CharField)

table gets char field info from ontology manager for column/int

in same checkin - related:
added new fields cos i can! evidence, description, absent, abnormal
made a slim of pato for abnormal & absent - 2 term slims
phenote can now read in slims - this will be useful for attribute slim
as well

Modified Paths:
--------------
    phenote/trunk/build.xml
    phenote/trunk/conf/initial-flybase.cfg
    phenote/trunk/conf/initial-zfin.cfg
    phenote/trunk/conf/phenote-config.rnc
    phenote/trunk/conf/phenote-config.xsd
    phenote/trunk/jars/BrowserLauncher2-10rc4.jar
    phenote/trunk/jars/commons-lang-2.1.jar
    phenote/trunk/jars/commons-logging-1.0.4.jar
    phenote/trunk/jars/jsr173_1.0_api.jar
    phenote/trunk/jars/jstl-1.1.jar
    phenote/trunk/jars/junit-4.0.jar
    phenote/trunk/jars/log4j-1.2.13.jar
    phenote/trunk/jars/oboedit.jar
    phenote/trunk/jars/org.geneontology.jar
    phenote/trunk/jars/phenoteconfigbeans.jar
    phenote/trunk/jars/phenoxmlbeans.jar
    phenote/trunk/jars/quartz-1.5.2.jar
    phenote/trunk/jars/spring.jar
    phenote/trunk/jars/standard-1.1.jar
    phenote/trunk/jars/te-common.jar
    phenote/trunk/jars/tomcat-servlet.jar
    phenote/trunk/jars/xbean.jar
    phenote/trunk/obo-files/quality.obo
    phenote/trunk/src/java/phenote/config/Config.java
    phenote/trunk/src/java/phenote/config/FieldConfig.java
    phenote/trunk/src/java/phenote/config/OntologyConfig.java
    phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
    phenote/trunk/src/java/phenote/datamodel/CharField.java
    phenote/trunk/src/java/phenote/datamodel/CharFieldEnum.java
    phenote/trunk/src/java/phenote/datamodel/CharFieldValue.java
    phenote/trunk/src/java/phenote/datamodel/Character.java
    phenote/trunk/src/java/phenote/datamodel/CharacterI.java
    phenote/trunk/src/java/phenote/datamodel/Ontology.java
    phenote/trunk/src/java/phenote/datamodel/OntologyManager.java
    phenote/trunk/src/java/phenote/edit/CompoundTransaction.java
    phenote/trunk/src/java/phenote/edit/EditManager.java
    phenote/trunk/src/java/phenote/edit/UpdateTransaction.java
    phenote/trunk/src/java/phenote/gui/CharacterTableModel.java
    phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java
    phenote/trunk/src/java/phenote/gui/field/FreeTextField.java
    phenote/trunk/src/java/phenote/gui/field/PostCompGui.java
    phenote/trunk/src/java/phenote/gui/field/TermCompList.java
    phenote/trunk/src/java/phenote/main/Phenote.java
    phenote/trunk/src/java/phenote/main/PhenoteVersion.java

Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml	2006-11-22 19:58:50 UTC (rev 218)
+++ phenote/trunk/build.xml	2006-11-22 20:26:15 UTC (rev 219)
@@ -375,9 +375,9 @@
 
 <!-- todo do all jars not just phenote - take out -signed -->
 <!-- depends on sym link phenote-webstart and env var PHENOTE_VERSION -->
-    <target name="phenote-webstart-website" depends="sign-jars">
+    <target name="webstart-website" depends="sign-jars">
       <copy todir="phenote-webstart">
-         <fileset file="doc/phenote-website/*.html">
+         <fileset file="doc/phenote-website/*.html"/>
        </copy>
       <mkdir dir="phenote-webstart/${env.PHENOTE_VERSION}"/>
       <copy todir="phenote-webstart/${env.PHENOTE_VERSION}">

Modified: phenote/trunk/conf/initial-flybase.cfg
===================================================================
--- phenote/trunk/conf/initial-flybase.cfg	2006-11-22 19:58:50 UTC (rev 218)
+++ phenote/trunk/conf/initial-flybase.cfg	2006-11-22 20:26:15 UTC (rev 219)
@@ -20,6 +20,12 @@
   </field>
 
   <field name="Quality" file="quality.obo"/>
-                      
 
+  <field name="Absent" file="quality.obo" slim="absent_slim" />
+  <field name="Abnormal" file="quality.obo" slim="abnormal_slim" />
+
+  <field name="Evidence" file="evidence_code.obo"/>
+
+  <field name="Description" />
+
 </phenote-configuration>

Modified: phenote/trunk/conf/initial-zfin.cfg
===================================================================
--- phenote/trunk/conf/initial-zfin.cfg	2006-11-22 19:58:50 UTC (rev 218)
+++ phenote/trunk/conf/initial-zfin.cfg	2006-11-22 20:26:15 UTC (rev 219)
@@ -18,8 +18,15 @@
      <ontology name="SP" file="spatial.obo"/>
   </field>
 
+  <field name="Stage" file="zebrafish_anatomy.obo" filter-out="ZFA:" />
+
   <field name="Quality" file="quality.obo"/>
 
-                      
+  <field name="Absent" file="quality.obo" slim="absent_slim" />
+  <field name="Abnormal" file="quality.obo" slim="abnormal_slim" />
 
+  <field name="Evidence" file="evidence_code.obo"/>
+
+  <field name="Description" />
+
 </phenote-configuration>

Modified: phenote/trunk/conf/phenote-config.rnc
===================================================================
--- phenote/trunk/conf/phenote-config.rnc	2006-11-22 19:58:50 UTC (rev 218)
+++ phenote/trunk/conf/phenote-config.rnc	2006-11-22 20:26:15 UTC (rev 219)
@@ -4,8 +4,6 @@
 start =
   element phenote-configuration {
     attribute version { xsd:float },
-    check-for-new-ontologies,
-    ontology-archive,
     log,
     dataadapter*,
     field*
@@ -32,12 +30,15 @@
 
 field = 
   element field {
-    attribute name { "Pub" | "Genotype" | "Genetic Context" | "Entity" | "Quality" },
+    ##attribute name { "Pub" | "Genotype" | "Genetic Context" | "Entity" | "Quality" },
+    attribute name { text },
     ## whether field is free text or constrained by ontology - take out?
     ## this is actually unnecasary - if there is no file free text is assumed    
     attribute type { "free_text" | "ontology" },  
     ## file is for single ontology - rename ontology_file?  
     attribute file { text },
+    attribute filter-out { text },
+    attribute slim { text },
     postcomp?,
     ontology*
   } 
@@ -47,7 +48,8 @@
     attribute name { text },
     ## obo file for ontology
     attribute file { text },
-    attribute filter-out { text }
+    attribute filter-out { text },
+    attribute slim { text }
   }
 
 postcomp =

Modified: phenote/trunk/conf/phenote-config.xsd
===================================================================
--- phenote/trunk/conf/phenote-config.xsd	2006-11-22 19:58:50 UTC (rev 218)
+++ phenote/trunk/conf/phenote-config.xsd	2006-11-22 20:26:15 UTC (rev 219)
@@ -3,7 +3,6 @@
   <xs:element name="phenote-configuration">
     <xs:complexType>
       <xs:sequence>
-        <xs:element ref="x:check-for-new-ontologies"/>
         <xs:element ref="x:log"/>
         <xs:element minOccurs="0" maxOccurs="unbounded" ref="x:dataadapter"/>
         <xs:element minOccurs="0" maxOccurs="unbounded" ref="x:field"/>
@@ -26,11 +25,6 @@
       </xs:attribute>
     </xs:complexType>
   </xs:element>
-  <xs:element name="check-for-new-ontologies">
-    <xs:complexType>
-      <xs:attribute name="intervalMinutes" use="required" type="xs:integer"/>
-    </xs:complexType>
-  </xs:element>
   <xs:element name="log">
     <xs:complexType>
       <xs:attribute name="config-file" use="required"/>
@@ -43,15 +37,9 @@
         <xs:element minOccurs="0" maxOccurs="unbounded" ref="x:ontology"/>
       </xs:sequence>
       <xs:attribute name="name" use="required">
-        <xs:simpleType>
-          <xs:restriction base="xs:token">
-            <xs:enumeration value="Pub"/>
-            <xs:enumeration value="Genotype"/>
-            <xs:enumeration value="Genetic Context"/>
-            <xs:enumeration value="Entity"/>
-            <xs:enumeration value="Quality"/>
-          </xs:restriction>
-        </xs:simpleType>
+        <xs:annotation>
+          <xs:documentation>attribute name { "Pub" | "Genotype" | "Genetic Context" | "Entity" | "Quality" },</xs:documentation>
+        </xs:annotation>
       </xs:attribute>
       <xs:attribute name="type" use="required">
         <xs:simpleType>
@@ -66,6 +54,8 @@
           <xs:documentation>file is for single ontology - rename ontology_file?  </xs:documentation>
         </xs:annotation>
       </xs:attribute>
+      <xs:attribute name="filter-out" use="required"/>
+      <xs:attribute name="slim" use="required"/>
     </xs:complexType>
   </xs:element>
   <xs:element name="ontology">
@@ -77,6 +67,7 @@
         </xs:annotation>
       </xs:attribute>
       <xs:attribute name="filter-out" use="required"/>
+      <xs:attribute name="slim" use="required"/>
     </xs:complexType>
   </xs:element>
   <xs:element name="postcomp">

Modified: phenote/trunk/jars/BrowserLauncher2-10rc4.jar
===================================================================
(Binary files differ)

Modified: phenote/trunk/jars/commons-lang-2.1.jar
===================================================================
(Binary files differ)

Modified: phenote/trunk/jars/commons-logging-1.0.4.jar
===================================================================
(Binary files differ)

Modified: phenote/trunk/jars/jsr173_1.0_api.jar
===================================================================
(Binary files differ)

Modified: phenote/trunk/jars/jstl-1.1.jar
===================================================================
(Binary files differ)

Modified: phenote/trunk/jars/junit-4.0.jar
===================================================================
(Binary files differ)

Modified: phenote/trunk/jars/log4j-1.2.13.jar
===================================================================
(Binary files differ)

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

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

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

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

Modified: phenote/trunk/jars/quartz-1.5.2.jar
===================================================================
(Binary files differ)

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

Modified: phenote/trunk/jars/standard-1.1.jar
===================================================================
(Binary files differ)

Modified: phenote/trunk/jars/te-common.jar
===================================================================
(Binary files differ)

Modified: phenote/trunk/jars/tomcat-servlet.jar
===================================================================
(Binary files differ)

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

Modified: phenote/trunk/obo-files/quality.obo
===================================================================
--- phenote/trunk/obo-files/quality.obo	2006-11-22 19:58:50 UTC (rev 218)
+++ phenote/trunk/obo-files/quality.obo	2006-11-22 20:26:15 UTC (rev 219)
@@ -1,3519 +1,2991 @@
 format-version: 1.0
-date: 11:08:2006 17:21
-saved-by: gg295
-auto-generated-by: OBO-Edit 1.000-beta16
-default-namespace: unknown
+date: 13:11:2006 14:30
+saved-by: George Gkoutos
+auto-generated-by: OBO-Edit 1.002
+subsetdef: absent_slim "Absent/Present slim"
+subsetdef: abnormal_slim "Abnormal/Normal slim"
+default-namespace: quality
 
 [Term]
 id: PATO:0000000
 name: pato
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000001
 name: quality
-namespace: attribute
+def: "A dependent entity that\ninheres in a bearer by virtue of how the bearer is related to other entities." [PATO GVG:]
 
 [Term]
 id: PATO:0000002
 name: value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000003
 name: assay
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000004
 name: mobility
-namespace: attribute
-def: "The quality of moving freely." [XX:<new dbxref>]
+def: "A quality of moving freely." [PATO GVG:]
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000005
 name: absolute activity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000006
 name: process
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000007
 name: relative activity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000008
-name: speed
-namespace: attribute
-def: "Rate of change of the position of an object." [XX:<new dbxref>]
+name: speed/velocity
+def: "A physical quality inhering in an object by virtue of the rate of change of its position." [Wikipedia:Wikipedia "http://en.wikipedia.org/"]
 is_a: PATO:0001018 ! physical quality
 
 [Term]
 id: PATO:0000009
 name: absolute speed
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000010
 name: relative speed
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000011
 name: age
-namespace: attribute
-is_a: PATO:0000050 ! life span
+is_a: PATO:0000165 ! time
 
 [Term]
 id: PATO:0000012
 name: absolute age
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000013
 name: relative age
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000014
 name: color
-namespace: attribute
-def: "Color is a property of light that is determined by its wavelength (or by its composition as a blend of several wavelengths). " [Wikipedia:]
-is_a: PATO:0001237 ! monadic quality of continuant
+def: "A composite chromatic quality composed of hue, saturation and intensity parts." [XX:<new dbxref>]
+is_a: PATO:0001301 ! chromatic property
 
 [Term]
 id: PATO:0000015
 name: color hue
-namespace: attribute
-is_obsolete: true
+def: "a chromatic scalar-circular quality inhering in an object that manifests in an observer by virtue of the dominant wavelength of the visible light; may be subject to fiat divisions, typically into 7 or 8 spectra" [XX:<new dbxref>]
+is_a: PATO:0001301 ! chromatic property
 
 [Term]
 id: PATO:0000016
-name: color intensity
-namespace: attribute
-is_obsolete: true
+name: color brightness
+def: "A scalar optical quality which obtains by the bearer producing the effects of light emittance in an observer." [XX:<new dbxref>]
+is_a: PATO:0001300 ! optical quality
 
 [Term]
 id: PATO:0000017
 name: color saturation
-namespace: attribute
-is_obsolete: true
+def: "a scalar chromatic quality that manifests by virtue of the range of wavelengths in perceived light." [XX:<new dbxref>]
+is_a: PATO:0001301 ! chromatic property
 
 [Term]
 id: PATO:0000018
-name: flourescence
-namespace: attribute
-def: "Fluorescence is a luminescence that is mostly found as an optical phenomenon in cold bodies, in which the molecular absorption of a photon triggers the emission of a lower-energy photon with a longer wavelength." [Wikipedia:]
-is_obsolete: true
+name: fluorescence
+def: "Luminosity in which the bearer emits longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together." [XX:<new dbxref>]
+is_a: PATO:0001296 ! luminosity
 
