The agINFRA Linked Data layer

Valeria PesceGlobal Forum on Agricultural Research (GFAR)

Giovanni L’AbateConsiglio per la Ricerca e la sperimentazione in Agricoltura

Centro di ricerca per l’agrobiologia e la pedologia (CRA-ABP)

Luca MatteisKoraljka Golub

Research Data Alliance 4th Plenary Meeting22-24 September 2014, Amsterdam

Agricultural Data Interoperability Interest Group

agINFRA projectEC 7th framework program INFRA-2011-1.2.2 - Grant agr. no: 283770

agINFRA - Background

• agINFRA: FP7 project EC 7th framework program INFRA-2011-1.2.2 - Grant agr. no: 283770

Objective: Promoting data sharing and development of trust in agricultural sciences

• agINFRA Knowledge Fair co-located with the Agricultural Data Interoperability Interest group meeting at the RDA 4th Plenary Meeting

• Types of data covered by agINFRA:bibliographic, educational, germplasm, soil

Interoperability 1

They are often both called vocabularies

Metadata elements to describe individual “things” (entities, datums, series…)

Aka metadata sets, metadata element sets, vocabularies

Sets of values for (some of) the metadata elements

Aka controlled vocabularies, authority data, value vocabularies, Knowledge Organization Systems (KOSs)

Various flavors of vocabularies

TitleAuthor(s)AbstractSubject(s)Publication datePublication placeType of documentother features…

Entity to be describedType?Bibliographic

resource

for describing bibliographic resources

Metadata vocabulary

Authority data

KOS

“Value vocabularies”

Data of type Person

Authority dataData of type Geographic location

“Des

crip

tio

n v

oca

bu

lari

es”

Controlled list

Concepts suitable for organizing by Topic

Concepts suitable for organizing by Type

for describing people

Metadata vocabularyfor describing

geographic places

Ontology

Names of things

URIs of things

Links to other URIs

Metadata vocabularies RDFs / OWL

KOS SKOS

Names of metadata elements

URIs of classes and properties

Links to other URIs

Design of the vocabulary / KOS

Controlled lists in

databases

Serialization into RDF

Interoperability 2: RDF and Linked Data

http://purl.org/dc/elements/1.1/contributor http://purl.org/ontology/bibo/editor “Editor”rdfs:subPropertyOf

http://aims.fao.org/aos/agrovoc/c_6599 http://id.loc.gov/authorities/sh85113862#concept “Rice”skos:exactMatch

Names of metadata elements URIs of classes and properties

Databases / tables / series

Names of things URIs of things Links to other URIs

http://vocabularies.aginfra.eu/soil#isObservedOnLocation

• Then, other complex things like “URI de-referencing” and “content negotiation”…(some good triple store platforms do it out of the box)

Interoperability 2: RDF and Linked Data

http://purl.org/ontology/bibo/editor “Editor”

https://aginfra-sg.ct.infn.it/rdf/cncp/resource/ObservedSoilSite/16.4CLcch1-1

http://vocabularies.aginfra.eu/soil#ObservedSoilProfile

“Observed soil 16.4CLcch1”

rdfs:type

Serialization into RDF

“Observed in location”

Tools used in agINFRA

• For building and managing SKOS: the FAO VocBench

• For publishing KOSs as Linked Data:SKOS loaded into Allegrograph

• For building and publishing RDF vocabularies: Neologism

• For publishing data as Linked Data:D2RQ from database to RDF

> mapping to published classes and propertiesLinks are provided in the last slide

Linked Data in agINFRA• Linked Data Vocabularies

– Reference to existing relevant RDF vocabularies and SKOS– New RDF vocabularies only when not existing (e.g. soil

ontology)– New KOS only when:

• Not existing• Mapping needed between local concepts and published concepts• Extension needed

• Linked Data datasets– Bibliographic data: AGRIS triple store– Germplasm data:

• CAAS Linked Data API (presented later)

• CRA triple store (presented later)

– Soil data: CRA triple store (presented later)

agINFRA LOD vocabularies

9

Voca

bula

ries.

agin

fra.

eu

agINFRAVocBench

agINFRANeologism

http://202.73.13.50:55481/aginfra/

VEST Registry

http://vocabularies.aginfra.eu

htt

p:/

/voca

bula

ries.

agin

fra.e

u

CIARD RING

Existing vocabularies

KOSs

Metadata / ontologies

New agINFRA vocabularies

http://aims.fao.org/vest-registry

http://ring.ciard.net

TOOLS agINFRA shop CIARD directories

http://202.45.139.84:10035/catalogs/fao/repositories/agINFRA

Triple store

URLs of agINFRA Linked Data vocabulary platforms

• agINFRA overview of vocabularies: http://vocabularies.aginfra.eu

• New agINFRA Soil Vocabulary:http://vocabularies.aginfra.eu/soil#

• VocBench instances:http://202.73.13.50:55481/aginfra/http://artemide.art.uniroma2.it/vocbench2

• Allegrograph triple store of agINFRA KOSs:http://202.45.139.84:10035/catalogs/fao/repositories/agINFRA

