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VIVO: enabling the discovery of research and scholarship

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An introduction to VIVO, an open source, semantic web application that enables discovery of research and scholarship across institutions and one library's role in its implementation and development.

Publicada em: Educação, Tecnologia
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VIVO: enabling the discovery of research and scholarship

  1. 1. VIVO: Enabling the Discovery of Research and Scholarship <ul><li>COLLEEN CUDDY, MA, MLS, AHIP </li></ul><ul><li>PAUL ALBERT, MA, MLS </li></ul><ul><li>Weill Cornell Medical Library </li></ul>library.weill.cornell.edu
  2. 2. BACKGROUND INFORMATION <ul><li>What is VIVO? </li></ul>
  3. 3. VIVO Defined <ul><li>VIVO promotes open standards and open linked data about research – people, papers/products, funding, events/presentations, resources, projects/studies, data, concepts – and the relationships between them. </li></ul><ul><li>VIVO is a set of open source, community-maintained software tools for research discovery and networking in science and other disciplines. </li></ul><ul><li>VIVO is a world community of collaborators – scientists, implementers, developers. </li></ul>
  4. 4. One Minute VIVO History <ul><li>2003 – VIVO created for local use at Cornell University (Ithaca) to support a university-wide life sciences initiative </li></ul><ul><li>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. </li></ul><ul><li>2010 Apr – Version 1.0 released </li></ul><ul><li>2010 July – Version 1.1 released </li></ul><ul><li>2010 Aug – First VIVO conference (NYC) </li></ul><ul><li>2011 Feb – Version 1.2 and Harvester version 1.0 </li></ul><ul><li>2011 July – Version 1.3 released </li></ul><ul><li>2011 Aug – Second VIVO conference (D.C.) </li></ul><ul><li>2012 Aug – Third VIVO conference (Miami) </li></ul>
  5. 5. Showcase credentials, expertise, skills, and professional achievements Connect within focus areas and geographic expertise Simplify reporting tasks and link data to external applications – e.g., to generate biosketches or CVs Publish the URL or populate profiles on other websites Find potential colleagues by research area, authorship, and collaborations Display visualizations of complex research networks and relationships What One Can (and Potentially Can) Do With VIVO
  6. 6. Who can use VIVO?
  7. 7. Reuse Data Across Applications
  8. 8. Original VIVO Implementation Sites <ul><li>University of Florida – Principal Investigator </li></ul><ul><li>Cornell University </li></ul><ul><li>Indiana University </li></ul><ul><li>Ponce School of Medicine </li></ul><ul><li>The Scripps Research Institute </li></ul><ul><li>Washington University School of Medicine </li></ul><ul><li>Weill Cornell Medical College (WCMC) </li></ul>
  9. 9. Current Pilot Implementation Sites and Collaborators <ul><li>University of Florida – Principe Investigator </li></ul><ul><li>Cornell University </li></ul><ul><li>Indiana University </li></ul><ul><li>Ponce School of Medicine </li></ul><ul><li>The Scripps Research Institute </li></ul><ul><li>Washington University School of Medicine </li></ul><ul><li>Weill Cornell Medical College (WCMC) </li></ul>
  10. 10. VIVO Collaborators Federal agencies – NIH, USDA, EPA, NSF, OSTP, FDP, STAR Metrics, NSF, NLM, VA, CENDI … Publishers and Aggregators – ORCID, Thomson Reuters, CiteSeer, arXiv, PLoS, BioMed Central, D-Space, Elsevier/Collexis … Press – Nature, Science, Cell, Genome Tech, SEED, The Chronicle, AP, Information Today, IEEE, Wired, … Professional Societies – APA, AAAS, AIRI, AAMC, ABRF, APA, … International – Australia, China, Netherlands, UK, Brazil, India, Costa Rica, Mexico, … Semantic Web community – eagle-i, DERI, Tim Berners-Lee, MyExperiment, ConceptWeb, Open Pharma Space (EU), Linked Data , … Social Network Analysis Community – Northwestern, Davis, UCF, … Schools and Consortia – CTSAs, CIC, SURA, FLR, Iowa, Harvard, UCSF, Pittsburgh, Stanford, MIT, Brown, Michigan, Colorado, OHSU, Duke, Minnesota, many more Sub-awards to Duke, Pittsburgh, Leicester, Stony Brook, Weill, Indiana Other Collaborators – Symplectic Elements, Wellspring, … Application and service providers – over 100 SourceForge File downloads – 10,000+ on SF since May 2010 Contact list – over 1,500
