VIVO: A SEMANTIC WEB NETWORK ENABLING COLLABORATION AMONG

SCIENTISTS

Mike Conlon, University of FloridaJohn Ruffing, Weill Cornell Medical College

Friday 21 October 2011

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

Data, Tools and Community

OVERVIEW

• Institutional Context• Data• Tools

• Consuming Data• Providing Data

• Community

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)

CURRENT PILOT IMPLEMENTATION SITES AND COLLABORATORS

DATA: LINKED AND OPEN

• Semantic Web• RDF• Ontology

VIVO’s semantic advantage

Data modeled as bidirectional relationships

All data has standard formatEv

eryt

hing

has

its

own

URI

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/

Andrew McDonald

author of

has author

research arearesearch 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 offaculty 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

Opendata

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

Alignment with eagle-I ontology

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

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

vivo.wustl.edu

Full integration with Digital Vita

CV

Faceted search, browse, and ontology hierarchy

VISUALIZATIONS ABOUT PEOPLE

INTER-INSTITUTIONAL COLLABORATION EXPLORER

http://xcite.hackerceo.org/VIVOviz

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

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

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

Providing Data

> > >

> RDF harvestSPARQL endpoint

VIVO(RDF)

data ingest ontologies

(RDF)shared as

RDF

interactiveinput

local systems of record

externalsources

DATA FLOW THROUGH A VIVO SYSTEM

VIVO

VIVO APPLICATION ARCHITECTURE

MySQLrelational database

JenaJava RDF library

TomcatJava servlet container

VIVOservlets, page templates,

javascript, css

Apacheweb server

Java Freemarker &

JSPs

local ontology

extensions

theming & branding,

navigation, browse tools

customization

applicationdelivery

foundation LuceneJava search

library

Pellet reasoning

engine

VIVO-Cornell: Harvester…and disseminator

Manual

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

Harvester design

POWER TOOL FOR DIRTY DATA – GOOGLE REFINE + VIVO

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

TARGETS FOR HARVESTING DATA

From local to national

> VIVO

local sources

nat’l sources

>share as RDF

website data

searchbrowse

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

Aggregatingand indexing RDF Exemplar

LINKED OPEN DATA

RDFTriples

RDFTriples

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.net

VIVO 2012, August 22-24, Hotel Intercontinental, Miami, Florida

Thank you!The VIVO Team 2011

LEARN 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/