Namespace: |
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Type: |
anonymous complexType |
Content: |
complex, 11 attributes, 5 elements |
Defined: |
globally in cmlreact.xsd; see XML source |
Includes: |
definitions of 5 elements |
Used: |
at 1 location |
XML Representation Summary |
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</spectrum> |
<xsd:element id="el.spectrum" name="spectrum"> <xsd:annotation> <xsd:documentation> <h:div class="summary">A spectrum and relevant data or metadata.</h:div> <h:div class="description"> The <h:tt>spectrum</h:tt> construct can hold <h:tt>metadataList</h:tt> , <h:tt>sample</h:tt> (which can contain molecule), <h:tt>conditionList</h:tt> (mainly for physical/chemical conditions, not instrumental), <h:tt>spectrumData</h:tt> for the actual data and instrumental settings/procedure and <h:tt>peakList</h:tt> for the assigned peaks. This approach puts the spectrum as the primary object of interest. It could also be possible to make <h:tt>spectrum</h:tt> a child of <h:tt>molecule</h:tt> (although a reference using <h:tt>ref</h:tt> might be preferable). </h:div> <h:div class="example" href="spectrum1.xml"/> </xsd:documentation> </xsd:annotation> <xsd:complexType> <xsd:sequence> <xsd:annotation> <xsd:documentation> <h:div> A (complete) description of the thing to which the spectrum relates. May contain <h:tt>molecule</h:tt> or <h:tt>substanceList</h:tt> . Solvents, mulls, etc should be described here. </h:div> </xsd:documentation> </xsd:annotation> </xsd:element> <xsd:annotation> <xsd:documentation> <h:div> The conditions relating to the spectrum (complementary to substanceList. </h:div> </xsd:documentation> </xsd:annotation> </xsd:element> <xsd:annotation> <xsd:documentation> <h:div> A list of peaks. This may occur independently of the xaxis/yaxis data. </h:div> </xsd:documentation> </xsd:annotation> </xsd:element> </xsd:sequence> <xsd:annotation> <xsd:documentation> <h:div class="specific">The molecule to which the spectrum refers.</h:div> </xsd:documentation> </xsd:annotation> </xsd:attributeGroup> <xsd:annotation> <xsd:documentation> <h:div class="specific"> Although this may also be contained in the <h:tt>sample</h:tt> element it is useful to state it here. No default. </h:div> </xsd:documentation> </xsd:annotation> </xsd:attributeGroup> </xsd:complexType> </xsd:element> |
Type: |
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Use: |
optional |
Defined: |
<xsd:attribute id="att.convention" name="convention" type="namespaceRefType"> <xsd:annotation> <xsd:documentation> <h:div class="summary">A reference to a convention.</h:div> <h:div class="description"> There is no controlled vocabulary for conventions, but the author must ensure that the semantics are openly available and that there are mechanisms for implementation. The convention is inherited by all the subelements, so that a convention for <h:tt>molecule</h:tt> would by default extend to its <h:tt>bond</h:tt> and <h:tt>atom</h:tt> children. This can be overwritten if necessary by an explicit <h:tt>convention</h:tt> . <h:p> It may be useful to create conventions with namespaces (e.g. <h:tt>iupac:name</h:tt> ). Use of <h:tt>convention</h:tt> will normally require non-STMML semantics, and should be used with caution. We would expect that conventions prefixed with "ISO" would be useful, such as ISO8601 for dateTimes. </h:p> <h:p> There is no default, but the conventions of STMML or the related language (e.g. CML) will be assumed. </h:p> </h:div> <h:div class="example" href="convGroup1.xml" id="ex"/> </xsd:documentation> </xsd:annotation> </xsd:attribute> |
Type: |
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Use: |
optional |
Defined: |
<xsd:attribute id="att.dictRef" name="dictRef" type="namespaceRefType"> <xsd:annotation> <xsd:documentation> <h:div class="summary">A reference to a dictionary entry.</h:div> <h:div class="description"> Elements in data instances such as _scalar_ may have a <h:tt>dictRef</h:tt> attribute to point to an entry in a dictionary. To avoid excessive use of (mutable) filenames and URIs we recommend a namespace prefix, mapped to a namespace URI in the normal manner. In this case, of course, the namespace URI must point to a real XML document containing _entry_ elements and validated against STMML Schema. <h:p> Where there is concern about the dictionary becoming separated from the document the dictionary entries can be physically included as part of the data instance and the normal XPointer addressing mechanism can be used. </h:p> <h:p> This attribute can also be used on _dictionary_ elements to define the namespace prefix </h:p> </h:div> <h:div class="example" href="dictRefGroup1.xml"/> </xsd:documentation> </xsd:annotation> </xsd:attribute> |
Type: |
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Use: |
optional |
Defined: |
Derivation: |
by union |
Derivation: |
restriction of xsd:string |
Derivation: |
restriction of namespaceRefType |
