BDML version 0.2 Specification

<BDBase>

Definition:

A single abstract base type for most elements in BDML.

Type:

BDBase

Attributes:

Attribute Name	Data Type	Use	Definition
metaid	xsd:ID	optional	Unique ID of metadata annotation.

Subelements:

Subelement Name	Data Type	min	max	Definition
notes	xsd:any	0	1	A container for comments about the element.
annotation	xsd:any	0	1	A container for optional software-generated content.

Notes:

<bdml>

Definition:

This is the root element for the BDML schema.

Type:

bdmlDocument

Attributes:

Attribute Name	Data Type	Use	Definition
version	xsd:positiveInteger	requied	The version of this BDML document.

Subelements:

Subelement Name	Data Type	min	max	Definition
info	Info	1	1	Information about the BDML file.
ontology	Ontology	0	1	Ontological references in the BDML file.
summary	Summary	1	1	Summary of data described in the BDML file.
contact	Contact	1	1	Contact information for the BDML file.
methods	Methods	1	1	Methods used to obtain data described in the BDML file.
data	Data	0	1	Data described in the BDML file.
series	Series	0	1	A sereis of data files which are obtained from the same experiment or simulation.
set	Set	0	1	A 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 Name	Data Type	min	max	Definition
bdmlID	UUIDType	1	1	Unique ID of the BDML file.
title	xsd:string	1	1	Title of the BDML file.
release	xsd:date	1	1	Release date of the BDML file.
license	xsd:string	1	1	License 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 Name	Data Type	min	max	Definition
ontologyTerm	ontologyTerm	0	1	Association 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 Name	Data Type	min	max	Definition
id	xsd:string	1	1	Unique ID for the ontology term.
term	xsd:string	1	1	The term itself.
ontologyID	xsd:string	1	1	Accession identifier of the ontology source.
ontologyRUI	xsd:URI	1	1	Unique 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 Name	Data Type	min	max	OntologyRef	Definition
description	xsd:string	1	1		Detailed information about the data described in the BDML file.
datatype	xsd:string	1	1	1	Describes specific type of data that was represented in the BDML file
organism	xsd:string	1	1	1	Name of a targeted organism being described. Name is based on the NCBI taxonomy definition.
localID	xsd:string	0	1		Internal or local identifier used to identify the BDML file.
basedon	BasedOn	1	1		Speficify Whether the data was gathered from an in vivo measurement or from a computer simulation.
contributors	xsd:string	1	1		Names of contributors who produce/collect the data.
citation	xsd:string	0	1		Detailed information about the original published paper.
PMID	xsd:positiveInteger	0	1		PubMed ID of the original published paper.
dblink	xsd:anyURI	0	1		A 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 Name	Data Type	min	max	Definition
name	xsd:string	1	1	Name of corresponding author of the BDML file.
E-mail	xsd:string	1	1	E-mail address of the corresponding author.
phone	xsd:string	0	1	Phone number of the corresponding author.
URL	xsd:anyURI	0	1	A URL link to corresponding author's laboratory or website.
organization	xsd:string	1	1	Affiliation of the corresponding author.
department	xsd:string	0	1	Department of the organization of the corresponding author.
laboratory	xsd:string	0	1	Name of the laboratory of the corresponding author.
address	xsd:string	0	1	Postal 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 Name	Data Type	min	max	Definition
summary	xsd:string	1	1	Detailed information about methods used to obtain the data.
source	xsd:anyURI	0	1	A URL link to original sources such as microscope images of an in vivo measurement or files of mathematical model of a computer simulation.
protocol	xsd:anyURI	0	1	A 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 Name	Data Type	min	max	Definition
scaleUnit	ScaleUnit	1	1	Scales and measurement units of spatial coordinates and time.
object	Object	1	unlimited	Types of object detected from microscope images used in an in vivo measurement or from the result of a computer simulation.
feature	Feature	0	unlimited	Types of feature within the objects.
component	Component	1	unlimited	A 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 Name	Data Type	min	max	OntologyRef	Definition
xScale	xsd:double	1	1		Scale in x dimension.
yScale	xsd:double	1	1		Scale in y dimension.
zScale	xsd:double	1	1		Scale in z dimension.
xyzUnit	UnitKind	1	1	1	Measurement unit of x, y and z dimensions.
tScale	xsd:double	0	1		Time scale.
tUnit	tUnitKind	1	1	1	Measurement 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 Name	Data Type	min	max	OntologyRef	Definition
objectName	xsd:string	1	1	1	Name of object.

