Documentation for Chemical Markup Language (CML)
Definition Type: Element
Name: reactionScheme
Namespace: http://www.xml-cml.org/schema
Containing Schema: schema.xsd
Abstract
Documentation:
A container for two or more related reactions and their relationships. Where reactions are closely related (and often formally dependent on each other) they should be contained within the reactionStepList of a reactionScheme. The semantics which have informed this design include: Steps within an organic synthesis. Two or more individual (primitive) steps provding the detailed mechanism for an overall reaction. Coupled or sequential reactions within biochemical pathways. This design is general because "reaction" is used in several ways. A biochemical pathway (e.g. oxidation of glucose to CO2 and water) involves many coupled enzyme reactions proceeding both in parallel and in sequence. Each of these steps ("reactions" in their own right) is itself complex and can include several mechanistics steps which are themselves reactions with products, reactants, etc. reactionScheme can therefore include reactionStepLists (with more reactionScheme children) which provide a more detailed view of the individual components. Where a set of reactions are primitives...
Collapse XSD Schema Diagram:
Drilldown into reactionScheme in schema schema_xsd Drilldown into reactionStepList in schema schema_xsd Drilldown into reaction in schema schema_xsd Drilldown into identifier in schema schema_xsd Drilldown into name in schema schema_xsd Drilldown into label in schema schema_xsd Drilldown into metadataList in schema schema_xsd Drilldown into format in schema schema_xsd Drilldown into reactionFormat in schema schema_xsd Drilldown into state in schema schema_xsd Drilldown into state in schema schema_xsd Drilldown into type in schema schema_xsd Drilldown into reactionType in schema schema_xsd Drilldown into role in schema schema_xsd Drilldown into reactionRole in schema schema_xsd Drilldown into ref in schema schema_xsd Drilldown into ref in schema schema_xsd Drilldown into id in schema schema_xsd Drilldown into id in schema schema_xsd Drilldown into title in schema schema_xsd Drilldown into title in schema schema_xsd Drilldown into convention in schema schema_xsd Drilldown into convention in schema schema_xsd Drilldown into dictRef in schema schema_xsd Drilldown into dictRef in schema schema_xsdXSD Diagram of reactionScheme in schema schema_xsd (Chemical Markup Language (CML))
Collapse XSD Schema Code: 
<xsd:element name="reactionScheme" id="el.reactionScheme">
    <xsd:annotation>
        <xsd:documentation>
            <h:div class="summary" xmlns:h="http://www.w3.org/1999/xhtml">A container for two or more related reactions and their relationships.</h:div>
            <h:div class="description" xmlns:h="http://www.w3.org/1999/xhtml">
                Where reactions are closely related (and often formally dependent on each other) they should be contained within the reactionStepList of a reactionScheme. The semantics which have informed this design include:
                <h:ul><h:li>Steps within an organic synthesis.</h:li>
                    <h:li>Two or more individual (primitive) steps provding the detailed mechanism for an overall reaction.</h:li>
                    <h:li>Coupled or sequential reactions within biochemical pathways.</h:li>
                </h:ul>
                <h:p>This design is general because "reaction" is used in several ways. A biochemical pathway (e.g. oxidation of glucose to CO2 and water) involves many coupled enzyme reactions proceeding both in parallel and in sequence. Each of these steps ("reactions" in their own right) is itself complex and can include several mechanistics steps which are themselves reactions with products, reactants, etc. <h:tt>reactionScheme</h:tt> can therefore include reactionStepLists (with more reactionScheme children) which provide a more detailed view of the individual components.</h:p>
                <h:p>Where a set of reactions are primitives...</h:p>
            </h:div>
            <h:div class="example" href="reactionScheme1.xml" xmlns:h="http://www.w3.org/1999/xhtml" />
            <h:div class="example" href="reactionScheme3.xml" xmlns:h="http://www.w3.org/1999/xhtml" />
            <h:div class="example" href="reactionScheme4a.xml" xmlns:h="http://www.w3.org/1999/xhtml" />
            <h:div class="example" href="reactionScheme4b.xml" xmlns:h="http://www.w3.org/1999/xhtml" />
        </xsd:documentation>
    </xsd:annotation>
    <xsd:complexType>
        <xsd:annotation>
            <xsd:documentation>
                <h:div class="description" xmlns:h="http://www.w3.org/1999/xhtml">
                    <h:p>The semantics of the content model are</h:p>
                    <h:ul>
                        <h:li>metadataList for general metadata</h:li>
                        <h:li>label for classifying or describing the reaction (e.g. "hydrolysis")</h:li>
                        <h:li>identifier for unique identification. This could be a classification such as EC (enzyme commission) or an IChI-like string generated from the components.</h:li>
                        <h:li>these are followed by the possible components of the reaction and/or a reactionList of further details.</h:li>
                    </h:ul>
                </h:div>
            </xsd:documentation>
        </xsd:annotation>
        <xsd:sequence>
            <xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded" />
            <xsd:choice minOccurs="0" maxOccurs="unbounded">
                <xsd:element ref="label" />
                <xsd:element ref="name" />
                <xsd:element ref="identifier" />
            </xsd:choice>
            <xsd:choice minOccurs="0" maxOccurs="unbounded">
                <xsd:element ref="reaction" />
                <xsd:element ref="reactionStepList" />
                <xsd:element ref="reactionScheme" />
            </xsd:choice>
        </xsd:sequence>
        <xsd:attributeGroup ref="dictRef" />
        <xsd:attributeGroup ref="convention" />
        <xsd:attributeGroup ref="title" />
        <xsd:attributeGroup ref="id" />
        <xsd:attributeGroup ref="ref" />
        <xsd:attributeGroup ref="reactionRole" />
        <xsd:attributeGroup ref="reactionType" />
        <xsd:attributeGroup ref="state" />
        <xsd:attributeGroup ref="reactionFormat" />
    </xsd:complexType>
</xsd:element>
Collapse Child Elements:
Name Type Min Occurs Max Occurs
metadataList nsA:metadataList 0 unbounded
label nsA:label (1) (1)
name nsA:name (1) (1)
identifier nsA:identifier (1) (1)
reaction nsA:reaction (1) (1)
reactionStepList nsA:reactionStepList (1) (1)
reactionScheme nsA:reactionScheme (1) (1)
Collapse Child Attributes:
Name Type Default Value Use
dictRef nsA:dictRef (Optional)
convention nsA:convention (Optional)
title nsA:title (Optional)
id nsA:id (Optional)
ref nsA:ref (Optional)
role nsA:role (Optional)
type nsA:type (Optional)
state nsA:state (Optional)
format nsA:format (Optional)
Documentation for Chemical Markup Language (CML)

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