  11. 11. Is VIVO Facebook for Researchers? <ul><li>No Mendeley is… (Ha) </li></ul>
  12. 12. KEY CONCEPTS OF VIVO <ul><li>What is VIVO? </li></ul>
  13. 13. Semantic representation of data
  14. 14. <ul><li>Data are structured in the form of “triples” as subject-predicate-object. </li></ul><ul><li>Information is stored using the Resource Description Framework (RDF). </li></ul><ul><li>Concepts and their relationships use a shared ontology to facilitate the harvesting of data from multiple sources. </li></ul>How does VIVO store data? Jane Smith is member of author of has affiliation with Dept. of Genetics College of Medicine Journal article Book chapter Book Genetics Institute Subject Predicate Object
  15. 15. <ul><li>Dublin core – description of resources </li></ul><ul><li>Event – arbitrary time/space regions </li></ul><ul><li>FOAF – people </li></ul><ul><li>Geopolitical – countries, regions </li></ul><ul><li>SKOS – thesauri, classification schemes, knowledge </li></ul><ul><li>BIBO – publications, citations </li></ul><ul><li>VIVO – additional classes and properties to meet VIVO application needs </li></ul>Selected Core Ontologies
  16. 16. <ul><li>Research (bibo:Document, vivo:Grant, vivo:Project, vivo:Software, vivo:Dataset, vivo:ResearchLaboratory) </li></ul><ul><li>Teaching (vivo:TeacherRole, vivo:AdvisingRelatioship) </li></ul><ul><li>Services (vivo:Service, vivo:CoreLaboratory, vivo:MemberRole) </li></ul><ul><li>Expertise (vivo:SubjectArea) </li></ul>Example: modeling a person
  17. 17. Alignment with eagle-I ontology
  18. 18. Local Dataflow into VIVO > > > > RDF harvest SPARQL endpoint interactive input VIVO (RDF) data ingest ontologies (RDF) shared as RDF local systems of record external sources
  19. 19. Linked Open Data RDF Triples RDF Triples
  20. 20. Community-Wide Semantic Search Search across VIVO sites
  21. 21. DATA VISUALIZATION <ul><li>What is VIVO? </li></ul>
  22. 22. Visualize co-author relationships
  23. 23. ScienceMap visualizes collections of publications
  24. 24. TOOLS & APPS FOR VIVO <ul><li>What is VIVO? </li></ul>
  25. 25. Draw organizational charts
  26. 26. VIVO produces both HTML and RDF Software reads VIVO RDF and displays
  27. 27. http://vivosearchlight.org/ @mileswortho
  28. 29. Inter-institutional Collaboration Explorer http://xcite.hackerceo.org/VIVOviz
  29. 30. Power Tool for Dirty Data – Google Refine + VIVO
  30. 31. LIBRARIES AS KEY PARTNERS <ul><li>What is VIVO? </li></ul>
  31. 32. VIVO Team at WCMC <ul><li>Curtis Cole, MD – Principal Investigator </li></ul><ul><li>Paul Albert – Data Architect </li></ul><ul><li>Mark Bronnimann – Systems Administrator </li></ul><ul><li>Eliza Chan – Developer </li></ul><ul><li>Dan Dickinson – Implementation/Technical Lead </li></ul><ul><li>Kenneth Lee – Project Manager </li></ul><ul><li>Grace Migliorosi, PhD – Outreach Coordinator </li></ul><ul><li>John Ruffing – Partner Site Integration Specialist </li></ul>
  32. 33. Why Libraries? <ul><li>Are a trusted, neutral space </li></ul><ul><li>Have a tradition of service and support </li></ul><ul><li>Strive to serve all missions of the institution </li></ul><ul><li>Are technology centers and have IT and data expertise </li></ul><ul><li>Have skills—information organization, instruction, usability, subject expertise, ontologies and controlled vocabularies </li></ul><ul><li>Have close relationships with their clients (buy in) </li></ul><ul><li>Understand user needs </li></ul><ul><li>Understand the importance of collaboration and know how to bring people together </li></ul><ul><li>Have knowledge of institution, research, education, clinical landscape </li></ul>Library Staff: Libraries:
  33. 34. The Library’ s Role in VIVO <ul><li>Identify target sources of data and set priorities </li></ul><ul><li>Resolve ambiguities between conflicting sources of data </li></ul><ul><li>Propose mappings to VIVO’ s classes and properties </li></ul><ul><li>Propose standards of data formatting </li></ul><ul><li>Create local extensions to the ontology (e.g. institutional identifier) </li></ul><ul><li>Create and implement policies for end users </li></ul>
  34. 35. COMING SOON <ul><li>What is VIVO? </li></ul>