 [Term]
 id: PATO:0000019
 name: color pattern
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000020
 name: relative color
-namespace: attribute
-is_a: PATO:0000014 ! color
+is_a: PATO:0001300 ! optical quality
 
 [Term]
 id: PATO:0000021
 name: compatibility
-namespace: attribute
-def: "The quality of having or lacking the ability harmonious coexistence." [gg:]
+def: "A quality of having or lacking the ability harmonious coexistence." [PATO GVG:]
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000022
 name: gametophytic compatability
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000023
 name: relative compatability
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000024
 name: sporophytic compatability
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000025
 name: composition
-namespace: attribute
+def: "A monadic quality of continuant inhering in an object by virtue of the quantities or relative ratios of subparts of the inhering entity; for example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood)" [PATO GVG:]
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000026
 name: carbohydrate composition
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000027
 name: electrolyte composition
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000028
 name: macromolecular composition
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000029
 name: protein composition
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000030
 name: enzyme composition
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000031
 name: metabolite composition
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000032
 name: secondary product composition
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000033
 name: concentration
-namespace: attribute
-def: "The proportion of the whole a subtance makes up in a mixture of two substances." [XX:<new dbxref>]
+def: "A physical quality inhering in a substance by \nvirtue of the amount of it there is mixed with another substance." [Wikipedia:Wikipedia "http://www.wikipedia.org/"]
 is_a: PATO:0001018 ! physical quality
 
 [Term]
 id: PATO:0000034
 name: protein concentration
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000035
 name: carbohydrate concentration
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000036
 name: water content
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000037
 name: consistency
-namespace: attribute
-def: "the property of holding together and retaining shape" [PATO:gg]
-is_obsolete: true
+def: "A physical quality that inheres in a continuant by\nvirtue of density, firmness, or viscosity." [PATO GVG:]
+is_a: PATO:0001018 ! physical quality
 
 [Term]
 id: PATO:0000038
 name: gel consistency
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000039
 name: direction
-namespace: attribute
-def: "The orientation of a line in space." [XX:<new dbxref>]
+def: "The orientation of a line in space." [: "http://thesaurus.maths.org/"]
 is_a: PATO:0001018 ! physical quality
 
 [Term]
 id: PATO:0000040
 name: distance
-namespace: attribute
 def: "The extent of space between two objects or places." [XX:<new dbxref>]
 is_a: PATO:0001018 ! physical quality
 
 [Term]
 id: PATO:0000041
 name: absolutedistance
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000042
 name: relative distance
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000043
 name: flavor
-namespace: attribute
-is_a: PATO:0001237 ! monadic quality of continuant
+def: "A relational quality inhering in an object or the molecules of an object, in which the molecules are perceived by a taste and odorant receptors." [XX:<new dbxref>]
+is_a: PATO:0001238 ! relational quality of continuant
 
 [Term]
 id: PATO:0000044
 name: frequency
-namespace: attribute
-def: "The number of times something happens in a period of time." [XX:<new dbxref>]
+def: "A physical quality which inhers to the bearer by virtue of the number of repetitive actions in a particular time." [Wikipedia:Wikipedia "http://en.wikipedia.org/"]
 is_a: PATO:0001018 ! physical quality
 
 [Term]
 id: PATO:0000045
 name: absolute frequency
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000046
 name: relative frequency
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000047
-name: gender
-namespace: attribute
+name: biological sex
+def: "A monadic quality of continuant inhering in an organism by virtue of its ability to undergo sexual reproduction in order to differentiate the individuals or types involved." [MGED:MGED]
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000048
 name: hardness
-namespace: attribute
-def: "The constant of proportionality of the force on an elastic body to the body's extension." [XX:<new dbxref>]
+def: "A physical quality inhering in a bearer as the constant of proportionality of the force on its elastic body to its body's extension." [: "http://thesaurus.maths.org/"]
 related_synonym: "stiffness" []
 is_a: PATO:0001018 ! physical quality
 
 [Term]
 id: PATO:0000049
 name: intensity
-namespace: attribute
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000050
 name: life span
-namespace: attribute
+def: "A time quality which is the expected maximum age." [XX:<new dbxref>]
 is_a: PATO:0000165 ! time
 
 [Term]
 id: PATO:0000051
 name: morphology
-namespace: attribute
+def: "A quality inhering in the bearer by virtue of its size, shape and structure" [PATO GVG:]
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000052
 name: shape
-namespace: attribute
+def: "A morphology quality inhering in a bearer by virtue of the ratios of distances between its features (points, edges, surfaces and also holes etc). " [PATO GVG:]
 is_a: PATO:0000051 ! morphology
 
 [Term]
 id: PATO:0000053
 name: count
-namespace: attribute
 is_a: PATO:0001226 ! quantitative
 
 [Term]
 id: PATO:0000054
 name: absolute number
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000055
 name: relative number
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000056
 name: nutritional
-namespace: attribute
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000057
-name: occurence
-namespace: attribute
+name: occurrence
 is_a: PATO:0001226 ! quantitative
 
 [Term]
 id: PATO:0000058
 name: odor
-namespace: attribute
-is_a: PATO:0001237 ! monadic quality of continuant
+def: "A relational quality inhering in an object by virtue of the molecules being are aerially dispersed and perceived by an odorant receptor. " [XX:<new dbxref>]
+is_a: PATO:0001238 ! relational quality of continuant
 
 [Term]
 id: PATO:0000059
 name: parental type
-namespace: attribute
-is_a: PATO:0000047 ! gender
+is_a: PATO:0000047 ! biological sex
 
 [Term]
 id: PATO:0000060
 name: pattern
-namespace: attribute
+def: "A monadic quality of continuant defined by the mathematic properties of the relative position of subparts" [XX:<new dbxref>]
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000061
 name: relative pattern
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000062
 name: sleep pattern
-namespace: attribute
 is_a: PATO:0000186 ! behavioral quality
 
 [Term]
 id: PATO:0000063
 name: percentage
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000064
 name: absolute percentage
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000065
 name: relative percentage
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000066
 name: pilosity
-namespace: attribute
-def: "The quality of having hair." [XX:<new dbxref>]
+def: "A quality of having hair." [PATO GVG:]
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000067
 name: relative pilosity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000068
 name: qualitative
-namespace: attribute
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000069
 name: deviation(from_normal)
-namespace: attribute
 is_a: PATO:0000068 ! qualitative
 
 [Term]
 id: PATO:0000070
 name: presence
-namespace: attribute
 is_a: PATO:0000068 ! qualitative
 
 [Term]
 id: PATO:0000071
 name: relative_quantity
-namespace: attribute
 is_a: PATO:0001226 ! quantitative
 
 [Term]
 id: PATO:0000072
 name: quality
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000073
 name: relative_quality
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000074
 name: shattering
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000075
 name: threshability
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000076
 name: regulation
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000077
 name: response
-namespace: attribute
+def: "A quality inhering in a bearer by virtue of \nits reaction to a stimulus or an agent." [PATO GVG:]
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000078
-name: rhythym
-namespace: attribute
+name: rhythm
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000079
 name: absolute rhythym
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000080
 name: amplitude
-namespace: attribute
-def: "The size of the maximum displacement from the 'normal' position, when periodic motion is taking place" [PATO:gg]
-is_a: PATO:0000078 ! rhythym
+def: "A physical quality inhering in a bearer by \nvirtue of the size of its maximum displacement from the 'normal' position, when periodic motion is taking place" [: "http://thesaurus.maths.org/"]
+is_a: PATO:0000078 ! rhythm
 is_a: PATO:0001018 ! physical quality
 
 [Term]
 id: PATO:0000081
 name: period
-namespace: attribute
-is_a: PATO:0000078 ! rhythym
+is_a: PATO:0000078 ! rhythm
 is_a: PATO:0000165 ! time
 
 [Term]
 id: PATO:0000082
 name: persistence
-namespace: attribute
-is_a: PATO:0000078 ! rhythym
+is_a: PATO:0000078 ! rhythm
 
 [Term]
 id: PATO:0000083
 name: phase
-namespace: attribute
-is_a: PATO:0000078 ! rhythym
+is_a: PATO:0000078 ! rhythm
 
 [Term]
 id: PATO:0000084
 name: relative rhythym
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000085
 name: sensitivity
-namespace: attribute
-is_a: PATO:0001237 ! monadic quality of continuant
+def: "A relational quality inhering in an entity by virtue of its capacity to respond to stimulation." [XX:<new dbxref>]
+is_a: PATO:0001238 ! relational quality of continuant
 
 [Term]
 id: PATO:0000086
 name: absolute sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000087
 name: disease sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000088
 name: absolute disease sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000089
 name: relative disease sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000090
 name: relative sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000091
 name: stress sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000092
 name: abiotic stress sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000093
 name: chemical sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000094
 name: drug sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000095
 name: absolute drug sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000096
 name: relative drug sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000097
 name: herbicide sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000098
 name: insecticide sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000099
 name: plant growth hormone sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000100
 name: soil composition sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000101
 name: soil nutrient sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000102
 name: macronutrient sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000103
 name: micronutrient sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000104
 name: osmotic response sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000105
 name: p h sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000106
 name: acid sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000107
 name: alkali sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000108
 name: salt sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000109
 name: water sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000110
 name: drought sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000111
 name: flooding sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000112
 name: humidity sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000113
 name: radiation sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000114
 name: temperature sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000115
 name: absolute temperature sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000116
 name: relative temperature sensitivity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000117
 name: size
-namespace: attribute
 is_a: PATO:0000051 ! morphology
 
 [Term]
 id: PATO:0000118
 name: absolute size
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000119
 name: height
-namespace: attribute
-def: "The vertical dimension of extension." [XX:<new dbxref>]
+def: "A physical quality which is equal to the vertical dimension of extension." [PATO GVG:]
 is_a: PATO:0001018 ! physical quality
 
 [Term]
 id: PATO:0000120
 name: absolute height
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000121
 name: relative height
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000122
 name: length
-namespace: attribute
-def: "The distance between two points." [XX:<new dbxref>]
+def: "A physical quality which is equal to the distance between two points." [PATO GVG:]
 is_a: PATO:0001018 ! physical quality
 
 [Term]
 id: PATO:0000123
 name: absolute length
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000124
 name: relative length
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000125
 name: mass
-namespace: attribute
-def: "The amount of matter in an object." [XX:<new dbxref>]
+def: "A physical quality that inheres in a bearer in proportion to the amount of matter it contains." [PATO GVG:]
 is_a: PATO:0001018 ! physical quality
 
 [Term]
 id: PATO:0000126
 name: absolute mass
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000127
 name: relative mass
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000128
 name: weight
-namespace: attribute
-def: "The size of the force which gravity exerts on a particular object. " [XX:<new dbxref>]
+def: "A quality inhering in an object with mass near a gravitational body." [Wikipedia:Wikipedia "http://www.wikipedia.org/"]
 is_a: PATO:0001035 ! force
 
 [Term]
 id: PATO:0000129
 name: absolute weight
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000130
 name: relative weight
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000131
 name: relative size
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000132
 name: spatial
-namespace: attribute
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000133
 name: angle
-namespace: attribute
-def: "The measure of a change in direction." [XX:<new dbxref>]
+def: "A physical quality inhering in a figure or space formed by the junction of two lines or planes." [Wikipedia :Wikipedia "http://www.wikipedia.org/"]
 is_a: PATO:0000132 ! spatial
 is_a: PATO:0001018 ! physical quality
 
 [Term]
 id: PATO:0000134
 name: absolute_angle
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000135
 name: relative_angle
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000136
 name: closure
-namespace: attribute
 is_a: PATO:0000132 ! spatial
 
 [Term]
 id: PATO:0000137
 name: orientation
-namespace: attribute
+def: "A quality of an object in which its \nlocation is defined by the angle between two axes, or an axis and another object" [XX:<new dbxref>]
 is_a: PATO:0000132 ! spatial
 
 [Term]
 id: PATO:0000138
 name: absolute orientation
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000139
 name: relative orientation
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000140
 name: placement
-namespace: attribute
-def: "The spatial property of the way in which something is placed" [PATO:gg]
+def: "A spatial quality of the way in which something is placed" [PATO:gg]
 is_a: PATO:0000132 ! spatial
 
 [Term]
 id: PATO:0000141
 name: structure
-namespace: attribute
+def: "A morphology quality inhering in a bearer by virtue of the relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.\n" [PATO GVG:]
 is_a: PATO:0000051 ! morphology
 
 [Term]
 id: PATO:0000142
 name: substance
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000143
 name: addictive substance
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000144
 name: solid substance
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000145
 name: liquid substance
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000146
 name: temperature
-namespace: attribute
-def: "The physical quality of the thermal energy of a system." [gg:]
+def: "A physical quality of the thermal energy of a system." [PATO GVG:]
 is_a: PATO:0001018 ! physical quality
 
 [Term]
 id: PATO:0000147
 name: absolute temperature
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000148
 name: body temperature
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000149
 name: relative temperature
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000150
 name: texture
-namespace: attribute
+def: "A morphology quality inhering in a bearer by virtue of the relative size and distribution of its surface elements or the representation or invention of the appearance of its surface. \n" [PATO GVG:]
 is_a: PATO:0000051 ! morphology
 
 [Term]
 id: PATO:0000151
 name: relative texture
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000152
 name: threshold
-namespace: attribute
+def: "A quality inhering in a bearer  by virtue of its sensitivity towards a fixed location or value where a change is observed; upper limit." [Wikipedia:Wikipedia "http://www.wikipedia.org/"]
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000153
 name: absolute threshold
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000154
 name: pain threshold
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000155
 name: relative threshold
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000156
 name: temporal
-namespace: attribute
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000157
 name: absolute temporal
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000158
 name: incidence
-namespace: attribute
 is_a: PATO:0000156 ! temporal
 
 [Term]
 id: PATO:0000159
 name: absolute incidence
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000160
 name: relative incidence
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000161
 name: rate
-namespace: attribute
 is_a: PATO:0000156 ! temporal
 
 [Term]
 id: PATO:0000162
 name: absolute rate
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000163
 name: relative rate
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000164
 name: relative temporal
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000165
 name: time
-namespace: attribute
+def: "A quality in which events occur in sequence" [XX:<new dbxref>]
 is_a: PATO:0001018 ! physical quality
 
