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S Cheng - eagle-i: development and expansion of a scientific resource discovery network
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Transcript of S Cheng - eagle-i: development and expansion of a scientific resource discovery network
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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
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eagle-i: Making Invisible Resources … Visible
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eagle-i: Describe Resources
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eagle-i: Share Resources
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eagle-i: Discover Resources
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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
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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
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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
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Open Access: Get the Resource Data
http://eagle-i.net/export
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Open Source: eagle-i Architecture
eagle-i ontology
Search Application
Repository 3rd Party Data Consumers
Data Client
. . .
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Open Source: Layered Ontology Approach
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Open Source: Get the Ontology
http://eagle-i.net/ontology
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Open Source: eagle-i Architecture
eagle-i ontology
Search Application
Repository 3rd Party Data Consumers
Data Client
. . .
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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
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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
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Open Source: Project Infrastructure
Bamboo
Nexus MailmanJira
ConfluenceSubversion
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Open Source: Get the Software
http://eagle-i.net/code(Open Source under BSD-3 license)
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Open Network: eagle-i Network
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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
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Open Network: Search & Learn
http://eagle-i.net
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Check it out …
• Search and Learn:
• http://eagle-i.net• Get the Data:
• http://eagle-i.net/export
Contact Me:[email protected]( Poster #21 )
• Get the Ontology:
• http://eagle-i.net/
ontology• Get the Code:
• http://eagle-i.net/
code
(Open Source Under BSD-3 license)