The eagle-i Network: enabling research resource discoveryMelissa Haendel

Oregon Health & Science University Library

03.15.13

LIBRARY

Outline

History of eagle-i Network

Basic features & functionality

Relationship to research lifecycle & community

Future collaborations

Dreams of a bench scientist

Better access to resources and expertise

More reproducible science

Credit where credit is due

Visible and interoperable data

Efficient science.

All of these dreams are aided by semantic technologies:

Uniform resource Identifiers

Ontologies (enabling common reference, differencing)

Linked Data

… and applications that use them

Helping researchers find invisible resourcesReagents, instruments, services, model and non-model organisms, protocols, biospecimens, human studies, software and research opportunities

Adding meaningful semantic relationships between resources

Making this data available using ontology-driven approach to research resource annotation and discovery

Reducing time-consuming and expensive duplication of resources

eagle-i Network

eagle-i Network

The problem

A

B

?

xFailed experiment

Polyclonal anti-TGFβ RISanta Cruz Biotechnology

A

Identifying resources

eagle-i: making research resources more visible

B

Successful experiment!

The problem

Information is context dependent

Ontologies provide links, or “context” for information

Nice automobile

is_a

Operating system

is_a

Fast mammal

is_a

named_after

named_after

SWEET: an ontology-driven data collection tool

www.eagle-i.net

How are resources shared in eagle-i?

eagle-i data with a new user-friendly user interface

Enables quality search of OHSU cores in Google

Enables an OHSU cross-core search for instruments and

services

Developed by UCSF: http://ctsiatucsf.github.com/plumage/

OHSU Core Search = leveraging eagle-i

www.ohsu.edu/research/coresearch/

ISF

ISF can be used by other applications

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.

CTSAconnect will produce a single Integrated Semantic Framework, a modular collection of ontologies

eagle-iResources

VIVO

Peopleeagle-i

VIVO

Inte

grat

edFram

ework

Semantic

Clinical activities

Merging VIVO and eagle-i semantic infrastructure

eagle-i

Identify potential collaborators, relevant

resources, and expertise across scientific disciplines

Assemble teams of scientists to address specific

research questions

Evaluate scientific outcomes

Oregon Health & Science University

Cornell University

University of Florida

Stony Brook University

University at Buffalo

Harvard University

CTSAconnect | Reveal Connections. Realize

Potential.

Antibody Registry and eagle-i use a shared ontology

Publishing unique identifiers can aid scientific reproducibility

Antibodies are not very uniquely identifiable in 57 publications

Perc

ent 0%

20%40%60%80%

100%

n=207

n=8

Working with publishers to increase reporting guidelines

Preserve

PublishResearch

CTSAconnect

Reveal Connections. Realize Potential.

Scholarly scientific research cycle

We can all work together to make research resources more visible and research more efficient.

Successful experiment!

Resources

Ontology Development Grouphttp://bit.ly/ohsuontdevgroup

CTSAconnect project ctsaconnect.org

CTSAconnect ontology

http://code.google.com/p/connect-isf/

VIVO integrated searchvivosearch.org

eagle-i federated searchhttp://www.eagle-i.net

eagle-i ontologyhttp://code.google.com/p/eagle-i/

eagle-i software code

https://open.med.harvard.edu/display/eaglei/Software

OHSU Cores Search www.ohsu.edu/research/coresearch

OHSU Library Ontology Development Group

Melissa Haendel – Co-Lead, Neuroscientist/Ontologist

Carlo Torniai – Co-Lead, Computer Scientist/Ontologist

Nicole Vasilevsky – Project Manager, Cell Biologist/

Ontologist

Scott Hoffmann – Engineer/Ontologist

Erik Segerdell – Biologist/Ontologist

Matthew Brush – Molecular biologist/Ontologist

Shahim Essaid – MD/Bioinformatist/Ontologist

CTSAconnect

eagle-i

OHSUMelissa HaendelCarlo TorniaiNicole VasilevskyChris KelleherShahim Essaid

Cornell UniversityDean KrafftJon Corson-RikertBrian Lowe

University of FloridaMike ConlonChris BarnesNicholas Rejack

OHSUMelissa HaendelCarlo TorniaiNicole VasilevskyScott HoffmannMatthew BrushJackie Wirz

Stony Brook UniversityMoises EisenbergErich BremerJanos Hajagos

Harvard UniversityDaniela BourgesSophia Cheng

University at BuffaloBarry SmithDagobert Soergel

ZaloniWill CorbettRanjit DasBen Sharma

Harvard UniversityLee NadlerDoug MacFaddenMarc CirielloRichard PearseDaniela BourgesTenille Johnson

Vanderbilt UniversityGordon BernardLisa Robins

PennGarret Fitzgerald Faith Coldren

Acknowledgements