 [Term]
 id: PATO:0000166
 name: absolute time
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000167
 name: bouts
-namespace: attribute
 is_a: PATO:0000165 ! time
 
 [Term]
 id: PATO:0000168
 name: relative time
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000169
 name: viability
-namespace: attribute
+def: "A quality inhering in a bearer or a population by virtue of the bearer's ability or inability to survive and develop normally or the number of surviving individuals in a given population." [PATO GVG:]
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000170
 name: yield
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000171
 name: absolute yield
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000172
 name: relative yield
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000173
 name: function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000174
 name: autonomic function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000175
 name: behavioral function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000176
 name: metabolic function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000177
 name: physiological function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000178
 name: relative function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000179
 name: body position
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000180
 name: body tone
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000181
 name: piloerection
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000182
 name: abdominal tone
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000183
 name: limb tone
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000184
 name: arousal
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000185
 name: balance
-namespace: attribute
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000186
 name: behavioral quality
-namespace: attribute
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000187
 name: consumption
-namespace: attribute
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000188
 name: coordination
-namespace: attribute
-def: "The quality of having or lacking skilful and effective interation of movemment." [gg:]
+def: "A quality of having or lacking skilful and effective interaction of movement." [PATO GVG:]
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000189
 name: discrimination
-namespace: attribute
-def: "The quality of perceiving differences between two or more stimuli." [XX:<new dbxref>]
+def: "A quality of perceiving differences between two or more stimuli." [PATO GVG:]
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000190
 name: gait
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000191
 name: learning_and memory
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000192
 name: locomotor_activity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000193
 name: mating
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000194
 name: spontaneous_activity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000195
 name: startle response
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000196
 name: vocalization
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000197
 name: transfer_arousal
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000198
 name: absolute consumption
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000199
 name: relative consumption
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000200
 name: learning
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000201
 name: memory
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000202
 name: long term memory
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000203
 name: short term memory
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000204
 name: absolute locomotor_activity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000205
 name: relative locomotor_activity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000206
 name: enzyme function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000207
 name: circulatory function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000208
 name: defensive function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000209
 name: digestive function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000210
 name: excretory function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000211
 name: muscle function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000212
 name: neural function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000213
 name: neurobehavioral function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000214
 name: reproductive function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000215
 name: respiratory function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000216
 name: heart rate
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000217
 name: immune function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000218
 name: repair function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000219
 name: healing
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000220
 name: regeneration
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000221
 name: urination
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000222
 name: muscle elevation
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000223
 name: muscle strength
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000224
 name: motor function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000225
 name: sensory function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000226
 name: tactile response
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000227
 name: motor performance
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000228
 name: auditory
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000229
 name: olfactory
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000230
 name: proprioreception
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000231
 name: reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000232
 name: taste
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000233
 name: touch
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000234
 name: visual
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000235
 name: odor_acuity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000236
 name: odor type
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000237
 name: absolute odor_acuity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000238
 name: relative odor_acuity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000239
 name: blinking reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000240
 name: contact righting reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000241
 name: corneal reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000242
 name: flinch reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000243
 name: lordosis reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000244
 name: ocular reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000245
 name: pinna reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000246
 name: postural reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000247
 name: proboscis extension reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000248
 name: pupillary reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000249
 name: righting reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000250
 name: spinal reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000251
 name: startle reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000252
 name: suckling reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000253
 name: swallowing reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000254
 name: vibrissae reflex
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000255
 name: taste_acuity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000256
 name: taste type
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000257
 name: absolute taste_acuity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000258
 name: relative taste_acuity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000259
 name: visual_ability
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000260
 name: visual_acuity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000261
 name: maturity
-namespace: attribute
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000262
 name: visual placing
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000263
 name: visual threshold
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000264
 name: absolute visual_ability
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000265
 name: relative visual_ability
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000266
 name: absolute visual_acuity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000267
 name: relative visual_acuity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000268
 name: absolute visual threshold
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000269
 name: relative visual threshold
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000270
 name: defecation
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000271
 name: prepulse inhibition
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000272
 name: relative neurobehavioral function
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000273
 name: fecundity
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000274
 name: fertility
-namespace: attribute
-def: "The quality of initiating, sustaining, or supporting reproduction." [XX:<new dbxref>]
+def: "A quality of initiating, sustaining, or supporting reproduction." [PATO GVG:]
 is_a: PATO:0001237 ! monadic quality of continuant
 
 [Term]
 id: PATO:0000275
 name: gestational period
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000276
 name: litter size
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000277
 name: female fertility
-namespace: attribute
-def: "The quality of female of initiating, sustaining, or supporting reproduction." [XX:<new dbxref>]
+def: "A fertility quality of the female of initiating, sustaining, or supporting reproduction." [PATO GVG:]
 is_a: PATO:0000274 ! fertility
 
 [Term]
 id: PATO:0000278
 name: hybrid fertility
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000279
 name: male fertility
-namespace: attribute
-def: "The quality of male of initiating, sustaining, or supporting reproduction." [XX:<new dbxref>]
+def: "A fertility quality of the male of initiating, sustaining, or supporting reproduction." [PATO GVG:]
 is_a: PATO:0000274 ! fertility
 
 [Term]
 id: PATO:0000280
 name: backcross fertility
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000281
 name: cytoplasmic sterility
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000282
 name: f1 fertility
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000283
 name: f2 fertility
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000284
 name: germ line dependent fertility
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000285
 name: soma dependent fertility
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000286
 name: cytoplasmic male sterility
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000287
 name: absolute litter size
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000288
 name: relative litter size
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000289
 name: respiratory rate
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000290
 name: absolute respiratory rate
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000291
 name: relative respiratory rate
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000292
 name: mobility value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000293
 name: absolute activity value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000294
 name: process value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000295
 name: relative activity value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000296
 name: speed value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000297
-name: arrested value
-namespace: attribute
-is_obsolete: true
+name: arrested
+def: "A duration in which the end point is shorted before natural end point (prematurely finishing)." [XX:<new dbxref>]
+related_synonym: "incomplete" []
+is_a: PATO:0001309 ! duration
 
 [Term]
 id: PATO:0000298
 name: not arrested value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000299
 name: mobile
-namespace: attribute
-def: "The quality of being incapable to move freely." [XX:<new dbxref>]
+def: "A mobility quality of being incapable to move freely." [PATO GVG:]
 is_a: PATO:0000004 ! mobility
 
 [Term]
 id: PATO:0000300
 name: immobile
-namespace: attribute
-def: "The quality of being capable to move freely." [XX:<new dbxref>]
+def: "A mobility quality of being capable to move freely." [PATO GVG:]
 is_a: PATO:0000004 ! mobility
 
 [Term]
 id: PATO:0000301
 name: absolute speed value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000302
 name: relative speed value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000303
 name: fast speed
-namespace: attribute
-def: "A speed which is relative high." [XX:<new dbxref>]
-is_a: PATO:0000008 ! speed
+def: "A speed which is relative high." [PATO GVG:]
+is_a: PATO:0000008 ! speed/velocity
 
 [Term]
 id: PATO:0000304
 name: slow speed
-namespace: attribute
 def: "A speed which is relative low." [XX:<new dbxref>]
-is_a: PATO:0000008 ! speed
+is_a: PATO:0000008 ! speed/velocity
 
 [Term]
 id: PATO:0000305
 name: age value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000306
 name: absolute age value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000307
 name: relative age value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000308
 name: old
-namespace: attribute
 is_a: PATO:0000011 ! age
 
 [Term]
 id: PATO:0000309
 name: young
-namespace: attribute
 is_a: PATO:0000011 ! age
 
 [Term]
 id: PATO:0000310
 name: color value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000311
 name: color hue value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000312
 name: color intensity value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000313
 name: color saturation value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000314
 name: flourescence value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000315
 name: color pattern value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000316
 name: relative color value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000317
 name: black
-namespace: attribute
-def: "Producing or reflecting comparatively little light and having no predominant hue." [Dictionary:http://dictionary.reference.com/]
+def: "A color that lacks any hues as parts." [XX:<new dbxref>]
 is_a: PATO:0000014 ! color
 
 [Term]
 id: PATO:0000318
 name: blue
-namespace: attribute
-def: "A hue of that portion of the visible spectrum lying between green and indigo, evoked in the human observer by radiant energy with wavelengths of approximately 420 to 490 nanometers;" [Dictionary:http://dictionary.reference.com/]
+def: "A hue of that portion of the visible spectrum lying between green and indigo, evoked in the human observer by radiant energy with wavelengths of approximately 420 to 490 nanometers;" [Dictionary:http\://dictionary.reference.com/]
 is_a: PATO:0000014 ! color
 
 [Term]
 id: PATO:0000319
 name: cyan
-namespace: attribute
 is_a: PATO:0000014 ! color
 
 [Term]
 id: PATO:0000320
 name: green
-namespace: attribute
-def: "A hue of that portion of the visible spectrum lying between yellow and blue, evoked in the human observer by radiant energy with wavelengths of approximately 490 to 570 nanometers;" [Dictionary:http://dictionary.reference.com/]
+def: "A hue of that portion of the visible spectrum lying between yellow and blue, evoked in the human observer by radiant energy with wavelengths of approximately 490 to 570 nanometers;" [Dictionary:http\://dictionary.reference.com/]
 is_a: PATO:0000014 ! color
 
 [Term]
 id: PATO:0000321
 name: magenta
-namespace: attribute
 is_a: PATO:0000322 ! red
 
 [Term]
 id: PATO:0000322
 name: red
-namespace: attribute
-def: "A hue of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers;" [Dictionary:http://dictionary.reference.com/]
+def: "A hue of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers;" [Dictionary:http\://dictionary.reference.com/]
 is_a: PATO:0000014 ! color
 
 [Term]
 id: PATO:0000323
 name: white
-namespace: attribute
-def: "An achromatic color of maximum lightness; the color of objects that reflect nearly all light of all visible wavelengths;" [Dictionary:http://dictionary.reference.com/]
+def: "An achromatic color of maximum lightness; the color of objects that reflect nearly all light of all visible wavelengths;" [Dictionary:http\://dictionary.reference.com/]
 is_a: PATO:0000014 ! color
 
 [Term]
 id: PATO:0000324
 name: yellow
-namespace: attribute
-def: "A hue of that portion of the visible spectrum lying between orange and green, evoked in the human observer by radiant energy with wavelengths of approximately 570 to 590 nanometers" [Dictionary:http://dictionary.reference.com/]
+def: "A hue of that portion of the visible spectrum lying between orange and green, evoked in the human observer by radiant energy with wavelengths of approximately 570 to 590 nanometers" [Dictionary:http\://dictionary.reference.com/]
 is_a: PATO:0000014 ! color
 
 [Term]
 id: PATO:0000325
 name: bright
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000326
 name: dim
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000327
 name: dark
-namespace: attribute
-is_obsolete: true
+is_a: PATO:0000016 ! color brightness
 
 [Term]
 id: PATO:0000328
 name: pale
-namespace: attribute
-is_obsolete: true
+related_synonym: "dull" []
+is_a: PATO:0000017 ! color saturation
 
 [Term]
 id: PATO:0000329
 name: blotchy
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000330
 name: irregular
-namespace: attribute
+def: "A physical quality inhering in a bearer by \nvirtue of lacking pattern." [PATO GVG:]
 is_a: PATO:0000060 ! pattern
 
 [Term]
 id: PATO:0000331
 name: discolored
-namespace: attribute
 is_a: PATO:0000020 ! relative color
 
 [Term]
 id: PATO:0000332
 name: pigmented
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000333
 name: spotted
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000334
 name: unpigmented
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000335
 name: variegated
-namespace: attribute
 related_synonym: "mottled (sensu Drosophila)" []
 is_obsolete: true
 
 [Term]
 id: PATO:0000336
 name: colored
-namespace: attribute
 is_a: PATO:0000020 ! relative color
 
 [Term]
 id: PATO:0000337
 name: colorless
-namespace: attribute
 is_a: PATO:0000020 ! relative color
 
 [Term]
 id: PATO:0000338
 name: compatability value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000339
 name: gametophytic compatability value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000340
 name: relative compatability value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000341
 name: sporophytic compatability value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000342
 name: gametophyte compatible value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000343
 name: gametophyte incompatible value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000344
 name: compatible
-namespace: attribute
-def: "The quality of being capable of harmonious coexistence." [gg:]
+def: "A compatibility quality of being capable of harmonious coexistence." [PATO GVG:]
 is_a: PATO:0000021 ! compatibility
 
 [Term]
 id: PATO:0000345
 name: incompatible
-namespace: attribute
-def: "The quality of being incapable of harmonious coexistence." [gg:]
+def: "A compatibility quality of being incapable of harmonious coexistence." [PATO GVG:]
 is_a: PATO:0000021 ! compatibility
 
 [Term]
 id: PATO:0000346
 name: sporophyte compatible value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000347
 name: sporophyte incompatible value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000348
 name: composition value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000349
 name: carbohydrate composition value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000350
 name: electrolyte composition value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000351
 name: macromolecular composition value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000352
 name: metabolite composition value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000353
 name: secondary product composition value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000354
 name: protein composition value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000355
 name: enzyme composition value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000356
 name: concentration value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000357
 name: protein concentration value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000358
 name: sugar concentration value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000359
 name: water content value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000360
 name: consistency value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000361
 name: gel consistency value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000362
 name: direction value
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000363
 name: away
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000364
 name: bi-directional
-namespace: attribute
 is_obsolete: true
 
 [Term]
 id: PATO:0000365
 name: down
-namespace: attribute
+def: "A direction from a higher to a lower point." [PATO GVG:]
 is_a: PATO:0000039 ! direction
 
 [Term]
 id: PATO:0000366
 name: left
-namespace: attribute
+def: "A direction that is similar to the direction of an object to the nor...
 
