June 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesHot Topics: The DuraSpaceCommunity Webinar SeriesSeries Five:“...
June 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesWebinar 3:VIVO Technical Deep DivePresented by:Brian Lowe, Sem...
VIVO “behind the curtain”June 11, 2013 Hot Topics: DuraSpace Community Webinar Series
Diving into VIVOJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
An “individual page”June 11, 2013 Hot Topics: DuraSpace Community Webinar Series
Not only people are individualsJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
Exposing the semanticsJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
Exposing the semanticsJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
A store of triplesJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
Basic patternsJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesUSDAfoaf:Organizationrdf:typetion
Basic patternsJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesUSDAfoaf:Organizationrdf:typetionvivo:awardsGran...
“Context node” patternJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesEat Smart NY
“Context node” patternJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesPersonInvestigator Rolehas rolerole inGr...
“Context node” patternJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesPersonhas rolerole inGrantDate/TimeInter...
“List views”June 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesEat Smart NY
“List views”June 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesEat Smart NYTripleStoreSPARQLqueriesdisplaytemplate
Triple storesJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesEat Smart NYTripleStoreSPARQLqueriesdisplaytempla...
ReasoningJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplate
ReasoningJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplate
Beyond the triple store:SOLR indexJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdis...
Beyond the triple store:SOLR indexJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdis...
Linked DataLinkSailor by Ian DavisHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplateJu...
Linked DataFollow your noseHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplateJune 11, ...
Linked DataFollow your noseHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplateJune 11, ...
Linked Data applicationsHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplateJune 11, 2013
Linked Data applicationsHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplatePonceVIVOWas...
Data integrationHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplate• Not just transform...
Data integrationHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplate• Disambiguating / d...
Data integration toolsHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplate• Lots of opti...
Data integration ToolsHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplate• VIVO Harvest...
Data integration toolsHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplateJune 11, 2013
Data integration toolsHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplateJune 11, 2013
THE VIVO APPLICATIONJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
From the outside• Supports browsing and searching withfaceted results• Usually populated by ingest• Supports authorized ed...
VIVO is open source• OSI BSD license– Moving to Apache 2 license• Built on open source components– Jena– Solr– jQuery– Fre...
VIVO plays well with others• Host operating system– Linux, Windows• Java web container– Tomcat, GlassFish, WebLogic• Datab...
The customary 3-layerarchitecture?Hot Topics: DuraSpace Community Webinar SeriesJune 11, 2013Presentation:HTML, CSS, JavaS...
A typical installationHot Topics: DuraSpace Community Webinar SeriesFirewallApacheHTTPserverTomcatVIVOSolrMySQLJune 11, 2013
Typical Apache functions• URL translation– http://vserver.domain.edu:8080/vivo http://vivo.domain.edu• Authentication sup...
VIVO is intended for customization• Themes and styles• Displays and editing• Static and dynamic pages• Extensions to the o...
VIVO is intended for customizationHot Topics: DuraSpace Community Webinar SeriesJune 11, 2013
VIVO is intended for customizationHot Topics: DuraSpace Community Webinar SeriesJune 11, 2013
VIVO is intended for customizationHot Topics: DuraSpace Community Webinar SeriesJune 11, 2013
VIVO is intended for customizationHot Topics: DuraSpace Community Webinar SeriesJune 11, 2013
VIVO is a customization• Vitro is a general-purpose web-basedontology and instanceeditor withcustomizable browsing• VIVO i...
Release 1.6 directions• Ontology normalization– Integrated Semantic Framework– Separating data content from displaycontext...
THE VIVO COMMUNITYJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
Who are we?• People who are developing VIVO• People who are installing VIVO• People who are customizing VIVO• People who a...
What does the community provide?• Mutual assistance on installations• Answers to questions about VIVO• Bug reports• Shared...
The front door – vivoweb.orgJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
vivoweb.org• Blog with info about– latest events– latest releases• Links to the other resources• “Contact Us” formJune 11,...
The conversation: open calls• Implementation and Development call– Every Thursday at 1:00 p.m., Eastern time– Full info an...
The conversation: mailing lists• Issues relating to VIVO implementation– https://lists.sourceforge.net/lists/listinfo/vivo...
The gatherings:The VIVO ConferenceJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
The gatherings:Implementation FestJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
Resources• Documentation– https://wiki.duraspace.org/display/VIVO• Tracking issues and progress– https://jira.duraspace.or...
Community Contributions• Ontology• Design• Code• Testing• Documentation• Outreach• “Ecosystem”June 11, 2013 Hot Topics: Du...
Find out more• Our web site:– http://vivoweb.org• The VIVO book:– VIVO: A Semantic Approach toScholarly Networking and Dis...
June 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesQuestions?Brian LoweCornell Universitybjl23@cornell.eduJim Bla...