<xsd:attribute id="att.format" name="format"> <xsd:annotation> <xsd:documentation> <h:div class="summary">Format of a spectrum.</h:div> <h:div class="description"> The data structure of the spectrum. (Not the format of the data). This describes how the data structure is to be interpreted. </h:div> </xsd:documentation> </xsd:annotation> <xsd:simpleType> <xsd:union> <xsd:simpleType> <xsd:restriction base="xsd:string"> <xsd:enumeration value="1D"> <xsd:annotation> <xsd:documentation> <h:div class="summary">one dimensional spectru.</h:div> <h:div class="description"> Data are represented by two _array_s, one representing the independent variable (e.g. wavelength, mass number) and the other the measured dependent variable (absorption, intensity, etc.). This can normally be plotted directly with the independent variable as the x-axis. The order of the points is not necessarily significant and may be increasing or decreasing. </h:div> </xsd:documentation> </xsd:annotation> </xsd:enumeration> <xsd:enumeration value="2Dsymm"> <xsd:annotation> <xsd:documentation> <h:div class="summary">Two dimensional spectru.</h:div> <h:div class="description"> Data are represented by a single symmetric _matrix_ with both axes identical (i.e. the same independent variable). A typical example is a "2D 1HNMR spectrum". The dependent variable is represented by the matrix elements. This can normally be plotted as a square symmentric about a diagonal. </h:div> </xsd:documentation> </xsd:annotation> </xsd:enumeration> <xsd:enumeration value="2Dasymm"> <xsd:annotation> <xsd:documentation> <h:div class="summary">Two dimensional spectrum with different axe.</h:div> <h:div class="description"> Data are represented by non-square _matrix_ with independent axes. A typical example is a "2D 1H 13C NMR spectrum". The dependent variable is represented by the matrix elements. . </h:div> </xsd:documentation> </xsd:annotation> </xsd:enumeration> </xsd:restriction> </xsd:simpleType> <xsd:simpleType> </xsd:simpleType> </xsd:union> </xsd:simpleType> </xsd:attribute> |
Type: |
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Use: |
optional |
Default: |
"none" |
Defined: |
Derivation: |
by union |
Derivation: |
restriction of xsd:string |
Derivation: |
restriction of namespaceRefType |
<xsd:attribute default="none" id="att.ft" name="ft"> <xsd:annotation> <xsd:documentation> <h:div class="summary">Domain of an FT spectrum.</h:div> <h:div class="description"> Indicates whether a spectrum is raw FID or has been transforme. </h:div> </xsd:documentation> </xsd:annotation> <xsd:simpleType> <xsd:union> <xsd:simpleType> <xsd:restriction base="xsd:string"> <xsd:enumeration value="raw"> <xsd:annotation> <xsd:documentation> <h:div class="summary"> Data are raw, so will normally require transforming. </h:div> </xsd:documentation> </xsd:annotation> </xsd:enumeration> <xsd:enumeration value="transformed"> <xsd:annotation> <xsd:documentation> <h:div class="summary"> Data have been transformed. This value indicates that an FT experiment and transformation have been performe. </h:div> </xsd:documentation> </xsd:annotation> </xsd:enumeration> <xsd:enumeration value="none"> <xsd:annotation> <xsd:documentation> <h:div class="summary"> This was not known to be an FT experiment. (It may have been, but the author or abstracter omitted to mention it). </h:div> </xsd:documentation> </xsd:annotation> </xsd:enumeration> </xsd:restriction> </xsd:simpleType> <xsd:simpleType> </xsd:simpleType> </xsd:union> </xsd:simpleType> </xsd:attribute> |
Type: |
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Use: |
optional |
Defined: |
Type: |
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Use: |
optional |
Defined: |
Derivation: |
by union |
Derivation: |
restriction of xsd:string |
Derivation: |
restriction of namespaceRefType |
<xsd:attribute id="att.measurement" name="measurement"> <xsd:annotation> <xsd:documentation> <h:div class="summary">Type of spectral measurement.</h:div> <h:div class="description"> The nature of the measured data. This is not an exhaustive list and should only be used if it affects the storage or immediate processing. </h:div> </xsd:documentation> </xsd:annotation> <xsd:simpleType> <xsd:union> <xsd:simpleType> <xsd:restriction base="xsd:string"> <xsd:enumeration value="transmittance"> <xsd:annotation> <xsd:documentation> <h:div class="summary"> Data are transmittance, so "peaks" are usually troughs. </h:div> </xsd:documentation> </xsd:annotation> </xsd:enumeration> <xsd:enumeration value="absorbance"> <xsd:annotation> <xsd:documentation> <h:div class="summary">Data are absorbanc.</h:div> <h:div class="description">so "peaks" are normally peaks.</h:div> </xsd:documentation> </xsd:annotation> </xsd:enumeration> </xsd:restriction> </xsd:simpleType> <xsd:simpleType> </xsd:simpleType> </xsd:union> </xsd:simpleType> </xsd:attribute> |
Type: |
|
Use: |
optional |
Defined: |