[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [218] phenote/trunk/doc/phenote-website

From: <mg...@us...> - 2006-11-22 19:58:53

Revision: 218
          http://svn.sourceforge.net/obo/?rev=218&view=rev
Author:   mgibson
Date:     2006-11-22 11:58:50 -0800 (Wed, 22 Nov 2006)

Log Message:
-----------
1.0

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/phenote-flybase.jnlp
    phenote/trunk/doc/phenote-website/phenote-human.jnlp
    phenote/trunk/doc/phenote-website/phenote-zfin.jnlp

Modified: phenote/trunk/doc/phenote-website/phenote-flybase.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-flybase.jnlp	2006-11-22 19:43:42 UTC (rev 217)
+++ phenote/trunk/doc/phenote-website/phenote-flybase.jnlp	2006-11-22 19:58:50 UTC (rev 218)
@@ -1,12 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <jnlp
 spec="1.0+"
-codebase="http://toy.lbl.gov:9010/phenote/0.9/"
+codebase="http://toy.lbl.gov:9010/phenote/1.0/"
 href="phenote-flybase.jnlp">
 <information>
-	<title>Phenote 0.9</title>
+	<title>Phenote 1.0</title>
 	<vendor>BBOP</vendor>
-	<description>Phenote 0.9</description>
+	<description>Phenote standalone app via webstart</description>
  	 <!-- Declares that the application can run without
          access to the server it was downloaded from -->
 	<offline-allowed />
@@ -25,17 +25,17 @@
          Multiple entries of this kind are allowed, in which
          case they are considered to be in order of preference -->
 	<j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
-	<jar href="jars/phenote-signed.jar" />
-	<jar href="jars/oboedit-signed.jar" />
-	<jar href="jars/org.geneontology-signed.jar" />
-	<jar href="jars/BrowserLauncher2-10rc4-signed.jar" />
-	<jar href="jars/jsr173_1.0_api-signed.jar" />
-	<jar href="jars/phenoxmlbeans-signed.jar" />
-	<jar href="jars/phenoteconfigbeans-signed.jar" />
-	<jar href="jars/xbean-signed.jar" />
-	<jar href="jars/tomcat-servlet-signed.jar" />
-	<jar href="jars/te-common-signed.jar" />
-	<jar href="jars/log4j-1.2.13-signed.jar" />
+	<jar href="jars/phenote.jar" />
+	<jar href="jars/oboedit.jar" />
+	<jar href="jars/org.geneontology.jar" />
+	<jar href="jars/BrowserLauncher2-10rc4.jar" />
+	<jar href="jars/jsr173_1.0_api.jar" />
+	<jar href="jars/phenoxmlbeans.jar" />
+	<jar href="jars/phenoteconfigbeans.jar" />
+	<jar href="jars/xbean.jar" />
+	<jar href="jars/tomcat-servlet.jar" />
+	<jar href="jars/te-common.jar" />
+	<jar href="jars/log4j-1.2.13.jar" />
 </resources>
 <application-desc main-class="phenote.main.Phenote">
         <argument>-c</argument>

Modified: phenote/trunk/doc/phenote-website/phenote-human.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-human.jnlp	2006-11-22 19:43:42 UTC (rev 217)
+++ phenote/trunk/doc/phenote-website/phenote-human.jnlp	2006-11-22 19:58:50 UTC (rev 218)
@@ -1,12 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <jnlp
 spec="1.0+"
-codebase="http://toy.lbl.gov:9010/phenote/0.9/"
+codebase="http://toy.lbl.gov:9010/phenote/1.0/"
 href="phenote-human.jnlp">
 <information>
-	<title>Phenote 0.9</title>
+	<title>Phenote 1.0</title>
 	<vendor>BBOP</vendor>
-	<description>Phenote 0.9</description>
+	<description>Phenote standalone app via webstart</description>
  	 <!-- Declares that the application can run without
          access to the server it was downloaded from -->
 	<offline-allowed />
@@ -26,16 +26,16 @@
          case they are considered to be in order of preference -->
 	<j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
 	<jar href="jars/phenote.jar" />
-	<jar href="jars/oboedit-signed.jar" />
-	<jar href="jars/org.geneontology-signed.jar" />
-	<jar href="jars/BrowserLauncher2-10rc4-signed.jar" />
-	<jar href="jars/jsr173_1.0_api-signed.jar" />
-	<jar href="jars/phenoxmlbeans-signed.jar" />
-	<jar href="jars/phenoteconfigbeans-signed.jar" />
-	<jar href="jars/tomcat-servlet-signed.jar" />
-	<jar href="jars/xbean-signed.jar" />
-        <jar href="jars/te-common-signed.jar" />
-        <jar href="jars/log4j-1.2.13-signed.jar" />
+	<jar href="jars/oboedit.jar" />
+	<jar href="jars/org.geneontology.jar" />
+	<jar href="jars/BrowserLauncher2-10rc4.jar" />
+	<jar href="jars/jsr173_1.0_api.jar" />
+	<jar href="jars/phenoxmlbeans.jar" />
+	<jar href="jars/phenoteconfigbeans.jar" />
+	<jar href="jars/tomcat-servlet.jar" />
+	<jar href="jars/xbean.jar" />
+        <jar href="jars/te-common.jar" />
+        <jar href="jars/log4j-1.2.13.jar" />
 <</resources>
 <application-desc main-class="phenote.gui.Phenote">
         <argument>-c</argument>

Modified: phenote/trunk/doc/phenote-website/phenote-zfin.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-zfin.jnlp	2006-11-22 19:43:42 UTC (rev 217)
+++ phenote/trunk/doc/phenote-website/phenote-zfin.jnlp	2006-11-22 19:58:50 UTC (rev 218)
@@ -1,12 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <jnlp
 spec="1.0+"
-codebase="http://toy.lbl.gov:9010/phenote/0.9/"
+codebase="http://toy.lbl.gov:9010/phenote/1.0/"
 href="phenote-zfin.jnlp">
 <information>
-	<title>Phenote 0.9</title>
+	<title>Phenote 1.0</title>
 	<vendor>BBOP</vendor>
-	<description>Phenote 0.9</description>
+	<description>Phenote standalone app via webstart</description>
  	 <!-- Declares that the application can run without
          access to the server it was downloaded from -->
 	<offline-allowed />
@@ -25,17 +25,17 @@
          Multiple entries of this kind are allowed, in which
          case they are considered to be in order of preference -->
 	<j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
-	<jar href="jars/phenote-signed.jar" />
-	<jar href="jars/oboedit-signed.jar" />
-	<jar href="jars/org.geneontology-signed.jar" />
-	<jar href="jars/BrowserLauncher2-10rc4-signed.jar" />
-	<jar href="jars/jsr173_1.0_api-signed.jar" />
-	<jar href="jars/phenoxmlbeans-signed.jar" />
-	<jar href="jars/phenoteconfigbeans-signed.jar" />
-	<jar href="jars/tomcat-servlet-signed.jar" />
-	<jar href="jars/xbean-signed.jar" />
-	<jar href="jars/te-common-signed.jar" />
-	<jar href="jars/log4j-1.2.13-signed.jar" />
+	<jar href="jars/phenote.jar" />
+	<jar href="jars/oboedit.jar" />
+	<jar href="jars/org.geneontology.jar" />
+	<jar href="jars/BrowserLauncher2-10rc4.jar" />
+	<jar href="jars/jsr173_1.0_api.jar" />
+	<jar href="jars/phenoxmlbeans.jar" />
+	<jar href="jars/phenoteconfigbeans.jar" />
+	<jar href="jars/tomcat-servlet.jar" />
+	<jar href="jars/xbean.jar" />
+	<jar href="jars/te-common.jar" />
+	<jar href="jars/log4j-1.2.13.jar" />
 </resources>
 <application-desc main-class="phenote.main.Phenote">
         <argument>-c</argument>


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[Obo-svn-commit] SF.net SVN: obo: [217] phenote/trunk/doc/phenote-website/phenote.html

From: <mg...@us...> - 2006-11-22 19:43:42

Revision: 217
          http://svn.sourceforge.net/obo/?rev=217&view=rev
Author:   mgibson
Date:     2006-11-22 11:43:42 -0800 (Wed, 22 Nov 2006)

Log Message:
-----------
1.0 dev version

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

Modified: phenote/trunk/doc/phenote-website/phenote.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.html	2006-11-22 19:38:48 UTC (rev 216)
+++ phenote/trunk/doc/phenote-website/phenote.html	2006-11-22 19:43:42 UTC (rev 217)
@@ -48,6 +48,14 @@
  href="https://sourceforge.net/tracker/?group_id=76834&amp;atid=887913">bug
 tracker</a>) and let me know what you
 think (mg...@fr...).<br>
+<br>
+Currently under development (still buggy):<br>
+<br>
+<a href="1.0/phenote-flybase.jnlp">Phenote dev 1.0 for fly</a><br>
+<br>
+<a href="1.0/phenote-zfin.jnlp">Phenote dev 1.0 for zfin</a><br>
+<br>
+<br>
 <h4>Phenote links:<br>
 </h4>
 <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Phenote


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[Obo-svn-commit] SF.net SVN: obo: [216] phenote/trunk/build.xml

From: <mg...@us...> - 2006-11-22 19:38:54

Revision: 216
          http://svn.sourceforge.net/obo/?rev=216&view=rev
Author:   mgibson
Date:     2006-11-22 11:38:48 -0800 (Wed, 22 Nov 2006)

Log Message:
-----------
ant for webstart deployment & docs

Modified Paths:
--------------
    phenote/trunk/build.xml

Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml	2006-11-22 19:35:16 UTC (rev 215)
+++ phenote/trunk/build.xml	2006-11-22 19:38:48 UTC (rev 216)
@@ -373,6 +373,31 @@
         </xmlbean>
     </target>
 
+<!-- todo do all jars not just phenote - take out -signed -->
+<!-- depends on sym link phenote-webstart and env var PHENOTE_VERSION -->
+    <target name="phenote-webstart-website" depends="sign-jars">
+      <copy todir="phenote-webstart">
+         <fileset file="doc/phenote-website/*.html">
+       </copy>
+      <mkdir dir="phenote-webstart/${env.PHENOTE_VERSION}"/>
+      <copy todir="phenote-webstart/${env.PHENOTE_VERSION}">
+        <fileset file="doc/phenote-website/*.jnlp"/>
+      </copy>
+      <copy todir="phenote-webstart/${env.PHENOTE_VERSION}/jars">
+        <fileset file="${lib}/*.jar"/>
+      </copy>
+    </target>
+
+    <target name="sign-jars" depends="build-all,jar">
+       <signjar keystore="plumpkey" alias="signFiles"
+                storepass="plumper" keypass="plumper">
+         <fileset dir="${lib}">
+            <include name="*.jar"/>
+         </fileset>
+       </signjar>
+    </target>
+
+
 </project>
 
 


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[Obo-svn-commit] SF.net SVN: obo: [215] phenote/trunk/doc/phenote-website/ phenote-release-notes.html

From: <mg...@us...> - 2006-11-22 19:35:18

Revision: 215
          http://svn.sourceforge.net/obo/?rev=215&view=rev
Author:   mgibson
Date:     2006-11-22 11:35:16 -0800 (Wed, 22 Nov 2006)

Log Message:
-----------
relase notes

Added Paths:
-----------
    phenote/trunk/doc/phenote-website/phenote-release-notes.html

Added: phenote/trunk/doc/phenote-website/phenote-release-notes.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.html	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.html	2006-11-22 19:35:16 UTC (rev 215)
@@ -0,0 +1,201 @@
+<!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>
+1.0
+will probably come out in December.<br>
+<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
+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
+webby phenote</a><br>
+<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
+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>
+<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
+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
+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>
+<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
+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>
+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
+(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
+here. Cleaned up and fixed a lot of the bugs in 0.2, which was rather
+buggy.<br>
+<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
+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>
+<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: [214] phenote/trunk/doc/phenote-web-site/

From: <mg...@us...> - 2006-11-22 19:33:10

Revision: 214
          http://svn.sourceforge.net/obo/?rev=214&view=rev
Author:   mgibson
Date:     2006-11-22 11:33:10 -0800 (Wed, 22 Nov 2006)

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

Removed Paths:
-------------
    phenote/trunk/doc/phenote-web-site/


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[Obo-svn-commit] SF.net SVN: obo: [213] phenote/trunk/doc/phenote-website

From: <mg...@us...> - 2006-11-22 19:32:11

Revision: 213
          http://svn.sourceforge.net/obo/?rev=213&view=rev
Author:   mgibson
Date:     2006-11-22 11:32:10 -0800 (Wed, 22 Nov 2006)

Log Message:
-----------
webstart
-This line, and those below, will be ignored--

A    phenote-website/phenote-flybase.jnlp
A    phenote-website/phenote-zfin.jnlp

Added Paths:
-----------
    phenote/trunk/doc/phenote-website/phenote-flybase.jnlp
    phenote/trunk/doc/phenote-website/phenote-zfin.jnlp

Added: phenote/trunk/doc/phenote-website/phenote-flybase.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-flybase.jnlp	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/phenote-flybase.jnlp	2006-11-22 19:32:10 UTC (rev 213)
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<jnlp
+spec="1.0+"
+codebase="http://toy.lbl.gov:9010/phenote/0.9/"
+href="phenote-flybase.jnlp">
+<information>
+	<title>Phenote 0.9</title>
+	<vendor>BBOP</vendor>
+	<description>Phenote 0.9</description>
+ 	 <!-- Declares that the application can run without
+         access to the server it was downloaded from -->
+	<offline-allowed />
+</information>
+<security>
+      <!-- Request that the application be given full
+           access to the local (executing) machine,
+           as if it were a regular Java application.
+           Requires that all JAR files be signed
+           by a trusted party -->
+	<all-permissions />
+</security>
+<resources>
+  	<!-- Specify the versions of the Java Runtime Environment
+         (JRE) that are supported by the application.
+         Multiple entries of this kind are allowed, in which
+         case they are considered to be in order of preference -->
+	<j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
+	<jar href="jars/phenote-signed.jar" />
+	<jar href="jars/oboedit-signed.jar" />
+	<jar href="jars/org.geneontology-signed.jar" />
+	<jar href="jars/BrowserLauncher2-10rc4-signed.jar" />
+	<jar href="jars/jsr173_1.0_api-signed.jar" />
+	<jar href="jars/phenoxmlbeans-signed.jar" />
+	<jar href="jars/phenoteconfigbeans-signed.jar" />
+	<jar href="jars/xbean-signed.jar" />
+	<jar href="jars/tomcat-servlet-signed.jar" />
+	<jar href="jars/te-common-signed.jar" />
+	<jar href="jars/log4j-1.2.13-signed.jar" />
+</resources>
+<application-desc main-class="phenote.main.Phenote">
+        <argument>-c</argument>
+        <argument>/initial-flybase.cfg</argument>
+</application-desc>
+</jnlp>
+
+
+

