1. Leveraging ontologies for research
reproducibility, resource sharing,
and researcher networking
Carlo Torniai and Melissa Haendel
Ontology Development Group
Oregon Health & Science University
Oregon Health & Science
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2. Topics
 Research reproducibility
 Ontology driven application for research resource
identification and sharing
 Team science
 Shared and computable expertise in support of
research profiling and building translational teams
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3. Supporting the translational lifecycle
Bench
experiments
Research
Clinical Trials resources
Shared
Knowledge
Clinical Publish
Research papers
Registries
and
Databases
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3/19/2013 3
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4. eagle-i: inventories “invisible” resources
Ontology-system for
collecting and querying
research resources
eagle-i.net net w o r k
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5. eagle-i: ontology driven application
Oregon Health & Science
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6. eagle-i: ontology driven application
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7. Leveraging ontologies for resource
representation
 Enables classification and unique reference of
resources in the literature and in clinical protocols
 Enables linkage with other standard vocabularies
and ontologies (MeSH, Gene Ontology, ICD)
 Facilitates semantic connections between
resources, people, and clinical research
 Standard representation of research
resources enables inference of expertise
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8. What is expertise?
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9. Leveraging expertise
 Innovation happens between publications
 Team science has a higher impact
 Clinical expertise isn’t well represented by
publications or grants
We need a system that can
connect basic and clinical
researchers
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10. CTSAConnect: using ontologies to
connect clinical and basic researchers
Goals:
– Identify potential collaborators, relevant resources, and
expertise across disciplines
– Assemble translational teams of scientists to address
specific research questions
Approach:
Create a semantic system to enable:
– Broad and computable representation of translational
expertise
– publication of expertise as Linked Data (LD) for use in
other applications
Oregon Health & Science
3/19/2013 10
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11. CTSAConnect
Semantic People
VIVO
VIVO
Coordination
Clinical
eagle-i eagle-i
activities
Resources
 eagle-i is an ontology-driven application . . . for collecting and
searching research resources.
 VIVO is an ontology-driven application . . . for collecting and
displaying information about people.
 Both publish Linked Data. Neither addresses clinical expertise.
 CTSAconnect will produce a single Integrated Semantic
Framework, a modular collection of ontologies — that also
includes clinical expertise
Oregon Health & Science
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12. Ontologies refactoring
ShareCenter
VIVO Discussions, requests, eagle-i
Person profiling share documents Research resources
ISF
Organizations Clinical Reagents
Contact Services Events Credentials
Affiliations Expertise Organisms
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13. Clinical Expertise Generation
Step 1 Step 2 Step 3 Step 4
Aggregate Compute Map Data to Publish Linked
Clinical Data Expertise Ontologies Data
Unique
3
Patient
Provider ID ICD Code Value Code Count Count Code Label
Unilateral or unspecified
femoral hernia with
1234567 552.00 1 1
obstruction (ICD9CM
552.00)
Bilateral femoral hernia
without mention of
1234567 553.02 8 6
obstruction or gangrene
(ICD9CM 553.02)
Regional enteritis of large
1234567 555.1 4 1
intestine (ICD9CM 555.1)
Corrected transposition of
1234568 745.12 10 5 great vessels (ICD9CM
745.12)
1
2 4
Come to my talk
tomorrow at 11.30
Electronic Health Record Data Mining

14. Putting it all together
No “biological” relationships between Stanley and Kelsey
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15. Our dream scenario
Researchers are connected based on relationships between resources, publications,
projects, pathways, phenotypes, etc.
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16. Monarch Initiative
www.monarchininitiative.org
Come see our poster this
Afternoon. N. 51
Enabling phenotype-based knowledge discovery tools
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17. Translational cross-institutional search
Type I diabetes
mellitus reference
Pathway
FAS
diabetes
Autoimmune
B6-H2g7 Lymphoproliferative Syndrome
Mus musculus
Evaluation of Dermal Myelinated Fibers
K. Hattori in Patients with Diabetic Polyneuropathy P. Kurre
CTSA1 A. Peltier
Figure form Kegg
www.genome.jp/kegg-bin/show_pathway?map04940
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18. Resources
eagle-i Support : NCRR / NCATS through
http://eagle-i.net Booz-Allen Hamilton
#U24 RR 029825
CTSAconnect Support : NCATS through Booz Allen
Hamilton
http://ctsaconnect.org CTSA 10-001: 100928SB23
Monarch Initiative Support : NIH Office of the Director
1R24OD011883-01
http://monarchinitiative.org
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