S Cheng - eagle-i: development and expansion of a scientific resource discovery network
Upcoming SlideShare
Loading in...5
×

Like this? Share it with your network

Share

S Cheng - eagle-i: development and expansion of a scientific resource discovery network

  • 538 views
Uploaded on

Presentation at BOSC2012 by S Cheng - eagle-i: development and expansion of a scientific resource discovery network

Presentation at BOSC2012 by S Cheng - eagle-i: development and expansion of a scientific resource discovery network

More in: Education
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Be the first to comment
    Be the first to like this
No Downloads

Views

Total Views
538
On Slideshare
538
From Embeds
0
Number of Embeds
0

Actions

Shares
Downloads
2
Comments
0
Likes
0

Embeds 0

No embeds

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
    No notes for slide
  • Eagle-I software   more – open source – access – network
  • 2009 – aim – invisible What Imagine – casey Needs – specific - [1] Doesn’t know [2] – to him – invisible Solve – network – connect – existing [3] – mouse model – equipment Accomplish – 3 complimentary
  • Here – screenshots Ontology browser – info – how – resources – described
  • Data client – research – resources – share
  • Search – research – need - discover
  • Heard – morning – open-ness – happens – specifically eagle-I open-ness Provide – open access – resource data – network [BREATHE] Our – code – ontology – open source [BREATHE] Finally – the network [BREATHE]
  • Able – provide – open access – data – building – semantic technologies – LOD Understand – how – semantic – LOD – enable – open access – quick overview – what   Data – expressed – RDF – stores – info – triple – form   LOD – principles – publish – machine – web [ < 3:00 ]
  • Not familiar – illustrate – quick - example   [ 1 ] RDF – visualized - Directed graph   [ 6 ] note - data separation – one source   Much more - out of scope [ < 4:00 ]
  • To download – resource data – point browser Note – network – information about – not data
  • Now – moving – open source component – here   Developed – federated network – each box   4 main   Search application Data repository Data clients Ontology   Ontology – also – open
  • Ontologists – layered approach –Lovingly – messy fish decouples – domain specific – application specific   Diagram - Can’t see – many ovals – represent – module – foaf – mesh   Theoretically – mix – match – modules – tailor
  • TO – download – ontology – learn – layered – visit
  • Coming back – architecture – look – 1 institution – talk software stack
  • Heart   Designed – interacting – vital – flexibility   Search – Harvest Data clients – SPARQL & CRUD Code – use Out of box APIs – develop – module Modify existing
  • Remember – LOD – strength – one source Challenge – federated – multi vs – common – manufacturer Global – link – earlier example   That’s – open source – nutshell
  • Open source – more – code Need – infrastructure – distribute – track – communicate Want – mention - Project – benefited – well thought out – stable Due – strong – open source – culture – Harvard – affiliates Decision – pool resources – one – host – tools   Nexus - Binary   Projects hosted get all with one click Extremely beneficial – just focus
  • MC: again, this is the place to say “And to get the actual code, go here”
  • Finally – mentioned   9 founding 25 partcipiating   anyone search – join
  • Addition – 25 Here – other – we know – downloaded Evaluating – modifying – adopting
  • To – search – or – learn - join
  • MC: consider saying that these are all on eagle-i.net/export, code, and ontology. Also, consider adding your poster/demo number/area/section to the slide. Also, consider saying that if they do come by, you’ll be able to show them the seach and data client in action. Woo hoo! You’re done! Say thanks, and walk off proud and tall!

Transcript

  • 1. eagle-i: Developmentand Expansion of aScientific ResourceDiscovery NetworkBOSC, June 2012 Sophia K. Cheng, MSc Senior Software EngineerCenter for Biomedical InformaticsHarvard Medical School
  • 2. eagle-i: Making Invisible Resources … Visible
  • 3. eagle-i: Describe Resources
  • 4. eagle-i: Share Resources
  • 5. eagle-i: Discover Resources
  • 6. eagle-i “Open-ness” • Open Access: Semantic web & Linked Open Data e’re in W • Open Source:Co e m OP EN Software and Ontology • Open Network: Anyone can search, any institution can join
  • 7. Open Access: Semantic Web & Linked OpenData • Semantic Web: • Set of standards for representing machine readable data •RDF – Data Predicate •OWL – Ontology Subject Object •SPARQL – Query •Linked Open Data: •Principles for publishing semantic web data •HTTP URLs for URIs •HTTP Protocol for content negotiation
  • 8. Open Access: Linked Open Data Example http:some.plasmid.emporiuminstance78 eagle-i rdf s s:la :ha b el pe ei:d http:some.university.netresource123 esc “Insulin” ro r e f:typ ipt :lo rd ca ion http:some.plasmid.emporiuminstance78 http:some.university.netresource123 tio l e n s ab ei:de :ha “Collection of plasmids fs:l ei:plasmid pe ro p e ei:d for PCR-based gene f:ty esc l:loc rd rd http:some.university.netresource456 ript targeting insulin” scrip e lab ati ion s: rdf on el :lab tion ei:de ei:plasmid “pBS Emporium Plasmid rat pe fs y f:t rd rd IRS-3” http:some.university.netresource456 “Collection of plasmids scrip rd fs: “Insulin” for PCR-based gene lab targeting insulin” e tion l ei:lab pe “pBS rat y “Insulin tagging f:t rd IRS-3” rd plasmid” fs: “Smith lab Laboratory” el ei:lab “Insulin tagging plasmid” “Smith Laboratory”
  • 9. Open Access: Get the Resource Data http://eagle-i.net/export
  • 10. Open Source: eagle-i Architecture Search Application eagle-i ontology ... Repository 3rd Party Data Consumers Data Client
  • 11. Open Source: Layered Ontology Approach
  • 12. Open Source: Get the Ontology http://eagle-i.net/ontology
  • 13. Open Source: eagle-i Architecture Search Application eagle-i ontology ... Repository 3rd Party Data Consumers Data Client
  • 14. Open Source: eagle-i Software Stack Search Application Repository Harvest REST API Sesame RDF store SPARQL REST API CRUD REST API Data ingest, transformation and integration toolkit SWEET 3rd Party Lab Pages Data collection LOD Integration and management Consumers module web client 3rd Party Consumers
  • 15. Open Source: eagle-i Global Repository Search Application Repository Harvest REST API Global Sesame RDF store Repository SPARQL REST API CRUD REST API Data ingest, transformation and integration toolkit SWEET 3rd Party Lab Pages Data collection LOD Integration and management Consumers module web client 3rd Party Consumers
  • 16. Open Source: Project Infrastructure Bamboo Subversion Confluence Nexus Jira Mailman
  • 17. Open Source: Get the Software http://eagle-i.net/code (Open Source under BSD-3 license)
  • 18. Open Network: eagle-i Network
  • 19. 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
  • 20. Open Network: Search & Learn http://eagle-i.net
  • 21. Check it out …• Search and Learn: • Get the Ontology: • http://eagle-i.net • http://eagle-i.net/ontology• Get the Data: • Get the Code:• http://eagle-i.net/export • http://eagle-i.net/code (Open Source Under BSD-3 license) Contact Me: sophia_cheng@hms.harvard.edu ( Poster #21 )