tumorml.xsd

<?xml version="1.0" encoding="UTF-8"?>
<!--
  XML schema for TumorML 1.2
  Author: David Johnson
  Contributors: Stelios Sfakianakis
  Created with oXygen XML editor
  
  Copyright (c) 2012-2013, University of Oxford; 2013-, TumorML contributors. 
  The TumorML schema is distributed under the terms of the GNU Lesser General Public License (LGPL)
  http://www.gnu.org/licenses/lgpl.html
-->
<xs:schema xmlns="http://www.tumorml.org/tumorml/1.2" targetNamespace="http://www.tumorml.org/tumorml/1.2" xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified">
  <!-- Regex for alphanumeric combinations w/ underscores OR MIRIAM URIs -->
  <xs:simpleType name="ident">
    <xs:restriction base="xs:token">
      <xs:pattern value="_*[0-9a-zA-Z][_0-9a-zA-Z]*|(urn:miriam:([\w\-\.]+\.[\w\-\.]+)+:[\w\-\.]+:[\w\-\.]+)"/>
    </xs:restriction>
  </xs:simpleType>
  <xs:simpleType name="url">
    <xs:restriction base="xs:token">
      <xs:pattern value="[hH][tT]{2}[pP]://[wW]{3}.*"/>
    </xs:restriction>
  </xs:simpleType>
  <!-- Tumor Model Taxonomy -->
  <xs:simpleType name="mathType">
    <xs:restriction base="xs:string">
      <xs:enumeration value="discrete"/>
      <xs:enumeration value="continuous"/>
      <xs:enumeration value="hybrid"/>
    </xs:restriction>
  </xs:simpleType>
  <xs:simpleType name="multiScaleType">
    <xs:restriction base="xs:string">
      <xs:enumeration value="topDown"/>
      <xs:enumeration value="bottomUp"/>
      <xs:enumeration value="middleOut"/>
    </xs:restriction>
  </xs:simpleType>
  <xs:simpleType name="singleScaleType">
    <xs:restriction base="xs:string">
      <xs:enumeration value="gene"/>
      <xs:enumeration value="subcellular"/>
      <xs:enumeration value="cell"/>
      <xs:enumeration value="tissue"/>
      <xs:enumeration value="organ"/>
    </xs:restriction>
  </xs:simpleType>
  <xs:simpleType name="cancerType">
    <xs:restriction base="xs:string">
      <xs:enumeration value="glioma"/>
      <xs:enumeration value="glioblastoma"/>
      <xs:enumeration value="nephroblastoma"/>
      <xs:enumeration value="lung"/>
      <xs:enumeration value="breast"/>
      <xs:enumeration value="generic"/>
    </xs:restriction>
  </xs:simpleType>
  <xs:simpleType name="homogeneityType">
    <xs:restriction base="xs:string">
      <xs:enumeration value="homogeneous"/>
      <xs:enumeration value="non-homogeneous"/>
    </xs:restriction>
  </xs:simpleType>
  <!--
    JSDL types
    n.b. Restricted due to TUMOR repository DB schema restrictions
  -->
  <xs:simpleType name="osType">
    <xs:restriction base="xs:string">
      <xs:enumeration value="unknown"/>
      <xs:enumeration value="linux"/>
      <xs:enumeration value="winNT"/>
      <xs:enumeration value="macOS"/>
      <xs:enumeration value="winXP"/>
      <xs:enumeration value="winVista"/>
      <xs:enumeration value="win7"/>
      <xs:enumeration value="solaris"/>
      <xs:enumeration value="sunOS"/>
      <xs:enumeration value="javaVM"/>
    </xs:restriction>
  </xs:simpleType>
  <xs:simpleType name="cpuType">
    <xs:restriction base="xs:string">
      <xs:enumeration value="sparc"/>
      <xs:enumeration value="powerpc"/>
      <xs:enumeration value="x86"/>
      <xs:enumeration value="x86_32"/>
      <xs:enumeration value="x86_64"/>
      <xs:enumeration value="parisc"/>
      <xs:enumeration value="mips"/>
      <xs:enumeration value="ia64"/>
      <xs:enumeration value="arm"/>
      <xs:enumeration value="other"/>
    </xs:restriction>
  </xs:simpleType>
  <xs:simpleType name="langType">
    <xs:restriction base="xs:string">
      <xs:enumeration value="c"/>
      <xs:enumeration value="cpp"/>
      <xs:enumeration value="java"/>
      <xs:enumeration value="python"/>
      <xs:enumeration value="perl"/>
