[MOBY-guts] biomoby commit
Pieter Neerincs
pieter at dev.open-bio.org
Tue Jul 31 13:48:31 UTC 2007
pieter
Tue Jul 31 09:48:30 EDT 2007
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API
In directory dev.open-bio.org:/tmp/cvs-serv10105
Modified Files:
DataClassOntology.html SecondaryArticle.html
Log Message:
Updated documentation for valid boolean values in primitives and secondaries.
moby-live/Docs/MOBY-S_API DataClassOntology.html,1.9,1.10 SecondaryArticle.html,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/DataClassOntology.html,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/DataClassOntology.html 2007/02/22 16:22:24 1.9
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/DataClassOntology.html 2007/07/31 13:48:30 1.10
@@ -55,11 +55,11 @@
<div class="post" id="post-2">
<!-- End of header boilerplate -->
-
-<h2><a name ="The_MOBY_Data_Class_Ontology"> </a>
-The MOBY Data Class Ontology </h2>
+<h2><a name="The_MOBY_Data_Class_Ontology"> </a> The MOBY Data Class Ontology </h2>
<div class="entrytext">
+<h3>"Standard" Objects</h3>
+
In the <a href="http://biomoby.org">BioMOBY</a> system, all
datatypes (Classes) are defined in an ontology, where each node
represents a named Class, and each arc represents one of two
@@ -69,13 +69,7 @@
"Object" Class, and (with the exception of the <a
href="#PrimitiveObjects">special-case
primitives</a>) may contain other objects which themselves inherit
-from the "Object" Class. This includes all primitive datatypes such
-as integers (class Integer), floating point numbers (class Float),
-dates and times (<a href="">DateTime</a>),
-and strings (class String). The class <a href="">DateTime</a>
-uses the <a href="http://www.w3.org/TR/NOTE-datetime"
-target="_top">W3C profile of the ISO-8601 specification</a> for
-specifying dates and times.</p>
+from the "Object" Class.
<p>
Given this structure, the relationship between any two objects
can be described in an RDF triple (subject1, predicate, subject2).
@@ -94,21 +88,21 @@
<pre class=MOBYcode> <Foo namespace="" id="" ></pre>
</p>
<p>
-<a name="PrimitiveObjects"></a>
-Another example of direct inheritence from the Object class is found
-in the classes representing primitives such as integers, floating
-point number, strings, and so on. The following RDF triple describes
-the Integer object:
-<pre class=MOBYcode> Integer - ISA - Object</pre>
-and as XML takes on the following structure:
-<pre class=MOBYcode>
- <Integer namespace="" id="" >966754</Integer>
-</pre>
-</p>
+<h3><a name="PrimitiveObjects"></a>"Primitive" Objects</h3>
+
+The BioMOBY Class ontology contains five special case primitives:
+<ul>
+<li> Integer </li>
+<li> Float </li>
+<li> <a href="#DateTime">DateTime</a> </li>
+<li> String </li>
+<li> <a href="#Boolean">Boolean</a> </li>
+</ul>
+
<p>
-Notice, these primitive types are the only cases where the content
-of the element is meant to be interpreted by the client or service.
+These primitive types are special as they are the only cases where the content
+of an element is meant to be interpreted by the client or service.
New classes <em>MUST NOT</em> inherit from the Primitive Classes. To obtain
content in another class, you must be a <em>container</em> of a
primitive class. The two relationship types - HASA and HAS - are used
@@ -118,7 +112,17 @@
parent object. HASA indicates that a single instance of the object is
contained, while HAS indicates that multiple instances of the object
are contained.
+
+The following RDF triple describes
+the Integer object:
+<pre class=MOBYcode> Integer - ISA - Object</pre>
+
+and as XML takes on the following structure:
+<pre class=MOBYcode>
+ <Integer namespace="" id="" >966754</Integer>
+</pre>
</p>
+
<p>
For example, one might imagine a <a href="">PlainText</a>
Object Class that needs to contain some stringified content. This
@@ -136,8 +140,21 @@
</moby:String>
</moby:PlainText>
</pre>
+</p>
+<p>
+The <a name="DateTime">DateTime class</a> uses the
+<a href="http://www.w3.org/TR/NOTE-datetime" target="_top">W3C profile of the ISO-8601 specification</a>
+for specifying dates and times.
+</p>
+<p>
+The <a name="Boolean">Boolean class</a> uses the
+<a href="http://www.w3.org/TR/xmlschema-2/#dt-boolean" target="_top">XML schema definition for valid boolean values</a>.
+Hence BioMOBY clients and services can send one of the following literals {true, false, 1, 0}
+and must understand all of {true, false, 1, 0}. Other commonly used boolean values like {T,F,TRUE,FALSE} etc.
+are not supported and illegal in BioMOBY lingua.
+</p>
<!-- Sidebar is boilerplate -->
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/SecondaryArticle.html,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/SecondaryArticle.html 2006/11/21 23:04:27 1.9
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/SecondaryArticle.html 2007/07/31 13:48:30 1.10
@@ -117,8 +117,8 @@
<p>
The components of the Parameter specification are:
<ul>
-<li> <em>datatype</em> - one of <code>Integer</code>, <code>Boolean</code>, <code>Float</code>,
- <code>String</code>, <code>DateTime</code>, which specifies the type of data
+<li> <em>datatype</em> - one of <code>Integer</code>, <a href="#Boolean"><code>Boolean</code></a>, <code>Float</code>,
+ <code>String</code>, <a href="#DateTime"><code>DateTime</code></a>, which specifies the type of data
involved</li>
<li> <em>description</em> - a description of this parameter.</li>
<li> <em>default</em> - an optional default value, in case none is specified</li>
@@ -131,6 +131,20 @@
</ul>
</p>
+<p>
+<a name="DateTime">DateTime secondaries</a> use the
+<a href="http://www.w3.org/TR/NOTE-datetime" target="_top">W3C profile of the ISO-8601 specification</a>
+for specifying dates and times.
+</p>
+
+<p>
+<a name="Boolean">Boolean secondaries</a> use the
+<a href="http://www.w3.org/TR/xmlschema-2/#dt-boolean" target="_top">XML schema definition for valid boolean values</a>.
+Hence BioMOBY clients and services can send one of the following literals {true, false, 1, 0}
+and must understand all of {true, false, 1, 0}. Other commonly used boolean values like {T,F,TRUE,FALSE} etc.
+are not supported and illegal in BioMOBY lingua.
+</p>
+
</div>
</div>
</div>
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