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VIVO: A Semantic Web Network Enabling Collaboration Among Scientists VIVO: A Semantic Web Network Enabling Collaboration Among Scientists

VIVO: A Semantic Web Network Enabling Collaboration Among Scientists - PowerPoint Presentation

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VIVO: A Semantic Web Network Enabling Collaboration Among Scientists - PPT Presentation

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

data vivo research rdf vivo data rdf research http faculty community university annual ontology open reporting search local subs

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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

Slide2

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

Slide3

Data, Tools

and Community

Slide4

overviewInstitutional ContextData

Tools

Consuming Data

Providing Data

Community

Slide5

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)

Slide6

Current Pilot Implementation Sites and Collaborators

Slide7

Data: linked and openSemantic WebRDF

Ontology

Slide8

VIVO’s

semantic advantage

Data modeled as bidirectional

relationships

All data has

standard format

Everything has its

own URI

Slide9

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/

Slide10

Andrew 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

Slide11

11

Open

data

Slide12

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

Slide13

Slide14

Alignment with eagle-I ontology

Slide15

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

Slide16

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

Slide17

vivo.wustl.edu

Slide18

Full integration with Digital Vita

CV

Slide19

Faceted search, browse, and ontology hierarchy

Slide20

Visualizations about people

Slide21

Inter-institutional Collaboration Explorer

http://xcite.hackerceo.org/VIVOviz

Slide22

Draw organizational charts

http://vivoweb.org/files/orgLast.pdf

Slide23

Slide24

Slide25

Slide26

Slide27

Slide28

Slide29

Repurpose content into

Drupal

http://bit.ly/gmm8Ng

Slide30

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

Slide31

Providing 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

Slide33

VIVO

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

Slide34

VIVO-Cornell: Harvester

…and disseminator

Slide35

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

Slide36

Harvester design

Slide37

Power Tool for Dirty Data – Google Refine + VIVO

Slide38

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

Slide39

Targets for harvesting data

Slide40

Slide41

From 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

Slide42

Linked Open Data

RDF

Triples

RDF

Triples

Slide43

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 festOn-line community

http://vivo.sourceforge.net

Slide44

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

Slide45

Thank you!

The VIVO Team 2011

Slide46

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

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