VIVO Community Day

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VIVO

Community Day


Melbourne, Australia

6 February 2012

Who are we?


Simon Porter


University of Melbourne


Brian Lowe


Semantic Applications Programmer, Mann Library Cornell
University


Semantic Team Lead for VIVO


Huda Khan


Semantic Applications Programmer, Mann Library Cornell
University


DataStaR



Stephen Williams


Senior Software Engineer, University of Florida


Originally VIVO Implementation IT


VIVO Data Ingest and Packaging Team

2

VIVO Vision


Towards building an
international network of
researchers

3


Showcase research and scholarly activity
across the university


Primary focus on people


Publications


Grants


Roles in activities


Coauthors and coinvestigators


4

VIVO Vision

Towards building an international network of researchers


Public data


Breaking out of institutional silos


Open technology


Open standards


Discover connections


Make connections


Promote better research


Within an institution


Nationally


Internationally


5

VIVO Vision

Towards building an international network of researchers

6

VIVO Vision

Towards building an international network of researchers

7

VIVO Vision

Towards building an international network of researchers

8

VIVO Vision

Towards building an international network of researchers

9

VIVO Vision

Towards building an international network of researchers

10

VIVO Vision

Towards building an international network of researchers

Semantic Web and Linked Data


Represent data as a big collection of simple (RDF)
statements





George Abawi a Faculty Member



VIVO Vision

Towards building an international network of researchers

Semantic Web and Linked Data


Use URIs to uniquely identify what we

re talking about




George Abawi

<
http://vivo.cornell.edu/individual/individual5320>


a


Faculty Member

<http://vivoweb.org/ontology/core#FacultyMember>

VIVO Vision

Towards building an international network of researchers

RDF Statements


Want to say something else? Just drop in some
more statements.



-

There

s always room for more


VIVO Vision

Towards building an international network of researchers

S P O

S P O

S P O

S P O

S P O

S P O

S P O


Ontologies


Help make sense of the statements



If someone is a faculty member, we can conclude she is
a person.



Not to tell us what we can and can

t say


VIVO Vision

Towards building an international network of researchers


Ontologies


Want to say something else?




Just extend the ontology


Add detail for your institution


Remain interoperable at more general level




Or load an additional ontology


Domain
-
specific data


Ontologies for data sources


VIVO Vision

Towards building an international network of researchers

Linked Data


Web of data, not just a web of text


Make triples


Mint URIs


Get your data out there!


-


Follow your nose



Serve HTML pages to web browsers


16

VIVO Vision

Towards building an international network of researchers

Linked Data


Serve HTML pages to web browsers


Serve RDF statements to machines


One URI leads to both


Just tell us which you want

17

VIVO Vision

Towards building an international network of researchers

Linked Data Enables Applications



national
search



ctsa

search



international
visualizer


18

VIVO Vision

Towards building an international network of researchers

VIVO Vision

Towards building an international network of researchers

VIVO

exemplar search




VIVO Vision

Towards building an international network of researchers

VIVO

exemplar search




VIVO Vision

Towards building an international network of researchers

VIVO is …


A data
-
driven application, not static HTML


An ontology
-
based data model that determines much
of the appearance and function of the application


OPEN (BSD software license)


VIVO Is not ..


A content management system for html pages not
modeled using the ontology



3 tools in one


Ontology editor


Comes with the VIVO core ontology


Ontology can be extended or other imported if
needed


Content editor


Add content through data ingest or interactive
editing


All content is modeled using the ontology


Website for display of that content


Presents the content for public display


Allows user authenticated by the institution to edit
their own content

VIVO Vision

Towards building an international network of researchers


Authoritative sources


-

university HR for positions


-

sponsored research office for grants and contracts


Institutional basis


-

Institution can vouch for who you are


Re
-
use Data


Data Collected should be available for anyone to use


Data Visualizations


Department Websites



VIVO Vision

Towards building an international network of researchers

The History of VIVO

Four phases of VIVO
development

24


o
build
it and they will come
--

early trials at Cornell


o
transition
to
W3C semantic standards


o
going
multi
-
institutional via the NIH
project


o
International open development and implementation

VIVO History

Four phases in the life of the VIVO Application

Cornell University, USA 2003





Increasingly interdisciplinary research



Complex institutional structure



Library saw need for system to connect the life sciences



VIVO borrowed Semantic Web Ideas



Later expanded to entire university


VIVO History

Four phases in the life of the VIVO Application

Semantic Web, 2007




Reengineered VIVO software to use W3C data:



RDF data



OWL ontologies


Adoption at University of Florida and


Chinese Academy of Sciences







Vitro software available for download


Blank slate


bring your own ontology

VIVO History

Four phases in the life of the VIVO Application

National Institutes of Health funding 2009




Focus on linked open data


Core ontology


Numerous application improvements


BSD license


Installation at 7 U.S. institutions


Many more downloading, evaluating, and planning


Cross
-
site search

VIVO History

Four phases in the life of the VIVO Application

VIVO Community

Developing VIVO across
multiple institutions and
countries

29


What is the VIVO Development Community


How to Participate


Meetings, programs and events to date


Highlights


Community Growth


Synergy with implementation


What have we learned here?


