The eagle-i Network:enabling research resourcediscoveryMelissa HaendelOregon Health & Science University Library03.15.13LI...
Outline History of eagle-i Network Basic features & functionality Relationship to research lifecycle & community Futur...
Dreams of a bench scientistBetter access to resources and expertiseMore reproducible scienceCredit where credit is dueVisi...
All of these dreams are aided bysemantic technologies: Uniform resourceIdentifiers Ontologies (enablingcommon reference,...
 Helping researchers find invisible resourcesReagents, instruments, services, model and non-model organisms,protocols, bi...
eagle-i Network
The problemAB
?xFailed experimentPolyclonal anti-TGFβ RISanta Cruz BiotechnologyAIdentifying resources
eagle-i: making research resourcesmore visibleBSuccessfulexperiment!
The problemInformation is context dependent
Ontologies provide links, or “context” forinformationNice automobileis_aOperating systemis_aFast mammalis_anamed_aftername...
SWEET: an ontology-driven data collectiontool
www.eagle-i.netHow are resources shared in eagle-i?
eagle-i data with a newuser-friendly user interfaceEnables quality search ofOHSU cores in GoogleEnables an OHSU cross-core...
www.ohsu.edu/research/coresearch/
ISFnet w o r kISF can be used by other applications
 eagle-i is an ontology-driven application . . . for collectingand searching research resources. VIVO is an ontology-dri...
Identify potentialcollaborators, relevantresources, and expertiseacross scientific disciplinesAssemble teams of scientists...
Antibody Registry and eagle-iuse a shared ontology
Publishing unique identifiers canaid scientific reproducibilityAntibodies are not very uniquely identifiable in 57 publica...
PreservePublishResearchCTSAconnectReveal Connections.Realize Potential.net w o r kScholarly scientific research cycle
We can all work together to make researchresourcesmore visibleand researchmore efficient.Successfulexperiment!net w o r k
ResourcesOntology Development Grouphttp://bit.ly/ohsuontdevgroupCTSAconnect projectctsaconnect.orgCTSAconnect ontologyhttp...
OHSU Library Ontology Development GroupMelissa Haendel – Co-Lead, Neuroscientist/OntologistCarlo Torniai – Co-Lead, Comput...
CTSAconnecteagle-iOHSUMelissa HaendelCarlo TorniaiNicole VasilevskyChris KelleherShahim EssaidCornell UniversityDean Kraff...
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eScience Institute presentation on eagle-i

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

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  • This is just a draft- copied from RedCap slides
  • Text -&gt; more complex on images Look for word “jaguar”- no meaning in the word- can be animal, car, operating system.Information is syntaxic not semantic, unable to know what we are referring to exactly
  • If we want to keep this slide, need to update the screenshot SWEET is an ontology-driven data collection tool
  • How are resources shared in eagle-i?
  • Include publication in landscape pictureFor commercial antibodies- identifiable/non-commercial identifiableNumber of antibodies and number of papersBring back to eagle-i
  • Move to end
  • eScience Institute presentation on eagle-i