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6-11-13 VIVO Technical Deep Dive Presentation Slides

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“Hot Topics: The DuraSpace Community Webinar Series, "Series Five: VIVO: Research Discovery and Networking.” Webinar #: 6-11-13 VIVO Technical Deep Dive, June 11, 2013
Presented by: Brian Lowe, Semantic Applications Programmer, Cornell University and Jim Blake, VIVO Release Manager, Cornell University.

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Transcript of "6-11-13 VIVO Technical Deep Dive Presentation Slides"

  1. 1. June 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesHot Topics: The DuraSpaceCommunity Webinar SeriesSeries Five:“VIVO: Research Discovery &Networking ”Curated by Dean Krafft
  2. 2. June 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesWebinar 3:VIVO Technical Deep DivePresented by:Brian Lowe, Semantic Applications Programmer, CornellJim Blake, VIVO Release Manager, Cornell
  3. 3. VIVO “behind the curtain”June 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  4. 4. Diving into VIVOJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  5. 5. An “individual page”June 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  6. 6. Not only people are individualsJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  7. 7. Exposing the semanticsJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  8. 8. Exposing the semanticsJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  9. 9. A store of triplesJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  10. 10. Basic patternsJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesUSDAfoaf:Organizationrdf:typetion
  11. 11. Basic patternsJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesUSDAfoaf:Organizationrdf:typetionvivo:awardsGrantEat Smart NY
  12. 12. “Context node” patternJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesEat Smart NY
  13. 13. “Context node” patternJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesPersonInvestigator Rolehas rolerole inGrant
  14. 14. “Context node” patternJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesPersonhas rolerole inGrantDate/TimeIntervalDate/Time ValueDate/Time Value Date/Time Value“2012”“2008”Investigator Role
  15. 15. “List views”June 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesEat Smart NY
  16. 16. “List views”June 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesEat Smart NYTripleStoreSPARQLqueriesdisplaytemplate
  17. 17. Triple storesJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesEat Smart NYTripleStoreSPARQLqueriesdisplaytemplate• Dump in whatever youwant (or can)• Extend the ontology;VIVO application adapts• Others take what theywant, ignore the rest• Reasoners add triplesautomatically
  18. 18. ReasoningJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplate
  19. 19. ReasoningJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplate
  20. 20. Beyond the triple store:SOLR indexJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplate
  21. 21. Beyond the triple store:SOLR indexJune 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplate
  22. 22. Linked DataLinkSailor by Ian DavisHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplateJune 11, 2013
  23. 23. Linked DataFollow your noseHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplateJune 11, 2013
  24. 24. Linked DataFollow your noseHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplateJune 11, 2013
  25. 25. Linked Data applicationsHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplateJune 11, 2013
  26. 26. Linked Data applicationsHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplatePonceVIVOWashUVIVOIUVIVOCornellIthacaVIVOWeillCornellVIVOeagle-IResearchresourcesOtherVIVOsDigitalVitaRDFIowaLokiRDFvivosearch.orgUFVIVOScrippsVIVOSolrsearchindexAlter-nateSolrindexLinked OpenDataJune 11, 2013HarvardProfilesRDF
  27. 27. Data integrationHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplate• Not just transforming one documentinto another• Turning strings into things• Making connections• Building a graph– Inside VIVO and linking out to theLinked Data cloudJune 11, 2013
  28. 28. Data integrationHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplate• Disambiguating / deduping• Dealing with dirty or incomplete dataJune 11, 2013
  29. 29. Data integration toolsHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplate• Lots of options• Triples just get dumped into triple storein the end• RDF can include additional source datanot needed for VIVO displayJune 11, 2013
  30. 30. Data integration ToolsHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplate• VIVO Harvester– developed at University of Florida– convert from XML, CSV, relationaldatabases– extensible architecture– fetch, translate, score and matchJune 11, 2013
  31. 31. Data integration toolsHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplateJune 11, 2013
  32. 32. Data integration toolsHot Topics: DuraSpace Community Webinar SeriesEat Smart NYSPARQLqueriesdisplaytemplateJune 11, 2013
  33. 33. THE VIVO APPLICATIONJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  34. 34. From the outside• Supports browsing and searching withfaceted results• Usually populated by ingest• Supports authorized editing of data• Supports Linked Open Data requestsHot Topics: DuraSpace Community Webinar SeriesJune 11, 2013
