BDML version 0.2 Specification

<BDBase>

Definition: A single abstract base type for most elements in BDML.
Type: BDBase
Attributes:
Attribute NameData TypeUseDefinition
metaidxsd:IDoptionalUnique ID of metadata annotation.
Subelements:
Subelement NameData TypeminmaxDefinition
notesxsd:any01A container for comments about the element.
annotationxsd:any01A container for optional software-generated content.
Notes:

<bdml>

Definition: This is the root element for the BDML schema.
Type: bdmlDocument
Attributes:
Attribute NameData TypeUseDefinition
versionxsd:positiveIntegerrequiedThe version of this BDML document.
Subelements:
Subelement NameData TypeminmaxDefinition
infoInfo11Information about the BDML file.
ontologyOntology01Ontological references in the BDML file.
summarySummary11Summary of data described in the BDML file.
contactContact11Contact information for the BDML file.
methodsMethods11Methods used to obtain data described in the BDML file.
dataData01Data described in the BDML file.
seriesSeries01A sereis of data files which are obtained from the same experiment or simulation.
setSet01A set of data files which are referenced in the same article.
Example:
<bdml version="0.2" xsi:schemaLocation="http://ssbd.qbic.riken.jp/bdml http://ssbd.qbic.riken.jp/bdml/bdml0.2.xsd">
  <info>
    <bdmlID>563d487f-1676-4159-a3ab-c25c2e198f6c</bdmlID>
    ...
  </info>
  <summary>
    <description>quantitative information about nuclear division dynamics in wild-type embryo</description>
    ...
  </summary>
  <contact>
    <name>Shuichi Onami</name>
    ...
  </contact>
  <methods>
    <summary>See details in Kyoda et al. (2013) Nucleic Acids Res 41, D732-D737.</summary>
    ...
  </methods>
  <data>
      ...
      ...
      ...
  </data>
</bdml>
Notes: Insted of <data>, <series> or <set> can be used for representing a set of data files which are obtained from the same experiment or simulation, or a set of data files which are referenced in the same article, respectively.

<info>

Definition: Information about the BDML file.
Type: Info
Subelements:
Subelement NameData TypeminmaxDefinition
bdmlIDUUIDType11Unique ID of the BDML file.
titlexsd:string11Title of the BDML file.
releasexsd:date11Release date of the BDML file.
licensexsd:string11License information of the BDML file.
Example:
<info>
  <bdmlID>563d487f-1676-4159-a3ab-c25c2e198f6c</bdmlID>
  <title>BDML file for quantitative information about nuclear division dynamics of wild-type embryo</title>
  <release>2012-05-18</release>
  <license>CC BY-SA</license>
</info>
Notes: The Creative Commons licenses are recommended for publishing data.

<ontology>

Definition: Ontological references used in the BDML file.
Type: Ontology
Subelements:
Subelement NameData TypeminmaxDefinition
ontologyTermontologyTerm01Association with a term from different ontology sources.
Example:
  <ontology>
    <ontologyTerm>...</ontologyTerm>
    ...
  </ontology>
Notes:

<ontologyTerm>

Definition: Association with a term from different ontology sources.
Type: ontologyTerm
Subelements:
Subelement NameData TypeminmaxDefinition
idxsd:string11Unique ID for the ontology term.
termxsd:string11The term itself.
ontologyIDxsd:string11Accession identifier of the ontology source.
ontologyRUIxsd:URI11Unique identifier of the ontology source.
Example:
  <ontologyTerm>
    <id>001</id>
    <term>nucleus</term>
    <ontologyID>GO:0005634</ontologyID>
    <ontologyURI>http://identifiers.org/go/</ontologyURI>
  </ontologyTerm>
Notes: The ontologyRef attribution refers to id defined in the ontologyTerm element.

