VIVO: A Semantic Web Network Enabling Collaboration Among Scientists

1. VIVO: A Semantic Web Network Enabling Collaboration Among Scientists Mike Conlon, University of Florida John Ruffing, Weill Cornell Medical College Friday 21 October 2011

2. 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

3. Data, Tools and Community

4. overview • Institutional Context • Data • Tools • Consuming Data • Providing Data • Community

5. 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)

6. Current Pilot Implementation Sites and Collaborators

7. Data: linked and open • Semantic Web • RDF • Ontology

8. VIVO’s semantic advantage Everything has its own URI All data has standard format Data modeled as bidirectional relationships

9. 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]

10. 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

11. Opendata 11

12. 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

14. Alignment with eagle-I ontology

15. 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

16. 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

17. vivo.wustl.edu

18. CV Full integration with Digital Vita

19. Faceted search, browse, and ontology hierarchy

20. Visualizations about people

21. Inter-institutional Collaboration Explorer http://xcite.hackerceo.org/VIVOviz

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

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

30. 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

31. Providing Data

32. 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

33. 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

34. VIVO-Cornell: Harvester…and disseminator

35. 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

36. Harvester design

37. Power Tool for Dirty Data – Google Refine + VIVO

38. 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

39. Targets for harvesting data

41. 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

42. Linked Open Data RDF Triples RDF Triples

43. 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

44. VIVO 2012, August 22-24, Hotel Intercontinental, Miami, Florida

45. Thank you! The VIVO Team 2011

46. 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/