      <xs:enumeration value="fortran"/>
      <xs:enumeration value="bash"/>
      <xs:enumeration value="multiple"/>
      <xs:enumeration value="matlab"/>
    </xs:restriction>
  </xs:simpleType>
  <xs:simpleType name="commandLineDataTypes">
    <xs:restriction base="xs:string">
      <xs:enumeration value="int"/>
      <xs:enumeration value="double"/>
      <xs:enumeration value="filename"/>
      <xs:enumeration value="string"/>
    </xs:restriction>
  </xs:simpleType>
  <!--
    some simple Dublin Core elements
    n.b. Simplified due to TUMOR repository DB schema restrictions
  -->
  <xs:group name="dc_elements">
    <xs:sequence>
      <xs:choice minOccurs="0" maxOccurs="unbounded">
        <xs:element ref="title"/>
        <xs:element ref="creator"/>
        <xs:element ref="description"/>
        <xs:element ref="publisher"/>
        <xs:element ref="contributor"/>
        <xs:element ref="date"/>
      </xs:choice>
    </xs:sequence>
  </xs:group>
  <xs:element name="title" type="xs:string"/>
  <xs:element name="creator" type="person"/>
  <xs:element name="description" type="xs:string"/>
  <xs:element name="publisher" type="person"/>
  <xs:element name="contributor" type="person"/>
  <xs:element name="date" type="xs:dateTime"/>
  <!--
    some simple xCard (vCard) elements describing an individual person, including a TUMOR user ID
    n.b. Simplified due to TUMOR repository DB schema restrictions
  -->
  <xs:complexType name="person">
    <xs:sequence>
      <xs:element ref="person"/>
    </xs:sequence>
  </xs:complexType>
  <xs:element name="person">
    <xs:complexType>
      <xs:sequence>
        <xs:element minOccurs="0" ref="fullname"/>
        <xs:element minOccurs="0" ref="name"/>
        <xs:element minOccurs="0" maxOccurs="unbounded" ref="email"/>
        <xs:element minOccurs="0" maxOccurs="unbounded" ref="org"/>
      </xs:sequence>
      <xs:attribute name="id" use="required" type="ident"/>
    </xs:complexType>
  </xs:element>
  <xs:element name="fullname" type="xs:string"/>
  <xs:element name="name">
    <xs:complexType>
      <xs:sequence>
        <xs:element ref="surname"/>
        <xs:element ref="given"/>
        <xs:element minOccurs="0" maxOccurs="unbounded" ref="prefix"/>
        <xs:element minOccurs="0" maxOccurs="unbounded" ref="suffix"/>
      </xs:sequence>
    </xs:complexType>
  </xs:element>
  <xs:element name="surname" type="xs:string"/>
  <xs:element name="given" type="xs:string"/>
  <xs:element name="prefix" type="xs:string"/>
  <xs:element name="suffix" type="xs:string"/>
  <xs:element name="email" type="xs:string"/>
  <xs:element name="org" type="xs:string"/>
  <!--
    TUMOR repository specific metadata
    n.b. Based on TUMOR repository DB schema
  -->
  <xs:group name="tumor_elements">
    <xs:sequence>
      <xs:choice minOccurs="0" maxOccurs="unbounded">
        <xs:element ref="math"/>
        <xs:element ref="singleScale"/>
        <xs:element ref="multiScale"/>
        <xs:element ref="cancer"/>
        <xs:element ref="homogeneity"/>
        <xs:element ref="freeGrowth"/>
        <xs:element ref="treatmentIncluded"/>
      </xs:choice>
    </xs:sequence>
  </xs:group>
  <xs:element name="math" type="xs:string"/>
  <xs:element name="singleScale" type="xs:string"/>
  <xs:element name="multiScale" type="xs:string"/>
  <xs:element name="cancer" type="xs:string"/>
  <xs:element name="homogeneity" type="xs:string"/>
  <xs:element name="freeGrowth" type="xs:boolean"/>
  <xs:element name="treatmentIncluded" type="xs:boolean"/>
  <!--
    External references
    n.b. Based on TUMOR repository DB schema
  -->
  <!-- bibType is based on BibTeX -->
  <xs:simpleType name="bibType">
    <xs:restriction base="xs:string">
      <xs:enumeration value="article"/>
