VIVO: enabling the discovery of research and scholarship
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VIVO: Enabling the Discovery of Research and Scholarship
COLLEEN CUDDY, MA, MLS, AHIPPAUL ALBERT, MA, MLS
Weill Cornell Medical Library library.weill.cornell.edu
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BACKGROUND INFORMATIONWhat is VIVO?
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VIVO Defined
• VIVO promotes open standards and open linked data about research – people, papers/products, funding, events/presentations, resources, projects/studies, data, concepts – and the relationships between them.
• VIVO is a set of open source, community-maintained software tools for research discovery and networking in science and other disciplines.
• VIVO is a world community of collaborators – scientists, implementers, developers.
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One Minute VIVO History
• 2003 – VIVO created for local use at Cornell University (Ithaca) to support a
university-wide life sciences initiative
• 2009 – The National Center for Research Resources (NIH) awards the VIVO
Collaboration a two-year, $12.2 million grant to VIVO for networking of researchers. A
parallel grant for collecting and networking research resources was awarded to the
eagle-i Consortium.
• 2010 Apr – Version 1.0 released
• 2010 July – Version 1.1 released
• 2010 Aug – First VIVO conference (NYC)
• 2011 Feb – Version 1.2 and Harvester version 1.0
• 2011 July – Version 1.3 released
• 2011 Aug – Second VIVO conference (D.C.)
• 2012 Aug – Third VIVO conference (Miami)
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Showcase credentials, expertise, skills, and professional achievementsShowcase credentials, expertise, skills, and professional achievements
Connect within focus areas and geographic expertise Connect within focus areas and geographic expertise
Simplify reporting tasks and link data to external applications – e.g., to generate biosketches or CVsSimplify reporting tasks and link data to external applications – e.g., to generate biosketches or CVs
Publish the URL or populate profiles on other websitesPublish the URL or populate profiles on other websites
Find potential colleagues by research area, authorship, and collaborationsFind potential colleagues by research area, authorship, and collaborations
Display visualizations of complex research networks and relationshipsDisplay visualizations of complex research networks and relationships
What One Can (and Potentially Can) Do With VIVO
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Who can use VIVO?
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Reuse Data Across Applications
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Original VIVO Implementation Sites
• University of Florida – Principal Investigator• Cornell University• Indiana University• Ponce School of Medicine• The Scripps Research Institute• Washington University School of Medicine• Weill Cornell Medical College (WCMC)
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Current Pilot Implementation Sites and Collaborators
• University of Florida – Principe Investigator• Cornell University• Indiana University• Ponce School of Medicine• The Scripps Research Institute• Washington University School of Medicine• Weill Cornell Medical College (WCMC)
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VIVO Collaborators
Federal agencies – NIH, USDA, EPA, NSF, OSTP, FDP, STAR Metrics, NSF, NLM, VA, CENDI …
Publishers and Aggregators – ORCID, Thomson Reuters, CiteSeer, arXiv, PLoS, BioMed Central, D-Space, Elsevier/Collexis …
Press – Nature, Science, Cell, Genome Tech, SEED, The Chronicle, AP, Information Today, IEEE, Wired, …
Professional Societies – APA, AAAS, AIRI, AAMC, ABRF, APA, …International – Australia, China, Netherlands, UK, Brazil, India, Costa Rica, Mexico, …Semantic Web community – eagle-i, DERI, Tim Berners-Lee, MyExperiment, ConceptWeb, Open
Pharma Space (EU), Linked Data, …Social Network Analysis Community – Northwestern, Davis, UCF, …Schools and Consortia – CTSAs, CIC, SURA, FLR, Iowa, Harvard, UCSF, Pittsburgh, Stanford,
MIT, Brown, Michigan, Colorado, OHSU, Duke, Minnesota, many moreSub-awards to Duke, Pittsburgh, Leicester, Stony Brook, Weill, IndianaOther Collaborators – Symplectic Elements, Wellspring, …Application and service providers – over 100SourceForge File downloads – 10,000+ on SF since May 2010Contact list – over 1,500
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Is VIVO Facebook for Researchers?