Added: phenote/trunk/doc/phenote-website/phenote-zfin.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-zfin.jnlp	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/phenote-zfin.jnlp	2006-11-22 19:32:10 UTC (rev 213)
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<jnlp
+spec="1.0+"
+codebase="http://toy.lbl.gov:9010/phenote/0.9/"
+href="phenote-zfin.jnlp">
+<information>
+	<title>Phenote 0.9</title>
+	<vendor>BBOP</vendor>
+	<description>Phenote 0.9</description>
+ 	 <!-- Declares that the application can run without
+         access to the server it was downloaded from -->
+	<offline-allowed />
+</information>
+<security>
+      <!-- Request that the application be given full
+           access to the local (executing) machine,
+           as if it were a regular Java application.
+           Requires that all JAR files be signed
+           by a trusted party -->
+	<all-permissions />
+</security>
+<resources>
+  	<!-- Specify the versions of the Java Runtime Environment
+         (JRE) that are supported by the application.
+         Multiple entries of this kind are allowed, in which
+         case they are considered to be in order of preference -->
+	<j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
+	<jar href="jars/phenote-signed.jar" />
+	<jar href="jars/oboedit-signed.jar" />
+	<jar href="jars/org.geneontology-signed.jar" />
+	<jar href="jars/BrowserLauncher2-10rc4-signed.jar" />
+	<jar href="jars/jsr173_1.0_api-signed.jar" />
+	<jar href="jars/phenoxmlbeans-signed.jar" />
+	<jar href="jars/phenoteconfigbeans-signed.jar" />
+	<jar href="jars/tomcat-servlet-signed.jar" />
+	<jar href="jars/xbean-signed.jar" />
+	<jar href="jars/te-common-signed.jar" />
+	<jar href="jars/log4j-1.2.13-signed.jar" />
+</resources>
+<application-desc main-class="phenote.main.Phenote">
+        <argument>-c</argument>
+        <argument>/initial-zfin.cfg</argument>
+</application-desc>
+</jnlp>
+
+
+


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[Obo-svn-commit] SF.net SVN: obo: [212] phenote/trunk/doc/phenote-web-site/phenote-human. jnlp

From: <mg...@us...> - 2006-11-22 19:13:35

Revision: 212
          http://svn.sourceforge.net/obo/?rev=212&view=rev
Author:   mgibson
Date:     2006-11-22 11:13:29 -0800 (Wed, 22 Nov 2006)

Log Message:
-----------
silly me web-site --> website

Removed Paths:
-------------
    phenote/trunk/doc/phenote-web-site/phenote-human.jnlp

Deleted: phenote/trunk/doc/phenote-web-site/phenote-human.jnlp
===================================================================
--- phenote/trunk/doc/phenote-web-site/phenote-human.jnlp	2006-11-22 19:13:10 UTC (rev 211)
+++ phenote/trunk/doc/phenote-web-site/phenote-human.jnlp	2006-11-22 19:13:29 UTC (rev 212)
@@ -1,47 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<jnlp
-spec="1.0+"
-codebase="http://toy.lbl.gov:9010/phenote/0.9/"
-href="phenote-human.jnlp">
-<information>
-	<title>Phenote 0.9</title>
-	<vendor>BBOP</vendor>
-	<description>Phenote 0.9</description>
- 	 <!-- Declares that the application can run without
-         access to the server it was downloaded from -->
-	<offline-allowed />
-</information>
-<security>
-      <!-- Request that the application be given full
-           access to the local (executing) machine,
-           as if it were a regular Java application.
-           Requires that all JAR files be signed
-           by a trusted party -->
-	<all-permissions />
-</security>
-<resources>
-  	<!-- Specify the versions of the Java Runtime Environment
-         (JRE) that are supported by the application.
-         Multiple entries of this kind are allowed, in which
-         case they are considered to be in order of preference -->
-	<j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
-	<jar href="jars/phenote.jar" />
-	<jar href="jars/oboedit-signed.jar" />
-	<jar href="jars/org.geneontology-signed.jar" />
-	<jar href="jars/BrowserLauncher2-10rc4-signed.jar" />
-	<jar href="jars/jsr173_1.0_api-signed.jar" />
-	<jar href="jars/phenoxmlbeans-signed.jar" />
-	<jar href="jars/phenoteconfigbeans-signed.jar" />
-	<jar href="jars/tomcat-servlet-signed.jar" />
-	<jar href="jars/xbean-signed.jar" />
-        <jar href="jars/te-common-signed.jar" />
-        <jar href="jars/log4j-1.2.13-signed.jar" />
-<</resources>
-<application-desc main-class="phenote.gui.Phenote">
-        <argument>-c</argument>
-        <argument>/human.cfg</argument>
-</application-desc>
-</jnlp>
-
-
-


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[Obo-svn-commit] SF.net SVN: obo: [211] phenote/trunk/doc/phenote-web-site/phenote.html

From: <mg...@us...> - 2006-11-22 19:13:16

Revision: 211
          http://svn.sourceforge.net/obo/?rev=211&view=rev
Author:   mgibson
Date:     2006-11-22 11:13:10 -0800 (Wed, 22 Nov 2006)

Log Message:
-----------
silly me web-site --> website

Removed Paths:
-------------
    phenote/trunk/doc/phenote-web-site/phenote.html

Deleted: phenote/trunk/doc/phenote-web-site/phenote.html
===================================================================
--- phenote/trunk/doc/phenote-web-site/phenote.html	2006-11-22 19:12:09 UTC (rev 210)
+++ phenote/trunk/doc/phenote-web-site/phenote.html	2006-11-22 19:13:10 UTC (rev 211)
@@ -1,117 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-  <meta content="text/html; charset=ISO-8859-1"
- http-equiv="content-type">
-  <title>Phenote</title>
-</head>
-<body>
-<h1 style="text-align: left;"><span style="font-weight: bold;"></span>Phenote<br>
-</h1>
-<br>
-Phenote is a tool to annotate phenotypes using the Entity Quality
-paradigm. It takes advantage of
-ontologies. It uses term completion to allow curators quick access to
-the ontology terms they want to use. <br>
-<br>
-<a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br>
-<br>
-<a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br>
-<br>
-To be clear the above webstart links for zfin &amp; fly were made via
-configuration not hard wired code. Thus one could in theory configure
-phenote for ones own purposes.<br>
-<br>
-Recent addditions include the ability to post compose terms, bul
-update, undo, spring framework, and
-synonyms now are shown in the completion list.<br>
-<br>
-Zebrafish requires
-components of phenote(to plug into their non-public
-website), not a full web app. Here is a proof of concept of some of
-those
-components:<br>
-<br>
-<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby
-Phenote(components used by Zfin)</a><br>
-<br>
-Webby phenote is a collaboration with Sohel Merchant at DichtyBase.
-Here is what they have done:<br>
-<br>
-<a
- href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DichtyBase
-webby phenote</a><br>
-<br>
-<br>
-I am doing these
-releases to get feedback. Please report any bugs (ideally through the <a
- href="https://sourceforge.net/tracker/?group_id=76834&amp;atid=887913">bug
-tracker</a>) and let me know what you
-think (mg...@fr...).<br>
-<h4>Phenote links:<br>
-</h4>
-<a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Phenote
-email list</a><br>
-<a href="https://sourceforge.net/tracker/?group_id=76834&amp;atid=887913">Phenote
-bug tracker</a><br>
-<a
- href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-bug-tracker">Bug
-tracker email list</a><br>
-<a href="https://sourceforge.net/svn/?group_id=76834">Phenote source
-code (obo sourceforge svn)</a><br>
-<a href="https://lists.sourceforge.net/lists/listinfo/obo-svn-commit">Phenote
-svn commit email list</a><br>
-<a
- href="http://wiki.dictybase.org/dictywiki/index.php/Phenotype_Curation_Tool_Documentation#Usage">Dichty
-webby phenote wiki developer docs</a><br>
-<a
- href="http://www.bioontology.org/wiki-internal/index.php/Phenotype_Annotation_Tool">Phenote
-ncbo internal wiki (ncbo folk only)</a><br>
-<br>
-<a href="phenote-release-notes.html">Phenote Release Notes and old
-webstart releases</a><br>
-<br>
-If the Phenote webstart link fails to do anything, then there are
-probably problems
-with webstart and/or java(has to be jdk 1.5). Take a look at my&nbsp; <a
- href="webstart-troubleshooting.html">webstart troubleshooting</a><br>
-page.<br>
-<br>
-Click here for <a href="phenote-java-requirements.html">phenote java
-requirements</a><br>
-<br>
-<br>
-<br>
-Old releases: <br>
-<br>
-<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>
-<br>
-<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>
-<br>
-<a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br>
-<br>
-<a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br>
-<br>
-<a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br>
-<br>
-<a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br>
-<br>
-<a href="0.4/phenote-flybase.jnlp">Phenote 0.4 webstart for FlyBase</a><br>
-<br>
-<a href="0.4/phenote-zfin.jnlp">Phenote 0.4 webstart for ZFIN</a><br>
-<br>
-<a href="0.3.1/phenote-webstart.jnlp">Phenote for CToL group (0.3.1)</a>&nbsp;&nbsp;
-(a special release for the CToL group that uses fish
-taxonomy)<br>
-<br>
-<a href="0.3/phenote-webstart.jnlp">Phenote 0.3</a><br>
-<br>
-<a href="0.2/phenote-webstart.jnlp">Phenote 0.2</a><br>
-<br>
-<a href="0.1/phenote-webstart.jnlp">Phenote 0.1</a><br>
-<br>
-<br>
-</body>
-</html>


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[Obo-svn-commit] SF.net SVN: obo: [210] phenote/trunk/doc

From: <mg...@us...> - 2006-11-22 19:12:14

Revision: 210
          http://svn.sourceforge.net/obo/?rev=210&view=rev
Author:   mgibson
Date:     2006-11-22 11:12:09 -0800 (Wed, 22 Nov 2006)

Log Message:
-----------
silly me web-site --> website

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

Copied: phenote/trunk/doc/phenote-website (from rev 208, phenote/trunk/doc/phenote-web-site)

Copied: phenote/trunk/doc/phenote-website/phenote-human.jnlp (from rev 209, phenote/trunk/doc/phenote-web-site/phenote-human.jnlp)
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-human.jnlp	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/phenote-human.jnlp	2006-11-22 19:12:09 UTC (rev 210)
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<jnlp
+spec="1.0+"
+codebase="http://toy.lbl.gov:9010/phenote/0.9/"
+href="phenote-human.jnlp">
+<information>
+	<title>Phenote 0.9</title>
+	<vendor>BBOP</vendor>
+	<description>Phenote 0.9</description>
+ 	 <!-- Declares that the application can run without
+         access to the server it was downloaded from -->
+	<offline-allowed />
+</information>
+<security>
+      <!-- Request that the application be given full
+           access to the local (executing) machine,
+           as if it were a regular Java application.
+           Requires that all JAR files be signed
+           by a trusted party -->
+	<all-permissions />
+</security>
+<resources>
+  	<!-- Specify the versions of the Java Runtime Environment
+         (JRE) that are supported by the application.
+         Multiple entries of this kind are allowed, in which
+         case they are considered to be in order of preference -->
+	<j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
+	<jar href="jars/phenote.jar" />
+	<jar href="jars/oboedit-signed.jar" />
+	<jar href="jars/org.geneontology-signed.jar" />
+	<jar href="jars/BrowserLauncher2-10rc4-signed.jar" />
+	<jar href="jars/jsr173_1.0_api-signed.jar" />
+	<jar href="jars/phenoxmlbeans-signed.jar" />
+	<jar href="jars/phenoteconfigbeans-signed.jar" />
+	<jar href="jars/tomcat-servlet-signed.jar" />
+	<jar href="jars/xbean-signed.jar" />
+        <jar href="jars/te-common-signed.jar" />
+        <jar href="jars/log4j-1.2.13-signed.jar" />
+<</resources>
+<application-desc main-class="phenote.gui.Phenote">
+        <argument>-c</argument>
+        <argument>/human.cfg</argument>
+</application-desc>
+</jnlp>
+
+
+


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[Obo-svn-commit] SF.net SVN: obo: [209] phenote/trunk/doc/phenote-web-site/phenote-human. jnlp

From: <mg...@us...> - 2006-11-22 19:01:46

Revision: 209
          http://svn.sourceforge.net/obo/?rev=209&view=rev
Author:   mgibson
Date:     2006-11-22 10:59:29 -0800 (Wed, 22 Nov 2006)

Log Message:
-----------
human webstart - need human.cfg!!!