      <xs:enumeration value="book"/>
      <xs:enumeration value="booklet"/>
      <xs:enumeration value="manual"/>
      <xs:enumeration value="techreport"/>
      <xs:enumeration value="mastersthesis"/>
      <xs:enumeration value="phdthesis"/>
      <xs:enumeration value="inbook"/>
      <xs:enumeration value="incollection"/>
      <xs:enumeration value="proceedings"/>
      <xs:enumeration value="inproceedings"/>
      <xs:enumeration value="conference"/>
      <xs:enumeration value="unpublished"/>
      <xs:enumeration value="misc"/>
    </xs:restriction>
  </xs:simpleType>
  <xs:element name="reference">
    <xs:complexType>
      <xs:all>
        <xs:element ref="title"/>
        <xs:element minOccurs="0" ref="source"/>
        <xs:element minOccurs="0" name="creator" type="xs:string"/>
        <xs:element minOccurs="0" ref="citation"/>
        <xs:element ref="type"/>
      </xs:all>
    </xs:complexType>
  </xs:element>
  <xs:element name="source" type="xs:string"/>
  <xs:element name="citation" type="xs:string"/>
  <xs:element name="type" type="xs:string"/>
  <!--
    SI base units based on NIST Reference
    http://physics.nist.gov/cuu/Units/current.html
  -->
  <xs:simpleType name="siBaseUnitTypes">
    <xs:restriction base="xs:string">
      <xs:enumeration value="meter"/>
      <xs:enumeration value="kilogram"/>
      <xs:enumeration value="second"/>
      <xs:enumeration value="ampere"/>
      <xs:enumeration value="kelvin"/>
      <xs:enumeration value="mole"/>
      <xs:enumeration value="candela"/>
    </xs:restriction>
  </xs:simpleType>
  <!-- Some extra non standard units used in cancer modelling, e.g. arbitrary counts -->
  <xs:simpleType name="tumorExtraUnitTypes">
    <xs:restriction base="xs:string">
      <xs:enumeration value="item"/>
      <xs:enumeration value="gray"/>
    </xs:restriction>
  </xs:simpleType>
  <!-- Combined lists of unit types used in TumorML -->
  <xs:simpleType name="unitTypes">
    <xs:union memberTypes="siBaseUnitTypes tumorExtraUnitTypes"/>
  </xs:simpleType>
  <!-- or derived unit name -->
  <!-- Units model -->
  <xs:element name="derivedUnit">
    <xs:complexType>
      <xs:sequence>
        <xs:element maxOccurs="unbounded" name="unit">
          <xs:complexType>
            <xs:attribute name="name" use="required"/>
            <xs:attribute name="multiplier" type="xs:int"/>
            <xs:attribute name="offset" type="xs:int"/>
            <xs:attribute name="scale" type="xs:int"/>
            <xs:attribute name="exp" type="xs:int"/>
          </xs:complexType>
        </xs:element>
      </xs:sequence>
      <xs:attribute name="name" use="required"/>
    </xs:complexType>
  </xs:element>
  <!-- Each TumorML model has an ID to lookup in the repository -->
  <xs:attributeGroup name="tumorml_id">
    <xs:attribute name="id" use="required" type="ident"/>
  </xs:attributeGroup>
  <!-- Basic structure is a model ID, header containing metadata, followed by the model description -->
  <xs:element name="tumorml">
    <xs:complexType>
      <xs:sequence>
        <xs:element ref="header"/>
        <xs:element ref="model"/>
      </xs:sequence>
      <xs:attributeGroup ref="tumorml_id"/>
    </xs:complexType>
  </xs:element>
  <!--
    The header contains metadata as: 
    * Dublin Core elements
    * TUMOR repository DB specific elements
    * Bibliographical references (optional)
  -->
  <xs:element name="header">
    <xs:complexType>
      <xs:choice minOccurs="0" maxOccurs="unbounded">
        <xs:group ref="dc_elements"/>
        <xs:group ref="tumor_elements"/>
        <xs:element ref="reference"/>
      </xs:choice>
    </xs:complexType>
  </xs:element>
  <!--
    The model description contains either:
    1) a simple model as
