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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. What is VIVO?.
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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
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
overview • Institutional Context • Data • Tools • Consuming Data • Providing Data • Community
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)
Data: linked and open • Semantic Web • RDF • Ontology
VIVO’s semantic advantage Everything has its own URI All data has standard format Data modeled as bidirectional relationships
Resource Description Framework (RDF) • simple data model for representing information • allows anyone to make statements about any resource • Can be represented in XML • based on “triples”: From: http://www.w3.org/TR/rdf-concepts/ Subject [Susan Riha] Object [NYS WRI] Predicate [head of]
Semantic representation of data has author Andrew McDonald Mining the record: Historical evidence for… author of academic staff in research area research area for academic staff has author author of taught by research area crop management Susan Riha teaches research area for headed by CSS 4830 NYS WRI head of faculty appointment in faculty members features person Earth and Atmospheric Sciences featured in Cornell’s supercomputers crunch weather data to help farmers manage chemicals
Opendata 11
Software reads VIVO RDF and displays 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
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
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
CV Full integration with Digital Vita
Inter-institutional Collaboration Explorer http://xcite.hackerceo.org/VIVOviz
Draw organizational charts http://vivoweb.org/files/orgLast.pdf
Repurpose content into Drupal http://bit.ly/gmm8Ng
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 – find investigators “like me” across the network • 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
local systems of record data ingest ontologies (RDF) VIVO (RDF) shared as RDF externalsources Data flow through a VIVO system > > > > RDF harvest SPARQL endpoint interactive input
VIVO application architecture VIVO local ontology extensions theming & branding, navigation, browse tools customization VIVO servlets, page templates, javascript, css Tomcat Java servlet container Apache web server application delivery Jena Java RDF library Lucene Java search library JavaFreemarker & JSPs Pellet reasoning engine foundation MySQL relational database
VIVO-Cornell as harvester: Content sources OSP data warehouse Course database OHR – appointment OHR – appointment Annual faculty reporting Annual faculty reporting Annual faculty reporting Manual Annual faculty reporting Annual faculty reporting Annual faculty reporting Manual Manual Annual faculty reporting PubMed Manual
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
From local to national National browse search share as RDF visualize Aggregating and indexing RDF Exemplar Local search browse visualize local sources • Cornell University • University of Florida • Indiana University • Ponce School of Medicine • The Scripps Research Institute • Washington University, St. Louis • Weill Cornell Medical College > > VIVO share as RDF nat’l sources website data
Linked Open Data RDF Triples RDF Triples
Building Community • Federal agencies – OSTP, NIH, NLM, NSF, USDA, FDP, FRPS, STAR Metrics, … • Publishers and Aggregators – Elsevier, Thomson Reuters, ORCID, CiteSeer, Arxiv, Dspace, … • Professional Societies – APA, AAAS, AIRI, AAMC, ABRF, … • International collaborators – Ireland, Germany, Australia, China, Netherlands, UK, Costa Rica, Iceland, Brazil, Mexico, … • Semantic Web community – DERI, Tim Berners-Lee, MyExperiment, ConceptWeb, Open Phacts (EU), Linked Data, … • Research resources – Eagle-I, BRO, eBIRT, RDS, … • Open Source cooperatives – Kuali, Sakai, Duraspace, … • Social Network Analysis Community – Northwestern, Davis, UCF, INSNA, … • Schools and Consortia – CTSAs, CIC, Pitt, Emory, Iowa, Harvard, UCSF, Stanford, MIT, Brown, Michigan, Nebraska, Colorado, Duke, Hunter, OHSU, Minnesota, … • Software downloads (>10,000) and contact list (>1,600) • Four annual events – conference, workshop, hackathon, implementation fest • On-line community http://vivo.sourceforge.net
VIVO 2012, August 22-24, Hotel Intercontinental, Miami, Florida
Thank you! The VIVO Team 2011
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/