• No Mendeley is… (Ha)
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KEY CONCEPTS OF VIVOWhat is VIVO?
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Semantic representation of data Semantic representation of data
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Data are structured in the form of “triples” as subject-predicate-object. Information is stored using the Resource Description Framework (RDF). Concepts and their relationships use a shared ontology to facilitate the harvesting
of data from multiple sources.
Jane Smith
is member of
author of
has affiliation with
Dept. of Genetics
College of Medicine
Journal article
Book chapter
Book
Genetics Institute
Subject Predicate Object
How does VIVO store data?
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Dublin core – description of resources Event – arbitrary time/space regions FOAF – people Geopolitical – countries, regions SKOS – thesauri, classification schemes, knowledge BIBO – publications, citations VIVO – additional classes and properties to meet VIVO application needs
Selected Core Ontologies
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Research (bibo:Document, vivo:Grant, vivo:Project, vivo:Software, vivo:Dataset, vivo:ResearchLaboratory)
Teaching (vivo:TeacherRole, vivo:AdvisingRelatioship) Services (vivo:Service, vivo:CoreLaboratory, vivo:MemberRole) Expertise (vivo:SubjectArea)
Example: modeling a person
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Alignment with eagle-I ontology
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> > >
> RDF harvestSPARQL endpoint
VIVO(RDF)
data ingest ontologies
(RDF)shared as
RDF
interactiveinput
local systems of record
externalsources
Local Dataflow into VIVO
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Linked Open Data
RDFTriples
RDFTriples
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Com
mun
ity-W
ide
Sem
antic
Sea
rch
Com
mun
ity-W
ide
Sem
antic
Sea
rch
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DATA VISUALIZATIONWhat is VIVO?
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Visualize co-author relationships Visualize co-author relationships
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ScienceMap visualizes collections of publications ScienceMap visualizes collections of publications
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TOOLS & APPS FOR VIVOWhat is VIVO?
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Draw organizational charts Draw organizational charts
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VIVO produces both HTML and RDF
Software reads VIVO RDF and displays
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http://vivosearchlight.org/@mileswortho
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Inter-institutional Collaboration Explorer
http://xcite.hackerceo.org/VIVOviz
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Power Tool for Dirty Data – Google Refine + VIVO
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LIBRARIES AS KEY PARTNERSWhat is VIVO?
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VIVO Team at WCMC
• Curtis Cole, MD – Principal Investigator• Paul Albert – Data Architect• Mark Bronnimann – Systems Administrator• Eliza Chan – Developer• Dan Dickinson – Implementation/Technical Lead• Kenneth Lee – Project Manager• Grace Migliorosi, PhD – Outreach Coordinator• John Ruffing – Partner Site Integration Specialist
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• Are a trusted, neutral space• Have a tradition of service and support• Strive to serve all missions of the institution• Are technology centers and have IT and data expertise
• Have skills—information organization, instruction, usability, subject expertise, ontologies and controlled vocabularies
• Have close relationships with their clients (buy in)• Understand user needs• Understand the importance of collaboration and know how to
bring people together• Have knowledge of institution, research, education, clinical
landscape
Library Staff:Library Staff:
Libraries:Libraries:
Why Libraries?
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The Library’s Role in VIVO
• Identify target sources of data and set priorities • Resolve ambiguities between conflicting sources of data• Propose mappings to VIVO’s classes and properties• Propose standards of data formatting• Create local extensions to the ontology (e.g. institutional identifier)• Create and implement policies for end users
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COMING SOONWhat is VIVO?
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What’s next at Weill Cornell
• Publications, publications, publications!!!• Implement self-edit • Internal outreach and training• Internal operations support• Upgrade to VIVO 1.3• Data exchange with CTSA partners – Hunter, Methodist, HSS, MSKCC• Establishing policies
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WCMC/CTSA Sources of Data
• Local Systems of Record– HR– RASP
• Data Aggregators and Repositories– PubMed– Web of Science– Grants.gov
• Individuals or their Proxies
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What’s next on the International Level
• Identify best practices for incorporating external data sources for publications and grants
• Support easier customization and improved semantic search• Extend the ontology to support intellectual property, research datasets, and more
detail about research resources• Identify and commit to a governance structure• Better provenance• and…
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Full integration with Digital Vita Full integration with Digital Vita
CV
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What’s next (National Level)
• Display visualizations of complex research networks and relationships.• Incorporate external data sources for publications and grants.• Support easier customization and improved semantic search.• Link data to external applications, e.g. generate CV’s or bio sketches.• Ability to search all VIVO sites/communities.
Improved search relevance and faceting Improved search relevance and faceting
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DEMONSTRATIONWhat is VIVO?
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Learn More About VIVO
• Project – http://vivoweb.org/
• Multi-site search (beta) – http://vivosearch.org/
• Sourceforge – http://sourceforge.net/projects/vivo/
• Facebook – http://facebook.com/VIVOcollaboration
• Twitter – http://twitter.com/VIVOcollab
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Cornell UniversityDean Krafft (Cornell PI)
Manolo BeviaJim Blake
Nick CappadonaBrian Caruso
Jon Corson-RikertElly Cramer
Medha DevareElizabeth Hines
Huda KhanDeepak Konidena
Brian LoweJoseph McEnerneyHolly Mistlebauer
Stella MitchellAnup Sawant
Christopher WestlingTim Worrall
Rebecca Younes
University of FloridaMike Conlon (VIVO and UF PI)
Beth AutenMichael Barbieri
Chris BarnesKaitlin Blackburn
Cecilia BoteroKerry Britt
Erin BrooksAmy Buhler
Ellie BushhousenLinda Butson
Chris CaseChristine Cogar
Valrie DavisMary Edwards
Nita FerreeRolando Garcia-Milan
George HackChris HainesSara HenningRae Jesano
Margeaux JohnsonMeghan Latorre
Yang LiJennifer LyonPaula Markes
Hannah NortonJames Pence
Narayan RaumNicholas Rejack
Alexander RockwellSara Russell Gonzalez
Nancy SchaeferDale SchepplerNicholas SkaggsMatthew Tedder
Michele R. TennantAlicia Turner
Stephen Williams
Indiana UniversityKaty Borner (IU PI)
Kavitha ChandrasekarBin Chen
Shanshan ChenRyan CobineJeni Coffey
Suresh DeivasigamaniYing Ding
Russell DuhonJon Dunn
Poornima GopinathJulie Hardesty
Brian KeeseNamrata Lele
Micah LinnemeierNianli Ma
Robert H. McDonaldAsik Pradhan Gongaju
Mark PriceMichael Stamper
Yuyin SunChintan TankAlan Walsh
Brian WheelerFeng Wu
Angela Zoss
Ponce School of MedicineRichard J. Noel, Jr. (Ponce PI)
Ricardo Espada ColonDamaris Torres Cruz
Michael Vega Negrón
This project is funded by the National Institutes of Health, U24 RR029822"VIVO: Enabling National Networking of Scientists”
The Scripps Research Institute
Gerald Joyce (Scripps PI)Catherine Dunn
Sam KatkovBrant KelleyPaula King
Angela MurrellBarbara NobleCary Thomas
Michaeleen Trimarchi
Washington University School of Medicine in St. Louis
Rakesh Nagarajan (WUSTL PI)Kristi L. HolmesCaerie HouchinsGeorge JosephSunita B. Koul
Leslie D. McIntosh
Weill Cornell Medical CollegeCurtis Cole (Weill PI)
Paul AlbertVictor Brodsky
Mark BronnimannAdam Cheriff
Oscar CruzDan Dickinson
Richard HuChris Huang
Itay KlazKenneth Lee
Peter MicheliniGrace Migliorisi
John RuffingJason Specland
Tru TranVinay Varughese
Virgil Wong
VIVO Collaboration
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QUESTIONS?Thank You!
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