        * One or more implementations
        * A input/output parameters profile
    or
    2) a complex model as
        * Multiple submodels
        * A model instance topology 
  -->
  <xs:element name="model">
    <xs:complexType>
      <xs:choice>
        <xs:group ref="simpleModel"/>
        <xs:group ref="complexModel"/>
      </xs:choice>
    </xs:complexType>
  </xs:element>
  <xs:group name="simpleModel">
    <xs:sequence>
      <xs:element ref="parameters"/>
      <xs:element maxOccurs="unbounded" ref="implementation"/>
    </xs:sequence>
  </xs:group>
  <xs:group name="complexModel">
    <xs:sequence>
      <xs:element ref="submodel"/>
      <xs:element maxOccurs="unbounded" ref="submodel"/>
      <xs:element ref="topology"/>
    </xs:sequence>
  </xs:group>
  <!--
    Each implementation contains:
     * Metadata as Dublin Core and any number of bibliographic references (optional)
     * A package file name
     * A command line to initiate model execution
     * A list of runtime environment requirements
  -->
  <xs:element name="implementation">
    <xs:complexType>
      <xs:choice minOccurs="0" maxOccurs="unbounded">
        <xs:group ref="dc_elements"/>
        <xs:element ref="reference"/>
        <xs:element ref="package"/>
        <xs:element ref="command"/>
        <xs:element ref="requirements"/>
      </xs:choice>
      <xs:attribute name="id" use="required" type="ident"/>
    </xs:complexType>
  </xs:element>
  <!-- A package consists of a package name and a list of files -->
  <xs:element name="package">
    <xs:complexType>
      <xs:sequence>
        <xs:element maxOccurs="unbounded" ref="file"/>
      </xs:sequence>
      <xs:attribute name="name" use="required"/>
      <xs:attribute name="checksum" use="required"/>
    </xs:complexType>
  </xs:element>
  <!-- A file has a name, a full path relative to the package root, and a checksum (optional) -->
  <xs:simpleType name="fname">
    <xs:restriction base="xs:token">
      <xs:pattern value="[A-Za-z0-9\\-\\._]+"/>
    </xs:restriction>
  </xs:simpleType>
  <!-- not tested yet -->
  <xs:simpleType name="dpath">
    <xs:restriction base="xs:token">
      <xs:pattern value="(/)?([^\\0]+(/)?)+"/>
    </xs:restriction>
  </xs:simpleType>
  <!-- not tested yet -->
  <xs:element name="file">
    <xs:complexType>
      <xs:attribute name="name" use="required" type="fname"/>
      <xs:attribute name="source" use="required" type="dpath"/>
      <xs:attribute name="checksum"/>
    </xs:complexType>
  </xs:element>
  <!-- A command is a simple string for now. -->
  <xs:element name="command" type="xs:string"/>
  <!-- TODO replace with a suitable regex -->
  <!--
    The requirements include:
     * Operating system (optional)
     * CPU architecture (optional)
     * Languages that need to be supported (optional, can be multiple)
  -->
  <xs:element name="requirements">
    <xs:complexType>
      <xs:choice minOccurs="0" maxOccurs="unbounded">
        <xs:element ref="operatingSystem"/>
        <xs:element ref="CPUArchitecture"/>
        <xs:element ref="language"/>
      </xs:choice>
    </xs:complexType>
  </xs:element>
  <xs:element name="operatingSystem" type="osType"/>
  <xs:element name="CPUArchitecture" type="cpuType"/>
  <xs:element name="language" type="langType"/>
  <!--
    Each submodel has a unique ID and:
     * All the elements of a simple model
    or
     * All the elements of a complex model
  -->
  <xs:element name="submodel">
    <xs:complexType>
      <xs:choice>
        <xs:group ref="simpleModel"/>
        <xs:group ref="complexModel"/>
      </xs:choice>
      <xs:attribute name="id" type="ident"/>
    </xs:complexType>
  </xs:element>
  <!-- A topology declares a 2 or more instances and at least one coupling of instance parameters together -->