Added Paths:
-----------
    phenote/trunk/doc/phenote-web-site/phenote-human.jnlp

Added: phenote/trunk/doc/phenote-web-site/phenote-human.jnlp
===================================================================
--- phenote/trunk/doc/phenote-web-site/phenote-human.jnlp	                        (rev 0)
+++ phenote/trunk/doc/phenote-web-site/phenote-human.jnlp	2006-11-22 18:59:29 UTC (rev 209)
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<jnlp
+spec="1.0+"
+codebase="http://toy.lbl.gov:9010/phenote/0.9/"
+href="phenote-human.jnlp">
+<information>
+	<title>Phenote 0.9</title>
+	<vendor>BBOP</vendor>
+	<description>Phenote 0.9</description>
+ 	 <!-- Declares that the application can run without
+         access to the server it was downloaded from -->
+	<offline-allowed />
+</information>
+<security>
+      <!-- Request that the application be given full
+           access to the local (executing) machine,
+           as if it were a regular Java application.
+           Requires that all JAR files be signed
+           by a trusted party -->
+	<all-permissions />
+</security>
+<resources>
+  	<!-- Specify the versions of the Java Runtime Environment
+         (JRE) that are supported by the application.
+         Multiple entries of this kind are allowed, in which
+         case they are considered to be in order of preference -->
+	<j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
+	<jar href="jars/phenote.jar" />
+	<jar href="jars/oboedit-signed.jar" />
+	<jar href="jars/org.geneontology-signed.jar" />
+	<jar href="jars/BrowserLauncher2-10rc4-signed.jar" />
+	<jar href="jars/jsr173_1.0_api-signed.jar" />
+	<jar href="jars/phenoxmlbeans-signed.jar" />
+	<jar href="jars/phenoteconfigbeans-signed.jar" />
+	<jar href="jars/tomcat-servlet-signed.jar" />
+	<jar href="jars/xbean-signed.jar" />
+        <jar href="jars/te-common-signed.jar" />
+        <jar href="jars/log4j-1.2.13-signed.jar" />
+<</resources>
+<application-desc main-class="phenote.gui.Phenote">
+        <argument>-c</argument>
+        <argument>/human.cfg</argument>
+</application-desc>
+</jnlp>
+
+
+


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: [208] phenote/trunk/obo-files

From: <mg...@us...> - 2006-11-22 13:58:19

Revision: 208
          http://svn.sourceforge.net/obo/?rev=208&view=rev
Author:   mgibson
Date:     2006-11-22 05:58:14 -0800 (Wed, 22 Nov 2006)

