Data Flows Pending Receipt RDF

From BiomedGT

1 Section 1: RDF General
2 Section 2: RDF Header
3 Section 3: Ontology header
4 Section 4: Workflow packages
- 4.1 First workflow package
- 4.2 Second Workflow Package
5 Section 5: Workflow Components

Section 1: RDF General

There are several mappings that need to be recognized to correctly parse the RDF:

3A - 3A represents a colon (:) in the RDF. As an example Category-3AWorkFlow_Pending_Receipt represents the entry Category:WorkFlow_Pending_Receipt.
28 and 29 - represents an open paren '(' and close paren ')' respectively. Needs to be accounted for.
&xxx; - represents an expanded entity. Look in the Header for its replacement. As an example, "<nowiki>&wikiurl;Category:WorkFlow_Pending_Receipt" expands to http://biomedgt.org/index.php?title=Category:WorkFlow_Pending_Receipt. Note that RDF parsers will do this automatically for you.

Section 2: RDF Header

The RDF header contains identifying information and links local names to namespaces.

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE rdf:RDF[
	<!ENTITY rdf 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'>
	<!ENTITY rdfs 'http://www.w3.org/2000/01/rdf-schema#'>
	<!ENTITY owl 'http://www.w3.org/2002/07/owl#'>
	<!ENTITY smw 'http://smw.ontoware.org/2005/smw#'>
	<!ENTITY smwdt 'http://smw.ontoware.org/2005/smw-datatype#'>
	<!ENTITY wiki 'http://biomedgt.org/index.php?title=Special:URIResolver/'>
	<!ENTITY property 'http://biomedgt.org/index.php?title=Special:URIResolver/Property-3A'>
	<!ENTITY wikiurl 'http://biomedgt.org/index.php?title='>
]>

<rdf:RDF
	xmlns:rdf="&rdf;"
	xmlns:rdfs="&rdfs;"
	xmlns:owl ="&owl;"
	xmlns:smw="&smw;"
	xmlns:wiki="&wiki;"
	xmlns:property="&property;">

NOTE: Some of the namespace prefixes are missing the octothorpe

Section 3: Ontology header

The ontology header provides the date and time that the information was retrieved (smw:exportDate) and identifies the fact that this node is about the Category:WorkFlow_Pending_Receipt (rdf:about). It also gives the URL that the information was retrieved from (rdf:isDefinedBy).

<!-- Ontology header -->
   <owl:Ontology rdf:about="">
      <smw:exportDate rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2007-10-15T14:09:40-06:00
</smw:exportDate>
   </owl:Ontology>
   <!-- exported page data -->
   <owl:Class rdf:about="&wiki;Category-3AWorkFlow_Pending_Receipt">
      <rdfs:label>WorkFlow Pending Receipt</rdfs:label>
      <smw:hasArticle rdf:resource="&wikiurl;Category:WorkFlow_Pending_Receipt"/>
      <rdfs:isDefinedBy rdf:resource="&wikiurl;Special:ExportRDF/Category:WorkFlow_Pending_Receipt"/>
   </owl:Class>

Section 4: Workflow packages

This section contains an entry for each workflow package that is ready to be processed in this category. Each workflow package begins with smw:Thing rdf:about="(package name)" and can be identified in RDF as it is an individual of rdf:type Category-3AWorkFlow_Package and rdf:type Category-3AWorkFlow_Pending_Receipt.

Each workflow package includes the name smw:hasArticle, the various bits of workflow metadata property:WorkFlow_Submission_Date, property:WorkFlow_Priority, property:WorkFlow_Submitter etc.

Each package then lists all of the structured proposals property:WorkFlow_Component rdf:resource=&wiki;Proposal-3A(name), unstructured proposals property:WorkFlow_Component rdf:resource=&wiki;Proposal_talk-3A(name), and ancillary discussion (any other property:WorkFlow_Component

