amia 2013: how can bio-ontologies support clinical and translational science?

3/19/13 1Oregon Health & Science

University

Leveraging ontologies for research reproducibility, resource sharing,

and researcher networking

Carlo Torniai and Melissa HaendelOntology Development Group

Oregon Health & Science University


University

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


University

Supporting the translational lifecycle

Research resources

Clinical Research

Publish papers

Registries and Databases

Clinical Trials

Bench experiments

SharedKnowledge

Research resources

Clinical Research

Bench experiments


University

eagle-i: inventories “invisible” resources Research generates many resources that are rarely shared or published:

Ontology-system for collecting and querying research resources

eagle-i.net


University

eagle-i: ontology driven application


University

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


University

What is expertise?


University

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


University

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


University

CTSAConnect

eagle-i is an ontology-driven application . . . for collecting and searching research resources.

VIVO is an ontology-driven application . . . for collecting anddisplaying 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

eagle-iResources

VIVO

People

Coordinationeagle-i

VIVO

Inte

grat

ed

Framework

Semantic

Clinical activities


University

Ontologies refactoring

eagle-iResearch resources

VIVOPerson profiling

ShareCenterDiscussions, requests,

share documents

ISF

Contact OrganizationsAffiliations

Services EventsClinical

ExpertiseReagents

OrganismsCredentials

Step 1Aggregate

Clinical Data

Step 2Compute Expertise

Step 4Publish Linked

Data

Step 3Map Data to Ontologies

Provider ID ICD Code Value Code Count

Unique Patient Count Code Label

1234567 552.00 1 1

Unilateral or unspecified femoral hernia with

obstruction (ICD9CM 552.00)

1234567 553.02 8 6

Bilateral femoral hernia without mention of

obstruction or gangrene (ICD9CM 553.02)

1234567 555.1 4 1 Regional enteritis of large intestine (ICD9CM 555.1)

1234568 745.12 10 5Corrected transposition of

great vessels (ICD9CM 745.12)

Clinical Expertise Generation

1 2 4

3

Come to my talk tomorrow at 11.30Electronic Health Record Data Mining


University

Putting it all together

No “biological” relationships between Stanley and Kelsey


University

Our dream scenario

Researchers are connected based on relationships between resources, publications, projects, pathways, phenotypes, etc.


University

Monarch Initiative

Enabling phenotype-based knowledge discovery tools

www.monarchininitiative.orgCome see our poster this Afternoon. N. 51

http://www.monarchininitiative.org/


University

Translational cross-institutional search

Autoimmune Lymphoproliferative SyndromeB6-H2g7

Mus musculus

CTSA1

K. Hattori P. KurreEvaluation of Dermal Myelinated Fibers in Patients with Diabetic Polyneuropathy

Figure form Keggwww.genome.jp/kegg-bin/show_pathway?map04940

FAS

Type I diabetes mellitus reference Pathway

diabetes

A. Peltier


University

Resources

CTSAconnecthttp://ctsaconnect.org

eagle-ihttp://eagle-i.net

Monarch Initiativehttp://monarchinitiative.org

Support : NCATS through Booz Allen HamiltonCTSA 10-001: 100928SB23

Support : NCRR / NCATS through Booz-Allen Hamilton #U24 RR 029825

Support : NIH Office of the Director 1R24OD011883-01

amia 2013: how can bio-ontologies support clinical and translational science?

Technology

map04940oregon health

querying research resources

computable expertise

ontologydriven application

clinical protocols

relevant resources

expertise innovation

leveraging ontologies