Facilitating Open Science and Research Discovery via VIVO and the

Semantic WebKristi Holmes, PhD

BioinformaticistBecker Medical Library

http://vivo.wustl.edu/display/n4754Twitter: @kristiholmes

December 5, 2011

Facilitating Open Science and Research Discovery via VIVO and the Semantic Web by Kristi L. Holmes is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

Information Overload

Public, structured linked data about investigators interests, activities and

accomplishments, and tools to use that data to advance science

What is VIVO?An open-source semantic web application that enables the discovery of research and scholarship across disciplines in an institution.

An open-source semantic 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.

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.

A powerful search functionality for locating people and information within or across institutions.

A VIVO profile allows you to:

Showcase credentials, expertise, skills, and professional achievements.Showcase 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 CVs.Simplify reporting tasks and link data to external applications – e.g., to generate biosketches or CVs.

Publish the URL or link the profile to other applications.Publish the URL or link the profile to other applications.

Find potential colleagues by research area, authorship, and collaborations.Find potential colleagues by research area, authorship, and collaborations.

Display visualizations of complex research networks and relationships.Display visualizations of complex research networks and relationships.

VIVO harvests data from verified sources

VIVO data is available for reuse by web pages, applications, and other consumers both within and outside the institution.

Data stored as RDF triples using standard

ontology

Data stored as RDF triples using standard

ontology

Internal data sources (I):• HR Directory• Office of Sponsored Research• Institutional Repositories• Registrar System• Faculty Activity Systems• Events and Seminars

Internal data sources (I):• HR Directory• Office of Sponsored Research• Institutional Repositories• Registrar System• Faculty Activity Systems• Events and Seminars

External data sources (I):• Publication warehouses-

e.g. PubMed, Web of Science, and more.

• Grant databases: e.g. NSF/ NIH

• National Organizations: AAAS, AMA, etc.

External data sources (I):• Publication warehouses-

e.g. PubMed, Web of Science, and more.

• Grant databases: e.g. NSF/ NIH

• National Organizations: AAAS, AMA, etc.

Faculty and unit administrators can then add additional information to their

profile. (M)

Faculty and unit administrators can then add additional information to their

profile. (M)

Information is stored using the Resource Description Framework (RDF) and data are structured in the form of “triples” as subject-predicate-object.

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 affiliations with

Dept. of Genetics

College of Medicine

Journal article

Book chapter

Book

Genetics Institute

Subject Predicate Object

How does VIVO store data?

Every piece of data has an addressEvery piece of data has an address

VIVO enables authoritative data about researchers to become part of the Linked Data cloud.

Using VIVO data By storing data in VIVO in RDF and using standard ontologies, the information in VIVO can either be displayed in a human readable web page or delivered directly to other systems as RDF. This allows the open researcher data in VIVO to be harvested, aggregated, and integrated into the Linked Open Data cloud.

The Semantic Web & Researcher Networking

• Increasing recognition of the value of semantic web standards • Increasing momentum in support of semantic web

technologies to facilitate research discovery• Recommendations for researcher networking recently

endorsed by the CTSA Consortium Steering Committee represent a new standard in researcher networking. – Read more at http://vivoweb.org/blog

• Examples of applications that consume these rich data include: visualizations, enhanced multi-site search, and VIVO Searchlight. Other utilities are in development across a wide range of topic areas.

Notable SemWeb projects• Dbpedia is a community effort to extract structured information from Wikipedia and to make this

information available on the Web. • NextBio is a database consolidating high-throughput life sciences experimental data tagged and

connected via biomedical ontologies. • GoPubMed a semantic search engine for the life sciences. It uses the GeneOntology (GO) and the

Medical Subject Headings (MeSH) to semantically filter millions of biomedical abstracts from MEDLINE.