First workflow package

<smw:Thing rdf:about="&wiki;WorkFlow-3AFrank_Hartels_Change_Request">
	<rdfs:label>WorkFlow:Frank Hartels Change Request</rdfs:label>
	<smw:hasArticle rdf:resource="&wikiurl;WorkFlow:Frank_Hartels_Change_Request"/>
	<rdfs:isDefinedBy rdf:resource="&wikiurl;Special:ExportRDF/WorkFlow:Frank_Hartels_Change_Request"/>
	<rdf:type rdf:resource="&wiki;Category-3AWorkFlow_Package"/>
	<rdf:type rdf:resource="&wiki;Category-3AWorkFlow_Pending_Receipt"/>
	<property:WorkFlow_Submission_Date 
	   rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2007-10-05T00:00:00</property:WorkFlow_Submission_Date>
	<property:WorkFlow_Submission_Priority 
	   rdf:datatype="http://www.w3.org/2001/XMLSchema#string">regular</property:WorkFlow_Submission_Priority>
	<property:WorkFlow_Submission_Required_By 
	   rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2007-11-04T00:00:00</property:WorkFlow_Submission_Required_By>
	<property:WorkFlow_Submission_Comment 
	    rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This is the package that the sandbox folks need to begin to play
	</property:WorkFlow_Submission_Comment>
	<property:WorkFlow_Component 
	    rdf:resource="&wiki;Proposal_talk-3ANCI_Apoptosis_Inhibitor_Gene-28C20347-29_by_Hsolbrig_at_20071011223308"/>
	<property:WorkFlow_Component
	    rdf:resource="&wiki;Proposal-3ANCI_BCAS1_Gene-28C20771-29_by_Hsolbrig_at_20071012004950"/>
	<property:WorkFlow_Component 
	    rdf:resource="&wiki;Category_talk-3ANCI_BCAS1_Gene-28C20771-29"/>
	<property:WorkFlow_Submitter 
	    rdf:resource="&wiki;User-3AHsolbrig"/>
</smw:Thing>

Second Workflow Package

<smw:Thing 
   rdf:about="http://biomedgt.org/index.php?title=Special:URIResolver/WorkFlow-3AAnother_Change_Request">
   <rdfs:label>WorkFlow:Another Change Request</rdfs:label>
   <smw:hasArticle rdf:resource="http://biomedgt.org/index.php?title=WorkFlow:Another_Change_Request"/>
   <rdfs:isDefinedBy 
       rdf:resource="http://biomedgt.org/index.php?title=Special:ExportRDF/WorkFlow:Another_Change_Request"/>
	<rdf:type 
	   rdf:resource="http://biomedgt.org/index.php?title=Special:URIResolver/Category-3AWorkFlow_Package"/>
	<rdf:type 
	   rdf:resource="http://biomedgt.org/index.php?title=Special:URIResolver/Category-3AWorkFlow_Pending_Receipt"/>
	<property:WorkFlow_Submission_Date 
	   rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2007-10-05T00:00:00</property:WorkFlow_Submission_Date>
	<property:WorkFlow_Submission_Priority 
	   rdf:datatype="http://www.w3.org/2001/XMLSchema#string">regular</property:WorkFlow_Submission_Priority>
	<property:WorkFlow_Submission_Required_By 
	   rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2007-11-04T00:00:00</property:WorkFlow_Submission_Required_By>
	<property:WorkFlow_Submission_Comment 
	   rdf:datatype="http://www.w3.org/2001/XMLSchema#string">
			This is the package that the sandbox folks need to begin to play
	</property:WorkFlow_Submission_Comment>
	<property:WorkFlow_Component 
	   rdf:resource="http://biomedgt.org/index.php?title=Special:URIResolver/Proposal-3ANCI_Trefoil_Family-28C21231-29_by_Hsolbrig_at_20071011222805"/>
	<property:WorkFlow_Component 
	   rdf:resource="http://biomedgt.org/index.php?title=Special:URIResolver/Proposal-3ANCI_Trefoil_Family-28C21231-29_by_Hsolbrig_at_20071011223603"/>
	<property:WorkFlow_Component 
	   rdf:resource="http://biomedgt.org/index.php?title=Special:URIResolver/Proposal-3ANCI_Trefoil_Family-28C21231-29_by_Hsolbrig_at_20071011230834"/>
	<property:WorkFlow_Component 
	   rdf:resource="http://biomedgt.org/index.php?title=Special:URIResolver/Proposal-3ANCI_Blue_Gene-28TC00001-29_by_Hsolbrig_at_00710120123"/>
	<property:WorkFlow_Submitter 
	   rdf:resource="http://biomedgt.org/index.php?title=Special:URIResolver/User-3AHsolbrig"/>
</smw:Thing>

Section 5: Workflow Components

The location of all of the resources in each workflow package workflow component can be found in the auxiliary definitions section. These are identified either as smw:Thing or owl:Class depending on whether the entity is structured or unstructured (technically, this distinction is between classes and individuals, but we have overloaded it for this purpose).

