
Koraljka Golub
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Papers by Koraljka Golub
1. The agINFRA Linked Data layer Valeria Pesce Global Forum on Agricultural Research (GFAR) Giovanni L’Abate Consiglio per la Ricerca e la sperimentazione in Agricoltura Centro di ricerca per l’agrobiologia e la pedologia (CRA-ABP) Luca Matteis Koraljka Golub Research Data Alliance 4th Plenary Meeting 22-24 September 2014, Amsterdam Agricultural Data Interoperability Interest Group agINFRA project EC 7th framework program INFRA-2011-1.2.2 - Grant agr. no: 283770
2. 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
3. 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)
4. Various flavors of vocabularies Title Author(s) Abstract Subject(s) Publication date Publication place Type of document other features… Entity to be describedType? Bibliographic resource for describing bibliographic resources Metadata vocabulary Authority data KOS “Value vocabularies” Data of type Person Authority data Data of type Geographic location “Description vocabularies” Controlled list Concepts suitable for organizing by Topic Concepts suitable for organizing by Type for describing people Metadata vocabularyfor describing geographic places Ontology
5. 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 Serialization into RDF Interoperability 2: RDF and Linked Data http://purl.org/dc/elements/1.1/contributorhttp://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
6. 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#Obs ervedSoilProfile “Observed soil 16.4CLcch1” rdfs:type Serialization into RDF “Observed in location”
7. 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 properties Links are provided in the last slide
8. 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)
9. agINFRA LOD vocabularies 9 Vocabularies. aginfra.eu agINFRA VocBench agINFRA Neologism http://202.73.13.50:55481/aginfra/ VEST Registry http://vocabularies.aginfra.eu http://vocabularies.aginfra.eu 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://202.45.139.84:100 35/catalogs/fao/repositori es/agINFRA Triple store
10. 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/ag INFRA
11. Namespaces of agINFRA new vocabularies • agINFRA Soil vocabulary: http://vocabularies.aginfra.eu/soil# • CRA Soil Terms: http://data.entecra.it/rdf/kos/soil/ or http://soilmaps.entecra.it/rdf/kos/soil/ • CRA Germplasm Terms: http://data.entecra.it/rdf/germplasm/soil/ or http://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/
12. 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
13. Soil Terms: starting from a database table Excel file
14. Table loaded into the VocBench as SKOS
15. Example 2: Resource types in AGRIS Starting from a table Concept Type of Concept Relationship among concepts Bibliography Top broadMatch http://purl.org/dc/dcmitype/Text Book Top NT Handbook/Manual broadMatch http://purl.org/dc/dcmitype/Text Conference BT Event broadMatch http://purl.org/dc/dcmitype/Event Dictionary Top broadMatch http://purl.org/dc/dcmitype/Text Directory Top relatedTerm http://purl.org/dc/dcmitype/Collection Drawing BT Image broadMatch http://purl.org/dc/dcmitype/Image Encyclopaedia Top broadMatch http://purl.org/dc/dcmitype/Text Event Top NT Conference exactMatch http://purl.org/dc/dcmitype/Event Extension Top Film Top broadMatch http://purl.org/dc/dcmitype/MovingImage Graphics BT Image broadMatch http://purl.org/dc/dcmitype/Image Handbook/Manual BT Book broadMatch http://purl.org/dc/dcmitype/Text Image Top NT Drawing, NT Graphics, NT MapsorAtlases exactMatch http://purl.org/dc/dcmitype/Image JournalArticle Top NT Preprint broadMatch http://purl.org/dc/dcmitype/Text Lit.Review Top broadMatch http://purl.org/dc/dcmitype/Text Manuscript Top broadMatch http://purl.org/dc/dcmitype/Text MapsorAtlases BT Image broadMatch http://purl.org/dc/dcmitype/Image News Top Non-Conventional Top NumericalData Top broadMatch http://purl.org/dc/dcmitype/Dataset Other Top Patent Top broadMatch http://purl.org/dc/dcmitype/Text Preprint BT JournalArticle broadMatch http://purl.org/dc/dcmitype/Text Report Top broadMatch http://purl.org/dc/dcmitype/Text Sound/Music Top broadMatch http://purl.org/dc/dcmitype/Sound Speech Top broadMatch http://purl.org/dc/dcmitype/Sound Standard Top broadMatch http://purl.org/dc/dcmitype/Text Summary Top broadMatch http://purl.org/dc/dcmitype/Text Thesaurus Top broadMatch http://purl.org/dc/dcmitype/Text Thesis Top broadMatch http://purl.org/dc/dcmitype/Text Website Top External mapping
16. AGRIS resource types in the VocBench http://aginfra.eu/voc/aginfra_doctypes/
17. Example 3: the Soil VocabularyStartingfromtheINSPIREUMLrepresentation
18. http://vocabularies.aginfra.eu/soil# INSPIRE data model agINFRA Soil Vocabulary RDF model
19. agINFRA LOD data 19 Germplasm data http://[CAAS-API-base-URL]/germplasm/rest https://aginfra-sg.ct.infn.it/rdf/cncp/ CIARD RING Existing datasets CAAS 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
20. 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
21. 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/
22. The end Thank you for your attention Valeria Pesce Giovanni L’Abate Luca Matteis Koraljka Golub