Connections with other communities


Priorities going forward

VIVO Community

Developing VIVO across multiple institutions and countries


The VIVO Development Community


Started as the 3 core teams


Crosses over into implementation &
customization


Especially with the harvester and other ingest efforts


Expanded via the Mini
-
Grants and the
Hackathon


Principles


Openness


Trying for a culture of explanation and mutual support


Engagement


responses coming increasingly from
beyond the original sites


VIVO Community

Developing VIVO across multiple institutions and countries


Vehicles for participation


SourceForge


Repositories


Wiki


Mail Lists


JIRA


IRC


Weekly calls


Release Testing

VIVO Community

Developing VIVO across multiple institutions and countries


Community Growth


List traffic in triple digits
since March 2011


Bug reports and
enhancements


Commits from outside
the project


Over 15,000 downloads

VIVO Community

Developing VIVO across multiple institutions and countries

VIVO Collaboration Initiatives




Oracle connectivity (Duke)


CAS Authentication (Georgia Tech)


Data re
-
use


Drupal RDFImporter module (
Miles Worthington
)


Web Services
(semanticsservice.svn.sourceforge.net)


UI to generate SPARQL queries (
Indiana
)


Google Refine Work at WCMC


ANDS

VIVO Collaboration Initiatives

Work on VIVO beyond the scope of the NIH Grant


Contributions to the Harvester


D2RMap enhancements (Eliza Chan, Brian
Keese)


MODS Harvester work (IU and UF)


Matching algorithms (chris westling)


Feedback from webinars


ease of use


Documentation of parameters


Allow Inspection at each Step

VIVO Collaboration Initiatives

Work on VIVO beyond the scope of the NIH Grant


Mini Grants


CV Generation


Content re
-
use in standard web pages


Controlled vocabularies


Interactively adding publications


Going beyond drupal in content
management support

VIVO Collaboration Initiatives

Work on VIVO beyond the scope of the NIH Grant


Digital Vita Docs


Tool to create CVs and
biosketches

from
VIVO


Data elements alignment between VIVO and
Digital Vita and export via one request


Mapping to Digital Vita XML Schema with
XPARQL


http://xsparql.deri.org


Conversion to PDF and rich text via Apache
FOP


http://xmlgraphics.apache.org/fop


VIVO Collaboration Initiatives

Work on VIVO beyond the scope of the NIH Grant


Duke VIVO Widgets


Concepts


Ease of re
-
use in any web page


Offer frequently requested content options


Interface for content selection and preview


Providing content in Open social containers

VIVO Collaboration Initiatives

Work on VIVO beyond the scope of the NIH Grant


Selecting content to bring to the website

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VIVO Collaboration Initiatives

Work on VIVO beyond the scope of the NIH Grant


Duke open social widget

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VIVO Collaboration Initiatives

Work on VIVO beyond the scope of the NIH Grant


Stony Brook UMLS web service


United Medical Language System (UMLS)


Why link to vocabularies outside of VIVO


Interface integrated for V1.4


Enables search enhancements leveraging
controlled vocabularies

VIVO Collaboration Initiatives

Work on VIVO beyond the scope of the NIH Grant

Stony Brook UMLS Service

43

Stony Brook UMLS Service

44

Stony Brook UMLS Service

45

Stony Brook UMLS Service


46


ORCID


Open Researcher and Contributor ID


Synergies with a large international
community


VIVO as a source of institutionally endorsed
information


VIVO as a platform for representing diverse non
-
traditional contributions to research


ORCID as a platform for linking individuals across
systems and making assertions about
provenance


EuroCRIS


Long
-
running European effort


CERIF data model largely for administrative
purposes


Interested in leveraging for researcher
networking


VIVO and EuroCRIS exploring interoperability
through ontologies and linked data


Extensions to publication editing

O
Q
-
&
,
:
6
)
,
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)
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VIVO Collaboration Initiatives

Work on VIVO beyond the scope of the NIH Grant


Hackathon


Sabaku conference attendee game


Exporting visualization data as datacube RDF


Submitting URIs to sameAs.org


Linking to DBPedia concepts to enhance
search


Drupal views


RDFa


Taverna Workflows

VIVO Collaboration Initiatives

Work on VIVO beyond the scope of the NIH Grant


Joomla


Expanding the range of content
management options for VIVO data


Large community


Links to eScience and grid computing


Enhanced SPARQL query module


Potential synergies with exhibit 3.0


(
http://www.simile
-
widgets.org/exhibit3/
)

VIVO Collaboration Initiatives

Work on VIVO beyond the scope of the NIH Grant


Ontology collaborations


Scientific resource ontology as a collaboration
with eagle


I


Mapping VIVO core to align underneath the
basic formal ontology (BFO)


Australian research data registry extensions


Visible at
https://rdf.unimelb.edu.au/vivo/


Rochester CTSA intellectual property data in
VIVO


OHSU Sharecenter CTSA supplement


Booz Allen Hamilton contract: connecting
clinicians and researchers

VIVO Collaboration Initiatives

Work on VIVO beyond the scope of the NIH Grant

Development Roadmap


Transitioning to open source community


Move towards greater modularity


Extensions, plug
-
ins


Clean separation of data model,
controllers, front
-
end (MVC)


Triple store independence


Provenance and update support


Named graphs

53

Development Roadmap


Better support for linking individuals with
different URIs in different sources


Displaying single cohesive view


Avoiding resource renaming after ingest


Editing and display ontology


E.g. configure what

s hidden/displayed


Better installation and deployment


Multiple language support