Mike Conlon University of Florida John Ruffing Weill Cornell Medical College Friday 21 October 2011 What is VIVO VIVO is open standards and linked open data regarding science people papersproducts funding events resources projects data concepts and the relationships betwee ID: 807106
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Slide1
VIVO: A Semantic Web Network Enabling Collaboration Among Scientists
Mike Conlon, University of Florida
John Ruffing, Weill Cornell Medical College
Friday 21 October 2011
Slide2What 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
Slide3Data, Tools
and Community
Slide4overviewInstitutional ContextData
Tools
Consuming Data
Providing Data
Community
Slide5VIVO 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)
Slide6Current Pilot Implementation Sites and Collaborators
Slide7Data: linked and openSemantic WebRDF
Ontology
Slide8VIVO’s
semantic advantage
Data modeled as bidirectional
relationships
All data has
standard format
Everything has its
own URI
Slide9Resource 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/
Slide10Andrew 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
Slide1111
Open
data
Slide12processOrg
<-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
Slide13Slide14Alignment with eagle-I ontology
Slide15VIVO 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
Slide16Providing 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
Slide17vivo.wustl.edu
Slide18Full integration with Digital Vita
CV
Slide19Faceted search, browse, and ontology hierarchy
Slide20Visualizations about people
Slide21Inter-institutional Collaboration Explorer
http://xcite.hackerceo.org/VIVOviz
Slide22Draw organizational charts
http://vivoweb.org/files/orgLast.pdf
Slide23Slide24Slide25Slide26Slide27Slide28Slide29Repurpose content into
Drupal
http://bit.ly/gmm8Ng
Slide30Research 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
Slide31Providing Data
Slide32>
>
>
>
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
Slide33VIVO
VIVO application architecture
MySQL
relational database
Jena
Java RDF library
Tomcat
Java servlet container
VIVO
servlets
, page templates,
javascript
,
css
Apache
web server
Java
Freemarker
&
JSPs
local ontology extensions
theming & branding, navigation, browse tools
customization
application
delivery
foundation
Lucene
Java search library
Pellet
reasoning engine
Slide34VIVO-Cornell: Harvester
…and disseminator
Slide35Manual
Annual faculty reporting
Manual
PubMed
Course database
Annual faculty reporting
Manual
Annual faculty reporting
OSP data warehouse
Annual faculty reporting
OHR – appointment
OHR
– appointment
Annual faculty reporting
Annual faculty reporting
Annual faculty reporting
Manual
VIVO-Cornell as harvester: Content sources
Slide36Harvester design
Slide37Power Tool for Dirty Data – Google Refine + VIVO
Slide38WCMC/CTSA Sources of Data
Local Systems of Record
HR
RASP
Data Aggregators and Repositories
PubMed
Web of Science
Grants.gov
Individuals or their Proxies
Slide39Targets for harvesting data
Slide40Slide41From 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
Slide42Linked Open Data
RDF
Triples
RDF
Triples
Slide43Building 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 festOn-line community
http://vivo.sourceforge.net
Slide44VIVO 2012, August 22-24, Hotel Intercontinental, Miami, Florida
Slide45Thank you!
The VIVO Team 2011
Slide46Learn 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
/