<summary>

Definition: Summary of the data described in the BDML file.
Type: Summary
Subelements:
Subelement NameData TypeminmaxOntologyRefDefinition
descriptionxsd:string11Detailed information about the data described in the BDML file.
datatypexsd:string111Describes specific type of data that was represented in the BDML file
organismxsd:string111Name of a targeted organism being described. Name is based on the NCBI taxonomy definition.
localIDxsd:string01Internal or local identifier used to identify the BDML file.
basedonBasedOn11Speficify Whether the data was gathered from an in vivo measurement or from a computer simulation.
contributorsxsd:string11Names of contributors who produce/collect the data.
citationxsd:string01Detailed information about the original published paper.
PMIDxsd:positiveInteger01PubMed ID of the original published paper.
dblinkxsd:anyURI01A URL link to the original database.
Example:
<summary>
  <description>quantitative information about nuclear division dynamics in wild-type embryo</description>
  <datatype>nuclear division dynamics</datatype>
  <organism>C. elegans</organism>
  <localID>wt(N2)030131_01</localID>
  <basedon>Experiment</basedon>
  <contributors>Kyoda, K., Furukawa, M., Arai, R., Onami, S.</contributors>
  <PMID>23172286</PMID>
  <dblink>http://so.qbic.riken.jp/wddd/</dblink>
</summary>
Notes:

<contact>

Definition: Contact information for the BDML file.
Type: Contact
Subelements:
Subelement NameData TypeminmaxDefinition
namexsd:string11Name of corresponding author of the BDML file.
E-mailxsd:string11E-mail address of the corresponding author.
phonexsd:string01Phone number of the corresponding author.
URLxsd:anyURI01A URL link to corresponding author's laboratory or website.
organizationxsd:string11Affiliation of the corresponding author.
departmentxsd:string01Department of the organization of the corresponding author.
laboratoryxsd:string01Name of the laboratory of the corresponding author.
addressxsd:string01Postal address of the corresponding author.
Example:
<contact>
  <name>Shuichi Onami</name>
  <E-mail>......@.......</E-mail>
  <organization>RIKEN</organization>
  <department>Quantitative Biology Center</department>
  <laboratory>Laboratory for Developmental Dynamics</laboratory>
  <address>2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan</address>
</contact>
Notes:

<methods>

Definition: Methods/procedures used to obtain the data described in the BDML file.
Type: Methods
Subelements:
Subelement NameData TypeminmaxDefinition
summaryxsd:string11Detailed information about methods used to obtain the data.
sourcexsd:anyURI01A URL link to original sources such as microscope images of an in vivo measurement or files of mathematical model of a computer simulation.
protocolxsd:anyURI01A URL link to a protocol file such as PDPML (Procedures for Data Processing Markup Language) file.
Example:
<methods>
  <summary>See details in Kyoda et al. (2013) Nucleic Acids Res 41, D732-D737.</summary>
  <source>http://ssbd.qbic.riken.jp/data/source/Ce_KK_P002/wt_N2_030131_01/wt_N2_030131_01.zip</source>
  <protocol>http://ssbd.qbic.riken.jp/data/pdpml/Ce_KK_P002.pdpml0.06.xml</protocol>
</methods>
Notes:

<data>

Definition: Numerical data described in the BDML file.
Type: Data
Subelements:
Subelement NameData TypeminmaxDefinition
scaleUnitScaleUnit11Scales and measurement units of spatial coordinates and time.
objectObject1unlimitedTypes of object detected from microscope images used in an in vivo measurement or from the result of a computer simulation.
featureFeature0unlimitedTypes of feature within the objects.
componentComponent1unlimitedA collection of objects and their spatial information at a given point of time.
Example:
<data>
  <scaleUnit>
    <xScale>0.105</xScale>
    ...
  </scaleUnit>
  <object>
    <objectName>
  </object>
  <component>
    <componentID>1000<componentID>
    ...
    ...
  </component>
  ...
</data>
Notes:

<scaleUnit>

Definition: Scale and unit of coordinates and time.
Type: ScaleUnit
Subelements:
Subelement NameData TypeminmaxOntologyRefDefinition
xScalexsd:double11Scale in x dimension.
yScalexsd:double11Scale in y dimension.
zScalexsd:double11Scale in z dimension.
xyzUnitUnitKind111Measurement unit of x, y and z dimensions.
tScalexsd:double01Time scale.
tUnittUnitKind111Measurement unit of time.
Example:
<scaleUnit>
  <xScale>0.105</xScale>
  <yScale>0.105</yScale>
  <zScale>0.5</zScale>
  <xyzUnit>micrometer</xyzUnit>
  <tScale>40.0</tSCale>
  <tUnit>second</tUnit>
</scaleUnit>
Notes: The zScale should be set to 0.0 for describing data in two dimension.