The rdf:about defines what the resource references. As an example, <smw:Thing rdf:about="&wiki;Proposal_talk-3ANCI_Apoptosis_Inhibitor_Gene-28C20347-29_by_Hsolbrig_at_20071011223308"> references an unstructured proposal referenced in the Frank_Hartels_Change_Request package and the <owl:Class rdf:about="&wiki;Proposal-3ANCI_Blue_Gene-28TC00001-29_by_Hsolbrig_at_00710120123"> references a structured proposal referenced in Another_Change_Request

<owl:Class rdf:about="&wiki;Proposal-3ANCI_Blue_Gene-28TC00001-29_by_Hsolbrig_at_00710120123">
   <rdfs:label>NCI Blue Gene(TC00001) by Hsolbrig at 00710120123</rdfs:label>
   <smw:hasArticle rdf:resource="&wikiurl;Proposal:NCI_Blue_Gene(TC00001)_by_Hsolbrig_at_00710120123"/>
   <rdfs:isDefinedBy
       rdf:resource="&wikiurl;Special:ExportRDF/Proposal:NCI_Blue_Gene(TC00001)_by_Hsolbrig_at_00710120123"/>
</owl:Class>
...
<smw:Thing rdf:about="&wiki;User-3AHsolbrig">
	<rdfs:label>User:Hsolbrig</rdfs:label>
	<smw:hasArticle rdf:resource="&wikiurl;User:Hsolbrig"/>
	<rdfs:isDefinedBy rdf:resource="&wikiurl;Special:ExportRDF/User:Hsolbrig"/>
</smw:Thing>
<smw:Thing rdf:about="&wiki;Proposal_talk-3ANCI_Apoptosis_Inhibitor_Gene-28C20347-29_by_Hsolbrig_at_20071011223308">
	<rdfs:label>Proposal_talk:NCI Apoptosis Inhibitor Gene(C20347) by Hsolbrig at 20071011223308</rdfs:label>
	<smw:hasArticle 
	   rdf:resource="&wikiurl;Proposal_talk:NCI_Apoptosis_Inhibitor_Gene(C20347)_by_Hsolbrig_at_20071011223308"/>
	<rdfs:isDefinedBy 
	   rdf:resource="&wikiurl;Special:ExportRDF/Proposal_talk:NCI_Apoptosis_Inhibitor_Gene(C20347)_by_Hsolbrig_at_20071011223308"/>
</smw:Thing>
<smw:Thing rdf:about="&wiki;Category_talk-3ANCI_BCAS1_Gene-28C20771-29">
	<rdfs:label>Category_talk:NCI BCAS1 Gene(C20771)</rdfs:label>
	<smw:hasArticle rdf:resource="&wikiurl;Category_talk:NCI_BCAS1_Gene(C20771)"/>
	<rdfs:isDefinedBy rdf:resource="&wikiurl;Special:ExportRDF/Category_talk:NCI_BCAS1_Gene(C20771)"/>
</smw:Thing>

<owl:Class rdf:about="&wiki;Proposal-3ANCI_BCAS1_Gene-28C20771-29_by_Hsolbrig_at_20071012004950">
	<rdfs:label>NCI BCAS1 Gene(C20771) by Hsolbrig at 20071012004950</rdfs:label>
	<smw:hasArticle rdf:resource="&wikiurl;Proposal:NCI_BCAS1_Gene(C20771)_by_Hsolbrig_at_20071012004950"/>
	<rdfs:isDefinedBy 
	     rdf:resource="&wikiurl;Special:ExportRDF/Proposal:NCI_BCAS1_Gene(C20771)_by_Hsolbrig_at_20071012004950"/>
</owl:Class>

NOTE: When pulling the URLs additional information from previous pages may appear but can be ignored

Retrieved from "http://biomedgt.nci.nih.gov/wiki/index.php/Data_Flows_Pending_Receipt_RDF"

Data Flows Pending Receipt RDF

From BiomedGT

Contents

Section 1: RDF General

Section 2: RDF Header

Section 3: Ontology header

Section 4: Workflow packages

First workflow package

Second Workflow Package

Section 5: Workflow Components

Views

Personal tools

Search

Navigation

terminologies

content search

workflow

Toolbox