• OpenPHACTS will create an open innovative platform, Open Pharmacological Space, which will be freely accessible for knowledge discovery and verification. Open PHACTS will provide a growing body of data on small molecules, their pharmacological profiles, pharmacokinetics, biological targets and pathways in a semantically interoperable format. Aligning and integrating proprietary and public data sources into a single system is currently a very difficult and time consuming task, repeated across companies, institutes and academic laboratories.

• Open Government initiatives• Publications efforts• DOD • Federal Profiling• Many others

Tools.

http://vivosearchlight.org/@mileswortho

http://xcite.hackerceo.org/VIVOviz/@hackerceo

Inter-Institutional Collaboration Explorer

http://vivo-vis.cns.iu.edu/vivo1/vis/map-of-science/CollegeofLiberalArtsandSciences

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A Growing Community of Collaboration• Federal agencies – White House OSTP, NIH, NLM, NSF, USDA, FDP/SciENCV, EPA, FRPS, STAR

Metrics, ...• Data Providers/Partnerships – euroCRIS, Wellspring Worldwide, Symplectic Elements, Thomson

Reuters, Elsevier, ORCID, CiteSeer, arXiv, PLoS, DSpace, BioMed Central,...• Professional Societies – APA, AAAS, AIRI, AAMC, ABRF, ... • International collaborators – Ireland, Germany, Australia, China, Netherlands, UK, Costa Rica,

Iceland, Brazil, Mexico, India, ...• Semantic Web community – DERI, Tim Berners-Lee, Jim Hendler, MyExperiment, ConceptWeb

Alliance, OpenPHACTS (EU), Linked Data, ...• Ontology – OBO, NBIC, Eagle-I, BRO, eBIRT, RDS, ...• Open Source cooperatives – Kuali, Sakai, DuraSpace, ... • Social Network Analysis Community – Northwestern, UC Davis, UCF, INSNA, ...• Collaborations with Schools and Consortia – CTSAs, Pittsburgh, Stony Brook, Duke, Weill Cornell,

Indiana, Cornell, Washington U, Ponce, Scripps, Emory, Iowa, Harvard, Rochester, UCSF, Stanford, MIT, Brown, Michigan, Nebraska, Colorado, Hunter, OHSU, Minnesota, Maastricht, ...

• Stats – downloads (>12,000), contact list (>1,600) • Four annual events – conference (08/22-24/2012, Miami) , workshop, hackathon,

implementation fest • Open Source Community – vivo.sourceforge.net• Learn more – vivoweb.org, @VIVOcollab on Twitter

vivo.sourceforge.net

open data, open tools, open process

Thank you!

VIVO CollaborationCornell UniversityDean Krafft (Cornell PI)

Manolo BeviaJim Blake

Nick CappadonaBrian Caruso

Jon Corson-RikertElly Cramer

Medha DevareElizabeth Hines

Huda KhanDepak 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

AcknowledgementsFunding:• VIVO, NIH award U24 RR029822• Washington University Institute

of Clinical and Translational Sciences, NIH award UL1 RR024992

Questions:• holmeskr@wustl.edu • Twitter: @kristiholmes• http://vivo.wustl.edu/display/n4754

Collaborations:• Washington University ICTS,

Departments • VIVO colleagues from across

the country• Becker Library colleagues• Library colleagues everywhere

Thanks!

Images and site creditsImages• http://www.joedeacon.com/news%20archive/data%20loss/blue_data.gif • http://i.telegraph.co.uk/multimedia/archive/02032/road-rail-us_2032312i.jpg • http://richard.cyganiak.de/2007/10/lod/lod-datasets_2011-09-19_colored.html• http://www.flickr.com/photos/matthileo/4826783509/

Websites, resources• http://vivoweb.org/• http://xcite.hackerceo.org/VIVOviz/ • http://vivo.sourceforge.net/ • http://vivosearch.org/ • http://vivosearchlight.org/ • http://vivo.cns.iu.edu/gallery.html/• http://dbpedia.org/About • http://www.gopubmed.com/ • http://www.openphacts.org/