eagle-i: Development and Expansion of a Scientific Resource Discovery Network

BOSC, June 2012

Sophia K. Cheng, MScSenior Software

Engineer

Center for Biomedical InformaticsHarvard Medical School

eagle-i: Making Invisible Resources … Visible

eagle-i: Describe Resources

eagle-i: Share Resources

eagle-i: Discover Resources

eagle-i “Open-ness”

• Open Access: Semantic web & Linked Open Data

• Open Source:Software and Ontology

• Open Network:

Anyone can search, any institution can join

Come in

We’re

OPENCome in

We’re

OPEN

Open Access: Semantic Web & Linked Open Data

• Semantic Web:

• Set of standards for representing machine readable data

•RDF – Data•OWL – Ontology•SPARQL – Query

•Linked Open Data:

•Principles for publishing semantic web data•HTTP URLs for URIs•HTTP Protocol for content negotiation

SubjectSubject ObjectObjectPredicate

Open Access: Linked Open Data Example

eagle-i

Plasmid Emporium

pe:has

http:\\some.university.net\resource123

http:\\some.university.net\resource123

http:\\some.university.net\resource456

http:\\some.university.net\resource456

“Insulin tagging

plasmid”

“Insulin tagging

plasmid”

“pBS rat IRS-3”

“pBS rat IRS-3”

rdf:type

rdfs

:labe

l ei:d

escrip

tion

ro:locationei:plasmidei:plasmid

“Smith Laboratory”

“Smith Laboratory”

ei:labei:lab

rdf:t

ype rdfs:label

http:\\some.plasmid.emporium\instance78

http:\\some.plasmid.emporium\instance78

“Collection of plasmids for PCR-

based gene targeting insulin”

“Collection of plasmids for PCR-

based gene targeting insulin”

“Insulin”“Insulin”

rdfs:label

ei:description

http:\\some.plasmid.emporium\instance78

http:\\some.plasmid.emporium\instance78

“Collection of plasmids for PCR-

based gene targeting insulin”

“Collection of plasmids for PCR-

based gene targeting insulin”

“Insulin”“Insulin”pe:has

rdfs:label

ei:descriptionhttp:\\some.university.net\resource123

http:\\some.university.net\resource123

http:\\some.university.net\resource456

http:\\some.university.net\resource456

“Insulin tagging

plasmid”

“Insulin tagging

plasmid”

“pBS rat IRS-3”

“pBS rat IRS-3”

rdf:type

rdfs

:labe

l ei:d

escrip

tion

ro:locationei:plasmidei:plasmid

“Smith Laboratory”

“Smith Laboratory”

ei:labei:labrd

f:typ

e rdfs:label

Open Access: Get the Resource Data

http://eagle-i.net/export

Open Source: eagle-i Architecture

eagle-i ontology

Search Application

Repository 3rd Party Data Consumers

Data Client

. . .

Open Source: Layered Ontology Approach

Open Source: Get the Ontology

http://eagle-i.net/ontology

Open Source: eagle-i Architecture

eagle-i ontology

Search Application

Repository 3rd Party Data Consumers

Data Client

. . .

Open Source: eagle-i Software Stack

Search Application

Repository Harvest REST API

Sesame RDF store

CRUD REST APISPARQL REST API

SWEETData collection

and managementweb client

Lab PagesIntegration

module

3rd PartyLOD

Consumers

3rd PartyConsumers

Data ingest, transformation andintegration toolkit

Open Source: eagle-i Global Repository

Search Application

Repository Harvest REST API

Sesame RDF store

CRUD REST APISPARQL REST API

SWEETData collection

and managementweb client

Lab PagesIntegration

module

3rd PartyLOD

Consumers

3rd PartyConsumers

Data ingest, transformation andintegration toolkit

Global

Repository

Open Source: Project Infrastructure

Bamboo

Nexus MailmanJira

ConfluenceSubversion

Open Source: Get the Software

http://eagle-i.net/code(Open Source under BSD-3 license)

Open Network: eagle-i Network

Open Network: Early Adopters & Evaluators

• University of North Carolina

• Fred Hutchinson Cancer Research

Center

• New York University

• University of California, San Francisco

• University of Leuven (Belgium)

• Brown University

Open Network: Search & Learn

http://eagle-i.net

Check it out …

• Search and Learn:

• http://eagle-i.net• Get the Data:

• http://eagle-i.net/export

Contact Me:sophia_cheng@hms.harvard.edu( Poster #21 )

• Get the Ontology:

• http://eagle-i.net/

ontology• Get the Code:

• http://eagle-i.net/

code

(Open Source Under BSD-3 license)