FOCUS MEETING ON FAIR DATA DEVELOPMENTS. Luiz Olavo Bonino -

Transcription

1 FOCUS MEETING ON FAIR DATA DEVELOPMENTS Luiz Olavo Bonino - luiz.bonino@dtls.nl

2 SUMMARY What is FAIR data? The FAIR ecosystem Plans and how to realise

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4 Produces Consumes

5 stewardship privacy? sustainability security Produces Consumes license access storage maintenance

6 RDF MIAPE DBMS Excel MIRIAM Semantics Produces Consumes API SQL SPARQL Metadata DICOM

7 access find format Produces Consumes license integrate query

8 WHAT IS FAIR DATA? FAIR Data aims to support existing communities in their attempts to enable valuable scientific data and knowledge to be published and utilised in a FAIR manner. Findable - (meta)data is uniquely and persistently identifiable. Should have basic machine readable descriptive metadata. Accessible - data is reachable and accessible by humans and machines using standard formats and protocols. Interoperable - (meta)data is machine readable and annotated with resolvable vocabularies/ontologies. Reusable - (meta)data is sufficiently well-described to allow (semi)automated integration with other compatible data sources.

9 THE FAIR ECOSYSTEM FAIR Data Principles FAIR Data Protocol FAIR Data Resources FAIR Data Core Technologies FAIR Data Systems/Tools Normative Artefact Software

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11 FAIR DATA RESOURCE Datasets expressed using one of the prescribed standards of the FAIR Data Protocol, with metadata complying with the protocol and license. The original dataset is transformed into a FAIR format and proper metadata and license are added to produce a FAIR Data Resource. The original and the FAIR version can co-exist, each one fulfilling its own purpose. FAIR Data Resource FAIR Conversion Original dataset Metadata License FAIR Format

12 Analysis transformation Analysis transformation FAIR transformation FAIR transformation

13 FAIR DATA APPLICATION ECOSYSTEM (NL APPROACH)

14 FAIR DATA RESOURCE FAIR Data Resource FAIR transformation

15 BRING YOUR OWN DATA - BYOD Goals: Learn how to make data linkable hands-on with experts Create a telling story to demonstrate its use Composition: Data owners specialists on given datasets Data interoperability experts Domain experts Source: Marcos Roos

16 BYOD

17 FAIRIFIER

18 FAIRIFIER FAIR Data Resource Non-FAIR Dataset input FAIRifier output Metadata License publish DataFAIRport Find,&Access,&Interoperate&&&Re3use&Data FAIR Format FAIR Data Resource Non-FAIR Dataset publish FAIRifier output Metadata License DataFAIRport Find,&Access,&Interoperate&&&Re3use&Data FAIR Format

19 FAIR DATA MODEL REGISTRY Data Model Dataset Data Model FAIR Data Model Registry Dataset Data Model Dataset

20 FAIRIFIER AND FAIR DATA MODEL REGISTRY Data Owner Non-FAIR Dataset submit FAIRifier search reference data model return reference FAIR Profile FAIR Data Model Registry output FAIR Data Resource F I A R Metadata License FAIR Format

21 A particular class of FAIR Data System that provides access to published datasets. The datasets can be external or internal to the FAIR Data Point. Also, the source data can be a regular (non- FAIR) dataset or a FAIR Data Resource. If the source data is non- FAIR, the FAIR Data Point needs to made the necessary FAIR transformations on the fly. FAIR Data Resource non-fair Data Resource Sensor

22 FAIR DATA POINT Dataset Data Producer Data Consumer Dataset Data Producer Dataset Data Producer Data Consumer Dataset Data Producer

23 FAIR DATA POINT Who are you? Can I trust you? FAIR Data Point

24 FAIR DATA POINT Here is information about myself FAIR Data Point FDP Metadata

25 FAIR DATA POINT Ok, now that I know you, tell me what you have to offer FAIR Data Point reads FDP Metadata

26 FAIR DATA POINT Here is information about my catalog of datasets FAIR Data Point Catalog Metadata

27 FAIR DATA POINT Tell me more about your genomic dataset FAIR Data Point reads Catalog Metadata

28 FAIR DATA POINT This is the detailed information about the genomic dataset FAIR Data Point Dataset & Data Record Metadata

