Idea: convert SDS-XML to RDF/XML

カテゴリー: CDISCラボ

An experimental idea to convert SDS-XML to RDF/XML.

Summary:
Typed SDS-XML may be interpreted as RDF/XML file by small changes. This means that 2 dimension data is transferred into network database. As the clinical data is often "sphere" rather than spreadsheet, this kind of exchange may be a benefit. This is just imagination. But we hope this inspires fellows/geeks in healthcare IT.

Note: This is not perfect conversion, but just a try to see what happens.

Step 1:
See SDS-XML. Here, we select Typed SDS-XML. It looks like as follows. Delete some attributes to symplify. Deleted parts are shown by strikethorugh.

<?xml version="1.0" encoding="UTF-8"?>
<ODM
 xmlns="http://www.cdisc.org/ns/odm/v1.3"
 xmlns:xlink="http://www.w3.org/1999/xlink"
 xmlns:sds="http://www.cdisc.org/ns/sds/v1.0"
 FileType="Snapshot"
 ODMVersion="1.3.2"
 sds:SDSVersion="1.0"
 FileOID="www.cdisc.org.Studycdisc01-Define-XML_2.0.0(IG.CM)"
 PriorFileOID="www.cdisc.org.Studycdisc01-Define-XML_2.0.0(IG.SV)"
 Originator="CDISC SDS-XML Team"
 CreationDateTime="2013-11-09T22:14:54">
 <ClinicalData
  StudyOID="cdisc01"
  MetaDataVersionOID="MDV.CDISC01.SDTMIG.3.1.2.SDTM.1.2">
  <ItemGroupData ItemGroupOID="IG.CM" sds:ItemGroupDataSeq="1">
   <ItemDataString ItemOID="IT.STUDYID">CDISC01</ItemDataString>
   <ItemDataString ItemOID="IT.CM.DOMAIN">CM</ItemDataString>
   <ItemDataString ItemOID="IT.USUBJID">CDISC01.100008</ItemDataString>
   <ItemDataInteger ItemOID="IT.CM.CMSEQ">1</ItemDataInteger>
   <ItemDataString ItemOID="IT.CM.CMTRT">PROCARDIA XL</ItemDataString>
  </ItemGroupData>
  <ItemGroupData ItemGroupOID="IG.CM" sds:ItemGroupDataSeq="2">
   <ItemDataString ItemOID="IT.STUDYID">CDISC01</ItemDataString>
   <ItemDataString ItemOID="IT.CM.DOMAIN">CM</ItemDataString>
   <ItemDataString ItemOID="IT.USUBJID">CDISC01.100008</ItemDataString>
   ...
  </ItemGroupData>
 </ClinicalData>
</ODM>

Step 2:
Insert <ex:has>. This is shown in red. it looks like as follows.

<?xml version="1.0" encoding="UTF-8"?>
<ODM>
 <ClinicalData StudyOID="cdisc01">
  <ex:has> 
  <ItemGroupData ItemGroupOID="IG.CM" sds:ItemGroupDataSeq="1">
   <ItemDataString ItemOID="IT.STUDYID">CDISC01</ItemDataString>
   <ItemDataString ItemOID="IT.CM.DOMAIN">CM</ItemDataString>
   <ItemDataString ItemOID="IT.USUBJID">CDISC01.100008</ItemDataString>
   <ItemDataInteger ItemOID="IT.CM.CMSEQ">1</ItemDataInteger>
   <ItemDataString ItemOID="IT.CM.CMTRT">PROCARDIA XL</ItemDataString>
  </ItemGroupData>
  </ex:has>  
  <ex:has> 
  <ItemGroupData ItemGroupOID="IG.CM" sds:ItemGroupDataSeq="2">
   <ItemDataString ItemOID="IT.STUDYID">CDISC01</ItemDataString>
   <ItemDataString ItemOID="IT.CM.DOMAIN">CM</ItemDataString>
   <ItemDataString ItemOID="IT.USUBJID">CDISC01.100008</ItemDataString>
   ...
  </ItemGroupData>
  </ex:has>  
 </ClinicalData>
</ODM>

Step 3:
Replace "ItemData*****" elements by "variable name in SDTM". Variable name can be retrieved from Define.XML based on ItemOID. Small changes are made at atrribute.

<?xml version="1.0" encoding="UTF-8"?>
<ODM>
 <ClinicalData rdf:about="cdisc01">
  <ex:has> 
  <ItemGroupData rdf:about="IG.CM1">
   <STUDYID>CDISC01</STUDYID>
   <DOMAIN>CM</DOMAIN>
   <USUBJID>CDISC01.100008</USUBJID>
   <CMSEQ>1</CMSEQ>
   <CMTRT>PROCARDIA XL</CMTRT>
  </ItemGroupData>
  </ex:has>  
  <ex:has> 
  <ItemGroupData rdf:about="IG.CM2">
   <STUDYID>CDISC01</STUDYID>
   <DOMAIN>CM</DOMAIN>
   <USUBJID>CDISC01.100008</USUBJID>
   ...
  </ItemGroupData>
  </ex:has>  
 </ClinicalData>
</ODM>

Step 4:
Interpret the XML above as RDF/XML. This is not validated RDF/XML. This is an experiment to draw RDF graph based on the modified SDS-XML. It generates RDF graph.

rdfgraph.jpg
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Jozef Aerts

URL | [ 編集 ] 2014/10/10(金) 12:42:21

There is currently a CDISC working group that is developing such graphs. As far as I know, they did not apply it on the clinical data itself, but only on the metadata. So this is an excellent idea.
The proposed transformation is easy to accomplish and I might give it a try this weekend (i.e. write a stylesheet).
With best regards,
Jozef











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