    1. 1. The eagle-i Network:enabling research resourcediscoveryMelissa HaendelOregon Health & Science University Library03.15.13LIBRARY
    2. 2. Outline History of eagle-i Network Basic features & functionality Relationship to research lifecycle & community Future collaborations
    3. 3. Dreams of a bench scientistBetter access to resources and expertiseMore reproducible scienceCredit where credit is dueVisible and interoperable dataEfficient science.
    4. 4. All of these dreams are aided bysemantic technologies: Uniform resourceIdentifiers Ontologies (enablingcommon reference,differencing) Linked Data … and applicationsthat use them
    5. 5.  Helping researchers find invisible resourcesReagents, instruments, services, model and non-model organisms,protocols, biospecimens, human studies, software and researchopportunities Adding meaningful semantic relationships betweenresources Making this data available using ontology-driven approachto research resource annotation and discovery Reducing time-consuming and expensive duplication ofresourceseagle-i Network
    6. 6. eagle-i Network
    7. 7. The problemAB
    8. 8. ?xFailed experimentPolyclonal anti-TGFβ RISanta Cruz BiotechnologyAIdentifying resources
    9. 9. eagle-i: making research resourcesmore visibleBSuccessfulexperiment!
    10. 10. The problemInformation is context dependent
    11. 11. Ontologies provide links, or “context” forinformationNice automobileis_aOperating systemis_aFast mammalis_anamed_afternamed_after
    12. 12. SWEET: an ontology-driven data collectiontool
    13. 13. www.eagle-i.netHow are resources shared in eagle-i?
    14. 14. eagle-i data with a newuser-friendly user interfaceEnables quality search ofOHSU cores in GoogleEnables an OHSU cross-coresearch for instruments andservicesDeveloped by UCSF:http://ctsiatucsf.github.com/plumage/OHSU Core Search = leveraging eagle-i
    15. 15. www.ohsu.edu/research/coresearch/
    16. 16. ISFnet w o r kISF can be used by other applications
    17. 17.  eagle-i is an ontology-driven application . . . for collectingand searching research resources. VIVO is an ontology-driven application . . . for collectinganddisplaying information about people. CTSAconnect will produce a single Integrated SemanticFramework, a modular collection of ontologieseagle-iResourcesVIVOPeopleeagle-iVIVOSemanticClinicalactivitiesMerging VIVO and eagle-i semanticinfrastructureeagle-i
    18. 18. Identify potentialcollaborators, relevantresources, and expertiseacross scientific disciplinesAssemble teams of scientiststo address specific researchquestionsEvaluate scientific outcomesOregon Health & ScienceUniversityCornell UniversityUniversity of FloridaStony Brook UniversityUniversity at BuffaloHarvard UniversityCTSAconnect | Reveal Connections. Realize Potential.
    19. 19. Antibody Registry and eagle-iuse a shared ontology
    20. 20. Publishing unique identifiers canaid scientific reproducibilityAntibodies are not very uniquely identifiable in 57 publicationsPercent0%20%40%60%80%100%Commercial antibodyidentifiableNon-commercial antibodyidentifiablen=207n=8Working with publishers to increasereporting guidelines
    21. 21. PreservePublishResearchCTSAconnectReveal Connections.Realize Potential.net w o r kScholarly scientific research cycle
    22. 22. We can all work together to make researchresourcesmore visibleand researchmore efficient.Successfulexperiment!net w o r k
    23. 23. ResourcesOntology Development Grouphttp://bit.ly/ohsuontdevgroupCTSAconnect projectctsaconnect.orgCTSAconnect ontologyhttp://code.google.com/p/connect-isf/VIVO integrated searchvivosearch.orgeagle-i federated searchhttp://www.eagle-i.neteagle-i ontologyhttp://code.google.com/p/eagle-i/eagle-i software codehttps://open.med.harvard.edu/display/eaglei/SoftwareOHSU Cores Searchwww.ohsu.edu/research/coresearch
    24. 24. OHSU Library Ontology Development GroupMelissa Haendel – Co-Lead, Neuroscientist/OntologistCarlo Torniai – Co-Lead, Computer Scientist/OntologistNicole Vasilevsky – Project Manager, Cell Biologist/OntologistScott Hoffmann – Engineer/OntologistErik Segerdell – Biologist/OntologistMatthew Brush – Molecular biologist/OntologistShahim Essaid – MD/Bioinformatist/Ontologist
    25. 25. CTSAconnecteagle-iOHSUMelissa HaendelCarlo TorniaiNicole VasilevskyChris KelleherShahim EssaidCornell UniversityDean KrafftJon Corson-RikertBrian LoweUniversity of FloridaMike ConlonChris BarnesNicholas RejackOHSUMelissa HaendelCarlo TorniaiNicole VasilevskyScott HoffmannMatthew BrushJackie WirzStony Brook UniversityMoises EisenbergErich BremerJanos HajagosHarvard UniversityDaniela BourgesSophia ChengUniversity at BuffaloBarry SmithDagobert SoergelZaloniWill CorbettRanjit DasBen SharmaHarvard UniversityLee NadlerDoug MacFaddenMarc CirielloRichard PearseDaniela BourgesTenille JohnsonVanderbilt UniversityGordon BernardLisa RobinsPennGarret FitzgeraldFaith ColdrenAcknowledgements

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