  35. 35. VIVO is open source• OSI BSD license– Moving to Apache 2 license• Built on open source components– Jena– Solr– jQuery– FreeMarker• Source code athttps://github.com/vivo-projectHot Topics: DuraSpace Community Webinar SeriesJune 11, 2013
  36. 36. VIVO plays well with others• Host operating system– Linux, Windows• Java web container– Tomcat, GlassFish, WebLogic• Database layer– MySQL, Oracle• Browsers– Firefox, Chrome, Safari– Internet Explorer 7, 8, 9Hot Topics: DuraSpace Community Webinar SeriesJune 11, 2013
  37. 37. The customary 3-layerarchitecture?Hot Topics: DuraSpace Community Webinar SeriesJune 11, 2013Presentation:HTML, CSS, JavaScript, AJAX, jQueryFreeMarker template engineBusiness logic:Java Web applicationData:A semantic triple store or SPARQL endpoint(frequently layered over a relational data base)
  38. 38. A typical installationHot Topics: DuraSpace Community Webinar SeriesFirewallApacheHTTPserverTomcatVIVOSolrMySQLJune 11, 2013
  39. 39. Typical Apache functions• URL translation– http://vserver.domain.edu:8080/vivo http://vivo.domain.edu• Authentication support– Shibboleth, CAS, LDAP• Security– Firewall, HTTPS enforcement• HTTP cachingHot Topics: DuraSpace Community Webinar SeriesJune 11, 2013
  40. 40. VIVO is intended for customization• Themes and styles• Displays and editing• Static and dynamic pages• Extensions to the ontology• OpenSocial gadgets• Backing technologiesHot Topics: DuraSpace Community Webinar SeriesJune 11, 2013
  41. 41. VIVO is intended for customizationHot Topics: DuraSpace Community Webinar SeriesJune 11, 2013
  42. 42. VIVO is intended for customizationHot Topics: DuraSpace Community Webinar SeriesJune 11, 2013
  43. 43. VIVO is intended for customizationHot Topics: DuraSpace Community Webinar SeriesJune 11, 2013
  44. 44. VIVO is intended for customizationHot Topics: DuraSpace Community Webinar SeriesJune 11, 2013
  45. 45. VIVO is a customization• Vitro is a general-purpose web-basedontology and instanceeditor withcustomizable browsing• VIVO is a thin layeraround VitroHot Topics: DuraSpace Community Webinar SeriesJune 11, 2013VIVOVitro
  46. 46. Release 1.6 directions• Ontology normalization– Integrated Semantic Framework– Separating data content from displaycontext• Full featured Web Service– Get data, modify data– Integrated authentication and indexing• Internationalization– Support for multiple languages• Performance improvementsHot Topics: DuraSpace Community Webinar SeriesJune 11, 2013
  47. 47. THE VIVO COMMUNITYJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  48. 48. Who are we?• People who are developing VIVO• People who are installing VIVO• People who are customizing VIVO• People who are re-purposing VIVO• People who are curious about VIVOJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  49. 49. What does the community provide?• Mutual assistance on installations• Answers to questions about VIVO• Bug reports• Shared code or configurations• Documentation• Ideas on how to improve VIVO• Use cases and requirements• Pre-release testingJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  50. 50. The front door – vivoweb.orgJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  51. 51. vivoweb.org• Blog with info about– latest events– latest releases• Links to the other resources• “Contact Us” formJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  52. 52. The conversation: open calls• Implementation and Development call– Every Thursday at 1:00 p.m., Eastern time– Full info and agendas on the wiki: search “WeeklyImplementation Calls”• Ontology call– Alternate Wednesdays at 11:00 a.m., Eastern time– Full info and agendas on the wiki: search“Ontology Calls”• WebEx conferencing provides simultaneousaudio, chat and screen-sharing• Everyone is welcomeJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  53. 53. The conversation: mailing lists• Issues relating to VIVO implementation– https://lists.sourceforge.net/lists/listinfo/vivo-imp-issues• Discussion of VIVO development– https://lists.sourceforge.net/lists/listinfo/vivo-dev-all• Discussion of the VIVO ontology– https://lists.sourceforge.net/lists/listinfo/vivo-ontology• Announcements of VIVO release candidates– https://lists.sourceforge.net/lists/listinfo/vivo-release-test• Anyone can join – archives are available forsearchingJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  54. 54. The gatherings:The VIVO ConferenceJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  55. 55. The gatherings:Implementation FestJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  56. 56. Resources• Documentation– https://wiki.duraspace.org/display/VIVO• Tracking issues and progress– https://jira.duraspace.orgJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  57. 57. Community Contributions• Ontology• Design• Code• Testing• Documentation• Outreach• “Ecosystem”June 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  58. 58. Find out more• Our web site:– http://vivoweb.org• The VIVO book:– VIVO: A Semantic Approach toScholarly Networking and Discovery• The 2013 VIVO Conference– August 14-16, St. Louis, MOJune 11, 2013 Hot Topics: DuraSpace Community Webinar Series
  59. 59. June 11, 2013 Hot Topics: DuraSpace Community Webinar SeriesQuestions?Brian LoweCornell Universitybjl23@cornell.eduJim BlakeCornell Universityjeb228@cornell.edu

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