<xsd:attribute id="att.moleculeRef" name="moleculeRef" type="moleculeRefType"> <xsd:annotation> <xsd:documentation> <h:div class="summary">A reference to a molecule.</h:div> <h:div class="description">Used by spectrum, etc.</h:div> </xsd:documentation> </xsd:annotation> </xsd:attribute> |
Type: |
|
Use: |
optional |
Defined: |
<xsd:attribute id="att.ref" name="ref" type="refType"> <xsd:annotation> <xsd:documentation> <h:div class="summary">A reference to an element of given type.</h:div> <h:div class="description"> <h:tt>ref</h:tt> modifies an element into a reference to an existing element of that type within the document. This is similar to a pointer and it can be thought of a strongly typed hyperlink. It may also be used for "subclassing" or "overriding" elements. <br xmlns=""/> When referring to an element most of the "data" such as attribute values and element content will be on the full instantiated element. Therefore ref (and possibly id) will normally be the only attributes on the pointing element. However there may be some attributes (title, count, etc.) which have useful semantics, but these are element-specific </h:div> <h:div class="example" href="refGroup1.xml"/> </xsd:documentation> </xsd:annotation> </xsd:attribute> |
Type: |
|
Use: |
optional |
Defined: |
Type: |
xsd:string, predefined |
Use: |
optional |
Defined: |
<xsd:attribute id="att.title" name="title" type="xsd:string"> <xsd:annotation> <xsd:documentation> <h:div class="summary">A title on an element.</h:div> <h:div class="description">No controlled value.</h:div> <h:div class="example" href="title1.xml"/> </xsd:documentation> </xsd:annotation> </xsd:attribute> |
Type: |
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Use: |
optional |
Defined: |
Derivation: |
by union |
Derivation: |
restriction of xsd:string |
Derivation: |
restriction of namespaceRefType |
<xsd:attribute id="att.spectrumType" name="type"> <xsd:annotation> <xsd:documentation> <h:div class="summary">The type of the spectrum.</h:div> </xsd:documentation> </xsd:annotation> <xsd:simpleType> <xsd:union> <xsd:simpleType> <xsd:restriction base="xsd:string"> <xsd:enumeration value="infrared"> <xsd:annotation> <xsd:documentation> <h:div class="summary">An infrared spectrum.</h:div> <h:div class="description"> The measurement should denote transmittance or absorbanc. </h:div> </xsd:documentation> </xsd:annotation> </xsd:enumeration> <xsd:enumeration value="massSpectrum"> <xsd:annotation> <xsd:documentation> <h:div class="summary">A "simple" mass spectrum.</h:div> <h:div class="description"> This excludes experiments such as GC/MS, MS/MS, etc. though these could be constructed out of individual spectra with some care. The spectrum may be continuous ( <h:tt>data</h:tt> or a <h:tt>peakList</h:tt> ). </h:div> </xsd:documentation> </xsd:annotation> </xsd:enumeration> <xsd:enumeration value="NMR"> <xsd:annotation> <xsd:documentation> <h:div class="summary">An NMR spectrum.</h:div> <h:div class="description"> This can include any experiment which creates a "1D" or "2D" data array. The symmetry of the spectrum can be specified but the details of the NMR experiment (COSY, NOESY, etc.) are not part of CMLSpect. They can be described though the normal <h:tt>dictRef</h:tt> mechanism. </h:div> </xsd:documentation> </xsd:annotation> </xsd:enumeration> <xsd:enumeration value="UV/VIS"> <xsd:annotation> <xsd:documentation> <h:div class="summary"> A spectrum somewhere in the UV VIS region of the spectrum. </h:div> <h:div class="description"> The measurement should denote transmittance or absorbance. </h:div> </xsd:documentation> </xsd:annotation> </xsd:enumeration> </xsd:restriction> </xsd:simpleType> <xsd:simpleType> </xsd:simpleType> </xsd:union> </xsd:simpleType> </xsd:attribute> |
Type: |
anonymous complexType, complex content |
Defined: |
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="conditionList"> <xsd:annotation> <xsd:documentation> <h:div> The conditions relating to the spectrum (complementary to substanceList. </h:div> </xsd:documentation> </xsd:annotation> </xsd:element> |
Type: |
anonymous complexType, complex content |
Defined: |
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="metadataList"/> |
Type: |
anonymous complexType, complex content |
Defined: |
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="peakList"> <xsd:annotation> <xsd:documentation> <h:div> A list of peaks. This may occur independently of the xaxis/yaxis data. </h:div> </xsd:documentation> </xsd:annotation> </xsd:element> |
Type: |
anonymous complexType, complex content |
Defined: |
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="sample"> <xsd:annotation> <xsd:documentation> <h:div> A (complete) description of the thing to which the spectrum relates. May contain <h:tt>molecule</h:tt> or <h:tt>substanceList</h:tt> . Solvents, mulls, etc should be described here. </h:div> </xsd:documentation> </xsd:annotation> </xsd:element> |
Type: |
anonymous complexType, complex content |
Defined: |
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="spectrumData"/> |
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