<object>

Definition: Types of object detected from microscope images in an in vivo measurement or from the result of a computer simulation.
Type: Object
Subelements:
Subelement NameData TypeminmaxOntologyRefDefinition
objectNamexsd:string111Name of object.
Example:
<object>
  <objectName>nucleus</objectName>
</object>
Notes:

<feature>

Definition: Types of feature within the objects.
Type: Feature
Subelements:
Subelement NameData TypeminmaxOntologyRefDefinition
featureNamexsd:string11Name of feature.
featureScalexsd:double11Scaling ratio of feature.
featureUnitUnitKind111Measurement unit of feature.
Example:
<feature>
  <featureName>total GFP signal</featureName>
  <featureScale>1.0</featureScale>
  <featureUnit>intensity</featureUnit>
</feature>
Notes:

<component>

Definition: A collection of objects and their spatial information at a given point of time.
Type: Component
Subelements:
Subelement NameData TypeminmaxDefinition
componentIDxsd:string11A unique ID of a component.
componentNamexsd:string01Name of the component.
timexsd:double11Time (e.g., time point/time frame).
prevIDxsd:string0unlimitedConnectivity with another component from a previous time point/frame.
measurementMeasurement1unlimitedSpatial information of objects.
Example:
<component>
  <componentID>2000</componentID>
  <componentName>P0</componentName>
  <time>2</time>
  <prevID>1000</prevID>
  <measurement>
    <objectRef>nucleus</objectRef>
    <line>
      ...
      ...
    </line>
  </measurement>
</component>
Notes:

<measurement>

Definition: Spatial information of objects.
Type: Measurement
Subelements:
Subelement NameData TypeminmaxDefinition
objectRefxsd:string11Reference to the objects defined in object.
pointPoint01Point entity type.
lineLine01Line entity type.
circleCircle01Circle entity type.
sphereSphere01Sphere entity type.
faceFace01Face entity type.
propertyProperty0unlimitedFeatures of an object.
Example:
<measurement>
  <objectRef>nucleus</objectRef>
  <line>
    <xyzSequence>
      ...
      ...
    </xyzSequence>
  </line>
</measurement>
Notes:

<point>

Definition: Point entity type.
Type: Point
Subelements:
Subelement NameData TypeminmaxDefinition
xyzXYZ1unlimited3-dimensional coordinates of a point.
Example:
<point>
  <xyz>
    <x>1.045</x>
    <y>4.421</y>
    <z>6.214</z>
  </xyz>
</point>
Notes:

<line>

Definition: Line entity type.
Type: Line
Subelements:
Subelement NameData TypeminmaxDefinition
xyzSequenceXYZSequence1unlimitedA continuous sequence points defined by a set of coordinates. If the line is closed, i.e. the starting point is the same as the end point, the sequence of points should be written in counter-clockwise direction.
Example:
<line>
  <xyzSequence>
    <xyz>
      ...
      ...
      ...
    </xyz>
  </xyzSequence>
</line>
Notes:

<circle>

Definition: Circle entity type.
Type: Circle
Subelements:
Subelement NameData TypeminmaxDefinition
xyzXYZ11Center of a circle.
radiusxsd:double11Radius of a circle.
Example:
<circle>
  <xyz>
    <x>163</x>
    <y>343</y>
    <z>0</z>
  </xyz>
  <radius>1.62</radius>
</circle>
Notes:

<sphere>

Definition: Sphere entity type.
Type: Sphere
Subelements:
Subelement NameData TypeminmaxDefinition
xyzXYZ11Center of a sphere.
radiusxsd:double11Radius of a sphere.
Example:
<sphere>
  <xyz>
    <x>163</x>
    <y>343</y>
    <z>6.1</z>
  </xyz>
  <radius>1.62</radius>
</sphere>
Notes:

<face>

Definition: Face entity type.
Type: Face
Subelements:
Subelement NameData TypeminmaxDefinition
xyzTripletXYZTriplet1unlimitedxyzTriplet is defined as a set of three points, Their coordinates are written in a counter-clockwise order when viewed from the outside of an object.
Example:
<face>
  <xyzTriplet>
    <xyz>
      ...
    </xyz>
    <xyz>
      ...
    </xyz>
    <xyz>
      ...
    </xyz>
  </xyzTriplet>
</face>
Notes: A face is defined by three points. Orientation of a face determines which side of the face is facing inside or outside of an object. To determine the orientation of a face, the coordinates of the face have to be written in counter clockwise order.

