View
615
Download
1
Category
Preview:
DESCRIPTION
Describes strategies for submission of clinical trial data to the NIAID Immunology Database and Analysis Portal in order to advance discoverability, comparability and analysis
Citation preview
1
ImmPort: Strategies to Enhance Discoverability of Clinical Trial Data
Barry Smithhttp://ontology.buffalo.edu/smith
https://immport.niaid.nih.gov
2
pipeline
3
BISC pipeline
PIs, hospitals, biostatisticians …
4
BISC pipeline
PIs, hospitals, biostatisticians …
NorthropGrumman
5
BISC pipeline
PIs, hospitals, biostatisticians …
NorthropGrumman
Max & Mindy
BISC pipeline
perform study &collect data
analyze data(SAS …)
submit data toImmPort
process & de-identify, data in ImmPort
discover, aggregate, analyze,data inImmPort
pipeline is siloed by heterogeneous terminologies and standards
perform study &collect data
analyze data(SAS …)
submit data toImmPort
process & de-identify, data in ImmPort
discover, aggregate, analyze,data inImmPort
siloes break discovery, comparability and analysis
perform study &collect data
analyze data(SAS …)
submit data toImmPort
process & de-identify, data in ImmPort
discover, compare, analyze,data inImmPort
9
10
76 results;0 results for ImmPort
11
how break down terminology-created silo walls?
perform study &collect data
analyze data(SAS …)
submit data toImmPort
process & de-identify, data in ImmPort
discover, aggregate, analyze,data inImmPort
standards and softwareCDISC, SDTM
EHRs, ELNs, CTMSs
standards and softwareImmPort templates
MYSQL …
12
Immune-Related Ontologies (examples)
Protein Ontology (PRO)Gene Ontology (GO) Cell Ontology (CL)Immune Epitope Ontology Beta Cell Genomics Ontology Infectious Disease Ontology
Allergy OntologyAntibody OntologyCDISC2RDFCL+ (for CyTOF)Cytokine OntologyImmunology OntologyVDJ Ontology
http://ncorwiki.buffalo.edu/index.php/Immunology_Ontologies
these ontologies are already being used by Max and Mindy
perform study &compile data
analyze data(SAS …)
submit data toImmPort
process & de-identify, data in ImmPort
discover, aggregate, analyze,data inImmPort
standards and softwareCDISC, SDTM
EHRs, ELNs, CTMSs
standards and softwareImmPort templates
html, SQL ..immune-related
ontologiesGO, PRO, CL,
…
14
pipeline
perform study &compile data
analyze data(SAS …)
submit data toImmPort
process & de-identify, data in ImmPort
discover, aggregate, analyze,data inImmPort
standards and softwareImmPort templates
html, SQL ..immune-related ontologiesGO, PRO, CL, … CDISC2RTF
standards and softwareCDISC, SDTM
EHRs, ELNs, CTMSs
15
strategies
• FDA-CDISC-CDISC2RDF• LabKey / Electronic Lab Notebook strategy• training submitters and users
16
Rho strategy
PIs, hospitals, contract research organizations (CROs):Rho Federal Systems Division
NorthropGrumman
Max, Mindy
17
ImmPort: Training and Strategy MeetingRho Federal Systems Division, Chapel Hill, Oct. 9-10
– to provide assistance to actual and potential submitters of data to ImmPort– to enable interaction between submitters and those charged with managing ImmPort– to improve discoverability and usability of data from ImmPortSpeakers
Ashley Xia (NIAID)Barry Smith (Buffalo / BISC)Jeff Wiser (NG / BISC)David Iklé, John Lim, Karen Kesler (Rho)
http://ncorwiki.buffalo.edu/index.php/ImmPort
18
one idea: an ontologically informed CTMS incrementally removing silos through the entire ImmPort pipeline
PIs, hospitals, CROs:Rho Federal Systems Division
NorthropGrumman
Max, Mindy
19
not only would this make life easier for all the participants listed here:
PIs, hospitals, CROs:Rho Federal Systems Division
NorthropGrumman
Max, Mindy, Atul …
20
it would also make ImmPort data discoverable by external researchers
PIs, hospitals, CROs
NorthropGrumman
de-identified patient data
Recommended