29 FAIR DATA POINT Ok, now that I know what you have, give me the data. FAIR Data Point reads Dataset & Data Record Metadata

30 FAIR DATA POINT Here is my data. FAIR Data Point FAIR Data

31 FAIR DATA POINT - GENERAL ARCHITECTURE FAIR Metadata FAIR Data FAIR API / GUI Metadata Provider FAIR Data Accessor Metrics Gatherer Access Controller

32 EMBEDDED FAIR DATA POINT FAIR Metadata FAIR Data EUDAT API / GUI FAIR API / GUI EUDAT EUDAT Current Current EUDAT Current EUDAT Current Components Metadata Provider FAIR Data Accessor Metrics Gatherer Access Controller B2FAIR

33 DISTRIBUTED FAIR DATA POINTS UNIPROT FAIR Data Point HPA FAIR Data Point Biobank FAIR Data Point Biobank Database Patient Registry FAIR Data Point

34 FAIR DATA POINT METADATA PROVIDER API

35 METADATA LAYERS Layer Description URL Example Standard FDP (Data repository) Information about the FDP as a data repository PID, title, description, license, owner, API version, etc. OAI-PMH (extended) Catalog Information about the catalog of datasets offered catalog PID, title, description, publisher, etc. W3C DCAT #Catalog Dataset Information about each of the offered datasets [datasetid]/ AccessURL, downloadurl, format, mediatype, etc. W3C DCAT #Dataset, #Distribution Data record Information about the actual data, types, identifiers, etc. [datarecordid] Community/ domain, ex.: DICOM, VCF,

36 FDP dbp: dcat: dct: lang: rdf: rdfs: xml: xsd: < < a dct:agent ; rdfs:label "FAIR Data Point of the Plant Breeding Group, Wageningen UR"^^xsd:string ; dct:description "This FDP provides metadata on plant-specific genotype/phenotype data sets"^^xsd:string ; dct:haspart "catalog-01"^^xsd:string ; dct:identifier "FDP-WUR-PB"^^xsd:string ; dct:issued " "^^xsd:date ; dct:language lang:en ; dct:modified " "^^xsd:date ; dct:publisher < ; dct:title "FAIR Data Point of the Plant Breeding Group, Wageningen UR"^^xsd:string ; dct:version "1.0"^^xsd:string ;

37 CATALOG dbp: dcat: dct: lang: rdf: rdfs: xml: xsd: < < a dcat:catalog ; rdfs:label "Plant Breeding Data Catalog"^^xsd:string ; dct:description "Plant Breeding Data Catalog"^^xsd:string ; dct:haspart <breedb> ; dct:issued " "^^xsd:date ; dct:language lang:en ; dct:modified " "^^xsd:date ; dct:publisher < ; dct:title "Plant Breeding Data Catalog"^^xsd:string ; dct:version "1.0"^^xsd:string ; dcat:dataset <breedb> ;

38 DATASET dbp: dcat: dct: lang: rdf: rdfs: xml: xsd: < < a dcat:dataset ; rdfs:label "BreeDB tomato passport data"^^xsd:string ; dct:description "BreeDB tomato passport data"^^xsd:string ; dct:issued " "^^xsd:date ; dct:language lang:en ; dct:modified " "^^xsd:date ; dct:publisher < ; dct:title "BreeDB tomato passport data"^^xsd:string ; dct:version "1.0"^^xsd:string ; dcat:distribution <breedb-sparql>, <breedb-sqldump> ;

