Presentation at the VIVO 2011 conference

CIARD - creating a global framework for
information sharing in agricultural research
and innovation – Role of VIVO
Talk at the VIVO 2011 conference

Dr. Johannes Keizer
Office of Knowledge Exchange, Research and Extension
Food and Agriculture Organization of the UN

Presentations by Johannes Keizer is licensed under a Creative Commons Attribution-
NonCommercial-ShareAlike 3.0 Unported License.

“... FAO’s principle task is to work
to ensure that the world’s
knowledge of food and
agriculture is available to those
who need it when they need it
and in a form which they can
access and use ...”

There will be generated more
scientific data in the next 5 years
than in the history of humankind

http://aims.fao.org johannes keizer

Contribution and Participation in Science

Territory size shows proportion of scientific papers published in 2001 by
authors living there.
Copyright SASI Group (University of Sheffield) and Mark Newman (University of Michigan)


Global Trends in Publishing


The Internet!


Aggregation States of Knowledge


Data and Information in Agricultural Research and
Extension


Distributed Repositories
• stats
• gene banks
• gis data
• blogs,
• journals
• open archives
• raw data
• technologies
• learning objects
• ………..


Task 1: making services

? ? ?


Task 2: getting knowledge

? ? ?


Task 3: working together

? ? ?
How can I get in real time all the specimen data on
useful insects from all people making research on this on
my desktop? How can I share in real time my data with
other colleagues working on that.


http://www.ciard.net


The Project: agINFRA

 Enforce Webpublishing of Data
 Produce linked open data from
all datasets
 Use common reference
vocabularies to interlink data
sets
 Don’t wait ! Wrap the Legacy


The Infrastructure elements

VocBench RING Tools
vocabulary server
LOD
concepts and entities routemap to information enabled software
triples nodes and gateways

Cloud Data Services LOD Generator

storage for RDF Webservices + APIs triplifier,
to triple stores concept and entity
triples
identifier


Lod Generator: process


Data Services: process


Under Construction!!!!!!!

 VocBench
VocBench RING Tools
 vocabulary server Linked Open Data LOD
AGROVOC
 AgroTagger

 Triplifying AGRIS
 Linking Data! Data Services
Cloud LOD Generator
 DrupalRDF
storage for front ends for triple stores
Webservices + APIs triplifier,
triples
 The CIARD R.I.N.G identifier

 “AgriVIVO

So…

Where does VIVO fit
in?


Background

 Many Agriculture Information
communities, how can we bring
together an international network of
researchers in this domain
 A precedent for a community open
source based solution


Many Agriculture Communities

• E-Agriculture site has 7111 members from
150 countries
• CIARD site: 6038 seeded from E-Agriculture
site
• AIMS site has 280 users
• SIDALC has 150+ institutions in 22 LAC
countries
• IAALD has 400+ members in 80 countries
• None of these user communities “talk” to
each other (though there is a lot of overlap

Precedent for Open Source Applications

 AgriDrupal – A content management
system based on Drupal with
Agriculture Information Systems
customizations
 AgriOceanDSpace – An institutional
repository platform, customized for the
Agriculture domain


How about “AgriVivo”?

 An open source semantic web
application, customized for managing
people (and their activities) that work in
the Agriculture domain.
 Enabling an International Network of
Agriculture researchers…


AgriVivo
Agri VIVO

Triple Store
AGRIS

E-AGRICULTURE

AIMS

SIDALC

IAALD


AgriVivo: Areas of Work

 Multi Language Support
 Integration of Agricultural Ontolologies
 Development of Harvesters for ingest
of Agricultural documents (AGRIS)
 Community Search of AgriVivo Sites


Linking Data

VocBench RING Tools
vocabulary server
LOD


triples
identifier


Serendipity linking


Semantic Linking

http://aims.fao.org/aos/agrovoc/c_7825


Semantic Linking

http://eurovoc.europa.eu/218754



http://agclass.nal.usda.gov
/nalt/2011.xml#1780



Linking data through common URIs

NALT
http://agclass.nal.usda.g http://www.agnic.
AGROVOC ov/nalt/2011.xml#1780 org/search/CAT8
http://aims.fao.org/aos/a 5822953
grovoc/c_7825

Eurovoc TOXIC UNBIS
http://eurovoc.euro
pa.eu/218754 SUBSTANCES

http://agris.fao.org/agris-
search/search/display.do?f=1996/TR
/TR96001.xml;TR9600026 http://unbisnet.un.org:8080/ipac20/
ipac.jsp?session=128F308557F34.
http://eur- 283092&profile=bib&uri=full=3100
lex.europa.eu/LexUriServ/LexUr 001~!685149~!1&ri=1&aspect=sub
iServ.do?uri=OJ:L:2010:202:00 tab124&menu=search&source=~!h
11:0015:EN:PDF orizon

http://aims.fao.org/aos/agrovoc/c_12332 owl:sameAs http://eurovoc.europa.eu/219871
skos: exact match UNBIS: Toxic Substances


http://lprapp14:8090/openagris/search.do?recordID=JP2010001379


Open AGRIS threads


The AIMS Community


Thank You!
Credits: John Ferreira, Imma Subirats, Yves
Jaques, Valeria Pesce, Fabrizio Celli, Ahsan
Morshed, Catarina Caracciolo, Dickson
Lukose, Gudrun Johannsen, Stefano
Anibaldi, Armando Stellato, Tom Baker and
many others

The VocBench

VocBench RING Tools
vocabulary server
LOD


triples
identifier


The VocBench


VocBench Features

 Domain independent
 Structure independent (i.e. thesauri, Glossaries,
etc)
 Supports RDF (SKOS, SKOS-XL), OWL
 Supports collaborative editing
 Supports editorial workflow, with user roles
 Simple and advanced search
 Supports data export: SKOS, Relational format
(MySQL)


The AGROVOC concept scheme
AGROVOC
Concept
Other scheme
skos:inScheme Scheme in FAO

skos:topConceptOf Another scheme
in FAO
6211 Further schemes
skos:broader skos:inScheme in FAO
8171
skos:broader
SKOS 1474 SKOS Label
Concept skos:broader
12332
rdf:type
skosxl:prefLabel :bar
skos:literalForm “maize”
skosxl:altLabel has_synonym :foo
rdf:type has_translation maïs (fr)
has_synonym
:foo
skos:literalForm “corn”
has_synonym :bar


LOD Generator/Agrotagger

VocBench RING Tools
vocabulary server
LOD


triples
identifier


AgroTagger

• Does Concept identification in unstructured
texts
• Uses Agrovoc as a controlled vocabulary
• Prototype under testing with excellent
results (entire repository of ICARDA
indexed)
• Will produce in future Structured RDF files
that can be used to link data like “open
Calais”


AGRIS Journal disambiguation
 2.644.818 AGRIS records
 2.171.113 records are journal records
(82.09%)
 1.788.083 journal records have been
covered by the disambiguation process
(82.35%)
 14.658 journals have been correctly
disambiguated
 ~20.000 strings must be examined yet:
they refer to journal’s titles
 Triples have been generated:


Triplifying AGRIS (small example)
<?xml version="1.0" encoding="utf-8"?>
<rdf:RDF xmlns:ags="http://purl.org/agmes/1.1/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-
syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:bibo="http://purl.org/ontology/bibo/"
xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dct="http://purl.org/dc/terms/">
<bibo:Journal rdf:about="http://aims.fao.org/aos/journal/c_b6e4ca85">
<bibo:ISSN>0101-9066</bibo:ISSN>
<bibo:ISSN>0101-9066</bibo:ISSN>
<dct:title><![CDATA[Circular técnica]]></dct:title>
<dct:alternative><![CDATA[Circular técnica (Centro Nacional de Pesquisa de Seringueira e Dendê)]]></dct:alternative>
<dct:alternative><![CDATA[Circular Tecnica - Centro Nacional de Pesquisa da Seringueira e Dende]]></dct:alternative>
<dct:alternative><![CDATA[Circular técnica - CNPSD]]></dct:alternative>
<dct:alternative><![CDATA[Circ. téc.]]></dct:alternative>
<ags:publisherPlace rdf:resource="http://aims.fao.org/aos/geopolitical.owl#Brazil"/>
<dct:publisher><![CDATA[Empresa Brasileira de Pesquisa Agropecuária, Centro Nacional de Pesquisa de Seringueira e
Dendê]]></dct:publisher>
<dct:language>por</dct:language>
<dct:date>1980</dct:date>
<dct:subject rdf:resource="http://aims.fao.org/aos/agrovoc/c_10795"/>
</bibo:Journal>


The CIARD RING

VocBench RING Tools
vocabulary server
LOD


triples
identifier


The CIARD RING

 Roadmap to information nodes and
gateways
 Community switchboard to find data
sources
 Not only registry, but dynamic
instrument for data linking


RING - Charts and numbers

http://ring.ciard.net


RING – Numbers
http://ring.ciard.net/totals
Number of
documents
potentially reachable
through the services
registered in the
RING.

Types of service
considered:
document
repositories and
bibliographic
databases.


http://aims.fao.org


Agricultural Information Management Standards

Tools Standards

http://www.ciard.net
http://ring.ciard.net
http://aims.fao.org
Advice http://agris.fao.org Services


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