  <xs:element name="topology">
    <xs:complexType>
      <xs:sequence>
        <xs:element ref="instance"/>
        <xs:element maxOccurs="unbounded" ref="instance"/>
        <xs:element maxOccurs="unbounded" ref="coupling"/>
      </xs:sequence>
    </xs:complexType>
  </xs:element>
  <!-- An instance has a unique ID, references a submodel by ID and has a multiplicity (currently fixed) -->
  <xs:element name="instance">
    <xs:complexType>
      <xs:attribute name="id" use="required" type="ident"/>
      <xs:attribute name="submodel" use="required" type="ident"/>
      <xs:attribute name="multiplicity" type="xs:int"/>
    </xs:complexType>
  </xs:element>
  <!--
    A coupling refers to a specific parameter of two different submodels
     * from submodel.parameter
     * to submodel.parameter
  -->
  <xs:element name="coupling">
    <xs:complexType>
      <xs:attribute name="from" use="required" type="ident"/>
      <xs:attribute name="to" use="required" type="ident"/>
    </xs:complexType>
  </xs:element>
  <!--
    The parameters element defines at least on input parameter and multiple output parameters
    n.b. There must be at least one input parameter
  -->
  <xs:element name="parameters">
    <xs:complexType>
      <xs:choice minOccurs="0" maxOccurs="unbounded">
        <xs:element ref="units"/>
        <xs:element ref="in"/>
        <xs:element ref="out"/>
      </xs:choice>
    </xs:complexType>
  </xs:element>
  <xs:element name="units">
    <xs:complexType>
      <xs:sequence>
        <xs:element maxOccurs="unbounded" ref="derivedUnit"/>
      </xs:sequence>
    </xs:complexType>
  </xs:element>
  <xs:element name="in" type="parameter"/>
  <xs:element name="out" type="parameter"/>
  <!--
    Parameters consist of:
     * A unique ID/name
     * A label (optional)
     * A description  (optional)
     * Whether or not this parameter is optional (optional)
     * A value descriptor (optional)
         * The descriptor contains a datatype, optional default value, and optional value range
     * A unit constraint, based on SI prefix and base units (optional)
    
    regardless of whether they are inputs or outputs
  -->
  <xs:complexType name="parameter">
    <xs:choice minOccurs="0" maxOccurs="unbounded">
      <xs:element ref="description"/>
      <xs:element ref="concept_id"/>
      <xs:element ref="value"/>
    </xs:choice>
    <xs:attribute name="name" use="required" type="ident"/>
    <xs:attribute name="label"/>
    <xs:attribute name="optional" type="xs:boolean"/>
  </xs:complexType>
  <xs:element name="concept_id" type="url"/>
  <xs:element name="value">
    <xs:complexType>
      <xs:all>
        <xs:element minOccurs="0" ref="range"/>
        <xs:element minOccurs="0" name="unit">
          <xs:complexType>
            <xs:attribute name="type" use="required">
              <xs:simpleType>
                <xs:union memberTypes="unitTypes ident"/>
              </xs:simpleType>
            </xs:attribute>
          </xs:complexType>
        </xs:element>
      </xs:all>
      <xs:attribute name="type" use="required" type="commandLineDataTypes"/>
      <xs:attribute name="default"/>
    </xs:complexType>
  </xs:element>
  <xs:element name="range">
    <xs:complexType>
      <xs:all>
        <xs:element minOccurs="0" ref="min"/>
        <xs:element minOccurs="0" ref="max"/>
      </xs:all>
    </xs:complexType>
  </xs:element>
  <xs:element name="min">
    <xs:complexType mixed="true">
      <xs:attribute name="inclusive" type="xs:boolean"/>
    </xs:complexType>
  </xs:element>
  <xs:element name="max">
    <xs:complexType mixed="true">
      <xs:attribute name="inclusive" type="xs:boolean"/>
    </xs:complexType>
  </xs:element>
</xs:schema>