Presentation at the eScience Institute on eagle-i and identification of research resources. http://nnlm.gov/2013escience/

1. The eagle-i Network:
enabling research resource
discovery
Melissa Haendel
Oregon Health & Science University Library
03.15.13
LIBRARY

2. Outline
 History of eagle-i Network
 Basic features & functionality
 Relationship to research lifecycle & community
 Future collaborations

3. 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.

4. All of these dreams are aided by
semantic technologies:
 Uniform resource
Identifiers
 Ontologies (enabling
common reference,
differencing)
 Linked Data
 … and applications
that use them

5.  Helping researchers find invisible resources
Reagents, 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

6. eagle-i Network

7. The problem
A
B

8. ?
x
Failed experiment
Polyclonal anti-TGFβ RI
Santa Cruz Biotechnology
A
Identifying resources

9. eagle-i: making research resourcesmore visible
B
Successful
experiment!

10. The problem
Information is context dependent

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

12. SWEET: an ontology-driven data collectiontool

13. www.eagle-i.net
How are resources shared in eagle-i?

14. 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

15. www.ohsu.edu/research/coresearch/

16. ISF
net w o r k
ISF can be used by other applications

17.  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.
 CTSAconnect will produce a single Integrated Semantic
Framework, a modular collection of ontologies
eagle-i
Resources
VIVO
Peopleeagle-i
VIVO
Semantic
Clinical
activities
Merging VIVO and eagle-i semanticinfrastructure
eagle-i

18. 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.

19. Antibody Registry and eagle-i
use a shared ontology

20. Publishing unique identifiers can
aid scientific reproducibility
Antibodies are not very uniquely identifiable in 57 publications
Percent
0%
20%
40%
60%
80%
100%
Commercial antibody
identifiable
Non-commercial antibody
identifiable
n=207
n=8
Working with publishers to increase
reporting guidelines

21. PreservePublishResearch
CTSAconnect
Reveal Connections.
Realize Potential.
net w o r k
Scholarly scientific research cycle

22. We can all work together to make research
resourcesmore visibleand researchmore efficient.
Successful
experiment!
net w o r k

23. Resources
Ontology Development Group
http://bit.ly/ohsuontdevgroup
CTSAconnect project
ctsaconnect.org
CTSAconnect ontology
http://code.google.com/p/connect-isf/
VIVO integrated search
vivosearch.org
eagle-i federated search
http://www.eagle-i.net
eagle-i ontology
http://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

24. 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

25. CTSAconnect
eagle-i
OHSU
Melissa Haendel
Carlo Torniai
Nicole Vasilevsky
Chris Kelleher
Shahim Essaid
Cornell University
Dean Krafft
Jon Corson-Rikert
Brian Lowe
University of Florida
Mike Conlon
Chris Barnes
Nicholas Rejack
OHSU
Melissa Haendel
Carlo Torniai
Nicole Vasilevsky
Scott Hoffmann
Matthew Brush
Jackie Wirz
Stony Brook University
Moises Eisenberg
Erich Bremer
Janos Hajagos
Harvard University
Daniela Bourges
Sophia Cheng
University at Buffalo
Barry Smith
Dagobert Soergel
Zaloni
Will Corbett
Ranjit Das
Ben Sharma
Harvard University
Lee Nadler
Doug MacFadden
Marc Ciriello
Richard Pearse
Daniela Bourges
Tenille Johnson
Vanderbilt University
Gordon Bernard
Lisa Robins
Penn
Garret Fitzgerald
Faith Coldren
Acknowledgements