Changeset 176 for Schemas

Timestamp:

05/21/08 20:46:07 (7 months ago)

Author:

andrew

Message:

Minor Update 2008-02 Version 2 May 2008

Location:

Schemas

Files:

• OME/2008-02/index.html (modified) (2 diffs)
• OME/2008-02/ome.xsd (modified) (9 diffs)
• index.html (modified) (3 diffs)

Schemas/OME/2008-02/index.html

@@ -8 +8 @@
 <h1>Open Microscopy Environment OME Schema</h1>
 <div class="head">
-<p>13th February 2008</p>
+<p>21st May 2008</p>
 </div>
 <div id="toc">
@@ -25 +25 @@
 <div id="status">
 <h2>Status</h2>
-<p>This schema is <strong>current</strong> and at version <strong>1</strong>.</p>
+<p>This schema is <strong>current</strong> and at version <strong>2</strong>.</p>
 <p>A list of the current versions of all the Open Microscopy Environment Group schemas is available at <a href="http://www.openmicroscopy.org/Schemas/">http://www.openmicroscopy.org/Schemas/</a></p>
 </div>

Schemas/OME/2008-02/ome.xsd

@@ -25 +25 @@
         xmlns:SPW="http://www.openmicroscopy.org/Schemas/SPW/2008-02" 
         xmlns:xml="http://www.w3.org/XML/1998/namespace"
-        version="1" 
+        version="2" 
         elementFormDefault="qualified">
         <xsd:import namespace="http://www.openmicroscopy.org/Schemas/AnalysisModule/2008-02" schemaLocation="http://www.openmicroscopy.org/Schemas/AnalysisModule/2008-02/AnalysisModule.xsd"/>
@@ -36 +36 @@
                 <xsd:documentation>
                         Open Microscopy Environment
-                        OME XML Schema February 2008 - Version 1
+                        OME XML Schema February 2008 - Update Version 21 May 2008
                         Author:  Ilya G. Goldberg, Andrew J Patterson
                         Copyright 2002 - 2008 OME. All rights reserved.
@@ -95 +95 @@
                                 <xsd:element ref="DatasetRef" minOccurs="0" maxOccurs="unbounded"/>
                                 <xsd:element ref="InstrumentRef" minOccurs="0"/>
-                                <xsd:element ref="ObjectiveSettingsRef" minOccurs="0"/>
+                                <xsd:element ref="ObjectiveRef" minOccurs="0"/>
                                 <xsd:element ref="ImagingEnvironment" minOccurs="0"/>
                                 <xsd:element ref="Thumbnail" minOccurs="0"/>
@@ -471 +471 @@
                                 The PhotometricInterpretation attribute is used to describe how to display a multi-component channel.  This attribute may be set to:
                                 'monochrome', 'RGB', 'ARGB', 'CMYK', 'HSV'.  The default for single-component channels is 'monochrome'.
-                                The Model attribute describes the type of microscopy performed for each channel.  This may be set to:
+                                The Mode attribute describes the type of microscopy performed for each channel.  This may be set to:
                                 'Wide-field','Wide-field','Laser Scanning Microscopy','Laser Scanning Confocal','Spinning Disk Confocal','Slit Scan Confocal','Multi-Photon Microscopy',
                                 'Structured Illumination','Single Molecule Imaging','Total Internal Reflection','Fluorescence-Lifetime','Spectral Imaging',
@@ -806 +806 @@
                         <xsd:documentation>
                                 A description of the microscope's objective lens.
-                                Required elements include the lens numerical aperture, and the magnification, both of which a floating point (real) numbers.
+                                Required elements include the lens numerical aperture, 
+                                and the magnification, both of which a floating 
+                                point (real) numbers.
+                                The values are those that are fixed for a particular 
+                                objective: either because it has been manufactured to 
+                                this specification or the value has been measured on 
+                                this particular objective.
+                                Correction: This is the type of correction coating applied to this lens.
+                                Immersion: This is the types of immersion medium the lens is designed to
+                                work with. It is not the same as 'Medium' in ObjectiveRef (a 
+                                single type) as here Immersion can have compound values like 'Multi'.
+                                LensNA: The numerical aperture of the lens (as a float)
+                                NominalMagnification: The specified magnification e.g. x10
+                                CalibratedMagnification: The measured magnification e.g. x10.3
+                                WorkingDistance: WorkingDistance of the lense. The Units are um.
                         </xsd:documentation>
                 </xsd:annotation>
@@ -827 +841 @@
                 </xsd:complexType>
         </xsd:element>
-        <xsd:element name="ObjectiveSettings">
-                <xsd:annotation>
-                        <xsd:documentation>
-                                A description of the user settings on a microscope's objective lens.
-                        </xsd:documentation>
-                </xsd:annotation>
-                <xsd:complexType>
-                        <xsd:sequence>
-                                <xsd:element ref="ObjectiveRef"/>
-                        </xsd:sequence>
-                        <xsd:attribute name="CorrectionCollar" type="xsd:float"/>
-                        <xsd:attribute name="Medium" type="Medium"/>
-                        <xsd:attribute name="RefractiveIndex" type="xsd:float"/>
-                </xsd:complexType>
-        </xsd:element>
         <xsd:simpleType name="Medium">
                 <xsd:annotation>
                         <xsd:documentation>
-                                A description of a Medium used either for the sample or the lens.
+                                A description of a Medium used for the lens.
                         </xsd:documentation>
                 </xsd:annotation>
@@ -1262 +1261 @@
                 </xsd:restriction>
         </xsd:simpleType>
-        <xsd:simpleType name="ObjectiveSettingsID">
-                <xsd:restriction base="LSID">
-                        <xsd:pattern value="(urn:lsid:([\w\-\.]+\.[\w\-\.]+)+:ObjectiveSettings:\S+)|(ObjectiveSettings:\S+)"/>
-                </xsd:restriction>
-        </xsd:simpleType>
         <xsd:simpleType name="LightSourceID">
                 <xsd:restriction base="LSID">
@@ -1831 +1825 @@
         </xsd:element>
         <xsd:element name="ObjectiveRef">
+                <xsd:annotation>
+                        <xsd:documentation> 
+                                This holds the setting applied to an objective as well as a
+                                reference to the objective. 
+                                The ID is the objective used in this case.
+                                The CorrectionCollar is it normal an adjustable ring on the 
+                                objective. Each has an arbitrary scale on it so the values 
+                                is unit-less.
+                                The Medium is the actual immersion medium used in this case.
+                                The RefractiveIndex is that of the immersion medium. This is
+                                a ratio so it also unit-less.
+                        </xsd:documentation>
+                </xsd:annotation>
                 <xsd:complexType>
                         <xsd:complexContent>
@@ -1840 +1847 @@
                                                 <xsd:annotation><xsd:documentation>This is unit-less, it is a ratio.</xsd:documentation></xsd:annotation>
                                         </xsd:attribute>
-                                </xsd:extension>
-                        </xsd:complexContent>
-                </xsd:complexType>
-        </xsd:element>
-        <xsd:element name="ObjectiveSettingsRef">
-                <xsd:complexType>
-                        <xsd:complexContent>
-                                <xsd:extension base="Reference">
-                                        <xsd:attribute name="ID" use="required" type="ObjectiveSettingsID"/>
                                 </xsd:extension>
                         </xsd:complexContent>

