<?xml version="1.0" encoding="UTF-8"?>
<xs:schema targetNamespace="http://morphml.org/metadata/schema"
xmlns="http://morphml.org/metadata/schema"
xmlns:xs="http://www.w3.org/2001/XMLSchema"
elementFormDefault="qualified" attributeFormDefault="unqualified">
<!--
This file specifies a number of basic elements which can be used by NeuroML v1.6 compliant files
Authors: Sharon Crook, Joe Svitak, Padraig Gleeson and members of the NeuroML project
-->
<xs:annotation>
<xs:documentation>Definition of elements common to a number of NeuroML files.</xs:documentation>
</xs:annotation>
<!-- Definition of a Point follows. -->
<xs:complexType name="Point">
<xs:annotation>
<xs:documentation>A 3D point with optional diameter. Note: the units for these values
will be specified in the file in which the element is used, e.g.
in a MorphML file with <b>lengthUnits="micron"</b> in the morphml element</xs:documentation>
</xs:annotation>
<xs:attribute name="x" type="xs:double" use="required"/>
<xs:attribute name="y" type="xs:double" use="required"/>
<xs:attribute name="z" type="xs:double" use="required"/>
<xs:attribute name="diameter" type="xs:double" use="optional"/>
</xs:complexType>
<!-- Definition of Points follows. -->
<xs:complexType name="Points">
<xs:annotation>
<xs:documentation>A collection of points.</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="point" type="Point" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="name" type="xs:string" use="optional"/>
</xs:complexType>
<!-- Definition of Sphere follows. -->
<xs:complexType name="Sphere">
<xs:annotation>
<xs:documentation>A spherical structure such as a cell body or cell.</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="center" type="Point">
<xs:annotation>
<xs:documentation>Diameter of sphere is obtained from center Point.</xs:documentation>
</xs:annotation>
</xs:element>
</xs:sequence>
<xs:attribute name="name" type="xs:string" use="optional"/>
</xs:complexType>
<!-- Definition of RectangularBox follows. -->
<xs:complexType name="RectangularBox">
<xs:annotation>
<xs:documentation>A Rectangular Box for locating cells in 3D.</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="corner" type="Point">
<xs:annotation>
<xs:documentation>Location of vertex with lowest x, y, z coords.</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="size">
<xs:annotation>
<xs:documentation>Size of box. Note if width, height or depth is zero, implies a lower dimension box, e.g. 2D plane.</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:attribute name="width" type="xs:double"/>
<xs:attribute name="height" type="xs:double"/>
<xs:attribute name="depth" type="xs:double"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="name" type="xs:string" use="optional"/>
</xs:complexType>
<!-- Definition of NonSpatialGrid follows. -->
<xs:complexType name="NonSpatialGrid">
<xs:annotation>
<xs:documentation>Specifies a grid of up to 3 dimensions, without any explicit 3D location information.</xs:documentation>
</xs:annotation>
<xs:attribute name="x" type="xs:positiveInteger" use="required"/>
<xs:attribute name="y" type="xs:positiveInteger" use="optional"/>
<xs:attribute name="z" type="xs:positiveInteger" use="optional"/>
</xs:complexType>
<!-- Definition of Manifold follows. -->
<xs:complexType name="Manifold">
<xs:annotation>
<xs:documentation>A surface.</xs:documentation>
</xs:annotation>
<xs:complexContent>
<xs:extension base="Points"/>
</xs:complexContent>
</xs:complexType>
<!-- Definition of Polygon follows. -->
<xs:complexType name="Polygon">
<xs:annotation>
<xs:documentation>A closed structure represented by a list of points where the first point connects with the last point.</xs:documentation>
</xs:annotation>
<xs:complexContent>
<xs:extension base="Points"/>
</xs:complexContent>
</xs:complexType>
<!-- Definition of Polyhedron follows. -->
<xs:complexType name="Polyhedron">
<xs:annotation>
<xs:documentation>A 3d surface to represent the cell body or histological structure.</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="polygons">
<xs:annotation>
<xs:documentation>Collection of polygons defining the polyhedron.</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element name="polygon" type="Polygon" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
<!-- Definition of Annotation follows -->
<xs:complexType name="Annotation">
<xs:annotation>
<xs:documentation>Concise processing directives for downstream applications.</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:any processContents="skip" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
<!-- Definition of LengthUnits follows. -->
<xs:simpleType name="LengthUnits">
<xs:annotation>
<xs:documentation>Enumeration of length units. Used in MorphML Level 1 files, where length is the only important dimension.</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:enumeration value="micron"/>
