[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) = $Central->findService(
input =>[
[DNASequence => ['NCBI_gi', 'NCBI_Acc']],
- ]);
+ ],
+ expandObjects => 1
+ );
unless ($Services){
- print "Service discovery failed with the following errror: "
+ print "Service discovery failed with the following errror: ";
print $REG->message;
end
}
@@ -110,8 +113,8 @@
URI => $URI},
}
- by default this becomes
- {MOBY_Central => {
- URL => '<a href="http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY-Central.pl">http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY-Central.pl</a>',
+ {mobycentral => {
+ URL => '<a href="http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl">http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl</a>',
URI => '<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 => $objectName (from Object ontology)</pre>
<p>
</p>
+<h2><a name="retrieveobjectdefinition">retrieveObjectDefinition</a></h2>
+<pre>
+ Title : retrieveObjectDefinition
+ Usage : $DEF = $MOBY->retrieveObjectDefinition($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 => "the name of the Object"
+ description => "a human-readable description of the object"
+ contactEmail => "your at email.address"
+ authURI => "URI of the registrar of this object"
+ Relationships => {
+ relationshipType1 => [
+ [Object1, articleName],
+ [Object2, articleName]],
+ relationshipType2 => [
+ [Object1, articleName]]}
+ XML => <....XML of object registration.../></pre>
+<pre>
+ Args : objectType => 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 "all" to get all objects</pre>
<p>
</p>
-<h2><a name="retrieveobjectdefinition">retrieveObjectDefinition</a></h2>
-<pre>
- Title : retrieveObjectDefinition
- Usage : $def = $MOBY->retrieveObjectDefinition($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->Relationships(%args)
- Function :
+ Function : traverse and return the relationships in the ontology
Returns : hashref of $hash{relationship_type}=\@lsids
Args : EITHER serviceType => $term_or_lsid
OR objectType => $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 = $MOBY->ISA($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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