Leslie McIntosh Vivo National Evaluator Washington University Jonathan Corson Rikert Vivo Development Lead Cornell University Ellen J Cramer Special Projects Lead Cornell University ID: 814707
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Slide1
April 5, 2011 1-2 p.m.
VIVO Researcher Networking Update
Leslie McIntosh
Vivo National EvaluatorWashington University
Jonathan Corson-RikertVivo Development LeadCornell University
Ellen
J.
Cramer
Special Projects Lead
Cornell
University
Slide2VIVO Collaboration
Cornell University
Dean
Krafft
(Cornell PI)Manolo Bevia
Jim Blake
Nick
Cappadona
Brian CarusoElly CramerMedha DevareElizabeth HinesHuda KhanBrian LoweJoseph McEnerneyHolly MistlebauerStella MitchellAnup SawantChristopher WestlingTim WorrallRebecca YounesJon Corson-Rikert
University of FloridaMike Conlon (VIVO and UF PI)Beth AutenChris BarnesCecilia BoteroKerry BrittErin BrooksAmy BuhlerEllie BushhousenLinda ButsonChris CaseChristine CogarValrie DavisMary EdwardsNita FerreeRolando Garcia-MilanGeorge HackChris HainesSara HenningRae JesanoMargeaux JohnsonMeghan LatorreYang LiPaula MarkesHannah NortonNarayan RaumAlexander RockwellSara Russell GonzalezNancy SchaeferDale SchepplerNicholas SkaggsSyraj SyedMatthew TedderMichele R. TennantAlicia TurnerStephen Williams
Indiana UniversityKaty Borner (IU PI)Kavitha ChandrasekarBin ChenShanshan ChenRyan CobineJeni CoffeySuresh DeivasigamaniYing DingRussell DuhonJon DunnPoornima GopinathJulie HardestyBrian KeeseNamrata LeleMicah LinnemeierNianli MaRobert H. McDonaldAsik Pradhan GongajuMark PriceMichael StamperYuyin SunChintan TankAlan WalshBrian WheelerFeng WuAngela Zoss
Ponce School of MedicineRichard J. Noel, Jr. (Ponce PI)Ricardo Espada ColonDamaris Torres CruzMichael Vega Negrón
This project is funded by the National Institutes of Health, U24 RR029822"VIVO: Enabling National Networking of Scientists”
The Scripps Research InstituteGerald Joyce (Scripps PI)Catherine DunnBrant KelleyPaula KingAngela MurrellBarbara NobleCary ThomasMichaeleen Trimarchi
Washington University School of Medicine in St. LouisRakesh Nagarajan (WUSTL PI)Kristi L. HolmesCaerie HouchinsGeorge JosephSunita B. KoulJasmine OwensLeslie D. McIntosh
Weill Cornell Medical CollegeCurtis Cole (Weill PI)Paul AlbertVictor BrodskyMark BronnimannAdam CheriffOscar CruzDan DickinsonRichard HuChris HuangItay KlazKenneth LeePeter MicheliniGrace MigliorisiJohn RuffingJason SpeclandTru TranVinay VarugheseVirgil Wong
Slide3Presentation Plan
Rough outline:Lessons learned from all sites (LESLIE) 15-20 min
Local implementation specifics (data sources, repurposing) (ELLY) 10-15 minDevelopment directions and multi-institutional perspectives (JON) 15-20 minTime for questions at the end.