<xs:enumeration value="millimetre"/>
<xs:enumeration value="metre"/>
</xs:restriction>
</xs:simpleType>
<!-- Definition of VolumeUnits follows. -->
<xs:simpleType name="VolumeUnits">
<xs:annotation>
<xs:documentation>Enumeration of volume units.</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:enumeration value="cubic_millimetre"/>
<xs:enumeration value="millilitre"/>
<xs:enumeration value="litre"/>
</xs:restriction>
</xs:simpleType>
<!-- Definition of Notes follows. -->
<xs:simpleType name="Notes">
<xs:annotation>
<xs:documentation>Textual human readable notes related to the element in question. It's useful to put these into
the NeuroML files instead of XML comments, as the notes can be extracted and repeated in the files to which the NeuroML is mapped.</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string"/>
</xs:simpleType>
<!-- Definition of Group follows. -->
<xs:simpleType name="Group">
<xs:annotation>
<xs:documentation>Allows elements to be associated, such as for grouping segments or cables into the basal arbor.</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string"/>
</xs:simpleType>
<!-- Definition of Property follows. -->
<xs:complexType name="Property">
<xs:annotation>
<xs:documentation>A Tag/Value/Type tuple.</xs:documentation>
</xs:annotation>
<xs:all>
<xs:element name="tag" type="xs:string"/>
<xs:element name="value" type="xs:string"/>
</xs:all>
</xs:complexType>
<!-- Definition of Properties follows. -->
<xs:complexType name="Properties">
<xs:annotation>
<xs:documentation>A collection of Properties</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="property" type="Property" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
<!-- Definition of PropertyDetail follows. -->
<xs:complexType name="PropertyDetail">
<xs:annotation>
<xs:documentation>Metadata for each Property.</xs:documentation>
</xs:annotation>
<xs:all>
<xs:element name="description" type="xs:string"/>
<xs:element name="type" type="xs:anyType"/>
</xs:all>
<xs:attribute name="property" type="xs:string"/>
</xs:complexType>
<!-- Definition of GroupDetail follows. -->
<xs:complexType name="GroupDetail">
<xs:annotation>
<xs:documentation>Metadata for each Group.</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="description" type="xs:string"/>
<xs:element name="properties" type="Properties" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="group" type="xs:string"/>
</xs:complexType>
<!-- Definition of metadata follows. -->
<xs:group name="metadata">
<xs:annotation>
<xs:documentation>General metadata which can be applied to a number of elements</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="notes" type="Notes" minOccurs="0"/>
<xs:element name="properties" type="Properties" minOccurs="0"/>
<xs:element name="annotation" type="Annotation" minOccurs="0"/>
<xs:element name="group" type="Group" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:group>
<!-- Definition of YesNo follows. -->
<xs:simpleType name="YesNo">
<xs:annotation>
<xs:documentation>String with only yes or no allowed</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:enumeration value="yes"/>
<xs:enumeration value="no"/>
</xs:restriction>
</xs:simpleType>
<!-- Definition of ZeroToOne follows. -->
<xs:simpleType name="ZeroToOne">
<xs:annotation>
<xs:documentation>Double restricted to between 1 and 0</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:double">
<xs:minInclusive value="0"/>
<xs:maxInclusive value="1"/>
</xs:restriction>
</xs:simpleType>
<!-- Definition of NonNegativeDouble follows. -->
<xs:simpleType name="NonNegativeDouble">
<xs:annotation>
<xs:documentation>Double restricted to 0 or greater</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:double">
<xs:minInclusive value="0"/>
</xs:restriction>
</xs:simpleType>
<!-- Definition of PositiveDouble follows. -->
<xs:simpleType name="PositiveDouble">
<xs:annotation>
<xs:documentation>Double restricted greater than 0</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:double">
<xs:minExclusive value="0"/>
</xs:restriction>
</xs:simpleType>
<!-- Definition of Units follows. -->
<xs:simpleType name="Units">
<xs:annotation>
<xs:documentation>Enumeration of unit scheme used. Only SI or Physiological units allowed</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:enumeration value="Physiological Units">
<xs:annotation>
<xs:documentation>Milisecond, millivolt, centimeter, etc</xs:documentation>
</xs:annotation>
</xs:enumeration>
<xs:enumeration value="SI Units">
<xs:annotation>
<xs:documentation>Second, volt, meter, etc.</xs:documentation>
</xs:annotation>
</xs:enumeration>
</xs:restriction>
</xs:simpleType>
<!-- Possible reference extensions. -->
<xs:group name="referencedata">
<xs:annotation>
<xs:documentation>General metadata about references for the model.