  35. 36. What’ s next at Weill Cornell <ul><li>Publications, publications, publications!!! </li></ul><ul><li>Implement self-edit </li></ul><ul><li>Internal outreach and training </li></ul><ul><li>Internal operations support </li></ul><ul><li>Upgrade to VIVO 1.3 </li></ul><ul><li>Data exchange with CTSA partners – Hunter, Methodist, HSS, MSKCC </li></ul><ul><li>Establishing policies </li></ul>
  36. 37. WCMC/CTSA Sources of Data <ul><li>Local Systems of Record </li></ul><ul><ul><li>HR </li></ul></ul><ul><ul><li>RASP </li></ul></ul><ul><li>Data Aggregators and Repositories </li></ul><ul><ul><li>PubMed </li></ul></ul><ul><ul><li>Web of Science </li></ul></ul><ul><ul><li>Grants.gov </li></ul></ul><ul><li>Individuals or their Proxies </li></ul>
  37. 38. What’ s next on the International Level <ul><li>Identify best practices for incorporating external data sources for publications and grants </li></ul><ul><li>Support easier customization and improved semantic search </li></ul><ul><li>Extend the ontology to support intellectual property, research datasets, and more detail about research resources </li></ul><ul><li>Identify and commit to a governance structure </li></ul><ul><li>Better provenance </li></ul><ul><li>and… </li></ul>
  38. 39. Full integration with Digital Vita CV
  39. 40. What ’s next (National Level) <ul><li>Display visualizations of complex research networks and relationships. </li></ul><ul><li>Incorporate external data sources for publications and grants. </li></ul><ul><li>Support easier customization and improved semantic search. </li></ul><ul><li>Link data to external applications, e.g. generate CV ’s or bio sketches. </li></ul><ul><li>Ability to search all VIVO sites/communities. </li></ul>Improved search relevance and faceting
  40. 41. DEMONSTRATION <ul><li>What is VIVO? </li></ul>
  41. 42. Learn More About VIVO <ul><li>Project – http://vivoweb.org/ </li></ul><ul><li>Multi-site search (beta) – http://vivosearch.org/ </li></ul><ul><li>Sourceforge – http://sourceforge.net/projects/vivo/ </li></ul><ul><li>Facebook – http://facebook.com/VIVOcollaboration </li></ul><ul><li>Twitter – http://twitter.com/VIVOcollab </li></ul>
  42. 43. Cornell University Dean Krafft (Cornell PI) Manolo Bevia Jim Blake Nick Cappadona Brian Caruso Jon Corson-Rikert Elly Cramer Medha Devare Elizabeth Hines Huda Khan Deepak Konidena Brian Lowe Joseph McEnerney Holly Mistlebauer Stella Mitchell Anup Sawant Christopher Westling Tim Worrall Rebecca Younes University of Florida Mike Conlon (VIVO and UF PI) Beth Auten Michael Barbieri Chris Barnes Kaitlin Blackburn Cecilia Botero Kerry Britt Erin Brooks Amy Buhler Ellie Bushhousen Linda Butson Chris Case Christine Cogar Valrie Davis Mary Edwards Nita Ferree Rolando Garcia-Milan George Hack Chris Haines Sara Henning Rae Jesano Margeaux Johnson Meghan Latorre Yang Li Jennifer Lyon Paula Markes Hannah Norton James Pence Narayan Raum Nicholas Rejack Alexander Rockwell Sara Russell Gonzalez Nancy Schaefer Dale Scheppler Nicholas Skaggs Matthew Tedder Michele R. Tennant Alicia Turner Stephen Williams Indiana University Katy Borner (IU PI) Kavitha Chandrasekar Bin Chen Shanshan Chen Ryan Cobine Jeni Coffey Suresh Deivasigamani Ying Ding Russell Duhon Jon Dunn Poornima Gopinath Julie Hardesty Brian Keese Namrata Lele Micah Linnemeier Nianli Ma Robert H. McDonald Asik Pradhan Gongaju Mark Price Michael Stamper Yuyin Sun Chintan Tank Alan Walsh Brian Wheeler Feng Wu Angela Zoss Ponce School of Medicine Richard J. Noel, Jr. (Ponce PI) Ricardo Espada Colon Damaris Torres Cruz Michael Vega Negrón This project is funded by the National Institutes of Health, U24 RR029822 &quot;VIVO: Enabling National Networking of Scientists ” The Scripps Research Institute Gerald Joyce (Scripps PI) Catherine Dunn Sam Katkov Brant Kelley Paula King Angela Murrell Barbara Noble Cary Thomas Michaeleen Trimarchi Washington University School of Medicine in St. Louis Rakesh Nagarajan (WUSTL PI) Kristi L. Holmes Caerie Houchins George Joseph Sunita B. Koul Leslie D. McIntosh Weill Cornell Medical College Curtis Cole (Weill PI) Paul Albert Victor Brodsky Mark Bronnimann Adam Cheriff Oscar Cruz Dan Dickinson Richard Hu Chris Huang Itay Klaz Kenneth Lee Peter Michelini Grace Migliorisi John Ruffing Jason Specland Tru Tran Vinay Varughese Virgil Wong VIVO Collaboration
  43. 44. QUESTIONS? <ul><li>Thank You! </li></ul>