What was submitted:The National Institutes of Health (NIH)-funded project, "VIVO: Enabling National Networking of Scientists," has just completed a fifth release of the VIVO software at the 18-month point of its current two-year grant. This presentation will focus on where VIVO is today, with a review of the implementation progress at all seven project sites, a detailed look into VIVO's integration into the institutional landscape at Cornell University, and a discussion of the national and international dimensions of VIVO and its future development directions
.VIVO highlights many of the opportunities and challenges of linked open data, including blending local and national data in a multi-institutional context, identifying authoritative information sources, disambiguating authors and organizations, providing appropriate temporal limits on relationships, and reconciling data differences in updates. Each institution on the VIVO project has faced unique challenges and achieved different successes, but common themes have emerged that will help potential adopters and highlight areas of remaining work. VIVO's role in serving the academic and research mission of a university, as illustrated at Cornell, also presents a compelling value proposition for administrators charged with sustaining the effort at the institutional level. This dynamic will have lasting implications for NIH's vision of a distributed, institutionally-sustained researcher networking solution serving large research consortia and national-level needs.
Slide4An open-source
s
emantic web application that enables the discovery of research and scholarship across disciplines in an institution.
Populated with
detailed profiles of faculty and researchers; displaying items such as publications, teaching, service, and professional affiliations.
A
powerful search functionality
for locating people and information within or across institutions.
Slide5Participating Institutions
National Network Team
University of Florida, Gainesville, FLCornell University, Ithaca, NYIndiana University, Bloomington, INThe Scripps Research Institute, La Jolla, CA
Institution
Acad. StaffStudent Pop.City
Pop.
Public/Private
Med
SchoolCornell (Ithaca)1,63920.9K100KBothUniversity of Florida4,53450.7K258KPublicYesIndiana University (Bloomington)2,97342.4K175K
PublicPonce School of Medicine 200475442KPrivateYesThe Scripps Research Institute225~22543KPrivateWashington University School of Medicine1,772~5002.8MPrivateYesWeill-Cornell Medical College 1,2354108.2MPrivateYes
Slide6Lessons Learned in VIVO Implementation
Slide7Data, Data, Data
Slide8Get the Data
Who owns the data?
Where are the data sources?What permissions do you need to use the data?
Manage the Data
Who owns the data now?Do you need to create a data management system?How will you refresh your data? How often?
Your data are only as good as the source.
Slide9Manage Expectations
Slide10Contribute to the Community
More to open-source than contributing codeDataDocumentation
IRC communicationListservsLessons learned
vivoweb.org
vivo.sourceforge.net
Slide11VIVO Cornell: In-house to National Cloud
2003-2007
Development of research profiles using ontologies in a database-driven website to meet the needs of the Life Sciences initiative.
2007
Converted to Semantic Web standards. Expanded to include disciplines across the institution
2007–2011+
With NIH grant, moved to national and international network of institutions and organizations and their faculty and researcher profiles
Slide12VIVO Cornell: Data Sources
Slide13VIVO Cornell: Data Sources
Slide14Repurposing and re-using data
Slide15Local Outreach
Provost Office - institutional support
Data providers – HR, Annual faculty reporting, Grants, Courses, Other
Librarian VIVO liaisons -subject areas
Web developers - repurposing of dataDepartment editors - training
Slide16Networking
Other sites piloting or adopting VIVO technology
Arizona State University, Duke University, IICA, Los Alamos National Laboratory, Northwestern University, Stony Brook University, University of Arkansas, University of Buffalo, University of Colorado – Boulder, University of Delaware, University of Oregon, University of Virginia,
USDA
Integration
partners
APA (Digital Trust), Duke (Widgets), Harvard University (Harvard Profiles), Indiana University (
HUBzero
), Orchid, Stony Brook University (UMLS), University of Hong Kong (Knowledge Exchange), University of Pittsburgh (Digital Vita), Weill Cornell Medical College (Google Refine).International effortsANDS-Vitro Consortium (Griffith, QUT, University of Melbourne, VeRSI)Chinese Academy of Sciences IICA (Inter-American Institute for Cooperation on Agriculture) isconsidering options like VIVO for a researcher network for their SIDALCApplication and there is a pilot VIVO implementation at the El Colegio de Postgraduados of Mexico.