Schemas/index.html

@@ -8 +8 @@
 <h1>Open Microscopy Environment Schemas</h1>
 <div class="head">
-<p>29th February 2008</p>
+<p>21st May 2008</p>
 </div>
 <div id="toc">
@@ -33 +33 @@
         <li>September 2007 - Minor release - version number increment</li>
         <li>February 2008 - Major release - new namespace /2008-02/</li>
+        <li>May 2008 - Minor release - version number increment</li>
 </ul>
 <p>For information on the schemas released before June 2007 is available at <a href="http://www.openmicroscopy.org/XMLschemas/">http://www.openmicroscopy.org/XMLschemas/</a>. This includes the schemas used by the original OME server.
@@ -48 +49 @@
         <li>DataHistory - February 2008 Version 1 [<a href="DataHistory/2008-02/DataHistory.xsd">DataHistory.xsd</a>] The Data History schema. Data history describes the data dependency in OME.</li>
         <li>MLI - February 2008 Version 1 [<a href="MLI/2008-02/MLI.xsd">MLI.xsd</a>] The Matlab Interface sub-schema.</li>
-        <li>OME - February 2008 Version 1 [<a href="OME/2008-02/ome.xsd">ome.xsd</a>] The main schema which defines the OME ontology for microscopy. This schema makes use of all of the others.</li>
+        <li>OME - February 2008 Version 2 [<a href="OME/2008-02/ome.xsd">ome.xsd</a>] The main schema which defines the OME ontology for microscopy. This schema makes use of all of the others.</li>
         <li>SPW - February 2008 Version 1 [<a href="SPW/2008-02/SPW.xsd">SPW.xsd</a>] Short Description</li>
         <li>STD - February 2008 Version 1 [<a href="STD/2008-02/STD.xsd">STD.xsd</a>] The Semantic Type definition schema. Once a Semantic Type is defined, data for the defined type can be imported into the OME server.</li>