Namespaces of agINFRA new vocabularies

• agINFRA Soil vocabulary: http://vocabularies.aginfra.eu/soil#

• CRA Soil Terms: http://data.entecra.it/rdf/kos/soil/ orhttp://soilmaps.entecra.it/rdf/kos/soil/

• CRA Germplasm Terms: http://data.entecra.it/rdf/germplasm/soil/ orhttp://planta-res.entecra.it/rdf/kos/germplasm/

• agINFRA Resource Types Terms: http://aginfra.eu/voc/aginfra_doctypes/

• agINFRA Educational Resources Terms: http://aginfra.eu/voc/aginfra_eduterms/

Example 1: the Soil Terms KOS

Rationale: • CRA had local lists of values for several soil

properties• In most cases those values mapped

conceptually with terms in published KOSs Local values published as new KOS with mappings to USDA Soil Taxonomy terms and/or WRB whenever possible

Soil Terms: starting from a database table Excel file

Table loaded into the VocBench as SKOS

Example 2: Resource types in AGRISStarting from a table

Concept Type of Concept Relationship among conceptsBibliography Top broadMatch http://purl.org/dc/dcmitype/TextBook Top NT Handbook/Manual broadMatch http://purl.org/dc/dcmitype/TextConference BT Event broadMatch http://purl.org/dc/dcmitype/EventDictionary Top broadMatch http://purl.org/dc/dcmitype/TextDirectory Top relatedTerm http://purl.org/dc/dcmitype/CollectionDrawing BT Image broadMatch http://purl.org/dc/dcmitype/ImageEncyclopaedia Top broadMatch http://purl.org/dc/dcmitype/TextEvent Top NT Conference exactMatch http://purl.org/dc/dcmitype/EventExtension TopFilm Top broadMatch http://purl.org/dc/dcmitype/MovingImageGraphics BT Image broadMatch http://purl.org/dc/dcmitype/ImageHandbook/Manual BT Book broadMatch http://purl.org/dc/dcmitype/TextImage Top NT Drawing, NT Graphics, NT MapsorAtlases exactMatch http://purl.org/dc/dcmitype/ImageJournalArticle Top NT Preprint broadMatch http://purl.org/dc/dcmitype/TextLit.Review Top broadMatch http://purl.org/dc/dcmitype/TextManuscript Top broadMatch http://purl.org/dc/dcmitype/TextMapsorAtlases BT Image broadMatch http://purl.org/dc/dcmitype/ImageNews TopNon-Conventional TopNumericalData Top broadMatch http://purl.org/dc/dcmitype/DatasetOther TopPatent Top broadMatch http://purl.org/dc/dcmitype/TextPreprint BT JournalArticle broadMatch http://purl.org/dc/dcmitype/TextReport Top broadMatch http://purl.org/dc/dcmitype/TextSound/Music Top broadMatch http://purl.org/dc/dcmitype/SoundSpeech Top broadMatch http://purl.org/dc/dcmitype/SoundStandard Top broadMatch http://purl.org/dc/dcmitype/TextSummary Top broadMatch http://purl.org/dc/dcmitype/TextThesaurus Top broadMatch http://purl.org/dc/dcmitype/TextThesis Top broadMatch http://purl.org/dc/dcmitype/TextWebsite Top

External mapping

AGRIS resource types in the VocBenchhttp://aginfra.eu/voc/aginfra_doctypes/

Example 3: the Soil VocabularySt

artin

g fr

om th

e IN

SPIR

E U

ML

repr

esen

tatio

n

http://vocabularies.aginfra.eu/soil#

INSPIRE data model

agINFRA Soil Vocabulary RDF model

agINFRA LOD data

19

Germplasm data

http://[CAAS-API-base-URL]/germplasm/rest

https://aginfra-sg.ct.infn.it/rdf/cncp/

CIARD RING

Existing datasetsCAAS

CRA

New agINFRA datasets

http://ring.ciard.net

DATASETS agINFRA shop? CIARD directories

Germplasm data

Soil data

API

https://aginfra-sg.ct.infn.it/rdf/... ?? CRA Triple store

CRA Triple store

CKAN

CKAN

Dataverse

AGRIS

GLN

Namespaces of agINFRA partners’ Linked Data

• Sustainability namespaces with the data owners • CRA data: data.entecra.it (presented

later)– http://data.entecra.it/rdf/soil/

temporarily at https://aginfra-sg.ct.infn.it/rdf/cncp/ – http://data.entecra.it/rdf/germplasm/

temporarily at http://93.63.35.32:8080/d2rq/

• CAAS data (presented later)– API: http://www.cgris.net/pquery.asp

• AGRIS data– http://agris.fao.org/aos/

20

Useful links

• agINFRA project: http://aginfra.eu• agINFRA vocabularies: http://vocabularies.aginfra.eu• Tools:

– VocBench: http://aims.fao.org/tools/vocbench-2 – Neologism: http://neologism.deri.ie/ – Allegrograph: http://franz.com/agraph/allegrograph/ – D2RQ: http://d2rq.org/

The end

Thank you for your attentionValeria Pesce

Giovanni L’AbateLuca Matteis

Koraljka Golub