Changeset 3926

Timestamp:

Nov 7, 2007, 2:41:54 PM (16 years ago)

Author:

Nicklas Nordborg

Message:

References #746: Transfer existing UML diagrams to latest MagicDraw?

• Added images for Array LIMS sections
• Added text to hybridizations and raw data section

Location:

trunk/doc/src

Files:

• docbook/developerdoc/api_overview.xml (modified) (2 diffs)
• uml/baseuml.mdzip (modified) (previous)

trunk/doc/src/docbook/developerdoc/api_overview.xml

@@ -1807 +1807 @@
     <sect2 id="data_api.plates">
       <title>Array LIMS - plates</title>
+
+      <sect3 id="data_api.plates.uml">
+        <title>UML diagram</title>
+        
+        <figure id="data_api.figures.plates">
+          <title>Array LIMS - plates</title>
+          <screenshot>
+            <mediaobject>
+              <imageobject>
+                <imagedata 
+                  fileref="figures/uml/datalayer.plates.png" format="PNG" />
+              </imageobject>
+            </mediaobject>
+          </screenshot>
+        </figure>
+      </sect3>
+
     </sect2>
 
     <sect2 id="data_api.arrays">
       <title>Array LIMS - arrays</title>
+      
+      <sect3 id="data_api.arrays.uml">
+        <title>UML diagram</title>
+        
+        <figure id="data_api.figures.arrays">
+          <title>Array LIMS - arrays</title>
+          <screenshot>
+            <mediaobject>
+              <imageobject>
+                <imagedata 
+                  fileref="figures/uml/datalayer.arrays.png" format="PNG" />
+              </imageobject>
+            </mediaobject>
+          </screenshot>
+        </figure>
+      </sect3>
+      
+      
     </sect2>
 
@@ -1832 +1867 @@
       </sect3>
       
+      <sect3 id="data_api.rawdata.hybridizations">
+        <title>Hybridizations</title>
+        
+        <para>
+        Hybridizations connects the slides from the Array LIMS part
+        with labeled extracts from the biomaterials part. The <property>creationEvent</property>
+        is used to register which labeled extracts that were used on the hybridization.
+        The relation to slides is a one-to-one relation. A slide can only be used on 
+        a single hybridization and a hybridization can only use a single slide. The relation
+        is optional from both sides.
+        </para>
+
+        <para>
+        The scanning of the hybridized slide is registered as separate scan events.
+        One or more images can optionally be attached to each scan. 
+        The images are not used by BASE.
+        </para>
+        
+      </sect3>
+      
+      <sect3 id="data_api.rawdata.description">
+        <title>Raw data</title>
+        
+        <para>
+        A <classname>RawBioAssayData</classname> object represents
+        the raw data that is produced by analysing the image(s) from a
+        single scan. You may register which software that was used, the
+        protocol and any parameters (through the annotation system).
+        </para>
+
+        <para>
+        Files with the analysed data values can be attached to the 
+        associated <classname>FileSetData</classname> object. The platform
+        and, optionally, the variant has information about the file types
+        that can be used for that platform. If the platform file types support 
+        metadata extraction, headers, the number of spots, and other 
+        information may be automatically extracted from the raw data file(s).
+        </para>
+        
+        <para>
+        If the platform support it, raw data can also be imported into the database.
+        This is handled by batchers and <classname>RawData</classname> objects.
+        Which table to store the data in depends on the <classname>rawDataType</classname>
+        property. The properties shown for the <classname>RawData</classname> class
+        in the diagram are the mandatory properties. Each raw data type defines additional
+        properties that are specific to that raw data type.
+        </para>
+        
+      </sect3>
+      
+      <sect3 id="data_api.rawdata.spotimages">
+        <title>Spot images</title>
+        
+        <para>
+        Spot images can be created if you have the original image
+        files. BASE can use 1-3 images as sources for the red, green
+        and blue channel respectively. The creation of spotimages requires
+        that x and y coordinates are given for each raw data spot. The scaling
+        and offset values are used to convert the coordinates to pixel
+        coordinates. With this information BASE is able to cut out a square
+        from the source images that, theoretically, contains a specific spot and 
+        nothing else. The spot images are gamma-corrected independently and then
+        put together into PNG images that are stored in a zip file. 
+        </para>
+      </sect3>
       
     </sect2>