Log Message:
-----------
evidence code ontology for evidence code field

Modified Paths:
--------------
    phenote/trunk/obo-files/spatial.obo

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

Added: phenote/trunk/obo-files/evidence_code.obo
===================================================================
--- phenote/trunk/obo-files/evidence_code.obo	                        (rev 0)
+++ phenote/trunk/obo-files/evidence_code.obo	2006-11-22 13:58:14 UTC (rev 208)
@@ -0,0 +1,873 @@
+format-version: 1.0
+date: 23:11:2005 19:45
+saved-by: ma11
+auto-generated-by: DAG-Edit 1.419-beta3
+default-namespace: evidence_code
+remark: cvs version: $Revision: 1.2 $
+
+[Term]
+id: ECO:0000000
+name: Evidence_Codes_Ontology
+
+[Term]
+id: ECO:0000001
+name: inferred by curator
+def: "To be used for those cases where an annotation is not supported by any evidence\, but can be reasonably inferred by a curator from other GO annotations\, for which evidence is available." [ECO:go ""]
+exact_synonym: "IC" []
+is_a: ECO:0000000 ! Evidence_Codes_Ontology
+xref_unknown: TAIR:TED\:0000013 ""
+
+[Term]
+id: ECO:0000002
+name: inferred from direct assay
+exact_synonym: "IDA" []
+is_a: ECO:0000033 ! traceable author statement
+xref_unknown: TAIR:TED\:0000002 ""
+
+[Term]
+id: ECO:0000003
+name: inferred from reconstitution assay
+is_a: ECO:0000006 ! inferred from experiment
+
+[Term]
+id: ECO:0000004
+name: inferred from cell fractionation
+def: "Used when an annotation is maded based on separation of subcellular components based on their physical properties\, such as density in sucrose density gradients. This evidence is used mostly for annotations to the cellular component ontology." [TAIR:TED ""]
+exact_synonym: "IDA\: cell fractionation" []
+is_a: ECO:0000100 ! inferred from fractionation
+xref_unknown: TAIR:TED\:0000015 ""
+
+[Term]
+id: ECO:0000005
+name: inferred from enzyme assay
+def: "Used when an annotation is maded based on assays that determine the catalytic activity of enzymes." [TAIR:TED ""]
+exact_synonym: "IDA\: enzyme assays" []
+is_a: ECO:0000039 ! inferred from protein assay
+xref_unknown: TAIR:TED\:0000018 ""
+
+[Term]
+id: ECO:0000006
+name: inferred from experiment
+is_a: ECO:0000002 ! inferred from direct assay
+
+[Term]
+id: ECO:0000007
+name: inferred from immunofluorescence
+def: "Used when an annotation is maded based on methods that detect the presence of macromolecules\, proteins\, and compounds by the use of a fluorescent-labeled antibody." [TAIR:TED ""]
+exact_synonym: "IDA\: immunofluorescence" []
+is_a: ECO:0000040 ! inferred from immunological assay
+xref_unknown: TAIR:TED\:0000019 ""
+
+[Term]
+id: ECO:0000008
+name: inferred from expression pattern
+exact_synonym: "IEP" []
+is_a: ECO:0000006 ! inferred from experiment
+xref_unknown: TAIR:TED\:0000005 ""
+
+[Term]
+id: ECO:0000009
+name: inferred from transcript expression
+is_a: ECO:0000008 ! inferred from expression pattern
+
+[Term]
+id: ECO:0000010
+name: inferred from protein expression
+is_a: ECO:0000008 ! inferred from expression pattern
+is_a: ECO:0000039 ! inferred from protein assay
+
+[Term]
+id: ECO:0000011
+name: inferred from genetic interaction
+exact_synonym: "IGI" []
+xref_analog: TAIR:TED\:0000006 ""
+is_a: ECO:0000059 ! inferred from genetic analysis
+
+[Term]
+id: ECO:0000012
+name: inferred from functional complementation
+def: "Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a mutant background in the organism of the gene's origin or a heterologous organism with a mutation in the homologous gene." [TAIR:TED ""]
+exact_synonym: "IGI\: functional complementation" []
+is_a: ECO:0000011 ! inferred from genetic interaction
+xref_unknown: TAIR:TED\:0000059 ""
+
+[Term]
+id: ECO:0000013
+name: inferred from transgenic rescue
+is_a: ECO:0000012 ! inferred from functional complementation
+
+[Term]
+id: ECO:0000014
+name: inferred from phenotype
+exact_synonym: "IMP" []
+is_a: ECO:0000059 ! inferred from genetic analysis
+xref_unknown: TAIR:TED\:0000007 ""
+
+[Term]
+id: ECO:0000015
+name: inferred from mutant phenotype
+is_a: ECO:0000014 ! inferred from phenotype
+
+[Term]
+id: ECO:0000016
+name: inferred from loss-of-function mutant phenotype
+is_a: ECO:0000015 ! inferred from mutant phenotype
+
+[Term]
+id: ECO:0000017
+name: inferred from ectopic expression
+def: "Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress or ectopically express the gene product in question." [TAIR:TED ""]
+exact_synonym: "IMP\: analysis of overexpression/ectopic expression phenotype" []
+is_a: ECO:0000014 ! inferred from phenotype
+xref_unknown: TAIR:TED\:0000067 ""
+
+[Term]
+id: ECO:0000018
+name: inferred from anti-sense experiment
+def: "Used when an annotation is based on a phenotype observed when expressing an anti-sense version of a gene product in a wild-type (for that gene product) background." [TAIR:TED ""]
+exact_synonym: "IMP\: anti-sense experiments" []
+is_a: ECO:0000014 ! inferred from phenotype
+xref_unknown: TAIR:TED\:0000070 ""
+
+[Term]
+id: ECO:0000019
+name: inferred from RNAi experiment
+def: "Inference based on a phenotype observed when expressing an RNAi construct that includes a fragment of the gene product in a wild-type (for that gene product) background.  A double-stranded RNA specifically suppresses the expression of the gene bearing its complementary sequence." [TAIR:TED ""]
+exact_synonym: "IMP\: RNAi experiments" []
+is_a: ECO:0000014 ! inferred from phenotype
+xref_unknown: TAIR:TED\:0000073 ""
+
+[Term]
+id: ECO:0000020
+name: inferred from specific protein inhibition
+is_a: ECO:0000039 ! inferred from protein assay
+
+[Term]
+id: ECO:0000021
+name: inferred from physical interaction
+exact_synonym: "IPI" []
+is_a: ECO:0000006 ! inferred from experiment
+xref_unknown: TAIR:TED\:0000008 ""
+
+[Term]
+id: ECO:0000022
+name: inferred from co-purification
+def: "Used in component annotations when a subunit is isolated as part of purification of its larger complex." [TAIR:TED ""]
+exact_synonym: "IPI\: co-purification" []
+is_a: ECO:0000021 ! inferred from physical interaction
+xref_unknown: TAIR:TED\:0000075 ""
+
+[Term]
+id: ECO:0000023
+name: inferred from ligand binding
+is_a: ECO:0000021 ! inferred from physical interaction
+
+[Term]
+id: ECO:0000024
+name: inferred from protein binding
+is_a: ECO:0000023 ! inferred from ligand binding
+is_a: ECO:0000039 ! inferred from protein assay
+
+[Term]
+id: ECO:0000025
+name: inferred from hybrid interaction
+is_a: ECO:0000023 ! inferred from ligand binding
+
+[Term]
+id: ECO:0000026
+name: inferred from nucleic acid hybridization
+is_a: ECO:0000006 ! inferred from experiment
+
+[Term]
+id: ECO:0000027
+name: inferred from structural similarity
+def: "Used when an annotation is made based on the structural similarity of the annotated gene/gene product to a single other gene or group of genes.  In the case of a single gene\, an accession for the related gene's sequence is entered in the evidence_with field." [TAIR:TED ""]
+exact_synonym: "ISS\: structural similarity" []
+is_a: ECO:0000041 ! inferred from similarity
+xref_unknown: TAIR:TED\:0000085 ""
+
+[Term]
+id: ECO:0000028
+name: inferred from motif similarity
+def: "Used when an annotation is made based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence." [TAIR:TED ""]
+exact_synonym: "ISS\: recognized domains" []
+is_a: ECO:0000044 ! inferred from sequence similarity
+xref_unknown: TAIR:TED\:0000082 ""
+
+[Term]
+id: ECO:0000029
+name: inferred from InterPro motif similarity
+is_a: ECO:0000028 ! inferred from motif similarity
+
+[Term]
+id: ECO:0000030
+name: inferred from curated BLAST match
+is_a: ECO:0000044 ! inferred from sequence similarity
+
+[Term]
+id: ECO:0000031
+name: inferred from curated BLAST match to protein
+is_a: ECO:0000030 ! inferred from curated BLAST match
+
+[Term]
+id: ECO:0000032
+name: inferred from curated BLAST match to nucleic acid
+is_a: ECO:0000030 ! inferred from curated BLAST match
+
+[Term]
+id: ECO:0000033
+name: traceable author statement
+exact_synonym: "TAS" []
+is_a: ECO:0000000 ! Evidence_Codes_Ontology
+xref_unknown: TAIR:TED\:0000012 ""
+
+[Term]
+id: ECO:0000034
+name: non-traceable author statement
+def: "Used for annotations based on statements in a publication or database record where the curator cannot\, from the publication\, trace the primary source of the evidence." [ECO:go ""]
+exact_synonym: "NAS" []
+is_a: ECO:0000000 ! Evidence_Codes_Ontology
+xref_unknown: TAIR:TED\:0000010 ""
+
+[Term]
+id: ECO:0000035
+name: no biological data
+exact_synonym: "ND" []
+is_a: ECO:0000000 ! Evidence_Codes_Ontology
+xref_unknown: TAIR:TED\:0000011 ""
+
+[Term]
+id: ECO:0000036
+name: inferred from electronic annotation
+def: "Used when an annotation is made solely based on a computational analysis of the gene product's sequence.  The prediction has not been examined by a curator." [ECO:go ""]
+exact_synonym: "IEA" []
+xref_analog: TAIR:TED\:0000004 ""
+is_a: ECO:0000043 ! inferred from in-silico analysis
+
+[Term]
+id: ECO:0000037
+name: not_recorded
+exact_synonym: "NR" []
+is_a: ECO:0000000 ! Evidence_Codes_Ontology
+
+[Term]
+id: ECO:0000038
+name: inferred from transient rescue
+is_a: ECO:0000012 ! inferred from functional complementation
+
+[Term]
+id: ECO:0000039
+name: inferred from protein assay
+is_a: ECO:0000006 ! inferred from experiment
+
+[Term]
+id: ECO:0000040
+name: inferred from immunological assay
+is_a: ECO:0000023 ! inferred from ligand binding
+is_a: ECO:0000039 ! inferred from protein assay
+
+[Term]
+id: ECO:0000041
+name: inferred from similarity
+is_a: ECO:0000033 ! traceable author statement
+is_a: ECO:0000043 ! inferred from in-silico analysis
+xref_unknown: TAIR:TED\:0000009 ""
+
+[Term]
+id: ECO:0000042
+name: inferred from gain-of-function mutant phenotype
+is_a: ECO:0000015 ! inferred from mutant phenotype
+
+[Term]
+id: ECO:0000043
+name: inferred from in-silico analysis
+is_a: ECO:0000000 ! Evidence_Codes_Ontology
+
+[Term]
+id: ECO:0000044
+name: inferred from sequence similarity
+def: "Used when an annotation is made based on the sequence similarity of the annotated gene/gene product to a single other gene or group of genes and this evidence has been examined by a curator." [TAIR:TED ""]
+exact_synonym: "ISS" []
+exact_synonym: "ISS\: sequence similarity (homologue of/most closely related to)" []
+is_a: ECO:0000041 ! inferred from similarity
+xref_unknown: TAIR:TED\:0000083 ""
+
+[Term]
+id: ECO:0000045
+name: inferred from spatial pattern of protein expression
+is_a: ECO:0000010 ! inferred from protein expression
+
+[Term]
+id: ECO:0000046
+name: inferred from level of protein expression
+is_a: ECO:0000010 ! inferred from protein expression
+
+[Term]
+id: ECO:0000047
+name: inferred from spatial pattern of transcript expression
+is_a: ECO:0000009 ! inferred from transcript expression
+
+[Term]
+id: ECO:0000048
+name: inferred from level of transcript expression
+is_a: ECO:0000009 ! inferred from transcript expression
+
+[Term]
+id: ECO:0000049
+name: inferred from reporter gene assay
+def: "Used when an annotation is made on the basis of the expression pattern of a reporter gene.  The reporter gene may consist of the native promoter of the gene in question that drives the expression of a readily assayable gene product such as GUS or GFP.  The reporter gene may also be a marker of a particular type of physiological response." [TAIR:TED ""]
+exact_synonym: " IEP\: expression of a reporter gene" []
+is_a: ECO:0000059 ! inferred from genetic analysis
+xref_unknown: TAIR:TED\:0000050 ""
+
+[Term]
+id: ECO:0000050
+name: inferred from loss of function mutant phenotype
+is_obsolete: true
+
+[Term]
+id: ECO:0000051
+name: inferred from gain of function mutant phenotype
+is_obsolete: true
+
+[Term]
+id: ECO:0000052
+name: inferred from supressor/enhancer interaction
+synonym: "IGI\: 'traditional' genetic interactions (e.g. suppressors\, synthetic lethals)" []
+xref_analog: TAIR:TED\:0000063 ""
+is_a: ECO:0000011 ! inferred from genetic interaction
+
+[Term]
+id: ECO:0000053
+name: inferred from reviewed computational analysis
+def: "Used for\: Predictions based on large-scale experiments (e.g. genome-wide two-hybrid\, genome-wide synthetic interactions); Predictions based on integration of large-scale datasets of several types; Text-based computation (e.g. text mining). This code is used for annotations based on a non-sequence-based computational method\,  where the results have been reviewed by an author or a curator. IEA should be used for any computational annotations that are not checked for accuracy by a curator (or by the authors of a paper describing such analysis)\, and sequence comparisons that have been reviewed use ISS. For microarray results alone\, IEP is preferred\, but RCA is used when microarray results are combined with results of other types of large-scale experiments.\n" [ECO:go]
+synonym: "RCA" []
+is_a: ECO:0000036 ! inferred from electronic annotation
+
+[Term]
+id: ECO:0000054
+name: inferred from double mutant analysis
+def: "Used when an annotation is made based on the phenotype of double mutant organism that contains a mutation in the gene product of interest in addition to a second mutation at an unrelated locus." [TAIT:TED ""]
+exact_synonym: "IGI\: double mutant analysis" []
+is_a: ECO:0000011 ! inferred from genetic interaction
+xref_unknown: TAIR:TED\:0000057 ""
+
+[Term]
+id: ECO:0000055
+name: inferred from array experiment
+is_a: ECO:0000006 ! inferred from experiment
+
+[Term]
+id: ECO:0000056
+name: inferred from epistatic interaction
+def: "Used when an annotation is based on results of epistatis analysis of an allele of the gene in question and a mutant allele at another locus." [TAIR:TED ""]
+exact_synonym: "IGI\: epistatic interactions" []
+is_a: ECO:0000011 ! inferred from genetic interaction
+xref_unknown: TAIR:TED\:0000058 ""
+
+[Term]
+id: ECO:0000058
+name: inferred from expression microarray experiment
+is_a: ECO:0000055 ! inferred from array experiment
+
+[Term]
+id: ECO:0000059
+name: inferred from genetic analysis
+is_a: ECO:0000006 ! inferred from experiment
+
+[Term]
+id: ECO:0000061
+name: inferred from quantitative trait analysis
+def: "Used when an annotation is made for a gene product that has not been cloned but is associated with a quantitative trait locus." [TAIR:tn ""]
+exact_synonym: "IGI\: quantitative trait analysis" []
+is_a: ECO:0000059 ! inferred from genetic analysis
+xref_unknown: TAIR:TED\:0000062 ""
+
+[Term]
+id: ECO:0000062
+name: inferred from genomic microarray experiment
+is_a: ECO:0000055 ! inferred from array experiment
+
+[Term]
+id: ECO:0000064
+name: inferred from functional complemtation in heterologous system
+def: "Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a heterologous organism with a mutation in the homologous gene." [TAIR:TED ""]
+exact_synonym: "IGI\: functional complementation in heterologous system" []
+is_a: ECO:0000012 ! inferred from functional complementation
+xref_unknown: TAIR:TED\:0000060 ""
+
+[Term]
+id: ECO:0000065
+name: inferred from CpG island microarray experiment
+is_a: ECO:0000055 ! inferred from array experiment
+
+[Term]
+id: ECO:0000066
+name: inferred from yeast one-hybrid assay
+def: "Used when an annotation is based on the interaction of a protein with a DNA fragment in a yeast one-hybrid assay.  The assay involves screening a library of candidate proteins for the ability bind to a target\, cis-regulatory element or any other short\, DNA binding sequence placed 5' to a yeast reporter gene." [TAIR:TED ""]
+exact_synonym: "IPI\: yeast one-hybrid assay" []
+is_a: ECO:0000025 ! inferred from hybrid interaction
+xref_unknown: TAIR:TED\:0000080 ""
+
+[Term]
+id: ECO:0000068
+name: inferred from yeast 2-hybrid assay
+def: "Used when an annotation is based on the interaction between two proteins in a yeast two-hybrid assay.  The assay involves screening a trap-tagged library with a bait-tagged vector.  The library is tagged with a DNA-binding domain (trap) and the bait is tagged with a transcriptional activation domain.  Interaction between a library-trap protein and the bait results in activation of a yeast reporter gene whose transcription can be experimentally assayed." [TAIR:TED ""]
+exact_synonym: "IPI\: yeast two-hybrid assay" []
+is_a: ECO:0000025 ! inferred from hybrid interaction
+xref_unknown: TAIR:TED\:0000081 ""
+
+[Term]
+id: ECO:0000069
+name: inferred from differential methylation hybridization
+is_a: ECO:0000026 ! inferred from nucleic acid hybridization
+
+[Term]
+id: ECO:0000070
+name: inferred from co-immunoprecipitation
+def: "Used when an annotation is based on the interaction of one gene product with another in a co-immunoprecipitation assay (two or more proteins are precipitated when treated with an antibody specific to a single protein).  The interacting protein is referenced in the evidence_with column." [TAIR:TED ""]
+exact_synonym: "IPI\: co-immunoprecipitation" []
+is_a: ECO:0000085 ! inferred from immunoprecipitation
+xref_unknown: TAIR:TED\:0000074 ""
+
+[Term]
+id: ECO:0000072
+name: inferred from Sos-recruitment assay
+def: "Used when an annotation is based on the interaction of two proteins in a sos-recruitment assay.  The assay is a genetic screening system that detects protein-protein interactions and is not based on a transcriptional readout.  " [TAIR:TED ""]
+exact_synonym: "IPI\: Sos-recruitment assay" []
+is_a: ECO:0000021 ! inferred from physical interaction
+xref_unknown: TAIR:TED\:0000078 ""
+
+[Term]
+id: ECO:0000073
+name: inferred from genomic analysis
+is_a: ECO:0000006 ! inferred from experiment
+
+[Term]
+id: ECO:0000074
+name: inferred from split-ubiquitin assay
+def: "Used when an annotation is based on the interaction of two proteins in a split-ubiquitin assay.  The bait protein is fused to the C-terminal ubiquitin (Cub) domain followed by a reporter protein\, and the prey protein is fused to a mutated N terminal ubiquiting (NubG) domain. If bait and prey interact\, their interaction brings the NubG and Cub domains close enough together to reconstitute split-ubiquitin\, resulting in the release of the reporter protein by the action of the UBPs." [TAIR:TED ""]
+exact_synonym: "IPI\: split-ubiquitin assay" []
+is_a: ECO:0000021 ! inferred from physical interaction
+xref_unknown: TAIR:TED\:0000079 ""
+
+[Term]
+id: ECO:0000076
+name: inferred from far-Western assay
+def: "Used when an annotation is based on the interaction of protein with another in a far-Western assay.  The assay involves separating target proteins on an SDS-PAGE gel\, blotting to a membrane\, hybridization with a protein probe and visualization using a probe-directed antibody.  The interacting protein is referenced in the evidence_with column." [TAIR:TED ""]
+exact_synonym: "IPI\: far-Western analysis" []
+is_a: ECO:0000021 ! inferred from physical interaction
+xref_unknown: TAIR:TED\:0000077 ""
+
+[Term]
+id: ECO:0000077
+name: inferred from methylation-specific PCR
+is_a: ECO:0000082 ! inferred from PCR experiment
+
+[Term]
+id: ECO:0000078
+name: inferred from Southern blot hybridization
+def: "Used when an annotation is based on the hybridization of a probe derived from the gene in question with a gene of known function/process/component.  Can also be used when a probe derived from a gene of known function/process/component hybridizes with the gene in question." [TAIR:TED ""]
+exact_synonym: "ISS\: Southern blotting" []
+is_a: ECO:0000026 ! inferred from nucleic acid hybridization
+xref_unknown: TAIR:TED\:0000084 ""
+
+[Term]
+id: ECO:0000079
+name: inferred from affinity chromatography
+def: "Used when an annotation is made based on affinity chromatography\, which is a selective separation technique by which a compound (e.g.\, an antibody) is immobilized on a polymeric matrix and used to bind selectively other compounds. Following removal of the unattached components\, the bound compound is displaced by changing the concentration of protons\, salts\, or cofactors in the eluent." [TAIR:TED ""]
+exact_synonym: "IDA\: affinity chromatography" []
+is_a: ECO:0000023 ! inferred from ligand binding
+xref_unknown: TAIR:TED\:0000003 ""
+
+[Term]
+id: ECO:0000081
+name: inferred from targeting sequence prediction
+def: "Used when a component annotation is made based on the presence of a targeting sequence in a protein's primary sequence.  The presence of the targeting sequence may be detected by computational prediction and/or the author's manual examination of the sequence." [TAIR:TED ""]
+exact_synonym: "ISS\: targeting sequence prediction" []
+is_a: ECO:0000028 ! inferred from motif similarity
+xref_unknown: TAIR:TED\:0000086 ""
+
+[Term]
+id: ECO:0000082
+name: inferred from PCR experiment
+is_a: ECO:0000073 ! inferred from genomic analysis
+
+[Term]
+id: ECO:0000083
+name: inferred from transmembrane domain prediction
+def: "Used when a component annotation is made based on the presence of one or more transmembrane domains in a protein's primary sequence.  The presence of the transmembrane domains may be detected by computational prediction and/or the author's manual examination of the sequence." [TAIR:TED ""]
+exact_synonym: "ISS\: transmembrane domain prediction" []
+is_a: ECO:0000028 ! inferred from motif similarity
+xref_unknown: TAIR:TED:0000087 ""
+
+[Term]
+id: ECO:0000085
+name: inferred from immunoprecipitation
+def: "Used when an annotation is made based on a method that precipitates a multivalent antigen by a bivalent antibody." [TAIR:TED ""]
+exact_synonym: "IDA\: immunoprecipitation" []
+is_a: ECO:0000040 ! inferred from immunological assay
+xref_unknown: TAIR:TED\:0000023 ""
+
+[Term]
+id: ECO:0000086
+name: inferred from amplification of intermethylated sites
+is_a: ECO:0000073 ! inferred from genomic analysis
+
+[Term]
+id: ECO:0000087
+name: inferred from immunolocalization
+def: "Used when an annotation is maded based on methods that detect the presence of macromolecules\, proteins\, and compounds by the use of antibodies." [TAIR:TED ""]
+exact_synonym: "IDA\: immunolocalization" []
+is_a: ECO:0000040 ! inferred from immunological assay
+is_a: ECO:0000122 ! inferred from protein localization
+xref_unknown: TAIR:TED\:0000020 ""
+
+[Term]
+id: ECO:0000089
+name: inferred from restriction landmark genomic scanning
+is_a: ECO:0000073 ! inferred from genomic analysis
+
+[Term]
+id: ECO:0000090
+name: inferred from immunogold labelling
+def: "Used when an annotation is made based on immunolocalization method that detects an antigen in cytological preparations by using a gold-labeled secondary antibody." [TAIR:TED ""]
+exact_synonym: "IDA\: immunogold labelling" []
+is_a: ECO:0000040 ! inferred from immunological assay
+xref_unknown: TAIR:TED\:0000022 ""
+
+[Term]
+id: ECO:0000092
+name: inferred from immunolocalization of epitope-tagged protein
+def: "Used when an annotation is maded based on immunolocalization of recombinant proteins fused with epitopes that are recognized by antibodies." [TAIR:TED ""]
+exact_synonym: "IDA\: immunolocalization of epitope-tagged protein" []
+is_a: ECO:0000087 ! inferred from immunolocalization
+xref_unknown: TAIR:TED\:0000021 ""
+
+[Term]
+id: ECO:0000093
+name: inferred from oligonucleotide microarray
+is_a: ECO:0000055 ! inferred from array experiment
+
+[Term]
+id: ECO:0000094
+name: inferred from bioassay
+def: "Used when an annotation is made based on assays using living organisms to measure the effect of a substance\, factor\, or condition." [TAIR:TED ""]
+exact_synonym: "IDA\: bioassay" []
+is_a: ECO:0000006 ! inferred from experiment
+xref_unknown: TAIR:TED\:0000014 ""
+
+[Term]
+id: ECO:0000096
+name: inferred from electrophoretic mobility shift assay
+def: "Used when an annotation is made based on electrophoretic mobility shift of macromolecules\, compounds\, and proteins. Most commonly used for detecting the binding of protein to DNA." [TAIR:TED ""]
+exact_synonym: "IDA\: electrophoretic mobility shift assay" []
+is_a: ECO:0000006 ! inferred from experiment
+xref_unknown: TAIR:TED\:0000017 ""
+
+[Term]
+id: ECO:0000097
+name: inferred from cDNA microarray
+is_a: ECO:0000055 ! inferred from array experiment
+
+[Term]
+id: ECO:0000098
+name: inferred from in situ hybridization
+def: "Used when an annotation is made based on a method that hybridizes a labeled nucleic acid probe to a tissue or cell specimen in which the cellular structures are still intact. Depending on the label and protocol used\, the probe may detect complementary DNA or RNA by hybridizing specifically to that gene or sequence." [TAIR:TED ""]
+exact_synonym: "IDA\: in situ hybridization" []
+is_a: ECO:0000026 ! inferred from nucleic acid hybridization
+xref_unknown: TAIR:TED\:0000024 ""
+
+[Term]
+id: ECO:0000100
+name: inferred from fractionation
+is_a: ECO:0000006 ! inferred from experiment
+
+[Term]
+id: ECO:0000101
+name: inferred from Affymetrix array
+is_a: ECO:0000055 ! inferred from array experiment
+
+[Term]
+id: ECO:0000102
+name: inferred from co-fractionation
+def: "Used when an annotation is maded based on fractionation of a protein with other compounds\, factors\, or macromolecules." [TAIR:TED ""]
+exact_synonym: "IDA\: co-fractionation" []
+is_a: ECO:0000100 ! inferred from fractionation
+xref_unknown: TAIR:TED\:0000016 ""
+
+[Term]
+id: ECO:0000104
+name: inferred from level of transcript expression determined by microarray analysis
+def: "Used when an annotation is made based on levels of RNA expression determined by microarray experiment." [TAIR:TED ""]
+synonym: "IEP\: transcript levels (e.g. microarray data)" []
+is_a: ECO:0000048 ! inferred from level of transcript expression
+is_a: ECO:0000058 ! inferred from expression microarray experiment
+xref_unknown: TAIR:TED\:0000055 ""
+
+[Term]
+id: ECO:0000105
+name: inferred from Nimblegen array
+is_a: ECO:0000055 ! inferred from array experiment
+
+[Term]
+id: ECO:0000106
+name: inferred from level of transcript expression determined by Northern assay
+def: "Used when an annotation is made based on levels of RNA expression determined by a Northern blot experiment." [TAIR:TED ""]
+synonym: "IEP\: transcript levels (e.g. Northerns)" []
+is_a: ECO:0000048 ! inferred from level of transcript expression
+xref_unknown: TAIR:TED\:0000054 ""
+
+[Term]
+id: ECO:0000108
+name: inferred from level of transcript expression determined by RT-PCR
+def: "Used when an annotation is made based on levels of RNA expression determined by an RT-PCR experiment (quantitative or otherwise)." [TAIR:TED ""]
+synonym: "IEP\: transcript levels (e.g. RT-PCR)" []
+is_a: ECO:0000048 ! inferred from level of transcript expression
+is_a: ECO:0000109 ! inferred from RT-PCR experiment
+xref_unknown: TAIR:TED\:0000056 ""
+
+[Term]
+id: ECO:0000109
+name: inferred from RT-PCR experiment
+is_a: ECO:0000082 ! inferred from PCR experiment
+
+[Term]
+id: ECO:0000110
+name: inferred from RNA protection assay
+def: "Used when an annotation is made based on levels of RNA expression determined by an RNA protection assay." [TAIR:TED ""]
+exact_synonym: "IEP\: RNA protection assay" []
+is_a: ECO:0000009 ! inferred from transcript expression
+xref_unknown: TAIR:TED\:0000052 ""
+
+[Term]
+id: ECO:0000112
+name: inferred from Western blot assay
+def: "Used when an annotation is made based on levels of protein expression determined by a Western blot assay." [TAIR:TED ""]
+synonym: "IEP\: protein levels (e.g. Western blots)" []
+is_a: ECO:0000046 ! inferred from level of protein expression
+xref_unknown: TAIR:TED\:0000051 ""
+
+[Term]
+id: ECO:0000114
+name: inferred from expression library screening
+def: "Used when an annotation is made on the basis of a protein expression library screen where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein." [TAIR:TED ""]
+exact_synonym: "IEP\: expression library screening" []
+is_a: ECO:0000010 ! inferred from protein expression
+is_a: ECO:0000040 ! inferred from immunological assay
+xref_unknown: TAIR:TED\:0000049 ""
+
+[Term]
+id: ECO:0000116
+name: inferred from differential hybridization
+def: "Used when an annotation is made based on results of a differential hybridization experiment that demonstrates expression of an RNA under one condition and not another." [TAIR:TED ""]
+exact_synonym: "IEP\: differential hybridization" []
+is_a: ECO:0000009 ! inferred from transcript expression
+is_a: ECO:0000026 ! inferred from nucleic acid hybridization
+xref_unknown: TAIR:TED\:0000048 ""
+
+[Term]
+id: ECO:0000118
+name: inferred from subtractive hybridization
+def: "Used when an annotation is made based on results of a subtractive hybridization experiment that demonstrates expression of an RNA under one condition and not another." [TAIR:TED ""]
+exact_synonym: "IEP\: subtractive hybridization" []
+is_a: ECO:0000009 ! inferred from transcript expression
+is_a: ECO:0000026 ! inferred from nucleic acid hybridization
+xref_unknown: TAIR:TED\:0000053 ""
+
+[Term]
+id: ECO:0000120
+name: inferred from over expression
+def: "Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress the gene product in question." [TAIR:TED ""]
+exact_synonym: "IMP\: analysis of overexpression/ectopic expression phenotype" []
+is_a: ECO:0000014 ! inferred from phenotype
+xref_unknown: TAIR:TED\:0000067 ""
+
+[Term]
+id: ECO:0000122
+name: inferred from protein localization
+is_a: ECO:0000039 ! inferred from protein assay
+
+[Term]
+id: ECO:0000124
+name: inferred from localization of fusion protein
+is_a: ECO:0000122 ! inferred from protein localization
+
+[Term]
+id: ECO:0000126
+name: inferred from localization of GFP fusion protein
+exact_synonym: "IDA\: localization of GFP/YFP fusion protein" []
+is_a: ECO:0000124 ! inferred from localization of fusion protein
+xref_unknown: TAIR:TED\:0000030 ""
+
+[Term]
+id: ECO:0000128
+name: inferred from localization of YFP fusion protein
+exact_synonym: "IDA\: localization of GFP/YFP fusion protein" []
+is_a: ECO:0000124 ! inferred from localization of fusion protein
+xref_unknown: TAIR:TED\:0000030 ""
+
+[Term]
+id: ECO:0000130
+name: inferred from localiztion of GUS fusion protein
+exact_synonym: "IDA\: localization of GUS fusion protein" []
+is_a: ECO:0000124 ! inferred from localization of fusion protein
+xref_unknown: TAIR:TED\:0000031 ""
+
+[Term]
+id: ECO:0000132
+name: inferred from localization of lacZ fusion protein
+is_a: ECO:0000124 ! inferred from localization of fusion protein
+
+[Term]
+id: ECO:0000134
+name: inferred from transport assay
+exact_synonym: "IDA\: transport assay" []
+is_a: ECO:0000006 ! inferred from experiment
+xref_unknown: TAIR:TED\:0000042 ""
+
+[Term]
+id: ECO:0000136
+name: inferred from nucleic acid binding assay
+is_a: ECO:0000023 ! inferred from ligand binding
+
+[Term]
+id: ECO:0000138
+name: inferred from ribohomopolymer binding assay
+exact_synonym: "IDA\: ribohomopolymer binding assay" []
+is_a: ECO:0000136 ! inferred from nucleic acid binding assay
+xref_unknown: TAIR:TED\:0000038 ""
+
+[Term]
+id: ECO:0000140
+name: inferred from thin layer chromatographic assay
+exact_synonym: "IDA\: thin layer chromatography" []
+is_a: ECO:0000006 ! inferred from experiment
+xref_unknown: TAIR:TED\:0000040 ""
+
+[Term]
+id: ECO:0000142
+name: inferred from protein:ion binding assay
+is_a: ECO:0000024 ! inferred from protein binding
+exact_exact_synonym: "IDA\: ion/protein binding experiments" []
+xref_unknown: TAIR:TED\:0000029 ""
+
+[Term]
+id: ECO:0000144
+name: inferred from Southwestern analysis
+def: "Used when an annotation is made based on a Southwestern blot analysis\, which detects DNA binding of proteins using labeled DNA as probe hybridizing to electrophoretically separated proteins." [TAIR:TED ""]
+exact_synonym: "IDA\: Southwestern analysis" []
+is_a: ECO:0000136 ! inferred from nucleic acid binding assay
+xref_unknown: TED:TED\:0000039 ""
+
+[Term]
+id: ECO:0000146
+name: inferred from Northwestern analysis
+def: "Used when an annotation is made based on a Northwestern blot analysis\, which detects RNA binding of proteins using labeled RNA as probe hybridizing to electrophoretically separated proteins." [TAIR:TED ""]
+exact_synonym: "IDA\: Northwestern analysis" []
+is_a: ECO:0000136 ! inferred from nucleic acid binding assay
+xref_unknown: TAIR:TED\:0000033 ""
+
+[Term]
+id: ECO:0000148
+name: inferred from in vitro binding assay
+exact_synonym: "IDA\: in vitro binding assay" []
+is_a: ECO:0000021 ! inferred from physical interaction
+xref_unknown: TAIR:TED\:0000026 ""
+
+[Term]
+id: ECO:0000150
+name: inferred from in vitro transcription reconstitution assay
+exact_synonym: "IDA\: in vitro reconstitution assay with recombinant protein" []
+is_a: ECO:0000003 ! inferred from reconstitution assay
+xref_unknown: TAIR:TED\:0000028 ""
+
+[Term]
+id: ECO:0000152
+name: inferred from in vitro transcription reconstitution assay with recombinant protein
+exact_synonym: "IDA\: in vitro reconstitution assay with recombinant protein" []
+is_a: ECO:0000150 ! inferred from in vitro transcription reconstitution assay
+xref_unknown: TAIR:TED\:0000027 ""
+
+[Term]
+id: ECO:0000154
+name: inferred from protein expression in heterologous system
+exact_synonym: "IDA\: protein expression in heterologous system" []
+is_a: ECO:0000010 ! inferred from protein expression
+xref_unknown: TAIR:TED\:0000034 ""
+
+[Term]
+id: ECO:0000156
+name: inferred from protein separation
+is_a: ECO:0000100 ! inferred from fractionation
+
+[Term]
+id: ECO:0000158
+name: inferred from protein separation followed by direct sequencing
+exact_synonym: "IDA\: protein separation and direct sequencing" []
+is_a: ECO:0000156 ! inferred from protein separation
+xref_unknown: TAIR:TED\:0000035 ""
+
+[Term]
+id: ECO:0000160
+name: inferred from protein separation followed by fragment identification
+exact_synonym: "IDA\: protein separation and fragment identification" []
+is_a: ECO:0000156 ! inferred from protein separation
+xref_unknown: TAIR:TED\:0000036 ""
+
+[Term]
+id: ECO:0000162
+name: inferred from uptake assay in a heterologous system
+def: "Used when an annotation is made based on small molecule update assays carried out in a heterologous system that contains a recombinant protein." [TAIR:TED ""]
+exact_synonym: "IDA\: uptake assay in heterologous system" []
+is_a: ECO:0000134 ! inferred from transport assay
+xref_unknown: TAIR:TED\:0000044 ""
+
+[Term]
+id: ECO:0000164
+name: inferred from electrophysiological experiment
+is_a: ECO:0000006 ! inferred from experiment
+
+[Term]
+id: ECO:0000166
+name: inferred from two-electrode voltage clamp technique
+exact_synonym: "IDA\: two-electrode voltage clamp technique" []
+is_a: ECO:0000164 ! inferred from electrophysiological experiment
+xref_unknown: TAIR:TED\:0000043 ""
+
+[Term]
+id: ECO:0000168
+name: inferred from transcription assay
+is_a: ECO:0000006 ! inferred from experiment
+
+[Term]
+id: ECO:0000170
+name: inferred from transcriptional activation assay
+def: "Used when an annotation is maded based on assays that show transcriptional activation of a specific target reporter gene." [TAIR:TED ""]
+exact_synonym: "IDA\: transcriptional activation assay" []
+is_a: ECO:0000168 ! inferred from transcription assay
+xref_unknown: TAIR:TED\:0000041 ""
+
+[Term]
+id: ECO:0000172
+name: inferred from biochemical trait
+def: "Used when an annotation is made based on the analysis of a biochemical aspect of a mutant phenotype; for example\, the accumulation of a biosynthetic intermediate." [TAIR:TED ""]
+exact_synonym: "IMP\: analysis of biochemical trait" []
+is_a: ECO:0000014 ! inferred from phenotype
+xref_unknown: TAIR:TED\:0000066 ""
+
+[Term]
+id: ECO:0000174
+name: inferred from physiological response
+def: "Used when an annotation is made based on the physiological response of a mutant to an external stimulus; for example\, abnormal growth of the root in response to gravity\, delay in flowering in response to varying light conditions." [TAIR:TED ""]
+exact_synonym: "IMP\: analysis of physiological response" []
+is_a: ECO:0000014 ! inferred from phenotype
+xref_unknown: TAIR:TED\:0000068 ""
+
+[Term]
+id: ECO:0000176
+name: inferred from visible phenotype
+def: "Used when an annotation is made based on the visual examination of a mutant phenotype; for example\, abnormalities in organism morphology." [TAIR:TED ""]
+exact_synonym: "IMP\: analysis of visible trait" []
+is_a: ECO:0000014 ! inferred from phenotype
+xref_unknown: TAIR:TED\:0000069 ""

