PDPML version 0.06 Specification

<pdpml>

Definition: This is the root element for the PDPML schema.
Type: pdpmlDocument
Attributes:
Attribute NameData TypeUseDefinition
versionxsd:positiveIntegerrequiedThe version of this PDPML document.
Subelements:
Subelement NameData TypeminmaxDefinition
infoInfo11Information about the PDPML file itself.
summarySummary11Summary of the procedures described in the PDPML file.
contactContact11Contact information for the PDPML file.
procedureProcedure11Procedure 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 NameData TypeminmaxDefinition
pdpmlIDUUIDType11Unique ID of the PDPML file.
titlexsd:string11Title of the PDPML file.
versionxsd:positiveInteger11Version of the PDPML file.
releasexsd:date11Relase 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 NameData TypeminmaxDefinition
descriptionxsd:string11Detailed explaination of the procedures.
contributorsxsd:string11Contributors 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 NameData TypeminmaxDefinition
namexsd:string11Name of the corresponding author of the PDPML file.
E-mailxsd:string11E-mail address of the corresponding author.
phonexsd:string01Phone number of the corresponding author.
URLxsd:anyURI01A URL link to the laboratory of the corresponding author.
organizationxsd:string11Organization, with which the corresponding author is affiliated.
departmentxsd:string01Department of the organization.
laboratoryxsd:string01Name of the laboratory.
addressxsd:string01Address 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 NameData TypeminmaxDefinition
descriptionxsd:string01Details of the procedure for data processing.
stepStep1unlimitedEach 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 NameData TypeUseDefinition
namexsd:stringrequiedThe name of the step.
orderxsd:positiveIntegeroptionalThe order of the step.
Subelements:
Subelement NameData TypeminmaxDefinition
annotationxsd:string01Details of each step.
programProgram11Program 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 NameData TypeminmaxDefinition
namexsd:string11The name of the program.
versionxsd:string01The version of the program.
urlxsd:anyURI01A URL to download site of the program.
descriptionxsd:string01Details 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: