VIVO: enabling the discovery of research and scholarship

library.weill.cornell.edu

VIVO: Enabling the Discovery of Research and Scholarship

COLLEEN CUDDY, MA, MLS, AHIPPAUL ALBERT, MA, MLS

Weill Cornell Medical Library library.weill.cornell.edu


BACKGROUND INFORMATIONWhat is VIVO?


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.


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)


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


Who can use VIVO?


Reuse Data Across Applications


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)


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)


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


Is VIVO Facebook for Researchers?

• No Mendeley is… (Ha)


KEY CONCEPTS OF VIVOWhat is VIVO?


Semantic representation of data Semantic representation of data


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?


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


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


Alignment with eagle-I ontology


> > >

> RDF harvestSPARQL endpoint

VIVO(RDF)

data ingest ontologies

(RDF)shared as

RDF

interactiveinput

local systems of record

externalsources

Local Dataflow into VIVO


Linked Open Data

RDFTriples

RDFTriples


Com

mun

ity-W

ide

Sem

antic

Sea

rch

Com

mun

ity-W

ide

Sem

antic

Sea

rch


DATA VISUALIZATIONWhat is VIVO?


Visualize co-author relationships Visualize co-author relationships


ScienceMap visualizes collections of publications ScienceMap visualizes collections of publications


TOOLS & APPS FOR VIVOWhat is VIVO?


Draw organizational charts Draw organizational charts


VIVO produces both HTML and RDF

Software reads VIVO RDF and displays


http://vivosearchlight.org/@mileswortho



Inter-institutional Collaboration Explorer

http://xcite.hackerceo.org/VIVOviz


Power Tool for Dirty Data – Google Refine + VIVO


LIBRARIES AS KEY PARTNERSWhat is VIVO?


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


• 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?


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


COMING SOONWhat is VIVO?


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


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


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…


Full integration with Digital Vita Full integration with Digital Vita

CV


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


DEMONSTRATIONWhat is VIVO?


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


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


QUESTIONS?Thank You!

Education

VIVO: enabling the discovery of research and scholarship