SDTM domains by query - is it possible?

Transcription

1 SDTM domains by query - is it possible? Johannes Ulander Standardisa8on and Harmonisa8on Specialist S-Cubed

2 Agenda What is data? Introduc8on to linked data and graphs Try some examples Where did my SDTM domain go? SDTM by Query Summary

3 What is data? 3

4 Introduc1on to graphs Node Site ID: 1 City: London Site Works at Inves8gator Name: Dr. X Property Rela)onship Triples 4

5 Introduc1on to graphs Node Site ID: 1 City: London Site Works at Inves8gator Name: Dr. X Property Node Property Value Site Site ID 1 Site City London Rela)onship Node Rela(on Node Inves8gator Works at Site Node Property Value Inves8gator Name Dr. X 5

6 Introduc1on to graphs Node Site ID: 1 City: London Site Works at Inves8gator Name: Dr. X Property Inves8gator Name: Dr. Who Site ID: 2 City: Leeds Site Works at Inves8gator Name: Dr. Y 6

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8 Race/Ethnicity MULTIPLE X + X Reported Ethnicity Ethnicity Name: Not Hispanic or La8no Subject Reported Race X X USUBJID: 1 Sex: Female Race Name: Asian Race Name: Black or African American 8

9 The graph can be queried Don t need to change the ques8on

10 The Graph is for storing informa1on = Visualiza8on is something different

11 TAUG Parkinson s Disease Diagnos8c Criteria Example CRF Medical History X X Graph representa8on 11

12 Medical History Significant pre-exis8ng condi8on Disease Name: Tinnitus USUBJID:S01 Subject First symptoms Date: Primary Diagnosis Date: Primary Diagnosis Date: Disease Name: Alzheimer s USUBJID:S02 Subject First symptoms Date: Significant pre-exis8ng condi8on 12

13 Where did my SDTM domain go?

14 Where did my SDTM domain go? MATCH (n) WHERE n.domain = MH AND n.usubjid = 1

15 Query Medical SDTM MH Domain MATCH (s:subject)-[]->(n), (s:subject)-[]-(study:study) WHERE s.usubjid = '1' AND n.domain = 'MH' RETURN study.name as STUDYID, s.usubjid as USUBJID, n.domain as DOMAIN, n.name as MHTERM, n.stdtc as MHSTDTC

16 SDTM domains are queries First exposure to study treatment EX Part of the query Not duplicated Not mapped DS DM

17 What about Analysis Data? EX DS DM

18 What about Analysis Data? Create average Systolic Blood Pressure MATCH (sbpnode:standardisedresult {name:"systolic Blood Pressure"})<-[]-(subjectNode:Subject {USUBJID:"1"}) CREATE (averagenode:average {name:"average SYSBP"}) WITH COLLECT(sbpNode) as sbpnodes, averagenode, AVG(sbpNode.STRESN) as theaveragevalue, subjectnode FOREACH (node in sbpnodes CREATE (node)-[source:sourcevalue]-(averagenode) ) SET averagenode.value = theaveragevalue CREATE (averagenode)<-[:derivedvalue]-(subjectnode) RETURN sbpnodes, averagenode, subjectnode

19 What about Analysis Data? EX Average SYSBP DS DM VS Averages ADVS

20 Add defini1on to query MATCH (sbpnode:standardisedresult {name:"systolic Blood Pressure"})<-[]-(subjectNode:Subject {USUBJID:"1"}) CREATE (averagenode:average {name:"average SYSBP"}) WITH COLLECT(sbpNode) as sbpnodes, averagenode, AVG(sbpNode.STRESN) as theaveragevalue, subjectnode FOREACH (node in sbpnodes CREATE (node)-[source:sourcevalue]-(averagenode) ) SET averagenode.value = theaveragevalue SET averagenode.value = theaveragevalue, averagenode.definition = " averagenode.method = "AVG() function" CREATE (averagenode)<-[:derivedvalue]-(subjectnode) RETURN sbpnodes, averagenode, subjectnode

21 The Galaxy of Clinical data meets the Universe EX DS DM VS Averages ADVS

22 Summary It is possible to create an SDTM domain by query Standardised structures Standardised queries In linked data there are no boundaries No mapping Linked data excels at handling complex informa1on Solves many of our current problems in rela1onal databases and standards management CDISC

23 Thank you for listening Johannes Ulander Standardisa8on and Harmonisa8on Specialist S-Cubed