PDPML version 0.06 Specification

<pdpml>

Definition:

This is the root element for the PDPML schema.

Type:

pdpmlDocument

Attributes:

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

Subelements:

Subelement Name	Data Type	min	max	Definition
info	Info	1	1	Information about the PDPML file itself.
summary	Summary	1	1	Summary of the procedures described in the PDPML file.
contact	Contact	1	1	Contact information for the PDPML file.
procedure	Procedure	1	1	Procedure for data processing.

Example:

<pdpml version="0.06" xsi:schemaLocation="http://ssbd.qbic.riken.jp/pdpml http://ssbd.qbic.riken.jp/pdpml/pdpml0.06.xsd">
  <info>
    <pdpmlID>0eb03d7c-cd2a-4198-bb0f-49fa43f629bd</pdpmlID>
    ...
  </info>
  <summary>
    <description>Method for obtaining cell division dynamics</description>
    ...
  </summary>
  <contact>
    <name>Shuichi Onami</name>
    ...
  </contact>
  <procedure>
      ...
      ...
      ...
  </procedure>
</pdpml>

Notes:

<info>

Definition:

Information about the PDPML file itself.

Type:

Info

Subelements:

Subelement Name	Data Type	min	max	Definition
pdpmlID	UUIDType	1	1	Unique ID of the PDPML file.
title	xsd:string	1	1	Title of the PDPML file.
version	xsd:positiveInteger	1	1	Version of the PDPML file.
release	xsd:date	1	1	Relase date of the PDPML file.

Example:

<info>
  <pdpmlID>0eb03d7c-cd2a-4198-bb0f-49fa43f629bd</pdpmlID>
  <title>File of the procedures for data processing to obtain cell division dynamics</title>
  <version>1</version>
  <release>2013-06-11</release>
</info>

Notes:

<summary>

Definition:

Summary of the data described in the PDPML file.

Type:

Summary

Subelements:

Subelement Name	Data Type	min	max	Definition
description	xsd:string	1	1	Detailed explaination of the procedures.
contributors	xsd:string	1	1	Contributors who designed the procedures.

Example:

<summary>
  <description>Method for obtaining cell division dynamics</description>
  <contributors>Koji Kyoda, Shugo Hamahashi, Mitsuru Urai, and Shuichi Onami</contributors>
</summary>

Notes:

<contact>

Definition:

Contact information for the PDPML file.

Type:

Contact

Subelements:

Subelement Name	Data Type	min	max	Definition
name	xsd:string	1	1	Name of the corresponding author of the PDPML 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 the laboratory of the corresponding author.
organization	xsd:string	1	1	Organization, with which the corresponding author is affiliated.
department	xsd:string	0	1	Department of the organization.
laboratory	xsd:string	0	1	Name of the laboratory.
address	xsd:string	0	1	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:

<procedure>

Definition:

Procedure for data processing described in the PDPML file.

Type:

Procedure

Subelements:

Subelement Name	Data Type	min	max	Definition
description	xsd:string	0	1	Details of the procedure for data processing.
step	Step	1	unlimited	Each step in the procedure.

Example:

<procedure>
  <description>We first automatically detected nuclear regions (step order=1).
		We next manually corrected some errors (step order=2).
		Lastly, we identified the trajectory of nuclear division dynamics.</description>
  <step name="automatic detection" order="1">
    ...
  </step>
  <step name="manual error correction" order="2">
    ...
  </step>
  <step name="tracking of nuclear regions" order="3">
    ...
  </step>
</procedure>

Notes:

<step>

Definition:

Each sep of the procedure.

Type:

Step

Attributes:

Attribute Name	Data Type	Use	Definition
name	xsd:string	requied	The name of the step.
order	xsd:positiveInteger	optional	The order of the step.

Subelements:

Subelement Name	Data Type	min	max	Definition
annotation	xsd:string	0	1	Details of each step.
program	Program	1	1	Program used in the step.

Example:

<step name="automatic detection" order="1">
  <annotation>
    automatic detection of nuclear regions
  </annotation>
  <program>
    ...
  </program>
</step>

Notes:

<program>

Definition:

Program used in the step.

Type:

Program

Subelements:

Subelement Name	Data Type	min	max	Definition
name	xsd:string	1	1	The name of the program.
version	xsd:string	0	1	The version of the program.
url	xsd:anyURI	0	1	A URL to download site of the program.
description	xsd:string	0	1	Details of configuration and the parameters used in the program.

Example:

<program>
  <name>nuclear_detection</name>
  <url>http://so.qbic.riken.jp/nuclear_detection/</url>
  <description>Use of nuclear_detection.tar.bz2 with a little modification. 
  list of parameters, window_size: 13x13; binary_threhold: 145; snakes_parameters: 0.9, 0.9, 0.9</description>
</program>

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:

SSBD:database