[MOBY-guts] biomoby commit

Mark Wilkinson mwilkinson at pub.open-bio.org
Wed Oct 22 11:29:09 EDT 2003


mwilkinson
Wed Oct 22 10:29:09 EDT 2003
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv7066/Perl/MOBY/Client

Modified Files:
	Central.html 
Log Message:
updating documentation for the website

moby-live/Perl/MOBY/Client Central.html,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html	2003/07/21 14:18:07	1.10
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html	2003/10/22 14:29:09	1.11
@@ -22,6 +22,7 @@
 		<li><a href="#new">new</a></li>
 		<li><a href="#registerobject_a.k.a_registerobjectclass">registerObject  a.k.a registerObjectClass</a></li>
 		<li><a href="#deregisterobject_a.k.a._deregisterobjectclass">deregisterObject a.k.a. deregisterObjectClass</a></li>
+		<li><a href="#retrieveobjectdefinition">retrieveObjectDefinition</a></li>
 		<li><a href="#registerservicetype">registerServiceType</a></li>
 		<li><a href="#deregisterservicetype">deregisterServiceType</a></li>
 		<li><a href="#registernamespace">registerNamespace</a></li>
@@ -37,8 +38,8 @@
 		<li><a href="#retrieveobjectnames">retrieveObjectNames</a></li>
 		<li><a href="#retrievenamespaces">retrieveNamespaces</a></li>
 		<li><a href="#retrieveobject">retrieveObject</a></li>
-		<li><a href="#retrieveobjectdefinition">retrieveObjectDefinition</a></li>
 		<li><a href="#relationships">Relationships</a></li>
+		<li><a href="#isa">ISA</a></li>
 		<li><a href="#dump">DUMP</a></li>
 	</ul>
 
@@ -61,9 +62,11 @@
  my ($Services, $REG) = $Central-&gt;findService(
             input =&gt;[
               [DNASequence =&gt; ['NCBI_gi', 'NCBI_Acc']],
-                ]);
+                ],
+                expandObjects =&gt; 1
+                );
  unless ($Services){
-         print &quot;Service discovery failed with the following errror: &quot;
+         print &quot;Service discovery failed with the following errror: &quot;;
          print $REG-&gt;message;
          end
  }
@@ -110,8 +113,8 @@
                                     URI =&gt; $URI},
                                 }
                             - by default this becomes
-                            {MOBY_Central =&gt; {
-                                 URL =&gt; '<a href="http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY-Central.pl">http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY-Central.pl</a>',
+                            {mobycentral =&gt; {
+                                 URL =&gt; '<a href="http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl">http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl</a>',
                                  URI =&gt; '<a href="http://mobycentral.cbr.nrc.ca/MOBY/Central">http://mobycentral.cbr.nrc.ca/MOBY/Central</a>'}
                              }
  Discussion:    Each registry must have a different
@@ -161,6 +164,30 @@
  Args      :    objectType =&gt; $objectName (from Object ontology)</pre>
 <p>
 </p>
+<h2><a name="retrieveobjectdefinition">retrieveObjectDefinition</a></h2>
+<pre>
+ Title     : retrieveObjectDefinition
+ Usage     : $DEF = $MOBY-&gt;retrieveObjectDefinition($objectType[,$registry])
+ Function  : retrieve the $XML that was used to register an object and its relationships
+ Returns   : hashref, identical to the hash sent during Object registration, plus
+             an additional XML hash key that contains the actual XML containing
+             the object definition as sent by MOBY Central (used for a visual
+                         overview, rather than parsing all of the hash keys)
+        objectType =&gt; &quot;the name of the Object&quot;
+    description =&gt; &quot;a human-readable description of the object&quot;
+    contactEmail =&gt; &quot;your at email.address&quot;
+    authURI =&gt; &quot;URI of the registrar of this object&quot;
+    Relationships =&gt; {
+      relationshipType1 =&gt; [
+        [Object1, articleName],
+        [Object2, articleName]],
+      relationshipType2 =&gt; [
+        [Object1, articleName]]}
+    XML =&gt; &lt;....XML of object registration.../&gt;</pre>
+<pre>
+ Args      : objectType =&gt;  the name or LSID URI for an object</pre>
+<p>
+</p>
 <h2><a name="registerservicetype">registerServiceType</a></h2>
 <pre>
  Title     :    registerServiceType
@@ -371,21 +398,11 @@
                 $name - object name (from ontology) or &quot;all&quot; to get all objects</pre>
 <p>
 </p>
-<h2><a name="retrieveobjectdefinition">retrieveObjectDefinition</a></h2>
-<pre>
- Title     :    retrieveObjectDefinition
- Usage     :    $def = $MOBY-&gt;retrieveObjectDefinition($name, [$regname])
- Function  :    To get the full definition of an object
- Returns   :    returns hashref to an identical hash to the one that was passed to
-                registerObjectClass during initial registration of the object
- Args      :    $name - object name (from ontology)</pre>
-<p>
-</p>
 <h2><a name="relationships">Relationships</a></h2>
 <pre>
  Title     :    Relationships
  Usage     :    $def = $MOBY-&gt;Relationships(%args)
- Function  :
+ Function  :    traverse and return the relationships in the ontology
  Returns   :    hashref of   $hash{relationship_type}=\@lsids
  Args      :    EITHER serviceType =&gt; $term_or_lsid
                 OR     objectType =&gt; $term_or_lsid
@@ -395,6 +412,17 @@
                 expandRelationships (NOT YET IMPLEMENTED)</pre>
 <p>
 </p>
+<h2><a name="isa">ISA</a></h2>
+<pre>
+ Title     :    ISA
+ Usage     :    $def = $MOBY-&gt;ISA($class1, $class2)
+ Function  :    a pre-canned use of the Relationships function
+                to quickly get an answer to whether class1 ISA class2
+ Returns   :    Boolean
+ Args      :    $class1  - an Object ontology term
+                $class2 - an Object ontology term</pre>
+<p>
+</p>
 <h2><a name="dump">DUMP</a></h2>
 <pre>
  Title     :    DUMP



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