39 METADATA DISTRIBUTION < a dcat:distribution ; rdfs:label "SPARQL endpoint for BreeDB tomato passport data"^^xsd:string ; dct:description "SPARQL endpoint for BreeDB tomato passport data"^^xsd:string ; dct:issued " "^^xsd:date ; dct:language lang:en ; dct:license < ; dct:modified " "^^xsd:date ; dct:publisher < ; dct:title "SPARQL endpoint for BreeDB tomato passport data"^^xsd:string ; dct:version "1.0"^^xsd:string ; dcat:accessurl < < a dcat:distribution ; rdfs:label "SQL dump of the BreeDB tomato passport data"^^xsd:string ; dct:description "SQL dump of the BreeDB tomato passport data"^^xsd:string ; dct:issued " "^^xsd:date ; dct:language lang:en ; dct:license < ; dct:modified " "^^xsd:date ; dct:publisher < ; dct:title "SQL dump of the BreeDB tomato passport data"^^xsd:string ; dct:version "1.0"^^xsd:string ; dcat:downloadurl < breedb.sql>.

40 CURRENT STATUS FDP, Catalog and Dataset metadata tested. FAIR Accessor tested. Demonstration application on rare diseases with FDPs exposing patient registry and biobank datasets. Working on FDP for BreeDB (WUR).

41 FDP DEMONSTRATION 60 dataset metadata 3 biobanks data 3 patient registries data Biobank FAIR Data Point Patient Registry FAIR Data Point

42 NEXT STEPS Extend the demonstration application with more types of datasets. Specific a metadata description format for the data record metadata. Implement the Security Enforcer and Metrics Gatherer components. Release version 1.0 Implement subscription/notification mechanism.

43 DataFAIRport Find,&Access,&Interoperate&&&Re3use&Data

44 DataFAIRport A particular class of FAIR Data System to provide support for data interoperability; Supports publication and access to FAIR data. Fosters an ecosystems of applications and services; Federated architecture: different FAIRports (and other FAIR Data Systems) are interconnectable; Supports citations of datasets and data items; Provides metrics for data usage and citation;

45 FAIR DATA PUBLICATION Concept 1 Concept 2 Concept 3 Concept 4 Dataset Metadata DataFAIRport Find,&Access,&Interoperate&&&Re3use&Data Concept 1 Data Owners/Creators Concept 3 Concept 2 Concept 4

46 FAIR DATA ACCESS Dataset Dataset Dataset DataFAIRport Find,&Access,&Interoperate&&&Re3use&Data Dataset Dataset Dataset Data User

47 DISTRIBUTED ARCHITECTURE Organiza(on X DataFAIRport Rare Diseases DataFAIRport Plant DataFAIRport VLPB/WUR Data FAIRport Organiza(on Y DataFAIRport DTL DataFAIRport

48 FAIR Data Search Engine R FAIRifier + (Meta)Data Publication FAIR Data Point DTL DataFAIRport Data storage (optional) Transformation Services Registry (optional) F A I Metadata storage NETHERLANDS

49 FAIRPORT ECOSYSTEM Application & Services [BRAIN] Data Consumer DataFAIRport Find,&Access,&Interoperate&&&Re3use&Data Infrastructural Services Data Producer

50 FAIRPORT Data Producer Data Data Mgmt Stewardship App Apps Data Consumer Apps Ex. *APInatomy, BRAIN, etc) Data Consumer Stewardship API FAIR Data API GUI (Data publishing, search, mgmt) DataFAIRport Find,&Access,&Interoperate&&&Re3use&Data Management component Data usage policy Metrics storage Semantic resolver Ontology storage (Meta)Data Storage component Data storage Metadata storage Data storage API / FAIR Data API FAIR Data System DataVerse EUDAT Data Repository

51 ROADMAP 2016 Implement the FAIR Data search engine Implement the FAIR Data publication mechanism Extend the demonstration application with more types of datasets. Specific a metadata description format for the data record metadata. Implement the Security Enforcer and Metrics Gatherer components on FAIR Data Points. Start work on the the encryption and pseudonymisation of Personal Health Train

52 QUESTIONS? Luiz Olavo Bonino