Modified: phenote/trunk/obo-files/spatial.obo
===================================================================
--- phenote/trunk/obo-files/spatial.obo	2006-11-21 21:06:59 UTC (rev 207)
+++ phenote/trunk/obo-files/spatial.obo	2006-11-22 13:58:14 UTC (rev 208)
@@ -583,4 +583,4 @@
 [Typedef]
 id: has_position
 name: has_position
-namespace: spatial
\ No newline at end of file
+namespace: spatial


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[Obo-svn-commit] SF.net SVN: obo: [206] phenote/trunk/doc/web-developer-docs

From: <mg...@us...> - 2006-11-20 20:50:56

Revision: 206
          http://svn.sourceforge.net/obo/?rev=206&view=rev
Author:   mgibson
Date:     2006-11-20 12:50:52 -0800 (Mon, 20 Nov 2006)

Log Message:
-----------
more web docs that i jotted down at ctol
needs more...

Modified Paths:
--------------
    phenote/trunk/doc/web-developer-docs

Modified: phenote/trunk/doc/web-developer-docs
===================================================================
--- phenote/trunk/doc/web-developer-docs	2006-11-17 18:29:07 UTC (rev 205)
+++ phenote/trunk/doc/web-developer-docs	2006-11-20 20:50:52 UTC (rev 206)
@@ -44,6 +44,33 @@
 </ul>
 
 
+so if you just want to grab pieces of the javascript
+
+ajax scripts:
+<script src="../javascript/ajax-lib/prototype.js" type="text/javascript"></script>
+<script src="../javascript/ajax-lib/effects.js"   type="text/javascript"></script>
+<script src="../javascript/ajax-lib/dragdrop.js"  type="text/javascript"></script>
+<script src="../javascript/ajax-lib/controls.js"  type="text/javascript"></script>
+
+
+EntityOntology Chooser:
+<script type="text/javascript">
+  function setEntityOntology(selectedOntology) {
+    if (selectedOntology == 'AO') {
+      ontologyName = 'ZF'; <!-- ZF Anatomy -->
+    } else if (selectedOntology == 'GO') {
+      ontologyName = 'GO';
+    }
+
+<!--    entityAutoCompleter.options.parameters = "ontologyName=" +    ontologyName; -->
+   entityAutoCompleter.options.defaultParams = "ontologyName="+ontologyName+"&field=ENTITY";
+    <!-- alert(entityAutoCompleter.options.defaultParams); -->
+
+  }
+
+</script>
+
+
 src/web documentation of js,html,ajax...:
 
 This is a web widget to search ontologies dynamically using Ajax. The


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