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
Ontologies provide links, or “context” for information
Nice automobile
is_a
Operating system
is_a
Fast mammal
is_a
named_after
named_after
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
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.
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