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 Data modeled as bidirectional relationships All data has standard format Everything has its own URI

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”: Subject [Susan Riha] Object [NYS WRI] Predicate [head of] From: http://www.w3.org/TR/rdf-concepts/

10. Andrew McDonald author of has author research area research area for academic staff in academic staff Susan Riha Mining the record: Historical evidence for… 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 Cornell’s supercomputers crunch weather data to help farmers manage chemicals Earth and Atmospheric Sciences

11. 11 Open data

12. 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

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. Full integration with Digital Vita CV

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

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

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

34. VIVO-Cornell: Harvester…and disseminator

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

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 > VIVO local sources nat’l 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

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.nethttp://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/http://vivoweb.org/ Sourceforge – http://sourceforge.net/projects/vivo/ http://sourceforge.net/projects/vivo/ Facebook – http://facebook.com/VIVOcollaboration http://facebook.com/VIVOcollaboration Twitter – http://twitter.com/VIVOcollabhttp://twitter.com/VIVOcollab Multi-site search (beta) – http://vivosearch.org/ http://vivosearch.org/