<xyzSequence>

Definition: A sequence of coordinates written in counter-clockwise direction.
Type: XYZSequence
Subelements:
Subelement NameData TypeminmaxDefinition
xyzXYZ1unlimited3-dimensional x, y, z coordinates.
Example:
<xyzSequence>
  <xyz>
    ...
  </xyz>
  <xyz>
    ...
  </xyz>
  ...
</xyzSequence>
Notes:

<xyzTriplet>

Definition: It is a set of three points. Their coordinates are written in a counter-clockwise order when viewed from the outside of an object.
Type: XYZTriplet
Subelements:
Subelement NameData TypeminmaxDefinition
xyzXYZ333-dimensional coordinate.
Example:
<xyzTriplet>
  <xyz>
    <x>0.5</x>
    <y>1.2</y>
    <z>0.0</z>
  </xyz>
  <xyz>
    <x>0.0</x>
    <y>1.0</y>
    <z>0.0</z>
  </xyz>
  <xyz>
    <x>0.2</x>
    <y>0.5</y>
    <z>0.0</z>
  </xyz>
</xyzTriplet>
Notes:

<xyz>

Definition: Three-dimensional coordinates.
Type: XYZ
Subelements:
Subelement NameData TypeminmaxDefinition
xxsd:double11X dimension.
yxsd:double11Y dimension.
zxsd:double11Z dimension.
Example:
<xyz>
  <x>0.5</x>
  <y>1.2</y>
  <z>0.0</z>
</xyz>
Notes:

<property>

Definition: The measured or computed feature and its numerical value of an object.
Type: Property
Subelements:
Subelement NameData TypeminmaxDefinition
featureRefxsd:double11Reference to the features defined in feature element.
featureValxsd:double11Value of the feature.
Example:
<property>
  <featureRef>total GFP signal</featureRef>
  <featureVal>103162</featureVal>
</property>
Notes:

<series>

Definition: A series of BDML data files which are obtained from the same experiment or simulation.
Type: Series
Subelements:
Subelement NameData TypeminmaxDefinition
bdmlIDRefUUIDType1unlimitedbdmlID of a BDML file.
Example:
<series>
  <bdmlIDRef>563d487f-1676-4159-a3ab-c25c2e198f6c</bdmlIDRef>
  ...
  ...
</series>
Notes:

<set>

Definition: A set of BDML data files which are referenced in the same article.
Type: Set
Subelements:
Subelement NameData TypeminmaxDefinition
bdmlIDRefUUIDType1unlimitedbdmlID of a BDML file.
Example:
<series>
  <bdmlIDRef>563d487f-1676-4159-a3ab-c25c2e198f6c</bdmlIDRef>
  ...
  ...
</series>
Notes:

UUIDType

Definition: A universally unique identifier.
Type: xsd:string
Pattern:
[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}
Notes:

BasedOn

Definition: Indicates whether data was produced from an in vivo measurement or from a computer simulation.
Type: xsd:string
Enumeration:
ExperimentSimulation
Notes:

UnitKind

Definition: Unit of numerical value in the data.
Type: xsd:string
Enumeration:
amperea.u.becquerelcandelaCelsiuscoulombdimensionlessfaradgramgrayhenryhertzitemjoule
katalkelvinkilogramliterlumenluxmetermetremicrometermicrometremolenewtonohmpascal
p.d.u.radiansiemenssievertsteradianteslavoltwattweber
Notes:

tUnitKind

Definition: Unit of time.
Type: xsd:string
Enumeration:
nanosecondmicrosecondmillisecond
secondminutehour
daymonthyear
Notes: