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VIVO: A Semantic Web Network Enabling Collaboration Among Scientists
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Permanent Link: http://ufdc.ufl.edu/IR00000627/00001
 Material Information
Title: VIVO: A Semantic Web Network Enabling Collaboration Among Scientists
Physical Description: Conference Presentation
Creator: Conlon, Michael
Ruffing, John
Publisher: University of Florida
Place of Publication: Philadelphia, PA
Publication Date: October 22, 2011
 Notes
Acquisition: Collected for University of Florida's Institutional Repository by the UFIR Self-Submittal tool. Submitted by Michael Conlon.
Publication Status: Published
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Source Institution: University of Florida Institutional Repository
Holding Location: University of Florida
Rights Management: All rights reserved by the submitter.
System ID: IR00000627:00001

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VIVO: A SEMANTIC WEB NETWORK ENABLING COLLABORATION AMONG SCIENTISTS Mike Conlon, University of Florida John Ruffing, Weill Cornell Medical College Friday 21 October 2011

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WHAT IS VIVO? VIVO is open standards and linked open data regarding science people, papers/products, funding, events, resources, projects, data, concepts and the relationships between them VIVO is open source, community maintained software tools for research discovery and networking VIVO is a world community of collaborators scientists, implementers, developers

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Data, Tools and Community

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OVERVIEW Institutional Context Data Tools Consuming Data Providing Data Community

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VIVO HISTORY AT A GLANCE 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 207 attendees) 2011 Feb Version 1.2 and Harvester version 1.0 2011 July Version 1.3 released 2011 Aug Second VIVO conference (D.C., 262 attendees) 2012 Aug Third VIVO conference (Miami)

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CURRENT PILOT IMPLEMENTATION SITES AND COLLABORATORS

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DATA: LINKED AND OPEN Semantic Web RDF Ontology

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semantic advantage Data modeled as bidirectional relationships

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Resource Description Framework (RDF) simple data model for representing information allows anyone to make statements about any resource Can be represented in XML Subject [Susan Riha ] Object [ NYS WRI] Predicate [head of] From: http://www.w3.org/TR/rdf concepts/

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Andrew McDonald author of has author research area research area for academic staff in academic staff Susan Riha author of has author teaches research area for research area headed by crop management CSS 4830 head of faculty appointment in faculty members taught by featured in features person Semantic representation of data NYS WRI farmers manage chemicals Earth and Atmospheric Sciences

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11 Open data

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processOrg < function( uri ){ x< xmlParse ( uri ) u< NULL name< xmlValue ( getNodeSet (x,"// rdfs:label ")[[1]] ) subs< getNodeSet (x,"//j.1:hasSubOrganization") if(length(subs)==0) list(name= name,subs =NULL) else { for( i in 1:length(subs)){ sub.uri< getURI ( xmlAttrs (subs[[ i ]])["resource"]) u< c( u,processOrg (sub.uri)) } list(name= name,subs =u) } } VIVO produces both HTML and RDF Software reads VIVO RDF and displays

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Alignment with eagle I ontology

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VIVO ENABLES AUTHORITATIVE DATA ABOUT RESEARCHERS TO JOIN THE LINKED DATA CLOUD. http://richard.cyganiak.de/2007/10/lod/lod datasets_2010 09 22_colored.png

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PROVIDING OPEN LINKED DATA VIVO version 1.3 completed. Includes spreadsheet upload. Google Refine. Harvester Fifty US schools adopting VIVO Harvard Profiles (30 sites) providing data using VIVO ontology and RDF SciVal experts (20 sites) working to provide VIVO ontology data American Psychological Association adopts VIVO for its 154,000 members USDA adopts VIVO. 40,000 scientists, 80,000 staff, 50 land grant universities CTSA SG3 to propose VIVO ontology as a consortium wide standard University of Rochester to provide CTSA IP as VIVO data Eagle I and VIVO working to produce common ontology via RDF ORCID, Community of Science interchange with VIVO Stonybrook producing UMLS concept linkages to VIVO profiles Indiana provides HubZero profiles (3,000) via VIVO. Iowa Loki profiles (1,000) via VIVO. Adoptions in Mexico, Costa Rica, Puerto Rico, India, China, UK, Netherlands, Brazil Eight major Australian research universities and Australian federal research adopt VIVO Thomson Reuters and Elsevier providing data to VIVO Wellspring offering individual VIVO profiles Wellspring, Elsevier, Symplectics offering VIVO implementation services OpenPhacts (EU) proposing VIVO Implementation Fest held June 22 23, St. Louis. 12 schools

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vivo.wustl.edu

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Full integration with Digital Vita CV

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Faceted search, browse, and ontology hierarchy

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VISUALIZATIONS ABOUT PEOPLE

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INTER INSTITUTIONAL COLLABORATION EXPLORER http://xcite.hackerceo.org/VIVOviz

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Draw organizational charts http://vivoweb.org/files/orgLast.pdf

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Repurpose content into Drupal http://bit.ly/gmm8Ng

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RESEARCH DISCOVERY AND NETWORKING TOOLS VIVO search research discovery and networking Duke, Florida web site plug ins for reuse of VIVO data Digital Enterprise Research Institute analytics for VIVO data VIVO Search Light find experts related to any page on the world wide web UCSF Harvard visualize publication collaboration patterns Northwestern C IKnow Recommender for team building APA society portal. Identity management CTSA consortium portal Pittsburgh Digital Vita produce vita and biosketches Direct2Experts get counts of researchers matching criteria and link to them Community of Science use VIVO data for faculty interests, route opportunities to faculty Federal Researcher Profile System avoid duplication of entry, simplify administration OpenPhacts (EU) provide provenance for assertions NRN visualization show data sources and their inventory of data VIVO concept what topic areas are covered by people, departments, universities

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Providing Data

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> > > > RDF harvest SPARQL endpoint VIVO (RDF) data ingest ontologies (RDF) shared as RDF interactive input local systems of record external sources DATA FLOW THROUGH A VIVO SYSTEM

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VIVO VIVO APPLICATION ARCHITECTURE Jena Java RDF library Tomcat Java servlet container VIVO servlets page templates, javascript css Apache web server Java Freemarker & JSPs local ontology extensions theming & branding, navigation, browse tools customization application delivery foundation Lucene Java search library Pellet reasoning engine

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VIVO Cornell: Harvester

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Manual Annual faculty reporting Manual PubMed Course database Annual faculty reporting Manual Annual faculty reporting OSP data warehouse Annual faculty reporting OHR appointment OHR appointment Annual faculty reporting Annual faculty reporting Annual faculty reporting Manual VIVO Cornell as harvester: Content sources

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Harvester design

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POWER TOOL FOR DIRTY DATA GOOGLE REFINE + VIVO

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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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TARGETS FOR HARVESTING DATA

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From local to national > VIVO local sources sources > share as RDF website data search browse visualize share as RDF search browse visualize Cornell University University of Florida Indiana University Ponce School of Medicine The Scripps Research Institute Washington University, St. Louis Weill Cornell Medical College Local National Aggregating and indexing RDF Exemplar

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LINKED OPEN DATA RDF Triples RDF Triples

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BUILDING COMMUNITY Federal agencies Publishers and Aggregators Elsevier, Thomson Reuters, ORCID, CiteSeer Arxiv Dspace Professional Societies International collaborators Ireland, Germany, Australia, China, Netherlands, UK, Costa Semantic Web community DERI, Tim Berners Lee, MyExperiment ConceptWeb Open Phacts Research resources Eagle I, BRO, eBIRT Open Source cooperatives Kuali Sakai, Duraspace Social Network Analysis Community Schools and Consortia CTSAs, CIC, Pitt, Emory, Iowa, Harvard, UCSF, Stanford, MIT, Software downloads (>10,000) and contact list (>1,600) Four annual events conference, workshop, hackathon implementation fest On line community http://vivo.sourceforge.net

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VIVO 2012, August 22 24, Hotel Intercontinental, Miami, Florida

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Thank you! The VIVO Team 2011

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LEARN MORE ABOUT VIVO Project http://vivoweb.org/ Sourceforge http://sourceforge.net/projects/vivo/ Facebook http://facebook.com/VIVOcollaboration Twitter http://twitter.com/VIVOcollab Multi site search (beta) http://vivosearch.org /