Note: This element will possibly change when a new set of schema
files is adopted for adding references, authors, citations, etc.</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="authorList" type="Authors" minOccurs="0"/>
<xs:element name="publication" type="Publication" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="neuronDBref" type="NeuronDBReference" minOccurs="0"/>
<xs:element name="modelDBref" type="ModelDBReference" minOccurs="0"/>
</xs:sequence>
</xs:group>
<xs:complexType name="NeuronDBReference">
<xs:annotation>
<xs:documentation>A reference to an entity in NeuronDB
Note: This element will possibly change when a new set of schema
files is adopted for adding references, authors, citations, etc. See
mailing lists for latest status</xs:documentation>
</xs:annotation>
<xs:all>
<xs:element name="modelName" type="xs:string"/>
<xs:element name="uri" type="xs:string"/>
</xs:all>
</xs:complexType>
<xs:complexType name="ModelDBReference">
<xs:annotation>
<xs:documentation>A reference to an entity in ModelDB
Note: This element will possibly change when a new set of schema
files is adopted for adding references, authors, citations, etc. See
mailing lists for latest status</xs:documentation>
</xs:annotation>
<xs:all>
<xs:element name="modelName" type="xs:string"/>
<xs:element name="uri" type="xs:string"/>
</xs:all>
</xs:complexType>
<xs:complexType name="Publication">
<xs:annotation>
<xs:documentation>A reference to a publication
Note: This element will possibly change when a new set of schema
files is adopted for adding references, authors, citations, etc. See
mailing lists for latest status</xs:documentation>
</xs:annotation>
<xs:all>
<xs:element name="fullTitle" type="xs:string">
<xs:annotation>
<xs:documentation>A reasonably complete reference to the paper, etc. including journal, authors, issue, year.
Mainly for quick recognition of the paper. The PubMed ref should contain the unique ID.</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="pubmedRef" type="xs:string">
<xs:annotation>
<xs:documentation>URL of paper in PubMed (starting with http://www.ncbi.nlm.nih.gov)</xs:documentation>
</xs:annotation>
</xs:element>
</xs:all>
</xs:complexType>
<xs:complexType name="Authors">
<xs:annotation>
<xs:documentation>A reference to an author
Note: This element will possibly change when a new set of schema
files is adopted for adding references, authors, citations, etc. See
mailing lists for latest status</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="modelAuthor" type="Person" maxOccurs="unbounded" minOccurs="0">
<xs:annotation>
<xs:documentation>Author of the original model</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="modelTranslator" type="Person" maxOccurs="unbounded" minOccurs="0">
<xs:annotation>
<xs:documentation>Person who translated the model to NeuroML</xs:documentation>
</xs:annotation>
</xs:element>
</xs:sequence>
</xs:complexType>
<xs:complexType name="Person">
<xs:annotation>
<xs:documentation>A generic reference to a person, for authorship, etc</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="name" type="xs:string">
</xs:element>
<xs:element name="institution" type="xs:string" minOccurs="0">
</xs:element>
<xs:element name="email" type="xs:string" minOccurs="0">
<xs:annotation>
<xs:documentation>Useful to have. Note: something like '- at -' replacing the @ might be wise</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="comment" type="xs:string" minOccurs="0">
<xs:annotation>
<xs:documentation>Optional comment on their specific contribution</xs:documentation>
</xs:annotation>
</xs:element>
</xs:sequence>
</xs:complexType>
<!-- Extensions for reusability etc.-->
<xs:simpleType name="StatusValue">
<xs:annotation>
<xs:documentation>Status enum for stability state of files. This is subject to change.</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:enumeration value="stable">
<xs:annotation><xs:documentation>File can be used with reasonable confidence</xs:documentation></xs:annotation>
</xs:enumeration>
<xs:enumeration value="in_progress">
<xs:annotation><xs:documentation>File can be used with caution, bearing in mind any comments present</xs:documentation></xs:annotation>
</xs:enumeration>
<xs:enumeration value="known_issues">
<xs:annotation><xs:documentation>File can be assumed to be erroneous and shouldn't be used</xs:documentation></xs:annotation>
</xs:enumeration>
</xs:restriction>
</xs:simpleType>
<xs:complexType name="Status">
<xs:annotation>
<xs:documentation>Status for stability state of files. Note this is still subject to change</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="comment" type="xs:string" maxOccurs="unbounded" minOccurs="0">
<xs:annotation>
<xs:documentation>A comment on the current status</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="issue" type="xs:string" maxOccurs="unbounded" minOccurs="0">
<xs:annotation>
<xs:documentation>An issue which need addressing</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="contributor" type="Person" maxOccurs="unbounded" minOccurs="0">
<xs:annotation>
<xs:documentation>Who added the comments?</xs:documentation>
</xs:annotation>
</xs:element>
</xs:sequence>
<xs:attribute name="value" type="StatusValue">
<xs:annotation>
<xs:documentation>Currently an enum value of status/in progress/etc.</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:schema>
|