Example:

<object>
  <objectName>nucleus</objectName>
</object>

Notes:

<feature>

Definition:

Types of feature within the objects.

Type:

Feature

Subelements:

Subelement Name	Data Type	min	max	OntologyRef	Definition
featureName	xsd:string	1	1		Name of feature.
featureScale	xsd:double	1	1		Scaling ratio of feature.
featureUnit	UnitKind	1	1	1	Measurement 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 Name	Data Type	min	max	Definition
componentID	xsd:string	1	1	A unique ID of a component.
componentName	xsd:string	0	1	Name of the component.
time	xsd:double	1	1	Time (e.g., time point/time frame).
prevID	xsd:string	0	unlimited	Connectivity with another component from a previous time point/frame.
measurement	Measurement	1	unlimited	Spatial 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 Name	Data Type	min	max	Definition
objectRef	xsd:string	1	1	Reference to the objects defined in object.
point	Point	0	1	Point entity type.
line	Line	0	1	Line entity type.
circle	Circle	0	1	Circle entity type.
sphere	Sphere	0	1	Sphere entity type.
face	Face	0	1	Face entity type.
property	Property	0	unlimited	Features of an object.

Example:

<measurement>
  <objectRef>nucleus</objectRef>
  <line>
    <xyzSequence>
      ...
      ...
    </xyzSequence>
  </line>
</measurement>

Notes:

<point>

Definition:

Point entity type.

Type:

Point

Subelements:

Subelement Name	Data Type	min	max	Definition
xyz	XYZ	1	unlimited	3-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 Name	Data Type	min	max	Definition
xyzSequence	XYZSequence	1	unlimited	A 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 Name	Data Type	min	max	Definition
xyz	XYZ	1	1	Center of a circle.
radius	xsd:double	1	1	Radius 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 Name	Data Type	min	max	Definition
xyz	XYZ	1	1	Center of a sphere.
radius	xsd:double	1	1	Radius 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 Name	Data Type	min	max	Definition
xyzTriplet	XYZTriplet	1	unlimited	xyzTriplet 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 Name	Data Type	min	max	Definition
xyz	XYZ	1	unlimited	3-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 Name	Data Type	min	max	Definition
xyz	XYZ	3	3	3-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 Name	Data Type	min	max	Definition
x	xsd:double	1	1	X dimension.
y	xsd:double	1	1	Y dimension.
z	xsd:double	1	1	Z 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 Name	Data Type	min	max	Definition
featureRef	xsd:double	1	1	Reference to the features defined in feature element.
featureVal	xsd:double	1	1	Value 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 Name	Data Type	min	max	Definition
bdmlIDRef	UUIDType	1	unlimited	bdmlID 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 Name	Data Type	min	max	Definition
bdmlIDRef	UUIDType	1	unlimited	bdmlID 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:

Experiment

Simulation

Notes:

UnitKind

Definition:

Unit of numerical value in the data.

Type:

xsd:string

Enumeration:

ampere

a.u.

becquerel

candela

Celsius

coulomb

dimensionless

farad

gram

gray

henry

hertz

item

joule

katal

kelvin

kilogram

liter

lumen

lux

meter

metre

micrometer

micrometre

mole

newton

ohm

pascal

p.d.u.

radian

siemens

sievert

steradian

tesla

volt

watt

weber

Notes:

tUnitKind

Definition:

Unit of time.

Type:

xsd:string

Enumeration:

nanosecond	microsecond	millisecond
second	minute	hour
day	month	year

Notes:

SSBD:database