Slide17VIVO update part III
VIVO core design principlesEnhancements during the NIH grantPlanned developmentVIVO at web scale
Mini-grants and collaborationsBuilding community and sustainability
Slide18First, it’s about data
Consistent formatting, in a language of the WebSelf-describingOntology
Context inherent in the dataDistributedDe-referenceableReusable without (or with) modificationPersistent independently of any application
Slide19VIVO is not just people or profiles
Anything can be a type (and have individuals)All individuals have the same structure
Varying attributes & relationshipsInheritanceExtend the ontology without modifying the appTradeoffs of generality vs. optimal interface
Slide20Highlights of recent improvements
Linked
Open Data
Application
n
avigation
t
heming
scalabilityMVC structureVIVOCore Ontologyeagle-iresearchresourcesself-editing
externalauthenticationHarvesterVisualizationspage templatesgrantsHR dataPubmed
Drupal importer
Slide21Deliverables by August, 2011
Linked
Open Data
Application
n
avigation
t
heming
scalabilityMVC structureVIVOCore Ontologyself-editing
externalauthenticationVisualizationspage templatesMap of ScienceGeoMaprole-basedauthorizationaggregatorsoftwareRDF to Solrindexer
local/nationalsearch UIlinkingbetweenVIVOsSearch-related functionalitiesBioportalsubmission
Harvestermore pubformats
nationalgrant data
Drupal importer
Slide22“National” search
NIH mandated no reliance on sustained centralized infrastructureAggregation of RDF from multiple sourcesHarvard Profiles, Collexis
, and likely othersSolr indexing leveraging the VIVO ontologyAggregator and indexing will be configurable to harvest any desired set of sources
Slide23National networking & search
Ponce
VIVO
WashU
VIVO
IU VIVO
Cornell
Ithaca
VIVO
Weill
Cornell VIVOVIVOaggregatortriple store
Other
VIVOs
OtherCTSAVIVOsHarvardProfilesRDFOther
VIVOsOtherRDFFuture CTSAtriple storeFuturestate or regionaltriple s
toreFutureCTSASolrindexOtherRDF
Solr
s
earch
index
Linked Open Data
future
Solr
index
VIVO
n
ational
network
search
UF VIVO
Scripps
VIVO
Slide24Slide25VIVO at web scale
Connections directly between VIVOsMultiple campuses of 1 institutionMultiple institutions within a consortium
Data resides & served from home institutionIndividuals linked by URI or common identifierUpdates via linked data harvesting or pingback
Slide26As the linked data cloud grows
Search enhanced by authoritative, structured, and updated dataRetrieval and filtering by type & relationship, not just textEnables better data mining and analysis
Reduces reporting burdenUnique semantic advantagesCategorization implicit in defined ontologiesCommon references to shared terminologiesORCID and other initiatives leading to common references to individuals
Slide27Community development
VIVOweb.orgVIVO on sourceforge
Fully open source (BSD license)Subversion repository – download or check outActive development and implementation mail lists & forumsInstallation and upgrade documentation
Wiki-based documentation effortSupplemental materialsMany ways to contribute and benefit
Slide28Mini-grants address key areas
Controlled vocabularies (Stony Brook)Author IDs and disambiguation (ORCID)Widgets to re-use VIVO data in standard web pages (Duke)
Direct output to biosketches and CVs (Pittsburgh)Connection to the HUBzero scientific simulation and grid services platform, via
Joomla CMS (IU)Google Refine for data cleanup and export (Weill Cornell)
Slide29VIVO Ecosystem Evolution
Slide30Community collaborations
ORCIDConnections to institutional repositories, as other libraries implement VIVOLibrary of Congress support for Exhibit API with VIVO as one target
Dataset metadata discovery and registry work, with Australian VIVO consortium
Slide31Questions yet to address
What access points and services need to be provided for national (or international) research networking to succeed?How will people be able to integrate this data into their daily workflow and research process?
How will boundaries between public and private data and services work?Federating group privileges as well as identities across multiple VIVOs and to other research-enabling tools
Slide32Thank you