6-11-13 VIVO Technical Deep Dive Presentation Slides

June 11, 2013 Hot Topics: DuraSpace Community Webinar Series
Hot Topics: The DuraSpace
Community Webinar Series
Series Five:
“VIVO: Research Discovery &
Networking ”
Curated by Dean Krafft

Webinar 3:
VIVO Technical Deep Dive
Presented by:
Brian Lowe, Semantic Applications Programmer, Cornell
Jim Blake, VIVO Release Manager, Cornell

VIVO “behind the curtain”

Diving into VIVO

An “individual page”

Not only people are individuals

Exposing the semantics

A store of triples

Basic patterns
USDA
foaf:Organization
rdf:typetion

Basic patterns
USDA
foaf:Organization
rdf:typetion
vivo:awardsGrant
Eat Smart NY

“Context node” pattern
Eat Smart NY

Person
Investigator Role
has role
role in
Grant

Person
has role
role in
Grant
Date/Time
Interval
Date/Time Value
Date/Time Value Date/Time Value
“2012”“2008”
Investigator Role

“List views”
Eat Smart NY

“List views”
Eat Smart NY
Triple
Store
SPARQL
queries
display
template

Triple stores
Eat Smart NY
Triple
Store
SPARQL
queries
display
template
• Dump in whatever you
want (or can)
• Extend the ontology;
VIVO application adapts
• Others take what they
want, ignore the rest
• Reasoners add triples
automatically

Reasoning
Eat Smart NY
SPARQL
queries
display
template

Beyond the triple store:
SOLR index
Eat Smart NY
SPARQL
queries
display
template

Linked Data
LinkSailor by Ian Davis
Hot Topics: DuraSpace Community Webinar Series
Eat Smart NY
SPARQL
queries
display
template
June 11, 2013

Linked Data
Follow your nose
Eat Smart NY
SPARQL
queries
display
template
June 11, 2013

Linked Data applications
Eat Smart NY
SPARQL
queries
display
template
June 11, 2013

Linked Data applications
Eat Smart NY
SPARQL
queries
display
template
Ponce
VIVO
WashU
VIVO
IU
VIVO
Cornell
Ithaca
VIVO
Weill
Cornel
l
VIVO
eagle-I
Research
resources
Other
VIVOs
Digita
l
Vita
RDF
Iowa
Loki
RDF
vivo
search.
org
UF
VIVO
Scripps
VIVO
Solr
search
index
Alter-
nate
Solr
indexLinked Open
Data
June 11, 2013
Harvard
Profiles
RDF

Data integration
Eat Smart NY
SPARQL
queries
display
template
• Not just transforming one document
into another
• Turning strings into things
• Making connections
• Building a graph
– Inside VIVO and linking out to the
Linked Data cloud
June 11, 2013

Data integration
Eat Smart NY
SPARQL
queries
display
template
• Disambiguating / deduping
• Dealing with dirty or incomplete data
June 11, 2013

Data integration tools
Eat Smart NY
SPARQL
queries
display
template
• Lots of options
• Triples just get dumped into triple store
in the end
• RDF can include additional source data
not needed for VIVO display
June 11, 2013

Data integration Tools
Eat Smart NY
SPARQL
queries
display
template
• VIVO Harvester
– developed at University of Florida
– convert from XML, CSV, relational
databases
– extensible architecture
– fetch, translate, score and match
June 11, 2013

Data integration tools
Eat Smart NY
SPARQL
queries
display
template
June 11, 2013

THE VIVO APPLICATION

From the outside
• Supports browsing and searching with
faceted results
• Usually populated by ingest
• Supports authorized editing of data
• Supports Linked Open Data requests
Hot Topics: DuraSpace Community Webinar SeriesJune 11, 2013

VIVO is open source
• OSI BSD license
– Moving to Apache 2 license
• Built on open source components
– Jena
– Solr
– jQuery
– FreeMarker
• Source code at
https://github.com/vivo-project

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, 9

The customary 3-layer
architecture?
Presentation:
HTML, CSS, JavaScript, AJAX, jQuery
FreeMarker template engine
Business logic:
Java Web application
Data:
A semantic triple store or SPARQL endpoint
(frequently layered over a relational data base)

A typical installation
Firewall
Apache
HTTP
server
Tomcat
VIVO
Solr
MySQL
June 11, 2013

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 caching

VIVO is intended for customization
• Themes and styles
• Displays and editing
• Static and dynamic pages
• Extensions to the ontology
• OpenSocial gadgets
• Backing technologies

VIVO is intended for customization

VIVO is a customization
• Vitro is a general-
purpose web-based
ontology and instance
editor with
customizable browsing
• VIVO is a thin layer
around Vitro
VIVO
Vitro

Release 1.6 directions
• Ontology normalization
– Integrated Semantic Framework
– Separating data content from display
context
• Full featured Web Service
– Get data, modify data
– Integrated authentication and indexing
• Internationalization
– Support for multiple languages
• Performance improvements

THE VIVO COMMUNITY

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 VIVO

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 testing

The front door – vivoweb.org

vivoweb.org
• Blog with info about
– latest events
– latest releases
• Links to the other resources
• “Contact Us” form

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 “Weekly
Implementation 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 simultaneous
audio, chat and screen-sharing
• Everyone is welcome

The conversation: mailing lists
• Issues relating to VIVO implementation
– https://lists.sourceforge.net/lists/listinfo/vivo-
imp-issues
• Discussion of VIVO development
dev-all
• Discussion of the VIVO ontology
ontology
• Announcements of VIVO release candidates
release-test
• Anyone can join – archives are available for
searching

The gatherings:
The VIVO Conference

The gatherings:
Implementation Fest

Resources
• Documentation
– https://wiki.duraspace.org/display/VI
VO
• Tracking issues and progress
– https://jira.duraspace.org

Community Contributions
• Ontology
• Design
• Code
• Testing
• Documentation
• Outreach
• “Ecosystem”

Find out more
• Our web site:
– http://vivoweb.org
• The VIVO book:
– VIVO: A Semantic Approach to
Scholarly Networking and Discovery
• The 2013 VIVO Conference
– August 14-16, St. Louis, MO

Questions?
Brian Lowe
Cornell University
bjl23@cornell.edu
Jim Blake
Cornell University
jeb228@cornell.edu

6-11-13 VIVO Technical Deep Dive Presentation Slides

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6-11-13 VIVO Technical Deep Dive Presentation Slides